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Revision 6615 - Directory Listing
Modified Thu Jun 22 08:24:11 2017 UTC (4 days, 15 hours ago) by jfenwick
Fix final warning in #402

Initialise an uninitialised fd_set


Revision 6614 - Directory Listing
Modified Thu Jun 22 06:37:41 2017 UTC (4 days, 17 hours ago) by jfenwick
Final tests for #269

Also, add explanation of how hasInf and hasNaN are not mutually exclusive.
To doc-strings


Revision 6613 - Directory Listing
Modified Tue Jun 20 10:09:18 2017 UTC (6 days, 14 hours ago) by jfenwick
Sigh


Revision 6612 - Directory Listing
Modified Tue Jun 20 03:21:40 2017 UTC (6 days, 20 hours ago) by jfenwick
Merging changes from release branch


Revision 6611 - Directory Listing
Modified Tue Jun 20 03:18:04 2017 UTC (6 days, 20 hours ago) by jfenwick
Removing to make way for more complete version from another branch.



Revision 6610 - Directory Listing
Modified Fri Jun 9 07:26:10 2017 UTC (2 weeks, 3 days ago) by jfenwick
More work on the _Inf functions


Revision 6609 - Directory Listing
Modified Thu Jun 8 07:08:54 2017 UTC (2 weeks, 4 days ago) by jfenwick
C++ functions Inf versions of the Nan replacement functions
No python interface or unit tests yet


Revision 6600 - Directory Listing
Modified Tue Jun 6 07:49:33 2017 UTC (2 weeks, 6 days ago) by jfenwick
Missing file


Revision 6592 - Directory Listing
Modified Mon Jun 5 02:15:01 2017 UTC (3 weeks ago) by jfenwick
Some notes on trilinos

Revision 6591 - Directory Listing
Modified Fri Jun 2 02:24:51 2017 UTC (3 weeks, 3 days ago) by jfenwick
Printing tagged Data now reports if tag is unused.

That is, a tag is part of the Data but not in the 
list of used tags for that function space.
(This will slow down this op a bit).


Revision 6590 - Directory Listing
Modified Fri Jun 2 01:10:53 2017 UTC (3 weeks, 3 days ago) by jfenwick
Only summarise data if it is expanded


Revision 6589 - Directory Listing
Modified Thu Jun 1 06:27:03 2017 UTC (3 weeks, 4 days ago) by jfenwick
Change list for 5.2.

Update dev list.
Tell people to look at install guide for discussion of Trilinos requirements
but haven't actually added that bit yet.


Revision 6588 - Directory Listing
Modified Thu Jun 1 01:25:24 2017 UTC (3 weeks, 4 days ago) by jfenwick
Describe mpi_no_host option


Revision 6587 - Directory Listing
Modified Wed May 24 07:50:23 2017 UTC (4 weeks, 5 days ago) by jfenwick
Fix lazy related test failures.


Revision 6586 - Directory Listing
Modified Tue May 23 07:00:19 2017 UTC (4 weeks, 6 days ago) by jfenwick
Fix broken symlinks in debian build

Add a dependency to doc package which has the targets in it.


Revision 6585 - Directory Listing
Modified Tue May 23 04:13:09 2017 UTC (4 weeks, 6 days ago) by caltinay
regenerated gradient tests for both real and complex data and moved them to a separate file.


Revision 6584 - Directory Listing
Modified Tue May 23 01:15:08 2017 UTC (4 weeks, 6 days ago) by caltinay
typos fixed.


Revision 6583 - Directory Listing
Modified Mon May 22 08:04:56 2017 UTC (5 weeks ago) by caltinay
Regenerated interpolation tests for both real and complex data.

Moved them into a separate file as with the integrals before.


Revision 6582 - Directory Listing
Modified Sun May 21 09:43:12 2017 UTC (5 weeks, 1 day ago) by caltinay
fixed typo.


Revision 6581 - Directory Listing
Modified Fri May 19 06:39:36 2017 UTC (5 weeks, 3 days ago) by caltinay
Implement #412 - complex support for paso's coupler.

Removed guards from domains accordingly as complex interpolations without
trilinos are supported now.


Revision 6580 - Directory Listing
Modified Fri May 19 04:05:40 2017 UTC (5 weeks, 3 days ago) by caltinay
Implemented complex dofToNodes in ripley which should fix the current segfaults.
NodesToDof still missing.

Also, builds without Trilinos will fail some complex tests as these
interpolations require trilinos.


Revision 6579 - Directory Listing
Modified Fri May 19 01:37:23 2017 UTC (5 weeks, 3 days ago) by caltinay
Regenerated tests for integration for real & complex Data. Moved them into a
separate file which is included from the spatial functions tests so will be
picked up without changes by the domains.


Revision 6578 - Directory Listing
Modified Wed May 17 04:16:40 2017 UTC (5 weeks, 5 days ago) by caltinay
Complex interpolation in speckley.


Revision 6577 - Directory Listing
Modified Wed May 17 02:34:45 2017 UTC (5 weeks, 5 days ago) by caltinay
complex integrals for speckley. Fixes #398


Revision 6576 - Directory Listing
Modified Wed May 17 01:42:26 2017 UTC (5 weeks, 5 days ago) by caltinay
Finished complex interpolation cases in dudley.


Revision 6575 - Directory Listing
Modified Wed May 17 01:04:36 2017 UTC (5 weeks, 5 days ago) by caltinay
complex integration and interpolation in dudley.


Revision 6574 - Directory Listing
Modified Wed May 17 00:53:31 2017 UTC (5 weeks, 5 days ago) by jfenwick
Don't call openmp function if you aren't in openmp


Revision 6573 - Directory Listing
Modified Wed May 17 00:02:42 2017 UTC (5 weeks, 6 days ago) by jfenwick
Add mpi_no_host option

Add option to prevent --host option being added to launcher.
Not sure how far this needs to be spread.


Revision 6572 - Directory Listing
Modified Tue May 16 23:16:45 2017 UTC (5 weeks, 6 days ago) by caltinay
implementation of complex integrals in finley. (#398)


Revision 6571 - Directory Listing
Modified Mon May 15 11:39:06 2017 UTC (6 weeks ago) by caltinay
Forgot to enable the code path.


Revision 6570 - Directory Listing
Modified Mon May 15 11:23:29 2017 UTC (6 weeks ago) by caltinay
Complex interpolation in finley is complete.


Revision 6569 - Directory Listing
Modified Mon May 15 10:17:13 2017 UTC (6 weeks ago) by caltinay
complex element data interpolation in finley.


Revision 6568 - Directory Listing
Modified Mon May 15 09:29:39 2017 UTC (6 weeks ago) by caltinay
Implemented remaining cases of complex nodal interpolation in finley.


Revision 6567 - Directory Listing
Modified Mon May 15 07:33:56 2017 UTC (6 weeks ago) by caltinay
This fixes #408 by implementing complex interpolation in finley from DOF to Nodes. The opposite direction is still missing.


Revision 6566 - Directory Listing
Modified Mon May 15 05:03:56 2017 UTC (6 weeks ago) by caltinay
Implement complex interpolation in finley. This does not include Copy/AverageNodalData yet.


Revision 6565 - Directory Listing
Modified Mon May 15 04:44:05 2017 UTC (6 weeks ago) by caltinay
Preparation for complex interpolation in finley. Throws exception instead of crashing now.


Revision 6559 - Directory Listing
Modified Wed May 10 06:21:29 2017 UTC (6 weeks, 5 days ago) by jfenwick
new test for tensor_transpose_mult

Revision 6558 - Directory Listing
Modified Wed May 10 04:55:32 2017 UTC (6 weeks, 5 days ago) by jfenwick
Finish phase()

Added phase() function to escript.util.
Added unit test for phase()

Fixes #385


Revision 6557 - Directory Listing
Modified Tue May 9 01:22:56 2017 UTC (6 weeks, 6 days ago) by jfenwick
Fix issue #409

minGlobalDataPoint will now throw if there are no values to process.


Revision 6556 - Directory Listing
Modified Mon May 8 02:42:09 2017 UTC (7 weeks ago) by jfenwick
Add compare tool.

Trying to get trilinos to build? Want to work out what is the difference between your configuration file and one that "works"?

Compile up tools.trconfcmp.cc and give it the too files.
It will tell you which variables are exclusive to one or the other as well as listing variables with different types and values.


Revision 6555 - Directory Listing
Modified Sun May 7 11:44:34 2017 UTC (7 weeks, 1 day ago) by caltinay
fixed minor typo.


Revision 6554 - Directory Listing
Modified Wed May 3 01:15:37 2017 UTC (7 weeks, 5 days ago) by jfenwick
Add a temporary work-around for #401.
Internally, tensor_transposed_mult(a,b) directly calls 
tensor_mult(a, tranpose(b)).

This is not efficient, but it should give the correct answers until we
can do a more efficient fix.

I've needed to modify some of the unit tests to account for the changed
behaviour.


Revision 6553 - Directory Listing
Modified Fri Apr 28 03:35:26 2017 UTC (8 weeks, 3 days ago) by jfenwick
Fix some unused vars


Revision 6552 - Directory Listing
Modified Wed Apr 26 02:33:23 2017 UTC (2 months ago) by jfenwick
Options for ferret

Revision 6551 - Directory Listing
Modified Tue Apr 4 06:17:09 2017 UTC (2 months, 3 weeks ago) by jfenwick
commenting some imports

Revision 6550 - Directory Listing
Modified Tue Apr 4 05:34:33 2017 UTC (2 months, 3 weeks ago) by jfenwick
minor tweaks

Revision 6549 - Directory Listing
Modified Mon Mar 27 06:32:03 2017 UTC (3 months ago) by jfenwick
Fixed various.

Mixed complex and reals are now tested properly in binary ops.
Overloaded ops are now tested.



Revision 6548 - Directory Listing
Modified Mon Mar 27 06:16:26 2017 UTC (3 months ago) by jfenwick
Fix a missing complex->data conversion

Revision 6547 - Directory Listing
Modified Mon Mar 27 06:15:05 2017 UTC (3 months ago) by jfenwick
Dont assume a tensor product has a real result

Revision 6546 - Directory Listing
Modified Mon Mar 27 00:00:49 2017 UTC (3 months ago) by jfenwick
Add test for overloaded +

Also add param to generator that will prevent
testing:
  numpy op Data
Because numpy applies its own interpretation


Revision 6545 - Directory Listing
Modified Fri Mar 24 00:21:35 2017 UTC (3 months ago) by jfenwick
Fixing the last commit.   (I did test it)

Revision 6544 - Directory Listing
Modified Thu Mar 23 23:59:21 2017 UTC (3 months ago) by jfenwick
Add two tests

Revision 6543 - Directory Listing
Modified Thu Mar 23 06:33:16 2017 UTC (3 months ago) by jfenwick
Adding eigenvalues_and_eigenvector test.

This one was a bit tricky and so it is tested with fewer 
steps.
Added option to not use update steps.


Revision 6542 - Directory Listing
Modified Thu Mar 23 00:35:22 2017 UTC (3 months ago) by jfenwick
Better version of earlier fix.

This version does not allow lazy non-expanded expressions of any depth other than 0.
Fixed missing POW operator collapsing.

Fixed height and child counts when collapsing (needed to make fields mutable)


Revision 6541 - Directory Listing
Modified Thu Mar 23 00:33:27 2017 UTC (3 months ago) by jfenwick
Remove unused test category

Revision 6540 - Directory Listing
Modified Wed Mar 22 06:50:34 2017 UTC (3 months ago) by jfenwick
Fix nasty concurrency bug.

Multiple threads were trying to collapse() subtrees.
Prevent POS from being called by c++ unit tests for lazy (python handles this differently).



Revision 6539 - Directory Listing
Modified Tue Mar 14 07:46:12 2017 UTC (3 months, 1 week ago) by jfenwick
Fix incorrect collapse behaviour

When nodes were collapsed, they weren't updating
m_op and m_opgroup properly.


Revision 6538 - Directory Listing
Modified Tue Mar 14 03:49:20 2017 UTC (3 months, 1 week ago) by jfenwick
Fix whereZero bugs

Add new opgroup G_UNARY_PR (always real) and put the
whereZero whereNonZero ops in it.

Reorder some declarations to stop the compiler complaining.


Revision 6537 - Directory Listing
Modified Tue Mar 14 00:01:31 2017 UTC (3 months, 1 week ago) by jfenwick
Add missing deepCopy cases


Revision 6536 - Directory Listing
Modified Mon Mar 13 06:30:35 2017 UTC (3 months, 2 weeks ago) by jfenwick
Bug fixes.

Correcting earlier correction.
Debug output now includes group information in some cases.
Fixed tree format output.
Fixed bug where G_UNARY_R with complex child was being resolved
as real.



Revision 6535 - Directory Listing
Modified Mon Mar 13 04:38:47 2017 UTC (3 months, 2 weeks ago) by jfenwick
Fix sign and abs

Sign now throws on complex inputs and abs is always real
... even abs(lazy)!


Revision 6534 - Directory Listing
Modified Fri Mar 10 04:47:23 2017 UTC (3 months, 2 weeks ago) by jfenwick
Fix crash


Revision 6533 - Directory Listing
Modified Fri Mar 10 04:08:40 2017 UTC (3 months, 2 weeks ago) by jfenwick
Lazy fixes

Make (anti)hermitian the same op type as symmetric.
Indicate complex lazy objects by including j in their description.
Add resolve routine for G_UNARY_C (promote) rather than trying
to shoehorn it into one of the existing routines.


Revision 6532 - Directory Listing
Modified Thu Mar 9 10:32:46 2017 UTC (3 months, 2 weeks ago) by jfenwick
More option files


Revision 6531 - Directory Listing
Modified Thu Mar 9 04:43:36 2017 UTC (3 months, 2 weeks ago) by jfenwick
Add Xenial options


Revision 6530 - Directory Listing
Modified Thu Mar 9 01:31:15 2017 UTC (3 months, 2 weeks ago) by jfenwick
Noting dependency on legacy-netcdf for debian styles


Revision 6529 - Directory Listing
Modified Thu Mar 9 01:29:12 2017 UTC (3 months, 2 weeks ago) by jfenwick
Adding yakkety options


Revision 6528 - Directory Listing
Modified Wed Mar 8 05:07:31 2017 UTC (3 months, 2 weeks ago) by jfenwick
Remove AUTOLAZY fiddles


Revision 6527 - Directory Listing
Modified Wed Mar 8 05:05:17 2017 UTC (3 months, 2 weeks ago) by jfenwick
Correct error messages about anti-hermitian


Revision 6526 - Directory Listing
Modified Wed Mar 8 03:48:11 2017 UTC (3 months, 2 weeks ago) by jfenwick
Fix error in m_iscompl determination


Revision 6525 - Directory Listing
Modified Wed Mar 8 02:11:25 2017 UTC (3 months, 2 weeks ago) by jfenwick
Stray print removal


Revision 6524 - Directory Listing
Modified Wed Mar 8 02:08:04 2017 UTC (3 months, 2 weeks ago) by jfenwick
"Reordering statements involving reference params" considered dangerous


Revision 6523 - Directory Listing
Modified Tue Mar 7 06:50:34 2017 UTC (3 months, 2 weeks ago) by jfenwick
UPDATE THE COPYRIGHT DATES


Revision 6522 - Directory Listing
Modified Tue Mar 7 05:55:32 2017 UTC (3 months, 2 weeks ago) by jfenwick
Various

Add complex version of isnan - here defined to be one or both components are nan.
Add typed version of ResolveSample.
Fix mistyping in Lsup


Revision 6521 - Directory Listing
Modified Tue Mar 7 04:24:20 2017 UTC (3 months, 2 weeks ago) by jfenwick
Merging clazy branch


Revision 6519 - Directory Listing
Modified Tue Mar 7 01:55:01 2017 UTC (3 months, 2 weeks ago) by jfenwick
Remove debug print


Revision 6515 - Directory Listing
Modified Mon Mar 6 01:54:53 2017 UTC (3 months, 3 weeks ago) by jfenwick
More helpful exception message


Revision 6510 - Directory Listing
Modified Thu Mar 2 23:47:07 2017 UTC (3 months, 3 weeks ago) by jfenwick
Move my netcdf variable fiddles after the environment is recreated



Revision 6509 - Directory Listing
Modified Thu Mar 2 07:36:17 2017 UTC (3 months, 3 weeks ago) by jfenwick
netcdf build option is now 3-state

no, 3, 4
I haven't bumped the options file version because
my changes should be backwards compatible 


Revision 6508 - Directory Listing
Modified Thu Mar 2 03:42:31 2017 UTC (3 months, 3 weeks ago) by jfenwick
Weipa netcdf update

passes unit tests -DNETCDF4 and only directly links:
  netcdf_c++4

Need to clean up scons options control


Revision 6507 - Directory Listing
Modified Wed Mar 1 06:19:04 2017 UTC (3 months, 3 weeks ago) by jfenwick
More netcdf4 work

Still need to convert weipa


Revision 6506 - Directory Listing
Modified Tue Feb 28 03:58:20 2017 UTC (3 months, 3 weeks ago) by jfenwick
Work on new netcdf


Revision 6505 - Directory Listing
Modified Tue Feb 21 06:11:12 2017 UTC (4 months ago) by jfenwick
Work on new netcdf interface

It passes unit tests ....


Revision 6504 - Directory Listing
Modified Tue Feb 21 01:00:17 2017 UTC (4 months ago) by jfenwick
Helper function to open netcdf


Revision 6503 - Directory Listing
Modified Mon Feb 20 03:39:19 2017 UTC (4 months ago) by jfenwick
netcdf4 version of load


Revision 6502 - Directory Listing
Modified Mon Feb 20 03:38:46 2017 UTC (4 months ago) by jfenwick
hiding some variables

Revision 6501 - Directory Listing
Modified Mon Feb 20 03:36:51 2017 UTC (4 months ago) by jfenwick
Removing debug vectors from debug builds since netcdfc++4 doesn\'t seem to like them

Revision 6500 - Directory Listing
Modified Fri Feb 17 04:54:25 2017 UTC (4 months, 1 week ago) by jfenwick
Forgot to check with MPI

Revision 6499 - Directory Listing
Modified Thu Feb 16 06:37:07 2017 UTC (4 months, 1 week ago) by jfenwick
Work towards netcdf4

Revision 6498 - Directory Listing
Modified Wed Feb 15 05:12:55 2017 UTC (4 months, 1 week ago) by jfenwick
partial workaround of complex testing issue

Revision 6497 - Directory Listing
Modified Wed Feb 15 00:44:55 2017 UTC (4 months, 1 week ago) by jfenwick
Reader for netcdf classic headers.



Revision 6496 - Directory Listing
Modified Tue Feb 14 00:38:08 2017 UTC (4 months, 1 week ago) by gross
bug to obtain function space fixed.

Revision 6495 - Directory Listing
Modified Fri Feb 10 08:16:28 2017 UTC (4 months, 2 weeks ago) by gross
magnetic intensity added.

Revision 6494 - Directory Listing
Modified Thu Feb 9 23:28:53 2017 UTC (4 months, 2 weeks ago) by jfenwick
This version seems to work


Revision 6493 - Directory Listing
Modified Thu Feb 9 23:23:37 2017 UTC (4 months, 2 weeks ago) by jfenwick
Added stdlocationisprefix option

This option will set the STD_LOCATION to the build prefix
Need this for building on magnus


Revision 6492 - Directory Listing
Modified Thu Feb 9 07:32:43 2017 UTC (4 months, 2 weeks ago) by gross
new section in inversion guide

Revision 6491 - Directory Listing
Modified Thu Feb 9 02:04:18 2017 UTC (4 months, 2 weeks ago) by jfenwick
fix name of macports boostio

Revision 6490 - Directory Listing
Modified Thu Feb 9 01:21:02 2017 UTC (4 months, 2 weeks ago) by jfenwick
because Darwin different

Revision 6489 - Directory Listing
Modified Thu Feb 9 00:28:44 2017 UTC (4 months, 2 weeks ago) by jfenwick
fix it

Revision 6488 - Directory Listing
Modified Wed Feb 8 23:55:10 2017 UTC (4 months, 2 weeks ago) by jfenwick
Attempt to make python detection better

Revision 6487 - Directory Listing
Modified Tue Feb 7 00:51:09 2017 UTC (4 months, 2 weeks ago) by caltinay
fix typo.


Revision 6486 - Directory Listing
Modified Fri Jan 27 00:13:27 2017 UTC (4 months, 4 weeks ago) by jfenwick
Another case of allowing complex


Revision 6485 - Directory Listing
Modified Wed Jan 25 04:45:38 2017 UTC (5 months ago) by jfenwick
Some more tests


Revision 6484 - Directory Listing
Modified Wed Jan 25 04:43:39 2017 UTC (5 months ago) by jfenwick
More helpful error message


Revision 6483 - Directory Listing
Modified Wed Jan 25 02:56:14 2017 UTC (5 months ago) by jfenwick
Biting bullet and doing separate generator for matrix


Revision 6482 - Directory Listing
Modified Tue Jan 24 07:45:33 2017 UTC (5 months ago) by jfenwick
More tests

Still need to look at the MVp testing


Revision 6481 - Directory Listing
Modified Tue Jan 24 07:34:24 2017 UTC (5 months ago) by jfenwick
Decree: Tensor products are not always real.


Revision 6480 - Directory Listing
Modified Tue Jan 24 05:01:31 2017 UTC (5 months ago) by jfenwick
Test for outer



Revision 6479 - Directory Listing
Modified Mon Jan 23 11:33:19 2017 UTC (5 months ago) by caltinay
Unbreak ripley Brick.


Revision 6478 - Directory Listing
Modified Mon Jan 23 10:15:02 2017 UTC (5 months ago) by caltinay
Let ripley's auto decomposition deal with this test. For <=4 ranks this
now succeeds, let's see what happens on Savanna...


Revision 6477 - Directory Listing
Modified Mon Jan 23 10:13:13 2017 UTC (5 months ago) by caltinay
Fixing default decomposition policy in ripley (ouch!).

Forgot to reset the grid spacing members so despite reporting the correct
values the domain did get expanded!


Revision 6476 - Directory Listing
Modified Mon Jan 23 08:32:07 2017 UTC (5 months ago) by caltinay
Fix test that was way too strict - obviously something in GDAL changed that
caused the failures when comparing data origin. But 7 digits are far too
many given the data is in meters.


Revision 6475 - Directory Listing
Modified Fri Jan 20 02:17:33 2017 UTC (5 months ago) by caltinay
syncing savanna options with actual dev-deps module. We had switched to
intel 17 a while back.


Revision 6474 - Directory Listing
Modified Fri Jan 20 00:12:46 2017 UTC (5 months ago) by gross
docstring updated.

Revision 6473 - Directory Listing
Modified Thu Jan 19 07:27:04 2017 UTC (5 months ago) by caltinay
complex integrals for ripley - part of #398. This is not properly tested.
Trying to integrate complex Data on other domains now throws rather than segfaulting.


Revision 6472 - Directory Listing
Modified Thu Jan 19 00:39:08 2017 UTC (5 months ago) by jfenwick
Fix failing unit tests


Revision 6471 - Directory Listing
Modified Wed Jan 18 06:09:47 2017 UTC (5 months, 1 week ago) by jfenwick
Make tuples acceptable to getRank and getShape


Revision 6470 - Directory Listing
Modified Wed Jan 18 05:37:05 2017 UTC (5 months, 1 week ago) by jfenwick
Initial tests binary operation


Revision 6469 - Directory Listing
Modified Tue Jan 17 07:45:36 2017 UTC (5 months, 1 week ago) by jfenwick
Add zeroed copy


Revision 6468 - Directory Listing
Modified Tue Jan 17 07:35:13 2017 UTC (5 months, 1 week ago) by jfenwick
reductions no longer ignore tags with default values

Also fix the tests which depended on broken Lsup
But it's better this way anyway


Revision 6467 - Directory Listing
Modified Wed Jan 11 03:13:14 2017 UTC (5 months, 2 weeks ago) by jfenwick
Fix unit test failure


Revision 6466 - Directory Listing
Modified Wed Jan 11 01:52:56 2017 UTC (5 months, 2 weeks ago) by jfenwick
Now includes tests of all ops in the original test set

These tests do not include tests of symbol inputs but those
aren't tested by the old set either


Revision 6465 - Directory Listing
Modified Wed Jan 11 01:28:23 2017 UTC (5 months, 2 weeks ago) by jfenwick
Fix bug in get_tagged
Adding test for eigenvalues - not currently testing the scalar input case


Revision 6464 - Directory Listing
Modified Wed Jan 11 00:00:46 2017 UTC (5 months, 2 weeks ago) by jfenwick
More tests

Rename data_only to no_scalars [which is more accurate]



Revision 6463 - Directory Listing
Modified Tue Jan 10 22:46:54 2017 UTC (5 months, 2 weeks ago) by jfenwick
Fix test failures

ensure inf and sup raise for complex ndarray
hasNaN does support complex



Revision 6462 - Directory Listing
Modified Tue Jan 10 06:37:50 2017 UTC (5 months, 2 weeks ago) by jfenwick
hermitian tests debug output


Revision 6461 - Directory Listing
Modified Tue Jan 10 06:29:51 2017 UTC (5 months, 2 weeks ago) by jfenwick
Stop (anit-)hermitian from using numpy.transpose

It doesn't default to the same axes swaps as our's does


Revision 6460 - Directory Listing
Modified Tue Jan 10 04:54:19 2017 UTC (5 months, 2 weeks ago) by jfenwick
Correct docstring for antihermitian


Revision 6459 - Directory Listing
Modified Tue Jan 10 04:28:51 2017 UTC (5 months, 2 weeks ago) by jfenwick
Fix build failure and add test

Used a common base type for exception which both py2 and py3 know about.
Can now specify that one expects certain ranks to throw and to specify
what sort of exceptions one expects.
   There is currently no way to specify which exceptions should be
thrown in which circumstances. I'm hoping that won't be required.



Revision 6458 - Directory Listing
Modified Tue Jan 10 03:04:13 2017 UTC (5 months, 2 weeks ago) by jfenwick
More debug and test for transpose


Revision 6457 - Directory Listing
Modified Tue Jan 10 02:05:39 2017 UTC (5 months, 2 weeks ago) by jfenwick
More tests

Added tests and reordered some.
Ensure that all complex possibilities are tested for exceptions not
just scalars.
Added min and max rank parameters - first use is to limit matrix
inversion to 2x2 cases.

Tests now check rank-4 cases.


Revision 6456 - Directory Listing
Modified Tue Jan 10 02:03:16 2017 UTC (5 months, 2 weeks ago) by jfenwick
Change in whereX semantics

The whereX functions now raise exceptions for complex numpy arrays.
They did not used to do this but this change brings them into line
with what Data does


Revision 6455 - Directory Listing
Modified Mon Jan 9 05:35:43 2017 UTC (5 months, 2 weeks ago) by jfenwick
Tests and fix to util.length

Added tests for maxval, minval and length.
util.length(z) now takes abs(z) of before applying inner product


Revision 6454 - Directory Listing
Modified Mon Jan 9 04:19:59 2017 UTC (5 months, 2 weeks ago) by jfenwick
Have unary tests for the trig now


Revision 6453 - Directory Listing
Modified Mon Jan 9 03:17:00 2017 UTC (5 months, 2 weeks ago) by jfenwick
More tests using the more general tester.

Added type to the Lsup type error message to help with future debugging.
The unary tests currently have some duplication because all of the old tests
run as well as the new tests but I'll fix that once the new tests cover everything.



Revision 6452 - Directory Listing
Modified Sun Jan 8 21:41:36 2017 UTC (5 months, 2 weeks ago) by jfenwick
Adapt to moving openmpi library

This fix assumes that the architecture you are linking to is
the one which the include headers are symlinked from.


Revision 6451 - Directory Listing
Modified Tue Dec 20 06:22:39 2016 UTC (6 months ago) by caltinay
Added '--mca io romio314' to guineapig options to get around a regression(?) in
OMPIO.
Basically it looks like current OpenMPI in Debian blocks when calling
MPI_File_write_shared from a subset of ranks only (which we do in a test).
My understanding of the spec is that this should not block as it's not a
collective operation and it certainly works with ROMIO and IntelMPI which is
why I think it may be a regression. This should probably be asked on the
OpenMPI mailing list. I have a test case if required.


Revision 6450 - Directory Listing
Modified Thu Dec 15 02:33:38 2016 UTC (6 months, 1 week ago) by jfenwick
Starting work on the unary ops


Revision 6449 - Directory Listing
Modified Wed Dec 14 01:01:48 2016 UTC (6 months, 1 week ago) by jfenwick
Removing references to the old util_reduction tests.
Note that this does weaken the ability to test domains which do not support
tagging because all types are tested together now.
However, if that becomes necessary, we can query the functionspace and 
not add tagged tests if it reports not supporting tagging.
At this point, more compact tests are more important.



Revision 6448 - Directory Listing
Modified Tue Dec 13 06:25:52 2016 UTC (6 months, 1 week ago) by jfenwick
Switch over to new util tests.
Fix some bugs


Revision 6447 - Directory Listing
Modified Tue Dec 13 05:07:30 2016 UTC (6 months, 1 week ago) by jfenwick
Reduction tests


Revision 6446 - Directory Listing
Modified Tue Dec 13 04:44:28 2016 UTC (6 months, 1 week ago) by jfenwick
Enable NAN_CHECK for all builds.
If you don't support std::isnan, then you don't support c++11


Revision 6445 - Directory Listing
Modified Wed Dec 7 07:01:18 2016 UTC (6 months, 2 weeks ago) by jfenwick
Make sure some of the test values are negative


Revision 6444 - Directory Listing
Modified Tue Dec 6 08:24:19 2016 UTC (6 months, 2 weeks ago) by jfenwick
More progress


Revision 6443 - Directory Listing
Modified Mon Dec 5 23:28:02 2016 UTC (6 months, 2 weeks ago) by jfenwick
Start on test restructure


Revision 6442 - Directory Listing
Modified Fri Dec 2 06:17:38 2016 UTC (6 months, 3 weeks ago) by gross
some modifications VGL

Revision 6441 - Directory Listing
Modified Tue Nov 29 07:27:03 2016 UTC (6 months, 3 weeks ago) by gross
arguments fixed

Revision 6440 - Directory Listing
Modified Tue Nov 29 07:26:33 2016 UTC (6 months, 3 weeks ago) by gross
namespace problem fixed

Revision 6439 - Directory Listing
Modified Tue Nov 29 05:35:33 2016 UTC (6 months, 3 weeks ago) by jfenwick
Adding a comment to explain what TestDomainTest is actually for.
Remove test_assemblage_* since all of those tests are covered by
test_assemblage [I'm sure Simon warned me about that].
Collapse the 3D2 parts which depended on them.
 Other than cleaning up, this should not change what is tested.



Revision 6438 - Directory Listing
Modified Mon Nov 7 08:30:55 2016 UTC (7 months, 2 weeks ago) by jfenwick
Remainder of this batch of default removing.


Revision 6437 - Directory Listing
Modified Mon Nov 7 04:20:32 2016 UTC (7 months, 2 weeks ago) by jfenwick
Fix compile error introduced last time.
Fix more calls in Dudley


Revision 6436 - Directory Listing
Modified Mon Nov 7 01:28:47 2016 UTC (7 months, 2 weeks ago) by jfenwick
Throw in some routines which don't support complex yet.
Fix some routines which rely on being able to get the entire 
vector by referencing relative to [0] (problem for lazy).
   This was addressed by adding a more explicit call.
Make calls to getSample?? pass explicit type parameter.

There is more to be done here.



Revision 6435 - Directory Listing
Modified Sat Nov 5 12:35:35 2016 UTC (7 months, 2 weeks ago) by caltinay
fix for #387 in ripley - implementation of complex straightforward interpolations.


Revision 6434 - Directory Listing
Modified Sat Nov 5 12:16:07 2016 UTC (7 months, 2 weeks ago) by caltinay
Final pieces for #386: Complex gradients for Speckley 3D order 2-10. Removed workaround from escript.


Revision 6433 - Directory Listing
Modified Sat Nov 5 12:14:52 2016 UTC (7 months, 2 weeks ago) by caltinay
#386: speckley complex gradients for 2D orders 3-10


Revision 6432 - Directory Listing
Modified Sat Nov 5 11:55:44 2016 UTC (7 months, 2 weeks ago) by caltinay
#386 - complex gradient for speckley 2D.


Revision 6431 - Directory Listing
Modified Sat Nov 5 11:38:07 2016 UTC (7 months, 2 weeks ago) by caltinay
#386: complex gradients for dudley.


Revision 6430 - Directory Listing
Modified Sat Nov 5 11:27:45 2016 UTC (7 months, 2 weeks ago) by caltinay
Part of #386 - complex gradients for finley.


Revision 6429 - Directory Listing
Modified Thu Nov 3 23:35:58 2016 UTC (7 months, 3 weeks ago) by caltinay
Part of #386 - complex gradient for ripley Brick.


Revision 6428 - Directory Listing
Modified Thu Nov 3 07:32:41 2016 UTC (7 months, 3 weeks ago) by gross
workaround for Bug #389 removed

Revision 6427 - Directory Listing
Modified Thu Nov 3 07:32:38 2016 UTC (7 months, 3 weeks ago) by jfenwick
Complex interpolation changes for ripley.
Needs better tests and removal of work-around once the other domains 
are done.


Revision 6426 - Directory Listing
Modified Thu Nov 3 05:07:00 2016 UTC (7 months, 3 weeks ago) by jfenwick
Initial work on fixing the complex interpolation issue.
This is just Ripley::Rectangle others to follow


Revision 6425 - Directory Listing
Modified Thu Nov 3 03:34:29 2016 UTC (7 months, 3 weeks ago) by jfenwick
Beginnings of interpolation fixes for complex.
I have not undone the python work-around because I still need to look
at the domains.
Starting with ripley


Revision 6424 - Directory Listing
Modified Thu Nov 3 02:13:09 2016 UTC (7 months, 3 weeks ago) by jfenwick
Fixing copyWithMask to work with complex Data (issue #389)

Revision 6423 - Directory Listing
Modified Wed Nov 2 13:05:29 2016 UTC (7 months, 3 weeks ago) by caltinay
prepare for complex gradients. Workaround in util.py still guards against badness.


Revision 6422 - Directory Listing
Modified Wed Nov 2 13:04:09 2016 UTC (7 months, 3 weeks ago) by caltinay
and the accompanying header changes to the last commit...


Revision 6421 - Directory Listing
Modified Wed Nov 2 13:03:45 2016 UTC (7 months, 3 weeks ago) by caltinay
implemented complex gradient for ripley 2D.

Code path is still disabled in escript until all other cases are implemented.


Revision 6420 - Directory Listing
Modified Wed Nov 2 06:35:58 2016 UTC (7 months, 3 weeks ago) by jfenwick
Fix Scalar with complex

#392



Revision 6419 - Directory Listing
Modified Wed Nov 2 06:09:25 2016 UTC (7 months, 3 weeks ago) by jfenwick
Fix segfault in slice assignment with complex.

Addresses issue #394



Revision 6418 - Directory Listing
Modified Wed Nov 2 05:04:51 2016 UTC (7 months, 3 weeks ago) by jfenwick
Fix TensorX factories to allow passing a complex scalar.

Issue described in #394 (although that wasn't the main point of that bug).



Revision 6417 - Directory Listing
Modified Wed Nov 2 03:57:52 2016 UTC (7 months, 3 weeks ago) by jfenwick
Fix setToZero


Revision 6416 - Directory Listing
Modified Wed Nov 2 03:01:53 2016 UTC (7 months, 3 weeks ago) by jfenwick
Prevent saveDataCSV from being called with complex values


Revision 6415 - Directory Listing
Modified Wed Nov 2 02:46:34 2016 UTC (7 months, 3 weeks ago) by gross
work around for bug #391 (right version now)

Revision 6414 - Directory Listing
Modified Wed Nov 2 02:44:31 2016 UTC (7 months, 3 weeks ago) by gross
work around for bug #391

Revision 6413 - Directory Listing
Modified Wed Nov 2 02:31:11 2016 UTC (7 months, 3 weeks ago) by jfenwick
Added untested .phase()  to Data.



Revision 6412 - Directory Listing
Modified Wed Nov 2 02:18:49 2016 UTC (7 months, 3 weeks ago) by gross
work around for bug #390

Revision 6411 - Directory Listing
Modified Wed Nov 2 01:48:58 2016 UTC (7 months, 3 weeks ago) by gross
work around for bug #386

Revision 6410 - Directory Listing
Modified Tue Nov 1 06:12:42 2016 UTC (7 months, 3 weeks ago) by jfenwick
Very minor fix towards more repeatable builds


Revision 6409 - Directory Listing
Modified Thu Oct 27 07:35:14 2016 UTC (7 months, 4 weeks ago) by gross
print statement removed

Revision 6408 - Directory Listing
Modified Thu Oct 27 03:29:59 2016 UTC (7 months, 4 weeks ago) by gross
work around for  Bug #389

Revision 6407 - Directory Listing
Modified Wed Oct 19 03:13:45 2016 UTC (8 months, 1 week ago) by gross
replaced complex argument by isComplex as complex is python keyword.

Revision 6406 - Directory Listing
Modified Wed Oct 19 02:16:52 2016 UTC (8 months, 1 week ago) by jfenwick
recording badgers trilinos options

Revision 6405 - Directory Listing
Modified Thu Oct 13 23:35:11 2016 UTC (8 months, 1 week ago) by gross
interpolation from reduced to full for finley Function. needs more work

Revision 6404 - Directory Listing
Modified Thu Sep 22 05:37:56 2016 UTC (9 months ago) by jfenwick
Fixing the openmp options for icpc


Revision 6400 - Directory Listing
Modified Thu Sep 8 13:09:10 2016 UTC (9 months, 2 weeks ago) by caltinay
Should fix #381 - Trilinos support for periodic boundaries.

An assumption was made which doesn't hold when periodic boundaries are used.
Removed that unnecessary assumption which fixes matrix size and indices.

Obviously we are lacking tests for this so will open up a ticket.


Revision 6399 - Directory Listing
Modified Wed Aug 3 00:21:25 2016 UTC (10 months, 3 weeks ago) by caltinay
fix warnings for paso-only build.


Revision 6398 - Directory Listing
Modified Tue Aug 2 12:39:07 2016 UTC (10 months, 3 weeks ago) by caltinay
update changelog.


Revision 6397 - Directory Listing
Modified Mon Aug 1 22:52:08 2016 UTC (10 months, 3 weeks ago) by caltinay
Implemented feature #281.

Ripley's default decomposition policy has now CHANGED. Domains will now
by default add elements only, leaving the lengths alone. Users can call
setDecompositionPolicy() to change that.


Revision 6396 - Directory Listing
Modified Mon Aug 1 22:27:28 2016 UTC (10 months, 3 weeks ago) by caltinay
changed order of direct solver preference as the Trilinos MUMPS interface clearly has issues.


Revision 6395 - Directory Listing
Modified Mon Aug 1 22:25:27 2016 UTC (10 months, 3 weeks ago) by caltinay
moving isDirectSolver() function to escript to correct solver library selection logic.

Also updated Ripley SystemMatrix overload with recent change.


Revision 6394 - Directory Listing
Modified Mon Aug 1 22:00:00 2016 UTC (10 months, 3 weeks ago) by caltinay
Work towards solving #281 - added static member but unused at the moment.


Revision 6393 - Directory Listing
Modified Mon Aug 1 06:20:09 2016 UTC (10 months, 3 weeks ago) by caltinay
Implement #379.

There is now a way to tell the PDE to retain preconditioner across solves
even when the matrix changes. This is enabled via pde.preservePreconditioner().
In conjunction with AMG and the reuse parameter this saves some time when
solving an almost identical system more than once.


Revision 6392 - Directory Listing
Modified Mon Aug 1 02:27:56 2016 UTC (10 months, 3 weeks ago) by caltinay
Implemented setting specific direct solver. Fixes #378


Revision 6391 - Directory Listing
Modified Thu Jul 28 05:44:42 2016 UTC (10 months, 4 weeks ago) by jfenwick
Removing instructions for installing from packages
Started changelog in user guide


Revision 6390 - Directory Listing
Modified Wed Jul 27 07:46:27 2016 UTC (11 months ago) by jfenwick
Fiddling with changelog


Revision 6389 - Directory Listing
Modified Wed Jul 27 07:39:57 2016 UTC (11 months ago) by jfenwick
Adding suitesparse to builddeps


Revision 6388 - Directory Listing
Modified Wed Jul 27 04:57:45 2016 UTC (11 months ago) by caltinay
add a way to modify solver options in simplesolve and use it to set
AMG block size so tests pass.


Revision 6387 - Directory Listing
Modified Mon Jul 25 06:11:40 2016 UTC (11 months ago) by caltinay
removed deprecated symbol, fixes #325


Revision 6386 - Directory Listing
Modified Mon Jul 25 06:01:14 2016 UTC (11 months ago) by caltinay
trying again to avoid mumps issue.


Revision 6385 - Directory Listing
Modified Mon Jul 25 03:17:21 2016 UTC (11 months ago) by caltinay
trying to fix remaining test failures which would have always failed but
only now are we actually running direct solvers under MPI...


Revision 6384 - Directory Listing
Modified Mon Jul 25 02:49:01 2016 UTC (11 months ago) by caltinay
modifying NE for ripley domain to circumvent Trilinos-MUMPS issue.

I have reported this (https://github.com/trilinos/Trilinos/issues/520)
and this should fix at least one test failure.


Revision 6383 - Directory Listing
Modified Mon Jul 25 02:47:11 2016 UTC (11 months ago) by caltinay
fixing parameter passing to Amesos2.


Revision 6382 - Directory Listing
Modified Mon Jul 25 00:02:08 2016 UTC (11 months ago) by caltinay
removing two duplicate tests.


Revision 6381 - Directory Listing
Modified Fri Jul 22 09:12:46 2016 UTC (11 months ago) by caltinay
changed some assertions so we get a better idea of values.

Not sure why current tests fail, some issues with Mumps?!


Revision 6380 - Directory Listing
Modified Fri Jul 22 06:32:45 2016 UTC (11 months ago) by caltinay
enable more tests that were skipped due to trilinos limitations.


Revision 6379 - Directory Listing
Modified Fri Jul 22 06:31:38 2016 UTC (11 months ago) by caltinay
fix indexing when adding to unrolled matrix...


Revision 6378 - Directory Listing
Modified Fri Jul 22 06:05:44 2016 UTC (11 months ago) by caltinay
added unroll flag to dudley and finley and enabled tests that were skipped
before.


Revision 6377 - Directory Listing
Modified Fri Jul 22 05:49:14 2016 UTC (11 months ago) by caltinay
add ILUT to the cases that require unrolling. Enable previously disabled tests
in ripley that now pass.
There are now bogus failures because the wrapper no longer throws for cases
that were not supported earlier. I can't fix that before changing finley and
dudley...


Revision 6376 - Directory Listing
Modified Fri Jul 22 05:35:20 2016 UTC (11 months ago) by caltinay
Woohoo! We can now 'unroll' Trilinos block matrices in order to get around the
limitations of Trilinos for solving block problems.
This commit adds the functionality to the wrapper and enables it for ripley.
dudley and finley will follow and I haven't enabled the tests yet.


Revision 6375 - Directory Listing
Modified Fri Jul 22 00:27:31 2016 UTC (11 months ago) by caltinay
finally, allow setting direct solver params from python.


Revision 6374 - Directory Listing
Modified Thu Jul 21 05:00:24 2016 UTC (11 months ago) by caltinay
Pass preconditioner options to Trilinos.


Revision 6373 - Directory Listing
Modified Wed Jul 20 23:47:10 2016 UTC (11 months ago) by caltinay
moved util method to separate header. Started setting options for preconditioners.


Revision 6372 - Directory Listing
Modified Wed Jul 20 06:14:51 2016 UTC (11 months, 1 week ago) by caltinay
We can now pass Trilinos options through the SolverBuddy.

Updated BelosWrapper to extract the supported options. Amesos2 & Ifpack2
to follow...


Revision 6371 - Directory Listing
Modified Wed Jul 20 03:02:32 2016 UTC (11 months, 1 week ago) by caltinay
replicated the changes that keep factorization/problem for block matrices.


Revision 6370 - Directory Listing
Modified Wed Jul 20 01:47:26 2016 UTC (11 months, 1 week ago) by caltinay
fix my launcher.


Revision 6369 - Directory Listing
Modified Tue Jul 19 07:11:15 2016 UTC (11 months, 1 week ago) by caltinay
Trilinoswrap now keeps previously computed factorizations in case of
direct solver, and previously set 'problem' in case of iterative solver.

This accelerates solve times substantially.
We currently do NOT check if the user changed solver options in between solves,
i.e. we do not detect if user does:
pde.setValue(...)
pde.getSolution()
pde.setValue(y=...)
solveroptions.setNewPreconditionerOrChangeSomeSolverRelevantOption(...)
pde.getSolution()

but one can always do: pde.resetOperator() to force reset (which happens
automatically if we change matrix values via A etc.)



Revision 6368 - Directory Listing
Modified Tue Jul 19 07:03:29 2016 UTC (11 months, 1 week ago) by caltinay
diagnostics reporting in block matrix wrapper.


Revision 6367 - Directory Listing
Modified Tue Jul 19 04:56:16 2016 UTC (11 months, 1 week ago) by caltinay
SolverBuddy: overload updateDiagnostics so we can call it from C++ - not ideal
but quick fix before a revamp of the whole class.
TrilinosMatrix: update solver diagnostics for time, residual and num iter.
RipleyMatrix: don't copy the SolverBuddy so the diags are actually returned.


Revision 6366 - Directory Listing
Modified Mon Jul 18 23:16:50 2016 UTC (11 months, 1 week ago) by caltinay
allow oversubscribe on guineapig for gmsh mpi invocation.


Revision 6365 - Directory Listing
Modified Mon Jul 18 11:23:09 2016 UTC (11 months, 1 week ago) by caltinay
remove -host arg on guineapig to avoid the new openmpi behaviour. We
probably need a bit more logic to fix this properly and more generally.


Revision 6364 - Directory Listing
Modified Mon Jul 18 02:25:04 2016 UTC (11 months, 1 week ago) by jfenwick
Force shorter trees to get lazy testing done in reasonable time


Revision 6363 - Directory Listing
Modified Tue Jul 12 06:23:40 2016 UTC (11 months, 2 weeks ago) by caltinay
update solver diagnostics for cusp solvers.


Revision 6362 - Directory Listing
Modified Thu Jul 7 03:12:06 2016 UTC (11 months, 2 weeks ago) by jfenwick
Doesn't fix any major problem bit closes #370

It wasn't actually a problem, but I've added explanatory text
to make it clear that something isn't going wrong.


Revision 6361 - Directory Listing
Modified Wed Jul 6 04:10:30 2016 UTC (11 months, 3 weeks ago) by caltinay
change solver tolerance for joint inversion test which takes too long with Lazy.


Revision 6360 - Directory Listing
Modified Wed Jul 6 03:02:30 2016 UTC (11 months, 3 weeks ago) by caltinay
complex finley contact elements.


Revision 6359 - Directory Listing
Modified Wed Jul 6 02:44:18 2016 UTC (11 months, 3 weeks ago) by caltinay
finley complex dirac.


Revision 6358 - Directory Listing
Modified Wed Jul 6 02:38:10 2016 UTC (11 months, 3 weeks ago) by caltinay
complex finley 3D PDE systems.


Revision 6357 - Directory Listing
Modified Wed Jul 6 02:24:03 2016 UTC (11 months, 3 weeks ago) by caltinay
complex finley 2D PDE systems.


Revision 6356 - Directory Listing
Modified Wed Jul 6 01:53:11 2016 UTC (11 months, 3 weeks ago) by caltinay
complex finley single 3D PDEs.


Revision 6355 - Directory Listing
Modified Wed Jul 6 01:03:10 2016 UTC (11 months, 3 weeks ago) by caltinay
fix compile without trilinos and add support for 2D complex single PDEs to finley.


Revision 6354 - Directory Listing
Modified Wed Jul 6 00:24:29 2016 UTC (11 months, 3 weeks ago) by caltinay
first step for complex PDEs in finley.


Revision 6353 - Directory Listing
Modified Tue Jul 5 06:36:20 2016 UTC (11 months, 3 weeks ago) by jfenwick
Another attempt to fix #372


Revision 6352 - Directory Listing
Modified Tue Jul 5 05:53:49 2016 UTC (11 months, 3 weeks ago) by jfenwick
Fixing summary for complex data


Revision 6351 - Directory Listing
Modified Tue Jul 5 05:47:29 2016 UTC (11 months, 3 weeks ago) by caltinay
dudley complex dirac.


Revision 6350 - Directory Listing
Modified Tue Jul 5 05:42:37 2016 UTC (11 months, 3 weeks ago) by caltinay
complex dudley 3D PDE systems.


Revision 6349 - Directory Listing
Modified Tue Jul 5 05:33:02 2016 UTC (11 months, 3 weeks ago) by caltinay
complex dudley 2D systems.


Revision 6348 - Directory Listing
Modified Tue Jul 5 05:31:48 2016 UTC (11 months, 3 weeks ago) by caltinay
interrogate coefficient for value type rather than PDE.

That way we get the correct type for
pde.createCoefficient("q")
even with complex-valued PDEs.


Revision 6347 - Directory Listing
Modified Tue Jul 5 04:50:14 2016 UTC (11 months, 3 weeks ago) by caltinay
complex support for dudley 3D single PDEs.


Revision 6346 - Directory Listing
Modified Mon Jul 4 07:27:36 2016 UTC (11 months, 3 weeks ago) by caltinay
oops, sorry.


Revision 6345 - Directory Listing
Modified Mon Jul 4 05:32:05 2016 UTC (11 months, 3 weeks ago) by jfenwick
Converting minGlobalDataPoint and maxGlobalDataPoint to internal_
That way people should not be using it and we can get rid of #5

Fixed a minor error in an error message.


Revision 6344 - Directory Listing
Modified Mon Jul 4 03:19:25 2016 UTC (11 months, 3 weeks ago) by jfenwick
Fix #372
Add some minimal testing
Change some references to "view"


Revision 6343 - Directory Listing
Modified Mon Jul 4 02:11:54 2016 UTC (11 months, 3 weeks ago) by caltinay
implemented complex-valued 2D single PDE solves with dudley.


Revision 6342 - Directory Listing
Modified Mon Jul 4 01:27:07 2016 UTC (11 months, 3 weeks ago) by caltinay
enable complex PDE solves in 3D with ripley.


Revision 6341 - Directory Listing
Modified Sun Jul 3 23:56:33 2016 UTC (11 months, 3 weeks ago) by caltinay
fixing type for smoother argument.


Revision 6340 - Directory Listing
Modified Fri Jul 1 12:58:45 2016 UTC (11 months, 3 weeks ago) by caltinay
Final piece of the puzzle: enable nullifyRowsAndCols for complex matrices.

There needs to be a new method to set diagonals to a complex value but I
haven't done that yet.

!! We can now solve a complex-valued 2D PDE with ripley !!


Revision 6339 - Directory Listing
Modified Fri Jul 1 12:56:43 2016 UTC (11 months, 3 weeks ago) by caltinay
(2.1) use the right type for solution vector.


Revision 6338 - Directory Listing
Modified Fri Jul 1 12:42:35 2016 UTC (11 months, 3 weeks ago) by caltinay
(5) this is the first big one -

template'ize ripley's DefaultAssembler2D and instantiate for both real_t and
cplx_t. Annoyingly, I had to replace all int-constants by doubles, as
2*c (where c is complex) does NOT compile. Also replaced all getSampleData*()
calls and initializers as required.


Revision 6337 - Directory Listing
Modified Fri Jul 1 12:38:18 2016 UTC (11 months, 3 weeks ago) by caltinay
(4) add complex argument to LinearProblem, LinearPDE and PDECoef.


Revision 6336 - Directory Listing
Modified Fri Jul 1 12:37:05 2016 UTC (11 months, 3 weeks ago) by caltinay
(3) add isComplex & setComplex to solver options.


Revision 6335 - Directory Listing
Modified Fri Jul 1 12:36:22 2016 UTC (11 months, 3 weeks ago) by caltinay
(2) use the right type to initialize Data object for mat-vec mult.


Revision 6334 - Directory Listing
Modified Fri Jul 1 12:35:42 2016 UTC (11 months, 3 weeks ago) by caltinay
The next few commits will start introducing complex-valued PDEs to escript.

Firstly, here is a C++ Data constructor that takes a complex constant. This
will be required by the mat-vec mult implementation.


Revision 6333 - Directory Listing
Modified Fri Jul 1 03:58:43 2016 UTC (11 months, 3 weeks ago) by caltinay
write some more features into buildvars.


Revision 6332 - Directory Listing
Modified Thu Jun 30 09:32:40 2016 UTC (11 months, 3 weeks ago) by caltinay
missed one.


Revision 6331 - Directory Listing
Modified Thu Jun 30 09:31:06 2016 UTC (11 months, 3 weeks ago) by caltinay
fixing unreachable code warnings issued by nvcc.


Revision 6330 - Directory Listing
Modified Sat Jun 25 11:36:26 2016 UTC (12 months ago) by caltinay
added missing x.


Revision 6329 - Directory Listing
Modified Fri Jun 24 04:19:10 2016 UTC (12 months ago) by caltinay
*sigh* add another barrier for file writer test - still not convinced openMPI
behaves properly.


Revision 6328 - Directory Listing
Modified Fri Jun 24 00:36:00 2016 UTC (12 months ago) by caltinay
try again - store exception in another var to avoid it becoming out of context.


Revision 6327 - Directory Listing
Modified Thu Jun 23 21:42:45 2016 UTC (12 months ago) by caltinay
tweak solver tolerance for all trilinos order 2 pde's in finley


Revision 6326 - Directory Listing
Modified Thu Jun 23 10:32:39 2016 UTC (12 months ago) by caltinay
more Amesos2 skips.


Revision 6325 - Directory Listing
Modified Thu Jun 23 09:12:54 2016 UTC (12 months ago) by caltinay
oops, these tests use pde systems so can't use Amesos2 yet.


Revision 6324 - Directory Listing
Modified Thu Jun 23 06:26:22 2016 UTC (12 months ago) by caltinay
fix.


Revision 6323 - Directory Listing
Modified Thu Jun 23 06:05:23 2016 UTC (12 months ago) by caltinay
skip ILUT block tests with trilinos.


Revision 6322 - Directory Listing
Modified Thu Jun 23 05:56:49 2016 UTC (12 months ago) by caltinay
don't reference e before assignment.


Revision 6321 - Directory Listing
Modified Thu Jun 23 05:38:50 2016 UTC (12 months ago) by caltinay
feature #3: this should fix up remaining tests that only checked paso_direct.
I also moved paso_direct to 'hasFeature' as it's a boolean...


Revision 6320 - Directory Listing
Modified Thu Jun 23 05:22:01 2016 UTC (12 months ago) by caltinay
i broke it.


Revision 6319 - Directory Listing
Modified Thu Jun 23 05:01:39 2016 UTC (12 months ago) by caltinay
remove Super LU from everywhere, we never supported it and never will directly.


Revision 6318 - Directory Listing
Modified Thu Jun 23 04:58:46 2016 UTC (12 months ago) by caltinay
remove pastix from everywhere. We never supported it and never will directly.


Revision 6317 - Directory Listing
Modified Thu Jun 23 04:48:29 2016 UTC (12 months ago) by caltinay
parts for feature #3 - automatically choose trilinos if:
1) package == default
2) method == direct
3) trilinos available
4) mpi size > 1


Revision 6316 - Directory Listing
Modified Thu Jun 23 04:25:56 2016 UTC (12 months ago) by caltinay
update tests, we now support pde systems with trilinos.


Revision 6315 - Directory Listing
Modified Wed Jun 22 03:59:33 2016 UTC (12 months ago) by caltinay
lookin' good so unskip more tests.


Revision 6314 - Directory Listing
Modified Tue Jun 21 23:27:35 2016 UTC (12 months ago) by caltinay
set mat error tolerance for LSQR as well.


Revision 6313 - Directory Listing
Modified Tue Jun 21 22:58:20 2016 UTC (12 months ago) by caltinay
forgot to change a line.


Revision 6312 - Directory Listing
Modified Tue Jun 21 06:51:27 2016 UTC (12 months ago) by caltinay
re-enable MueLu with long-index builds. There are only a few tweaks required
in Trilinos which I have done locally so if the tests pass we can go from
there.


Revision 6311 - Directory Listing
Modified Tue Jun 21 06:41:55 2016 UTC (12 months ago) by caltinay
lots of noise due to reformatting but mainly added braces around parallel
loops within switch so nvcc doesn't choke.


Revision 6310 - Directory Listing
Modified Tue Jun 21 04:18:28 2016 UTC (12 months ago) by jfenwick
Bringing in some changes from debian


Revision 6309 - Directory Listing
Modified Tue Jun 21 01:15:15 2016 UTC (12 months ago) by caltinay
updated mole py3 options.


Revision 6308 - Directory Listing
Modified Mon Jun 20 01:59:34 2016 UTC (12 months ago) by caltinay
trying to fix remaining trilinos errors.


Revision 6307 - Directory Listing
Modified Sun Jun 19 11:05:47 2016 UTC (12 months, 1 week ago) by caltinay
fixing order of expressions in nlpde so Lsup works in MPI.
Also only do the lsup's if required (debug output).


Revision 6306 - Directory Listing
Modified Sat Jun 18 13:26:00 2016 UTC (12 months, 1 week ago) by caltinay
fix test

Revision 6305 - Directory Listing
Modified Sat Jun 18 11:11:30 2016 UTC (12 months, 1 week ago) by caltinay
suppress sympy warning with py3


Revision 6304 - Directory Listing
Modified Sat Jun 18 11:00:33 2016 UTC (12 months, 1 week ago) by caltinay
tweak.


Revision 6303 - Directory Listing
Modified Sat Jun 18 10:53:18 2016 UTC (12 months, 1 week ago) by caltinay
changed default value for ILUT drop tolerance and fixed a typo.


Revision 6302 - Directory Listing
Modified Fri Jun 17 09:27:13 2016 UTC (12 months, 1 week ago) by caltinay
off-by-one errors.


Revision 6301 - Directory Listing
Modified Fri Jun 17 07:45:23 2016 UTC (12 months, 1 week ago) by caltinay
yes

Revision 6300 - Directory Listing
Modified Fri Jun 17 07:03:44 2016 UTC (12 months, 1 week ago) by caltinay
another attempt to fix the logic.


Revision 6299 - Directory Listing
Modified Fri Jun 17 05:53:58 2016 UTC (12 months, 1 week ago) by caltinay
fix paso direct solver detection logic in tests.


Revision 6298 - Directory Listing
Modified Fri Jun 17 04:00:35 2016 UTC (12 months, 1 week ago) by caltinay
type fixes in debug mode and savanna lib reference fix.


Revision 6297 - Directory Listing
Modified Fri Jun 17 00:05:11 2016 UTC (12 months, 1 week ago) by caltinay
make lazy-related config options tristate variables.


Revision 6296 - Directory Listing
Modified Thu Jun 16 23:58:54 2016 UTC (12 months, 1 week ago) by caltinay
don't claim to have paso direct solvers without paso.
Fix tests accordingly as well.


Revision 6295 - Directory Listing
Modified Thu Jun 16 23:53:23 2016 UTC (12 months, 1 week ago) by caltinay
mara options update.


Revision 6294 - Directory Listing
Modified Thu Jun 16 10:35:10 2016 UTC (12 months, 1 week ago) by caltinay
added default trilinos options to savanna.


Revision 6293 - Directory Listing
Modified Thu Jun 16 08:34:17 2016 UTC (12 months, 1 week ago) by caltinay
more test fixes.


Revision 6292 - Directory Listing
Modified Thu Jun 16 06:18:23 2016 UTC (12 months, 1 week ago) by caltinay
fix for non-mpi build. this time tested.


Revision 6291 - Directory Listing
Modified Thu Jun 16 05:47:55 2016 UTC (12 months, 1 week ago) by caltinay
advertise if escript was built with long indices as this means we can't run
MueLu (AMG) tests. Increased number of GS sweeps for a test that hangs again.


Revision 6290 - Directory Listing
Modified Thu Jun 16 01:49:20 2016 UTC (12 months, 1 week ago) by caltinay
attempt to fix non-mpi build. not tested.


Revision 6289 - Directory Listing
Modified Wed Jun 15 22:43:24 2016 UTC (12 months, 1 week ago) by caltinay
ILUT does not appear to work with Trilinos block matrices


Revision 6288 - Directory Listing
Modified Wed Jun 15 13:23:14 2016 UTC (12 months, 1 week ago) by caltinay
starting to move savanna to py3 toolchain.


Revision 6287 - Directory Listing
Modified Wed Jun 15 06:33:57 2016 UTC (12 months, 1 week ago) by caltinay
add c++11 flag to all compilers by default.


Revision 6286 - Directory Listing
Modified Wed Jun 15 06:21:00 2016 UTC (12 months, 1 week ago) by caltinay
added trilinos options (not actually installed yet).


Revision 6285 - Directory Listing
Modified Wed Jun 15 06:19:18 2016 UTC (12 months, 1 week ago) by caltinay
new mole options. There doesn't seem to be a boost-python3 yet so
the py3 builds will fail.


Revision 6284 - Directory Listing
Modified Wed Jun 15 06:05:20 2016 UTC (12 months, 1 week ago) by caltinay
newton changes for buildbot.


Revision 6283 - Directory Listing
Modified Wed Jun 15 05:58:34 2016 UTC (12 months, 1 week ago) by caltinay
Preparing for buildbot changes.


Revision 6282 - Directory Listing
Modified Tue Jun 14 04:54:01 2016 UTC (12 months, 1 week ago) by caltinay
changes to finley tests. See last few commits for details.


Revision 6281 - Directory Listing
Modified Tue Jun 14 02:42:32 2016 UTC (12 months, 1 week ago) by caltinay
Changes to dudley tests. See last commit.
The main things are: separated all test classes that were inheriting from more
than one base class. Also switched to a glob in SConscript as some tests files
were not even in the list to be run.


Revision 6280 - Directory Listing
Modified Tue Jun 14 02:39:13 2016 UTC (12 months, 1 week ago) by caltinay
BIG FAT MAJOR OOPS!
It looks like some of our tests have never actually run because something
goes wrong when a test class inherits from multiple test classes in escript.
Dudley never supported contact elements, yet only some of the tests were marked
as skipped. Symfuncs refers to self.RES_TOL which was never defined.

This commit adds some relevant skip's and the next ones will actually enable
the tests in the domains.


Revision 6279 - Directory Listing
Modified Mon Jun 13 07:05:21 2016 UTC (12 months, 1 week ago) by caltinay
this should fix most of the remaining trilinos test failures.


Revision 6278 - Directory Listing
Modified Mon Jun 13 06:39:59 2016 UTC (12 months, 1 week ago) by caltinay
trilinos-based interpolation from DOF->ReducedNodes in finley.


Revision 6277 - Directory Listing
Modified Mon Jun 13 06:18:44 2016 UTC (12 months, 1 week ago) by caltinay
implemented trilinos-based interpolation from red. DOF -> reducedNodes in finley.
Replaced some assertTrue's by more specific tests for more useful output.


Revision 6276 - Directory Listing
Modified Mon Jun 13 05:27:47 2016 UTC (12 months, 1 week ago) by caltinay
get around the fact that we're overriding cxx_extra on the command line.


Revision 6275 - Directory Listing
Modified Mon Jun 13 03:28:07 2016 UTC (12 months, 1 week ago) by caltinay
missing dependency?


Revision 6274 - Directory Listing
Modified Mon Jun 13 02:02:34 2016 UTC (12 months, 1 week ago) by caltinay
another one.


Revision 6273 - Directory Listing
Modified Mon Jun 13 01:01:53 2016 UTC (12 months, 1 week ago) by caltinay
same as last one.


Revision 6272 - Directory Listing
Modified Mon Jun 13 01:00:49 2016 UTC (12 months, 1 week ago) by caltinay
don't sys.exit if there is no pyproj.


Revision 6271 - Directory Listing
Modified Thu Jun 9 04:30:10 2016 UTC (12 months, 2 weeks ago) by caltinay
work around the fact that closing a MPI shared file does not always
have barrier semantics.


Revision 6270 - Directory Listing
Modified Thu Jun 9 00:46:11 2016 UTC (12 months, 2 weeks ago) by caltinay
added preliminary tinaroo options

Revision 6269 - Directory Listing
Modified Wed Jun 8 04:29:26 2016 UTC (12 months, 2 weeks ago) by caltinay
fix intel warnings

Revision 6268 - Directory Listing
Modified Wed Jun 8 02:14:17 2016 UTC (12 months, 2 weeks ago) by caltinay
use configured python in launcher

Revision 6267 - Directory Listing
Modified Wed Jun 8 01:57:48 2016 UTC (12 months, 2 weeks ago) by caltinay
Fixing test that appears to depend on filesystem type/MPI implementation.

Revision 6266 - Directory Listing
Modified Fri Jun 3 12:00:02 2016 UTC (12 months, 3 weeks ago) by caltinay
avoid the oversubscribing issue by disabling cpu binding on guineapig.


Revision 6265 - Directory Listing
Modified Fri Jun 3 06:31:31 2016 UTC (12 months, 3 weeks ago) by caltinay
update to guineapig options file. We now inherit from sid.


Revision 6264 - Directory Listing
Modified Fri Jun 3 06:23:10 2016 UTC (12 months, 3 weeks ago) by caltinay
fixing last dudley failures with trilinos. MueLu is not compatible with
block matrices yet so skip those tests. On the other hand we can now run
AMG tests with >1 rank.


Revision 6263 - Directory Listing
Modified Fri Jun 3 06:03:20 2016 UTC (12 months, 3 weeks ago) by caltinay
fixing another shared pointer race condition by caching a value.


Revision 6262 - Directory Listing
Modified Fri Jun 3 05:14:55 2016 UTC (12 months, 3 weeks ago) by caltinay
fix some tests with trilinos.
We now support direct solvers with mpi but not with pde systems.


Revision 6261 - Directory Listing
Modified Fri Jun 3 05:13:03 2016 UTC (12 months, 3 weeks ago) by caltinay
fixed shared ptr race in dudley. Store pointer to matrix rather than
shared ptr when assembling PDE. This could be considered part of #365


Revision 6260 - Directory Listing
Modified Fri Jun 3 04:15:26 2016 UTC (12 months, 3 weeks ago) by caltinay
modify solver tolerance for trilinos for some tests.
Paso's Jacobi seems to do a better job.


Revision 6259 - Directory Listing
Modified Fri Jun 3 03:07:20 2016 UTC (12 months, 3 weeks ago) by caltinay
do not require Zoltan2.


Revision 6258 - Directory Listing
Modified Fri Jun 3 00:34:00 2016 UTC (12 months, 3 weeks ago) by caltinay
ditto for assertAlmostEquals


Revision 6257 - Directory Listing
Modified Fri Jun 3 00:30:37 2016 UTC (12 months, 3 weeks ago) by caltinay
s/assertEquals/assertEqual/g since the former is deprecated.


Revision 6256 - Directory Listing
Modified Thu Jun 2 23:03:48 2016 UTC (12 months, 3 weeks ago) by caltinay
added missing requireWrite().


Revision 6255 - Directory Listing
Modified Thu Jun 2 06:52:06 2016 UTC (12 months, 3 weeks ago) by caltinay
modified build summary so we save some space and make clear what solvers
are available.


Revision 6254 - Directory Listing
Modified Thu Jun 2 05:22:41 2016 UTC (12 months, 3 weeks ago) by jfenwick
Standards bump


Revision 6253 - Directory Listing
Modified Thu Jun 2 05:04:41 2016 UTC (12 months, 3 weeks ago) by caltinay
...final?


Revision 6252 - Directory Listing
Modified Thu Jun 2 05:02:50 2016 UTC (12 months, 3 weeks ago) by caltinay
brrr, they switched from reporting via stderr to stdout...


Revision 6251 - Directory Listing
Modified Thu Jun 2 04:58:45 2016 UTC (12 months, 3 weeks ago) by jfenwick
Hoping to make lintian happier


Revision 6250 - Directory Listing
Modified Thu Jun 2 04:44:29 2016 UTC (12 months, 3 weeks ago) by jfenwick
Change the ssh agent to use when there is no ssh.
Since this situation only arises in debian testing in chroots,
I think it is ok not to expose this as a configuration option.


Revision 6249 - Directory Listing
Modified Thu Jun 2 04:37:00 2016 UTC (12 months, 3 weeks ago) by caltinay
fixes #368 - if this is openmpi try to get the version to determine default
options.


Revision 6248 - Directory Listing
Modified Thu Jun 2 04:13:21 2016 UTC (12 months, 3 weeks ago) by caltinay
more scons changes:
- replaced p.stdout.read... by p.communicate as recommended by doco
- moved python lib name enquiry logic from options file into dependencies.py
- reporting python version in summary now.


Revision 6247 - Directory Listing
Modified Thu Jun 2 02:35:41 2016 UTC (12 months, 3 weeks ago) by caltinay
Another change that may break things...
- added new TristateVariable to scons
- use it only for lapack for now whose value now defaults to 'auto', i.e.
   if mkl is installed, use it, otherwise try to link with atlas, all
   unless longindices is True.
- updated options files accordingly.


Revision 6246 - Directory Listing
Modified Thu Jun 2 00:47:54 2016 UTC (12 months, 3 weeks ago) by jfenwick
Let's try this


Revision 6245 - Directory Listing
Modified Thu Jun 2 00:35:02 2016 UTC (12 months, 3 weeks ago) by caltinay
do not override launcher on guineapig - py3 tests failed because we used
mpirun for a non-mpi build and ran gmsh twice in a row.


Revision 6244 - Directory Listing
Modified Wed Jun 1 10:41:29 2016 UTC (12 months, 3 weeks ago) by jfenwick
Fixing imports after options file changes


Revision 6243 - Directory Listing
Modified Wed Jun 1 09:50:18 2016 UTC (12 months, 3 weeks ago) by jfenwick
move overlord path setting to cxx_extra after options file changes

Revision 6242 - Directory Listing
Modified Wed Jun 1 07:57:06 2016 UTC (12 months, 3 weeks ago) by jfenwick
Try to get build testing working


Revision 6241 - Directory Listing
Modified Wed Jun 1 06:00:06 2016 UTC (12 months, 3 weeks ago) by caltinay
**Warning, this may break your build**
- Bumped required options version to 203 - new options for trilinos, paso, weipa
- scons/templates/README_FIRST is now the file that explains all the options,
  added comment to README but need to change install guide still.
- removed some obsolete options files
- removed most comments from template files, they now refer to README_FIRST
- removed usepython3 option as we now determine this based on python version
  string.
- enabled use of numpy.h with python 3 (last commit should have fixed the
  issues)


Revision 6240 - Directory Listing
Modified Wed Jun 1 05:52:38 2016 UTC (12 months, 3 weeks ago) by caltinay
WrappedArray is now compatible with python 3, i.e. we can now use numpy.h
with python 3.


Revision 6239 - Directory Listing
Modified Wed Jun 1 01:34:54 2016 UTC (12 months, 3 weeks ago) by caltinay
intialize sin_zero to be on the safe side (CID 99655)


Revision 6238 - Directory Listing
Modified Wed Jun 1 01:24:29 2016 UTC (12 months, 3 weeks ago) by caltinay
fixing coverity-detected leaks CID 99614,99615



Revision 6237 - Directory Listing
Modified Wed Jun 1 01:17:10 2016 UTC (12 months, 3 weeks ago) by caltinay
fixing coverity-detected leak CID 99603



Revision 6236 - Directory Listing
Modified Wed Jun 1 01:09:03 2016 UTC (12 months, 3 weeks ago) by caltinay
fixing coverity-detected leaks CID 115857,115858.



Revision 6235 - Directory Listing
Modified Wed Jun 1 01:05:29 2016 UTC (12 months, 3 weeks ago) by caltinay
fixing coverity-detected leaks CID 115859,115860,115861.



Revision 6234 - Directory Listing
Modified Wed Jun 1 01:00:21 2016 UTC (12 months, 3 weeks ago) by caltinay
fixing coverity-detected leaks CID 115863,115864,115865.



Revision 6233 - Directory Listing
Modified Mon May 30 23:45:53 2016 UTC (12 months, 3 weeks ago) by caltinay
i broke the other end. Hope this fixes it.


Revision 6232 - Directory Listing
Modified Mon May 30 04:21:28 2016 UTC (12 months, 3 weeks ago) by jfenwick
Other changes to match the previous commit.



Revision 6231 - Directory Listing
Modified Mon May 30 03:50:37 2016 UTC (12 months, 3 weeks ago) by jfenwick
I don't think we need this (and debian points out that it doesn't have a copyright notice).


Revision 6230 - Directory Listing
Modified Sun May 29 10:46:41 2016 UTC (12 months, 4 weeks ago) by caltinay
unfortunately we need to skip this test now when both escript and gmsh
is built with MPI. Another solution would be to add another function to
gmshrunner for merging meshes and call it instead of subprocess.call(...)


Revision 6229 - Directory Listing
Modified Sun May 29 10:42:41 2016 UTC (12 months, 4 weeks ago) by caltinay
how on earth did we miss this before??!


Revision 6228 - Directory Listing
Modified Sat May 28 10:21:18 2016 UTC (12 months, 4 weeks ago) by caltinay
non-mpi is a thing

Revision 6227 - Directory Listing
Modified Fri May 27 09:59:21 2016 UTC (13 months ago) by caltinay
change to a cppunit assertion which currently fails on guineapig to make it
output a sane error.

The reason for the failure is not entirely clear.
We are closing a parallel file which, according to doco, is a collective
operation, however the subsequent check for file size almost certainly returns
the wrong value on at least one rank.
This could be easily fixed by a barrier but we never saw this behaviour so
I suggest we investigate.


Revision 6226 - Directory Listing
Modified Fri May 27 02:55:38 2016 UTC (13 months ago) by caltinay
fix modellib test to use feature checker for gmsh.


Revision 6225 - Directory Listing
Modified Fri May 27 01:47:50 2016 UTC (13 months ago) by caltinay
fixed deprecation warning


Revision 6224 - Directory Listing
Modified Thu May 26 06:33:37 2016 UTC (13 months ago) by caltinay
fix newton options file.


Revision 6223 - Directory Listing
Modified Thu May 26 01:06:02 2016 UTC (13 months ago) by jfenwick
Fixes to itest.sh and extract tests


Revision 6222 - Directory Listing
Modified Wed May 25 23:36:21 2016 UTC (13 months ago) by caltinay
updated gp options for stretch.


Revision 6221 - Directory Listing
Modified Wed May 25 12:26:50 2016 UTC (13 months ago) by caltinay
don't use MueLu with index type long - lapack is incompatible.


Revision 6220 - Directory Listing
Modified Wed May 25 09:48:35 2016 UTC (13 months ago) by caltinay
add some colour to my compiler errors


Revision 6219 - Directory Listing
Modified Wed May 25 07:00:28 2016 UTC (13 months ago) by caltinay
skip paso test in finley without paso and fix assemble parameter issue
without paso.


Revision 6218 - Directory Listing
Modified Mon May 23 13:42:19 2016 UTC (13 months ago) by caltinay
fixed typo.


Revision 6217 - Directory Listing
Modified Mon May 23 06:57:40 2016 UTC (13 months ago) by caltinay
increase GS sweeps once more.


Revision 6216 - Directory Listing
Modified Mon May 23 06:52:32 2016 UTC (13 months ago) by caltinay
trying to support 2nd order elements in finley with trilinos. WIP


Revision 6215 - Directory Listing
Modified Mon May 23 02:58:03 2016 UTC (13 months ago) by caltinay
trilinos-based DOF->node interpolation in finley. Not complete yet.


Revision 6214 - Directory Listing
Modified Fri May 20 07:04:31 2016 UTC (13 months, 1 week ago) by caltinay
implemented trilinos interpolation from DOF->nodes in dudley.


Revision 6213 - Directory Listing
Modified Fri May 20 04:32:25 2016 UTC (13 months, 1 week ago) by caltinay
can now interpolate multi-component Data objects from DOF -> nodes with
trilinos in ripley.


Revision 6212 - Directory Listing
Modified Tue May 17 00:52:16 2016 UTC (13 months, 1 week ago) by caltinay
typo with trilinos.


Revision 6211 - Directory Listing
Modified Mon May 16 11:48:02 2016 UTC (13 months, 1 week ago) by caltinay
guard slave-only functions in readgmsh to avoid unused func warnings in
non-MPI builds.


Revision 6210 - Directory Listing
Modified Mon May 16 08:42:05 2016 UTC (13 months, 1 week ago) by caltinay
more test adjustments.


Revision 6209 - Directory Listing
Modified Mon May 16 04:32:21 2016 UTC (13 months, 1 week ago) by caltinay
fixed typo.


Revision 6208 - Directory Listing
Modified Mon May 16 02:17:37 2016 UTC (13 months, 1 week ago) by caltinay
rebaseline test meshes.


Revision 6207 - Directory Listing
Modified Mon May 16 00:49:48 2016 UTC (13 months, 1 week ago) by caltinay
merged finley Mesh and MeshAdapter into FinleyDomain.


Revision 6206 - Directory Listing
Modified Sun May 15 12:18:58 2016 UTC (13 months, 1 week ago) by caltinay
fix test.


Revision 6205 - Directory Listing
Modified Sun May 15 09:40:50 2016 UTC (13 months, 1 week ago) by caltinay
minor changes to sync dudley and finley.


Revision 6204 - Directory Listing
Modified Thu May 12 23:05:56 2016 UTC (13 months, 2 weeks ago) by caltinay
fixed types for index type long.


Revision 6203 - Directory Listing
Modified Wed May 11 06:13:51 2016 UTC (13 months, 2 weeks ago) by caltinay
dudley: merged Mesh and MeshAdapter into DudleyDomain to finally remove the
now unnecessary indirection. If all builders are happy we can do the same
for finley.


Revision 6202 - Directory Listing
Modified Thu May 5 04:47:09 2016 UTC (13 months, 3 weeks ago) by caltinay
slightly better error messages on test failure in pdetools.


Revision 6201 - Directory Listing
Modified Thu May 5 04:32:02 2016 UTC (13 months, 3 weeks ago) by caltinay
re-increase num GS sweeps in test now that it succeeds with paso. Trilinos
requires this


Revision 6200 - Directory Listing
Modified Wed May 4 23:57:49 2016 UTC (13 months, 3 weeks ago) by caltinay
paso: allow saving to matrix market with >1 rank by collecting matrix on master.


Revision 6199 - Directory Listing
Modified Wed May 4 23:56:52 2016 UTC (13 months, 3 weeks ago) by caltinay
addresses #366. Gauss-Seidel sweeps now only use the main block of the
system matrix.


Revision 6198 - Directory Listing
Modified Wed May 4 06:17:49 2016 UTC (13 months, 3 weeks ago) by caltinay
resetting number of GS sweeps to 1 in MINRES test. See bug #366


Revision 6197 - Directory Listing
Modified Fri Apr 29 14:02:32 2016 UTC (13 months, 4 weeks ago) by caltinay
moved Distribution struct to escript and updated domains accordingly.
We can now build the full escript suite without paso (-:


Revision 6196 - Directory Listing
Modified Thu Apr 28 03:38:25 2016 UTC (13 months, 4 weeks ago) by caltinay
It looks like there is an issue with paso's GAUSS-SEIDEL and parallel domains
where some ranks have no element, or similar(?)
Getting around this in the unit tests now by optimizing domain distribution,
obviously that only works with parmetis. Alternative would be to use slightly
larger test domains.


Revision 6195 - Directory Listing
Modified Thu Apr 28 01:10:46 2016 UTC (13 months, 4 weeks ago) by caltinay
more tweaking.


Revision 6194 - Directory Listing
Modified Wed Apr 27 23:46:30 2016 UTC (13 months, 4 weeks ago) by caltinay
lowering number of GS sweeps again to see if intel-hybrid likes it.


Revision 6193 - Directory Listing
Modified Wed Apr 27 06:11:40 2016 UTC (13 months, 4 weeks ago) by caltinay
preparations for paso-less dudley.


Revision 6192 - Directory Listing
Modified Wed Apr 27 05:53:11 2016 UTC (13 months, 4 weeks ago) by caltinay
moved createRandomVector from distribution to AMG, the only place it is
needed. This is in preparation for moving the lightweight Distribution
struct to escript so it can be used without paso.


Revision 6191 - Directory Listing
Modified Wed Apr 27 05:24:32 2016 UTC (13 months, 4 weeks ago) by caltinay
use omp reduction operator now that we don't care about gcc 4.4.


Revision 6190 - Directory Listing
Modified Wed Apr 27 05:23:15 2016 UTC (13 months, 4 weeks ago) by caltinay
moved numPositives from paso::Distribution to paso::util.


Revision 6189 - Directory Listing
Modified Wed Apr 27 03:39:21 2016 UTC (14 months ago) by caltinay
PRES20 is synonymous with GMRES and ILU0 with RILU in trilinos for now until
we have the proper options in place.


Revision 6188 - Directory Listing
Modified Wed Apr 27 03:38:10 2016 UTC (14 months ago) by caltinay
silence trilinos matrix constructors and remove unneeded code as the devs
confirmed we don't need resumeFill/fillComplete for block matrices.


Revision 6187 - Directory Listing
Modified Wed Apr 27 03:36:18 2016 UTC (14 months ago) by caltinay
don't test REC_ILU which has never been supported (and paso silently fell
back to Jacobi). Test ILUT instead which is not supported by paso either but
Trilinos.


Revision 6186 - Directory Listing
Modified Wed Apr 27 01:34:39 2016 UTC (14 months ago) by caltinay
fixed typo for block matrices.


Revision 6185 - Directory Listing
Modified Wed Apr 27 01:34:17 2016 UTC (14 months ago) by caltinay
only run paso tests when paso is installed - for now in ripley.


Revision 6184 - Directory Listing
Modified Wed Apr 27 01:30:57 2016 UTC (14 months ago) by caltinay
more fixes to weipa readerlib build


Revision 6183 - Directory Listing
Modified Wed Apr 27 00:09:32 2016 UTC (14 months ago) by caltinay
fix weipa readerlib build.


Revision 6182 - Directory Listing
Modified Tue Apr 26 06:31:51 2016 UTC (14 months ago) by caltinay
rather than skipping pde system tests with trilinos we now expect failures,
which actually translate to quite a few unexpected successes.
There is still a threading issue somewhere...


Revision 6181 - Directory Listing
Modified Tue Apr 26 06:16:15 2016 UTC (14 months ago) by caltinay
added support for (experimental) block matrices in Trilinos.
They appear to be much slower and only a limited number of
solvers/preconditioners are supported but it's a start.
Test updates pending.


Revision 6180 - Directory Listing
Modified Sat Apr 16 04:53:19 2016 UTC (14 months, 1 week ago) by caltinay
fix escriptreader dependencies


Revision 6179 - Directory Listing
Modified Fri Apr 15 12:48:58 2016 UTC (14 months, 1 week ago) by caltinay
ditto.


Revision 6178 - Directory Listing
Modified Fri Apr 15 10:43:52 2016 UTC (14 months, 1 week ago) by caltinay
missed these.


Revision 6177 - Directory Listing
Modified Fri Apr 15 08:26:07 2016 UTC (14 months, 1 week ago) by caltinay
fixed typo


Revision 6176 - Directory Listing
Modified Fri Apr 15 07:10:51 2016 UTC (14 months, 1 week ago) by caltinay
fix OMP race conditions in trilinos matrix.


Revision 6175 - Directory Listing
Modified Fri Apr 15 06:59:14 2016 UTC (14 months, 1 week ago) by caltinay
make sure to copy python lists rather than adding on or PrependUnique is
useless.


Revision 6174 - Directory Listing
Modified Fri Apr 15 03:41:03 2016 UTC (14 months, 1 week ago) by caltinay
Some reorganisation of EscriptParams and related changes.
We now distinguish between modifiable parameters and build features.
To interrogate the latter use:
escript::hasFeature()  [ python: escript.hasFeature() ]
and
escript::listFeatures() [ python: escript.listFeatures() ]

I have decided to add specific getters for the remaining few parameters to
avoid the penalty of string comparisons and to remove the wealth of friend
declarations with Data* classes.

Also made some changes in SConstruct to make sure we set *all* preprocessor
directives *before* building anything.

Still to do is dealing with checks for direct solver and gmsh. The latter needs
to be a runtime check rather than a compile time check.


Revision 6173 - Directory Listing
Modified Thu Apr 14 05:56:55 2016 UTC (14 months, 1 week ago) by caltinay
moved reference to JMPI down to Coupler.


Revision 6172 - Directory Listing
Modified Thu Apr 14 05:15:27 2016 UTC (14 months, 1 week ago) by caltinay
type change in paso.


Revision 6171 - Directory Listing
Modified Wed Apr 13 13:39:08 2016 UTC (14 months, 1 week ago) by jfenwick
adding tests to tagged versions

Revision 6170 - Directory Listing
Modified Wed Apr 13 07:46:34 2016 UTC (14 months, 1 week ago) by caltinay
moved common code to base class in ripley and implemented single-component
dofToNodes with trilinos.


Revision 6169 - Directory Listing
Modified Wed Apr 13 05:24:45 2016 UTC (14 months, 1 week ago) by caltinay
ripley now builds without paso but dof2nodes is currently unimplemented then.


Revision 6168 - Directory Listing
Modified Wed Apr 13 03:08:12 2016 UTC (14 months, 2 weeks ago) by jfenwick
Making Lazy and the rest of escript use the same operator enumeration



Revision 6167 - Directory Listing
Modified Tue Apr 12 09:34:03 2016 UTC (14 months, 2 weeks ago) by caltinay
forgot to commit.


Revision 6166 - Directory Listing
Modified Tue Apr 12 06:51:37 2016 UTC (14 months, 2 weeks ago) by caltinay
Starting to make Paso optional in ripley.


Revision 6165 - Directory Listing
Modified Mon Apr 11 10:25:51 2016 UTC (14 months, 2 weeks ago) by caltinay
limit number of elements in speckley test.


Revision 6164 - Directory Listing
Modified Mon Apr 11 06:06:43 2016 UTC (14 months, 2 weeks ago) by jfenwick
Test fixes and more tests


Revision 6163 - Directory Listing
Modified Sun Apr 10 23:44:11 2016 UTC (14 months, 2 weeks ago) by jfenwick
Fix to prevent complex tests running with lazy.


Revision 6162 - Directory Listing
Modified Fri Apr 8 09:46:26 2016 UTC (14 months, 2 weeks ago) by caltinay
Data() constructor fix.


Revision 6161 - Directory Listing
Modified Fri Apr 8 06:57:08 2016 UTC (14 months, 2 weeks ago) by caltinay
report filename in error message.


Revision 6160 - Directory Listing
Modified Fri Apr 8 06:24:27 2016 UTC (14 months, 2 weeks ago) by jfenwick
Bump standards version to see what happens



Revision 6159 - Directory Listing
Modified Fri Apr 8 06:22:04 2016 UTC (14 months, 2 weeks ago) by jfenwick
Non-backwards compatible change!

The way the Data constructor operates from python has been changed.
  Data(v, shape, functionspace, expand=True)
no longer works.
The keyword part is not allowed now.
This used to work automatically because boost recognised the name
and allowed use as a keyword.
To get complex to work, we now take (object, object, object, object)
and workout what the args mean in the function (which means keywords
are out).

Adds some additional tests for complex.


Revision 6158 - Directory Listing
Modified Fri Apr 8 05:00:26 2016 UTC (14 months, 2 weeks ago) by caltinay
create test directory. This was always failing but buildbot only now
stops to report this.


Revision 6157 - Directory Listing
Modified Fri Apr 8 04:43:52 2016 UTC (14 months, 2 weeks ago) by caltinay
fixed savanna options file for noomp.


Revision 6156 - Directory Listing
Modified Fri Apr 8 04:39:55 2016 UTC (14 months, 2 weeks ago) by caltinay
index type fix.


Revision 6155 - Directory Listing
Modified Fri Apr 8 00:48:28 2016 UTC (14 months, 2 weeks ago) by caltinay
index type long fixes in weipa. Weipa does not support long but converts
at the moment...


Revision 6154 - Directory Listing
Modified Thu Apr 7 02:52:30 2016 UTC (14 months, 2 weeks ago) by jfenwick
Complex fixes and a small number of tests


Revision 6153 - Directory Listing
Modified Thu Apr 7 00:35:31 2016 UTC (14 months, 2 weeks ago) by caltinay
no-op - remove parmetis line from netwon options.


Revision 6152 - Directory Listing
Modified Thu Apr 7 00:33:51 2016 UTC (14 months, 2 weeks ago) by caltinay
we should now properly catch segfaults when testing.


Revision 6151 - Directory Listing
Modified Wed Apr 6 23:44:46 2016 UTC (14 months, 2 weeks ago) by jfenwick
Remove getsubst


Revision 6150 - Directory Listing
Modified Wed Apr 6 23:44:12 2016 UTC (14 months, 2 weeks ago) by caltinay
fix newton options file.


Revision 6149 - Directory Listing
Modified Wed Apr 6 23:36:42 2016 UTC (14 months, 2 weeks ago) by caltinay
fix a typo introduced in r6144. Buildbot reported success since then but
was actually segfaulting!!


Revision 6148 - Directory Listing
Modified Wed Apr 6 10:28:13 2016 UTC (14 months, 2 weeks ago) by caltinay
fix savanna options file and make sure libraries get added once only.


Revision 6147 - Directory Listing
Modified Wed Apr 6 07:57:22 2016 UTC (14 months, 2 weeks ago) by jfenwick
Complex changes

Testing reveals holes in the complex code big enough to
drive a truck through.
This commit means you will however need a slightly 
smaller truck



Revision 6146 - Directory Listing
Modified Wed Apr 6 07:10:59 2016 UTC (14 months, 2 weeks ago) by caltinay
add lib path for trilinos.


Revision 6145 - Directory Listing
Modified Wed Apr 6 06:28:57 2016 UTC (14 months, 2 weeks ago) by caltinay
now refraining from adding all libraries to all targets. So we don't link
unnecessary libraries, e.g. escript does not need parmetis etc...


Revision 6144 - Directory Listing
Modified Wed Apr 6 05:25:13 2016 UTC (14 months, 2 weeks ago) by caltinay
last round of namespacing defines.


Revision 6143 - Directory Listing
Modified Wed Apr 6 03:59:15 2016 UTC (14 months, 3 weeks ago) by caltinay
try to fix another warning.


Revision 6142 - Directory Listing
Modified Wed Apr 6 03:57:28 2016 UTC (14 months, 3 weeks ago) by caltinay
two fixes.


Revision 6141 - Directory Listing
Modified Wed Apr 6 03:51:30 2016 UTC (14 months, 3 weeks ago) by caltinay
more namespacing of defines.


Revision 6140 - Directory Listing
Modified Wed Apr 6 03:17:31 2016 UTC (14 months, 3 weeks ago) by jfenwick
Eigenvectors for _some_ complex cases

escript is cowardly refusing to compute eigenvalues
for 3x3 complex matricies because the 3x3 alg has 
< in it.


Revision 6139 - Directory Listing
Modified Wed Apr 6 02:58:19 2016 UTC (14 months, 3 weeks ago) by caltinay
fix for scons versions < 2.4


Revision 6138 - Directory Listing
Modified Wed Apr 6 02:10:10 2016 UTC (14 months, 3 weeks ago) by caltinay
starting to 'namespace' our way too generic defines...


Revision 6137 - Directory Listing
Modified Wed Apr 6 01:57:52 2016 UTC (14 months, 3 weeks ago) by caltinay
new configure check for working complex std::acos


Revision 6136 - Directory Listing
Modified Wed Apr 6 01:45:53 2016 UTC (14 months, 3 weeks ago) by jfenwick
Swap axes for complex


Revision 6135 - Directory Listing
Modified Wed Apr 6 01:07:38 2016 UTC (14 months, 3 weeks ago) by jfenwick
transpose for complex


Revision 6134 - Directory Listing
Modified Wed Apr 6 00:48:07 2016 UTC (14 months, 3 weeks ago) by jfenwick
trace for non-constant data



Revision 6133 - Directory Listing
Modified Wed Apr 6 00:33:10 2016 UTC (14 months, 3 weeks ago) by jfenwick
trace() now supports complex


Revision 6132 - Directory Listing
Modified Wed Apr 6 00:14:03 2016 UTC (14 months, 3 weeks ago) by caltinay
don't skip test with #ranks=1 and fix it (readGmsh).


Revision 6131 - Directory Listing
Modified Tue Apr 5 23:55:59 2016 UTC (14 months, 3 weeks ago) by jfenwick
Bug fix and test for complex NaN replacement


Revision 6130 - Directory Listing
Modified Tue Apr 5 07:05:01 2016 UTC (14 months, 3 weeks ago) by caltinay
more index_t != int fixes in dudley and finley. Both compile now with index
type long. Weipa doesn't.


Revision 6129 - Directory Listing
Modified Tue Apr 5 06:12:25 2016 UTC (14 months, 3 weeks ago) by caltinay
rebaseline.


Revision 6128 - Directory Listing
Modified Tue Apr 5 05:19:48 2016 UTC (14 months, 3 weeks ago) by jfenwick
Hopefully fix OSX problem.




Revision 6127 - Directory Listing
Modified Tue Apr 5 04:39:31 2016 UTC (14 months, 3 weeks ago) by jfenwick
Rename nonsymmetric to antisymmetric in tests



Revision 6126 - Directory Listing
Modified Tue Apr 5 04:29:41 2016 UTC (14 months, 3 weeks ago) by caltinay
more index_t != int fixes in dudley.


Revision 6125 - Directory Listing
Modified Tue Apr 5 04:12:13 2016 UTC (14 months, 3 weeks ago) by jfenwick
Fix incorrect behaviour of anti-symmetric for scalars.

Also add hermitian and antihermitian.
Very quick check looks ok but really not tested yet.


Revision 6124 - Directory Listing
Modified Tue Apr 5 03:23:12 2016 UTC (14 months, 3 weeks ago) by caltinay
Fixing python module build on OS X. Added PythonModule builder so we do this generically now.

Revision 6123 - Directory Listing
Modified Mon Apr 4 06:24:25 2016 UTC (14 months, 3 weeks ago) by jfenwick
Fixes to debian build


Revision 6122 - Directory Listing
Modified Mon Apr 4 04:15:50 2016 UTC (14 months, 3 weeks ago) by caltinay
two fixes for long int build.


Revision 6121 - Directory Listing
Modified Mon Apr 4 03:47:52 2016 UTC (14 months, 3 weeks ago) by caltinay
fix dudley test.


Revision 6120 - Directory Listing
Modified Mon Apr 4 01:33:51 2016 UTC (14 months, 3 weeks ago) by caltinay
guilty as charged.


Revision 6119 - Directory Listing
Modified Sun Apr 3 23:36:59 2016 UTC (14 months, 3 weeks ago) by caltinay
merging trilinos branch to trunk.
We can now build with trilinos and use it instead of paso for single PDEs.
There are some more things to be done...


Revision 6114 - Directory Listing
Modified Fri Apr 1 03:37:52 2016 UTC (14 months, 3 weeks ago) by jfenwick
symmetric and antisymmetric now support complex

Also a number of methods are renamed from nonsymmetric


Revision 6113 - Directory Listing
Modified Fri Apr 1 00:22:23 2016 UTC (14 months, 3 weeks ago) by caltinay
trying to fix deb build.


Revision 6112 - Directory Listing
Modified Thu Mar 31 09:40:10 2016 UTC (14 months, 3 weeks ago) by jfenwick
Relicense all the things!



Revision 6110 - Directory Listing
Modified Thu Mar 31 06:31:03 2016 UTC (14 months, 3 weeks ago) by jfenwick
Rename nonsymetric to antisymmetric.

nonsymmetric is now an alias to antisymmetric.
At some stage later, we can try to remove nonsymmetric



Revision 6107 - Directory Listing
Modified Thu Mar 31 00:47:21 2016 UTC (14 months, 3 weeks ago) by jfenwick
Use tags in test


Revision 6103 - Directory Listing
Modified Wed Mar 30 05:01:49 2016 UTC (14 months, 3 weeks ago) by jfenwick
Add variable to control using replacement acos on broken OSX

Revision 6102 - Directory Listing
Modified Wed Mar 30 05:00:20 2016 UTC (14 months, 3 weeks ago) by jfenwick
Add some missing functions.

There may be others


Revision 6099 - Directory Listing
Modified Tue Mar 29 03:50:14 2016 UTC (14 months, 4 weeks ago) by jfenwick
Don't expect an exception is we aren't doing that check.


Revision 6098 - Directory Listing
Modified Tue Mar 29 02:21:44 2016 UTC (14 months, 4 weeks ago) by jfenwick
Remove "within object" checks for sharing from normal codepath

Something about the way the checks were being done, slowed things down.
Now, you will only get those checks if you define SLOWSHARECHECK



Revision 6097 - Directory Listing
Modified Sun Mar 27 03:31:00 2016 UTC (15 months ago) by jfenwick
Tricky race condition hidden in duplicate code

Not sure now why I needed two paths for this.



Revision 6096 - Directory Listing
Modified Sun Mar 27 03:30:14 2016 UTC (15 months ago) by jfenwick
Don\'t know why the other builders didn't need this

Revision 6095 - Directory Listing
Modified Sat Mar 26 03:06:30 2016 UTC (15 months ago) by jfenwick
Fixing remaining examples


Revision 6094 - Directory Listing
Modified Fri Mar 25 14:19:11 2016 UTC (15 months ago) by jfenwick
Fix more tests.  Note needed to change example to add another import.

This isn't all of the problems fixed.
There is at least one more import os missing.
But it's late.


Revision 6093 - Directory Listing
Modified Thu Mar 24 07:18:55 2016 UTC (15 months ago) by jfenwick
Removing unintended inclusions in __all__ for esys.escript

Patched some unit tests which were affected.


Revision 6092 - Directory Listing
Modified Thu Mar 24 05:43:00 2016 UTC (15 months ago) by jfenwick
Adding some complex versions to ops.

And some tests but not enough yet


Revision 6091 - Directory Listing
Modified Thu Mar 24 04:52:53 2016 UTC (15 months ago) by jfenwick
Fix race condition in checking for sharing.

Bit tricky to find this one.


Revision 6088 - Directory Listing
Modified Wed Mar 23 00:44:58 2016 UTC (15 months ago) by jfenwick
Removing old shared tracking


Revision 6087 - Directory Listing
Modified Tue Mar 22 22:32:12 2016 UTC (15 months ago) by jfenwick
Fixing tests


Revision 6086 - Directory Listing
Modified Tue Mar 22 09:54:51 2016 UTC (15 months ago) by jfenwick
Trying to switch over to using shared_ptr.use_count()

Let's see how the buildbot likes it


Revision 6084 - Directory Listing
Modified Tue Mar 22 04:23:02 2016 UTC (15 months ago) by jfenwick
Renaming headers for (hopefully) easier understanding



Revision 6083 - Directory Listing
Modified Tue Mar 22 03:30:18 2016 UTC (15 months ago) by jfenwick
Removing the DataMaths namespace


Revision 6082 - Directory Listing
Modified Tue Mar 22 02:57:49 2016 UTC (15 months ago) by jfenwick
More cleanup

Moving some includes around.
The plan is to rename some includes to better reflect their purpose.
Removing inheritance from std::binary_function   (since that is deprecated).
Replacing some doubles with real_t.



Revision 6078 - Directory Listing
Modified Mon Mar 21 06:02:29 2016 UTC (15 months ago) by caltinay
please keep third-party includes after our own to avoid reintroducing
the "python has to be first" issue.


Revision 6077 - Directory Listing
Modified Mon Mar 21 06:00:21 2016 UTC (15 months ago) by jfenwick
Compile error fix.

Not sure why my system didn't pick it up.


Revision 6076 - Directory Listing
Modified Fri Mar 18 12:06:46 2016 UTC (15 months, 1 week ago) by jfenwick
Fixing some namespaces and includes

Revision 6075 - Directory Listing
Modified Fri Mar 18 06:30:04 2016 UTC (15 months, 1 week ago) by jfenwick
More code removal and test fixing.

A number of operations were tested via binaryOp
and unaryOp rather than via Data methods.
   I hope these operations 
are tested elsewhere.



Revision 6074 - Directory Listing
Modified Fri Mar 18 02:42:48 2016 UTC (15 months, 1 week ago) by jfenwick
Starting to remove dead code.

DataAlgorithmAdapter is only used by the code which tests it.


Revision 6073 - Directory Listing
Modified Thu Mar 17 03:30:53 2016 UTC (15 months, 1 week ago) by jfenwick
sigh use the correct version of abs()

Added test to detect this particular break again.


Revision 6072 - Directory Listing
Modified Thu Mar 17 00:34:01 2016 UTC (15 months, 1 week ago) by jfenwick
Remove horrible debug output


Revision 6071 - Directory Listing
Modified Wed Mar 16 07:07:05 2016 UTC (15 months, 1 week ago) by jfenwick
More test fixes. Better error message on TestDomain.

That throw should probably be an assert though


Revision 6070 - Directory Listing
Modified Wed Mar 16 07:05:32 2016 UTC (15 months, 1 week ago) by jfenwick
Ensure that objects with no samples do not contribute to inf and sup.




Revision 6069 - Directory Listing
Modified Wed Mar 16 04:30:40 2016 UTC (15 months, 1 week ago) by jfenwick
Passes a few more tests.

Some more bugfixes regarding empty processes.
For convienience, added DataAbstracts::hasNoSamples


Revision 6068 - Directory Listing
Modified Wed Mar 16 03:37:43 2016 UTC (15 months, 1 week ago) by jfenwick
Remove some tests which expect illegal index lookups to throw.

Fix some other tests which try to compare results on empty procs


Revision 6067 - Directory Listing
Modified Wed Mar 16 02:47:38 2016 UTC (15 months, 1 week ago) by caltinay
Back to having a single ESYS_ASSERT macro BUT when built with MPI we
are now merely printing the error message and calling MPI_Abort on COMM_WORLD.
My understanding is that this should work on subworlds as well as all
processes are part of COMM_WORLD...

Addresses #362


Revision 6066 - Directory Listing
Modified Tue Mar 15 06:42:55 2016 UTC (15 months, 1 week ago) by jfenwick
Code path conversions.

TestDomain can now return a JMPI.
Some tests now use TestDomain (didn't want to undo all that work
from before I found the ASSERT fix).
Moving more code to new path.
Commenting out a bunch of old ops.



Revision 6065 - Directory Listing
Modified Tue Mar 15 06:29:38 2016 UTC (15 months, 1 week ago) by jfenwick
A bit of a hack.

This can be improved. But the idea is to prevent checks from
throwing where no domain is available.


Revision 6064 - Directory Listing
Modified Mon Mar 14 01:06:18 2016 UTC (15 months, 1 week ago) by jfenwick
Data::hasNoSamples()  now actually looks at how many samples we have.




Revision 6063 - Directory Listing
Modified Mon Mar 14 00:50:44 2016 UTC (15 months, 1 week ago) by jfenwick
Fix to prevent new codepath from trying to act on locally empty data.

I've "corrected" the tests to do what I think is the correct thing.



Revision 6061 - Directory Listing
Modified Fri Mar 11 04:40:28 2016 UTC (15 months, 2 weeks ago) by caltinay
Undoing the switch to use MPI-aware assert in Data.h because some
functions are only called from a subset of ranks which would then
cause definite hangs due to the error reduction operation. We need
to find a better way of dealing with this.


Revision 6060 - Directory Listing
Modified Fri Mar 11 02:51:26 2016 UTC (15 months, 2 weeks ago) by caltinay
added an MPI-aware version of ESYS_ASSERT and replaced suitable places.
This will not fix the current buildbot hang as that is within a block
where we don't have a JMPI intance.


Revision 6057 - Directory Listing
Modified Thu Mar 10 06:00:58 2016 UTC (15 months, 2 weeks ago) by jfenwick
Well it passes my tests



Revision 6056 - Directory Listing
Modified Thu Mar 10 04:29:53 2016 UTC (15 months, 2 weeks ago) by jfenwick
Small fix - hard to find



Revision 6050 - Directory Listing
Modified Wed Mar 9 22:44:52 2016 UTC (15 months, 2 weeks ago) by caltinay
make it compile on savanna again.


Revision 6048 - Directory Listing
Modified Wed Mar 9 07:34:47 2016 UTC (15 months, 2 weeks ago) by jfenwick
Relocating binaryDataOp to Data.cpp



Revision 6047 - Directory Listing
Modified Wed Mar 9 07:25:42 2016 UTC (15 months, 2 weeks ago) by jfenwick
Removing code some code not used by new path



Revision 6046 - Directory Listing
Modified Wed Mar 9 07:05:48 2016 UTC (15 months, 2 weeks ago) by jfenwick
More pruning and switching

All self-update operations use the new path


Revision 6045 - Directory Listing
Modified Wed Mar 9 06:28:47 2016 UTC (15 months, 2 weeks ago) by jfenwick
Adding more operations to the alternate binary codepath




Revision 6044 - Directory Listing
Modified Wed Mar 9 05:57:27 2016 UTC (15 months, 2 weeks ago) by caltinay
next try to fix the getopts issue.


Revision 6043 - Directory Listing
Modified Wed Mar 9 04:44:10 2016 UTC (15 months, 2 weeks ago) by jfenwick
Making a macro


Revision 6042 - Directory Listing
Modified Wed Mar 9 04:30:36 2016 UTC (15 months, 2 weeks ago) by jfenwick
Preliminary to lazy cleanup


Lazy is not templated for complex as yet but hopefully
we can relieve the dependency on the briarpatch of
the current methods.



Revision 6041 - Directory Listing
Modified Wed Mar 9 03:48:05 2016 UTC (15 months, 2 weeks ago) by caltinay
the -- appears to break parsing properly...


Revision 6039 - Directory Listing
Modified Wed Mar 9 01:56:34 2016 UTC (15 months, 2 weeks ago) by jfenwick
Enable alternate path.

Let's see what the buildbot thinks of it.


Revision 6038 - Directory Listing
Modified Wed Mar 9 01:32:00 2016 UTC (15 months, 2 weeks ago) by jfenwick
Bug fixes and function for unary ops.

This commit does not actually switch the alternate functionality on.
I'll do that separately


Revision 6037 - Directory Listing
Modified Wed Mar 9 01:28:53 2016 UTC (15 months, 2 weeks ago) by jfenwick
It turns out that explict can be helpful.



Revision 6036 - Directory Listing
Modified Wed Mar 9 00:41:26 2016 UTC (15 months, 2 weeks ago) by caltinay
grr, another revert.


Revision 6035 - Directory Listing
Modified Wed Mar 9 00:39:20 2016 UTC (15 months, 2 weeks ago) by caltinay
reverted accidental commit of SConstruct.


Revision 6034 - Directory Listing
Modified Wed Mar 9 00:37:57 2016 UTC (15 months, 2 weeks ago) by caltinay
a few changes to GroupTest / utest:
GroupTest class now takes a name parameter that is used as (shell) function
name in utest for the test group.
By default all tests are run as before but one can now do:
./utest.sh build '-t2' escriptcpp
to only run the escript c++ unit tests.
Also tweaked a couple things so utest.sh does now work with dash.


Revision 6033 - Directory Listing
Modified Wed Mar 9 00:13:29 2016 UTC (15 months, 2 weeks ago) by jfenwick
More tests for addition



Revision 6032 - Directory Listing
Modified Tue Mar 8 10:02:26 2016 UTC (15 months, 2 weeks ago) by caltinay
hmm, I thought we're using globs...


Revision 6031 - Directory Listing
Modified Tue Mar 8 06:27:14 2016 UTC (15 months, 2 weeks ago) by caltinay
added a generic baseclass for PDE solver tests which is used by all domains.
Renamed test files to prepare for Trilinos merge at some point.


Revision 6029 - Directory Listing
Modified Mon Mar 7 11:16:41 2016 UTC (15 months, 2 weeks ago) by caltinay
increase domain size. Not entirely sure why we get spurious runtime errors
only for this test case but we shall see...


Revision 6028 - Directory Listing
Modified Mon Mar 7 05:55:01 2016 UTC (15 months, 2 weeks ago) by jfenwick
Modify TestDomain to generate correct coordinates in MPI.

This was breaking testing because the coords were inputs to the
testing function.


Revision 6027 - Directory Listing
Modified Mon Mar 7 03:01:22 2016 UTC (15 months, 2 weeks ago) by caltinay
fix for serial.


Revision 6026 - Directory Listing
Modified Mon Mar 7 01:58:51 2016 UTC (15 months, 2 weeks ago) by caltinay
Fixes #361 - bug in readGmsh + MPI reading nodes
Also fixes another related issue reading elements with a certain number of ranks


Revision 6025 - Directory Listing
Modified Fri Mar 4 05:47:57 2016 UTC (15 months, 3 weeks ago) by jfenwick
Added more tests for + operator.

This time we test inplace updates


Revision 6024 - Directory Listing
Modified Fri Mar 4 04:14:27 2016 UTC (15 months, 3 weeks ago) by jfenwick
Fixing testing.

Pulling alernative binary op skeleton.


Revision 6023 - Directory Listing
Modified Fri Mar 4 01:38:00 2016 UTC (15 months, 3 weeks ago) by caltinay
clear error code when restarting solver!


Revision 6022 - Directory Listing
Modified Fri Mar 4 00:02:44 2016 UTC (15 months, 3 weeks ago) by jfenwick
Additional test for various combinations of Data

It turns out we didn't have good enough tests for binary operators
which try various combinations of types.
This adds a new test and extends TestDomain to allow control of
tags in use (and mapping of tags to samples)



Revision 6021 - Directory Listing
Modified Thu Mar 3 23:56:55 2016 UTC (15 months, 3 weeks ago) by caltinay
fix for non-MPI builds.


Revision 6020 - Directory Listing
Modified Thu Mar 3 23:51:14 2016 UTC (15 months, 3 weeks ago) by caltinay
This should fix current test failures with Multiresolution domains.
The assumption that all ranks have the same number of DOF does not hold for
these domains but the distribution vector did not reflect that.


Revision 6019 - Directory Listing
Modified Thu Mar 3 04:01:30 2016 UTC (15 months, 3 weeks ago) by caltinay
adjusted number of elements in test so we get results with 20 ranks.


Revision 6018 - Directory Listing
Modified Thu Mar 3 03:57:34 2016 UTC (15 months, 3 weeks ago) by caltinay
adjusted speckley test tolerance and changed reporting so we don't get
60 != 60 :-)


Revision 6017 - Directory Listing
Modified Thu Mar 3 03:06:42 2016 UTC (15 months, 3 weeks ago) by caltinay
fixing a few more POSIX_C redefinition warnings.


Revision 6016 - Directory Listing
Modified Thu Mar 3 03:00:24 2016 UTC (15 months, 3 weeks ago) by caltinay
increase test size so we have enough elements for MPI size 20.


Revision 6015 - Directory Listing
Modified Thu Mar 3 01:56:12 2016 UTC (15 months, 3 weeks ago) by caltinay
try new obspy interface first to silence deprecation warning.


Revision 6014 - Directory Listing
Modified Thu Mar 3 01:50:06 2016 UTC (15 months, 3 weeks ago) by caltinay
hopefully fixing dirac point mapping by adding/subtracting epsilon from
boundaries.
We were getting different results with intel and gnu because we were
essentially checking 0.5 < 0.5


Revision 6013 - Directory Listing
Modified Wed Mar 2 06:16:47 2016 UTC (15 months, 3 weeks ago) by caltinay
Incompressible Flow test case fails for NE > ~24 independent on number
of ranks, might be a tolerance issue but I'm patching the test for now.


Revision 6012 - Directory Listing
Modified Wed Mar 2 05:06:18 2016 UTC (15 months, 3 weeks ago) by caltinay
copied fix from finley to dudley.


Revision 6011 - Directory Listing
Modified Wed Mar 2 05:05:16 2016 UTC (15 months, 3 weeks ago) by caltinay
more special case issues (segfault due to empty rank).


Revision 6010 - Directory Listing
Modified Wed Mar 2 04:26:26 2016 UTC (15 months, 3 weeks ago) by caltinay
silence the auto_ptr deprecation warning on savanna.


Revision 6008 - Directory Listing
Modified Wed Mar 2 04:09:58 2016 UTC (15 months, 3 weeks ago) by caltinay
don't call collective within conditional! This was fixed in finley
before.


Revision 6007 - Directory Listing
Modified Wed Mar 2 03:06:07 2016 UTC (15 months, 3 weeks ago) by caltinay
Fixed another exception hang case. Again this didn't trigger before
because we didn't run with >10 ranks.


Revision 6006 - Directory Listing
Modified Wed Mar 2 01:58:31 2016 UTC (15 months, 3 weeks ago) by caltinay
Fixed a corner case in finley where some ranks have no reduced DOFs.
This came to light when bumping the number of testing ranks to 20 on
Savanna.


Revision 6005 - Directory Listing
Modified Wed Mar 2 00:26:33 2016 UTC (15 months, 3 weeks ago) by caltinay
fixed another current exception hang.


Revision 6004 - Directory Listing
Modified Tue Mar 1 23:43:55 2016 UTC (15 months, 3 weeks ago) by caltinay
removed build_shared from most files.
esysUtils is gone and paso now has to be a shared lib to allow python
bindings.
I haven't bumped the options file version yet as there's more to come
before the release (trilinos etc) and the plan is to overhaul the scons
stuff once again.


Revision 6003 - Directory Listing
Modified Tue Mar 1 23:33:52 2016 UTC (15 months, 3 weeks ago) by caltinay
removed useless include.


Revision 6002 - Directory Listing
Modified Tue Mar 1 23:12:14 2016 UTC (15 months, 3 weeks ago) by caltinay
Making sure that the exception is raised in all ranks in SystemMatrixPattern
so we know why the current tests fail.

This demonstrates two things:
1) we have been hiding error conditions previously where we used Esys_SetError
rather than throwing exceptions. I have confirmed that the current test
failures should have been triggered "long ago" but since rank 0 has no error
condition this never happened. Annoyingly the tests succeeded despite
ignoring the error!

2) eventually we will have to replace the ad-hoc exception throwing by a
similar pattern to this to avoid the unit tests getting stuck when only
a subset of ranks throws.


Revision 6001 - Directory Listing
Modified Tue Mar 1 05:01:49 2016 UTC (15 months, 3 weeks ago) by caltinay
Bye bye esysUtils.
Also removed first.h as escript/DataTypes.h is now required everywhere
and fulfills that role by including a boost python header first.


Revision 6000 - Directory Listing
Modified Tue Mar 1 00:24:43 2016 UTC (15 months, 3 weeks ago) by caltinay
a few more include rearrangements.


Revision 5999 - Directory Listing
Modified Mon Feb 29 23:49:08 2016 UTC (15 months, 3 weeks ago) by caltinay
include reorder to try and get rid of POSIX_C... redef warnings.


Revision 5998 - Directory Listing
Modified Mon Feb 29 08:57:28 2016 UTC (15 months, 3 weeks ago) by caltinay
removed some macros and moved index.h to escript.


Revision 5997 - Directory Listing
Modified Mon Feb 29 07:24:47 2016 UTC (15 months, 3 weeks ago) by caltinay
moved esys MPI to escript.


Revision 5996 - Directory Listing
Modified Mon Feb 29 05:39:02 2016 UTC (15 months, 3 weeks ago) by caltinay
1) finally put dudley into its own namespace
2) replaced all Esys*Error calls by exceptions in dudley and paso


Revision 5995 - Directory Listing
Modified Mon Feb 29 00:01:56 2016 UTC (15 months, 3 weeks ago) by caltinay
removed pasowrap from doxyfile.


Revision 5994 - Directory Listing
Modified Sun Feb 28 10:20:49 2016 UTC (15 months, 4 weeks ago) by caltinay
update 2.


Revision 5993 - Directory Listing
Modified Sun Feb 28 10:19:30 2016 UTC (15 months, 4 weeks ago) by caltinay
update.


Revision 5992 - Directory Listing
Modified Fri Feb 26 23:55:23 2016 UTC (15 months, 4 weeks ago) by jfenwick
Enable hasNaN and replaceNaN for complex


Revision 5991 - Directory Listing
Modified Fri Feb 26 23:11:08 2016 UTC (15 months, 4 weeks ago) by jfenwick
Enabling more ops for complex

Commenting out the templated C_TensorUnaryOperation.
Want to remove the equivalent binary versions as well


Revision 5990 - Directory Listing
Modified Fri Feb 26 07:23:48 2016 UTC (16 months ago) by caltinay
small fix.


Revision 5989 - Directory Listing
Modified Fri Feb 26 07:00:48 2016 UTC (16 months ago) by jfenwick
Enabling neg and exp for complex


Revision 5988 - Directory Listing
Modified Fri Feb 26 06:59:38 2016 UTC (16 months ago) by caltinay
eliminated Esys_setError() et al from finley. We do have the issue of
potentially throwing exceptions in some ranks and not others but I'd claim
that was the case before in various places.


Revision 5987 - Directory Listing
Modified Fri Feb 26 04:34:10 2016 UTC (16 months ago) by jfenwick
Fix to allow packages to build for sid


Revision 5986 - Directory Listing
Modified Fri Feb 26 04:10:41 2016 UTC (16 months ago) by caltinay
more test fixes.


Revision 5985 - Directory Listing
Modified Fri Feb 26 02:21:44 2016 UTC (16 months ago) by jfenwick
Adding #define for namespace on dynamic_pointer_cast<>

Also for static_pointer_cast<>
The plan is to make it easy to switch between boost::
and std::  for shared_ptr

This will be important if we start to rely on more recent
share_ptr features (guaranteed to be in c++11 not necessarily in boost)


Revision 5984 - Directory Listing
Modified Fri Feb 26 02:00:45 2016 UTC (16 months ago) by caltinay
Added IOError. Also started replacing some 'setError()' calls by exception
throws as the latest test failures are bogus because an error was set but
never checked for.


Revision 5983 - Directory Listing
Modified Thu Feb 25 07:18:06 2016 UTC (16 months ago) by caltinay
bye bye DataC!
Fixes #248


Revision 5982 - Directory Listing
Modified Thu Feb 25 07:16:26 2016 UTC (16 months ago) by caltinay
all of dudley's Assemble* routines are now in namespace and
I think I removed all DataC use.


Revision 5981 - Directory Listing
Modified Thu Feb 25 07:12:18 2016 UTC (16 months ago) by caltinay
fixed a few exception types in tests.


Revision 5980 - Directory Listing
Modified Thu Feb 25 04:03:21 2016 UTC (16 months ago) by caltinay
oops :-)


Revision 5979 - Directory Listing
Modified Wed Feb 24 23:03:17 2016 UTC (16 months ago) by caltinay
fix for serial.


Revision 5978 - Directory Listing
Modified Wed Feb 24 22:02:37 2016 UTC (16 months ago) by caltinay
don't check for exception string contents.


Revision 5977 - Directory Listing
Modified Wed Feb 24 07:15:04 2016 UTC (16 months ago) by caltinay
replaced some DataC usage by equivalent method calls.


Revision 5976 - Directory Listing
Modified Wed Feb 24 06:57:20 2016 UTC (16 months ago) by caltinay
squashed last instances of checkPtr.


Revision 5975 - Directory Listing
Modified Wed Feb 24 06:56:51 2016 UTC (16 months ago) by caltinay
updated unit tests to reflect changed exception class.


Revision 5974 - Directory Listing
Modified Wed Feb 24 04:40:24 2016 UTC (16 months ago) by caltinay
update some tests.


Revision 5973 - Directory Listing
Modified Wed Feb 24 04:27:52 2016 UTC (16 months ago) by caltinay
trying to fix the "python include must come first" issue on savanna and
fix for serial build.


Revision 5972 - Directory Listing
Modified Wed Feb 24 04:05:30 2016 UTC (16 months ago) by caltinay
Major rework of our exceptions. We now have specific
AssertException
NotImplementedError
ValueError
which translate to the corresponding python exception type.
I have gone through a few places and replaced things but not everywhere.



Revision 5971 - Directory Listing
Modified Wed Feb 24 03:22:58 2016 UTC (16 months ago) by caltinay
disable cuda on savanna as it's incompatible with c++11 at the moment.


Revision 5970 - Directory Listing
Modified Tue Feb 23 08:30:40 2016 UTC (16 months ago) by jfenwick
To keep the mac happy

Revision 5969 - Directory Listing
Modified Tue Feb 23 06:22:10 2016 UTC (16 months ago) by caltinay
forgot to move file writer unit test.


Revision 5968 - Directory Listing
Modified Tue Feb 23 06:08:37 2016 UTC (16 months ago) by caltinay
moved file writer to escript and added explicit link to escript in paso.


Revision 5967 - Directory Listing
Modified Tue Feb 23 05:46:09 2016 UTC (16 months ago) by caltinay
found a few instances of MPI_COMM_WORLD and squashed them.
Added member to AbstractDomain that returns a JMPI so we ensure all
domains support that.
Moved appendRankToFilename into class.


Revision 5966 - Directory Listing
Modified Tue Feb 23 03:31:17 2016 UTC (16 months ago) by caltinay
fixed serial compile and moved mod_rank into class.


Revision 5965 - Directory Listing
Modified Tue Feb 23 01:45:40 2016 UTC (16 months ago) by caltinay
removed more useless #defines.


Revision 5964 - Directory Listing
Modified Tue Feb 23 01:20:19 2016 UTC (16 months ago) by jfenwick
Hopefully fix the numpy/py3 bug



Revision 5962 - Directory Listing
Modified Mon Feb 22 06:46:23 2016 UTC (16 months ago) by caltinay
removed types.h and adapted quite a bit of code...


Revision 5961 - Directory Listing
Modified Mon Feb 22 05:37:35 2016 UTC (16 months ago) by jfenwick
Fixing badger options to deal with the MPI/c++11 macro warning


Revision 5960 - Directory Listing
Modified Mon Feb 22 05:37:05 2016 UTC (16 months ago) by jfenwick
Support for setting data point values.


Revision 5959 - Directory Listing
Modified Mon Feb 22 01:32:59 2016 UTC (16 months ago) by caltinay
removed a few macros.


Revision 5958 - Directory Listing
Modified Mon Feb 22 01:05:32 2016 UTC (16 months ago) by caltinay
moved random to escript.


Revision 5957 - Directory Listing
Modified Mon Feb 22 00:56:47 2016 UTC (16 months ago) by jfenwick
Enable toListOfTuples

Expand some THROWONCOMPLEX macros for cases where the 
 situation is permanent.



Revision 5956 - Directory Listing
Modified Mon Feb 22 00:33:39 2016 UTC (16 months ago) by jfenwick
Expanding some tabs. Replace more unaries

The where? family of functions is now done via the enum



Revision 5955 - Directory Listing
Modified Sun Feb 21 23:04:50 2016 UTC (16 months ago) by caltinay
initialize member to avoid random segfaults in threaded mode.


Revision 5954 - Directory Listing
Modified Sun Feb 21 22:40:27 2016 UTC (16 months ago) by caltinay
moved exception translators to escript.


Revision 5953 - Directory Listing
Modified Fri Feb 19 11:07:39 2016 UTC (16 months ago) by caltinay
remove 'nasty hack' and fix a typo in escript.


Revision 5952 - Directory Listing
Modified Fri Feb 19 07:27:31 2016 UTC (16 months, 1 week ago) by caltinay
bye bye blocktimer.
I just tried to use it and the things it reports were plain wrong.
No wonder given the few places it was ever put in.
Also, it seems it has caused more problems than helped over the years
(see svn log).
If we are ever keen to time our code again we might as well do it properly
using PAPI or similar...
 


Revision 5951 - Directory Listing
Modified Fri Feb 19 06:56:19 2016 UTC (16 months, 1 week ago) by caltinay
might be able to remove this "old hack" but for now I moved it into the right
place.


Revision 5950 - Directory Listing
Modified Fri Feb 19 06:49:07 2016 UTC (16 months, 1 week ago) by caltinay
metis kindly put its own real_t typedef in the global namespace so
we need to be careful not to clash with that :-(


Revision 5949 - Directory Listing
Modified Fri Feb 19 06:06:01 2016 UTC (16 months, 1 week ago) by jfenwick
Do unary expanded ops in a single chunk for each thread to avoid multiple switches



Revision 5948 - Directory Listing
Modified Fri Feb 19 05:02:39 2016 UTC (16 months, 1 week ago) by caltinay
moved index_t & dim_t into escript::DataTypes and updated files
accordingly. Dudley needs a full sweep of namespacing at some not-distant
future.


Revision 5947 - Directory Listing
Modified Fri Feb 19 03:11:05 2016 UTC (16 months, 1 week ago) by caltinay
forgot to build dudley. fixed.


Revision 5946 - Directory Listing
Modified Fri Feb 19 03:02:56 2016 UTC (16 months, 1 week ago) by caltinay
some baby steps towards removing esysUtils and making escript
our main library/module. Added real_t_max() and real_t_eps() functions.



Revision 5945 - Directory Listing
Modified Fri Feb 19 02:25:44 2016 UTC (16 months, 1 week ago) by jfenwick
Can now take .real() and .imag() on all types.

imag() on real is not especially efficient.
May want to look at how the local ops are called to
see if we can reduce the loop overhead (given that each call
incurs a switch() cost now).


Revision 5944 - Directory Listing
Modified Fri Feb 19 00:54:36 2016 UTC (16 months, 1 week ago) by jfenwick
Can now take conjugates of complexes

Also fixed a bug related to unary operations on complexes


Revision 5943 - Directory Listing
Modified Thu Feb 18 23:36:21 2016 UTC (16 months, 1 week ago) by jfenwick
Remove unused var


Revision 5942 - Directory Listing
Modified Thu Feb 18 22:53:49 2016 UTC (16 months, 1 week ago) by caltinay
Argh! "No more C-code lurking in our base"
Simon says....nothing.


Revision 5939 - Directory Listing
Modified Thu Feb 18 10:04:32 2016 UTC (16 months, 1 week ago) by caltinay
added -std=c++11 unconditionally in sconstruct since we can't compile
without.


Revision 5938 - Directory Listing
Modified Thu Feb 18 06:30:35 2016 UTC (16 months, 1 week ago) by jfenwick
Merging from 5937 on the complex branch

Some parts of complex work but all of it is
not unit tested and it is certainly not feature
complete (I haven't put any time into dealing with
subworld for complex).

The other important aspect of this merge is that
c++11 is now required to build escript.



Revision 5936 - Directory Listing
Modified Thu Feb 18 04:11:21 2016 UTC (16 months, 1 week ago) by caltinay
re-added check for esys errors.
The seterror function should really throw itself now!!


Revision 5932 - Directory Listing
Modified Wed Feb 17 23:12:24 2016 UTC (16 months, 1 week ago) by caltinay
disable cuda on guineapig due to a nvcc/boost compile issue.


Revision 5931 - Directory Listing
Modified Wed Feb 17 22:50:34 2016 UTC (16 months, 1 week ago) by caltinay
unset build_shared for gp and newton. The static string definition is
causing trouble now.


Revision 5930 - Directory Listing
Modified Wed Feb 17 22:17:30 2016 UTC (16 months, 1 week ago) by caltinay
fixed a type error.


Revision 5929 - Directory Listing
Modified Wed Feb 17 07:40:00 2016 UTC (16 months, 1 week ago) by caltinay
Merged pasowrap into paso.
Unfortunately, this required touching quite a few files.
build_shared now defaults to true but will likely disappear altogether
once esysUtils disappears.


Revision 5923 - Directory Listing
Modified Mon Feb 15 03:39:22 2016 UTC (16 months, 1 week ago) by jfenwick
Enable d+=d

Seems like an obscure case but it failed because
,in order to allow for possible interpolation, it
created a temporary object which looked to the lazy
system as if the data was suddenly shared.



Revision 5900 - Directory Listing
Modified Fri Feb 5 04:02:20 2016 UTC (16 months, 3 weeks ago) by caltinay
removed two macros which conflict with third party libs.
The whole header should probably be culled and we should remove its inclusion
from other headers. Later...


Revision 5899 - Directory Listing
Modified Fri Feb 5 03:55:35 2016 UTC (16 months, 3 weeks ago) by caltinay
basically a no-op but c++11 rightfully complains that we're trying to
operator<< a stringstream object.


Revision 5863 - Directory Listing
Modified Wed Jan 13 02:25:48 2016 UTC (17 months, 1 week ago) by jfenwick
Copyright dates updated.
\version for doxygen to read


Revision 5857 - Directory Listing
Modified Tue Dec 15 07:30:34 2015 UTC (18 months, 1 week ago) by caltinay
hmm, this change was necessary on Trusty for some reason, it shouldn't break
other builds...


Revision 5856 - Directory Listing
Modified Tue Dec 15 06:31:27 2015 UTC (18 months, 1 week ago) by jfenwick
Removed dependency on lsb-release
Added new entry to debian/changelog
debian/rules now does not make any use of custom subst files (always 
builds for "sid")

Updated makesrc.sh    to build an "orig" tarball which we can use as our source release.



Revision 5855 - Directory Listing
Modified Tue Dec 15 03:38:42 2015 UTC (18 months, 1 week ago) by caltinay
options file for our new slave.


Revision 5854 - Directory Listing
Modified Tue Dec 15 02:51:21 2015 UTC (18 months, 1 week ago) by jfenwick
Updated version info and remove all applied patches from the quilt series


Revision 5853 - Directory Listing
Modified Tue Dec 15 01:19:33 2015 UTC (18 months, 1 week ago) by jfenwick
bringing changes over from debian for 4.1
The quilt patch series do not make sense at the moment because most of them will already be encorporated 


Revision 5852 - Directory Listing
Modified Mon Dec 14 23:52:02 2015 UTC (18 months, 1 week ago) by jfenwick
Added non-version specific options file for debian


Revision 5851 - Directory Listing
Modified Thu Dec 10 05:09:35 2015 UTC (18 months, 2 weeks ago) by jfenwick
changes to support fixing libraries build on osx - enable with osx_dependency_fix.  Also added options file for OSX.11 and homebrew

Revision 5845 - Directory Listing
Modified Fri Nov 27 05:24:13 2015 UTC (18 months, 4 weeks ago) by sshaw
removing dud commmented code

Revision 5835 - Directory Listing
Modified Thu Nov 26 07:42:03 2015 UTC (19 months ago) by gross
MT allows now a background field

Revision 5834 - Directory Listing
Modified Thu Nov 26 06:28:05 2015 UTC (19 months ago) by jfenwick
More lintian fixes


Revision 5833 - Directory Listing
Modified Thu Nov 26 04:37:32 2015 UTC (19 months ago) by jfenwick
Fixing some lintian objections

Revision 5832 - Directory Listing
Modified Thu Nov 26 01:16:43 2015 UTC (19 months ago) by jfenwick
Minor cleanup

Revision 5831 - Directory Listing
Modified Thu Nov 26 00:26:52 2015 UTC (19 months ago) by jfenwick
Produces what looks like correct answers on Jaco's example.

Still to do:
. Clean up extraneous output
. Doco on what the various variables do
. Discussion on difference between this mode and the normal
downunder. (Should the same changes be made to normal downunder?)
. Document more clearly assumptions which have been made. 
  - The only one which comes to mind is the one where only the 
    regularisation term actually matters for one of the calculations.
 


Revision 5830 - Directory Listing
Modified Tue Nov 24 23:55:20 2015 UTC (19 months ago) by jfenwick
not supposed to do that

Revision 5829 - Directory Listing
Modified Tue Nov 24 00:37:43 2015 UTC (19 months ago) by jfenwick
Added debian/watch file
It turns out that 
  uscan --no-download --verbose  
does not like ~ in upstream version numbers.
We may need to do a mini re-release of 4.1 to fix that 


Revision 5828 - Directory Listing
Modified Mon Nov 23 00:43:19 2015 UTC (19 months ago) by jfenwick
Provide access to splitworld via the escript package


Revision 5827 - Directory Listing
Modified Thu Nov 19 05:32:16 2015 UTC (19 months, 1 week ago) by jfenwick
Fix to stop clang complaining.  Adding a script to change references in libraries on osx

Revision 5826 - Directory Listing
Modified Tue Nov 17 03:28:56 2015 UTC (19 months, 1 week ago) by jfenwick
Removing unnescessary .dirs files

Revision 5825 - Directory Listing
Modified Tue Nov 17 02:41:49 2015 UTC (19 months, 1 week ago) by jfenwick
Removing unnecessary dep - it is picked up by the auto-stuff

Revision 5824 - Directory Listing
Modified Tue Nov 10 12:49:22 2015 UTC (19 months, 2 weeks ago) by caltinay
updating savanna options to use intel 2016 and cuda 7.5


Revision 5823 - Directory Listing
Modified Wed Nov 4 08:32:50 2015 UTC (19 months, 3 weeks ago) by jfenwick
Changes for new interface


Revision 5822 - Directory Listing
Modified Fri Oct 30 06:32:34 2015 UTC (19 months, 3 weeks ago) by jduplessis
turns out x should be because sigmaprim - sigma this is because there is a negative in the x template


Revision 5821 - Directory Listing
Modified Fri Oct 16 00:59:07 2015 UTC (20 months, 1 week ago) by caltinay
Type fix for parmetis with long indices

Revision 5820 - Directory Listing
Modified Thu Oct 15 05:38:49 2015 UTC (20 months, 1 week ago) by caltinay
removed obsolete comment.


Revision 5819 - Directory Listing
Modified Fri Oct 9 04:21:49 2015 UTC (20 months, 2 weeks ago) by caltinay
and another skip without gmsh.


Revision 5818 - Directory Listing
Modified Fri Oct 9 03:42:53 2015 UTC (20 months, 2 weeks ago) by caltinay
skip test without gmsh.


Revision 5817 - Directory Listing
Modified Fri Oct 9 00:07:06 2015 UTC (20 months, 2 weeks ago) by caltinay
fixed failures for MPI builds with single-rank runs


Revision 5816 - Directory Listing
Modified Thu Oct 8 23:44:31 2015 UTC (20 months, 2 weeks ago) by caltinay
fix running unit tests when prefix is set to somewhere else.


Revision 5815 - Directory Listing
Modified Thu Oct 8 02:49:13 2015 UTC (20 months, 2 weeks ago) by jfenwick
Working on package testing

Revision 5814 - Directory Listing
Modified Fri Oct 2 04:52:56 2015 UTC (20 months, 3 weeks ago) by jfenwick
Allow openmpi to execute when there is no rsh/ssh

Revision 5813 - Directory Listing
Modified Tue Sep 29 03:48:17 2015 UTC (20 months, 4 weeks ago) by caltinay
Fixed a bug in saveDataCSV where mask could be on a different domain
and/or function space than the data objects.


Revision 5812 - Directory Listing
Modified Sat Sep 26 02:44:57 2015 UTC (21 months ago) by jfenwick
Adding the mpi binaries for building


Revision 5811 - Directory Listing
Modified Sat Sep 26 02:10:31 2015 UTC (21 months ago) by jfenwick
Running sanity check from build directory


Revision 5810 - Directory Listing
Modified Fri Sep 25 06:17:26 2015 UTC (21 months ago) by caltinay
DOF and reduced DOF can now be passed to ownSample() in Finley.


Revision 5809 - Directory Listing
Modified Fri Sep 25 00:54:38 2015 UTC (21 months ago) by caltinay
another fix for _XOPEN_SOURCE warning in tests.


Revision 5808 - Directory Listing
Modified Fri Sep 25 00:17:38 2015 UTC (21 months ago) by caltinay
The MPI file view resets file pointer offset so explicitly
set to EOF when appending. Should fix test failures.


Revision 5807 - Directory Listing
Modified Thu Sep 24 06:40:11 2015 UTC (21 months ago) by caltinay
fix for non-MPI build


Revision 5806 - Directory Listing
Modified Thu Sep 24 06:36:22 2015 UTC (21 months ago) by caltinay
DataExpanded: avoid lockups in dump() due to unnecessary MPI comms.
Also code cleanup.


Revision 5805 - Directory Listing
Modified Thu Sep 24 04:18:13 2015 UTC (21 months ago) by caltinay
Cleanup in escript utils and use FileWriter to avoid code
duplication.
Also added sanity checks to FileWriter.


Revision 5804 - Directory Listing
Modified Thu Sep 24 03:51:27 2015 UTC (21 months ago) by caltinay
actually *USE* MPI IO in ripley rather than pretending, d'oh.


Revision 5803 - Directory Listing
Modified Thu Sep 24 01:29:17 2015 UTC (21 months ago) by jfenwick
Hopefully addressing some of the packaging issues

Revision 5802 - Directory Listing
Modified Wed Sep 23 05:17:26 2015 UTC (21 months ago) by jfenwick
Trying again to default to sanity.


Revision 5801 - Directory Listing
Modified Tue Sep 22 10:37:07 2015 UTC (21 months ago) by jfenwick
move sanity out of always build until ordering can be resolved

Revision 5800 - Directory Listing
Modified Tue Sep 22 09:42:58 2015 UTC (21 months ago) by jfenwick
Fixing default builds

Revision 5799 - Directory Listing
Modified Tue Sep 22 06:54:28 2015 UTC (21 months ago) by gross
fix for Bug #326

Revision 5798 - Directory Listing
Modified Tue Sep 22 04:22:12 2015 UTC (21 months ago) by jfenwick
Added a sanity check for builds as requested by Anton.
This will just check to see if the libraries built.

Feel free to add other checks to scripts/release_sanity  BUT they are not
to create files which pollute the source directory.



Revision 5797 - Directory Listing
Modified Tue Sep 22 01:32:21 2015 UTC (21 months ago) by jfenwick
Moving /debian out of the way to /localdebian


Revision 5796 - Directory Listing
Modified Mon Sep 21 03:43:09 2015 UTC (21 months ago) by caltinay
Removed some order 2 tests in dudley and fixed docstring to make
clear that dudley only supports order 1.


Revision 5795 - Directory Listing
Modified Mon Sep 21 03:37:30 2015 UTC (21 months ago) by caltinay
Avoid netCDF warning by calling del on local references to mmap'ed data


Revision 5794 - Directory Listing
Modified Fri Sep 18 02:32:59 2015 UTC (21 months, 1 week ago) by caltinay
Fix for bug #328


Revision 5793 - Directory Listing
Modified Wed Sep 16 05:02:36 2015 UTC (21 months, 1 week ago) by caltinay
Commented use of makeZeroRowSums in Transport solver, see bug #326


Revision 5792 - Directory Listing
Modified Wed Sep 16 05:01:47 2015 UTC (21 months, 1 week ago) by caltinay
Fixed typo in datamanager.


Revision 5791 - Directory Listing
Modified Wed Sep 16 02:24:07 2015 UTC (21 months, 1 week ago) by caltinay
x!=None -> x is not None fixes


Revision 5790 - Directory Listing
Modified Wed Sep 9 04:56:37 2015 UTC (21 months, 2 weeks ago) by jduplessis
wrong order for subtraction. based on ralfs notes.


Revision 5789 - Directory Listing
Modified Mon Sep 7 01:01:53 2015 UTC (21 months, 2 weeks ago) by caltinay
index_t fixes in DataExpanded.


Revision 5788 - Directory Listing
Modified Mon Sep 7 01:00:49 2015 UTC (21 months, 2 weeks ago) by caltinay
switch to impi 5.1


Revision 5787 - Directory Listing
Modified Fri Sep 4 06:00:20 2015 UTC (21 months, 3 weeks ago) by caltinay
64-bit index fixes in finley.


Revision 5786 - Directory Listing
Modified Thu Sep 3 05:03:25 2015 UTC (21 months, 3 weeks ago) by caltinay
Another case of 'we are setting the wrong params for third-party libs' +
we are now setting a flag to use two-level factorization with more than
8 OpenMP threads.
--> runtime for a 2000x2000 poisson problem with block size 3 running on 20
threads is down from 168 seconds to 91.5 seconds! (Paso PCG: 466
seconds)



Revision 5785 - Directory Listing
Modified Thu Sep 3 03:15:25 2015 UTC (21 months, 3 weeks ago) by caltinay
Can compile with MKL and long indices now.


Revision 5784 - Directory Listing
Modified Thu Sep 3 02:43:08 2015 UTC (21 months, 3 weeks ago) by caltinay
updated templates to use correct type for domains parameter.


Revision 5783 - Directory Listing
Modified Wed Sep 2 23:27:34 2015 UTC (21 months, 3 weeks ago) by caltinay
another non-finley test failure fixed.


Revision 5782 - Directory Listing
Modified Tue Sep 1 06:00:44 2015 UTC (21 months, 3 weeks ago) by caltinay
added guards for non-finley builds.


Revision 5781 - Directory Listing
Modified Mon Aug 31 05:52:20 2015 UTC (21 months, 3 weeks ago) by caltinay
made finley::Mesh::write long index compatible.


Revision 5780 - Directory Listing
Modified Mon Aug 31 05:37:39 2015 UTC (21 months, 3 weeks ago) by sshaw
makeTranformation deprecated, left as a wrapper of the new makeTransformation

Revision 5779 - Directory Listing
Modified Fri Aug 28 06:27:41 2015 UTC (21 months, 4 weeks ago) by sshaw
fixing UMFPACK numerical issues due to implicit METIS ordering not existin gin newer UMFPACK versions (>5.2)


Revision 5778 - Directory Listing
Modified Mon Aug 10 05:43:52 2015 UTC (22 months, 2 weeks ago) by jduplessis
added bessel function of first and second kind


Revision 5775 - Directory Listing
Modified Thu Jul 30 08:01:06 2015 UTC (22 months, 4 weeks ago) by sshaw
pushing release to trunk

Revision 5760 - Directory Listing
Modified Wed Jul 22 11:30:28 2015 UTC (23 months ago) by sshaw
fixing the python3 fix that was fixed for python2 but broke 3

Revision 5759 - Directory Listing
Modified Wed Jul 22 05:26:42 2015 UTC (23 months ago) by sshaw
undoing mistaken commit of types.h

Revision 5758 - Directory Listing
Modified Wed Jul 22 05:25:45 2015 UTC (23 months ago) by sshaw
fixing python 3 compatibility change where overriding a type in scope destroys the global type referece completely (result is py2 no longer complaining)

Revision 5756 - Directory Listing
Modified Fri Jul 17 05:20:47 2015 UTC (23 months, 1 week ago) by sshaw
making long as a type work in python3

Revision 5753 - Directory Listing
Modified Fri Jul 17 01:06:22 2015 UTC (23 months, 1 week ago) by sshaw
replacing xrange for py3 compatibility

Revision 5752 - Directory Listing
Modified Fri Jul 17 00:05:18 2015 UTC (23 months, 1 week ago) by sshaw
fixing MT tests for MPI

Revision 5751 - Directory Listing
Modified Wed Jul 15 10:25:45 2015 UTC (23 months, 1 week ago) by jfenwick
Tests and tweaks for magneto-telluric

Revision 5750 - Directory Listing
Modified Wed Jul 15 09:59:49 2015 UTC (23 months, 1 week ago) by jfenwick
Fixing a python3 issue with voxet example

Revision 5749 - Directory Listing
Modified Wed Jul 15 08:23:11 2015 UTC (23 months, 1 week ago) by sshaw
now with proper namespacing on MT example fixes

Revision 5748 - Directory Listing
Modified Wed Jul 15 06:49:05 2015 UTC (23 months, 1 week ago) by sshaw
python3 prints for 2D MT source

Revision 5747 - Directory Listing
Modified Wed Jul 15 06:44:38 2015 UTC (23 months, 1 week ago) by sshaw
tab->space replacements again

Revision 5746 - Directory Listing
Modified Wed Jul 15 05:29:59 2015 UTC (23 months, 1 week ago) by sshaw
adding detection of missing direct solvers to MT tests

Revision 5745 - Directory Listing
Modified Wed Jul 15 03:24:37 2015 UTC (23 months, 1 week ago) by sshaw
python3ifying inequality tests in MT

Revision 5744 - Directory Listing
Modified Wed Jul 15 00:01:00 2015 UTC (23 months, 1 week ago) by jduplessis
somehow ReadGmsh escaped

Revision 5743 - Directory Listing
Modified Tue Jul 14 07:24:22 2015 UTC (23 months, 2 weeks ago) by jduplessis
removed dcresdomgen

Revision 5742 - Directory Listing
Modified Tue Jul 14 05:52:56 2015 UTC (23 months, 2 weeks ago) by jduplessis
removal of dcdomaingen from trunk for now


Revision 5741 - Directory Listing
Modified Tue Jul 14 01:16:47 2015 UTC (23 months, 2 weeks ago) by sshaw
making MT examples python3 and MPI safe

Revision 5740 - Directory Listing
Modified Mon Jul 13 10:28:24 2015 UTC (23 months, 2 weeks ago) by jfenwick
Remove blanket import of escript into inversions.
Modify __all__ to allow "hiding" some members of escript from a blanket import


Revision 5739 - Directory Listing
Modified Mon Jul 13 07:54:16 2015 UTC (23 months, 2 weeks ago) by jfenwick
Changing scoping for splitworld internals.
Experiments on hiding them to follow later.



Revision 5738 - Directory Listing
Modified Mon Jul 13 07:52:05 2015 UTC (23 months, 2 weeks ago) by jfenwick
Added Ralf's examples.
Tests for correctness to follow later.


Revision 5737 - Directory Listing
Modified Mon Jul 13 04:51:55 2015 UTC (23 months, 2 weeks ago) by jduplessis
updates of test to prepare for removal of dcresdomgen


Revision 5736 - Directory Listing
Modified Fri Jul 10 00:34:03 2015 UTC (23 months, 2 weeks ago) by sshaw
made namespace use consistent between header and cpp to help poor doxygen find the right functions

Revision 5735 - Directory Listing
Modified Fri Jul 10 00:03:36 2015 UTC (23 months, 2 weeks ago) by sshaw
updating doxygen config file version


Revision 5734 - Directory Listing
Modified Thu Jul 9 23:16:37 2015 UTC (23 months, 2 weeks ago) by jfenwick
Removing subworlds from the user guide until we tweak the interface.



Revision 5733 - Directory Listing
Modified Thu Jul 9 22:24:46 2015 UTC (23 months, 2 weeks ago) by jfenwick
Minor fixes to splitworld doco


Revision 5731 - Directory Listing
Modified Thu Jul 9 02:27:37 2015 UTC (23 months, 2 weeks ago) by jfenwick
An attempt to provide some prior warning about situations described in issue#309.
If -DEXWRITECHK is defined, any attempt to get RW access to a data object
without requireWrite() will throw an exception.

This does not ultimately address the issue of dirac but will hopefully
catch problems.


Revision 5728 - Directory Listing
Modified Wed Jul 8 04:33:25 2015 UTC (23 months, 2 weeks ago) by sshaw
fixing some issues in splitworld doco


Revision 5727 - Directory Listing
Modified Wed Jul 8 04:29:40 2015 UTC (23 months, 2 weeks ago) by sshaw
correcting exception message text


Revision 5726 - Directory Listing
Modified Wed Jul 8 04:28:55 2015 UTC (23 months, 2 weeks ago) by jduplessis
commiting updates before removal


Revision 5725 - Directory Listing
Modified Tue Jul 7 04:09:10 2015 UTC (23 months, 3 weeks ago) by jfenwick
Adding split example to example dir

Revision 5724 - Directory Listing
Modified Mon Jul 6 05:40:35 2015 UTC (23 months, 3 weeks ago) by jfenwick
Added text for SubWorlds.


Revision 5723 - Directory Listing
Modified Mon Jul 6 01:51:13 2015 UTC (23 months, 3 weeks ago) by sshaw
adding division to future imports for voxet reader example

Revision 5722 - Directory Listing
Modified Mon Jul 6 01:43:30 2015 UTC (23 months, 3 weeks ago) by sshaw
doco updates, adding example gocad reader to user guide examples

Revision 5721 - Directory Listing
Modified Fri Jul 3 04:06:55 2015 UTC (23 months, 3 weeks ago) by jfenwick
Fixing tests to account for MultiBrick's non-MPI ness


Revision 5720 - Directory Listing
Modified Thu Jul 2 22:55:42 2015 UTC (23 months, 3 weeks ago) by sshaw
updating multibrick exception message to be accurate


Revision 5719 - Directory Listing
Modified Thu Jul 2 07:09:20 2015 UTC (23 months, 3 weeks ago) by jfenwick
Allow launching using fewer nodes than are in the host file


Revision 5718 - Directory Listing
Modified Thu Jul 2 05:02:26 2015 UTC (23 months, 3 weeks ago) by jfenwick
Added tests for Multi-Brick and Rectangle


Revision 5717 - Directory Listing
Modified Thu Jul 2 04:39:14 2015 UTC (23 months, 3 weeks ago) by sshaw
some minor cleanup of splitworlds


Revision 5716 - Directory Listing
Modified Thu Jul 2 04:24:13 2015 UTC (23 months, 3 weeks ago) by jfenwick
Avoid aliased buffer


Revision 5715 - Directory Listing
Modified Thu Jul 2 01:37:02 2015 UTC (23 months, 3 weeks ago) by jfenwick
Some unit test updates


Revision 5714 - Directory Listing
Modified Wed Jul 1 03:57:45 2015 UTC (23 months, 3 weeks ago) by sshaw
fix for build failures on x86 machines due to underlying type of size_t being different for a format string

Revision 5713 - Directory Listing
Modified Tue Jun 30 05:54:14 2015 UTC (23 months, 4 weeks ago) by sshaw
cleanup of finley test imports and docstrings

Revision 5712 - Directory Listing
Modified Tue Jun 30 05:43:48 2015 UTC (23 months, 4 weeks ago) by caltinay
fixing second domain generation.


Revision 5711 - Directory Listing
Modified Tue Jun 30 05:15:54 2015 UTC (23 months, 4 weeks ago) by sshaw
fixing doxygen warnings


Revision 5710 - Directory Listing
Modified Tue Jun 30 03:42:04 2015 UTC (23 months, 4 weeks ago) by caltinay
Work around gmsh issue when optimizing mesh by disabling optimization for a test

Revision 5709 - Directory Listing
Modified Mon Jun 29 06:13:31 2015 UTC (23 months, 4 weeks ago) by caltinay
fixed an issue introduced in last commit.


Revision 5708 - Directory Listing
Modified Mon Jun 29 05:25:51 2015 UTC (23 months, 4 weeks ago) by caltinay
index fixes and some code cleanup in finley.
Introduced index_size attribute to finley dump (netCDF) files.


Revision 5707 - Directory Listing
Modified Mon Jun 29 03:59:06 2015 UTC (23 months, 4 weeks ago) by sshaw
adding copyright headers to files without copyright info, moved header to top of file in some cases where it wasn't

Revision 5706 - Directory Listing
Modified Mon Jun 29 03:41:36 2015 UTC (23 months, 4 weeks ago) by sshaw
all python files now force use of python3 prints and division syntax to stop sneaky errors appearing in py3 environs

Revision 5705 - Directory Listing
Modified Mon Jun 29 01:07:07 2015 UTC (23 months, 4 weeks ago) by sshaw
no more tab characters in python files

Revision 5704 - Directory Listing
Modified Mon Jun 29 01:03:48 2015 UTC (23 months, 4 weeks ago) by jfenwick
Adding forgotten ripley

Revision 5703 - Directory Listing
Modified Mon Jun 29 00:56:26 2015 UTC (23 months, 4 weeks ago) by jfenwick
Adding/fixing split world tests for domains except speckley


Revision 5702 - Directory Listing
Modified Mon Jun 29 00:05:03 2015 UTC (23 months, 4 weeks ago) by sshaw
finley util tests with contact now test properly for multi-process and skip if so

Revision 5701 - Directory Listing
Modified Fri Jun 26 05:48:11 2015 UTC (2 years ago) by caltinay
more work towards long indices.


Revision 5700 - Directory Listing
Modified Fri Jun 26 05:18:37 2015 UTC (2 years ago) by sshaw
changing silo module test to be a skip message rather than a failure

Revision 5699 - Directory Listing
Modified Fri Jun 26 05:01:26 2015 UTC (2 years ago) by sshaw
removing dudley tests that will never work

Revision 5698 - Directory Listing
Modified Fri Jun 26 04:40:42 2015 UTC (2 years ago) by sshaw
adding a test for silo being available but broken (as it currently is in debian/jessie

Revision 5697 - Directory Listing
Modified Fri Jun 26 04:29:19 2015 UTC (2 years ago) by jfenwick
Now we consider MPI_COMM_NULL in the MPI wrapper constructor
Added checks to see if reductions can clash
Make use of our MPI wrapper
Remove the unused "active" param.
Added a missing const 




Revision 5696 - Directory Listing
Modified Fri Jun 26 04:00:56 2015 UTC (2 years ago) by caltinay
Added version check to parmetis to get size of index types.
Also reporting boost & parmetis version now in summary.


Revision 5695 - Directory Listing
Modified Fri Jun 26 03:28:21 2015 UTC (2 years ago) by sshaw
some testfile cleanup: python3ifying, unskipping, and less '= False and True'

Revision 5694 - Directory Listing
Modified Fri Jun 26 02:10:39 2015 UTC (2 years ago) by caltinay
index type fixes.


Revision 5693 - Directory Listing
Modified Fri Jun 26 01:13:47 2015 UTC (2 years ago) by sshaw
added info on multi-resolution ripley to user guide

Revision 5692 - Directory Listing
Modified Thu Jun 25 06:16:17 2015 UTC (2 years ago) by caltinay
Work to get finley compiling with long indices.


Revision 5691 - Directory Listing
Modified Thu Jun 25 04:58:26 2015 UTC (2 years ago) by sshaw
adding multires domains to changelist

Revision 5690 - Directory Listing
Modified Thu Jun 25 04:25:44 2015 UTC (2 years ago) by caltinay
ripley compiles again with index type long.


Revision 5689 - Directory Listing
Modified Thu Jun 25 04:04:38 2015 UTC (2 years ago) by caltinay
Bail out if trying to build with long indices and lapack.


Revision 5688 - Directory Listing
Modified Thu Jun 25 03:30:29 2015 UTC (2 years ago) by sshaw
first pass at a changelist for 4.1

Revision 5687 - Directory Listing
Modified Thu Jun 25 01:47:50 2015 UTC (2 years ago) by jfenwick
isValid() allows testing if the wrapped communicator is actually valid 
in this process.

Also, will not try to free a communicator if it is MPI_COMM_NULL



Revision 5686 - Directory Listing
Modified Wed Jun 24 04:54:08 2015 UTC (2 years ago) by sshaw
updated comment in gmsh reader to explain the 'unsure why'


Revision 5685 - Directory Listing
Modified Wed Jun 24 04:53:16 2015 UTC (2 years ago) by sshaw
no more unexpected multi-process DIRECT exceptions in tests, no more unexpected direct solver missing exceptions in tests


Revision 5684 - Directory Listing
Modified Wed Jun 24 04:52:14 2015 UTC (2 years ago) by sshaw
no more multi-process segy exceptions in wave examples


Revision 5683 - Directory Listing
Modified Wed Jun 24 02:00:12 2015 UTC (2 years ago) by jfenwick
Removing debug output.
SUM variables now reset properly.
More forms of reduction supported.


Revision 5682 - Directory Listing
Modified Tue Jun 23 05:59:29 2015 UTC (2 years ago) by jduplessis
fixing Dudley help comments


Revision 5681 - Directory Listing
Modified Tue Jun 23 03:05:16 2015 UTC (2 years ago) by sshaw
currently is now currecntly spelled

Revision 5680 - Directory Listing
Modified Tue Jun 23 01:55:20 2015 UTC (2 years ago) by jfenwick
Bug fixes exposed by unit tests


Revision 5679 - Directory Listing
Modified Tue Jun 23 01:52:59 2015 UTC (2 years ago) by jfenwick
More informative error messages for people acting on DataEmpty

Revision 5678 - Directory Listing
Modified Tue Jun 23 00:08:37 2015 UTC (2 years ago) by sshaw
fixing synth TTI example: domain subdivision, spelling errors, and multi-proc SEGY exceptions

Revision 5677 - Directory Listing
Modified Mon Jun 22 08:05:28 2015 UTC (2 years ago) by jduplessis
brick and rectangle documentations updates


Revision 5676 - Directory Listing
Modified Mon Jun 22 06:53:36 2015 UTC (2 years ago) by sshaw
missing output directory created


Revision 5675 - Directory Listing
Modified Mon Jun 22 03:42:31 2015 UTC (2 years ago) by jduplessis
excetion for mpi and direct solver


Revision 5674 - Directory Listing
Modified Mon Jun 22 02:46:40 2015 UTC (2 years ago) by caltinay
Fixed a few typos


Revision 5673 - Directory Listing
Modified Mon Jun 22 02:43:20 2015 UTC (2 years ago) by jduplessis
makes meaning of solver options more clear


Revision 5672 - Directory Listing
Modified Mon Jun 22 01:14:00 2015 UTC (2 years ago) by jduplessis
added other solver methods. Also made error message more clear


Revision 5671 - Directory Listing
Modified Fri Jun 19 07:15:38 2015 UTC (2 years ago) by gross
start dirac example added

Revision 5670 - Directory Listing
Modified Fri Jun 19 07:14:10 2015 UTC (2 years ago) by gross
documenation fro Dirac added

Revision 5669 - Directory Listing
Modified Fri Jun 19 05:18:05 2015 UTC (2 years ago) by sshaw
trying to set a DIRECT solver method without libsuitesparse throws an exception


Revision 5668 - Directory Listing
Modified Fri Jun 19 04:22:12 2015 UTC (2 years ago) by sshaw
and now with the correct function names being used

Revision 5667 - Directory Listing
Modified Fri Jun 19 04:19:54 2015 UTC (2 years ago) by sshaw
stopping example wave scripts from trying to write SEGYs if obspy not installed

Revision 5666 - Directory Listing
Modified Fri Jun 19 02:09:55 2015 UTC (2 years ago) by sshaw
adding example wave scripts to the built examples collection and to testing, shortened length of simulations to make testing bearable

Revision 5665 - Directory Listing
Modified Fri Jun 19 02:08:01 2015 UTC (2 years ago) by sshaw
cleaning up seismic.py whitespace and fixing spelling mistakes in function names and params, the existing ones have been left with warnings about them being deprecated (createAbsorptionLayerFunction)


Revision 5664 - Directory Listing
Modified Thu Jun 18 23:34:12 2015 UTC (2 years ago) by sshaw
making the pdetools.Defect class abstract methods more obvious in documentation


Revision 5663 - Directory Listing
Modified Thu Jun 18 07:09:05 2015 UTC (2 years ago) by jfenwick
Further progress but still not right

Revision 5662 - Directory Listing
Modified Thu Jun 18 04:40:34 2015 UTC (2 years ago) by caltinay
Fixes #259 - replaced all references to mayavi by Mayavi2 in the docs.
The arguments were already correct.


Revision 5661 - Directory Listing
Modified Thu Jun 18 04:15:51 2015 UTC (2 years ago) by caltinay
use a placeholder that is more unlikely to be in the real data as suggested
by Jaco.


Revision 5660 - Directory Listing
Modified Thu Jun 18 04:06:31 2015 UTC (2 years ago) by caltinay
Fix for #266 - replace NaNs by large number before masking so it
actually works.


Revision 5659 - Directory Listing
Modified Thu Jun 18 01:35:56 2015 UTC (2 years ago) by caltinay
some typo and whitespace fixes


Revision 5658 - Directory Listing
Modified Wed Jun 17 23:39:18 2015 UTC (2 years ago) by jfenwick
Add brief text about dudley to finley section and tweak ripley description.


Revision 5657 - Directory Listing
Modified Wed Jun 17 07:23:39 2015 UTC (2 years ago) by jfenwick
SUM type variables, no longer accumulate forever

Revision 5656 - Directory Listing
Modified Tue Jun 16 07:11:02 2015 UTC (2 years ago) by jfenwick
Fixed incorrect package name in centos install instructions

Revision 5655 - Directory Listing
Modified Mon Jun 15 06:10:26 2015 UTC (2 years ago) by caltinay
Fixed tests.


Revision 5654 - Directory Listing
Modified Mon Jun 15 05:21:00 2015 UTC (2 years ago) by jfenwick
further

Revision 5653 - Directory Listing
Modified Mon Jun 15 03:48:49 2015 UTC (2 years ago) by caltinay
Implementation for #314. Minimizer callbacks in downunder are now passed
appropriate norm(s) that are used to check for convergence.


Revision 5652 - Directory Listing
Modified Mon Jun 15 02:48:17 2015 UTC (2 years ago) by gross
typo fixed

Revision 5651 - Directory Listing
Modified Sun Jun 14 23:24:48 2015 UTC (2 years ago) by jfenwick
turns out the consts are important

Revision 5650 - Directory Listing
Modified Sun Jun 14 23:02:39 2015 UTC (2 years ago) by sshaw
more xrange->range conversion for python3 compatibility

Revision 5649 - Directory Listing
Modified Sun Jun 14 06:38:00 2015 UTC (2 years ago) by jfenwick
Got stuck

Revision 5648 - Directory Listing
Modified Sat Jun 13 04:36:22 2015 UTC (2 years ago) by jfenwick
Can now get doubles out of python reducers


Revision 5647 - Directory Listing
Modified Fri Jun 12 05:16:33 2015 UTC (2 years ago) by jfenwick
Fixed the getPyObj on MPIDataReducer.
Note: the boost::python::object constructor can do things implicit conversion can't.


Revision 5646 - Directory Listing
Modified Fri Jun 12 04:04:58 2015 UTC (2 years ago) by sshaw
some more python3 fixing, better sorting of dicts/sets->lists for some cases

Revision 5645 - Directory Listing
Modified Fri Jun 12 02:56:30 2015 UTC (2 years ago) by jfenwick
more

Revision 5644 - Directory Listing
Modified Thu Jun 11 23:50:17 2015 UTC (2 years ago) by sshaw
fixing test_getPotential3dSchlumberger syntax errors

Revision 5643 - Directory Listing
Modified Thu Jun 11 22:50:48 2015 UTC (2 years ago) by jfenwick
adding set only reducer

Revision 5642 - Directory Listing
Modified Thu Jun 11 07:53:22 2015 UTC (2 years ago) by jfenwick
Start on converting _zoom and line_search

Revision 5641 - Directory Listing
Modified Thu Jun 11 05:59:46 2015 UTC (2 years ago) by sshaw
adjusted dict->list conversions to be deterministic under python3 (fixes ranks operating on elements in different orders)

Revision 5640 - Directory Listing
Modified Thu Jun 11 05:32:09 2015 UTC (2 years ago) by sshaw
utest now properly catches errors in test scripts, not just failures

Revision 5639 - Directory Listing
Modified Thu Jun 11 01:34:26 2015 UTC (2 years ago) by caltinay
make conversion of dict to list deterministic.
This should fix the MPI_Waitall failures we are seeing with python 3
and multiple ranks.


Revision 5638 - Directory Listing
Modified Wed Jun 10 03:45:27 2015 UTC (2 years ago) by jfenwick
fixing tabs and updating options file

Revision 5637 - Directory Listing
Modified Wed Jun 10 03:34:10 2015 UTC (2 years ago) by jfenwick
further

Revision 5636 - Directory Listing
Modified Tue Jun 9 23:44:22 2015 UTC (2 years ago) by jfenwick
Remove some debug prints


Revision 5635 - Directory Listing
Modified Tue Jun 9 23:41:14 2015 UTC (2 years ago) by jfenwick
Some more work on splits. Next target is gradient calculation

Revision 5634 - Directory Listing
Modified Tue Jun 9 00:27:13 2015 UTC (2 years ago) by jfenwick
fixing my tab crimes

Revision 5633 - Directory Listing
Modified Fri Jun 5 01:08:43 2015 UTC (2 years ago) by jfenwick
And the domestication of the dog continued unabated


Revision 5632 - Directory Listing
Modified Thu Jun 4 07:14:39 2015 UTC (2 years ago) by jfenwick
Adding options file for me


Revision 5631 - Directory Listing
Modified Thu Jun 4 07:13:11 2015 UTC (2 years ago) by jfenwick
More


Revision 5630 - Directory Listing
Modified Thu Jun 4 06:25:57 2015 UTC (2 years ago) by jfenwick
Some work towards split inversion

Revision 5629 - Directory Listing
Modified Thu Jun 4 03:49:45 2015 UTC (2 years ago) by jduplessis
temporary increase in tolerance.


Revision 5628 - Directory Listing
Modified Thu Jun 4 01:27:34 2015 UTC (2 years ago) by caltinay
fixAboveLevel takes now precedence over fixAtTop as required by TM mode
forward model constructor.


Revision 5627 - Directory Listing
Modified Thu Jun 4 01:26:55 2015 UTC (2 years ago) by caltinay
Fixed a few gcc 5 warnings.


Revision 5626 - Directory Listing
Modified Wed Jun 3 02:21:06 2015 UTC (2 years ago) by caltinay
revert obvious unintended comment changes.


Revision 5625 - Directory Listing
Modified Mon Jun 1 05:01:54 2015 UTC (2 years ago) by jduplessis
fixed electrodelist


Revision 5624 - Directory Listing
Modified Mon Jun 1 04:49:20 2015 UTC (2 years ago) by jduplessis
electrode list rather than dictionary


Revision 5623 - Directory Listing
Modified Mon Jun 1 04:21:26 2015 UTC (2 years ago) by jfenwick
With some help from Cihan, we now have exception traces for python code called from C++.
It also works with python3.


Revision 5622 - Directory Listing
Modified Thu May 28 02:37:12 2015 UTC (2 years, 1 month ago) by jfenwick
Small improvements towards split inversion


Revision 5621 - Directory Listing
Modified Wed May 27 03:25:41 2015 UTC (2 years, 1 month ago) by sshaw
cookbook examples now using correct indices

Revision 5620 - Directory Listing
Modified Mon May 25 03:16:41 2015 UTC (2 years, 1 month ago) by jfenwick
badger is on Jessie now.


Revision 5619 - Directory Listing
Modified Mon May 25 01:38:10 2015 UTC (2 years, 1 month ago) by jfenwick
Cleanup of scripts directory
There is now a single python suppressions file for both py2.7 and py3.
makesrc.py will make an orig.tar.gz with the appropriate name for building debs.


Revision 5618 - Directory Listing
Modified Mon May 25 00:05:26 2015 UTC (2 years, 1 month ago) by jfenwick
Remove comment about Python3 support being experimental


Revision 5617 - Directory Listing
Modified Tue May 19 01:03:17 2015 UTC (2 years, 1 month ago) by jfenwick
Fix out of bounds in FinleyElement handling

Revision 5616 - Directory Listing
Modified Mon May 18 05:01:33 2015 UTC (2 years, 1 month ago) by jfenwick
Added debian build flags


Revision 5615 - Directory Listing
Modified Mon May 18 04:47:57 2015 UTC (2 years, 1 month ago) by jfenwick
Fixing doco links

Revision 5614 - Directory Listing
Modified Fri May 15 05:37:34 2015 UTC (2 years, 1 month ago) by caltinay
Fixes #311 - avoid accessing last+1 element although it is never used.


Revision 5613 - Directory Listing
Modified Fri May 15 04:49:58 2015 UTC (2 years, 1 month ago) by sshaw
fixing bad meshinfo when saving speckley metadata to VTK

Revision 5612 - Directory Listing
Modified Fri May 15 03:29:02 2015 UTC (2 years, 1 month ago) by jfenwick
Moving guineapig to jessie


Revision 5611 - Directory Listing
Modified Wed May 13 23:36:01 2015 UTC (2 years, 1 month ago) by jfenwick
Changes to reflect new debian and ubuntu releases.


Revision 5610 - Directory Listing
Modified Wed May 13 00:40:26 2015 UTC (2 years, 1 month ago) by jfenwick
Added missing \n to test footer.
Added check to stop me from nuking my src dir when extracting tests


Revision 5609 - Directory Listing
Modified Wed May 6 23:57:42 2015 UTC (2 years, 1 month ago) by sshaw
making itest do the summary of failures the same as utest

Revision 5608 - Directory Listing
Modified Wed May 6 02:38:03 2015 UTC (2 years, 1 month ago) by jfenwick
Builds and passes at least some tests on all packages.
We need to evaluate the test failures a bit more carefully though.


Revision 5607 - Directory Listing
Modified Tue May 5 06:35:41 2015 UTC (2 years, 1 month ago) by caltinay
added missing **2 to MT forward model


Revision 5606 - Directory Listing
Modified Tue May 5 05:17:34 2015 UTC (2 years, 1 month ago) by jfenwick
Fix tests I broke


Revision 5605 - Directory Listing
Modified Tue May 5 02:13:51 2015 UTC (2 years, 1 month ago) by gross
fix for a more robust setting of an initial value

Revision 5604 - Directory Listing
Modified Tue May 5 01:45:11 2015 UTC (2 years, 1 month ago) by jfenwick
We can now build a directory of tests to validate an install.


Revision 5603 - Directory Listing
Modified Mon May 4 04:15:50 2015 UTC (2 years, 1 month ago) by jfenwick
Fix unintended revert in copyright

Revision 5602 - Directory Listing
Modified Mon May 4 04:14:21 2015 UTC (2 years, 1 month ago) by jfenwick
Fix email addr and remove stray subst file

Revision 5601 - Directory Listing
Modified Mon May 4 03:25:18 2015 UTC (2 years, 1 month ago) by jfenwick
Now with correct priorities for alternatives, paths to overlord binary, other fixes

Revision 5600 - Directory Listing
Modified Mon May 4 00:07:53 2015 UTC (2 years, 1 month ago) by jfenwick
Remove "Standalone" from run-escript.

It is not longer updated.


Revision 5599 - Directory Listing
Modified Mon May 4 00:05:46 2015 UTC (2 years, 1 month ago) by jfenwick
More general ESCRIPT_ROOT use


Revision 5598 - Directory Listing
Modified Sun May 3 23:06:36 2015 UTC (2 years, 1 month ago) by jfenwick
Changes which got sent to the wrong branch


Revision 5594 - Directory Listing
Modified Wed Apr 29 02:45:11 2015 UTC (2 years, 1 month ago) by jfenwick
Further tweaks

Revision 5593 - Directory Listing
Modified Fri Apr 24 01:36:26 2015 UTC (2 years, 2 months ago) by jfenwick
Fixing institution name to comply with policy

Revision 5592 - Directory Listing
Modified Fri Apr 24 01:09:11 2015 UTC (2 years, 2 months ago) by jfenwick
Spelling error

Revision 5591 - Directory Listing
Modified Fri Apr 24 01:02:33 2015 UTC (2 years, 2 months ago) by jfenwick
Fixing bad path in help message.

Revision 5590 - Directory Listing
Modified Wed Apr 22 05:54:02 2015 UTC (2 years, 2 months ago) by jfenwick
Recording current debianisation efforts

Revision 5589 - Directory Listing
Modified Wed Apr 22 03:13:44 2015 UTC (2 years, 2 months ago) by jfenwick
Changes brought across from the debian preparation branch.



Revision 5588 - Directory Listing
Modified Tue Apr 21 05:07:16 2015 UTC (2 years, 2 months ago) by caltinay
Update to copyright headers in cusp library.


Revision 5587 - Directory Listing
Modified Mon Apr 20 00:40:57 2015 UTC (2 years, 2 months ago) by caltinay
Fixed a typo in error case.


Revision 5586 - Directory Listing
Modified Tue Apr 14 03:27:59 2015 UTC (2 years, 2 months ago) by sshaw
making speckley gradients faster

Revision 5585 - Directory Listing
Modified Fri Apr 10 06:00:39 2015 UTC (2 years, 2 months ago) by sshaw
MPI optimisations for speckley Brick corners and edges


Revision 5584 - Directory Listing
Modified Fri Apr 10 04:31:52 2015 UTC (2 years, 2 months ago) by sshaw
improved speckley Rectangle MPI use

Revision 5583 - Directory Listing
Modified Fri Apr 10 04:28:07 2015 UTC (2 years, 2 months ago) by sshaw
better MPI utilisation when sharing speckley Brick's faces


Revision 5582 - Directory Listing
Modified Fri Apr 10 00:58:52 2015 UTC (2 years, 2 months ago) by sshaw
Fixing dirac point hangs in ripley when using lazy


Revision 5581 - Directory Listing
Modified Tue Apr 7 06:25:20 2015 UTC (2 years, 2 months ago) by jduplessis
fixed missing self.__w for when w is a list rather than a float


Revision 5580 - Directory Listing
Modified Tue Apr 7 04:25:01 2015 UTC (2 years, 2 months ago) by caltinay
do not run MT tests without direct solver.


Revision 5579 - Directory Listing
Modified Tue Apr 7 01:19:53 2015 UTC (2 years, 2 months ago) by sshaw
fixing lazy breakages with speckley waves

Revision 5576 - Directory Listing
Modified Wed Apr 1 07:38:51 2015 UTC (2 years, 2 months ago) by jfenwick
Fixed missing optionfile message

Revision 5575 - Directory Listing
Modified Wed Apr 1 03:17:22 2015 UTC (2 years, 2 months ago) by sshaw
sphinx now builds python doco including module-level docstrings and class __init__ docstrings, also cleared up some doco errors and added multires documentation

Revision 5574 - Directory Listing
Modified Mon Mar 30 03:14:06 2015 UTC (2 years, 2 months ago) by sshaw
adding speckley wave assemblers and associated tests


Revision 5573 - Directory Listing
Modified Mon Mar 30 03:13:41 2015 UTC (2 years, 2 months ago) by sshaw
more robust ripley wave assemblers and new wave assembler tests


Revision 5572 - Directory Listing
Modified Mon Mar 30 03:13:13 2015 UTC (2 years, 2 months ago) by sshaw
altering NullDomain's reported function space type code to avoid collisions with real domains


Revision 5571 - Directory Listing
Modified Mon Mar 30 01:04:27 2015 UTC (2 years, 2 months ago) by sshaw
adding a future import for printing to stop pycad designs printing tuples in py2


Revision 5568 - Directory Listing
Modified Fri Mar 27 01:34:10 2015 UTC (2 years, 3 months ago) by sshaw
more informative exceptions from ripley's WaveAssemblers


Revision 5567 - Directory Listing
Modified Fri Mar 27 00:50:15 2015 UTC (2 years, 3 months ago) by sshaw
HTIWave and VTIWave models: disabling default absorption zone, adding option to disable fast assemblers, adding interface for setting PDE's q value for custom boundary conditions

Revision 5565 - Directory Listing
Modified Thu Mar 26 21:52:47 2015 UTC (2 years, 3 months ago) by jfenwick
That python define problem

Revision 5564 - Directory Listing
Modified Thu Mar 26 07:10:44 2015 UTC (2 years, 3 months ago) by jduplessis
changed eletrode dict to electrodelst


Revision 5563 - Directory Listing
Modified Thu Mar 26 07:03:32 2015 UTC (2 years, 3 months ago) by jfenwick
Fixed indenting and accounted for py3 RuntimeException not having .message


Revision 5562 - Directory Listing
Modified Thu Mar 26 01:36:21 2015 UTC (2 years, 3 months ago) by jfenwick
More split world functions

Revision 5561 - Directory Listing
Modified Thu Mar 26 01:33:52 2015 UTC (2 years, 3 months ago) by jfenwick
Improving error message on interpolation failure.

Revision 5560 - Directory Listing
Modified Wed Mar 25 23:29:59 2015 UTC (2 years, 3 months ago) by caltinay
make slurm cpu binding quiet on savanna.


Revision 5559 - Directory Listing
Modified Wed Mar 25 05:32:01 2015 UTC (2 years, 3 months ago) by caltinay
changed axis of subdivision to avoid element stretching effects.


Revision 5558 - Directory Listing
Modified Wed Mar 25 02:13:05 2015 UTC (2 years, 3 months ago) by caltinay
Updated MT TM gradient which fixes test.
Also fixed some doc strings and replaced some asserts for better test
output.


Revision 5557 - Directory Listing
Modified Wed Mar 25 01:34:51 2015 UTC (2 years, 3 months ago) by caltinay
do not expose 'duv'.


Revision 5556 - Directory Listing
Modified Wed Mar 25 00:11:28 2015 UTC (2 years, 3 months ago) by gross
test added to fail TM forward

Revision 5555 - Directory Listing
Modified Tue Mar 24 06:31:43 2015 UTC (2 years, 3 months ago) by caltinay
Correction to TM mode gradient


Revision 5554 - Directory Listing
Modified Mon Mar 23 06:54:53 2015 UTC (2 years, 3 months ago) by gross
fixes and test for TM mode 

Revision 5553 - Directory Listing
Modified Mon Mar 23 05:42:53 2015 UTC (2 years, 3 months ago) by gross
fixes to MT-TE forward.

Revision 5550 - Directory Listing
Modified Fri Mar 20 01:03:01 2015 UTC (2 years, 3 months ago) by caltinay
some corrections to TM


Revision 5549 - Directory Listing
Modified Thu Mar 19 07:42:14 2015 UTC (2 years, 3 months ago) by caltinay
2D MT TM mode. Incomplete.


Revision 5548 - Directory Listing
Modified Thu Mar 19 06:30:13 2015 UTC (2 years, 3 months ago) by caltinay
Split forward models into separate files as it's getting very crowded now.


Revision 5547 - Directory Listing
Modified Thu Mar 19 01:20:20 2015 UTC (2 years, 3 months ago) by jfenwick
Modify centos install instructions to always add epel.
Have the correct macro expansion for \downunder


Revision 5546 - Directory Listing
Modified Thu Mar 19 01:18:23 2015 UTC (2 years, 3 months ago) by gross
fixes on MT forward and testing

Revision 5545 - Directory Listing
Modified Wed Mar 18 06:18:19 2015 UTC (2 years, 3 months ago) by caltinay
MT TE: merge data points and weights into a Data object each to save time.
Also some cleanup.


Revision 5544 - Directory Listing
Modified Wed Mar 18 05:30:09 2015 UTC (2 years, 3 months ago) by sshaw
stripping out some unchanged and inheritable methods from multirectangle, converting some last calculations to their relevant method

Revision 5543 - Directory Listing
Modified Wed Mar 18 03:23:05 2015 UTC (2 years, 3 months ago) by gross
grad fixed

Revision 5542 - Directory Listing
Modified Wed Mar 18 01:55:21 2015 UTC (2 years, 3 months ago) by gross
some fixws to ME

Revision 5541 - Directory Listing
Modified Wed Mar 18 00:05:15 2015 UTC (2 years, 3 months ago) by gross
some modifications to the boundary condition

Revision 5540 - Directory Listing
Modified Tue Mar 17 06:55:35 2015 UTC (2 years, 3 months ago) by sshaw
multi-resolution domains now support multi-process if the multi-dimension doesn't exceed 2 (MultiRectangle now supports MPI)

Revision 5539 - Directory Listing
Modified Tue Mar 17 05:56:07 2015 UTC (2 years, 3 months ago) by jfenwick
Made the docstrings for finley and dudley wrappers echo the docstrings from the c++drivers. Removed some old commented out boost.

Revision 5538 - Directory Listing
Modified Tue Mar 17 00:24:11 2015 UTC (2 years, 3 months ago) by caltinay
updated MT TE forward model. This might break a test depending on tolerances...


Revision 5537 - Directory Listing
Modified Fri Mar 13 00:12:23 2015 UTC (2 years, 3 months ago) by jfenwick
removing using statement

Revision 5536 - Directory Listing
Modified Fri Mar 13 00:11:40 2015 UTC (2 years, 3 months ago) by jfenwick
IS_NAN removed

Revision 5535 - Directory Listing
Modified Thu Mar 12 23:05:26 2015 UTC (2 years, 3 months ago) by jfenwick
Switch to boost::math::isnan

Revision 5534 - Directory Listing
Modified Thu Mar 12 06:01:50 2015 UTC (2 years, 3 months ago) by caltinay
A bit of no-op cleanup in forwardmodels before adding things.


Revision 5533 - Directory Listing
Modified Thu Mar 12 03:13:35 2015 UTC (2 years, 3 months ago) by sshaw
fixing ripley and multires ripley dirac tests

Revision 5532 - Directory Listing
Modified Thu Mar 12 02:59:34 2015 UTC (2 years, 3 months ago) by caltinay
Moved element ownership knowledge from weipa to ripley and made a few
corrections.
Multidomains not checked.


Revision 5531 - Directory Listing
Modified Wed Mar 11 23:59:10 2015 UTC (2 years, 3 months ago) by sshaw
returning non-multires ripley dirac tests to the working version

Revision 5529 - Directory Listing
Modified Wed Mar 11 04:03:12 2015 UTC (2 years, 3 months ago) by sshaw
finishing std namespace changes to speckley and ripley so they compile again

Revision 5528 - Directory Listing
Modified Wed Mar 11 03:48:47 2015 UTC (2 years, 3 months ago) by sshaw
adding single-process multi-resolution ripley domains

Revision 5527 - Directory Listing
Modified Wed Mar 11 03:48:13 2015 UTC (2 years, 3 months ago) by sshaw
test dependencies now use desired build path as check


Revision 5526 - Directory Listing
Modified Wed Mar 11 03:20:28 2015 UTC (2 years, 3 months ago) by sshaw
returning import exceptions to normal behaviour for testruns

Revision 5525 - Directory Listing
Modified Wed Mar 11 01:17:16 2015 UTC (2 years, 3 months ago) by jfenwick
Getting isnan from boost::math which should help address issue 283
Removing top level using of std



Revision 5524 - Directory Listing
Modified Wed Mar 11 01:05:39 2015 UTC (2 years, 3 months ago) by sshaw
and stifling the right output


Revision 5523 - Directory Listing
Modified Wed Mar 11 01:04:43 2015 UTC (2 years, 3 months ago) by sshaw
adding ommitted and import cat from command


Revision 5522 - Directory Listing
Modified Tue Mar 10 23:26:03 2015 UTC (2 years, 3 months ago) by sshaw
adding error summary to tail of utest runs and keeping a non-zero exit status if any failures

Revision 5521 - Directory Listing
Modified Tue Mar 10 06:27:59 2015 UTC (2 years, 3 months ago) by sshaw
adding failure logs and continuing after failing when using utest.sh

Revision 5520 - Directory Listing
Modified Tue Mar 10 05:34:14 2015 UTC (2 years, 3 months ago) by caltinay
Fixing parmetis options. We've been passing an array that's too small
according to current parmetis doco.


Revision 5519 - Directory Listing
Modified Tue Mar 10 05:32:16 2015 UTC (2 years, 3 months ago) by jfenwick
Reverting commit to allow it to be fixed more generally



Revision 5518 - Directory Listing
Modified Tue Mar 10 04:47:02 2015 UTC (2 years, 3 months ago) by jfenwick
Hack to avoid non-deterministic map order

Revision 5517 - Directory Listing
Modified Mon Mar 9 00:55:49 2015 UTC (2 years, 3 months ago) by jfenwick
Using // for integer division, in accordance with the prophecy.


Revision 5516 - Directory Listing
Modified Sun Mar 8 23:56:39 2015 UTC (2 years, 3 months ago) by jfenwick
hopefully fix mac problem

Revision 5515 - Directory Listing
Modified Fri Mar 6 06:33:33 2015 UTC (2 years, 3 months ago) by caltinay
Memory access changes ripley Wave 2D+3D.


Revision 5514 - Directory Listing
Modified Fri Mar 6 05:38:48 2015 UTC (2 years, 3 months ago) by caltinay
Memory access changes ripley Lame 2D+3D.


Revision 5513 - Directory Listing
Modified Fri Mar 6 05:06:13 2015 UTC (2 years, 3 months ago) by caltinay
Memory access changes ripley default 3D.


Revision 5510 - Directory Listing
Modified Fri Mar 6 01:29:46 2015 UTC (2 years, 3 months ago) by caltinay
Memory access changes ripley default 2D.


Revision 5508 - Directory Listing
Modified Thu Mar 5 06:31:38 2015 UTC (2 years, 3 months ago) by caltinay
More hand-optimization of generated code to save unnecessary memory ops.


Revision 5507 - Directory Listing
Modified Thu Mar 5 06:26:14 2015 UTC (2 years, 3 months ago) by sshaw
adjusting cblib for examples to not use matplotlib's default of natgrid which is also by default not installed

Revision 5506 - Directory Listing
Modified Thu Mar 5 04:14:49 2015 UTC (2 years, 3 months ago) by caltinay
Avoid unnecessary allocs/frees in parallel region which caused hangs
using many threads and intel OMP on savanna (probably due to a bug in
the intel library or glibc).


Revision 5503 - Directory Listing
Modified Wed Mar 4 04:52:23 2015 UTC (2 years, 3 months ago) by jfenwick
Removing some traces of implied windows support

Revision 5502 - Directory Listing
Modified Mon Mar 2 01:09:24 2015 UTC (2 years, 3 months ago) by jfenwick
Removing Vince from active developer lists

Revision 5499 - Directory Listing
Modified Thu Feb 26 07:07:43 2015 UTC (2 years, 4 months ago) by jduplessis
fixing print function

Revision 5498 - Directory Listing
Modified Thu Feb 26 06:39:12 2015 UTC (2 years, 4 months ago) by sshaw
fixing broken header guard

Revision 5497 - Directory Listing
Modified Thu Feb 26 01:16:45 2015 UTC (2 years, 4 months ago) by jduplessis
sigmoid tuning

Revision 5496 - Directory Listing
Modified Thu Feb 26 00:36:29 2015 UTC (2 years, 4 months ago) by sshaw
fixing a missing build dependency of pythonMPI existing before individual tests are run

Revision 5495 - Directory Listing
Modified Wed Feb 25 05:32:12 2015 UTC (2 years, 4 months ago) by jduplessis
changed to sigmoid mapping

Revision 5494 - Directory Listing
Modified Tue Feb 24 23:18:59 2015 UTC (2 years, 4 months ago) by jduplessis
improved error checking in gmshreader suite


Revision 5493 - Directory Listing
Modified Tue Feb 24 22:37:24 2015 UTC (2 years, 4 months ago) by jfenwick
Added forgotten files

Revision 5492 - Directory Listing
Modified Tue Feb 24 09:33:32 2015 UTC (2 years, 4 months ago) by jfenwick
fixed linking problem

Revision 5491 - Directory Listing
Modified Tue Feb 24 06:49:15 2015 UTC (2 years, 4 months ago) by caltinay
- adding process ID to valgrind logs
- disabled generation of suppressions
- added commented options to use MPT


Revision 5490 - Directory Listing
Modified Tue Feb 24 05:54:13 2015 UTC (2 years, 4 months ago) by jfenwick
Renaming the reducer root include and adding missing files


Revision 5489 - Directory Listing
Modified Tue Feb 24 05:12:12 2015 UTC (2 years, 4 months ago) by jfenwick
splitting reducer files

Revision 5488 - Directory Listing
Modified Tue Feb 24 01:13:15 2015 UTC (2 years, 4 months ago) by sshaw
examples used in testing no longer follow the test rules

Revision 5487 - Directory Listing
Modified Mon Feb 23 06:49:16 2015 UTC (2 years, 4 months ago) by sshaw
adding pycad back into the python compile stage

Revision 5486 - Directory Listing
Modified Mon Feb 23 05:00:59 2015 UTC (2 years, 4 months ago) by sshaw
removed skip tracking for tools

Revision 5485 - Directory Listing
Modified Mon Feb 23 03:41:02 2015 UTC (2 years, 4 months ago) by sshaw
adding an omitted /

Revision 5484 - Directory Listing
Modified Mon Feb 23 01:06:38 2015 UTC (2 years, 4 months ago) by sshaw
adjusting utest to use the same testing framework as scons for skipped test logging

Revision 5483 - Directory Listing
Modified Thu Feb 19 04:28:56 2015 UTC (2 years, 4 months ago) by jfenwick
More python fixes

Revision 5482 - Directory Listing
Modified Wed Feb 18 05:41:09 2015 UTC (2 years, 4 months ago) by jfenwick
Fixing a missing const chain

Revision 5481 - Directory Listing
Modified Wed Feb 18 05:07:25 2015 UTC (2 years, 4 months ago) by sshaw
fixing a memory leak in the new MPI wrapper, along with some comment updating to satisfy doxygen a bit better

Revision 5480 - Directory Listing
Modified Wed Feb 18 04:35:50 2015 UTC (2 years, 4 months ago) by jfenwick
Stage 1 of removing escriptDataC



Revision 5479 - Directory Listing
Modified Wed Feb 18 04:09:13 2015 UTC (2 years, 4 months ago) by jduplessis
updated old script

Revision 5478 - Directory Listing
Modified Wed Feb 18 01:57:49 2015 UTC (2 years, 4 months ago) by sshaw
introducing shiny new reduced function spaces to speckley

Revision 5477 - Directory Listing
Modified Wed Feb 18 00:32:21 2015 UTC (2 years, 4 months ago) by sshaw
fixing an older example script


Revision 5476 - Directory Listing
Modified Wed Feb 18 00:02:32 2015 UTC (2 years, 4 months ago) by jfenwick
passing tests on badger

Revision 5475 - Directory Listing
Modified Tue Feb 17 06:08:16 2015 UTC (2 years, 4 months ago) by sshaw
fixed gmsh named tags, along with a little more cleanup

Revision 5474 - Directory Listing
Modified Tue Feb 17 04:08:35 2015 UTC (2 years, 4 months ago) by jfenwick
Fix for one of the splitworld test issues

Revision 5473 - Directory Listing
Modified Mon Feb 16 06:56:25 2015 UTC (2 years, 4 months ago) by sshaw
fixing NULL statuses in MPI calls on savanna

Revision 5472 - Directory Listing
Modified Mon Feb 16 05:44:59 2015 UTC (2 years, 4 months ago) by sshaw
more python define conflict fixes


Revision 5471 - Directory Listing
Modified Mon Feb 16 05:16:20 2015 UTC (2 years, 4 months ago) by sshaw
fixing invalid tag errors with MPI on savanna

Revision 5470 - Directory Listing
Modified Mon Feb 16 04:23:17 2015 UTC (2 years, 4 months ago) by jfenwick
Fix some more. Make savanna warnings into errors.

Revision 5469 - Directory Listing
Modified Mon Feb 16 04:03:24 2015 UTC (2 years, 4 months ago) by jfenwick
fixes I forgot to commit

Revision 5468 - Directory Listing
Modified Mon Feb 16 03:52:35 2015 UTC (2 years, 4 months ago) by sshaw
and that concludes our story of how the gmsh ruined christmas

Revision 5467 - Directory Listing
Modified Mon Feb 16 00:24:20 2015 UTC (2 years, 4 months ago) by jfenwick
Removing DBADPYTHONMACRO workarounds

Revision 5466 - Directory Listing
Modified Mon Feb 16 00:07:23 2015 UTC (2 years, 4 months ago) by sshaw
correcting readGmsh failures with older version meshes

Revision 5465 - Directory Listing
Modified Mon Feb 16 00:03:05 2015 UTC (2 years, 4 months ago) by jfenwick
We now have an arena where any headers which insist on being first
because they do bad things, can battle to the death.

esysutils/first.h

should only be included in .cpp files.
#define the macros for the features you need in that .cpp

For this to work, any such claims to primacy must be resolved in
first.h, so please don't try to hack pretenders to the throne into the
include hierachy.

Next, will be removing some older attempts at the same thing.




Revision 5464 - Directory Listing
Modified Sat Feb 14 00:25:03 2015 UTC (2 years, 4 months ago) by jfenwick
Fix for python compile warnings

Revision 5463 - Directory Listing
Modified Fri Feb 13 06:54:08 2015 UTC (2 years, 4 months ago) by sshaw
fixing uninitialised int that really was initialised before use

Revision 5462 - Directory Listing
Modified Fri Feb 13 06:30:33 2015 UTC (2 years, 4 months ago) by sshaw
a more improved readGmsh for less awkward MPI silences

Revision 5461 - Directory Listing
Modified Fri Feb 13 04:37:51 2015 UTC (2 years, 4 months ago) by jfenwick
Passes some tests. Still has bug

Revision 5460 - Directory Listing
Modified Fri Feb 13 04:29:26 2015 UTC (2 years, 4 months ago) by sshaw
removing permanently true comparison that blocks compilation with -Werror=type-limits

Revision 5459 - Directory Listing
Modified Wed Feb 11 04:31:31 2015 UTC (2 years, 4 months ago) by jduplessis
run dcforward: schlumberger tests uses analytic solver
dcresistivityforwardmodeling:added numeric solver for schlumberger 
domaingeneratordcresistivity:non layered meshses can set field size




Revision 5458 - Directory Listing
Modified Wed Feb 11 03:05:41 2015 UTC (2 years, 4 months ago) by jfenwick
Adding max and min as reduction operations

Revision 5457 - Directory Listing
Modified Tue Feb 10 04:51:15 2015 UTC (2 years, 4 months ago) by jfenwick
adjust globalvarinfo to account for automatic import assumptions

Revision 5456 - Directory Listing
Modified Tue Feb 10 01:41:59 2015 UTC (2 years, 4 months ago) by jfenwick
Tidier. Debugging HO!

Revision 5455 - Directory Listing
Modified Tue Feb 10 01:27:57 2015 UTC (2 years, 4 months ago) by jfenwick
more pruning

Revision 5454 - Directory Listing
Modified Tue Feb 10 00:49:28 2015 UTC (2 years, 4 months ago) by jfenwick
improvements and compilability

Revision 5453 - Directory Listing
Modified Mon Feb 9 23:46:17 2015 UTC (2 years, 4 months ago) by jfenwick
Passes simple test with auto imports, still in need of cleanup

Revision 5452 - Directory Listing
Modified Mon Feb 9 03:39:06 2015 UTC (2 years, 4 months ago) by sshaw
fixing wrong equality

Revision 5451 - Directory Listing
Modified Mon Feb 9 02:58:12 2015 UTC (2 years, 4 months ago) by jfenwick
updates

Revision 5450 - Directory Listing
Modified Mon Feb 9 01:39:26 2015 UTC (2 years, 4 months ago) by sshaw
Solving MPI gmsh invocation race conditions via network-IPC with the help of escript-overlord.
I, for one, welcome it.


Revision 5449 - Directory Listing
Modified Sun Feb 8 23:46:01 2015 UTC (2 years, 4 months ago) by jfenwick
Modified checkError function to play nicely with overlapping communicators.
Added a function to get a string from a python exception in boost.


Revision 5448 - Directory Listing
Modified Fri Feb 6 05:31:37 2015 UTC (2 years, 4 months ago) by jfenwick
Updating all the dates

Revision 5447 - Directory Listing
Modified Fri Feb 6 04:52:30 2015 UTC (2 years, 4 months ago) by jfenwick
Changes to subworlds

Revision 5446 - Directory Listing
Modified Thu Feb 5 04:34:12 2015 UTC (2 years, 4 months ago) by jduplessis
removed random file opens


Revision 5445 - Directory Listing
Modified Thu Feb 5 04:02:54 2015 UTC (2 years, 4 months ago) by jduplessis
0 rather than 1 equals error for gmshpy


Revision 5444 - Directory Listing
Modified Tue Feb 3 08:02:56 2015 UTC (2 years, 4 months ago) by jfenwick
Fixing intel warning

Revision 5443 - Directory Listing
Modified Tue Feb 3 07:11:01 2015 UTC (2 years, 4 months ago) by jfenwick
Adding local value import. Remote import still to do

Revision 5442 - Directory Listing
Modified Tue Feb 3 07:10:21 2015 UTC (2 years, 4 months ago) by jfenwick
Fix to utest construction

Revision 5441 - Directory Listing
Modified Tue Feb 3 06:38:11 2015 UTC (2 years, 4 months ago) by jduplessis
changed the refrence for domain generator every now based around 0
made delphiIn accesable


Revision 5440 - Directory Listing
Modified Mon Feb 2 01:07:51 2015 UTC (2 years, 4 months ago) by caltinay
fixed srun spec for savanna.


Revision 5439 - Directory Listing
Modified Thu Jan 29 05:28:34 2015 UTC (2 years, 4 months ago) by jduplessis
updates and fix for layered domain


Revision 5438 - Directory Listing
Modified Wed Jan 28 10:38:11 2015 UTC (2 years, 4 months ago) by caltinay
ice noomp options file.


Revision 5437 - Directory Listing
Modified Wed Jan 28 06:47:42 2015 UTC (2 years, 4 months ago) by jduplessis
updated dc res mapping


Revision 5436 - Directory Listing
Modified Tue Jan 27 05:16:42 2015 UTC (2 years, 4 months ago) by caltinay
export slurm env for tests. Added ice options file.


Revision 5435 - Directory Listing
Modified Tue Jan 27 00:15:26 2015 UTC (2 years, 4 months ago) by caltinay
option 'thrust_prefix' was never used - updated to cuda_prefix and added
detection code. Updated savanna options.


Revision 5434 - Directory Listing
Modified Fri Jan 23 04:29:09 2015 UTC (2 years, 5 months ago) by jfenwick
Trying to fix mac tests

Revision 5433 - Directory Listing
Modified Fri Jan 23 03:35:22 2015 UTC (2 years, 5 months ago) by caltinay
DUDLEY!!


Revision 5432 - Directory Listing
Modified Fri Jan 23 02:40:32 2015 UTC (2 years, 5 months ago) by caltinay
dudley needs a serious review!


Revision 5431 - Directory Listing
Modified Fri Jan 23 02:32:53 2015 UTC (2 years, 5 months ago) by caltinay
updated savanna options file.


Revision 5430 - Directory Listing
Modified Fri Jan 23 01:11:09 2015 UTC (2 years, 5 months ago) by gross
fixes in teh DCREs mapping

Revision 5429 - Directory Listing
Modified Fri Jan 23 00:19:43 2015 UTC (2 years, 5 months ago) by caltinay
Looks like debian has a very old version of parmetis so deal with that.


Revision 5428 - Directory Listing
Modified Thu Jan 22 23:16:00 2015 UTC (2 years, 5 months ago) by caltinay
Fixed types for parmetis.


Revision 5427 - Directory Listing
Modified Thu Jan 22 05:04:49 2015 UTC (2 years, 5 months ago) by jduplessis
can be a list of tuples or list of lists


Revision 5426 - Directory Listing
Modified Thu Jan 22 04:35:31 2015 UTC (2 years, 5 months ago) by jduplessis
source sample tags


Revision 5425 - Directory Listing
Modified Wed Jan 21 06:17:21 2015 UTC (2 years, 5 months ago) by jfenwick
Fix build error and add comment

Revision 5424 - Directory Listing
Modified Wed Jan 21 04:29:51 2015 UTC (2 years, 5 months ago) by jfenwick
Tweaks to parallel

Revision 5423 - Directory Listing
Modified Tue Jan 20 06:59:42 2015 UTC (2 years, 5 months ago) by caltinay
current magnus options file.


Revision 5422 - Directory Listing
Modified Mon Jan 19 04:36:08 2015 UTC (2 years, 5 months ago) by jduplessis
error check for 3d support

Revision 5421 - Directory Listing
Modified Mon Jan 19 00:40:53 2015 UTC (2 years, 5 months ago) by jduplessis
added resuse so use can specify wether or not to use the current meshfile or to over write it
the surface tagging was providing some issues commented out for now


Revision 5420 - Directory Listing
Modified Thu Jan 15 04:03:40 2015 UTC (2 years, 5 months ago) by jfenwick
Do not ignore gmshGeo2Msh return value

Revision 5419 - Directory Listing
Modified Wed Jan 14 09:14:05 2015 UTC (2 years, 5 months ago) by jfenwick
Make tests write to the correct directories

Revision 5418 - Directory Listing
Modified Wed Jan 14 05:34:55 2015 UTC (2 years, 5 months ago) by jfenwick
Fixing some unit test failures on osx

Revision 5417 - Directory Listing
Modified Wed Jan 14 01:54:19 2015 UTC (2 years, 5 months ago) by jfenwick
Fixing more tests to check for the optional natgrid package

Revision 5416 - Directory Listing
Modified Wed Dec 24 00:23:14 2014 UTC (2 years, 6 months ago) by jfenwick
Try a version number debtools accept. Updated subst files. Still missing trusty

Revision 5414 - Directory Listing
Modified Tue Dec 23 07:53:35 2014 UTC (2 years, 6 months ago) by jfenwick
Bump version to allow experiments to not clash

Revision 5413 - Directory Listing
Modified Tue Dec 23 07:17:43 2014 UTC (2 years, 6 months ago) by jfenwick
First steps towards python3 packages.
Problems still to be resolved:
  doesn't remove cleanly (esys/__init__.pyc is created)

Need to test interactions between the new packages and the old package 


Revision 5412 - Directory Listing
Modified Mon Dec 22 06:40:31 2014 UTC (2 years, 6 months ago) by jfenwick
Adding options files for jessie


Revision 5411 - Directory Listing
Modified Mon Dec 22 01:39:10 2014 UTC (2 years, 6 months ago) by jfenwick
Fixed py3 matplotlib detection. Converted a division for py3

Revision 5410 - Directory Listing
Modified Sun Dec 21 23:24:54 2014 UTC (2 years, 6 months ago) by jfenwick
Switching versions back to development and using a single reference file for version and date.

Revision 5408 - Directory Listing
Modified Thu Dec 18 03:54:12 2014 UTC (2 years, 6 months ago) by jfenwick
fixing stuff

Revision 5407 - Directory Listing
Modified Thu Dec 18 02:48:24 2014 UTC (2 years, 6 months ago) by jfenwick
release changes

Revision 5405 - Directory Listing
Modified Thu Dec 18 00:41:39 2014 UTC (2 years, 6 months ago) by caltinay
next try.


Revision 5404 - Directory Listing
Modified Thu Dec 18 00:10:22 2014 UTC (2 years, 6 months ago) by caltinay
Disabled OMP binding by default because it interfers with mpi binding
- threads were all running on one core on guineapig.


Revision 5403 - Directory Listing
Modified Wed Dec 17 08:24:44 2014 UTC (2 years, 6 months ago) by caltinay
no need to bind procs on guineapig


Revision 5402 - Directory Listing
Modified Wed Dec 17 05:44:00 2014 UTC (2 years, 6 months ago) by jfenwick
True location of runMPIProgram

Revision 5401 - Directory Listing
Modified Wed Dec 17 04:09:16 2014 UTC (2 years, 6 months ago) by jduplessis
mpirank added

Revision 5400 - Directory Listing
Modified Wed Dec 17 02:59:38 2014 UTC (2 years, 6 months ago) by jduplessis
added unlink

Revision 5399 - Directory Listing
Modified Wed Dec 17 02:53:58 2014 UTC (2 years, 6 months ago) by caltinay
commented obsolete test.


Revision 5398 - Directory Listing
Modified Wed Dec 17 02:51:41 2014 UTC (2 years, 6 months ago) by caltinay
#$@!#@$ typo


Revision 5397 - Directory Listing
Modified Wed Dec 17 01:35:43 2014 UTC (2 years, 6 months ago) by caltinay
new, single interface to gmsh in escriptcore used by pycad and downunder.


Revision 5394 - Directory Listing
Modified Wed Dec 17 00:11:29 2014 UTC (2 years, 6 months ago) by caltinay
made pycad tests accept some whitespace differences


Revision 5392 - Directory Listing
Modified Tue Dec 16 07:01:26 2014 UTC (2 years, 6 months ago) by caltinay
formatting fixes in gmsh design.


Revision 5391 - Directory Listing
Modified Tue Dec 16 06:59:58 2014 UTC (2 years, 6 months ago) by caltinay
report gmshpy availability


Revision 5384 - Directory Listing
Modified Tue Dec 16 01:33:35 2014 UTC (2 years, 6 months ago) by caltinay
added commented setOrderN() call to gmshpy.


Revision 5383 - Directory Listing
Modified Tue Dec 16 00:44:47 2014 UTC (2 years, 6 months ago) by sshaw
replacing dcresistivity gmsh runner with pycads

Revision 5382 - Directory Listing
Modified Tue Dec 16 00:42:01 2014 UTC (2 years, 6 months ago) by sshaw
fix for exit status being destroyed in serial gmsh execution


Revision 5381 - Directory Listing
Modified Tue Dec 16 00:40:47 2014 UTC (2 years, 6 months ago) by sshaw
simple fix for dudley's finley dependency


Revision 5378 - Directory Listing
Modified Mon Dec 15 23:48:54 2014 UTC (2 years, 6 months ago) by jfenwick
Adding boostrandom to requirements

Revision 5377 - Directory Listing
Modified Mon Dec 15 23:35:27 2014 UTC (2 years, 6 months ago) by jfenwick
Updating debian changelog

Revision 5376 - Directory Listing
Modified Mon Dec 15 23:20:01 2014 UTC (2 years, 6 months ago) by jfenwick
Broadening tolerance for utopic version

Revision 5375 - Directory Listing
Modified Mon Dec 15 23:16:39 2014 UTC (2 years, 6 months ago) by sshaw
removing mixed tabs and spaces for python3


Revision 5374 - Directory Listing
Modified Mon Dec 15 06:10:16 2014 UTC (2 years, 6 months ago) by caltinay
updated raijin options file.


Revision 5373 - Directory Listing
Modified Mon Dec 15 06:09:58 2014 UTC (2 years, 6 months ago) by caltinay
Fixing OMP build with icc13 on raijin.


Revision 5372 - Directory Listing
Modified Mon Dec 15 05:48:55 2014 UTC (2 years, 6 months ago) by sshaw
removing parallel section on map inserts

Revision 5371 - Directory Listing
Modified Mon Dec 15 05:46:14 2014 UTC (2 years, 6 months ago) by jfenwick
Adding subst for utopic

Revision 5370 - Directory Listing
Modified Mon Dec 15 05:25:42 2014 UTC (2 years, 6 months ago) by jfenwick
Fix debian rules to account for different way to generate run-escript

Revision 5369 - Directory Listing
Modified Mon Dec 15 04:23:38 2014 UTC (2 years, 6 months ago) by jfenwick
Fixing getsubst for long past directory move.
Also removing obsolete releases.


Revision 5368 - Directory Listing
Modified Mon Dec 15 04:04:51 2014 UTC (2 years, 6 months ago) by caltinay
Added commented changes so they don't get lost.


Revision 5367 - Directory Listing
Modified Mon Dec 15 04:02:21 2014 UTC (2 years, 6 months ago) by caltinay
Undoing parts of r5363 until tests reflect the change.


Revision 5366 - Directory Listing
Modified Mon Dec 15 03:51:02 2014 UTC (2 years, 6 months ago) by jduplessis
fixed naming conventions + comments

Revision 5365 - Directory Listing
Modified Mon Dec 15 01:46:14 2014 UTC (2 years, 6 months ago) by caltinay
mara options.


Revision 5364 - Directory Listing
Modified Mon Dec 15 01:45:43 2014 UTC (2 years, 6 months ago) by caltinay
Fixed Voxet origin which refers to cell centre in Voxet lingo.


Revision 5363 - Directory Listing
Modified Mon Dec 15 01:45:09 2014 UTC (2 years, 6 months ago) by caltinay
Added 'pressure at 0' option to Isostatic Pressure calculation.


Revision 5362 - Directory Listing
Modified Mon Dec 15 01:36:27 2014 UTC (2 years, 6 months ago) by sshaw
making DipoleDipole test more tolerant to cope with gmsh's filthy non-deterministic seeding by output filename


Revision 5361 - Directory Listing
Modified Mon Dec 15 00:53:41 2014 UTC (2 years, 6 months ago) by jfenwick
Partial better fix for natgrid problem

Revision 5360 - Directory Listing
Modified Sun Dec 14 23:57:33 2014 UTC (2 years, 6 months ago) by sshaw
fixing sillyness from my previous commit

Revision 5359 - Directory Listing
Modified Sun Dec 14 23:17:37 2014 UTC (2 years, 6 months ago) by sshaw
making dcforward tests more verbose when failing

Revision 5358 - Directory Listing
Modified Fri Dec 12 06:25:52 2014 UTC (2 years, 6 months ago) by jduplessis
removed debug

Revision 5357 - Directory Listing
Modified Fri Dec 12 06:09:59 2014 UTC (2 years, 6 months ago) by jduplessis
faster test

Revision 5356 - Directory Listing
Modified Fri Dec 12 04:04:33 2014 UTC (2 years, 6 months ago) by caltinay
guineapig intel options files.


Revision 5355 - Directory Listing
Modified Fri Dec 12 03:57:25 2014 UTC (2 years, 6 months ago) by jfenwick
New options file for openSuse. Add natgridchecking for openSuse

Revision 5354 - Directory Listing
Modified Fri Dec 12 03:36:34 2014 UTC (2 years, 6 months ago) by jfenwick
Install guide fixes

Revision 5353 - Directory Listing
Modified Fri Dec 12 03:22:41 2014 UTC (2 years, 6 months ago) by jduplessis
adding dc_forward example

Revision 5352 - Directory Listing
Modified Fri Dec 12 03:13:14 2014 UTC (2 years, 6 months ago) by jfenwick
Adding new fedora. removing old ones

Revision 5351 - Directory Listing
Modified Fri Dec 12 03:06:55 2014 UTC (2 years, 6 months ago) by jfenwick
removing some old templates. updating the centos one

Revision 5350 - Directory Listing
Modified Fri Dec 12 03:00:37 2014 UTC (2 years, 6 months ago) by sshaw
updating reference meshes to take into account first-tag method


Revision 5349 - Directory Listing
Modified Fri Dec 12 01:32:05 2014 UTC (2 years, 6 months ago) by sshaw
more informative skip messages, first tagged element applies for readgmsh instead of last

Revision 5348 - Directory Listing
Modified Fri Dec 12 01:04:31 2014 UTC (2 years, 6 months ago) by sshaw
replacing mixed tabs with spaces


Revision 5347 - Directory Listing
Modified Fri Dec 12 01:01:27 2014 UTC (2 years, 6 months ago) by jfenwick
Check if pyproj is available before running example

Revision 5346 - Directory Listing
Modified Thu Dec 11 23:55:13 2014 UTC (2 years, 6 months ago) by sshaw
fixing more cases of indexing empty vectors

Revision 5345 - Directory Listing
Modified Thu Dec 11 23:25:08 2014 UTC (2 years, 6 months ago) by sshaw
updating reference meshes

Revision 5344 - Directory Listing
Modified Thu Dec 11 23:01:16 2014 UTC (2 years, 6 months ago) by sshaw
fixing non-mpi builds

Revision 5343 - Directory Listing
Modified Thu Dec 11 08:21:01 2014 UTC (2 years, 6 months ago) by sshaw
some fixes for the new node tagging from gmshreader


Revision 5342 - Directory Listing
Modified Thu Dec 11 03:56:23 2014 UTC (2 years, 6 months ago) by sshaw
fixes to readGmsh off-by-one


Revision 5341 - Directory Listing
Modified Thu Dec 11 03:20:36 2014 UTC (2 years, 6 months ago) by sshaw
fixing some indexing into empty vectors, related to #291

Revision 5340 - Directory Listing
Modified Thu Dec 11 00:24:58 2014 UTC (2 years, 6 months ago) by jduplessis
updated tags in fly files


Revision 5339 - Directory Listing
Modified Thu Dec 11 00:08:58 2014 UTC (2 years, 6 months ago) by sshaw
added an exception for trying to set an escript param that doesn't exist

Revision 5338 - Directory Listing
Modified Wed Dec 10 07:03:24 2014 UTC (2 years, 6 months ago) by sshaw
fix for gmsh permissive use of scoped i

Revision 5337 - Directory Listing
Modified Wed Dec 10 05:58:33 2014 UTC (2 years, 6 months ago) by jduplessis
added a nodeid map so that node id's can be used to index the node arrays such as the tag array


Revision 5336 - Directory Listing
Modified Wed Dec 10 05:23:51 2014 UTC (2 years, 6 months ago) by jfenwick
Making params more visible

Revision 5335 - Directory Listing
Modified Wed Dec 10 05:22:27 2014 UTC (2 years, 6 months ago) by jfenwick
install guide culling

Revision 5334 - Directory Listing
Modified Wed Dec 10 04:10:41 2014 UTC (2 years, 6 months ago) by sshaw
more finley test cleanup


Revision 5333 - Directory Listing
Modified Wed Dec 10 02:53:03 2014 UTC (2 years, 6 months ago) by sshaw
some more readGmsh cleaning


Revision 5332 - Directory Listing
Modified Wed Dec 10 01:49:15 2014 UTC (2 years, 6 months ago) by sshaw
readability cleanup on readGmsh


Revision 5331 - Directory Listing
Modified Wed Dec 10 01:13:34 2014 UTC (2 years, 6 months ago) by jfenwick
Disabling gmshpy until after the release

Revision 5330 - Directory Listing
Modified Wed Dec 10 00:20:05 2014 UTC (2 years, 6 months ago) by jfenwick
Use gmshpy for preference


Revision 5329 - Directory Listing
Modified Tue Dec 9 23:44:48 2014 UTC (2 years, 6 months ago) by jfenwick
Not sure how I missed this one

Revision 5328 - Directory Listing
Modified Tue Dec 9 06:34:08 2014 UTC (2 years, 6 months ago) by sshaw
removing unused test file

Revision 5327 - Directory Listing
Modified Tue Dec 9 06:32:11 2014 UTC (2 years, 6 months ago) by jduplessis
fixed continuousFunction mesh tagging


Revision 5326 - Directory Listing
Modified Tue Dec 9 05:04:34 2014 UTC (2 years, 6 months ago) by sshaw
reinstating old dudley tests that weren't properly being tested due to constructor problems

Revision 5325 - Directory Listing
Modified Tue Dec 9 04:53:14 2014 UTC (2 years, 6 months ago) by sshaw
9000 less tests are skipped, partly removing skips, partly removing duplicate test file

Revision 5324 - Directory Listing
Modified Tue Dec 9 04:43:02 2014 UTC (2 years, 6 months ago) by sshaw
fixing python 3 dealing badly with str(generators)

Revision 5323 - Directory Listing
Modified Tue Dec 9 04:01:35 2014 UTC (2 years, 6 months ago) by sshaw
fixing another sillyness with import errors


Revision 5322 - Directory Listing
Modified Tue Dec 9 03:53:35 2014 UTC (2 years, 6 months ago) by jfenwick
Added NETCDF_BUILD to escript params. Tests now check this before testing netcdf dependent stuff

Revision 5321 - Directory Listing
Modified Tue Dec 9 03:27:32 2014 UTC (2 years, 6 months ago) by sshaw
adding omitted 3D diracdelta interpolation tests

Revision 5320 - Directory Listing
Modified Tue Dec 9 01:39:46 2014 UTC (2 years, 6 months ago) by sshaw
new EscriptParam GMSH_SUPPORT and GMSH_MPI for use in python-land, included associated exceptions in DCRes gmsh use and assocaiated skips in relevant tests

Revision 5319 - Directory Listing
Modified Tue Dec 9 00:58:32 2014 UTC (2 years, 6 months ago) by jduplessis
small changes to indentation etc


Revision 5318 - Directory Listing
Modified Tue Dec 9 00:37:06 2014 UTC (2 years, 6 months ago) by sshaw
change of speckleys test to match speckleys name

Revision 5317 - Directory Listing
Modified Tue Dec 9 00:36:08 2014 UTC (2 years, 6 months ago) by sshaw
speckley and ripley can now interpolate from DiracDeltaFunctions to ContinuousFunction

Revision 5316 - Directory Listing
Modified Mon Dec 8 06:30:49 2014 UTC (2 years, 6 months ago) by sshaw
better cleanup of dcres tempfiles

Revision 5315 - Directory Listing
Modified Mon Dec 8 05:08:54 2014 UTC (2 years, 6 months ago) by sshaw
resistivity style fixes for consistency, adding skips for non-finley builds

Revision 5314 - Directory Listing
Modified Mon Dec 8 04:28:28 2014 UTC (2 years, 6 months ago) by jfenwick
Trying again to fix this without messing up mpi

Revision 5313 - Directory Listing
Modified Mon Dec 8 04:03:52 2014 UTC (2 years, 6 months ago) by jfenwick
Hide unused mpit thing from non-mpi

Revision 5312 - Directory Listing
Modified Mon Dec 8 00:44:04 2014 UTC (2 years, 6 months ago) by jfenwick
Added 10.10 homebrew template

Revision 5311 - Directory Listing
Modified Mon Dec 8 00:35:45 2014 UTC (2 years, 6 months ago) by jfenwick
Adding 10.10 mp template

Revision 5310 - Directory Listing
Modified Mon Dec 8 00:10:01 2014 UTC (2 years, 6 months ago) by caltinay
slurm runner for savanna.


Revision 5309 - Directory Listing
Modified Mon Dec 8 00:08:32 2014 UTC (2 years, 6 months ago) by sshaw
catching other case of domainGenerator tests failing

Revision 5308 - Directory Listing
Modified Fri Dec 5 04:58:53 2014 UTC (2 years, 6 months ago) by sshaw
more silly importerror fixes in tests

Revision 5307 - Directory Listing
Modified Fri Dec 5 04:30:05 2014 UTC (2 years, 6 months ago) by sshaw
fixing inverted boolean for ripley presence

Revision 5306 - Directory Listing
Modified Fri Dec 5 01:49:46 2014 UTC (2 years, 6 months ago) by jduplessis
added skip if gmsh missing

Revision 5305 - Directory Listing
Modified Thu Dec 4 06:48:39 2014 UTC (2 years, 6 months ago) by caltinay
This looks like unintended by the last commit.


Revision 5304 - Directory Listing
Modified Thu Dec 4 06:29:13 2014 UTC (2 years, 6 months ago) by caltinay
make MPI build work again.


Revision 5303 - Directory Listing
Modified Thu Dec 4 06:17:11 2014 UTC (2 years, 6 months ago) by jfenwick
Changes to keep clang happy

Revision 5302 - Directory Listing
Modified Thu Dec 4 06:16:28 2014 UTC (2 years, 6 months ago) by caltinay
some more.


Revision 5301 - Directory Listing
Modified Thu Dec 4 05:58:49 2014 UTC (2 years, 6 months ago) by caltinay
A lil' bit more meat in ripley.


Revision 5300 - Directory Listing
Modified Thu Dec 4 05:44:25 2014 UTC (2 years, 6 months ago) by jduplessis
added missing init

Revision 5299 - Directory Listing
Modified Thu Dec 4 04:07:23 2014 UTC (2 years, 6 months ago) by jduplessis
all classes tested, documentation and small fixes to follow

Revision 5298 - Directory Listing
Modified Thu Dec 4 02:54:50 2014 UTC (2 years, 6 months ago) by caltinay
Doco updates.


Revision 5297 - Directory Listing
Modified Thu Dec 4 01:58:53 2014 UTC (2 years, 6 months ago) by caltinay
More user doco updates.


Revision 5296 - Directory Listing
Modified Wed Dec 3 07:22:17 2014 UTC (2 years, 6 months ago) by caltinay
More updates to user doc.


Revision 5295 - Directory Listing
Modified Wed Dec 3 05:35:28 2014 UTC (2 years, 6 months ago) by caltinay
fixed undef error and some content.


Revision 5294 - Directory Listing
Modified Wed Dec 3 05:30:18 2014 UTC (2 years, 6 months ago) by sshaw
working around oddness when catching ImportErrors after catching a propagated ImportError, cleaning up last of finley examples without domain checks

Revision 5293 - Directory Listing
Modified Wed Dec 3 04:28:17 2014 UTC (2 years, 6 months ago) by caltinay
added missing copyright headers in user guide plus fixed minor typo.


Revision 5292 - Directory Listing
Modified Wed Dec 3 04:08:14 2014 UTC (2 years, 6 months ago) by sshaw
more corrections to tests

Revision 5291 - Directory Listing
Modified Wed Dec 3 03:55:26 2014 UTC (2 years, 6 months ago) by jfenwick
version number hack to allow older versions to run

Revision 5290 - Directory Listing
Modified Wed Dec 3 01:15:33 2014 UTC (2 years, 6 months ago) by sshaw
fixing some broken imports from earlier commit

Revision 5289 - Directory Listing
Modified Tue Dec 2 23:43:22 2014 UTC (2 years, 6 months ago) by sshaw
updating hamster options


Revision 5288 - Directory Listing
Modified Tue Dec 2 23:18:40 2014 UTC (2 years, 6 months ago) by sshaw
fixing tests for cases where required domains not built

Revision 5287 - Directory Listing
Modified Tue Dec 2 05:36:36 2014 UTC (2 years, 6 months ago) by jfenwick
Fix for bug#284. Added dummify=False to lambdify calls.

Revision 5286 - Directory Listing
Modified Tue Dec 2 03:45:09 2014 UTC (2 years, 6 months ago) by caltinay
removed obsolete (?) tests...


Revision 5285 - Directory Listing
Modified Tue Dec 2 00:52:50 2014 UTC (2 years, 6 months ago) by jfenwick
Fixed array overflow issue#285

Revision 5284 - Directory Listing
Modified Tue Dec 2 00:44:49 2014 UTC (2 years, 6 months ago) by sshaw
Lame is now accented in user doc where appropriate

Revision 5283 - Directory Listing
Modified Fri Nov 28 05:38:33 2014 UTC (2 years, 6 months ago) by sshaw
updating older templates with v202 options

Revision 5282 - Directory Listing
Modified Fri Nov 28 04:04:10 2014 UTC (2 years, 6 months ago) by jduplessis
dcres inversions won't be added yet


Revision 5281 - Directory Listing
Modified Fri Nov 28 02:43:30 2014 UTC (2 years, 6 months ago) by sshaw
updating current dev list, should probably add Ralf for DCres too

Revision 5280 - Directory Listing
Modified Fri Nov 28 02:23:08 2014 UTC (2 years, 6 months ago) by sshaw
adding initial 4.0 changelog

Revision 5279 - Directory Listing
Modified Thu Nov 27 00:26:18 2014 UTC (2 years, 7 months ago) by sshaw
adding ripley and speckley to user guide, a bit barebones still

Revision 5278 - Directory Listing
Modified Thu Nov 27 00:25:49 2014 UTC (2 years, 7 months ago) by sshaw
sphinxifying older style python doco, including order shifting of module doc

Revision 5277 - Directory Listing
Modified Mon Nov 24 03:29:15 2014 UTC (2 years, 7 months ago) by caltinay
added missing cpus-per-rank option for OpenMPI


Revision 5276 - Directory Listing
Modified Fri Nov 21 04:27:37 2014 UTC (2 years, 7 months ago) by jduplessis
fixed pole-pole gradient


Revision 5275 - Directory Listing
Modified Thu Nov 20 01:27:04 2014 UTC (2 years, 7 months ago) by caltinay
Fixed problem introduced earlier.


Revision 5274 - Directory Listing
Modified Wed Nov 19 03:44:48 2014 UTC (2 years, 7 months ago) by sshaw
python3ifying division in downunder, stripping some debug prints

Revision 5273 - Directory Listing
Modified Tue Nov 18 01:08:29 2014 UTC (2 years, 7 months ago) by caltinay
fixing some intel warnings.


Revision 5272 - Directory Listing
Modified Tue Nov 18 00:56:54 2014 UTC (2 years, 7 months ago) by sshaw
adding coupler doco, adjusting sphinx to use a math extension to deal with many warnings

Revision 5271 - Directory Listing
Modified Tue Nov 18 00:46:29 2014 UTC (2 years, 7 months ago) by caltinay
Re-enabled process binding params for OpenMPI. Not sure if this is a good default though...


Revision 5270 - Directory Listing
Modified Tue Nov 18 00:26:31 2014 UTC (2 years, 7 months ago) by jduplessis
fixed extra brace


Revision 5269 - Directory Listing
Modified Mon Nov 17 23:17:34 2014 UTC (2 years, 7 months ago) by sshaw
removing early return in copuler test

Revision 5268 - Directory Listing
Modified Mon Nov 17 07:10:40 2014 UTC (2 years, 7 months ago) by sshaw
completed speckley->ripley interpolation across multi-axial subdivisions

Revision 5267 - Directory Listing
Modified Mon Nov 17 06:48:27 2014 UTC (2 years, 7 months ago) by caltinay
template is not executable...


Revision 5266 - Directory Listing
Modified Mon Nov 17 06:45:01 2014 UTC (2 years, 7 months ago) by caltinay
New options 'launcher', 'prelaunch' and 'postlaunch'.
The idea is to avoid system/env-specific hacks to run-escript and provide
a means to configure launchers (i.e. mpirun and friends) at build-time.
Thus bin/run-escript now lives as a template run-escript.in and the actual
launcher is created using the above options when running scons.
Technically not much should have changed as I have tried to set the defaults
to what they were in the original launcher.

Only wheezy_options updated so far until I get feedback...



Revision 5265 - Directory Listing
Modified Mon Nov 17 04:59:25 2014 UTC (2 years, 7 months ago) by jfenwick
Adding missing include which clang noticed.

Revision 5264 - Directory Listing
Modified Mon Nov 17 03:04:10 2014 UTC (2 years, 7 months ago) by sshaw
python3ifying xrange calls

Revision 5263 - Directory Listing
Modified Sun Nov 16 23:35:59 2014 UTC (2 years, 7 months ago) by sshaw
python3ifying prints

Revision 5262 - Directory Listing
Modified Thu Nov 13 08:11:40 2014 UTC (2 years, 7 months ago) by gross
Some fixes to the dcresitivity forward model. simple test added. 

Revision 5261 - Directory Listing
Modified Thu Nov 13 04:40:28 2014 UTC (2 years, 7 months ago) by jfenwick
uint ->unsigned int;  using namespace std in speckly Rectangle to allow isnan to work.

Revision 5260 - Directory Listing
Modified Wed Nov 12 05:19:36 2014 UTC (2 years, 7 months ago) by jduplessis
changed to primary potential as an input


Revision 5259 - Directory Listing
Modified Wed Nov 12 01:20:34 2014 UTC (2 years, 7 months ago) by jfenwick
fixed error which I did not know about

Revision 5258 - Directory Listing
Modified Tue Nov 11 04:29:54 2014 UTC (2 years, 7 months ago) by sshaw
replacing a sleep with an MPIbarrier because it's much, much faster in block testing

Revision 5257 - Directory Listing
Modified Tue Nov 11 04:11:28 2014 UTC (2 years, 7 months ago) by sshaw
added a flush and delay to fix race conditions hiding testing summaries from rank zero


Revision 5256 - Directory Listing
Modified Tue Nov 11 03:18:41 2014 UTC (2 years, 7 months ago) by jfenwick
Doesn't work yet but getting some subworld changes in.


Revision 5255 - Directory Listing
Modified Tue Nov 11 01:55:44 2014 UTC (2 years, 7 months ago) by sshaw
adding support for biaxial MPI subdivision for speckly->ripley coupler

Revision 5254 - Directory Listing
Modified Mon Nov 10 09:30:53 2014 UTC (2 years, 7 months ago) by caltinay
Fixed indexing of dirac point data while assembling PDE in ripley.


Revision 5253 - Directory Listing
Modified Mon Nov 10 07:07:34 2014 UTC (2 years, 7 months ago) by gross
some work on the DcRes

Revision 5252 - Directory Listing
Modified Mon Nov 10 05:01:31 2014 UTC (2 years, 7 months ago) by caltinay
update of other template options files.


Revision 5251 - Directory Listing
Modified Mon Nov 10 04:34:39 2014 UTC (2 years, 7 months ago) by gross
Ricker support velocity outout

Revision 5250 - Directory Listing
Modified Mon Nov 10 04:05:11 2014 UTC (2 years, 7 months ago) by caltinay
Updated wheezy template options file and made our rodents import from there.
Had to rename scons/os -> scons/templates to avoid import conflicts.
Removed obsolete option vsl_random and added new options.
Other templates are yet to be updated.


Revision 5249 - Directory Listing
Modified Mon Nov 10 00:47:47 2014 UTC (2 years, 7 months ago) by jduplessis
further name changes


Revision 5248 - Directory Listing
Modified Mon Nov 10 00:37:31 2014 UTC (2 years, 7 months ago) by jduplessis
debug and name changes


Revision 5247 - Directory Listing
Modified Fri Nov 7 02:44:08 2014 UTC (2 years, 7 months ago) by sshaw
fixing non-MPI builds with couplers

Revision 5246 - Directory Listing
Modified Fri Nov 7 01:41:18 2014 UTC (2 years, 7 months ago) by sshaw
adding speckley->ripley MPI Brick coupling for single axis subdivisions

Revision 5245 - Directory Listing
Modified Thu Nov 6 11:14:08 2014 UTC (2 years, 7 months ago) by caltinay
CPU optimizations for block size 1 symmetric spmv (DIA) which is now also
faster than non-symmetric on i7.


Revision 5244 - Directory Listing
Modified Thu Nov 6 11:03:58 2014 UTC (2 years, 7 months ago) by caltinay
block size 2 optimizations.


Revision 5243 - Directory Listing
Modified Thu Nov 6 10:09:23 2014 UTC (2 years, 7 months ago) by caltinay
Significant speed-up for symmetric spmv on CPU. This is now faster than
non-symmetric on i7.


Revision 5242 - Directory Listing
Modified Wed Nov 5 01:34:55 2014 UTC (2 years, 7 months ago) by jduplessis
python 3 print 


Revision 5241 - Directory Listing
Modified Tue Nov 4 06:47:42 2014 UTC (2 years, 7 months ago) by jduplessis
non exponential mapping


Revision 5240 - Directory Listing
Modified Tue Nov 4 03:47:26 2014 UTC (2 years, 7 months ago) by sshaw
adding options to record time and cycle number in silo and VTK files

Revision 5239 - Directory Listing
Modified Thu Oct 30 05:36:00 2014 UTC (2 years, 7 months ago) by caltinay
More cache-friendly version of CPU-based symmetric-CDS-SpMV for block sizes >2.


Revision 5238 - Directory Listing
Modified Wed Oct 29 05:26:36 2014 UTC (2 years, 7 months ago) by caltinay
block size 3 special case on GPU.


Revision 5237 - Directory Listing
Modified Wed Oct 29 04:28:59 2014 UTC (2 years, 7 months ago) by caltinay
-Enabled use of texture memory by default (needs config option).
-split symmetric spmv to separate file and added specialized version
for block size 2.


Revision 5236 - Directory Listing
Modified Wed Oct 29 03:19:11 2014 UTC (2 years, 7 months ago) by caltinay
well, this was embarrassing...


Revision 5235 - Directory Listing
Modified Wed Oct 29 01:01:44 2014 UTC (2 years, 7 months ago) by caltinay
Tweaks to the forward model tests and finally silenced all but rank 0
for unit test output. I don't think this will hide useful info as all
ranks should output the same thing by the TextTestRunner...


Revision 5234 - Directory Listing
Modified Wed Oct 29 00:54:43 2014 UTC (2 years, 7 months ago) by jduplessis
commented out prints


Revision 5233 - Directory Listing
Modified Wed Oct 29 00:49:32 2014 UTC (2 years, 7 months ago) by jduplessis
added changes for polepole models


Revision 5232 - Directory Listing
Modified Wed Oct 29 00:19:06 2014 UTC (2 years, 7 months ago) by caltinay
array of mu's should be float even if someone does [1,2].



Revision 5231 - Directory Listing
Modified Tue Oct 28 21:21:15 2014 UTC (2 years, 7 months ago) by caltinay
Skipping ripley SystemMatrix tests with >1 rank, some formatting and minor
changes.


Revision 5230 - Directory Listing
Modified Tue Oct 28 07:38:38 2014 UTC (2 years, 7 months ago) by caltinay
lowered tolerance so cusp BiCGSTAB solves to required accuracy by this test.


Revision 5229 - Directory Listing
Modified Mon Oct 27 23:39:15 2014 UTC (2 years, 7 months ago) by caltinay
build_dir->BUILD_DIR in testrunner


Revision 5228 - Directory Listing
Modified Mon Oct 27 23:31:46 2014 UTC (2 years, 7 months ago) by caltinay
updated UMFPACK def in places...


Revision 5227 - Directory Listing
Modified Mon Oct 27 06:09:03 2014 UTC (2 years, 8 months ago) by sshaw
adding forgotten files

Revision 5226 - Directory Listing
Modified Mon Oct 27 05:04:07 2014 UTC (2 years, 8 months ago) by sshaw
extending speckley->ripley interpolation to support MPI


Revision 5225 - Directory Listing
Modified Mon Oct 27 01:33:45 2014 UTC (2 years, 8 months ago) by caltinay
dummy commit to see if submin is happy now.


Revision 5224 - Directory Listing
Modified Mon Oct 27 01:23:31 2014 UTC (2 years, 8 months ago) by jduplessis
fixed issue with point elements

Revision 5223 - Directory Listing
Modified Fri Oct 24 04:34:07 2014 UTC (2 years, 8 months ago) by caltinay
Fixed CDS->CDS copy and implemented a kernel for symmetric spmv which is
currently not optimized and thus slow.


Revision 5222 - Directory Listing
Modified Fri Oct 24 04:29:46 2014 UTC (2 years, 8 months ago) by jduplessis
getNumberOfDataPoints is a per rank operation


Revision 5221 - Directory Listing
Modified Thu Oct 23 04:01:49 2014 UTC (2 years, 8 months ago) by caltinay
Actually implement transposed SpMV for blocksizes >=3


Revision 5220 - Directory Listing
Modified Thu Oct 23 03:50:37 2014 UTC (2 years, 8 months ago) by caltinay
Fixes to CDS SpMV symmetric and tests for blocksizes 1-4 symm/non-symm.


Revision 5219 - Directory Listing
Modified Thu Oct 23 03:47:27 2014 UTC (2 years, 8 months ago) by jduplessis
should now work with mpi

Revision 5218 - Directory Listing
Modified Thu Oct 23 00:37:38 2014 UTC (2 years, 8 months ago) by jduplessis
debug removings

Revision 5217 - Directory Listing
Modified Thu Oct 23 00:18:44 2014 UTC (2 years, 8 months ago) by jduplessis
further debug removings

Revision 5216 - Directory Listing
Modified Thu Oct 23 00:12:22 2014 UTC (2 years, 8 months ago) by jduplessis
further removal of print statements

Revision 5215 - Directory Listing
Modified Thu Oct 23 00:10:19 2014 UTC (2 years, 8 months ago) by jduplessis
fixed mpi version for when mesh does not exists and removed some print statements

Revision 5214 - Directory Listing
Modified Wed Oct 22 23:42:01 2014 UTC (2 years, 8 months ago) by caltinay
enable thrust/CUDA on guineapig for testing ripley SystemMatrix.


Revision 5213 - Directory Listing
Modified Wed Oct 22 05:59:37 2014 UTC (2 years, 8 months ago) by jduplessis
nlpde example for user guide

Revision 5212 - Directory Listing
Modified Wed Oct 22 05:06:48 2014 UTC (2 years, 8 months ago) by caltinay
Preparing ripley SystemMatrix tests.


Revision 5211 - Directory Listing
Modified Wed Oct 22 04:26:03 2014 UTC (2 years, 8 months ago) by sshaw
fixed infinite loop in gmsh reader

Revision 5210 - Directory Listing
Modified Wed Oct 22 03:50:06 2014 UTC (2 years, 8 months ago) by jduplessis
added copyright message

Revision 5209 - Directory Listing
Modified Tue Oct 21 06:50:20 2014 UTC (2 years, 8 months ago) by caltinay
Adding memory optimization for symmetric CDS matrices (in ripley).
Only main and upper diagonal blocks are now stored.
SpMV not updated on GPUs yet but we get a speed-up on Xeons.



Revision 5208 - Directory Listing
Modified Tue Oct 21 03:43:14 2014 UTC (2 years, 8 months ago) by jduplessis
fixed may be unitialised error reworked code to add more openMpness


Revision 5207 - Directory Listing
Modified Tue Oct 21 00:51:22 2014 UTC (2 years, 8 months ago) by jduplessis
fixed compiler errors


Revision 5206 - Directory Listing
Modified Mon Oct 20 06:59:57 2014 UTC (2 years, 8 months ago) by jduplessis
working mpi version of readGmsh. tweaks and unit tests to come


Revision 5205 - Directory Listing
Modified Wed Oct 15 22:39:30 2014 UTC (2 years, 8 months ago) by caltinay
writeBinaryGrid should check for ReducedSolution as well since a
Projector returns a data object on that function space.


Revision 5204 - Directory Listing
Modified Tue Oct 14 22:33:56 2014 UTC (2 years, 8 months ago) by jduplessis
removed debug print


Revision 5203 - Directory Listing
Modified Tue Oct 14 06:46:34 2014 UTC (2 years, 8 months ago) by jduplessis
removed debug print statement


Revision 5202 - Directory Listing
Modified Mon Oct 13 00:53:00 2014 UTC (2 years, 8 months ago) by caltinay
comment debug output (py3 errors)


Revision 5201 - Directory Listing
Modified Fri Oct 10 06:23:03 2014 UTC (2 years, 8 months ago) by sshaw
fixing errors in speckley bricks node referencing in multidimensional subdivisions, fixes recent VTK failures

Revision 5200 - Directory Listing
Modified Thu Oct 9 05:18:45 2014 UTC (2 years, 8 months ago) by sshaw
removing prints from tests

Revision 5199 - Directory Listing
Modified Thu Oct 9 05:17:02 2014 UTC (2 years, 8 months ago) by sshaw
adjusting tests to allow for domain resizing under MPI


Revision 5198 - Directory Listing
Modified Wed Oct 8 08:28:35 2014 UTC (2 years, 8 months ago) by caltinay
fixed longstanding lazy test failures due to calling getDataRO() without
resolving Data object first (only in finley).


Revision 5197 - Directory Listing
Modified Wed Oct 8 04:41:15 2014 UTC (2 years, 8 months ago) by sshaw
allows absorption zones of zero size in seismic models

Revision 5196 - Directory Listing
Modified Tue Oct 7 02:00:59 2014 UTC (2 years, 8 months ago) by caltinay
more type changes/fixes.


Revision 5195 - Directory Listing
Modified Fri Oct 3 02:12:56 2014 UTC (2 years, 8 months ago) by sshaw
speckley: more informative functionspace errors for coupled interpolation, removed points from tagsinuse to match ripley

Revision 5194 - Directory Listing
Modified Thu Oct 2 06:36:02 2014 UTC (2 years, 8 months ago) by caltinay
Some more long-index work.


Revision 5193 - Directory Listing
Modified Thu Oct 2 06:19:08 2014 UTC (2 years, 8 months ago) by sshaw
adding test skip for couplers and multiprocess

Revision 5192 - Directory Listing
Modified Thu Oct 2 04:42:23 2014 UTC (2 years, 8 months ago) by sshaw
adding omitted copyright header

Revision 5191 - Directory Listing
Modified Thu Oct 2 04:40:20 2014 UTC (2 years, 8 months ago) by sshaw
adding speckley to ripley interpolation (single process only)

Revision 5190 - Directory Listing
Modified Thu Oct 2 01:15:32 2014 UTC (2 years, 8 months ago) by sshaw
removing accidentally included and incomplete cross domain work

Revision 5189 - Directory Listing
Modified Thu Oct 2 01:12:57 2014 UTC (2 years, 8 months ago) by sshaw
fixing badly behaved dirac points in speckley

Revision 5188 - Directory Listing
Modified Wed Oct 1 21:54:07 2014 UTC (2 years, 8 months ago) by caltinay
Fixed logic error.


Revision 5187 - Directory Listing
Modified Wed Oct 1 06:49:24 2014 UTC (2 years, 8 months ago) by caltinay
escript, paso, ripley now compiles with index type long.


Revision 5186 - Directory Listing
Modified Wed Oct 1 06:18:02 2014 UTC (2 years, 8 months ago) by sshaw
fixing misplaced dirac points in ripley domains with enormous elements

Revision 5185 - Directory Listing
Modified Wed Oct 1 05:33:55 2014 UTC (2 years, 8 months ago) by caltinay
typo.


Revision 5184 - Directory Listing
Modified Wed Oct 1 04:19:22 2014 UTC (2 years, 8 months ago) by caltinay
New scons option 'domains' to build only specified domains.
Defaults to all. Implements #257


Revision 5183 - Directory Listing
Modified Tue Sep 30 05:55:37 2014 UTC (2 years, 8 months ago) by caltinay
More long-index work. Added scons option 'longindices'.
Parts will not compile yet if set to true.


Revision 5182 - Directory Listing
Modified Tue Sep 30 04:03:34 2014 UTC (2 years, 8 months ago) by caltinay
more work towards allowing non-int indices.


Revision 5181 - Directory Listing
Modified Tue Sep 30 01:42:49 2014 UTC (2 years, 8 months ago) by gross
for buildbot testing

Revision 5180 - Directory Listing
Modified Thu Sep 25 11:25:29 2014 UTC (2 years, 9 months ago) by caltinay
Postpone closing netcdf file to avoid numpy segfault.


Revision 5179 - Directory Listing
Modified Thu Sep 25 07:18:20 2014 UTC (2 years, 9 months ago) by caltinay
Work towards allowing non-int index type.


Revision 5178 - Directory Listing
Modified Thu Sep 25 06:31:12 2014 UTC (2 years, 9 months ago) by caltinay
updated silo deps on guineapig.


Revision 5177 - Directory Listing
Modified Thu Sep 25 04:37:54 2014 UTC (2 years, 9 months ago) by sshaw
more speckley type cleanup (and unused function cleanup)

Revision 5176 - Directory Listing
Modified Thu Sep 25 04:36:28 2014 UTC (2 years, 9 months ago) by sshaw
fixes to wave models using wavelet acceleration instead of value


Revision 5175 - Directory Listing
Modified Thu Sep 25 03:58:06 2014 UTC (2 years, 9 months ago) by sshaw
some speckley type corrections

Revision 5174 - Directory Listing
Modified Thu Sep 25 01:45:59 2014 UTC (2 years, 9 months ago) by caltinay
Report number of matrix entries if verbosity is on.


Revision 5173 - Directory Listing
Modified Thu Sep 25 01:04:26 2014 UTC (2 years, 9 months ago) by sshaw
fixing a sillyness in speckley dirac point assignment

Revision 5172 - Directory Listing
Modified Wed Sep 24 06:59:22 2014 UTC (2 years, 9 months ago) by caltinay
Implemented writeBinaryGrid for Solution (DegreesOfFreedom). Fixes #280


Revision 5171 - Directory Listing
Modified Wed Sep 24 06:57:33 2014 UTC (2 years, 9 months ago) by sshaw
removing leftover dummy test

Revision 5170 - Directory Listing
Modified Wed Sep 24 00:30:39 2014 UTC (2 years, 9 months ago) by sshaw
fixing bug in multi-process speckley with dirac points, some test cleanup

Revision 5169 - Directory Listing
Modified Mon Sep 22 08:46:58 2014 UTC (2 years, 9 months ago) by gross
tIsostaticPressure testing added

Revision 5168 - Directory Listing
Modified Mon Sep 22 05:22:06 2014 UTC (2 years, 9 months ago) by jduplessis
changed version number


Revision 5167 - Directory Listing
Modified Thu Sep 18 04:04:33 2014 UTC (2 years, 9 months ago) by caltinay
updated mole options file.


Revision 5166 - Directory Listing
Modified Wed Sep 17 21:44:41 2014 UTC (2 years, 9 months ago) by sshaw
added missed test files

Revision 5165 - Directory Listing
Modified Wed Sep 17 11:40:57 2014 UTC (2 years, 9 months ago) by caltinay
savanna: removed ipo to speed up linking, moved to new intel 15 tool chain,
removed umfpack dependency since we are using MKL.


Revision 5164 - Directory Listing
Modified Wed Sep 17 11:26:09 2014 UTC (2 years, 9 months ago) by caltinay
Slightly better error reporting from CUDA.


Revision 5163 - Directory Listing
Modified Wed Sep 17 08:56:09 2014 UTC (2 years, 9 months ago) by gross
subsidence forward model and testing added

Revision 5162 - Directory Listing
Modified Wed Sep 17 06:38:15 2014 UTC (2 years, 9 months ago) by caltinay
added missing guards


Revision 5161 - Directory Listing
Modified Wed Sep 17 06:37:39 2014 UTC (2 years, 9 months ago) by sshaw
fixing odd crashes in speckley saving to silo

Revision 5160 - Directory Listing
Modified Wed Sep 17 05:20:34 2014 UTC (2 years, 9 months ago) by caltinay
Commit 2/2 - .cpp -> .cu


Revision 5159 - Directory Listing
Modified Wed Sep 17 05:19:56 2014 UTC (2 years, 9 months ago) by caltinay
cusp requires thrust which is unlikely to be installed without the CUDA tk.
-> decided to remove cusp-based solvers/matrices for non-CUDA builds.
Commit 1/2 (svn rejects type change in single commit)


Revision 5158 - Directory Listing
Modified Wed Sep 17 04:33:42 2014 UTC (2 years, 9 months ago) by sshaw
removed vestigal FunctionOnBoundary and reduced functionspaces from speckley

Revision 5157 - Directory Listing
Modified Wed Sep 17 01:02:58 2014 UTC (2 years, 9 months ago) by sshaw
fixing non-MPI builds of speckley

Revision 5156 - Directory Listing
Modified Wed Sep 17 00:40:33 2014 UTC (2 years, 9 months ago) by caltinay
intel 15 doesn't like this.


Revision 5155 - Directory Listing
Modified Tue Sep 16 04:21:15 2014 UTC (2 years, 9 months ago) by sshaw
stripping out some leftover commented debug from previous commit

Revision 5154 - Directory Listing
Modified Tue Sep 16 04:19:03 2014 UTC (2 years, 9 months ago) by sshaw
updating speckley binary grid reads to interpolate all missing quad points

Revision 5153 - Directory Listing
Modified Tue Sep 16 03:34:31 2014 UTC (2 years, 9 months ago) by caltinay
bump guineapig's options file version.


Revision 5152 - Directory Listing
Modified Tue Sep 16 01:29:30 2014 UTC (2 years, 9 months ago) by jduplessis
add dcresistivity inversion


Revision 5151 - Directory Listing
Modified Mon Sep 15 06:11:46 2014 UTC (2 years, 9 months ago) by sshaw
adding simple read/write tests for speckley

Revision 5150 - Directory Listing
Modified Mon Sep 15 06:09:42 2014 UTC (2 years, 9 months ago) by sshaw
type corrections to speckley and adding in binarygrid support for brick (element corners only)

Revision 5149 - Directory Listing
Modified Mon Sep 15 01:57:06 2014 UTC (2 years, 9 months ago) by sshaw
removed transport from speckley, added read/write binary grids for rectangles

Revision 5148 - Directory Listing
Modified Mon Sep 15 01:25:23 2014 UTC (2 years, 9 months ago) by caltinay
Merging ripley diagonal storage + CUDA support into trunk.
Options file version has been incremented due to new options
'cuda' and 'nvccflags'.


Revision 5145 - Directory Listing
Modified Thu Sep 11 03:28:37 2014 UTC (2 years, 9 months ago) by sshaw
fixed corner issue in three-dimensional speckley subdivisions

Revision 5143 - Directory Listing
Modified Wed Sep 10 07:27:59 2014 UTC (2 years, 9 months ago) by sshaw
removing some of those omp loop sections until they play well

Revision 5142 - Directory Listing
Modified Wed Sep 10 07:18:34 2014 UTC (2 years, 9 months ago) by sshaw
marked loops as omp, wrapped remaining MPI-only function call

Revision 5140 - Directory Listing
Modified Wed Sep 10 05:49:19 2014 UTC (2 years, 9 months ago) by sshaw
stripping debug print out of speckley section of weipa

Revision 5139 - Directory Listing
Modified Wed Sep 10 05:42:46 2014 UTC (2 years, 9 months ago) by sshaw
speckley brick now supports MPI

Revision 5138 - Directory Listing
Modified Wed Sep 10 04:12:47 2014 UTC (2 years, 9 months ago) by caltinay
Added ABS which was obviously missing in a function that is used to
create balance vector in paso.


Revision 5133 - Directory Listing
Modified Fri Sep 5 00:07:34 2014 UTC (2 years, 9 months ago) by sshaw
fixed non-MPI builds with speckley

Revision 5132 - Directory Listing
Modified Thu Sep 4 07:02:24 2014 UTC (2 years, 9 months ago) by sshaw
added MPI support and tests to speckley, cleaned out more ghostzone code

Revision 5129 - Directory Listing
Modified Fri Aug 29 05:10:48 2014 UTC (2 years, 9 months ago) by sshaw
fixing missed MPI type merge from ripley

Revision 5128 - Directory Listing
Modified Fri Aug 29 00:52:35 2014 UTC (2 years, 9 months ago) by sshaw
fixing a bad index calculation

Revision 5127 - Directory Listing
Modified Fri Aug 29 00:30:34 2014 UTC (2 years, 9 months ago) by sshaw
more redundant includes removed

Revision 5126 - Directory Listing
Modified Thu Aug 28 23:32:59 2014 UTC (2 years, 9 months ago) by sshaw
fixing last remnants of speckley::SystemMatrix


Revision 5125 - Directory Listing
Modified Thu Aug 28 23:16:21 2014 UTC (2 years, 9 months ago) by sshaw
removing troublesome future-predicting #include

Revision 5124 - Directory Listing
Modified Thu Aug 28 07:02:55 2014 UTC (2 years, 9 months ago) by sshaw
minor comment fix for ripley

Revision 5123 - Directory Listing
Modified Thu Aug 28 07:02:11 2014 UTC (2 years, 9 months ago) by sshaw
Adding speckley (high-order) domain family, doesn't yet support MPI, Reduced functionspaces, or PDEs using A, B and/or C



Revision 5121 - Directory Listing
Modified Wed Aug 20 10:32:40 2014 UTC (2 years, 10 months ago) by caltinay
Made more methods pure virtual in AbstractDomain and moved the generic
implementation into NullDomain.
Made TestDomain derive from NullDomain to inherit the methods.


Revision 5120 - Directory Listing
Modified Wed Aug 20 06:19:20 2014 UTC (2 years, 10 months ago) by caltinay
Some code cleanup and int->dim_t replacements in ripley.


Revision 5119 - Directory Listing
Modified Wed Aug 20 04:10:01 2014 UTC (2 years, 10 months ago) by caltinay
Separated pattern generation from connector generation in ripley Brick
to allow using alternative System Matrices.


Revision 5118 - Directory Listing
Modified Mon Aug 18 11:28:55 2014 UTC (2 years, 10 months ago) by caltinay
Separated generation of paso matrix pattern and coupler/DOF Map
in Rectangle. This is in preparation for introducing non-Paso matrices.
Brick still to do.


Revision 5117 - Directory Listing
Modified Mon Aug 18 05:42:09 2014 UTC (2 years, 10 months ago) by caltinay
Further untangled/simplified paso pattern generation in ripley.


Revision 5116 - Directory Listing
Modified Mon Aug 18 01:56:41 2014 UTC (2 years, 10 months ago) by caltinay
making an example slightly more generic.


Revision 5115 - Directory Listing
Modified Thu Aug 14 05:36:58 2014 UTC (2 years, 10 months ago) by caltinay
Minor tweaks.


Revision 5114 - Directory Listing
Modified Thu Aug 14 05:15:31 2014 UTC (2 years, 10 months ago) by caltinay
Preliminary changes to make ripley ready for other System Matrixes.


Revision 5113 - Directory Listing
Modified Tue Aug 12 23:06:07 2014 UTC (2 years, 10 months ago) by caltinay
new directory for boost install.


Revision 5112 - Directory Listing
Modified Mon Aug 11 04:17:17 2014 UTC (2 years, 10 months ago) by caltinay
Report regularization terms separately when debug output is enabled.


Revision 5111 - Directory Listing
Modified Tue Aug 5 00:19:56 2014 UTC (2 years, 10 months ago) by caltinay
replaced '@expectedFailure' by '@skip' since py3 does not support the former
for test classes.


Revision 5110 - Directory Listing
Modified Fri Aug 1 05:04:59 2014 UTC (2 years, 10 months ago) by jduplessis
replaced atomic with critical


Revision 5109 - Directory Listing
Modified Fri Aug 1 04:39:53 2014 UTC (2 years, 10 months ago) by jduplessis
fix indentation


Revision 5108 - Directory Listing
Modified Fri Aug 1 04:37:45 2014 UTC (2 years, 10 months ago) by jduplessis
removing renamed tests


Revision 5107 - Directory Listing
Modified Thu Jul 24 14:07:14 2014 UTC (2 years, 11 months ago) by caltinay
It appears critical for scaling in finley/dudley that IndexList does not
realloc so reimplemented original idea.


Revision 5106 - Directory Listing
Modified Mon Jul 21 11:57:42 2014 UTC (2 years, 11 months ago) by caltinay
Avoid some unnecessary reallocation.


Revision 5105 - Directory Listing
Modified Mon Jul 21 10:08:43 2014 UTC (2 years, 11 months ago) by caltinay
fix for parmetis-enabled build


Revision 5104 - Directory Listing
Modified Mon Jul 21 07:47:55 2014 UTC (2 years, 11 months ago) by caltinay
Fixed a threading performance issue in finley/dudley by preallocating
chunk in vector and using dynamic arrays directly for parallel region.


Revision 5103 - Directory Listing
Modified Thu Jul 17 13:39:02 2014 UTC (2 years, 11 months ago) by caltinay
use a vector for index list because we need contiguous storage for efficiency.


Revision 5102 - Directory Listing
Modified Wed Jul 16 00:46:22 2014 UTC (2 years, 11 months ago) by caltinay
We were setting --cpus-per-rank without a --bind... option under OpenMPI
but the latter is required according to doco.
This, in combination with setting OMP_PROC_BIND=true, caused all ranks
to run on the same core when running without hostfile (e.g. on guineapig)
so the runtimes exploded.
Added --bind-to-core to fix that issue.


Revision 5101 - Directory Listing
Modified Tue Jul 15 09:50:20 2014 UTC (2 years, 11 months ago) by caltinay
Fixed another race with file deletion.


Revision 5100 - Directory Listing
Modified Tue Jul 15 07:36:29 2014 UTC (2 years, 11 months ago) by jduplessis
minor revisions


Revision 5099 - Directory Listing
Modified Mon Jul 14 00:41:14 2014 UTC (2 years, 11 months ago) by caltinay
Fix recent mpi test failures by giving ranks>0 some time to check their
output before deleting test files.


Revision 5098 - Directory Listing
Modified Sun Jul 13 14:33:43 2014 UTC (2 years, 11 months ago) by caltinay
Finally implemented multipliers for readBinaryGrid under MPI and fixed tests
accordingly.
We can now read data at resolution x into a domain at resolution N*x properly.



Revision 5097 - Directory Listing
Modified Sun Jul 13 01:02:24 2014 UTC (2 years, 11 months ago) by caltinay
Fixed undefined behaviour when indexing empty stl containers to pass
pointers (i.e. &vec[0]).


Revision 5096 - Directory Listing
Modified Fri Jul 11 12:32:49 2014 UTC (2 years, 11 months ago) by caltinay
More readBinaryGrid tests. There are a few 'expectedFailure's for
>1 rank. This is a shortcoming of the tests, not of the actual
implementation, so they need more work.


Revision 5094 - Directory Listing
Modified Thu Jul 10 02:46:33 2014 UTC (2 years, 11 months ago) by caltinay
Back to sh-compatibility


Revision 5093 - Directory Listing
Modified Tue Jul 8 01:54:09 2014 UTC (2 years, 11 months ago) by jfenwick
Document range of random number generator.


Revision 5092 - Directory Listing
Modified Mon Jul 7 00:47:44 2014 UTC (2 years, 11 months ago) by sshaw
fixing lack of thread binding for intel-based OpenMP, gcc unaffected

Revision 5091 - Directory Listing
Modified Wed Jul 2 05:19:02 2014 UTC (2 years, 11 months ago) by jduplessis
NaN tests for ripley

Revision 5090 - Directory Listing
Modified Wed Jul 2 05:14:11 2014 UTC (2 years, 11 months ago) by jduplessis
tests for replace and has NaN


Revision 5089 - Directory Listing
Modified Tue Jul 1 01:07:16 2014 UTC (2 years, 11 months ago) by jduplessis
fix missing self.__


Revision 5088 - Directory Listing
Modified Tue Jul 1 00:32:22 2014 UTC (2 years, 11 months ago) by jduplessis
option for direct solver with mtInversion

Revision 5082 - Directory Listing
Modified Fri Jun 27 05:36:01 2014 UTC (3 years ago) by jfenwick
Thanks to Cihan. Silence annoying warngings

Revision 5081 - Directory Listing
Modified Fri Jun 27 03:48:06 2014 UTC (3 years ago) by jduplessis
squirrel options

Revision 5080 - Directory Listing
Modified Wed Jun 25 02:50:56 2014 UTC (3 years ago) by sshaw
more StringIO replacements for py3 compatibility

Revision 5079 - Directory Listing
Modified Tue Jun 24 22:50:50 2014 UTC (3 years ago) by caltinay
bump to py3.4 on piggy.


Revision 5078 - Directory Listing
Modified Tue Jun 24 06:50:21 2014 UTC (3 years ago) by sshaw
fixing silly leftovers that were missed in previous commits

Revision 5077 - Directory Listing
Modified Tue Jun 24 03:51:19 2014 UTC (3 years ago) by caltinay
Make readBinaryGrid "public" within the ripley module.


Revision 5076 - Directory Listing
Modified Tue Jun 24 03:41:42 2014 UTC (3 years ago) by sshaw
more python3 compatibility fixes

Revision 5074 - Directory Listing
Modified Tue Jun 24 00:44:50 2014 UTC (3 years ago) by sshaw
python3 compatibility fix

Revision 5073 - Directory Listing
Modified Mon Jun 23 22:22:44 2014 UTC (3 years ago) by caltinay
fixing some py3 warnings.


Revision 5072 - Directory Listing
Modified Mon Jun 23 05:13:30 2014 UTC (3 years ago) by jduplessis
paralelize hasNaN and replaceNaN


Revision 5071 - Directory Listing
Modified Mon Jun 23 04:36:14 2014 UTC (3 years ago) by sshaw
fixing python 3 xrange unfriendliness

Revision 5069 - Directory Listing
Modified Fri Jun 20 06:54:20 2014 UTC (3 years ago) by sshaw
fixing mismatching identifiers

Revision 5067 - Directory Listing
Modified Fri Jun 20 06:04:58 2014 UTC (3 years ago) by sshaw
actually fixing python 3 breakage and not the previous commits rewrite of lots of code repetition

Revision 5066 - Directory Listing
Modified Fri Jun 20 06:04:02 2014 UTC (3 years ago) by sshaw
fixing python 3 breakage

Revision 5061 - Directory Listing
Modified Fri Jun 20 04:10:59 2014 UTC (3 years ago) by jfenwick
Added descriptive information to functionspace names

Revision 5060 - Directory Listing
Modified Fri Jun 20 03:29:11 2014 UTC (3 years ago) by sshaw
more reporting of previously silently skipped/passing tests

Revision 5059 - Directory Listing
Modified Fri Jun 20 03:10:19 2014 UTC (3 years ago) by sshaw
more test renames, more marking non-test classes, fixed broken test in run_xml

Revision 5058 - Directory Listing
Modified Fri Jun 20 02:03:28 2014 UTC (3 years ago) by sshaw
more test renames, marking some that look wrongly named as subclass required

Revision 5057 - Directory Listing
Modified Fri Jun 20 01:53:38 2014 UTC (3 years ago) by gross
some fixes for MT-TE

Revision 5056 - Directory Listing
Modified Fri Jun 20 01:37:28 2014 UTC (3 years ago) by jduplessis
replace nan stuff

Revision 5055 - Directory Listing
Modified Fri Jun 20 01:21:43 2014 UTC (3 years ago) by sshaw
more test renaming, less silent skipping of tests

Revision 5054 - Directory Listing
Modified Fri Jun 20 00:59:16 2014 UTC (3 years ago) by caltinay
test name changes so they run again.


Revision 5051 - Directory Listing
Modified Wed Jun 18 05:08:02 2014 UTC (3 years ago) by caltinay
Added base readBinaryGrid tests and fixed reading doubles with non-native
endianness.


Revision 5050 - Directory Listing
Modified Wed Jun 18 04:17:54 2014 UTC (3 years ago) by sshaw
more comment cleanup

Revision 5049 - Directory Listing
Modified Wed Jun 18 04:17:26 2014 UTC (3 years ago) by sshaw
small code documentation cleanup

Revision 5048 - Directory Listing
Modified Fri Jun 13 05:41:15 2014 UTC (3 years ago) by caltinay
fixed typo in lbfgs-SetOptions.


Revision 5047 - Directory Listing
Modified Fri Jun 13 05:12:03 2014 UTC (3 years ago) by sshaw
removing dumb 'False and' that was leftover

Revision 5046 - Directory Listing
Modified Fri Jun 13 02:54:29 2014 UTC (3 years ago) by caltinay
std::isnan -> isnan


Revision 5045 - Directory Listing
Modified Fri Jun 13 02:53:39 2014 UTC (3 years ago) by caltinay
minor fixes required on cray/py26


Revision 5044 - Directory Listing
Modified Fri Jun 13 01:51:58 2014 UTC (3 years ago) by caltinay
fixed compiler warnings that appeared due to removing the exceptions.


Revision 5043 - Directory Listing
Modified Thu Jun 12 07:07:27 2014 UTC (3 years ago) by jduplessis
skip gmshnamedtags for mpi

Revision 5042 - Directory Listing
Modified Thu Jun 12 06:40:11 2014 UTC (3 years ago) by caltinay
HTI and VTI are the only cases as ensured by the constructor so don't
throw in parallel region.


Revision 5041 - Directory Listing
Modified Thu Jun 12 05:28:22 2014 UTC (3 years ago) by sshaw
fixed domainreader test sillyness and moved gmsh detection into testfile from SConscript

Revision 5040 - Directory Listing
Modified Thu Jun 12 05:12:33 2014 UTC (3 years ago) by caltinay
gravity constant scaling for geodetic coordinates does not appear to be
right so reverting for now.


Revision 5039 - Directory Listing
Modified Thu Jun 12 05:10:38 2014 UTC (3 years ago) by caltinay
compiler help


Revision 5038 - Directory Listing
Modified Thu Jun 12 04:58:56 2014 UTC (3 years ago) by caltinay
Missed a few. Should be almost done.


Revision 5037 - Directory Listing
Modified Thu Jun 12 04:39:23 2014 UTC (3 years ago) by caltinay
more on CAP.


Revision 5036 - Directory Listing
Modified Thu Jun 12 04:37:33 2014 UTC (3 years ago) by caltinay
CAP#4


Revision 5035 - Directory Listing
Modified Thu Jun 12 03:52:39 2014 UTC (3 years ago) by caltinay
csp#3


Revision 5034 - Directory Listing
Modified Thu Jun 12 03:14:56 2014 UTC (3 years ago) by caltinay
More omp compiler helps.


Revision 5033 - Directory Listing
Modified Thu Jun 12 01:04:42 2014 UTC (3 years ago) by jduplessis
test file for named tags

Revision 5032 - Directory Listing
Modified Thu Jun 12 01:03:00 2014 UTC (3 years ago) by jduplessis
added test for named tags

Revision 5031 - Directory Listing
Modified Thu Jun 12 01:01:21 2014 UTC (3 years ago) by sshaw
retrieving LinearMappingX from the lost and found bin

Revision 5030 - Directory Listing
Modified Thu Jun 12 00:37:33 2014 UTC (3 years ago) by sshaw
more missing tests added

Revision 5029 - Directory Listing
Modified Wed Jun 11 23:52:36 2014 UTC (3 years ago) by caltinay
Continuing the compiler assistance package...


Revision 5028 - Directory Listing
Modified Wed Jun 11 22:49:41 2014 UTC (3 years ago) by caltinay
this fails without abspath on a system.


Revision 5027 - Directory Listing
Modified Wed Jun 11 07:32:26 2014 UTC (3 years ago) by caltinay
First commit of a 'compiler assistance package', i.e.
making it easier for compilers to understand OMP loop limits.


Revision 5026 - Directory Listing
Modified Wed Jun 11 06:07:03 2014 UTC (3 years ago) by jduplessis
reading physical names should now work properly


Revision 5025 - Directory Listing
Modified Wed Jun 11 05:44:31 2014 UTC (3 years ago) by caltinay
Fix to gravity model with geodetic coords and another instance of
== badness.


Revision 5024 - Directory Listing
Modified Tue Jun 10 08:46:07 2014 UTC (3 years ago) by jfenwick
Fixing more == None


Revision 5023 - Directory Listing
Modified Tue Jun 10 06:37:50 2014 UTC (3 years ago) by jfenwick
Replacing ==None and variants with is None in accordance with new warnings.


Revision 5022 - Directory Listing
Modified Tue Jun 10 05:02:47 2014 UTC (3 years ago) by sshaw
scons runs now remove prior skipped files on a per-file basis

Revision 5021 - Directory Listing
Modified Tue Jun 10 04:44:52 2014 UTC (3 years ago) by jfenwick
Making == and != on Data objects throw exceptions to warn people that they probably don't do what they might think they do.
Credit to Jaco and Cihan.


Revision 5020 - Directory Listing
Modified Tue Jun 10 04:07:00 2014 UTC (3 years ago) by caltinay
remember the good ol' days where no newline at end of files were frowned upon? 
Thanks to crayc++ they're back.


Revision 5019 - Directory Listing
Modified Tue Jun 10 03:57:55 2014 UTC (3 years ago) by sshaw
scons ends if tests fail again

Revision 5018 - Directory Listing
Modified Tue Jun 10 03:38:29 2014 UTC (3 years ago) by caltinay
byteswap.h availability does not mean bswapXXX works so check that.
(crayc++ does not support inline assembly)


Revision 5017 - Directory Listing
Modified Tue Jun 10 02:16:18 2014 UTC (3 years ago) by sshaw
scons now runs tests via a testrunner to collect lists of skipped tests in build/ (examples have their own builder since they aren't unit tests)
fixed hessian regularisation tests falling over by adding a shortcircuit optional arg that returns the pde, not the solution
added missing/omitted tests back into scons tests


Revision 5016 - Directory Listing
Modified Mon Jun 9 09:54:18 2014 UTC (3 years ago) by caltinay
"The Queen's commit". Happy birthday,


Revision 5015 - Directory Listing
Modified Sun Jun 8 13:09:16 2014 UTC (3 years ago) by caltinay
Implemented writing of binary grids for FLOAT64 in non-native byte order.
Write tests pass now fully on debian.

This depends on uint64_t which is assumed to be available...


Revision 5014 - Directory Listing
Modified Sun Jun 8 12:05:22 2014 UTC (3 years ago) by caltinay
built boost 1.55.0 on savanna which fixes the segfaults we have been seeing
for a long time when using shared_from_this() with the intel compiler.

(While Intel couldn't reproduce, I could on epic, magnus, and raijin w/ system
boost+python. Finally found that using 1.53+ modules on raijin did no longer
exhibit the problem.)



Revision 5013 - Directory Listing
Modified Fri Jun 6 07:25:13 2014 UTC (3 years ago) by caltinay
fix minor typo


Revision 5012 - Directory Listing
Modified Fri Jun 6 07:23:36 2014 UTC (3 years ago) by caltinay
writeBinaryGrid tests. big endian doubles fail currently.


Revision 5011 - Directory Listing
Modified Fri Jun 6 07:05:50 2014 UTC (3 years ago) by jduplessis
updates getInverse for mt


Revision 5010 - Directory Listing
Modified Fri Jun 6 07:00:28 2014 UTC (3 years ago) by caltinay
fixes #270 (pathological case).


Revision 5009 - Directory Listing
Modified Fri Jun 6 04:36:13 2014 UTC (3 years ago) by caltinay
deleted strange file which doesn't belong here.


Revision 5008 - Directory Listing
Modified Fri Jun 6 04:31:41 2014 UTC (3 years ago) by caltinay
some cleanup, renaming and fixing of ripley tests.


Revision 5006 - Directory Listing
Modified Fri Jun 6 03:40:44 2014 UTC (3 years ago) by gross
Cross-Gradient testing added. No dramas.

Revision 5005 - Directory Listing
Modified Fri Jun 6 03:11:14 2014 UTC (3 years ago) by gross
test for Hessian added. Cross  gradient is still missing.

Revision 5004 - Directory Listing
Modified Fri Jun 6 02:34:27 2014 UTC (3 years ago) by gross
two bug fixes in the cross gradient term

Revision 5003 - Directory Listing
Modified Fri Jun 6 00:34:33 2014 UTC (3 years ago) by sshaw
a more forgiving test class prefix check

Revision 5002 - Directory Listing
Modified Fri Jun 6 00:21:58 2014 UTC (3 years ago) by sshaw
tweaking test class name to allow unittest to function

Revision 5001 - Directory Listing
Modified Thu Jun 5 23:59:21 2014 UTC (3 years ago) by gross
regularization test added.

Revision 5000 - Directory Listing
Modified Thu Jun 5 23:33:16 2014 UTC (3 years ago) by jfenwick
Recent release of g++ no longer accepts isnan outside of the std namespace.
Added a general using namespace std _inside_ the function to catch both cases.

Also, 5000th commit


Revision 4999 - Directory Listing
Modified Thu Jun 5 06:39:52 2014 UTC (3 years ago) by jfenwick
Fixing weirdness


Revision 4998 - Directory Listing
Modified Thu Jun 5 06:03:08 2014 UTC (3 years ago) by jduplessis
implemented hasNaN


Revision 4997 - Directory Listing
Modified Thu Jun 5 05:23:41 2014 UTC (3 years ago) by jfenwick
Added missing link


Revision 4996 - Directory Listing
Modified Thu Jun 5 03:56:33 2014 UTC (3 years ago) by jfenwick
Changed cookbook back to single spacing from double spacing.
All pdfs now link in the same docguide.tex file which explains what the
various bits of doco are.



Revision 4995 - Directory Listing
Modified Thu Jun 5 03:44:16 2014 UTC (3 years ago) by caltinay
Doc fixes and ensuring that expensive debug ops will not be processed if debug
mode is disabled.


Revision 4994 - Directory Listing
Modified Thu Jun 5 03:04:57 2014 UTC (3 years ago) by jfenwick
Ensure isnan calls the c++ version except on windows compilers


Revision 4993 - Directory Listing
Modified Thu Jun 5 03:04:56 2014 UTC (3 years ago) by sshaw
fixing the launcher to run on all nodes for savanna

Revision 4992 - Directory Listing
Modified Thu Jun 5 01:38:33 2014 UTC (3 years ago) by caltinay
Don't obtain/report UTM zone for non-cartesian coordinate systems.


Revision 4991 - Directory Listing
Modified Thu Jun 5 01:01:41 2014 UTC (3 years ago) by jduplessis
adding MT data


Revision 4990 - Directory Listing
Modified Wed Jun 4 13:17:15 2014 UTC (3 years ago) by jduplessis
added mtMappings


Revision 4989 - Directory Listing
Modified Wed Jun 4 06:22:36 2014 UTC (3 years ago) by sshaw
marking pdetools.Defect as abstract in doco and preventing it from silently returning lots of zeroes instead of being subclassed

Revision 4986 - Directory Listing
Modified Tue Jun 3 03:09:14 2014 UTC (3 years ago) by sshaw
adding skips for those tests not previously tested and which will need checking

Revision 4985 - Directory Listing
Modified Mon Jun 2 05:45:58 2014 UTC (3 years ago) by sshaw
uncommenting decorator that shouldn't have been commented

Revision 4984 - Directory Listing
Modified Mon Jun 2 02:50:34 2014 UTC (3 years ago) by sshaw
revamping testrunners, now uses automated discovery and allows running specific tests without modifying files (see escriptcore/py_src/testing.py for more info/examples)


Revision 4983 - Directory Listing
Modified Mon Jun 2 02:32:23 2014 UTC (3 years ago) by sshaw
removing missing/leftover test files from test list

Revision 4982 - Directory Listing
Modified Mon Jun 2 00:41:30 2014 UTC (3 years ago) by sshaw
removing run_utilOnFinley3.py as it is a duplicate of run_utilOnFinley.py

Revision 4981 - Directory Listing
Modified Mon Jun 2 00:26:35 2014 UTC (3 years ago) by gross
MT tests added

Revision 4980 - Directory Listing
Modified Sun Jun 1 23:53:11 2014 UTC (3 years ago) by gross
more fixes on MT

Revision 4979 - Directory Listing
Modified Sun Jun 1 22:36:16 2014 UTC (3 years ago) by gross
some fixes to the MT forward model

Revision 4978 - Directory Listing
Modified Thu May 29 11:55:53 2014 UTC (3 years ago) by caltinay
Make clear that reversing is not implemented yet for Rectangle.
Implemented reversing in z for Brick.
This needs proper testing...


Revision 4977 - Directory Listing
Modified Thu May 29 08:51:43 2014 UTC (3 years ago) by caltinay
la la la....


Revision 4976 - Directory Listing
Modified Thu May 29 08:27:53 2014 UTC (3 years ago) by gross
gradient for coordinate systems added

Revision 4975 - Directory Listing
Modified Thu May 29 03:44:49 2014 UTC (3 years ago) by caltinay
Don't cast p0 to a float as it might be a data object.


Revision 4974 - Directory Listing
Modified Wed May 28 08:02:02 2014 UTC (3 years, 1 month ago) by jduplessis
added a data source object for MT2DTE


Revision 4973 - Directory Listing
Modified Wed May 28 06:02:38 2014 UTC (3 years, 1 month ago) by sshaw
making verbose-mode logging accurate

Revision 4972 - Directory Listing
Modified Tue May 27 05:33:10 2014 UTC (3 years, 1 month ago) by sshaw
small doc grammar changes

Revision 4971 - Directory Listing
Modified Tue May 27 04:52:52 2014 UTC (3 years, 1 month ago) by caltinay
debug output clean up.


Revision 4970 - Directory Listing
Modified Tue May 27 03:47:04 2014 UTC (3 years, 1 month ago) by caltinay
more bashisms removed (valgrind run) from launcher.


Revision 4969 - Directory Listing
Modified Mon May 26 23:50:52 2014 UTC (3 years, 1 month ago) by sshaw
fixing intel's hidden function warning

Revision 4968 - Directory Listing
Modified Mon May 26 04:20:22 2014 UTC (3 years, 1 month ago) by jfenwick
One more time for the dummies

Revision 4967 - Directory Listing
Modified Mon May 26 04:18:19 2014 UTC (3 years, 1 month ago) by sshaw
5.1e-8 is close enough to zero, rounding is breaking this on clang/mac so making it strict <

Revision 4966 - Directory Listing
Modified Mon May 26 02:55:33 2014 UTC (3 years, 1 month ago) by jfenwick
Dealing with non-determinism. We hope.

Revision 4965 - Directory Listing
Modified Fri May 23 22:07:32 2014 UTC (3 years, 1 month ago) by jfenwick
Try to fix this for MPI again

Revision 4964 - Directory Listing
Modified Fri May 23 07:14:25 2014 UTC (3 years, 1 month ago) by gross
MT2D forward pproblem

Revision 4963 - Directory Listing
Modified Fri May 23 05:12:40 2014 UTC (3 years, 1 month ago) by jfenwick
Removed JMPI from ScriptMPI.cpp.
Changed options file to build shared libraries.
Fixed error in unit tests



Revision 4962 - Directory Listing
Modified Fri May 23 02:53:00 2014 UTC (3 years, 1 month ago) by jfenwick
Tests for adding dirac points. There are no tests for what dirac points appear on which ranks.

Revision 4961 - Directory Listing
Modified Thu May 22 03:53:31 2014 UTC (3 years, 1 month ago) by sshaw
another two epydoc leftovers that were missed

Revision 4960 - Directory Listing
Modified Thu May 22 03:35:41 2014 UTC (3 years, 1 month ago) by sshaw
removing vestigal epydoc markup and replacing with sphinx markup


Revision 4959 - Directory Listing
Modified Wed May 21 04:22:14 2014 UTC (3 years, 1 month ago) by gross
added some text on 2D MT TE inversion

Revision 4957 - Directory Listing
Modified Wed May 21 01:31:23 2014 UTC (3 years, 1 month ago) by caltinay
Missed a few unittest wrapper imports.


Revision 4947 - Directory Listing
Modified Mon May 19 03:58:03 2014 UTC (3 years, 1 month ago) by sshaw
adding build fail message for when a boost lib is too old to compile everything anyway (minimum version is currently 1.46)

Revision 4945 - Directory Listing
Modified Thu May 15 09:07:06 2014 UTC (3 years, 1 month ago) by jfenwick
Untested code for adding dirac points to finley domains. Still to do: load(), unit tests

Revision 4943 - Directory Listing
Modified Thu May 15 04:58:35 2014 UTC (3 years, 1 month ago) by sshaw
moving abstract assemblers back into ripley since only ripley uses them (for now)

Revision 4942 - Directory Listing
Modified Thu May 15 03:42:28 2014 UTC (3 years, 1 month ago) by sshaw
each PDE now is responsible for its own assembler, allows multiple types of PDEs to share a domain without interference

Revision 4939 - Directory Listing
Modified Wed May 14 03:56:47 2014 UTC (3 years, 1 month ago) by caltinay
close the file after finishing reading to avoid segfault on centos.


Revision 4938 - Directory Listing
Modified Wed May 14 01:13:23 2014 UTC (3 years, 1 month ago) by jfenwick
Modify unit tests to read their classes from
esys.escriptcore.utestselect

Change the line in that file to switch between unittest and unittest2



Revision 4937 - Directory Listing
Modified Tue May 13 07:07:32 2014 UTC (3 years, 1 month ago) by caltinay
gcc 4.9: error: type qualifiers ignored on function return type [-Werror=ignored-qualifiers]


Revision 4936 - Directory Listing
Modified Tue May 13 07:00:36 2014 UTC (3 years, 1 month ago) by caltinay
Wait a bit after running the mpi-enabled gmsh version to increase probability
of success (yes it's a hack).


Revision 4935 - Directory Listing
Modified Tue May 13 03:49:09 2014 UTC (3 years, 1 month ago) by jfenwick
Fixes for Python3


Revision 4934 - Directory Listing
Modified Tue May 13 00:28:11 2014 UTC (3 years, 1 month ago) by jfenwick
This commit is brought to you by the number 4934 and the tool "meld".
Merge of partially complete split world code from branch.




Revision 4931 - Directory Listing
Modified Mon May 12 02:27:34 2014 UTC (3 years, 1 month ago) by jduplessis
this is a fix for older versions of numpy where passing in an a list of ints causes
 the inver code to break.


Revision 4930 - Directory Listing
Modified Mon May 12 01:56:16 2014 UTC (3 years, 1 month ago) by caltinay
a few constness fixes in abstract and pasowrap SystemMatrix.


Revision 4929 - Directory Listing
Modified Mon May 5 06:20:20 2014 UTC (3 years, 1 month ago) by caltinay
a few non-invasive const fixes in AbstractSystemMatrix.


Revision 4928 - Directory Listing
Modified Mon May 5 03:02:04 2014 UTC (3 years, 1 month ago) by caltinay
fixed a very bad doc string in abstract class.


Revision 4927 - Directory Listing
Modified Fri May 2 02:47:44 2014 UTC (3 years, 1 month ago) by caltinay
Removed the remaining (2) bashism's in run-escript so bash is no longer required.


Revision 4926 - Directory Listing
Modified Thu May 1 05:29:12 2014 UTC (3 years, 1 month ago) by caltinay
trying to make centos happy.


Revision 4920 - Directory Listing
Modified Wed Apr 30 10:17:05 2014 UTC (3 years, 1 month ago) by caltinay
Fixes #253 (unused var in weipa)


Revision 4918 - Directory Listing
Modified Wed Apr 30 06:20:47 2014 UTC (3 years, 1 month ago) by caltinay
instructions for FreeBSD 10.0


Revision 4917 - Directory Listing
Modified Wed Apr 30 05:58:08 2014 UTC (3 years, 1 month ago) by caltinay
export LD_PRELOAD for tests.
added freebsd 10.0 options file.


Revision 4916 - Directory Listing
Modified Wed Apr 30 05:30:36 2014 UTC (3 years, 1 month ago) by sshaw
updating deb changelog

Revision 4915 - Directory Listing
Modified Wed Apr 30 05:29:23 2014 UTC (3 years, 1 month ago) by jfenwick
Fixes for macports

Revision 4914 - Directory Listing
Modified Wed Apr 30 04:58:45 2014 UTC (3 years, 1 month ago) by sshaw
removing spare 'as'


Revision 4913 - Directory Listing
Modified Wed Apr 30 04:57:21 2014 UTC (3 years, 1 month ago) by jfenwick
Reorder homebrew install

Revision 4912 - Directory Listing
Modified Wed Apr 30 04:57:01 2014 UTC (3 years, 1 month ago) by jduplessis
update to comments and fixing of docstring


Revision 4911 - Directory Listing
Modified Wed Apr 30 04:43:23 2014 UTC (3 years, 1 month ago) by jfenwick
fix unused var

Revision 4910 - Directory Listing
Modified Wed Apr 30 02:21:59 2014 UTC (3 years, 1 month ago) by jduplessis
fix docstring error


Revision 4909 - Directory Listing
Modified Wed Apr 30 01:20:22 2014 UTC (3 years, 1 month ago) by caltinay
Fixed Wunused-functions picked up by g++ 4.9


Revision 4908 - Directory Listing
Modified Wed Apr 30 00:24:38 2014 UTC (3 years, 1 month ago) by sshaw
removing runmodel from /bin given it doesn't have x-permissions

Revision 4907 - Directory Listing
Modified Tue Apr 29 12:58:43 2014 UTC (3 years, 1 month ago) by jduplessis
fix docstring indentation isssue for accousticwaveform


Revision 4906 - Directory Listing
Modified Tue Apr 29 05:27:34 2014 UTC (3 years, 1 month ago) by sshaw
restoring lost changes

Revision 4905 - Directory Listing
Modified Tue Apr 29 05:16:13 2014 UTC (3 years, 1 month ago) by sshaw
updated install doc


Revision 4904 - Directory Listing
Modified Tue Apr 29 04:40:30 2014 UTC (3 years, 1 month ago) by jduplessis
removing test print


Revision 4903 - Directory Listing
Modified Tue Apr 29 04:12:59 2014 UTC (3 years, 1 month ago) by jduplessis
updates for centos 6.5 install instructions


Revision 4902 - Directory Listing
Modified Tue Apr 29 04:07:28 2014 UTC (3 years, 1 month ago) by jduplessis
add centos 6.5 scons option file.

Revision 4901 - Directory Listing
Modified Tue Apr 29 03:55:00 2014 UTC (3 years, 1 month ago) by jfenwick
Updated info about macos commandline tools to note existance of xcodebuild command.


Revision 4900 - Directory Listing
Modified Tue Apr 29 01:44:02 2014 UTC (3 years, 1 month ago) by jduplessis
update sympy version check


Revision 4899 - Directory Listing
Modified Tue Apr 29 01:42:23 2014 UTC (3 years, 1 month ago) by jduplessis
sympy version check


Revision 4898 - Directory Listing
Modified Tue Apr 29 01:03:58 2014 UTC (3 years, 1 month ago) by jduplessis
sympy version check


Revision 4897 - Directory Listing
Modified Tue Apr 29 00:43:58 2014 UTC (3 years, 1 month ago) by jduplessis
sympy version check


Revision 4896 - Directory Listing
Modified Tue Apr 29 00:35:22 2014 UTC (3 years, 1 month ago) by jfenwick
Added missing backslash
Corrected spelling mistake


Revision 4895 - Directory Listing
Modified Tue Apr 29 00:21:43 2014 UTC (3 years, 1 month ago) by sshaw
affected tests now skipped if pyproj not installed

Revision 4894 - Directory Listing
Modified Mon Apr 28 04:28:28 2014 UTC (3 years, 1 month ago) by sshaw
adding options for fedora 20, only changes boost_python-mt for now

Revision 4893 - Directory Listing
Modified Mon Apr 28 04:03:41 2014 UTC (3 years, 2 months ago) by caltinay
typo


Revision 4892 - Directory Listing
Modified Mon Apr 28 03:30:29 2014 UTC (3 years, 2 months ago) by caltinay
scaled down grav_netcdf test...


Revision 4891 - Directory Listing
Modified Mon Apr 28 03:20:38 2014 UTC (3 years, 2 months ago) by caltinay
some changes to user guide.


Revision 4890 - Directory Listing
Modified Mon Apr 28 01:24:21 2014 UTC (3 years, 2 months ago) by jduplessis
added suggestion to copy options file from os directory.


Revision 4889 - Directory Listing
Modified Mon Apr 28 01:17:41 2014 UTC (3 years, 2 months ago) by jduplessis
Updated warning message when no options file is provided


Revision 4888 - Directory Listing
Modified Mon Apr 28 00:52:20 2014 UTC (3 years, 2 months ago) by jfenwick
Removing manual pagebreaks

Revision 4887 - Directory Listing
Modified Mon Apr 28 00:34:35 2014 UTC (3 years, 2 months ago) by jduplessis
Minor updates


Revision 4886 - Directory Listing
Modified Sun Apr 27 13:12:23 2014 UTC (3 years, 2 months ago) by jduplessis
rewording and checking


Revision 4885 - Directory Listing
Modified Sun Apr 27 11:48:36 2014 UTC (3 years, 2 months ago) by jduplessis
Small changes


Revision 4884 - Directory Listing
Modified Thu Apr 24 04:47:39 2014 UTC (3 years, 2 months ago) by jduplessis
this file is added so that we can import Symbolic by doing:
    import esys.escript.symbolic as symb instead of 
    import esys.escriptcore.symbolic as symb

the one line containined in the file is on line five for reasons prettiness



Revision 4883 - Directory Listing
Modified Thu Apr 24 00:00:33 2014 UTC (3 years, 2 months ago) by jfenwick
Updated changes list and sorted dev lists


Revision 4882 - Directory Listing
Modified Wed Apr 23 14:54:26 2014 UTC (3 years, 2 months ago) by jduplessis
fixing small errors


Revision 4881 - Directory Listing
Modified Wed Apr 23 14:20:28 2014 UTC (3 years, 2 months ago) by jduplessis
grammar, spelling and formating changes.


Revision 4880 - Directory Listing
Modified Wed Apr 23 06:10:16 2014 UTC (3 years, 2 months ago) by jduplessis
added sympy to bib and making small grammar, spelling and style changes.


Revision 4879 - Directory Listing
Modified Wed Apr 23 00:50:36 2014 UTC (3 years, 2 months ago) by jduplessis
symbolic part of user guide nearly complete


Revision 4878 - Directory Listing
Modified Wed Apr 23 00:49:10 2014 UTC (3 years, 2 months ago) by jduplessis
adding figures for symbolic part of user guide.


Revision 4877 - Directory Listing
Modified Tue Apr 22 07:24:32 2014 UTC (3 years, 2 months ago) by caltinay
new intel cc,mkl & mpi on savanna.


Revision 4876 - Directory Listing
Modified Tue Apr 22 05:43:36 2014 UTC (3 years, 2 months ago) by sshaw
fixing package requirements for ubuntu trusty packages

Revision 4875 - Directory Listing
Modified Thu Apr 17 06:14:54 2014 UTC (3 years, 2 months ago) by jfenwick
Updated changelog

Revision 4874 - Directory Listing
Modified Thu Apr 17 01:13:10 2014 UTC (3 years, 2 months ago) by sshaw
fixed ripley dirac test for multiple ranks and added protections against MPI causing problems due to premature exits by some ranks

Revision 4873 - Directory Listing
Modified Wed Apr 16 06:38:51 2014 UTC (3 years, 2 months ago) by caltinay
whitespace only changes.


Revision 4872 - Directory Listing
Modified Wed Apr 16 06:08:06 2014 UTC (3 years, 2 months ago) by sshaw
adding dirac point interpolation tests for ripley, all ranks will be used in subdividing each axis in turn

Revision 4871 - Directory Listing
Modified Wed Apr 16 05:28:27 2014 UTC (3 years, 2 months ago) by jduplessis
changed symconsts to symconsts to fit the rest of escript 


Revision 4870 - Directory Listing
Modified Mon Apr 14 10:50:41 2014 UTC (3 years, 2 months ago) by caltinay
Q: ...so what does this papi flag do?
A: darn, you got me.
[now it prints errors with the papi version shipped with debian, hooray]


Revision 4869 - Directory Listing
Modified Mon Apr 14 10:39:22 2014 UTC (3 years, 2 months ago) by caltinay
all of paso now lives in its own namespace.


Revision 4868 - Directory Listing
Modified Sat Apr 12 01:50:15 2014 UTC (3 years, 2 months ago) by caltinay
don't report an error when there isn't one.....


Revision 4867 - Directory Listing
Modified Fri Apr 11 12:29:49 2014 UTC (3 years, 2 months ago) by caltinay
paso: starting to polish


Revision 4866 - Directory Listing
Modified Fri Apr 11 03:28:35 2014 UTC (3 years, 2 months ago) by jfenwick
Remove reference to epydoc documentation from doxygen (since our debian doc package uses sphinx).


Revision 4865 - Directory Listing
Modified Fri Apr 11 02:38:11 2014 UTC (3 years, 2 months ago) by sshaw
bringing doxygen reported version number up to date

Revision 4864 - Directory Listing
Modified Fri Apr 11 02:04:18 2014 UTC (3 years, 2 months ago) by caltinay
fixing mkl build.


Revision 4863 - Directory Listing
Modified Thu Apr 10 06:24:55 2014 UTC (3 years, 2 months ago) by caltinay
cleansing


Revision 4862 - Directory Listing
Modified Thu Apr 10 05:35:56 2014 UTC (3 years, 2 months ago) by sshaw
removing leftover debug prints

Revision 4861 - Directory Listing
Modified Thu Apr 10 05:17:47 2014 UTC (3 years, 2 months ago) by sshaw
added exception for domain sizes that cause integer overflows

Revision 4860 - Directory Listing
Modified Thu Apr 10 04:08:42 2014 UTC (3 years, 2 months ago) by sshaw
wrapping resize exceptions for overly large domains (previous message to user was: 'RuntimeError: vector::_M_fill_insert')

Revision 4859 - Directory Listing
Modified Thu Apr 10 00:23:29 2014 UTC (3 years, 2 months ago) by jfenwick
Avoid division by zero


Revision 4858 - Directory Listing
Modified Wed Apr 9 23:34:17 2014 UTC (3 years, 2 months ago) by sshaw
skipping multirank segywriter tests now that multirank writes throw exceptions

Revision 4857 - Directory Listing
Modified Wed Apr 9 06:54:59 2014 UTC (3 years, 2 months ago) by jduplessis
modified atoms code that when type is set to escript.Symbol, sympy.symbol get added to the type list. This is because escript.symbols are represented by sympy symbols in the _arr list


Revision 4856 - Directory Listing
Modified Wed Apr 9 06:46:55 2014 UTC (3 years, 2 months ago) by caltinay
some mopping in paso


Revision 4855 - Directory Listing
Modified Wed Apr 9 06:19:59 2014 UTC (3 years, 2 months ago) by sshaw
removing leftover python solveroptions

Revision 4854 - Directory Listing
Modified Wed Apr 9 06:17:09 2014 UTC (3 years, 2 months ago) by gross
FWI is running

Revision 4853 - Directory Listing
Modified Wed Apr 9 05:41:57 2014 UTC (3 years, 2 months ago) by jfenwick
Added import division and changed a few / to //


Revision 4852 - Directory Listing
Modified Wed Apr 9 03:58:08 2014 UTC (3 years, 2 months ago) by caltinay
paso util sweep


Revision 4851 - Directory Listing
Modified Wed Apr 9 03:30:36 2014 UTC (3 years, 2 months ago) by sshaw
added exceptions to ripley for more informative deaths to negative element counts

Revision 4850 - Directory Listing
Modified Wed Apr 9 02:26:22 2014 UTC (3 years, 2 months ago) by sshaw
adding exception for multi-rank segy write instead of failing to write correctly and reporting success

Revision 4849 - Directory Listing
Modified Wed Apr 9 02:14:58 2014 UTC (3 years, 2 months ago) by caltinay
More vacuuming.


Revision 4848 - Directory Listing
Modified Wed Apr 9 00:26:32 2014 UTC (3 years, 2 months ago) by jfenwick
lots of future print_function

Revision 4847 - Directory Listing
Modified Wed Apr 9 00:11:55 2014 UTC (3 years, 2 months ago) by sshaw
fixed awkard integer division in LinearMapping (py3 unaffected)

Revision 4846 - Directory Listing
Modified Tue Apr 8 23:55:38 2014 UTC (3 years, 2 months ago) by caltinay
paso::Options.


Revision 4845 - Directory Listing
Modified Tue Apr 8 11:35:27 2014 UTC (3 years, 2 months ago) by caltinay
I fink I broke it - now I thixed it.


Revision 4844 - Directory Listing
Modified Tue Apr 8 07:56:52 2014 UTC (3 years, 2 months ago) by jfenwick
Removing MPIInfo from pythonMPI

Revision 4843 - Directory Listing
Modified Tue Apr 8 05:32:07 2014 UTC (3 years, 2 months ago) by caltinay
checkpointing paso::Preconditioner.


Revision 4842 - Directory Listing
Modified Tue Apr 8 04:50:05 2014 UTC (3 years, 2 months ago) by jduplessis
Removing variational problem as it will not be part of the release


Revision 4841 - Directory Listing
Modified Tue Apr 8 03:49:18 2014 UTC (3 years, 2 months ago) by jfenwick
keeping older compilers happy

Revision 4840 - Directory Listing
Modified Tue Apr 8 03:24:47 2014 UTC (3 years, 2 months ago) by jfenwick
scons options for trusty

Revision 4839 - Directory Listing
Modified Tue Apr 8 03:14:23 2014 UTC (3 years, 2 months ago) by jfenwick
Adding initial support for ubuntu trusty

Revision 4838 - Directory Listing
Modified Mon Apr 7 10:16:21 2014 UTC (3 years, 2 months ago) by caltinay
Fixing non-mpi build.


Revision 4837 - Directory Listing
Modified Mon Apr 7 05:59:24 2014 UTC (3 years, 2 months ago) by jduplessis
added test for evalf


Revision 4836 - Directory Listing
Modified Mon Apr 7 05:51:55 2014 UTC (3 years, 2 months ago) by caltinay
"Some" SystemMatrix clean up.....


Revision 4835 - Directory Listing
Modified Mon Apr 7 04:29:20 2014 UTC (3 years, 2 months ago) by jfenwick
removing unused MIS


Revision 4834 - Directory Listing
Modified Mon Apr 7 00:32:14 2014 UTC (3 years, 2 months ago) by jfenwick
Added Jaco


Revision 4833 - Directory Listing
Modified Sun Apr 6 23:30:34 2014 UTC (3 years, 2 months ago) by jfenwick
Adding missing names.



Revision 4832 - Directory Listing
Modified Fri Apr 4 05:03:45 2014 UTC (3 years, 2 months ago) by sshaw
some incredibly long lines are now much, much nicer to read/wrap

Revision 4831 - Directory Listing
Modified Fri Apr 4 02:42:52 2014 UTC (3 years, 2 months ago) by caltinay
fixing MKL compile.


Revision 4830 - Directory Listing
Modified Thu Apr 3 04:45:06 2014 UTC (3 years, 2 months ago) by caltinay
Removed obsolete file, reverted verbosity of test and a bit more cleanup.


Revision 4829 - Directory Listing
Modified Thu Apr 3 04:02:53 2014 UTC (3 years, 2 months ago) by caltinay
checkpointing some SparseMatrix cleanup.


Revision 4828 - Directory Listing
Modified Wed Apr 2 07:01:38 2014 UTC (3 years, 2 months ago) by sshaw
more tightly constrained checks on types and lengths of dirac points and tags in ripley python constructors

Revision 4827 - Directory Listing
Modified Wed Apr 2 07:00:15 2014 UTC (3 years, 2 months ago) by sshaw
dropping out of domain dirac points for ripley Brick as well

Revision 4826 - Directory Listing
Modified Wed Apr 2 03:54:18 2014 UTC (3 years, 2 months ago) by sshaw
changing ripley to drop dirac points outside domain rather than try to map them, matches finley behaviour

Revision 4825 - Directory Listing
Modified Wed Apr 2 03:53:23 2014 UTC (3 years, 2 months ago) by jfenwick
Addresses issue 241

Revision 4824 - Directory Listing
Modified Tue Apr 1 06:40:19 2014 UTC (3 years, 2 months ago) by sshaw
fixed sillyness with serial builds reporting as MPI

Revision 4823 - Directory Listing
Modified Tue Apr 1 05:46:07 2014 UTC (3 years, 2 months ago) by sshaw
SolverBuddy documentation changes from old python docstrings to doxygen format

Revision 4822 - Directory Listing
Modified Tue Apr 1 05:05:45 2014 UTC (3 years, 2 months ago) by sshaw
now with all required files at no extra cost

Revision 4821 - Directory Listing
Modified Tue Apr 1 04:58:33 2014 UTC (3 years, 2 months ago) by sshaw
moved SolverOptions to c++, split into SolverOptions for the options and SolverBuddy as the state as a precursor to per-pde solving... does break some use cases (e.g. pde.getSolverOptions().DIRECT will now fail, new value access is with SolverOptions.DIRECT), examples and documentation updated to match

Revision 4820 - Directory Listing
Modified Tue Apr 1 04:55:49 2014 UTC (3 years, 2 months ago) by sshaw
allowing for larger amounts of variable tracking with debug=true (mostly for escriptcpp.cpp)

Revision 4819 - Directory Listing
Modified Tue Apr 1 03:50:23 2014 UTC (3 years, 2 months ago) by caltinay
Pattern shared ptrs


Revision 4818 - Directory Listing
Modified Mon Mar 31 00:16:20 2014 UTC (3 years, 2 months ago) by caltinay
SystemMatrixPattern shptr


Revision 4817 - Directory Listing
Modified Fri Mar 28 08:04:09 2014 UTC (3 years, 3 months ago) by caltinay
Coupler/Connector shared ptrs.


Revision 4816 - Directory Listing
Modified Fri Mar 28 06:16:02 2014 UTC (3 years, 3 months ago) by caltinay
paso::SharedComponents now header-only and shared ptr managed.


Revision 4815 - Directory Listing
Modified Fri Mar 28 05:25:56 2014 UTC (3 years, 3 months ago) by sshaw
replacing awful config file debugthing

Revision 4814 - Directory Listing
Modified Fri Mar 28 04:31:02 2014 UTC (3 years, 3 months ago) by caltinay
paso::Distribution instances are now managed by a boost::shared_ptr, methods
are all inline.


Revision 4811 - Directory Listing
Modified Thu Mar 27 07:00:46 2014 UTC (3 years, 3 months ago) by sshaw
moving away from shared pointers in domain components

Revision 4810 - Directory Listing
Modified Thu Mar 27 07:00:30 2014 UTC (3 years, 3 months ago) by caltinay
Removed some obsolete checkPtr's. More to come...


Revision 4809 - Directory Listing
Modified Thu Mar 27 05:52:41 2014 UTC (3 years, 3 months ago) by caltinay
Removed code duplication and moved IndexList to esysUtils header only.
Renamed AML.cpp which is old,unused code.


Revision 4807 - Directory Listing
Modified Thu Mar 27 04:49:38 2014 UTC (3 years, 3 months ago) by caltinay
2 fixes to dirac points which fixes #240.


Revision 4806 - Directory Listing
Modified Thu Mar 27 03:03:13 2014 UTC (3 years, 3 months ago) by sshaw
fixed fetch error in type collation for lame assembler

Revision 4805 - Directory Listing
Modified Thu Mar 27 01:31:59 2014 UTC (3 years, 3 months ago) by sshaw
changing 2D wave assembler to use shared domain pointer

Revision 4803 - Directory Listing
Modified Wed Mar 26 06:52:28 2014 UTC (3 years, 3 months ago) by caltinay
Removed obsolete wrappers for malloc and friends.
Paso_Pattern -> paso::Pattern


Revision 4801 - Directory Listing
Modified Wed Mar 26 03:26:58 2014 UTC (3 years, 3 months ago) by caltinay
paso::Coupler and paso::Connector.


Revision 4800 - Directory Listing
Modified Wed Mar 26 01:50:04 2014 UTC (3 years, 3 months ago) by caltinay
paso::SystemMatrixPattern


Revision 4799 - Directory Listing
Modified Wed Mar 26 00:37:59 2014 UTC (3 years, 3 months ago) by sshaw
storing the code generators for the relevant chunks of the lame assembler

Revision 4798 - Directory Listing
Modified Tue Mar 25 22:08:30 2014 UTC (3 years, 3 months ago) by caltinay
added missing const.


Revision 4797 - Directory Listing
Modified Mon Mar 24 05:42:42 2014 UTC (3 years, 3 months ago) by caltinay
put SparseMatrix into paso namespace, accompanied by minor code cleanup.


Revision 4795 - Directory Listing
Modified Mon Mar 24 01:50:32 2014 UTC (3 years, 3 months ago) by caltinay
code cleanup of paso::SparseMatrix_MatrixVector and variants.
Mostly a no-op.


Revision 4794 - Directory Listing
Modified Mon Mar 24 01:01:30 2014 UTC (3 years, 3 months ago) by jduplessis
adding symbolic to user guide, work in progress


Revision 4793 - Directory Listing
Modified Fri Mar 21 06:44:26 2014 UTC (3 years, 3 months ago) by jduplessis
changed 'dict_keys' object to list so that it can be indexed

Revision 4792 - Directory Listing
Modified Fri Mar 21 05:06:11 2014 UTC (3 years, 3 months ago) by jfenwick
make escriptcore/ visible

Revision 4791 - Directory Listing
Modified Fri Mar 21 03:32:56 2014 UTC (3 years, 3 months ago) by jduplessis
changed has_key to in for python 3

Revision 4789 - Directory Listing
Modified Fri Mar 21 00:30:32 2014 UTC (3 years, 3 months ago) by sshaw
changing more awkward logic into more obvious (and correct, though i doubt a negative length ever happens) logic

Revision 4788 - Directory Listing
Modified Fri Mar 21 00:11:09 2014 UTC (3 years, 3 months ago) by sshaw
fixed a broken numerical comparison

Revision 4787 - Directory Listing
Modified Fri Mar 21 00:08:15 2014 UTC (3 years, 3 months ago) by sshaw
changed header guard definition to match header guard check

Revision 4786 - Directory Listing
Modified Thu Mar 20 23:53:44 2014 UTC (3 years, 3 months ago) by sshaw
fixed silly naming issue

Revision 4783 - Directory Listing
Modified Thu Mar 20 06:23:23 2014 UTC (3 years, 3 months ago) by sshaw
refactored linearPDE tests (removing repetition)

Revision 4782 - Directory Listing
Modified Thu Mar 20 05:16:16 2014 UTC (3 years, 3 months ago) by sshaw
cleaned up and simplified run_seismic tests, including specific checking for obspy not being installed

Revision 4781 - Directory Listing
Modified Thu Mar 20 04:57:07 2014 UTC (3 years, 3 months ago) by jduplessis
added test for preservation of data substitutions

Revision 4780 - Directory Listing
Modified Thu Mar 20 03:19:54 2014 UTC (3 years, 3 months ago) by sshaw
fixing a race condition in file tests

Revision 4779 - Directory Listing
Modified Thu Mar 20 01:52:49 2014 UTC (3 years, 3 months ago) by jfenwick
Temporarily adjusting magic numbers

Revision 4778 - Directory Listing
Modified Thu Mar 20 00:41:58 2014 UTC (3 years, 3 months ago) by sshaw
python3ified tests using deprecated test methods ( #89 and #106 ), added run_seismic into downunder tests (with skips if obspy/segywriters fail to write)

Revision 4777 - Directory Listing
Modified Wed Mar 19 23:52:36 2014 UTC (3 years, 3 months ago) by sshaw
replacing xrange with range for python3 compatibility, refs #106

Revision 4776 - Directory Listing
Modified Wed Mar 19 23:31:00 2014 UTC (3 years, 3 months ago) by caltinay
Removed some superfluous checks and typos.


Revision 4775 - Directory Listing
Modified Wed Mar 19 23:12:53 2014 UTC (3 years, 3 months ago) by caltinay
Moved matrix format exception further up the stack which fixes #109.
Also, removed default defines CORE_ID1 and BLOCKTIMER, added the former to
savanna's options.


Revision 4772 - Directory Listing
Modified Wed Mar 19 04:28:53 2014 UTC (3 years, 3 months ago) by sshaw
removing ridiculous remaining return

Revision 4771 - Directory Listing
Modified Wed Mar 19 04:22:37 2014 UTC (3 years, 3 months ago) by sshaw
fixed multiple ranks trying to unlink tempfiles

Revision 4770 - Directory Listing
Modified Wed Mar 19 03:48:43 2014 UTC (3 years, 3 months ago) by sshaw
relevant tests skipped if not built with USE_BOOSTIO

Revision 4769 - Directory Listing
Modified Wed Mar 19 03:43:52 2014 UTC (3 years, 3 months ago) by sshaw
added missing ifdefs for library presence

Revision 4768 - Directory Listing
Modified Wed Mar 19 02:51:33 2014 UTC (3 years, 3 months ago) by jduplessis
Removed commented for loops


Revision 4767 - Directory Listing
Modified Wed Mar 19 02:48:33 2014 UTC (3 years, 3 months ago) by jduplessis
Major issues with subs and data objects have been rectified. subs was also not working properly for symbol to symbol substitutions this has been rectified.


Revision 4766 - Directory Listing
Modified Wed Mar 19 00:57:21 2014 UTC (3 years, 3 months ago) by sshaw
allowed custom assemblers a value tolerance in tests (for case of 0 to 1 in objects, tolerance of 1e-8)

Revision 4765 - Directory Listing
Modified Wed Mar 19 00:17:16 2014 UTC (3 years, 3 months ago) by sshaw
added ripley rectangle reading from compressed files, added unit tests for binaryGrid reads and writes (only single ranks for compressed thus far) (#104)

Revision 4764 - Directory Listing
Modified Tue Mar 18 15:58:21 2014 UTC (3 years, 3 months ago) by gross
mapping test fixed

Revision 4761 - Directory Listing
Modified Tue Mar 18 00:25:55 2014 UTC (3 years, 3 months ago) by sshaw
fixed partially overridden class warnings with intel compiler

Revision 4760 - Directory Listing
Modified Mon Mar 17 23:48:37 2014 UTC (3 years, 3 months ago) by sshaw
moved functionspace type collation from RipleyDomain into custom assemblers, refs #102

Revision 4759 - Directory Listing
Modified Mon Mar 17 07:52:26 2014 UTC (3 years, 3 months ago) by jfenwick
Throw TypeError on any attempt to use relational ops on Data, FunctionSpace and Domain.  Also fixes a type error in run_mappings.py but the test still fails.

Revision 4758 - Directory Listing
Modified Mon Mar 17 05:00:27 2014 UTC (3 years, 3 months ago) by sshaw
fixed classname typo for AcousticVelocityMapping, added exceptions for ordered comparisons with Data objects from python (#107)

Revision 4755 - Directory Listing
Modified Mon Mar 17 02:58:52 2014 UTC (3 years, 3 months ago) by sshaw
added conflict test for ripley Brick

Revision 4754 - Directory Listing
Modified Mon Mar 17 02:51:12 2014 UTC (3 years, 3 months ago) by sshaw
now with 0% missing files!

Revision 4753 - Directory Listing
Modified Mon Mar 17 02:39:44 2014 UTC (3 years, 3 months ago) by sshaw
added exceptions for conflicting assembler types, added tests for lame assemblers

Revision 4751 - Directory Listing
Modified Fri Mar 14 06:49:06 2014 UTC (3 years, 3 months ago) by sshaw
completed LameAssemblers

Revision 4749 - Directory Listing
Modified Fri Mar 14 03:05:07 2014 UTC (3 years, 3 months ago) by sshaw
making inversioncostfunctions python3 compatible

Revision 4748 - Directory Listing
Modified Fri Mar 14 00:30:51 2014 UTC (3 years, 3 months ago) by sshaw
adjusted InversionCostFunction tests to run on arbitrary numbers of ranks

Revision 4744 - Directory Listing
Modified Wed Mar 12 21:30:10 2014 UTC (3 years, 3 months ago) by gross
first version of a FWI

Revision 4743 - Directory Listing
Modified Wed Mar 12 21:09:20 2014 UTC (3 years, 3 months ago) by gross
mapping for FWI added

Revision 4742 - Directory Listing
Modified Wed Mar 12 07:21:24 2014 UTC (3 years, 3 months ago) by jduplessis
updated setitem and getitem to preserve data substitutions


Revision 4741 - Directory Listing
Modified Wed Mar 12 03:31:10 2014 UTC (3 years, 3 months ago) by jfenwick
Fix scoping because my compiler complained. g++4.8 thing?

Revision 4740 - Directory Listing
Modified Wed Mar 12 03:26:13 2014 UTC (3 years, 3 months ago) by sshaw
exporting compression support to buildvars

Revision 4739 - Directory Listing
Modified Wed Mar 12 03:25:32 2014 UTC (3 years, 3 months ago) by sshaw
fixing test file filename mismatch

Revision 4738 - Directory Listing
Modified Wed Mar 12 01:32:36 2014 UTC (3 years, 3 months ago) by sshaw
adding support for reading binary grids from gzip compressed binary files, ripley brick only so far

Revision 4737 - Directory Listing
Modified Tue Mar 11 13:23:21 2014 UTC (3 years, 3 months ago) by gross
missing file

Revision 4735 - Directory Listing
Modified Mon Mar 10 07:44:58 2014 UTC (3 years, 3 months ago) by sshaw
fixing/completing 2D lame assembler


Revision 4733 - Directory Listing
Modified Mon Mar 10 05:57:11 2014 UTC (3 years, 3 months ago) by jduplessis
added a check to only get data substitutions on symbols


Revision 4729 - Directory Listing
Modified Sat Mar 8 00:56:37 2014 UTC (3 years, 3 months ago) by gross
a more general for of the inversioncostfunction has required for waveform inversin

Revision 4728 - Directory Listing
Modified Fri Mar 7 05:29:06 2014 UTC (3 years, 3 months ago) by jduplessis
renamed

Revision 4727 - Directory Listing
Modified Fri Mar 7 05:28:12 2014 UTC (3 years, 3 months ago) by jduplessis
added an optional evalf input to the evaluator, without this constants such as pi etc wont get evaluated. and renamed constants symconstants


Revision 4726 - Directory Listing
Modified Fri Mar 7 00:23:44 2014 UTC (3 years, 3 months ago) by sshaw
Added a success/fail line below config in build process ( redmine #26 )

Revision 4723 - Directory Listing
Modified Wed Mar 5 05:40:25 2014 UTC (3 years, 3 months ago) by jduplessis
fixed presenservation of data objects(data substitutions) when subs is called on a symbol



Revision 4722 - Directory Listing
Modified Wed Mar 5 05:29:25 2014 UTC (3 years, 3 months ago) by sshaw
vastly decreased ripley domain setup time under MPI (approximately from O(n*m) to O(n+m), n being shared nodes, m being the rank DOF)

Revision 4721 - Directory Listing
Modified Fri Feb 28 03:51:07 2014 UTC (3 years, 3 months ago) by jfenwick
Fixing strange casts.
Removed old methods.


Revision 4720 - Directory Listing
Modified Fri Feb 28 01:38:09 2014 UTC (3 years, 3 months ago) by sshaw
ripley now tested with lame, helmholtz and nolumping linear PDEs

Revision 4719 - Directory Listing
Modified Fri Feb 28 00:27:29 2014 UTC (3 years, 3 months ago) by jfenwick
Modify run_forward test to account for small negative results.

Revision 4718 - Directory Listing
Modified Thu Feb 27 23:43:12 2014 UTC (3 years, 3 months ago) by sshaw
Added a missed include guard


Revision 4717 - Directory Listing
Modified Thu Feb 27 12:30:04 2014 UTC (3 years, 3 months ago) by jfenwick
Fix copy error from 3d down to 2d.



Revision 4716 - Directory Listing
Modified Thu Feb 27 11:02:55 2014 UTC (3 years, 3 months ago) by jfenwick
Fixed some bad indenting.
Skip non-linear tests if sympy is not available.



Revision 4715 - Directory Listing
Modified Thu Feb 27 07:57:45 2014 UTC (3 years, 3 months ago) by jfenwick
Fixing print statement

Revision 4714 - Directory Listing
Modified Thu Feb 27 05:04:15 2014 UTC (3 years, 3 months ago) by sshaw
made non-linearPDE tests on ripley work with any number of ranks

Revision 4713 - Directory Listing
Modified Thu Feb 27 02:00:15 2014 UTC (3 years, 3 months ago) by jfenwick
Added a temporay fix to get some of the unit tests passing again.
This mechanism will be removed before the release so don't get used to it.

Revision 4712 - Directory Listing
Modified Wed Feb 26 04:08:41 2014 UTC (3 years, 4 months ago) by sshaw
adding skeleton of fast Lame assemblers
adjusted automatic ripley domain subdivision ( should solve issue #94 )
more tab->space conversions


Revision 4711 - Directory Listing
Modified Tue Feb 25 00:04:04 2014 UTC (3 years, 4 months ago) by jfenwick
Another try at this test.



Revision 4710 - Directory Listing
Modified Mon Feb 24 03:41:06 2014 UTC (3 years, 4 months ago) by jfenwick
Fixing not enough elements for small numbers of ranks in test

Revision 4709 - Directory Listing
Modified Mon Feb 24 01:31:00 2014 UTC (3 years, 4 months ago) by jfenwick
Failed to take ripley padding into account when constructing tests.



Revision 4708 - Directory Listing
Modified Fri Feb 21 03:08:05 2014 UTC (3 years, 4 months ago) by jduplessis
Removed rotation from ydirection test


Revision 4707 - Directory Listing
Modified Fri Feb 21 03:07:09 2014 UTC (3 years, 4 months ago) by jduplessis
Modified domain in tests


Revision 4706 - Directory Listing
Modified Fri Feb 21 02:39:58 2014 UTC (3 years, 4 months ago) by jfenwick
Some additional cleanup I missed


Revision 4705 - Directory Listing
Modified Fri Feb 21 02:36:15 2014 UTC (3 years, 4 months ago) by jfenwick
Set the randomfill back to generating randoms and updated doco to tell people how to use it.


Revision 4704 - Directory Listing
Modified Fri Feb 21 01:11:30 2014 UTC (3 years, 4 months ago) by jduplessis
added modification

double *F_p=NULL;
if(!p.F.isEmpty()) {
	p.F.requireWrite();
        F_p=p.F.getSampleDataRW(0);     
}

to all files such they will not operate on an empty F.

 


Revision 4703 - Directory Listing
Modified Fri Feb 21 00:55:31 2014 UTC (3 years, 4 months ago) by jfenwick
This version has been tested in some detail. It does not actually do randoms though (since that wrecks the testing).  In will do a commit soon which puts the randomness back

Revision 4702 - Directory Listing
Modified Thu Feb 20 06:36:00 2014 UTC (3 years, 4 months ago) by jduplessis
updated test_yDirection fixed a couple of small bugs


Revision 4701 - Directory Listing
Modified Thu Feb 20 06:32:12 2014 UTC (3 years, 4 months ago) by jduplessis
Put in a check to make sure F is not used when empty. This prevents an exception.


Revision 4700 - Directory Listing
Modified Thu Feb 20 03:57:17 2014 UTC (3 years, 4 months ago) by gross
some more work toward seismic data

Revision 4699 - Directory Listing
Modified Wed Feb 19 09:31:45 2014 UTC (3 years, 4 months ago) by jduplessis
Added test when adding incorrect Dim And Shape, for tryin to set Unknown Perameter and a test to make sure the definition of y is correct




Revision 4698 - Directory Listing
Modified Wed Feb 19 08:10:12 2014 UTC (3 years, 4 months ago) by gross
data sources support tags now

Revision 4697 - Directory Listing
Modified Wed Feb 19 08:03:56 2014 UTC (3 years, 4 months ago) by gross
data sources support tags now

Revision 4696 - Directory Listing
Modified Wed Feb 19 07:29:50 2014 UTC (3 years, 4 months ago) by jfenwick
Correcting python libname for sage.
Fixing bug where the number of values in the shape was not considered for buffer and message size.


Revision 4695 - Directory Listing
Modified Wed Feb 19 06:58:41 2014 UTC (3 years, 4 months ago) by sshaw
added warning output when saving as silo but not built with silo support (redmine #87 )

Revision 4694 - Directory Listing
Modified Wed Feb 19 06:25:55 2014 UTC (3 years, 4 months ago) by jduplessis
fixed __getitem__ such that the symbol it return will have the same dimentionality as its parent symbol


Revision 4693 - Directory Listing
Modified Wed Feb 19 06:04:28 2014 UTC (3 years, 4 months ago) by sshaw
adding HTI support to 3D wave assembler

Revision 4692 - Directory Listing
Modified Wed Feb 19 05:26:55 2014 UTC (3 years, 4 months ago) by sshaw
fixed duplication for 2D constant data in wave assembler

Revision 4691 - Directory Listing
Modified Wed Feb 19 05:23:17 2014 UTC (3 years, 4 months ago) by sshaw
added support for HTI waves to the fast wave assembler

Revision 4690 - Directory Listing
Modified Wed Feb 19 05:22:16 2014 UTC (3 years, 4 months ago) by sshaw
adjusting porcupine config to use MPI by default

Revision 4689 - Directory Listing
Modified Wed Feb 19 05:13:17 2014 UTC (3 years, 4 months ago) by jfenwick
Give the unit test enough room


Revision 4688 - Directory Listing
Modified Wed Feb 19 03:18:58 2014 UTC (3 years, 4 months ago) by gross
acoustic forward problem + testing add

Revision 4687 - Directory Listing
Modified Wed Feb 19 00:03:29 2014 UTC (3 years, 4 months ago) by jfenwick
Remove randomFill python method from ripley domains.
All random data objects (for all domain types) should be generated 
using esys.escript.RandomData()

The only filtered random we have is gaussian on ripley but
it is triggered by passing the tuple as the last arg of RandomData().

While the interface is a bit more complicated (in that you always need
 to pass in shape and functionspace) it does mean we have a 
common interface for all domains. 

Removed randomFill from DataExpanded.
The reasoning behind this is to force domains to call the util function
themselves and enforce whatever consistancy requirements they have.

Added version of blocktools to deal with 2D case in Ripley.
Use blocktools for the 2D transfers [This was cleaner than modifying the
previous implementation to deal with variable shaped points].

Note that under MPI, ripley can not generate random data (even unfiltered)
if any of its per rank dimensions is <4 elements on any side.

Unit tests for these calls are in but some extra checks still needed.




Revision 4686 - Directory Listing
Modified Tue Feb 18 06:04:13 2014 UTC (3 years, 4 months ago) by jduplessis
modified nonlinearPDE to be compatible with python 3.


Revision 4685 - Directory Listing
Modified Tue Feb 18 04:19:27 2014 UTC (3 years, 4 months ago) by jduplessis
Replaced python dictionary iteritems with item for python 3.0 compatibility


Revision 4684 - Directory Listing
Modified Tue Feb 18 01:17:02 2014 UTC (3 years, 4 months ago) by jduplessis
Removing Finley mesh import which was copied from run_linearPdeOnFinley... as it is not used.


Revision 4683 - Directory Listing
Modified Mon Feb 17 07:03:40 2014 UTC (3 years, 4 months ago) by jduplessis
adding nonlinearpde test for ripley.


Revision 4682 - Directory Listing
Modified Mon Feb 17 05:24:14 2014 UTC (3 years, 4 months ago) by jduplessis


Revision 4681 - Directory Listing
Modified Mon Feb 17 04:05:11 2014 UTC (3 years, 4 months ago) by jduplessis


Revision 4680 - Directory Listing
Modified Mon Feb 17 04:04:40 2014 UTC (3 years, 4 months ago) by jduplessis
changed name


Revision 4679 - Directory Listing
Modified Mon Feb 17 04:02:56 2014 UTC (3 years, 4 months ago) by jduplessis
Changed name


Revision 4678 - Directory Listing
Modified Mon Feb 17 03:35:08 2014 UTC (3 years, 4 months ago) by jduplessis
adding ripley test for nlpde


Revision 4677 - Directory Listing
Modified Mon Feb 17 02:49:59 2014 UTC (3 years, 4 months ago) by jduplessis
adding nlpde tests


Revision 4676 - Directory Listing
Modified Mon Feb 17 02:41:15 2014 UTC (3 years, 4 months ago) by jduplessis
Unit test for nonlinear pde. 
test that it can generate a solution without error and that the appropriate coefficients are generated when setValue is called. 



Revision 4675 - Directory Listing
Modified Mon Feb 17 01:07:12 2014 UTC (3 years, 4 months ago) by sshaw
expanded tab chars for consistentcy and removed trailing whitespace

Revision 4674 - Directory Listing
Modified Thu Feb 13 23:47:04 2014 UTC (3 years, 4 months ago) by jfenwick
Not using GNU only getopt arguments

Revision 4673 - Directory Listing
Modified Thu Feb 13 08:14:11 2014 UTC (3 years, 4 months ago) by jfenwick
Ammended install doco for OSX

Revision 4672 - Directory Listing
Modified Thu Feb 13 01:10:29 2014 UTC (3 years, 4 months ago) by sshaw
compacted older style C comparison structure

Revision 4671 - Directory Listing
Modified Thu Feb 13 00:18:10 2014 UTC (3 years, 4 months ago) by jfenwick
Fixed another comparator which wasn't strict


Revision 4670 - Directory Listing
Modified Wed Feb 12 08:24:31 2014 UTC (3 years, 4 months ago) by jfenwick
Correcting comparator function so it acts as < rather than <=

Revision 4669 - Directory Listing
Modified Tue Feb 11 06:10:27 2014 UTC (3 years, 4 months ago) by jfenwick
Replacing .eps figures in user guide with their pdf versions.
If you are creating new figures, then please don't use .eps



Revision 4668 - Directory Listing
Modified Tue Feb 11 03:44:10 2014 UTC (3 years, 4 months ago) by jfenwick
Improvements but still needs more validation


Revision 4667 - Directory Listing
Modified Tue Feb 11 00:47:26 2014 UTC (3 years, 4 months ago) by sshaw
adjusted launcher to run efficiently/properly on raijin

Revision 4666 - Directory Listing
Modified Mon Feb 10 03:33:51 2014 UTC (3 years, 4 months ago) by jduplessis
check in util no longer necassary due to wrappings in contants.py


Revision 4665 - Directory Listing
Modified Mon Feb 10 03:29:02 2014 UTC (3 years, 4 months ago) by caltinay
This should help running on raijin without damaging anything.


Revision 4664 - Directory Listing
Modified Mon Feb 10 01:57:11 2014 UTC (3 years, 4 months ago) by caltinay
Trying to make the shell on osx happy.


Revision 4663 - Directory Listing
Modified Mon Feb 10 00:48:49 2014 UTC (3 years, 4 months ago) by jduplessis
Adding wrapper for Symbolic constants such as pi
usage:
	symconsts.pi  ---> gives escript Symbol(sympy.pi)



Revision 4662 - Directory Listing
Modified Sun Feb 9 23:03:45 2014 UTC (3 years, 4 months ago) by caltinay
Cater for changed interface in sympy 0.7.2.
Also silenced a harmless warning.


Revision 4661 - Directory Listing
Modified Fri Feb 7 03:10:15 2014 UTC (3 years, 4 months ago) by sshaw
more informative exception for unsupported error message

Revision 4660 - Directory Listing
Modified Fri Feb 7 03:08:49 2014 UTC (3 years, 4 months ago) by sshaw
fixed dirac point->node mapping issues in ripley when using mpi

Revision 4659 - Directory Listing
Modified Fri Feb 7 00:13:47 2014 UTC (3 years, 4 months ago) by jduplessis
New solution to cos(sympy.pi). This solution help to keep sympy optional in escript and provides the desired functionality.


Revision 4658 - Directory Listing
Modified Thu Feb 6 13:28:56 2014 UTC (3 years, 4 months ago) by caltinay
This seems to fix #65 but is a bit scary.
netcdf and gdal (and others?) seem to return bytearrays instead of strings in
py3, which when fed back into a library function caused a segfault.
Not sure if I caught every case and whether this is actually a bug in the lib...


Revision 4657 - Directory Listing
Modified Thu Feb 6 06:12:20 2014 UTC (3 years, 4 months ago) by jfenwick
I changed some files.
Updated copyright notices, added GeoComp.




Revision 4656 - Directory Listing
Modified Thu Feb 6 05:12:01 2014 UTC (3 years, 4 months ago) by gross
removed unwanted table

Revision 4655 - Directory Listing
Modified Thu Feb 6 04:15:42 2014 UTC (3 years, 4 months ago) by jfenwick
Reverting r4654

Revision 4654 - Directory Listing
Modified Wed Feb 5 06:55:35 2014 UTC (3 years, 4 months ago) by jduplessis
Modified some of the util function so that they will operate with general sympy objects such as pi.

This is usefull when you want to do 

sin(pi) or cos(pi) for example 

where pi is a sympy object.



Revision 4653 - Directory Listing
Modified Wed Feb 5 05:20:41 2014 UTC (3 years, 4 months ago) by jfenwick
Made index chars unsigned to prevent warnings

Revision 4652 - Directory Listing
Modified Wed Feb 5 05:15:07 2014 UTC (3 years, 4 months ago) by jfenwick
Made index chars unsigned to prevent warnings

Revision 4651 - Directory Listing
Modified Wed Feb 5 05:00:34 2014 UTC (3 years, 4 months ago) by jfenwick
Fixed missing include

Revision 4650 - Directory Listing
Modified Wed Feb 5 04:16:01 2014 UTC (3 years, 4 months ago) by jfenwick
Fixed a spelling error and missing virtual (not sure that one matters).
Added _untested_ 3D gaussian smoothed random data



Revision 4649 - Directory Listing
Modified Wed Feb 5 02:09:21 2014 UTC (3 years, 4 months ago) by caltinay
Forgot something...


Revision 4648 - Directory Listing
Modified Wed Feb 5 02:03:08 2014 UTC (3 years, 4 months ago) by caltinay
Fix segfault reported in #57.


Revision 4647 - Directory Listing
Modified Mon Feb 3 03:29:43 2014 UTC (3 years, 4 months ago) by jduplessis
Commiting to make sure line 309 doesn't contain print len(u_syms)\n


Revision 4646 - Directory Listing
Modified Mon Feb 3 00:25:58 2014 UTC (3 years, 4 months ago) by gross
some extensions to synthetic_sonicHTI.py

Revision 4645 - Directory Listing
Modified Mon Feb 3 00:06:24 2014 UTC (3 years, 4 months ago) by sshaw
further optimisation of wave assemblers, added support for constant data

Revision 4644 - Directory Listing
Modified Mon Feb 3 00:03:52 2014 UTC (3 years, 4 months ago) by sshaw
fixed indent errors in coalgas, added future print import to seismic_wave, since it was using py3 style prints

Revision 4643 - Directory Listing
Modified Sun Feb 2 23:52:38 2014 UTC (3 years, 4 months ago) by sshaw
fixed some error message formatting interpreting tuples badly

Revision 4642 - Directory Listing
Modified Fri Jan 31 02:16:45 2014 UTC (3 years, 4 months ago) by jfenwick
Renamed the default options file to make it clear that it was used for g++.
There is now no default mole options file.
This is deliberate. You need to configure your environment based on the compiler you wish to use. (See scripts in /usr/local/env).

If you are doing a lot of building, symlink your chosen file to scons/mole_options.py. DO NOT COMMIT it though.



Revision 4641 - Directory Listing
Modified Fri Jan 31 02:13:47 2014 UTC (3 years, 4 months ago) by jduplessis
line 966 

	"if not args.has_key(n): args[n]=Data()" was changed to "if not args.has_key(n) and not constants.has_key(n): args[n]=Data()".

also added: 

	args=dict(args.items()+constants.items())

to merge the two dictionaries.



Revision 4640 - Directory Listing
Modified Fri Jan 31 00:56:51 2014 UTC (3 years, 4 months ago) by jfenwick
Ensure that DYLD_LIBRARY_PATH is passed into scons.
Update mole_options to work with g++
(To get this to work, you will need to set up your env vars).



Revision 4639 - Directory Listing
Modified Thu Jan 30 06:43:03 2014 UTC (3 years, 4 months ago) by jfenwick
They should be equivalent but just in case ! ==  is treated differently to !=

Revision 4638 - Directory Listing
Modified Thu Jan 30 06:25:10 2014 UTC (3 years, 4 months ago) by jfenwick
Fixes necessary to get a clang/macports build working on 10.9

Revision 4637 - Directory Listing
Modified Thu Jan 30 00:01:47 2014 UTC (3 years, 4 months ago) by gross
TTI fixes

Revision 4636 - Directory Listing
Modified Tue Jan 28 04:24:30 2014 UTC (3 years, 4 months ago) by sshaw
fixed more whitespace issues


Revision 4635 - Directory Listing
Modified Tue Jan 28 03:34:04 2014 UTC (3 years, 4 months ago) by sshaw
fixed mixed tabs/spaces for python 3 compatibility

Revision 4634 - Directory Listing
Modified Tue Jan 28 03:33:03 2014 UTC (3 years, 4 months ago) by jfenwick
Fixes to keep clang happy

Revision 4633 - Directory Listing
Modified Tue Jan 28 01:04:17 2014 UTC (3 years, 4 months ago) by caltinay
Fixed failure for lazy data when interpolating.


Revision 4632 - Directory Listing
Modified Tue Jan 28 00:22:53 2014 UTC (3 years, 4 months ago) by gross
missing file

Revision 4631 - Directory Listing
Modified Fri Jan 24 04:13:56 2014 UTC (3 years, 5 months ago) by gross
2d TTI added

Revision 4630 - Directory Listing
Modified Fri Jan 24 03:32:11 2014 UTC (3 years, 5 months ago) by sshaw
fixed a leftover from testin gin seismic, changed synthetic_VTI example back to original large 2D problem

Revision 4629 - Directory Listing
Modified Fri Jan 24 03:29:25 2014 UTC (3 years, 5 months ago) by sshaw
added dirac point interpolation to ripley (and fixed dirac points in Brick)
added fast wave assembler for Brick and minor correction to fast wave assembler for Rectangle


Revision 4628 - Directory Listing
Modified Fri Jan 24 02:09:19 2014 UTC (3 years, 5 months ago) by jduplessis
Modifying nonlinearPDE.py comments to make the meaning clearer


Revision 4627 - Directory Listing
Modified Fri Jan 24 01:53:33 2014 UTC (3 years, 5 months ago) by jduplessis
fixing error in comment


Revision 4626 - Directory Listing
Modified Wed Jan 22 06:07:34 2014 UTC (3 years, 5 months ago) by caltinay
Eliminated all const_cast<Data*> hacks in ripley and finley now that
Data.getSampleDataRO returns a const pointer.


Revision 4625 - Directory Listing
Modified Mon Jan 20 03:42:55 2014 UTC (3 years, 5 months ago) by sshaw
amalgamated waveassembler constant construction into the one place

Revision 4624 - Directory Listing
Modified Sun Jan 19 23:03:59 2014 UTC (3 years, 5 months ago) by sshaw
removed some leftover debug prints

Revision 4623 - Directory Listing
Modified Fri Jan 17 05:53:17 2014 UTC (3 years, 5 months ago) by sshaw
added missing files and a spare missing comma, also the ability for finley VTIWaves to not crash

Revision 4622 - Directory Listing
Modified Fri Jan 17 04:55:41 2014 UTC (3 years, 5 months ago) by sshaw
Added dirac support to ripley, added interface for custom assemblers for ripleydomains (also added the custom assembler for 2D VTI waves), changed synthetic_VTI example to use the new, faster custom assembler


Revision 4621 - Directory Listing
Modified Thu Jan 16 10:07:44 2014 UTC (3 years, 5 months ago) by jfenwick
getSampleDataRO is now const

Revision 4620 - Directory Listing
Modified Thu Jan 16 03:17:20 2014 UTC (3 years, 5 months ago) by caltinay
py3 RuntimeError does not have 'message' member.


Revision 4619 - Directory Listing
Modified Thu Jan 16 02:10:26 2014 UTC (3 years, 5 months ago) by caltinay
updated gp py3 options.


Revision 4618 - Directory Listing
Modified Wed Jan 15 04:35:19 2014 UTC (3 years, 5 months ago) by caltinay
Implemented reverse reading of grid data from netcdf files.
Fixes #44.


Revision 4617 - Directory Listing
Modified Wed Jan 15 03:49:19 2014 UTC (3 years, 5 months ago) by caltinay
new name for boost library on guineapig


Revision 4616 - Directory Listing
Modified Tue Jan 14 22:57:47 2014 UTC (3 years, 5 months ago) by caltinay
- Fixed unit test failure by populating missing parts of the struct
- prepared for reversing read order from grids
- worked around a segfault caused by python version in jessie (2.7.6) in
  combination with gdal,pyproj and RTLD_GLOBAL in dlopen flags.



Revision 4615 - Directory Listing
Modified Mon Jan 13 05:05:33 2014 UTC (3 years, 5 months ago) by caltinay
Step 1 for #31: wrap parameters in an object.


Revision 4614 - Directory Listing
Modified Mon Jan 13 02:44:07 2014 UTC (3 years, 5 months ago) by caltinay
Corrected a faulty test.


Revision 4613 - Directory Listing
Modified Mon Jan 13 01:09:01 2014 UTC (3 years, 5 months ago) by caltinay
Addresses #43 - altitude is now scaled according to reference system height
unit.
Also separated out UTM zone determination from the actual projection code
to silence bogus output.


Revision 4612 - Directory Listing
Modified Thu Jan 9 05:30:27 2014 UTC (3 years, 5 months ago) by gross
modifications to sonic seismic

Revision 4611 - Directory Listing
Modified Mon Dec 23 04:03:00 2013 UTC (3 years, 6 months ago) by gross
scaling corrected

Revision 4610 - Directory Listing
Modified Mon Dec 23 00:01:23 2013 UTC (3 years, 6 months ago) by gross
exposed createAbsorbtionLayerFunction

Revision 4609 - Directory Listing
Modified Fri Dec 20 07:56:56 2013 UTC (3 years, 6 months ago) by gross
fix to deal with empty right hand side vector F.



Revision 4608 - Directory Listing
Modified Fri Dec 20 01:53:04 2013 UTC (3 years, 6 months ago) by sshaw
tiny grammar fix in user guide

Revision 4607 - Directory Listing
Modified Wed Dec 18 09:46:16 2013 UTC (3 years, 6 months ago) by jfenwick
include cmath in all cases rather than math.h - the mathinf for intel on windows is still there (in part because we have no way to test if it is still relevant)

Revision 4606 - Directory Listing
Modified Wed Dec 18 08:21:25 2013 UTC (3 years, 6 months ago) by jfenwick
Updating run_models to not call the old DarcyFlow methods



Revision 4605 - Directory Listing
Modified Wed Dec 18 06:05:43 2013 UTC (3 years, 6 months ago) by jfenwick
Mantis issue #675 said

Cihan:
while merging symbolic into trunk I noticed that most dudley tests are
disabled. This happened in revision 3261 where you wrote:

"Disable some unit tests for dudley until I can fix MPI failures"

Is that fixed?

=== I'm renabling most of the test (which pass without difficulty).
But one of them appears to be out of date or something.
More investigation required.




Revision 4604 - Directory Listing
Modified Wed Dec 18 03:29:26 2013 UTC (3 years, 6 months ago) by sshaw
fixed tabs/space mix for python3

Revision 4603 - Directory Listing
Modified Wed Dec 18 02:24:32 2013 UTC (3 years, 6 months ago) by jfenwick
Added boost::noncopyable to remaining abstract base classes in the module file.
ie escriptcpp.cpp
Note I have not altered the c++ inheritance (this just just for the boost::python import)


Revision 4602 - Directory Listing
Modified Wed Dec 18 01:15:22 2013 UTC (3 years, 6 months ago) by jfenwick
Fixed missing \


Revision 4601 - Directory Listing
Modified Tue Dec 17 23:37:08 2013 UTC (3 years, 6 months ago) by gross
downunder: self-demagnetization added as forward model. 



Revision 4600 - Directory Listing
Modified Tue Dec 17 04:28:40 2013 UTC (3 years, 6 months ago) by jfenwick
Using section: science in debian/control instead of main.
This new value for section has the virtue of actually existing


Revision 4599 - Directory Listing
Modified Sun Dec 15 23:51:13 2013 UTC (3 years, 6 months ago) by sshaw
merged 3.4.1 release changes into trunk

Revision 4598 - Directory Listing
Modified Sun Dec 15 23:39:16 2013 UTC (3 years, 6 months ago) by rschaa
Minor change to figure.
Replaced .pdf with .png


Revision 4597 - Directory Listing
Modified Sun Dec 15 22:36:24 2013 UTC (3 years, 6 months ago) by gross
unused variable fixed

Revision 4586 - Directory Listing
Modified Wed Dec 11 06:03:27 2013 UTC (3 years, 6 months ago) by jfenwick
2D guassian smoothing of random data done.
Added more memory non-leaks to the supp file


Revision 4585 - Directory Listing
Modified Wed Dec 11 04:39:54 2013 UTC (3 years, 6 months ago) by sshaw
uint -> unsigned int

Revision 4584 - Directory Listing
Modified Wed Dec 11 04:24:15 2013 UTC (3 years, 6 months ago) by sshaw
more buildbot commit testing

Revision 4583 - Directory Listing
Modified Wed Dec 11 02:09:19 2013 UTC (3 years, 6 months ago) by jfenwick
deliberate error to test buildbot

Revision 4582 - Directory Listing
Modified Wed Dec 11 02:08:41 2013 UTC (3 years, 6 months ago) by jfenwick
Added libpython version of suppressions to the aggressive file.
Rectangle now passes correct values around.
Random still to come.


Revision 4581 - Directory Listing
Modified Tue Dec 10 09:32:50 2013 UTC (3 years, 6 months ago) by jfenwick
Some more work on random
Added a more agressive (And smaller) supressions file for python


Revision 4580 - Directory Listing
Modified Tue Dec 10 06:10:44 2013 UTC (3 years, 6 months ago) by sshaw
fixed doc building relying on potentially missing python package installs (bug #739)

Revision 4579 - Directory Listing
Modified Tue Dec 10 04:08:20 2013 UTC (3 years, 6 months ago) by sshaw
adding porcupine's scons options file

Revision 4578 - Directory Listing
Modified Tue Dec 10 04:07:51 2013 UTC (3 years, 6 months ago) by sshaw
fixed gmsh Design deconstructor attempting to access non-existing members or files that were never created
also fixed a loose (non-)integer division for python3


Revision 4577 - Directory Listing
Modified Tue Dec 10 00:50:55 2013 UTC (3 years, 6 months ago) by sshaw
Undoing unintended commit of omp wrapper removal

Revision 4576 - Directory Listing
Modified Mon Dec 9 23:35:30 2013 UTC (3 years, 6 months ago) by sshaw
python3ified things, replaced mixed whitespace and xrange calls

Revision 4575 - Directory Listing
Modified Mon Dec 9 22:59:31 2013 UTC (3 years, 6 months ago) by jfenwick
Some more work on this


Revision 4574 - Directory Listing
Modified Mon Dec 9 04:29:44 2013 UTC (3 years, 6 months ago) by gross
some corrections

Revision 4573 - Directory Listing
Modified Mon Dec 9 03:42:50 2013 UTC (3 years, 6 months ago) by gross
HTI added

Revision 4572 - Directory Listing
Modified Sun Dec 8 00:54:37 2013 UTC (3 years, 6 months ago) by jfenwick
Some work on rectangle random MPI

Revision 4571 - Directory Listing
Modified Fri Dec 6 02:47:14 2013 UTC (3 years, 6 months ago) by sshaw
replaced a deliberate NULL dereference with abort() to satisfy lion-clang

Revision 4570 - Directory Listing
Modified Fri Dec 6 02:22:37 2013 UTC (3 years, 6 months ago) by gross
strain convention corrected.

Revision 4569 - Directory Listing
Modified Fri Dec 6 02:21:12 2013 UTC (3 years, 6 months ago) by gross
some update

Revision 4568 - Directory Listing
Modified Thu Dec 5 23:13:26 2013 UTC (3 years, 6 months ago) by jfenwick
Package building files for saucy


Revision 4567 - Directory Listing
Modified Thu Dec 5 09:00:23 2013 UTC (3 years, 6 months ago) by jfenwick
Options file for ubuntu 13.10


Revision 4566 - Directory Listing
Modified Thu Dec 5 01:02:47 2013 UTC (3 years, 6 months ago) by sshaw
fixed Dudley saveVTK crash on world size > 6 (mantis bug #738)

Revision 4565 - Directory Listing
Modified Wed Dec 4 06:42:30 2013 UTC (3 years, 6 months ago) by gross
and another typo fixed.

Revision 4564 - Directory Listing
Modified Wed Dec 4 06:34:14 2013 UTC (3 years, 6 months ago) by gross
VTI wave added  

Revision 4563 - Directory Listing
Modified Wed Dec 4 06:30:59 2013 UTC (3 years, 6 months ago) by gross
typo fixed

Revision 4562 - Directory Listing
Modified Wed Dec 4 05:41:10 2013 UTC (3 years, 6 months ago) by gross
VTI wave added  

Revision 4561 - Directory Listing
Modified Wed Dec 4 05:19:32 2013 UTC (3 years, 6 months ago) by caltinay
Removed spurious print and some minor changes in inversion example.


Revision 4560 - Directory Listing
Modified Wed Dec 4 03:43:57 2013 UTC (3 years, 6 months ago) by rschaa
Options file for ferret


Revision 4559 - Directory Listing
Modified Wed Dec 4 02:05:34 2013 UTC (3 years, 6 months ago) by sshaw
renamed design.Design to design.AbstractDesign as a more explicit/descriptive name, this will break any existing custom implementation until changed to match

updated gmsh.Design docstring to match that of the code

Revision 4558 - Directory Listing
Modified Tue Dec 3 22:37:38 2013 UTC (3 years, 6 months ago) by jfenwick
Moving MeshAdapter constructor call out of smartptr constructor.  I think a throw in there would lead to undefined behaviour

Revision 4557 - Directory Listing
Modified Tue Dec 3 12:53:38 2013 UTC (3 years, 6 months ago) by caltinay
Fixed boost/intel issue in dudley and synced options file with module on
savanna.


Revision 4556 - Directory Listing
Modified Tue Dec 3 05:40:53 2013 UTC (3 years, 6 months ago) by sshaw
fixed mixed tabs/spaces and py2 prints breaking the python3 compiler

Revision 4555 - Directory Listing
Modified Tue Dec 3 03:54:20 2013 UTC (3 years, 6 months ago) by sshaw
updated doc install instructions to match that required

Revision 4554 - Directory Listing
Modified Tue Dec 3 03:45:56 2013 UTC (3 years, 6 months ago) by sshaw
documentation spelling and whitespace corrections, added some Design.setOptions params that were missing from the userguide

Revision 4553 - Directory Listing
Modified Mon Dec 2 07:18:02 2013 UTC (3 years, 6 months ago) by gross
clarification on receiver array

Revision 4552 - Directory Listing
Modified Mon Dec 2 06:13:47 2013 UTC (3 years, 6 months ago) by sshaw
Replaced non-visible (when built) unicode endash with single dash in user guide source

Revision 4551 - Directory Listing
Modified Mon Dec 2 03:32:23 2013 UTC (3 years, 6 months ago) by sshaw
Fixed missing install keyword in instructions


Revision 4550 - Directory Listing
Modified Fri Nov 29 07:44:37 2013 UTC (3 years, 6 months ago) by gross
some modifications

Revision 4549 - Directory Listing
Modified Fri Nov 29 05:24:40 2013 UTC (3 years, 6 months ago) by gross
argument for lumping added.

Revision 4548 - Directory Listing
Modified Fri Nov 29 04:39:15 2013 UTC (3 years, 6 months ago) by gross
renamed file

Revision 4547 - Directory Listing
Modified Thu Nov 28 23:47:27 2013 UTC (3 years, 6 months ago) by jfenwick
Added msec unit


Revision 4546 - Directory Listing
Modified Thu Nov 28 05:30:48 2013 UTC (3 years, 6 months ago) by gross
sonic wave propagation added

Revision 4545 - Directory Listing
Modified Thu Nov 28 05:02:43 2013 UTC (3 years, 6 months ago) by gross
wave simulator base added

Revision 4544 - Directory Listing
Modified Thu Nov 28 04:01:46 2013 UTC (3 years, 6 months ago) by gross
wave simulator base added

Revision 4543 - Directory Listing
Modified Thu Nov 28 03:42:10 2013 UTC (3 years, 6 months ago) by gross
missing retirn statement added

Revision 4542 - Directory Listing
Modified Thu Nov 28 01:33:22 2013 UTC (3 years, 6 months ago) by jfenwick
Moving to new icc and associated modules.




Revision 4541 - Directory Listing
Modified Thu Nov 28 01:17:19 2013 UTC (3 years, 6 months ago) by gross
Ricker wavelet added

Revision 4540 - Directory Listing
Modified Thu Nov 28 01:06:10 2013 UTC (3 years, 6 months ago) by gross
segy writer added

Revision 4539 - Directory Listing
Modified Thu Nov 28 00:38:10 2013 UTC (3 years, 6 months ago) by gross
segy writer test added.

Revision 4538 - Directory Listing
Modified Thu Nov 28 00:37:48 2013 UTC (3 years, 6 months ago) by gross
segy writer added

Revision 4537 - Directory Listing
Modified Mon Nov 25 06:44:46 2013 UTC (3 years, 7 months ago) by gross
missing references and double labeling fixed.

Revision 4536 - Directory Listing
Modified Thu Nov 21 07:58:32 2013 UTC (3 years, 7 months ago) by jfenwick
Working around intelcc s seeming dislike of boost smart pointers

Revision 4535 - Directory Listing
Modified Wed Nov 20 06:37:53 2013 UTC (3 years, 7 months ago) by gross
strong correlation joint inversion fixed.

Revision 4534 - Directory Listing
Modified Thu Nov 7 08:17:02 2013 UTC (3 years, 7 months ago) by gross
typo fixed

Revision 4533 - Directory Listing
Modified Thu Nov 7 04:56:11 2013 UTC (3 years, 7 months ago) by gross
typo fixed

Revision 4532 - Directory Listing
Modified Thu Nov 7 04:54:56 2013 UTC (3 years, 7 months ago) by gross
strongly coupled joint inversion added

Revision 4531 - Directory Listing
Modified Mon Nov 4 02:09:05 2013 UTC (3 years, 7 months ago) by jfenwick
Removed strange looking dead code to resolve issue #710

Revision 4530 - Directory Listing
Modified Wed Oct 30 04:34:21 2013 UTC (3 years, 7 months ago) by caltinay
Fix in finley loadMesh which needs to call updateTagList() for all ranks, even
if a rank has no elements.


Revision 4529 - Directory Listing
Modified Fri Oct 25 01:23:27 2013 UTC (3 years, 8 months ago) by caltinay
Ripley can now read grids in non-native byte order. This is in preparation for
Gocad Voxet import.


Revision 4528 - Directory Listing
Modified Sun Sep 29 23:12:19 2013 UTC (3 years, 8 months ago) by caltinay
Added timeStepFormat option to saveESD (mantis 723).


Revision 4527 - Directory Listing
Modified Mon Sep 2 21:54:35 2013 UTC (3 years, 9 months ago) by jfenwick
use enums

Revision 4526 - Directory Listing
Modified Mon Sep 2 06:34:25 2013 UTC (3 years, 9 months ago) by jfenwick
Single rank rectangle randoms.


Revision 4525 - Directory Listing
Modified Fri Aug 30 09:14:35 2013 UTC (3 years, 9 months ago) by jfenwick
try this

Revision 4524 - Directory Listing
Modified Tue Aug 27 01:32:10 2013 UTC (3 years, 10 months ago) by jfenwick
Steube!!!!!


Revision 4523 - Directory Listing
Modified Mon Aug 26 23:04:07 2013 UTC (3 years, 10 months ago) by caltinay
New working raijin options.


Revision 4522 - Directory Listing
Modified Mon Aug 26 22:15:26 2013 UTC (3 years, 10 months ago) by caltinay
Newer versions of proj require specifying ellipsoid parameter.


Revision 4521 - Directory Listing
Modified Mon Aug 26 11:51:30 2013 UTC (3 years, 10 months ago) by jfenwick
Remove bool_t
Part of random.



Revision 4520 - Directory Listing
Modified Thu Aug 22 06:42:57 2013 UTC (3 years, 10 months ago) by caltinay
Removing spurious usage of C compiler:
-Changed all scons tests to use C++ compiler
-Renamed paso profiling files (unused)
-Updated most options files (removal of options and updated comments)


Revision 4519 - Directory Listing
Modified Mon Aug 19 05:56:22 2013 UTC (3 years, 10 months ago) by caltinay
Initial raijin options file.


Revision 4518 - Directory Listing
Modified Tue Aug 13 01:49:59 2013 UTC (3 years, 10 months ago) by caltinay
The line search step length caching should only be used within esys.downunder
inversions where the inverse Hessian approximation is not very good at the
moment.


Revision 4517 - Directory Listing
Modified Mon Aug 12 05:56:54 2013 UTC (3 years, 10 months ago) by caltinay
Implemented caching (and relaxation) of line search step size alpha.
Experiments show a significant decrease in the number of  iterations required
to converge with this change.


Revision 4516 - Directory Listing
Modified Thu Aug 8 05:41:49 2013 UTC (3 years, 10 months ago) by caltinay
Implemented more CF conventions for the netCDF datasource.
Also added a check to LatLonToUTM to pass through coordinates that are already
projected.
Data gridded by GDAL is now understood.


Revision 4515 - Directory Listing
Modified Mon Aug 5 06:09:01 2013 UTC (3 years, 10 months ago) by jfenwick
Intel compiler mutter grumble

Revision 4514 - Directory Listing
Modified Mon Aug 5 03:28:44 2013 UTC (3 years, 10 months ago) by jfenwick
Look at the MPI

Revision 4513 - Directory Listing
Modified Mon Aug 5 00:57:34 2013 UTC (3 years, 10 months ago) by jfenwick
Dropping VSL random. Random data now uses more general routine.

Revision 4512 - Directory Listing
Modified Mon Jul 29 05:27:16 2013 UTC (3 years, 10 months ago) by caltinay
With current Intel compiler (13.5.192) on savanna any build with OMP and without MPI
will segfault in AbstractDomain->getPtr() for unknown reasons.
Trying a workaround for finley which can be adapted to dudley and ripley if it works.


Revision 4511 - Directory Listing
Modified Thu Jul 25 04:51:02 2013 UTC (3 years, 11 months ago) by caltinay
Print a warning on savanna if dev-deps is not loaded when building and add
debug symbols by default.


Revision 4510 - Directory Listing
Modified Thu Jul 25 04:02:07 2013 UTC (3 years, 11 months ago) by caltinay
Fixed a path which should fix unit tests.


Revision 4509 - Directory Listing
Modified Wed Jul 24 08:37:29 2013 UTC (3 years, 11 months ago) by jfenwick
Fixed paths for utest.sh


Revision 4508 - Directory Listing
Modified Wed Jul 24 04:23:22 2013 UTC (3 years, 11 months ago) by jfenwick
Moving to escriptcore

Revision 4507 - Directory Listing
Modified Wed Jul 24 02:50:22 2013 UTC (3 years, 11 months ago) by jfenwick
It begins

Revision 4506 - Directory Listing
Modified Wed Jul 24 01:28:42 2013 UTC (3 years, 11 months ago) by caltinay
run-escript -m now takes an optional argument to allow for different valgrind
tools (callgrind & memcheck supported at the moment).


Revision 4505 - Directory Listing
Modified Tue Jul 23 02:09:45 2013 UTC (3 years, 11 months ago) by jfenwick
Hopefully addresses mantis721

Revision 4504 - Directory Listing
Modified Mon Jul 22 02:04:34 2013 UTC (3 years, 11 months ago) by caltinay
Fix to verbose parameter reporting in linear pdes


Revision 4503 - Directory Listing
Modified Wed Jul 17 05:27:36 2013 UTC (3 years, 11 months ago) by caltinay
Skip new test with >1 rank.


Revision 4502 - Directory Listing
Modified Wed Jul 17 03:12:28 2013 UTC (3 years, 11 months ago) by caltinay
Test reading IEEE8ByteReal data from ER Mapper files.


Revision 4501 - Directory Listing
Modified Wed Jul 17 00:02:26 2013 UTC (3 years, 11 months ago) by caltinay
This time I fixed the comment instead of the code for this special case.


Revision 4500 - Directory Listing
Modified Tue Jul 16 05:47:11 2013 UTC (3 years, 11 months ago) by caltinay
updated scons script


Revision 4499 - Directory Listing
Modified Tue Jul 16 05:42:19 2013 UTC (3 years, 11 months ago) by caltinay
finley: mainly const'ness fixes, some formatting.


Revision 4498 - Directory Listing
Modified Tue Jul 16 01:56:37 2013 UTC (3 years, 11 months ago) by caltinay
Another special case fix.


Revision 4497 - Directory Listing
Modified Mon Jul 15 23:32:28 2013 UTC (3 years, 11 months ago) by caltinay
Small fix for non-mpi build.


Revision 4496 - Directory Listing
Modified Mon Jul 15 06:53:44 2013 UTC (3 years, 11 months ago) by caltinay
finley (WIP):
-moved all of finley into its namespace
-introduced some shared pointers
-Mesh is now a class
-other bits and pieces...


Revision 4495 - Directory Listing
Modified Fri Jul 5 02:19:47 2013 UTC (3 years, 11 months ago) by caltinay
Added support for more input data types in ER Mapper files.
Tests will follow soon.


Revision 4494 - Directory Listing
Modified Thu Jul 4 02:53:47 2013 UTC (3 years, 11 months ago) by caltinay
Suppressions for savanna runs.


Revision 4493 - Directory Listing
Modified Wed Jul 3 06:32:11 2013 UTC (3 years, 11 months ago) by caltinay
Fixed omp typo - gcc didn't pick it up...


Revision 4492 - Directory Listing
Modified Tue Jul 2 01:44:11 2013 UTC (3 years, 11 months ago) by caltinay
Finley changes that were held back while in release mode - moved more stuff
into finley namespace.


Revision 4491 - Directory Listing
Modified Tue Jul 2 01:10:41 2013 UTC (3 years, 11 months ago) by caltinay
Reintegrating changes from 3.4 branch (with changes).


Revision 4490 - Directory Listing
Modified Tue Jul 2 00:38:44 2013 UTC (3 years, 11 months ago) by caltinay
More python suppressions from savanna.


Revision 4489 - Directory Listing
Modified Fri Jun 28 00:05:31 2013 UTC (4 years ago) by caltinay
Moved to update 5 of intel libraries/compiler on savanna.


Revision 4483 - Directory Listing
Modified Wed Jun 26 02:36:15 2013 UTC (4 years ago) by caltinay
Added option to easily run escript with valgrind memcheck.


Revision 4482 - Directory Listing
Modified Tue Jun 25 05:20:01 2013 UTC (4 years ago) by caltinay
More leak fixes and suppression file additions.


Revision 4481 - Directory Listing
Modified Mon Jun 24 06:22:27 2013 UTC (4 years ago) by caltinay
Hmm. That's a nasty undocumented "feature"...


Revision 4480 - Directory Listing
Modified Mon Jun 24 05:09:52 2013 UTC (4 years ago) by caltinay
More valgrind suppressions and memory leak fixes identified in various places.


Revision 4479 - Directory Listing
Modified Thu Jun 20 10:54:09 2013 UTC (4 years ago) by caltinay
Missed a subtle fact about the stringstream constructor...


Revision 4478 - Directory Listing
Modified Thu Jun 20 06:34:02 2013 UTC (4 years ago) by caltinay
Moved appendRankToFilename to header within namespace to remove code duplication
and fixed memory leaks this way.


Revision 4477 - Directory Listing
Modified Thu Jun 20 02:41:28 2013 UTC (4 years ago) by caltinay
escript: use scoped_array instead of scoped_ptr
ripley: netcdf returns a copy of an array so use scoped_array
downunder: s/Sperical/Spherical/
scripts: added a few more suppressions


Revision 4476 - Directory Listing
Modified Thu Jun 20 00:05:53 2013 UTC (4 years ago) by caltinay
Revised valgrind suppressions file with more generic Python & OpenMPI
suppressions.


Revision 4474 - Directory Listing
Modified Wed Jun 19 06:44:47 2013 UTC (4 years ago) by caltinay
Brought over leak fix, gcc 4.8 fix and mismatched new[]/delete fix from release
branch.


Revision 4465 - Directory Listing
Modified Mon Jun 17 06:49:39 2013 UTC (4 years ago) by caltinay
Remove superfluous \label


Revision 4463 - Directory Listing
Modified Mon Jun 17 06:11:32 2013 UTC (4 years ago) by gross
missing file

Revision 4462 - Directory Listing
Modified Mon Jun 17 04:12:06 2013 UTC (4 years ago) by caltinay
Raise exception if background magnetic field has not been set but is required.


Revision 4461 - Directory Listing
Modified Sun Jun 16 23:39:31 2013 UTC (4 years ago) by caltinay
small py3 fix.


Revision 4455 - Directory Listing
Modified Thu Jun 13 03:13:36 2013 UTC (4 years ago) by caltinay
Removed \LG etc. from inversion document.
Documented new GOCAD Voxet writer. Needs to be mentioned in 'changes' too.


Revision 4454 - Directory Listing
Modified Thu Jun 13 03:12:17 2013 UTC (4 years ago) by caltinay
More "delete test output files after checking"


Revision 4451 - Directory Listing
Modified Thu Jun 13 01:38:56 2013 UTC (4 years ago) by jfenwick
some pending changes on badger

Revision 4450 - Directory Listing
Modified Thu Jun 13 00:45:59 2013 UTC (4 years ago) by jfenwick
install docs - still waiting on Mac. Removing debug output.

Revision 4449 - Directory Listing
Modified Thu Jun 13 00:24:00 2013 UTC (4 years ago) by jfenwick
Finishing off this end.


Revision 4448 - Directory Listing
Modified Wed Jun 12 23:05:12 2013 UTC (4 years ago) by caltinay
Only one rank should delete file in tests.


Revision 4447 - Directory Listing
Modified Wed Jun 12 13:55:53 2013 UTC (4 years ago) by caltinay
Clean up some generated test files.


Revision 4446 - Directory Listing
Modified Tue Jun 11 04:00:15 2013 UTC (4 years ago) by caltinay
This should fix the py3 error...


Revision 4445 - Directory Listing
Modified Tue Jun 11 03:35:55 2013 UTC (4 years ago) by caltinay
Apply weight rescaling to input weights before the coordinate scaling.
Also skipping a check when more than 1 rank is used.


Revision 4444 - Directory Listing
Modified Mon Jun 10 07:55:05 2013 UTC (4 years ago) by caltinay
Converted IndexList to a std::list.


Revision 4443 - Directory Listing
Modified Mon Jun 10 04:50:27 2013 UTC (4 years ago) by caltinay
Update test to take into account changed height scale.


Revision 4442 - Directory Listing
Modified Fri Jun 7 07:04:44 2013 UTC (4 years ago) by caltinay
cosmetic changes.


Revision 4441 - Directory Listing
Modified Fri Jun 7 02:23:49 2013 UTC (4 years ago) by caltinay
finley now uses Data objects directly instead of going through the C wrapper.


Revision 4440 - Directory Listing
Modified Wed Jun 5 05:22:20 2013 UTC (4 years ago) by jfenwick
options files changes and install changes

Revision 4439 - Directory Listing
Modified Wed Jun 5 02:09:35 2013 UTC (4 years ago) by jfenwick
some work on install doco

Revision 4438 - Directory Listing
Modified Tue Jun 4 09:00:50 2013 UTC (4 years ago) by jfenwick
Some changes to packaging

Revision 4437 - Directory Listing
Modified Tue Jun 4 05:37:18 2013 UTC (4 years ago) by caltinay
finley:
-Removed obsolete reference files (OpenDX)
-Converted tag map to a std::map
-loosened tests to ignore tag order in file
-added some decorators for test skips


Revision 4436 - Directory Listing
Modified Mon Jun 3 05:37:31 2013 UTC (4 years ago) by caltinay
Tweak.


Revision 4435 - Directory Listing
Modified Mon Jun 3 04:27:57 2013 UTC (4 years ago) by caltinay
Fixed a few scaling problems for non-cartesian coordinates in domainbuilder.


Revision 4434 - Directory Listing
Modified Mon Jun 3 00:43:29 2013 UTC (4 years ago) by caltinay
tab-fixes and an indexing fix.


Revision 4433 - Directory Listing
Modified Fri May 31 12:09:58 2013 UTC (4 years ago) by gross
some clarifications on geodetic coordinates. 
order of background magnetic flux density component has been corrected: input is now B_east, B_north, B_vertical.



Revision 4432 - Directory Listing
Modified Fri May 31 07:13:38 2013 UTC (4 years ago) by caltinay
updated sconscript file


Revision 4431 - Directory Listing
Modified Fri May 31 07:09:03 2013 UTC (4 years ago) by caltinay
finley ElementFile is now a class...


Revision 4430 - Directory Listing
Modified Fri May 31 00:38:42 2013 UTC (4 years ago) by caltinay
Don't panic - just forgot some brackets... D'oh!


Revision 4429 - Directory Listing
Modified Thu May 30 13:52:01 2013 UTC (4 years ago) by caltinay
Okay I now know that std::vector<bool> is evil, but WTF happens in this context???
It only crashes with more than one thread and more than one MPI process.



Revision 4428 - Directory Listing
Modified Thu May 30 06:39:10 2013 UTC (4 years ago) by caltinay
finley's NodeFile is now a class.
Associated changes:
- use of some C++ constructs/functions/types (1st pass)
- removal of obsolete pointer check
- merging of some duplicated code
- ...


Revision 4426 - Directory Listing
Modified Mon May 27 06:14:19 2013 UTC (4 years, 1 month ago) by jfenwick
Testing commit


Revision 4425 - Directory Listing
Modified Mon May 27 05:44:28 2013 UTC (4 years, 1 month ago) by caltinay
svn server test and finley stuff.


Revision 4424 - Directory Listing
Modified Mon May 27 04:48:31 2013 UTC (4 years, 1 month ago) by caltinay
SVN server test.


Revision 4423 - Directory Listing
Modified Mon May 27 04:38:59 2013 UTC (4 years, 1 month ago) by caltinay
finley bits.


Revision 4422 - Directory Listing
Modified Fri May 24 04:42:29 2013 UTC (4 years, 1 month ago) by caltinay
s/jacobeans/jacobians and other bits and pieces.


Revision 4421 - Directory Listing
Modified Tue May 21 05:16:39 2013 UTC (4 years, 1 month ago) by caltinay
Finley... there were actually some long-standing errors in the checks.


Revision 4420 - Directory Listing
Modified Mon May 20 07:12:15 2013 UTC (4 years, 1 month ago) by caltinay
Enabled metis on guineapig.


Revision 4419 - Directory Listing
Modified Mon May 20 05:03:35 2013 UTC (4 years, 1 month ago) by caltinay
Fixed a typo.


Revision 4418 - Directory Listing
Modified Mon May 20 04:08:16 2013 UTC (4 years, 1 month ago) by caltinay
Try...


Revision 4417 - Directory Listing
Modified Mon May 20 02:15:47 2013 UTC (4 years, 1 month ago) by caltinay
Retab regularizations.


Revision 4416 - Directory Listing
Modified Fri May 17 02:32:33 2013 UTC (4 years, 1 month ago) by jfenwick
Renaming a thing and adding some doco.

Revision 4415 - Directory Listing
Modified Fri May 17 00:33:02 2013 UTC (4 years, 1 month ago) by caltinay
Commented unused var to make compiler happy.


Revision 4414 - Directory Listing
Modified Thu May 16 05:37:32 2013 UTC (4 years, 1 month ago) by caltinay
Few more bits and pieces in finley.


Revision 4410 - Directory Listing
Modified Tue May 14 11:29:23 2013 UTC (4 years, 1 month ago) by caltinay
Oops, I saw this coming.


Revision 4408 - Directory Listing
Modified Tue May 14 06:58:43 2013 UTC (4 years, 1 month ago) by caltinay
Mostly no-op - trying to get some consistency in style while going through a
few files.
Also some minor changes related to C->C++ (e.g. no need to copy vector to pass
to functions etc.)


Revision 4407 - Directory Listing
Modified Tue May 14 05:17:24 2013 UTC (4 years, 1 month ago) by jfenwick
Added output function to arithmetic tuple

Revision 4406 - Directory Listing
Modified Tue May 14 02:54:09 2013 UTC (4 years, 1 month ago) by caltinay
Removed references to pyvisi which disappeared a few releases ago...


Revision 4405 - Directory Listing
Modified Sun May 12 23:27:33 2013 UTC (4 years, 1 month ago) by caltinay
Once again..


Revision 4404 - Directory Listing
Modified Sun May 12 23:25:10 2013 UTC (4 years, 1 month ago) by caltinay
Retab forwardmodels


Revision 4400 - Directory Listing
Modified Fri May 10 04:05:00 2013 UTC (4 years, 1 month ago) by caltinay
Uaaargh - the minimizer ate my files! Fixed reporting of iteration number in
callback.


Revision 4399 - Directory Listing
Modified Thu May 9 10:46:41 2013 UTC (4 years, 1 month ago) by jfenwick
just fiddling

Revision 4398 - Directory Listing
Modified Thu May 9 08:42:44 2013 UTC (4 years, 1 month ago) by jfenwick
support for supressing doco subpackages. fiddling with one of the imports to try to reduce the number of places where Data appears.  Seriously it looks like we have 8 different Data classes

Revision 4397 - Directory Listing
Modified Thu May 9 06:17:15 2013 UTC (4 years, 1 month ago) by jfenwick
Added some doco to make it a little easier to work out what is going on.
Cleaned up some reST ugliness


Revision 4396 - Directory Listing
Modified Wed May 8 09:27:10 2013 UTC (4 years, 1 month ago) by jfenwick
fix extraction script to pick up more classes. Stop models from importing escript into its namespace

Revision 4395 - Directory Listing
Modified Wed May 8 03:05:05 2013 UTC (4 years, 1 month ago) by caltinay
Changed trade-off factors for example to avoid unit test failures due to
scaling issues.


Revision 4394 - Directory Listing
Modified Tue May 7 04:56:59 2013 UTC (4 years, 1 month ago) by caltinay
Fixed rounding with lat/lon coordinates and removed stray print statements.


Revision 4393 - Directory Listing
Modified Mon May 6 03:35:48 2013 UTC (4 years, 1 month ago) by caltinay
Correct indexing of forward models.


Revision 4392 - Directory Listing
Modified Mon May 6 02:18:33 2013 UTC (4 years, 1 month ago) by caltinay
More saveSilo checks.


Revision 4391 - Directory Listing
Modified Mon May 6 02:15:48 2013 UTC (4 years, 1 month ago) by caltinay
Do not claim success when saving silo without silo support.


Revision 4390 - Directory Listing
Modified Mon May 6 01:59:34 2013 UTC (4 years, 1 month ago) by caltinay
Fixed advertising of NetCdfData availability.


Revision 4389 - Directory Listing
Modified Mon May 6 01:52:05 2013 UTC (4 years, 1 month ago) by caltinay
retab coordinates.py


Revision 4388 - Directory Listing
Modified Thu May 2 01:55:08 2013 UTC (4 years, 1 month ago) by jfenwick
I need this

Revision 4387 - Directory Listing
Modified Thu May 2 00:46:49 2013 UTC (4 years, 1 month ago) by jfenwick
The future is now

Revision 4386 - Directory Listing
Modified Tue Apr 30 02:58:02 2013 UTC (4 years, 1 month ago) by jfenwick
Add missing [0]

Revision 4385 - Directory Listing
Modified Mon Apr 29 06:03:30 2013 UTC (4 years, 1 month ago) by jfenwick
It was bugging me

Revision 4384 - Directory Listing
Modified Sat Apr 27 05:09:37 2013 UTC (4 years, 2 months ago) by jfenwick
Partially complete new install instructions

Revision 4383 - Directory Listing
Modified Fri Apr 26 06:13:12 2013 UTC (4 years, 2 months ago) by jfenwick
Changes to install doco


Revision 4382 - Directory Listing
Modified Thu Apr 25 04:44:14 2013 UTC (4 years, 2 months ago) by caltinay
Finalised ripley PDE assembly optimisation work.

Stats (combined Rectangle & Brick):
  rev.4369: 7440 constants, 16985 lines, ~17m to compile w/ icc
       NOW: 4038 constants, 13579 lines, ~6.5m to compile w/ icc

Runtime of unit tests a few seconds shorter as well :-)


Revision 4381 - Directory Listing
Modified Thu Apr 25 01:57:54 2013 UTC (4 years, 2 months ago) by caltinay
Prescribe data scale in tests to silence message.


Revision 4380 - Directory Listing
Modified Wed Apr 24 23:59:49 2013 UTC (4 years, 2 months ago) by jfenwick
Attempt to help windows

Revision 4379 - Directory Listing
Modified Wed Apr 24 20:31:19 2013 UTC (4 years, 2 months ago) by gross
more documentation on geodetic coordinates.

Revision 4378 - Directory Listing
Modified Wed Apr 24 06:21:42 2013 UTC (4 years, 2 months ago) by caltinay
ripley work: Almost done - one more round in Brick left....


Revision 4377 - Directory Listing
Modified Tue Apr 23 05:30:02 2013 UTC (4 years, 2 months ago) by caltinay
More work on ripley - Brick is under 10000 lines now.


Revision 4376 - Directory Listing
Modified Mon Apr 22 08:44:45 2013 UTC (4 years, 2 months ago) by gross
domumentation update on coordinate systems - part I

Revision 4375 - Directory Listing
Modified Mon Apr 22 05:35:52 2013 UTC (4 years, 2 months ago) by caltinay
More ripley code cleaning/optimisation.


Revision 4374 - Directory Listing
Modified Mon Apr 22 03:21:48 2013 UTC (4 years, 2 months ago) by gross
some typo fixed.

Revision 4373 - Directory Listing
Modified Mon Apr 22 03:16:24 2013 UTC (4 years, 2 months ago) by gross
more on geodetic coordinates

Revision 4372 - Directory Listing
Modified Mon Apr 22 00:02:36 2013 UTC (4 years, 2 months ago) by caltinay
Retab...


Revision 4371 - Directory Listing
Modified Fri Apr 19 08:47:57 2013 UTC (4 years, 2 months ago) by jfenwick
As far as I can tell, passes unit tests on freebsd with non-default compiler==gcc46

Revision 4370 - Directory Listing
Modified Fri Apr 19 06:15:24 2013 UTC (4 years, 2 months ago) by caltinay
WIP: ripley hand-optimisation & further rules to generator
-> drastically reduced number of constants
-> compile time of Brick.cpp less than half of what it was on savanna
-> additional runtime savings
-> to be continued...


Revision 4369 - Directory Listing
Modified Fri Apr 19 02:32:34 2013 UTC (4 years, 2 months ago) by jfenwick
fix problems revealed on freebsd

Revision 4368 - Directory Listing
Modified Thu Apr 18 02:26:35 2013 UTC (4 years, 2 months ago) by jfenwick
put back std::

Revision 4367 - Directory Listing
Modified Wed Apr 17 09:55:25 2013 UTC (4 years, 2 months ago) by plaub
Allow access to the individual components of the weighted sum cost function.


Revision 4366 - Directory Listing
Modified Wed Apr 17 04:41:16 2013 UTC (4 years, 2 months ago) by caltinay
Be more careful with namespace & includes.


Revision 4365 - Directory Listing
Modified Wed Apr 17 03:46:22 2013 UTC (4 years, 2 months ago) by caltinay
Skip tests for #ranks > 1 again.


Revision 4364 - Directory Listing
Modified Wed Apr 17 01:56:00 2013 UTC (4 years, 2 months ago) by caltinay
Decorated some test cases.


Revision 4363 - Directory Listing
Modified Wed Apr 17 01:07:38 2013 UTC (4 years, 2 months ago) by caltinay
retab coordinates.py.


Revision 4362 - Directory Listing
Modified Tue Apr 16 04:37:13 2013 UTC (4 years, 2 months ago) by caltinay
Implemented NumpyData downunder source (w/ tests).
Added check of data dimensionality to domainbuilder since data_dim must equal
domain_dim-1 at the moment.


Revision 4361 - Directory Listing
Modified Mon Apr 15 04:43:19 2013 UTC (4 years, 2 months ago) by jfenwick
beginnings of an option file for macports

Revision 4360 - Directory Listing
Modified Mon Apr 15 02:41:42 2013 UTC (4 years, 2 months ago) by jfenwick
some mismatched memory ops

Revision 4359 - Directory Listing
Modified Fri Apr 12 04:54:20 2013 UTC (4 years, 2 months ago) by gross
more on coordinate systems

Revision 4358 - Directory Listing
Modified Fri Apr 12 04:54:00 2013 UTC (4 years, 2 months ago) by gross
more on coordinate systems

Revision 4357 - Directory Listing
Modified Thu Apr 11 06:07:14 2013 UTC (4 years, 2 months ago) by caltinay
templated writeBinaryGrid and a bit of cleanup.


Revision 4356 - Directory Listing
Modified Tue Apr 9 00:15:59 2013 UTC (4 years, 2 months ago) by caltinay
Retabbed file for py3 pleasure.


Revision 4355 - Directory Listing
Modified Fri Apr 5 07:25:02 2013 UTC (4 years, 2 months ago) by jfenwick
start install guide overhall

Revision 4354 - Directory Listing
Modified Fri Apr 5 03:55:03 2013 UTC (4 years, 2 months ago) by jfenwick
adding option files for distros

Revision 4353 - Directory Listing
Modified Fri Apr 5 00:14:35 2013 UTC (4 years, 2 months ago) by caltinay
For some reason std::isnan<float> is not available on NCI so changed this
to ::isnan. Added options file for NCI vayu.


Revision 4352 - Directory Listing
Modified Thu Apr 4 04:28:57 2013 UTC (4 years, 2 months ago) by jfenwick


Revision 4349 - Directory Listing
Modified Wed Apr 3 09:37:54 2013 UTC (4 years, 2 months ago) by gross
first contributions for geodeic coordinates

Revision 4348 - Directory Listing
Modified Tue Apr 2 07:15:43 2013 UTC (4 years, 2 months ago) by caltinay
Reapply some of the spelling fixes that got lost....


Revision 4347 - Directory Listing
Modified Tue Apr 2 04:58:44 2013 UTC (4 years, 2 months ago) by jfenwick
Fixed some const char* conversions


Revision 4346 - Directory Listing
Modified Tue Apr 2 04:46:45 2013 UTC (4 years, 2 months ago) by jfenwick
Bringing the changes from doubleplusgood branch.
Can't merge directly because svn doesn't transfer changes to renamed files (mutter grumble).

Revision 4344 - Directory Listing
Modified Wed Mar 27 07:58:34 2013 UTC (4 years, 3 months ago) by gross
fix potential at botttom added.

Revision 4343 - Directory Listing
Modified Wed Mar 27 06:44:36 2013 UTC (4 years, 3 months ago) by gross
 

Revision 4342 - Directory Listing
Modified Tue Mar 26 02:31:41 2013 UTC (4 years, 3 months ago) by jfenwick
get rid of the escript link that snuck in somehow.   deal with cases where the root of the install is in a path with spaces in it.

Revision 4341 - Directory Listing
Modified Mon Mar 25 04:01:25 2013 UTC (4 years, 3 months ago) by caltinay
GOCAD Voxet writer in weipa.


Revision 4340 - Directory Listing
Modified Fri Mar 22 04:38:36 2013 UTC (4 years, 3 months ago) by caltinay
added ripley method that returns grid parameters as python tuple.


Revision 4339 - Directory Listing
Modified Fri Mar 22 02:25:37 2013 UTC (4 years, 3 months ago) by jfenwick
options file for all standalone builds

Revision 4337 - Directory Listing
Modified Fri Mar 22 00:05:25 2013 UTC (4 years, 3 months ago) by caltinay
Detect a few more byte swap/endianness headers and silence output from
'detectModule' scons helper


Revision 4334 - Directory Listing
Modified Thu Mar 21 06:00:14 2013 UTC (4 years, 3 months ago) by caltinay
Preparations for Voxet (GOCAD) binary grid output + code clean up.
Changed node id's order to remove code duplication in weipa.
More work to do...


Revision 4326 - Directory Listing
Modified Wed Mar 20 02:50:46 2013 UTC (4 years, 3 months ago) by caltinay
Removed stray print statement.


Revision 4323 - Directory Listing
Modified Tue Mar 19 00:17:36 2013 UTC (4 years, 3 months ago) by jfenwick
Bringing across changes from release3.3.1. (Version names are set back to Development).

Revision 4322 - Directory Listing
Modified Mon Mar 18 00:09:02 2013 UTC (4 years, 3 months ago) by caltinay
Test for calling I/O redirect or not was wrong... fixed.


Revision 4320 - Directory Listing
Modified Fri Mar 15 02:57:15 2013 UTC (4 years, 3 months ago) by caltinay
Moved file writer helper class to esysUtils and made it header-only. It will
be used by ripley writer methods.


Revision 4311 - Directory Listing
Modified Tue Mar 12 04:26:24 2013 UTC (4 years, 3 months ago) by jfenwick
gracefully end if pyproj is not installed

Revision 4310 - Directory Listing
Modified Tue Mar 12 03:23:26 2013 UTC (4 years, 3 months ago) by jfenwick
examples don't FAIL if tool is not installed

Revision 4309 - Directory Listing
Modified Mon Mar 11 05:07:39 2013 UTC (4 years, 3 months ago) by caltinay
Temporary workaround for sys.exit() causing unclean exit with MPI.


Revision 4308 - Directory Listing
Modified Mon Mar 11 02:47:59 2013 UTC (4 years, 3 months ago) by caltinay
Added missing import.


Revision 4307 - Directory Listing
Modified Mon Mar 11 02:46:17 2013 UTC (4 years, 3 months ago) by azadeh
shake29->weasel


Revision 4306 - Directory Listing
Modified Mon Mar 11 02:36:55 2013 UTC (4 years, 3 months ago) by caltinay
python 3 compat.


Revision 4303 - Directory Listing
Modified Mon Mar 11 01:17:39 2013 UTC (4 years, 3 months ago) by caltinay
Enabled index in inversion doc. Eliminated some typos.


Revision 4301 - Directory Listing
Modified Mon Mar 11 00:52:31 2013 UTC (4 years, 3 months ago) by jfenwick
Updated copyright on doco that has not existed all the way back to 2003.
Added Azadeh and Vince to credits


Revision 4300 - Directory Listing
Modified Mon Mar 11 00:50:19 2013 UTC (4 years, 3 months ago) by caltinay
Always invoke external python to check for modules. For some reason scipy
detection did not work properly using the old way.


Revision 4299 - Directory Listing
Modified Mon Mar 11 00:40:09 2013 UTC (4 years, 3 months ago) by caltinay
Exit with a warning in example files that require unavailable scipy.
bollide->hamster
added warnings to scons for scipy and gdal


Revision 4298 - Directory Listing
Modified Mon Mar 11 00:03:22 2013 UTC (4 years, 3 months ago) by azadeh
changing Magnetic Images


Revision 4297 - Directory Listing
Modified Fri Mar 8 06:14:17 2013 UTC (4 years, 3 months ago) by jfenwick
Removing the sphinx spelling checker since it breaks my build.  Updated the genrst script so that non-package modules still show up in the doco. Still needs a bit of a tweak in the long term

Revision 4296 - Directory Listing
Modified Fri Mar 8 05:37:44 2013 UTC (4 years, 3 months ago) by caltinay
Oopsie


Revision 4295 - Directory Listing
Modified Fri Mar 8 04:42:01 2013 UTC (4 years, 3 months ago) by caltinay
de-cluttered sconstruct a bit and fixed a script.


Revision 4294 - Directory Listing
Modified Fri Mar 8 03:37:10 2013 UTC (4 years, 3 months ago) by gross
text for magnetic inversion tutorial added.

Revision 4293 - Directory Listing
Modified Fri Mar 8 00:07:07 2013 UTC (4 years, 3 months ago) by jfenwick
fixing sneaky bug in grouptest

Revision 4292 - Directory Listing
Modified Thu Mar 7 22:39:32 2013 UTC (4 years, 3 months ago) by caltinay
Broken? It ain't broken ;-) Sorry Joel.


Revision 4290 - Directory Listing
Modified Thu Mar 7 07:04:29 2013 UTC (4 years, 3 months ago) by jfenwick
Ignore __pycache__ when generating sphinx docs

Revision 4289 - Directory Listing
Modified Thu Mar 7 07:02:59 2013 UTC (4 years, 3 months ago) by jfenwick
including inversion examples in bundles and tests

Revision 4288 - Directory Listing
Modified Thu Mar 7 06:35:14 2013 UTC (4 years, 3 months ago) by gross
some modifications clarifying the B field orientation

Revision 4287 - Directory Listing
Modified Thu Mar 7 05:26:44 2013 UTC (4 years, 3 months ago) by caltinay
Removed simpleGeoMagnetic field function from doco and example source.


Revision 4286 - Directory Listing
Modified Thu Mar 7 04:28:11 2013 UTC (4 years, 3 months ago) by caltinay
Assorted spelling fixes.


Revision 4285 - Directory Listing
Modified Thu Mar 7 01:08:43 2013 UTC (4 years, 3 months ago) by caltinay
Corrected some spelling.


Revision 4284 - Directory Listing
Modified Thu Mar 7 00:43:48 2013 UTC (4 years, 3 months ago) by caltinay
Replaced dummy implementations by pure virtual methods.


Revision 4283 - Directory Listing
Modified Thu Mar 7 00:11:36 2013 UTC (4 years, 3 months ago) by caltinay
Minor epydoc fixes.


Revision 4282 - Directory Listing
Modified Wed Mar 6 08:33:59 2013 UTC (4 years, 3 months ago) by gross
first contribution for the magnetic cookbook.

Revision 4281 - Directory Listing
Modified Wed Mar 6 07:08:36 2013 UTC (4 years, 3 months ago) by gross
typo - sorry

Revision 4279 - Directory Listing
Modified Wed Mar 6 05:10:44 2013 UTC (4 years, 3 months ago) by caltinay
Update to API doco and separate section for multiple data sets.


Revision 4278 - Directory Listing
Modified Wed Mar 6 04:45:40 2013 UTC (4 years, 3 months ago) by gross
joint inversion chapter in part I replaced by announcment

Revision 4277 - Directory Listing
Modified Wed Mar 6 01:30:41 2013 UTC (4 years, 3 months ago) by caltinay
Implemented claimed support for mixing data with different resolutions.


Revision 4274 - Directory Listing
Modified Tue Mar 5 06:10:17 2013 UTC (4 years, 3 months ago) by caltinay
Small fix to example file.


Revision 4273 - Directory Listing
Modified Tue Mar 5 04:14:44 2013 UTC (4 years, 3 months ago) by caltinay
More doco updates and change to the return value of minimizers.


Revision 4272 - Directory Listing
Modified Tue Mar 5 01:06:45 2013 UTC (4 years, 3 months ago) by caltinay
Finished gravity part in cookbook. Started review of class descriptions.


Revision 4271 - Directory Listing
Modified Mon Mar 4 05:59:59 2013 UTC (4 years, 3 months ago) by caltinay
Finished data-with-holes section and added a few more notes about optional
arguments further up. Changed example scripts to show usage of special
features.


Revision 4270 - Directory Listing
Modified Mon Mar 4 04:01:28 2013 UTC (4 years, 3 months ago) by caltinay
Corrected test for modified handling of ER Mapper origin.


Revision 4269 - Directory Listing
Modified Mon Mar 4 00:54:29 2013 UTC (4 years, 3 months ago) by caltinay
Some more work.


Revision 4268 - Directory Listing
Modified Mon Mar 4 00:41:08 2013 UTC (4 years, 3 months ago) by gross
some citation fixed.


Revision 4267 - Directory Listing
Modified Fri Mar 1 04:50:54 2013 UTC (4 years, 3 months ago) by caltinay
Updated inversion example scripts, added ER Mapper data, checked results
and corrected some issues. Cookbook does not reflect the changes yet.


Revision 4266 - Directory Listing
Modified Fri Mar 1 01:37:41 2013 UTC (4 years, 3 months ago) by caltinay
Deleted old data files.


Revision 4265 - Directory Listing
Modified Fri Mar 1 00:52:30 2013 UTC (4 years, 3 months ago) by jfenwick
because we arent using python 2.5 anymore

Revision 4264 - Directory Listing
Modified Thu Feb 28 11:32:57 2013 UTC (4 years, 3 months ago) by jfenwick
Trying

Revision 4263 - Directory Listing
Modified Thu Feb 28 05:59:04 2013 UTC (4 years, 3 months ago) by caltinay
No more xrange in downunder.


Revision 4262 - Directory Listing
Modified Thu Feb 28 05:49:11 2013 UTC (4 years, 3 months ago) by caltinay
removed use of xrange and hack.


Revision 4260 - Directory Listing
Modified Wed Feb 27 04:58:47 2013 UTC (4 years, 3 months ago) by azadeh
adding gravity and magnetic data files which used for inversions


Revision 4259 - Directory Listing
Modified Wed Feb 27 03:52:35 2013 UTC (4 years, 3 months ago) by azadeh
cookmagnetic


Revision 4258 - Directory Listing
Modified Wed Feb 27 03:50:08 2013 UTC (4 years, 3 months ago) by azadeh
cookmagnetic


Revision 4256 - Directory Listing
Modified Wed Feb 27 03:25:05 2013 UTC (4 years, 3 months ago) by azadeh
changing some magnetic result image names


Revision 4255 - Directory Listing
Modified Wed Feb 27 03:06:21 2013 UTC (4 years, 3 months ago) by jfenwick
Hopefully, this will address the interpolation problems.

New canInterpolate() function exposed to python which calls probeInterpolation

AbstractDomain now has an additional virtual.
preferredIntrpolationOnDomain()

This will return 0 if interpolation is impossible, 1 if possible and preferred.
It will return -1 if interpolation is possible and preferred in the 
oposite direction.

A value of -1 does not say that the proposed interpolation is possible or not.
Rather it indicates "please use the other way".
If you really _need_ to test it that way, use probeInterpolationOnDomain 



Revision 4254 - Directory Listing
Modified Wed Feb 27 02:59:29 2013 UTC (4 years, 3 months ago) by azadeh
added joint result 


Revision 4253 - Directory Listing
Modified Wed Feb 27 02:55:32 2013 UTC (4 years, 3 months ago) by azadeh
removed joint result


Revision 4252 - Directory Listing
Modified Wed Feb 27 02:49:06 2013 UTC (4 years, 3 months ago) by azadeh
added magnetic inversion results


Revision 4251 - Directory Listing
Modified Wed Feb 27 02:47:10 2013 UTC (4 years, 3 months ago) by azadeh
removed old magnetic images
This line, and those below, will be ignored--

D    QLDMagMu10Contour.png
D    QLDMagMu01Slice.png
D    QLDMagMu1Contour.png
D    QLDMagMu100Slice.png
D    QLDMagMu01Contour.png
D    QLDMagMu10Slice.png
D    QLDMagMu100Contour.png
D    QLDMagMu1Slice.png


Revision 4250 - Directory Listing
Modified Wed Feb 27 00:26:12 2013 UTC (4 years, 3 months ago) by caltinay
Fix for joint example.


Revision 4249 - Directory Listing
Modified Tue Feb 26 01:01:59 2013 UTC (4 years, 4 months ago) by caltinay
s/shake75/bollide. Made build_full succeed without cppunit.


Revision 4248 - Directory Listing
Modified Mon Feb 25 05:53:55 2013 UTC (4 years, 4 months ago) by jfenwick
This should not trigger the build

Revision 4247 - Directory Listing
Modified Mon Feb 25 05:51:41 2013 UTC (4 years, 4 months ago) by jfenwick


Revision 4246 - Directory Listing
Modified Mon Feb 25 05:49:49 2013 UTC (4 years, 4 months ago) by jfenwick
still testing

Revision 4245 - Directory Listing
Modified Mon Feb 25 05:45:06 2013 UTC (4 years, 4 months ago) by jfenwick
again

Revision 4244 - Directory Listing
Modified Mon Feb 25 05:37:50 2013 UTC (4 years, 4 months ago) by jfenwick
More testing and a target in scons for the pdf docs


Revision 4243 - Directory Listing
Modified Mon Feb 25 05:33:01 2013 UTC (4 years, 4 months ago) by jfenwick
For testing buildbot


Revision 4242 - Directory Listing
Modified Mon Feb 25 03:16:14 2013 UTC (4 years, 4 months ago) by jfenwick
Allow pure virtual classes to be exported to python.
Temporary fix for a ripley interpolation issue


Revision 4241 - Directory Listing
Modified Fri Feb 22 11:35:11 2013 UTC (4 years, 4 months ago) by jfenwick
Added py3 config

Revision 4240 - Directory Listing
Modified Fri Feb 22 01:51:19 2013 UTC (4 years, 4 months ago) by jfenwick
options file for a clang buildbot

Revision 4239 - Directory Listing
Modified Fri Feb 22 00:35:01 2013 UTC (4 years, 4 months ago) by caltinay
initialize utm zone in er mapper reader.


Revision 4238 - Directory Listing
Modified Thu Feb 21 09:58:49 2013 UTC (4 years, 4 months ago) by jfenwick
fixed some relative imports and uses of xrange

Revision 4237 - Directory Listing
Modified Thu Feb 21 07:27:36 2013 UTC (4 years, 4 months ago) by jfenwick
Fixed bad tabbing so this revision works with python3 or clang.
(clang at least up to the tests which need pyproj)


Revision 4236 - Directory Listing
Modified Thu Feb 21 05:05:05 2013 UTC (4 years, 4 months ago) by jfenwick
Noted that saveDX and saveVTK have been removed.


Revision 4235 - Directory Listing
Modified Thu Feb 21 04:05:53 2013 UTC (4 years, 4 months ago) by caltinay
small fix.


Revision 4234 - Directory Listing
Modified Thu Feb 21 04:00:31 2013 UTC (4 years, 4 months ago) by gross
typo fixed

Revision 4233 - Directory Listing
Modified Thu Feb 21 02:00:09 2013 UTC (4 years, 4 months ago) by caltinay
updated content file (wishlist). Added byte swapping to plotter.


Revision 4232 - Directory Listing
Modified Wed Feb 20 08:31:31 2013 UTC (4 years, 4 months ago) by jfenwick
Fixed the WrappedArray class so it doesn't generate warnings


Revision 4231 - Directory Listing
Modified Wed Feb 20 07:41:52 2013 UTC (4 years, 4 months ago) by jfenwick
Updating doco for pyproj and a few other minor inconsistancies.  The inversion doco still needs to mention them.

Revision 4230 - Directory Listing
Modified Wed Feb 20 03:57:37 2013 UTC (4 years, 4 months ago) by caltinay
Removed some superfluous files.


Revision 4229 - Directory Listing
Modified Wed Feb 20 03:39:46 2013 UTC (4 years, 4 months ago) by azadeh
cookgravity


Revision 4228 - Directory Listing
Modified Wed Feb 20 03:34:07 2013 UTC (4 years, 4 months ago) by caltinay
Tweak & fix for data plotters


Revision 4227 - Directory Listing
Modified Wed Feb 20 03:10:50 2013 UTC (4 years, 4 months ago) by caltinay
ER Mapper data source updates.


Revision 4226 - Directory Listing
Modified Wed Feb 20 03:07:36 2013 UTC (4 years, 4 months ago) by caltinay
typo.


Revision 4225 - Directory Listing
Modified Wed Feb 20 02:45:09 2013 UTC (4 years, 4 months ago) by azadeh
moving images to figures folder


Revision 4224 - Directory Listing
Modified Wed Feb 20 02:34:18 2013 UTC (4 years, 4 months ago) by azadeh
changing images in cook gravity


Revision 4223 - Directory Listing
Modified Wed Feb 20 01:47:26 2013 UTC (4 years, 4 months ago) by caltinay
$#@%%^@(!


Revision 4222 - Directory Listing
Modified Wed Feb 20 01:27:40 2013 UTC (4 years, 4 months ago) by caltinay
Disabled docs about NonlinearPDE and removed inversion from user's guide.


Revision 4221 - Directory Listing
Modified Wed Feb 20 01:24:29 2013 UTC (4 years, 4 months ago) by caltinay
The numpy 1.7 macro does not help since the new style API/macros are not
present in 1.6. So when compiling with numpy 1.7 werror needs to be set to
False.


Revision 4220 - Directory Listing
Modified Wed Feb 20 01:17:30 2013 UTC (4 years, 4 months ago) by azadeh
adding gravity images with color bar in a folder


Revision 4219 - Directory Listing
Modified Wed Feb 20 00:26:19 2013 UTC (4 years, 4 months ago) by caltinay
Not sure why, but this fixes all failures in the linearPDE tests with ripley.


Revision 4218 - Directory Listing
Modified Tue Feb 19 06:11:35 2013 UTC (4 years, 4 months ago) by caltinay
Added gravity data in ER Mapper format and inversion script for it.


Revision 4217 - Directory Listing
Modified Tue Feb 19 06:09:51 2013 UTC (4 years, 4 months ago) by caltinay
numpy 1.7 introduced a warning for deprecation of certain APIs. We have to
acknowledge that to get rid of the warning...


Revision 4216 - Directory Listing
Modified Tue Feb 19 05:15:38 2013 UTC (4 years, 4 months ago) by caltinay
Report if pyproj is available.


Revision 4215 - Directory Listing
Modified Tue Feb 19 02:52:40 2013 UTC (4 years, 4 months ago) by azadeh
adding gravity coarse data


Revision 4214 - Directory Listing
Modified Tue Feb 19 02:42:43 2013 UTC (4 years, 4 months ago) by caltinay
Added capstartfalse/true to escript cookbook figures with no caption so
the build succeeds with the hypcap package enabled.


Revision 4213 - Directory Listing
Modified Tue Feb 19 01:16:29 2013 UTC (4 years, 4 months ago) by caltinay
Some cleanup and more consistent logging.


Revision 4212 - Directory Listing
Modified Tue Feb 19 00:11:28 2013 UTC (4 years, 4 months ago) by caltinay
Even friendlier message when pyproj is not installed but required.


Revision 4211 - Directory Listing
Modified Mon Feb 18 23:54:46 2013 UTC (4 years, 4 months ago) by caltinay
Implemented interpolation from Reduced[Face]Elements to [Face]Elements and
changed regularization to compute gradient on Function instead of
ReducedFunction. Results differ slightly so this should help with the accuracy.


Revision 4210 - Directory Listing
Modified Mon Feb 18 23:47:09 2013 UTC (4 years, 4 months ago) by jfenwick
Added suggests for new libraries used by downunder.


Revision 4209 - Directory Listing
Modified Mon Feb 18 06:00:56 2013 UTC (4 years, 4 months ago) by caltinay
Fixed joint example file, added ER Mapper plot script, updated content file.


Revision 4208 - Directory Listing
Modified Mon Feb 18 05:02:28 2013 UTC (4 years, 4 months ago) by jfenwick
rename so the poor case-sensitive mac can checkout

Revision 4207 - Directory Listing
Modified Mon Feb 18 03:17:11 2013 UTC (4 years, 4 months ago) by azadeh
adding bar for gravity image


Revision 4206 - Directory Listing
Modified Sun Feb 17 23:32:07 2013 UTC (4 years, 4 months ago) by caltinay
Import minimizers by default so the exception classes are exposed.


Revision 4205 - Directory Listing
Modified Fri Feb 15 06:02:07 2013 UTC (4 years, 4 months ago) by caltinay
Work on inversion cookbook. Also tweak to hyperref and a few more references.


Revision 4204 - Directory Listing
Modified Thu Feb 14 08:06:26 2013 UTC (4 years, 4 months ago) by gross
more on gravity and cleaning up file names

Revision 4203 - Directory Listing
Modified Thu Feb 14 07:05:58 2013 UTC (4 years, 4 months ago) by gross
Clarification of file names.

Revision 4202 - Directory Listing
Modified Thu Feb 14 06:53:41 2013 UTC (4 years, 4 months ago) by gross
Some adjustments to the sturture and naming

Revision 4201 - Directory Listing
Modified Thu Feb 14 06:40:01 2013 UTC (4 years, 4 months ago) by caltinay
DomainBuilder now ensures all data is in same UTM zone (with test).


Revision 4200 - Directory Listing
Modified Thu Feb 14 04:35:38 2013 UTC (4 years, 4 months ago) by azadeh
adding content folder to show input files


Revision 4199 - Directory Listing
Modified Wed Feb 13 08:39:05 2013 UTC (4 years, 4 months ago) by gross
more in the inversion cook-book

Revision 4198 - Directory Listing
Modified Wed Feb 13 06:49:10 2013 UTC (4 years, 4 months ago) by gross
name adjustments and remove unused files

Revision 4197 - Directory Listing
Modified Wed Feb 13 05:53:19 2013 UTC (4 years, 4 months ago) by caltinay
Changes to netCDF data source:
-removed assumptions
-added parameters to override data/error variable names, scale factor and null
value.


Revision 4196 - Directory Listing
Modified Wed Feb 13 00:58:37 2013 UTC (4 years, 4 months ago) by caltinay
Small fix so ERS files with DOS newline are parsed correctly.


Revision 4195 - Directory Listing
Modified Tue Feb 12 04:08:19 2013 UTC (4 years, 4 months ago) by jfenwick
Fixing case mismatch that was preventing bibtex from building

Revision 4194 - Directory Listing
Modified Tue Feb 12 03:04:17 2013 UTC (4 years, 4 months ago) by azadeh
Fixing some naming clashes

Revision 4193 - Directory Listing
Modified Tue Feb 12 00:59:49 2013 UTC (4 years, 4 months ago) by azadeh
reference


Revision 4192 - Directory Listing
Modified Tue Feb 12 00:28:47 2013 UTC (4 years, 4 months ago) by gross
problem with nc reader for dudley and finley fixed: the reader builds now the taginuse lists.

Revision 4191 - Directory Listing
Modified Mon Feb 11 08:22:47 2013 UTC (4 years, 4 months ago) by gross
more on gravity cook book

Revision 4190 - Directory Listing
Modified Mon Feb 11 05:10:00 2013 UTC (4 years, 4 months ago) by gross
unit gal added

Revision 4189 - Directory Listing
Modified Mon Feb 11 04:17:00 2013 UTC (4 years, 4 months ago) by gross
some images added

Revision 4188 - Directory Listing
Modified Mon Feb 11 01:51:22 2013 UTC (4 years, 4 months ago) by caltinay
Removed unneeded (large) result files.


Revision 4187 - Directory Listing
Modified Mon Feb 11 01:05:10 2013 UTC (4 years, 4 months ago) by azadeh
adding gravity magnetic and joint inversion files in netcdf format 


Revision 4186 - Directory Listing
Modified Mon Feb 11 00:47:34 2013 UTC (4 years, 4 months ago) by azadeh
adding gravity plots with different Mu


Revision 4185 - Directory Listing
Modified Fri Feb 8 09:06:21 2013 UTC (4 years, 4 months ago) by gross
modifications to cookbook

Revision 4184 - Directory Listing
Modified Fri Feb 8 04:33:48 2013 UTC (4 years, 4 months ago) by azadeh
new images in cookgravity


Revision 4183 - Directory Listing
Modified Mon Feb 4 02:58:02 2013 UTC (4 years, 4 months ago) by azadeh
joint result image updated


Revision 4182 - Directory Listing
Modified Fri Feb 1 02:29:53 2013 UTC (4 years, 4 months ago) by caltinay
Revised Intro/Overview text.


Revision 4181 - Directory Listing
Modified Fri Feb 1 02:16:56 2013 UTC (4 years, 4 months ago) by azadeh
cook joint


Revision 4180 - Directory Listing
Modified Thu Jan 31 04:58:16 2013 UTC (4 years, 4 months ago) by azadeh
updating


Revision 4179 - Directory Listing
Modified Thu Jan 31 04:30:50 2013 UTC (4 years, 4 months ago) by caltinay
More doco.


Revision 4178 - Directory Listing
Modified Thu Jan 31 03:18:56 2013 UTC (4 years, 4 months ago) by caltinay
Some more doco.


Revision 4177 - Directory Listing
Modified Thu Jan 31 02:23:02 2013 UTC (4 years, 4 months ago) by azadeh
cook joint and magnetic


Revision 4176 - Directory Listing
Modified Wed Jan 30 05:30:30 2013 UTC (4 years, 4 months ago) by caltinay
Removed tests that are known not to work.


Revision 4175 - Directory Listing
Modified Wed Jan 30 05:01:50 2013 UTC (4 years, 4 months ago) by caltinay
joint netcdf example and some minor fixes to other example/test case.


Revision 4174 - Directory Listing
Modified Wed Jan 30 03:21:27 2013 UTC (4 years, 4 months ago) by caltinay
ripley's readBinaryGrid and readNcGrid now filter out NaN leaving the relevant
destination data points untouched.


Revision 4173 - Directory Listing
Modified Wed Jan 30 03:05:01 2013 UTC (4 years, 4 months ago) by caltinay
Do not use -ffast-math by default (see mantis 691).


Revision 4172 - Directory Listing
Modified Wed Jan 30 01:24:03 2013 UTC (4 years, 4 months ago) by azadeh
cookjoint
--This line, and those below, will be ignored

M    CookJoint.tex


Revision 4168 - Directory Listing
Modified Fri Jan 25 07:31:47 2013 UTC (4 years, 5 months ago) by jfenwick
Release title and dep fix

Revision 4167 - Directory Listing
Modified Fri Jan 25 05:21:30 2013 UTC (4 years, 5 months ago) by jfenwick
fixes for doco for earlier releases

Revision 4166 - Directory Listing
Modified Fri Jan 25 04:18:45 2013 UTC (4 years, 5 months ago) by azadeh
gravity


Revision 4165 - Directory Listing
Modified Fri Jan 25 01:07:57 2013 UTC (4 years, 5 months ago) by azadeh
joint


Revision 4164 - Directory Listing
Modified Thu Jan 24 05:34:13 2013 UTC (4 years, 5 months ago) by caltinay
netcdf data source description.


Revision 4163 - Directory Listing
Modified Thu Jan 24 05:03:48 2013 UTC (4 years, 5 months ago) by azadeh
changing


Revision 4162 - Directory Listing
Modified Thu Jan 24 03:53:19 2013 UTC (4 years, 5 months ago) by caltinay
Added missing example file to display netcdf data.


Revision 4161 - Directory Listing
Modified Thu Jan 24 03:22:38 2013 UTC (4 years, 5 months ago) by azadeh
modifying 


Revision 4160 - Directory Listing
Modified Thu Jan 24 00:13:32 2013 UTC (4 years, 5 months ago) by caltinay
Moved figures to subdir and added more DataSource doco.


Revision 4159 - Directory Listing
Modified Thu Jan 24 00:05:28 2013 UTC (4 years, 5 months ago) by azadeh
dding magnetic images


Revision 4158 - Directory Listing
Modified Wed Jan 23 07:02:21 2013 UTC (4 years, 5 months ago) by caltinay
Write output even when max iterations reached.


Revision 4157 - Directory Listing
Modified Wed Jan 23 03:52:07 2013 UTC (4 years, 5 months ago) by caltinay
added magnetic netcdf example (no data yet).


Revision 4156 - Directory Listing
Modified Wed Jan 23 03:45:14 2013 UTC (4 years, 5 months ago) by azadeh
changes in document


Revision 4155 - Directory Listing
Modified Wed Jan 23 00:05:03 2013 UTC (4 years, 5 months ago) by jfenwick
Removed some incorrect ACcESS copyright attributions [2010 or later] since ACcESS did not exist at that point. Also added 2013 to a couple of files which I missed.

Revision 4154 - Directory Listing
Modified Tue Jan 22 09:30:23 2013 UTC (4 years, 5 months ago) by jfenwick
Round 1 of copyright fixes

Revision 4153 - Directory Listing
Modified Tue Jan 22 01:57:50 2013 UTC (4 years, 5 months ago) by gross
no driver example added. Doe not work yet.

Revision 4152 - Directory Listing
Modified Tue Jan 22 00:29:03 2013 UTC (4 years, 5 months ago) by caltinay
Moved figures to subdirectory.


Revision 4151 - Directory Listing
Modified Tue Jan 22 00:23:39 2013 UTC (4 years, 5 months ago) by azadeh
update joint and magnetic cookbook.


Revision 4150 - Directory Listing
Modified Mon Jan 21 04:14:24 2013 UTC (4 years, 5 months ago) by caltinay
Raise an exception if some methods are called after domain creation.


Revision 4149 - Directory Listing
Modified Mon Jan 21 02:03:31 2013 UTC (4 years, 5 months ago) by caltinay
Checkpoint - DomainBuilder documented.


Revision 4148 - Directory Listing
Modified Mon Jan 21 01:04:20 2013 UTC (4 years, 5 months ago) by caltinay
Updated netcdf gravity inversion example.


Revision 4147 - Directory Listing
Modified Fri Jan 18 03:35:15 2013 UTC (4 years, 5 months ago) by gross
added some words in the overview and clean-up of bib.

Revision 4146 - Directory Listing
Modified Fri Jan 18 01:36:49 2013 UTC (4 years, 5 months ago) by gross
some remarks on the class dependency added.

Revision 4145 - Directory Listing
Modified Fri Jan 18 00:51:49 2013 UTC (4 years, 5 months ago) by caltinay
Checkpoint.


Revision 4144 - Directory Listing
Modified Fri Jan 18 00:34:21 2013 UTC (4 years, 5 months ago) by gross
new diagrams

Revision 4143 - Directory Listing
Modified Thu Jan 17 08:48:47 2013 UTC (4 years, 5 months ago) by gross
documentation of minimizer update plus clarification of notations on the code

Revision 4142 - Directory Listing
Modified Tue Jan 15 09:06:06 2013 UTC (4 years, 5 months ago) by gross
documentation of inversion cost function added

Revision 4141 - Directory Listing
Modified Tue Jan 15 04:11:12 2013 UTC (4 years, 5 months ago) by jfenwick
Fixed to scripts to allow doco to build in pbuilder.
Looking for libraries in the place they were built is a good I've found.


Revision 4140 - Directory Listing
Modified Tue Jan 15 02:34:41 2013 UTC (4 years, 5 months ago) by caltinay
Updated example inversion files.


Revision 4139 - Directory Listing
Modified Tue Jan 15 00:13:28 2013 UTC (4 years, 5 months ago) by caltinay
Added L-BFGS reference and some minor changes.


Revision 4138 - Directory Listing
Modified Mon Jan 14 23:57:00 2013 UTC (4 years, 5 months ago) by gross
some rearrangement of part II

Revision 4137 - Directory Listing
Modified Mon Jan 14 22:59:13 2013 UTC (4 years, 5 months ago) by caltinay
Disabled another test.


Revision 4136 - Directory Listing
Modified Mon Jan 14 05:20:34 2013 UTC (4 years, 5 months ago) by caltinay
clarifications about cartesian domain


Revision 4135 - Directory Listing
Modified Mon Jan 14 04:54:14 2013 UTC (4 years, 5 months ago) by caltinay
Fixed test file.


Revision 4134 - Directory Listing
Modified Sun Jan 13 23:24:35 2013 UTC (4 years, 5 months ago) by caltinay
Removed failing test.


Revision 4133 - Directory Listing
Modified Fri Jan 11 06:41:10 2013 UTC (4 years, 5 months ago) by gross
some documentation on Inversion Cost function added.

Revision 4132 - Directory Listing
Modified Fri Jan 11 05:46:49 2013 UTC (4 years, 5 months ago) by caltinay
Range of epydoc fixes.


Revision 4131 - Directory Listing
Modified Fri Jan 11 03:54:16 2013 UTC (4 years, 5 months ago) by gross
documentaion of inversion driver API added.

Revision 4130 - Directory Listing
Modified Thu Jan 10 03:38:17 2013 UTC (4 years, 5 months ago) by caltinay
Do not end document after chapter :-)


Revision 4129 - Directory Listing
Modified Thu Jan 10 03:30:45 2013 UTC (4 years, 5 months ago) by caltinay
Fixed small typo


Revision 4128 - Directory Listing
Modified Thu Jan 10 02:04:08 2013 UTC (4 years, 5 months ago) by caltinay
Use fixed low number of iterations for the callback test.


Revision 4127 - Directory Listing
Modified Thu Jan 10 00:46:56 2013 UTC (4 years, 5 months ago) by azadeh
add documentation for gravity.


Revision 4126 - Directory Listing
Modified Tue Jan 8 02:37:48 2013 UTC (4 years, 5 months ago) by gross
some work on the level set class. no testing yet.

Revision 4125 - Directory Listing
Modified Wed Jan 2 06:15:00 2013 UTC (4 years, 5 months ago) by gross
some fixes in the inversion set-up

Revision 4124 - Directory Listing
Modified Fri Dec 21 01:35:43 2012 UTC (4 years, 6 months ago) by gross
joint inversion added

Revision 4123 - Directory Listing
Modified Thu Dec 20 23:47:55 2012 UTC (4 years, 6 months ago) by gross
small fix

Revision 4122 - Directory Listing
Modified Thu Dec 20 05:42:35 2012 UTC (4 years, 6 months ago) by gross
More work towards joint inversion. There is now one class for inversion cost function which can handle all relevant cases 
for a single model inversion, cross gradient case and functional dependence of physical parameters.



Revision 4121 - Directory Listing
Modified Wed Dec 19 00:24:50 2012 UTC (4 years, 6 months ago) by gross
changes to the boundary conditions.

Revision 4120 - Directory Listing
Modified Tue Dec 18 04:49:37 2012 UTC (4 years, 6 months ago) by gross
some improvements to the robutness of the minimizer:
  a break down in the orthogonalization is hnadles via a restart.
  a restart can now be set manually
  the iteration throughs now an exception in case of failure.

It is also possible to set the density anomaly to zero for regions below a certain depth. 





Revision 4119 - Directory Listing
Modified Mon Dec 17 04:53:15 2012 UTC (4 years, 6 months ago) by gross
some adjustments to the documentation

Revision 4118 - Directory Listing
Modified Mon Dec 17 00:50:47 2012 UTC (4 years, 6 months ago) by jfenwick
Some tweaks for auto building - need more though

Revision 4117 - Directory Listing
Modified Fri Dec 14 07:29:35 2012 UTC (4 years, 6 months ago) by gross
some adjustments with names

Revision 4116 - Directory Listing
Modified Fri Dec 14 07:21:14 2012 UTC (4 years, 6 months ago) by gross
tests for oscillatory data added.

Revision 4115 - Directory Listing
Modified Fri Dec 14 04:48:48 2012 UTC (4 years, 6 months ago) by gross
terminolgy for magnetic flux density clarified. clean up on synthetic data

Revision 4114 - Directory Listing
Modified Fri Dec 14 04:24:46 2012 UTC (4 years, 6 months ago) by caltinay
Time to remove deprecated saveVTK/DX methods from Data and Domain.


Revision 4113 - Directory Listing
Modified Fri Dec 14 01:54:53 2012 UTC (4 years, 6 months ago) by caltinay
shake29 options file.


Revision 4112 - Directory Listing
Modified Fri Dec 14 01:51:30 2012 UTC (4 years, 6 months ago) by caltinay
Added simple gravity inversion example to be included in cookbook.


Revision 4111 - Directory Listing
Modified Fri Dec 14 01:46:13 2012 UTC (4 years, 6 months ago) by jfenwick
Fixed the genrst script to be executable

Revision 4110 - Directory Listing
Modified Fri Dec 14 01:21:33 2012 UTC (4 years, 6 months ago) by jfenwick
Fixed to use whatever python is leading the path.
Disabled epydoc


Revision 4109 - Directory Listing
Modified Fri Dec 14 01:08:52 2012 UTC (4 years, 6 months ago) by caltinay
Fixed tests.


Revision 4108 - Directory Listing
Modified Thu Dec 13 06:38:11 2012 UTC (4 years, 6 months ago) by caltinay
Changed methods to add padding areas.


Revision 4107 - Directory Listing
Modified Thu Dec 13 05:54:03 2012 UTC (4 years, 6 months ago) by jfenwick
Now building doc using sphinx. Doc builds will fail until I get stuff installed on savanna

Revision 4106 - Directory Listing
Modified Thu Dec 13 05:08:44 2012 UTC (4 years, 6 months ago) by gross
some clarification on how to handle back ground magnetic field plus renaming of SyntheticData

Revision 4105 - Directory Listing
Modified Thu Dec 13 04:11:59 2012 UTC (4 years, 6 months ago) by caltinay
Updated test to reflect interface changes.


Revision 4104 - Directory Listing
Modified Thu Dec 13 03:30:23 2012 UTC (4 years, 6 months ago) by jfenwick
Ensuring we are using new-style classes
This may not be strictly necessary since our code does not depend on the difference.


Revision 4103 - Directory Listing
Modified Wed Dec 12 07:03:02 2012 UTC (4 years, 6 months ago) by jfenwick
Got rid of some unwanted sidebar elts. Correctly detect standalone functions exposed by boost

Revision 4102 - Directory Listing
Modified Wed Dec 12 06:17:03 2012 UTC (4 years, 6 months ago) by gross
more improvements on rescaling of weights. We now try to balance the gradients rather than the values.

Revision 4101 - Directory Listing
Modified Wed Dec 12 04:22:58 2012 UTC (4 years, 6 months ago) by jfenwick
First attempt at a sphinx generated API docs
In the project root:

mkdir doctest
python doc/sphinx_api/genrst.py
cd doctest
make html

should do



Revision 4100 - Directory Listing
Modified Tue Dec 11 06:55:20 2012 UTC (4 years, 6 months ago) by gross
minimizer uses now a relative change to solution to terminate iteration. Gravity still has problems

Revision 4099 - Directory Listing
Modified Tue Dec 11 04:04:47 2012 UTC (4 years, 6 months ago) by gross
Clarification of terminology and scaling.
Joint inversion is not working yet.


Revision 4098 - Directory Listing
Modified Fri Dec 7 03:45:20 2012 UTC (4 years, 6 months ago) by caltinay
Unbroke my breakage.


Revision 4097 - Directory Listing
Modified Fri Dec 7 01:18:35 2012 UTC (4 years, 6 months ago) by caltinay
Minor edits.


Revision 4096 - Directory Listing
Modified Thu Dec 6 04:05:29 2012 UTC (4 years, 6 months ago) by jfenwick
temporary doc fixes and moving tsunami out of the way

Revision 4095 - Directory Listing
Modified Wed Dec 5 05:32:22 2012 UTC (4 years, 6 months ago) by caltinay
A bit of doco cleanup.


Revision 4094 - Directory Listing
Modified Mon Dec 3 23:28:38 2012 UTC (4 years, 6 months ago) by caltinay
Fixed typo.


Revision 4093 - Directory Listing
Modified Fri Nov 30 04:52:01 2012 UTC (4 years, 6 months ago) by gross
There is now a coherent implementation of gravity and magnetic forward model including an update of the user's guide.

Revision 4092 - Directory Listing
Modified Thu Nov 29 10:42:39 2012 UTC (4 years, 6 months ago) by caltinay
Minor change. Test commit.


Revision 4091 - Directory Listing
Modified Mon Nov 26 10:27:29 2012 UTC (4 years, 7 months ago) by gross
Some terminology introduced and magnetic inversion corrected.

Revision 4090 - Directory Listing
Modified Mon Nov 26 03:51:04 2012 UTC (4 years, 7 months ago) by caltinay
Savanna tweaks.


Revision 4089 - Directory Listing
Modified Fri Nov 23 04:41:54 2012 UTC (4 years, 7 months ago) by caltinay
Switch to new toolchain on Savanna.


Revision 4088 - Directory Listing
Modified Thu Nov 22 23:31:37 2012 UTC (4 years, 7 months ago) by caltinay
Use kronecker, not numpy's identity in wave (why do these issues come up now?)


Revision 4087 - Directory Listing
Modified Thu Nov 22 22:28:01 2012 UTC (4 years, 7 months ago) by caltinay
Moved matplotlib imports in test scripts before escript since there is an
import chain which pulls it so the use() function has no effect.


Revision 4086 - Directory Listing
Modified Wed Nov 21 02:48:12 2012 UTC (4 years, 7 months ago) by jfenwick
Doco for 1D interpolation [resolves #631]

Revision 4085 - Directory Listing
Modified Tue Nov 20 07:04:11 2012 UTC (4 years, 7 months ago) by jfenwick
nonuniformInterolate and Slope added.
Doco later


Revision 4084 - Directory Listing
Modified Tue Nov 20 06:22:07 2012 UTC (4 years, 7 months ago) by jfenwick
Adding some linebreaks

Revision 4083 - Directory Listing
Modified Mon Nov 19 22:19:42 2012 UTC (4 years, 7 months ago) by caltinay
removed manually set weights from scripts.


Revision 4082 - Directory Listing
Modified Mon Nov 19 06:16:06 2012 UTC (4 years, 7 months ago) by jfenwick
Minor changes to install doco

Revision 4081 - Directory Listing
Modified Mon Nov 19 02:35:18 2012 UTC (4 years, 7 months ago) by caltinay
Updated unit test to test LinearMapping instead of old ScalingMapping


Revision 4080 - Directory Listing
Modified Mon Nov 19 01:45:38 2012 UTC (4 years, 7 months ago) by jfenwick
Epydoc fixes


Revision 4079 - Directory Listing
Modified Fri Nov 16 07:59:01 2012 UTC (4 years, 7 months ago) by gross
some modifications to scaling in downunder. still not perfect.

Revision 4078 - Directory Listing
Modified Fri Nov 16 07:50:49 2012 UTC (4 years, 7 months ago) by jfenwick
Unit tests for binary install with no scons and no source tree.
Script for installing and testing a .deb within a chroot.




Revision 4077 - Directory Listing
Modified Fri Nov 16 04:31:02 2012 UTC (4 years, 7 months ago) by caltinay
Minor change.


Revision 4076 - Directory Listing
Modified Thu Nov 15 03:45:24 2012 UTC (4 years, 7 months ago) by gross
    def getDirectionalDerivative(self, m, d, grad_m):
        

Revision 4075 - Directory Listing
Modified Thu Nov 15 03:31:37 2012 UTC (4 years, 7 months ago) by gross
missing latex files

Revision 4074 - Directory Listing
Modified Thu Nov 15 03:30:59 2012 UTC (4 years, 7 months ago) by gross
this will break the downundermodule: major revision of the classes.

Revision 4073 - Directory Listing
Modified Thu Nov 15 03:28:33 2012 UTC (4 years, 7 months ago) by jfenwick
Fixing doco build error


Revision 4072 - Directory Listing
Modified Thu Nov 15 01:58:35 2012 UTC (4 years, 7 months ago) by jfenwick
Fix to prevent escript from segfaulting on quantal


Revision 4071 - Directory Listing
Modified Tue Nov 13 21:43:11 2012 UTC (4 years, 7 months ago) by gross
small fix

Revision 4070 - Directory Listing
Modified Tue Nov 13 07:55:22 2012 UTC (4 years, 7 months ago) by jfenwick
File for quantal. Now to work out why on earth quantal manages to make epydoc segfault


Revision 4069 - Directory Listing
Modified Tue Nov 13 07:47:16 2012 UTC (4 years, 7 months ago) by gross
ArithmeticTuple supports empty data object as components now.

Revision 4068 - Directory Listing
Modified Tue Nov 13 04:42:08 2012 UTC (4 years, 7 months ago) by vboros
Small corrections to the magnetic forward model



Revision 4067 - Directory Listing
Modified Mon Nov 12 07:35:14 2012 UTC (4 years, 7 months ago) by vboros
Magnetostatics background added



Revision 4066 - Directory Listing
Modified Mon Nov 12 06:18:47 2012 UTC (4 years, 7 months ago) by jfenwick
renaming wheezyoptions file

Revision 4065 - Directory Listing
Modified Mon Nov 12 04:47:32 2012 UTC (4 years, 7 months ago) by jfenwick
Trying without uml

Revision 4064 - Directory Listing
Modified Fri Nov 9 07:25:14 2012 UTC (4 years, 7 months ago) by jfenwick
Tweaks

Revision 4063 - Directory Listing
Modified Fri Nov 9 06:15:00 2012 UTC (4 years, 7 months ago) by caltinay
Fixed a typo in method description.


Revision 4062 - Directory Listing
Modified Fri Nov 9 04:53:08 2012 UTC (4 years, 7 months ago) by caltinay
Start of module reference section in inversion guide.


Revision 4061 - Directory Listing
Modified Fri Nov 9 04:05:28 2012 UTC (4 years, 7 months ago) by caltinay
Updated data source test cases.


Revision 4060 - Directory Listing
Modified Fri Nov 9 03:50:19 2012 UTC (4 years, 7 months ago) by caltinay
-Overhaul of inversion data sources. Domain is now generated and managed by separate class.
-Removed UBCDataSource which was only used for testing.
-Updated example scripts.


Revision 4059 - Directory Listing
Modified Fri Nov 9 03:20:23 2012 UTC (4 years, 7 months ago) by jfenwick
Start of substitution for rules


Revision 4058 - Directory Listing
Modified Fri Nov 2 06:47:06 2012 UTC (4 years, 7 months ago) by caltinay
-Ripley now checks for input fs when calling gradient
-interactive mode works again when filename is supplied (typo)
-forward model PDE sets symmetry on now


Revision 4057 - Directory Listing
Modified Fri Nov 2 04:15:09 2012 UTC (4 years, 7 months ago) by caltinay
toc/hyperref fixes for inversion pdf.


Revision 4056 - Directory Listing
Modified Thu Nov 1 07:20:38 2012 UTC (4 years, 7 months ago) by jfenwick
Allow doxygen to build in another target
Debian build stuff begins


Revision 4055 - Directory Listing
Modified Thu Nov 1 00:22:01 2012 UTC (4 years, 7 months ago) by gross
Renaming of filenames

Revision 4054 - Directory Listing
Modified Wed Oct 31 23:27:57 2012 UTC (4 years, 7 months ago) by gross
prilimary checkin 

Revision 4053 - Directory Listing
Modified Wed Oct 31 07:27:35 2012 UTC (4 years, 7 months ago) by caltinay
Do not fix potential on sides of domain by default.


Revision 4052 - Directory Listing
Modified Wed Oct 31 05:50:35 2012 UTC (4 years, 7 months ago) by gross
missing references added (mantis id=683)

Revision 4051 - Directory Listing
Modified Wed Oct 31 03:40:47 2012 UTC (4 years, 7 months ago) by caltinay
Split inversion cookbook into two parts...


Revision 4050 - Directory Listing
Modified Wed Oct 31 01:01:24 2012 UTC (4 years, 7 months ago) by caltinay
Changed initial Hessian in magnetic test and removed some debug output.


Revision 4049 - Directory Listing
Modified Wed Oct 31 00:50:50 2012 UTC (4 years, 7 months ago) by caltinay
Fixed typos.


Revision 4048 - Directory Listing
Modified Tue Oct 30 21:54:15 2012 UTC (4 years, 7 months ago) by gross
fixed modification in the DataSource creator

Revision 4047 - Directory Listing
Modified Tue Oct 30 09:10:07 2012 UTC (4 years, 7 months ago) by gross
More on magnetic inversion

Revision 4046 - Directory Listing
Modified Tue Oct 30 04:43:25 2012 UTC (4 years, 7 months ago) by caltinay
Deprecated saveDX and made sure DeprecationWarnings are shown (py2.7 disabled
those). Also a fix to $BUILD_DIR being non-absolute.


Revision 4045 - Directory Listing
Modified Tue Oct 30 03:57:22 2012 UTC (4 years, 7 months ago) by caltinay
Imported inversion cookbook.


Revision 4044 - Directory Listing
Modified Tue Oct 30 03:35:17 2012 UTC (4 years, 7 months ago) by caltinay
Some doco fixes for downunder.


Revision 4043 - Directory Listing
Modified Tue Oct 30 03:34:43 2012 UTC (4 years, 7 months ago) by caltinay
Compile fixes for install guide.


Revision 4042 - Directory Listing
Modified Mon Oct 29 05:55:58 2012 UTC (4 years, 7 months ago) by caltinay
New SaveSilo tests (only run if Silo module available and MPI size=1).
Tests are somewhat limited due to missing functionality in Silo module (devs
contacted about that).


Revision 4041 - Directory Listing
Modified Sun Oct 28 23:42:35 2012 UTC (4 years, 7 months ago) by caltinay
Fixed a typo


Revision 4040 - Directory Listing
Modified Sun Oct 28 22:37:45 2012 UTC (4 years, 7 months ago) by jfenwick
Some py3 changes that didn't get committed for some reason


Revision 4039 - Directory Listing
Modified Fri Oct 26 07:34:06 2012 UTC (4 years, 8 months ago) by gross
magnetic inversion added

Revision 4038 - Directory Listing
Modified Fri Oct 26 04:47:25 2012 UTC (4 years, 8 months ago) by jfenwick
Minor fix to control file

Revision 4037 - Directory Listing
Modified Fri Oct 26 03:04:30 2012 UTC (4 years, 8 months ago) by gross
some modifictaions to make implementation for magnetic inversion easier

Revision 4036 - Directory Listing
Modified Thu Oct 25 06:21:03 2012 UTC (4 years, 8 months ago) by caltinay
Added saveVTK tests for ripley domains.


Revision 4035 - Directory Listing
Modified Thu Oct 25 03:10:14 2012 UTC (4 years, 8 months ago) by caltinay
Tweaked scons files so tests work even when specifying non-absolute build_dir.


Revision 4034 - Directory Listing
Modified Thu Oct 25 02:54:01 2012 UTC (4 years, 8 months ago) by caltinay
Fixes to inversion. Using resetRightHandSideCoefficients() now.


Revision 4033 - Directory Listing
Modified Wed Oct 24 08:14:41 2012 UTC (4 years, 8 months ago) by gross
some typos fixed.

Revision 4032 - Directory Listing
Modified Wed Oct 24 08:06:15 2012 UTC (4 years, 8 months ago) by gross
Gravity inversion is disconnect from DataSource objects now in order to allow for more  flexibility
when it comes to the definition of of Mapping and Regulariztion. GravityInversion does not hold a reference to the datasource object anymore.

use   inv=GravityInversion()
      inv.setUp(datasource) 

rather than inv.setDataSource(datasource); inv.setUp()




Revision 4031 - Directory Listing
Modified Wed Oct 24 03:36:37 2012 UTC (4 years, 8 months ago) by caltinay
Added option -x to run xterm to run-escript and replaced a few bashims.


Revision 4030 - Directory Listing
Modified Wed Oct 24 00:57:36 2012 UTC (4 years, 8 months ago) by caltinay
Silenced the no-visit-in-path warning and fixed not-in-path run-escript in
utest.sh.


Revision 4029 - Directory Listing
Modified Wed Oct 24 00:29:15 2012 UTC (4 years, 8 months ago) by caltinay
Reapplied changes from rev. 3853 which got lost in a merge...


Revision 4028 - Directory Listing
Modified Tue Oct 23 05:16:38 2012 UTC (4 years, 8 months ago) by gross
changes in pycad to address feature request 0000661

Revision 4027 - Directory Listing
Modified Tue Oct 23 04:56:33 2012 UTC (4 years, 8 months ago) by gross
setting a constant value to the initial solution of the Transport problem 
had a problem. initial data object needs to be expanded before copied to the 
paso transport object.




Revision 4026 - Directory Listing
Modified Tue Oct 23 03:12:50 2012 UTC (4 years, 8 months ago) by gross
missing file

Revision 4025 - Directory Listing
Modified Mon Oct 22 08:18:47 2012 UTC (4 years, 8 months ago) by gross
 linearPDE.resetRightHandSideCoefficients has been implemented and tested.

Revision 4024 - Directory Listing
Modified Mon Oct 22 06:11:29 2012 UTC (4 years, 8 months ago) by gross
tag testing for finley and dudley files added.

Revision 4023 - Directory Listing
Modified Tue Oct 16 04:17:48 2012 UTC (4 years, 8 months ago) by caltinay
Another fix to the PDE assembly logic in ripley.


Revision 4022 - Directory Listing
Modified Mon Oct 15 23:52:24 2012 UTC (4 years, 8 months ago) by caltinay
Fixed checks in ripley::addPDEToRHS().


Revision 4021 - Directory Listing
Modified Mon Oct 15 02:31:00 2012 UTC (4 years, 8 months ago) by jfenwick
Doco fixes.
Unit test fix for sys.version_info type change


Revision 4020 - Directory Listing
Modified Thu Oct 11 22:27:33 2012 UTC (4 years, 8 months ago) by caltinay
Removed print() that slipped in in last commit.


Revision 4019 - Directory Listing
Modified Thu Oct 11 08:12:55 2012 UTC (4 years, 8 months ago) by jfenwick
More tabbing errors,
range/xrange
...

Revision 4018 - Directory Listing
Modified Thu Oct 11 04:43:39 2012 UTC (4 years, 8 months ago) by jfenwick
Used "new" raise syntax in a few places
Fixed some tabbing
Fixed some funnies involving changes to xrange/range
added a quick and nasty __hash__ function to Symbol
   def __hash__(self):
        return id(self)
This does mean that __hash__ and == do not match exactly.   Not sure if that matters for our purposes

Revision 4017 - Directory Listing
Modified Thu Oct 11 03:13:28 2012 UTC (4 years, 8 months ago) by caltinay
Modified a test so roundoff errors don't cause failures.


Revision 4016 - Directory Listing
Modified Tue Oct 9 03:50:27 2012 UTC (4 years, 8 months ago) by caltinay
Skip data source tests under MPI for now as there is no straightforward way
of comparing the data (saveVTK appears to be the best option).


Revision 4015 - Directory Listing
Modified Mon Oct 8 01:19:04 2012 UTC (4 years, 8 months ago) by caltinay
Updated savanna options file to use latest compiler, mkl


Revision 4014 - Directory Listing
Modified Thu Oct 4 03:28:35 2012 UTC (4 years, 8 months ago) by caltinay
Changed data source to use ripley's netCDF reader,
added tests and changed ERMapper test to have different x and y sizes.


Revision 4013 - Directory Listing
Modified Thu Oct 4 03:13:27 2012 UTC (4 years, 8 months ago) by caltinay
Implemented netCDF grid reader analogous to binary grid reader in ripley.


Revision 4012 - Directory Listing
Modified Wed Oct 3 02:25:10 2012 UTC (4 years, 8 months ago) by caltinay
Initialize X_reduced in forward model to avoid issues later on.


Revision 4011 - Directory Listing
Modified Wed Oct 3 00:47:55 2012 UTC (4 years, 8 months ago) by caltinay
Updated test reference file.


Revision 4010 - Directory Listing
Modified Tue Oct 2 06:57:11 2012 UTC (4 years, 8 months ago) by caltinay
Fixed a potential div by zero in ripley's automatic domain subdivider....


Revision 4009 - Directory Listing
Modified Tue Oct 2 05:53:37 2012 UTC (4 years, 8 months ago) by caltinay
don't try to flip y-coord in reader. some more fixes and doco.


Revision 4008 - Directory Listing
Modified Tue Oct 2 04:33:27 2012 UTC (4 years, 8 months ago) by gross
point coordinates are now written in %.14e rather then %f. This fixes accuracy problems when it comes to geometrically small domains.



Revision 4007 - Directory Listing
Modified Tue Oct 2 02:12:01 2012 UTC (4 years, 8 months ago) by caltinay
Doco updates.
Data source paddings now take x,y not xy,z as Z padding can be done by setting
vertical extents.


Revision 4006 - Directory Listing
Modified Fri Sep 28 06:16:46 2012 UTC (4 years, 8 months ago) by caltinay
Update vm options to use pip-installed numpy.


Revision 4005 - Directory Listing
Modified Fri Sep 28 06:09:03 2012 UTC (4 years, 8 months ago) by caltinay
test fixes, doco updates, annoyance removals.


Revision 4004 - Directory Listing
Modified Fri Sep 28 04:45:25 2012 UTC (4 years, 8 months ago) by caltinay
don't use escript.escript.Data...


Revision 4003 - Directory Listing
Modified Fri Sep 28 00:20:01 2012 UTC (4 years, 8 months ago) by jfenwick
Load balancing on unit tests

Revision 4002 - Directory Listing
Modified Fri Sep 28 00:16:56 2012 UTC (4 years, 8 months ago) by caltinay
Fixed a memory leak (freeing paso coupler) in ripley.


Revision 4001 - Directory Listing
Modified Thu Sep 27 01:35:52 2012 UTC (4 years, 9 months ago) by caltinay
Removed obsolete files.


Revision 4000 - Directory Listing
Modified Thu Sep 27 01:32:07 2012 UTC (4 years, 9 months ago) by caltinay
s/escript/escore/


Revision 3999 - Directory Listing
Modified Thu Sep 27 01:31:07 2012 UTC (4 years, 9 months ago) by jfenwick
Splitting tests


Revision 3998 - Directory Listing
Modified Thu Sep 27 01:17:28 2012 UTC (4 years, 9 months ago) by caltinay
Finley now throws in ownSample() for reduced function with mpisize>1.


Revision 3997 - Directory Listing
Modified Thu Sep 27 01:09:12 2012 UTC (4 years, 9 months ago) by caltinay
Add note to documentation that saveDataCSV will not work in all cases.


Revision 3996 - Directory Listing
Modified Thu Sep 27 00:54:10 2012 UTC (4 years, 9 months ago) by caltinay
Don't test saveCSV for cases it does not work with.


Revision 3995 - Directory Listing
Modified Wed Sep 26 12:43:17 2012 UTC (4 years, 9 months ago) by jfenwick
More module fiddles

Revision 3994 - Directory Listing
Modified Wed Sep 26 07:38:38 2012 UTC (4 years, 9 months ago) by jfenwick
Install doco still needs work.
Removing some of the weird:
     esys.finley.finley
type modules

Revision 3993 - Directory Listing
Modified Wed Sep 26 07:00:55 2012 UTC (4 years, 9 months ago) by caltinay
Addressing mantis 651. Test for finley will fail under MPI since there is
sth wrong with the way ReducedContinuousFunction samples are interrogated.


Revision 3992 - Directory Listing
Modified Wed Sep 26 02:50:48 2012 UTC (4 years, 9 months ago) by caltinay
Data.cpp: Removed some namespace ambiguities which fixes doxygen warnings, some
cleanup and reindent.
*: doxygen fixes.


Revision 3991 - Directory Listing
Modified Tue Sep 25 23:52:22 2012 UTC (4 years, 9 months ago) by caltinay
Updated doxygen cfg file and made a few first changes to doco.


Revision 3990 - Directory Listing
Modified Tue Sep 25 05:03:20 2012 UTC (4 years, 9 months ago) by caltinay
First set of assorted epydoc fixes/additions.


Revision 3989 - Directory Listing
Modified Tue Sep 25 02:21:54 2012 UTC (4 years, 9 months ago) by jfenwick
More copyright fixes.
pyvisi traces removed.
Some install doco

Revision 3988 - Directory Listing
Modified Mon Sep 24 01:08:19 2012 UTC (4 years, 9 months ago) by caltinay
Scale coordinates if pyproj is not available


Revision 3987 - Directory Listing
Modified Sun Sep 23 23:24:37 2012 UTC (4 years, 9 months ago) by caltinay
Fix to test which fails when ripley adjusts number of elements (domain decomp.)


Revision 3986 - Directory Listing
Modified Sun Sep 23 23:01:10 2012 UTC (4 years, 9 months ago) by caltinay
Added explicit cast to make osx happy.


Revision 3985 - Directory Listing
Modified Fri Sep 21 06:44:17 2012 UTC (4 years, 9 months ago) by caltinay
Unit test for ER Mapper reader.


Revision 3984 - Directory Listing
Modified Fri Sep 21 06:41:54 2012 UTC (4 years, 9 months ago) by caltinay
invert Y coordinate in ripley's 3d data reader. This needs to be configurable
and added to 2d as well...


Revision 3983 - Directory Listing
Modified Fri Sep 21 06:41:03 2012 UTC (4 years, 9 months ago) by caltinay
Use ReducedFunction for data sources.


Revision 3982 - Directory Listing
Modified Fri Sep 21 03:23:22 2012 UTC (4 years, 9 months ago) by jfenwick
More edits + removing pyvisi from trunk


Revision 3981 - Directory Listing
Modified Fri Sep 21 02:47:54 2012 UTC (4 years, 9 months ago) by jfenwick
First pass of updating copyright notices

Revision 3980 - Directory Listing
Modified Fri Sep 21 01:55:39 2012 UTC (4 years, 9 months ago) by caltinay
Now using NullCellValue to initialise data object for ERS reader.


Revision 3979 - Directory Listing
Modified Thu Sep 20 06:18:49 2012 UTC (4 years, 9 months ago) by caltinay
Fixed tests under MPI.


Revision 3978 - Directory Listing
Modified Thu Sep 20 04:36:17 2012 UTC (4 years, 9 months ago) by caltinay
Make sympy optional as it was intended initially. Trying to instantiate anything
from symbolic will raise an exception if sympy is not available.


Revision 3977 - Directory Listing
Modified Thu Sep 20 04:27:10 2012 UTC (4 years, 9 months ago) by caltinay
Export KMP_MONITOR_STACKSIZE so tests work on savanna.


Revision 3976 - Directory Listing
Modified Thu Sep 20 03:26:47 2012 UTC (4 years, 9 months ago) by caltinay
fixed python-2.7'ism.


Revision 3975 - Directory Listing
Modified Thu Sep 20 01:54:06 2012 UTC (4 years, 9 months ago) by caltinay
Merged symbolic branch into trunk. Curious what daniel and spartacus have to
say...


Revision 3972 - Directory Listing
Modified Wed Sep 19 03:08:39 2012 UTC (4 years, 9 months ago) by caltinay
Can now constrain sides of domain.


Revision 3971 - Directory Listing
Modified Wed Sep 19 02:55:35 2012 UTC (4 years, 9 months ago) by caltinay
Implemented binary grid reader in ripley which is now used in ER Mapper source.
Interface/details likely to change but need to get this running now.


Revision 3970 - Directory Listing
Modified Wed Sep 19 02:28:27 2012 UTC (4 years, 9 months ago) by jfenwick
More install doc fixes


Revision 3969 - Directory Listing
Modified Tue Sep 18 05:34:38 2012 UTC (4 years, 9 months ago) by jfenwick
Removing reference to nose


Revision 3968 - Directory Listing
Modified Mon Sep 17 06:30:02 2012 UTC (4 years, 9 months ago) by jfenwick
Starting updates to the install guide


Revision 3967 - Directory Listing
Modified Mon Sep 17 04:02:58 2012 UTC (4 years, 9 months ago) by jfenwick
Changes to SConstruct to allow building with clang


Revision 3966 - Directory Listing
Modified Mon Sep 17 00:45:39 2012 UTC (4 years, 9 months ago) by caltinay
Changed unit scale for ER Mapper files. Fixed an issue with UBC source.


Revision 3965 - Directory Listing
Modified Fri Sep 14 01:23:17 2012 UTC (4 years, 9 months ago) by caltinay
Data sources have to end up in the Function fs or we get into trouble when
interpolating. Now using setValueOfDataPoint() which doesn't seem to slow
things down too much.


Revision 3964 - Directory Listing
Modified Thu Sep 13 03:49:55 2012 UTC (4 years, 9 months ago) by caltinay
Hopefully this will fix the interpolation in data sources.


Revision 3963 - Directory Listing
Modified Thu Sep 13 01:39:00 2012 UTC (4 years, 9 months ago) by jfenwick
Fix to keep the warning-free-build happy


Revision 3962 - Directory Listing
Modified Tue Sep 11 09:12:07 2012 UTC (4 years, 9 months ago) by jfenwick
Fix in brick for ambiguous typing.

Python work around for unit tests.
Passing cpp tests as well.

omp is disabled due to a weird linking error.


Revision 3961 - Directory Listing
Modified Tue Sep 11 07:21:41 2012 UTC (4 years, 9 months ago) by jfenwick
Options file for mole.
Work around for python compile errors


Revision 3960 - Directory Listing
Modified Mon Sep 10 01:39:40 2012 UTC (4 years, 9 months ago) by caltinay
Added accessors to fwd model, regularization and cost function plus access
to gravity survey data.


Revision 3959 - Directory Listing
Modified Fri Sep 7 04:48:07 2012 UTC (4 years, 9 months ago) by caltinay
support for geodetic coordinates in ER Mapper files. Correction to UTM
conversion (now assumes southern hemisphere).


Revision 3958 - Directory Listing
Modified Fri Sep 7 02:56:42 2012 UTC (4 years, 9 months ago) by caltinay
Fixes to netcdf data source and new ERS (ER Mapper) datasource.


Revision 3957 - Directory Listing
Modified Wed Sep 5 23:49:23 2012 UTC (4 years, 9 months ago) by caltinay
Do not require pyproj module-wide. Print a warning if it is not available but
needed instead of raising an exception.


Revision 3956 - Directory Listing
Modified Wed Sep 5 04:57:43 2012 UTC (4 years, 9 months ago) by caltinay
Fixes to netcdf reader for inversions.


Revision 3955 - Directory Listing
Modified Tue Sep 4 01:44:41 2012 UTC (4 years, 9 months ago) by caltinay
Added CentOS 6 vm options file.


Revision 3954 - Directory Listing
Modified Tue Sep 4 01:43:58 2012 UTC (4 years, 9 months ago) by caltinay
Fixed an issue with incompatible nose.


Revision 3953 - Directory Listing
Modified Mon Sep 3 00:57:12 2012 UTC (4 years, 9 months ago) by caltinay
Some test output adjustments.


Revision 3952 - Directory Listing
Modified Sun Sep 2 23:42:25 2012 UTC (4 years, 9 months ago) by caltinay
Made a test slightly more relaxed since roundoff errors caused it to fail on
one system.


Revision 3951 - Directory Listing
Modified Tue Aug 28 23:58:08 2012 UTC (4 years, 9 months ago) by caltinay
Fixed tests with python versions <2.7.


Revision 3950 - Directory Listing
Modified Fri Aug 24 06:10:02 2012 UTC (4 years, 10 months ago) by caltinay
More tests and corrections in the alternative minimizers.


Revision 3949 - Directory Listing
Modified Fri Aug 24 02:37:47 2012 UTC (4 years, 10 months ago) by caltinay
Added tests for mappings.


Revision 3948 - Directory Listing
Modified Fri Aug 24 01:01:34 2012 UTC (4 years, 10 months ago) by caltinay
Some interface changes to make the inversion more flexible.


Revision 3947 - Directory Listing
Modified Wed Aug 22 23:19:10 2012 UTC (4 years, 10 months ago) by caltinay
Compiling and installing downunder module now. Adjusted import statements
accordingly. Added a gravity test run.


Revision 3946 - Directory Listing
Modified Wed Aug 22 02:08:12 2012 UTC (4 years, 10 months ago) by caltinay
Initial import of inversion code from devteam area, rev. 51.
Nothing is scons built/installed/tested yet.


Revision 3945 - Directory Listing
Modified Tue Aug 21 04:11:13 2012 UTC (4 years, 10 months ago) by jfenwick
Changing utest behaviour for MPI


Revision 3944 - Directory Listing
Modified Mon Aug 20 02:11:22 2012 UTC (4 years, 10 months ago) by caltinay
Fixed ordering of Hex's in weipa's ripley writer.
Fixed an issue with auto domain subdivisions in ripley Brick.


Revision 3943 - Directory Listing
Modified Thu Aug 9 04:43:24 2012 UTC (4 years, 10 months ago) by caltinay
Added heuristics for number of domain subdivisions to ripley so ripley domains
can now be created without specifying the values manually (but a warning will
be printed).


Revision 3942 - Directory Listing
Modified Fri Jul 27 01:04:48 2012 UTC (4 years, 11 months ago) by jfenwick
Porting changes back from 3.3 release branch


Revision 3941 - Directory Listing
Modified Fri Jul 27 00:38:10 2012 UTC (4 years, 11 months ago) by jfenwick
Some more test disabling


Revision 3940 - Directory Listing
Modified Thu Jul 26 05:54:58 2012 UTC (4 years, 11 months ago) by jfenwick
Disabling tests which do not allow MPI
Previously we allowed these if there was only one rank


Revision 3939 - Directory Listing
Modified Mon Jul 23 01:50:46 2012 UTC (4 years, 11 months ago) by caltinay
Added return value checks for freopen in mpi redirect code. Ubuntu has a
warn_unused_result attribute set for the function.
Re-indented the file while at it.


Revision 3934 - Directory Listing
Modified Fri Jul 13 09:01:16 2012 UTC (4 years, 11 months ago) by jfenwick
Added unit test for tagreader


Revision 3931 - Directory Listing
Modified Tue Jul 10 00:39:09 2012 UTC (4 years, 11 months ago) by jfenwick
Fixing spelling


Revision 3928 - Directory Listing
Modified Mon Jul 9 23:23:43 2012 UTC (4 years, 11 months ago) by jfenwick
Do not allow attempts to setValue using a Locator which does not match the funcionSpace of the Data


Revision 3927 - Directory Listing
Modified Mon Jul 9 11:11:47 2012 UTC (4 years, 11 months ago) by jfenwick
Avoid warning


Revision 3923 - Directory Listing
Modified Mon Jul 9 05:12:12 2012 UTC (4 years, 11 months ago) by jfenwick
Fixing build error.


Revision 3922 - Directory Listing
Modified Mon Jul 9 02:19:51 2012 UTC (4 years, 11 months ago) by jfenwick
Adds setvalue to locator
Addresses mantis #531


Revision 3921 - Directory Listing
Modified Thu Jul 5 05:02:49 2012 UTC (4 years, 11 months ago) by jfenwick
Fix build error


Revision 3920 - Directory Listing
Modified Thu Jul 5 03:42:30 2012 UTC (4 years, 11 months ago) by jfenwick
Copied over tagname reading stuff from finley


Revision 3919 - Directory Listing
Modified Thu Jul 5 03:12:02 2012 UTC (4 years, 11 months ago) by jfenwick
Don't know what caused this to show as an error.
Compiler update perhaps?




Revision 3918 - Directory Listing
Modified Thu Jul 5 02:44:07 2012 UTC (4 years, 11 months ago) by jfenwick
Added unit test which uses the TestDomain to check reduction.
TestDomains can no longer be created directly from python 
(fixes problem I had earlier)

TestDomain can now create testdomains with aribtrarily sized 
coordinate vectors.


Revision 3917 - Directory Listing
Modified Thu Jul 5 00:17:50 2012 UTC (4 years, 11 months ago) by jfenwick
Fixing a bug in lazy reduction operations.
Will add extra test to prevent regression once I can find out why the test is crashing


Revision 3916 - Directory Listing
Modified Wed Jul 4 06:16:52 2012 UTC (4 years, 11 months ago) by jfenwick
Deal correctly with scalars passed into inplace update operators.
Fixes mantis 669

Revision 3915 - Directory Listing
Modified Mon Jun 25 02:17:58 2012 UTC (5 years ago) by caltinay
Added declspecs for all ripley classes.


Revision 3914 - Directory Listing
Modified Wed Jun 20 04:51:47 2012 UTC (5 years ago) by jfenwick
Only allow setX from ContinuousFunctions.
This addresses mantis 644.

Revision 3913 - Directory Listing
Modified Tue Jun 19 06:21:58 2012 UTC (5 years ago) by caltinay
Fixed misuse of getSampleDataRO with lazy data in ripley.


Revision 3912 - Directory Listing
Modified Fri Jun 15 05:02:42 2012 UTC (5 years ago) by jfenwick
GetMeshFromFile wrapper to load .fly or .msh depending on the extension.
Note that this only works on one of the two formats named .msh

Addresses mantis issue 641.



Revision 3911 - Directory Listing
Modified Thu Jun 14 01:01:03 2012 UTC (5 years ago) by jfenwick
Copyright changes

Revision 3910 - Directory Listing
Modified Thu Jun 14 00:45:03 2012 UTC (5 years ago) by gross
Small bug fixed.

Revision 3909 - Directory Listing
Modified Wed Jun 13 07:03:06 2012 UTC (5 years ago) by gross
darcy solver removes hydrostatic pressure from problem now

Revision 3908 - Directory Listing
Modified Wed Jun 13 05:43:45 2012 UTC (5 years ago) by caltinay
Fixed an error in ripley computing shared node id's.
pythonMPIredirect now redirects again.


Revision 3907 - Directory Listing
Modified Fri Jun 8 01:20:09 2012 UTC (5 years ago) by jfenwick
Only switch on useElementsOnFace  by default where we actually support it


Revision 3906 - Directory Listing
Modified Thu Jun 7 11:00:50 2012 UTC (5 years ago) by jfenwick
Disable AMG on MPI builds


Revision 3905 - Directory Listing
Modified Tue Jun 5 08:33:41 2012 UTC (5 years ago) by gross
length scale changed

Revision 3904 - Directory Listing
Modified Tue Jun 5 08:30:24 2012 UTC (5 years ago) by gross
incorrect macro element argument removed

Revision 3903 - Directory Listing
Modified Tue Jun 5 08:26:20 2012 UTC (5 years ago) by gross
offset removed: not clear why this was there

Revision 3901 - Directory Listing
Modified Wed May 23 08:09:45 2012 UTC (5 years, 1 month ago) by jfenwick
Rectangle and Brick use rich face element by default. 
This is to address issue #653

Updated unit tests to explicitly not use them where they didn't
specify previoulsy



Revision 3897 - Directory Listing
Modified Wed May 16 03:17:26 2012 UTC (5 years, 1 month ago) by jfenwick
correcting example

Revision 3896 - Directory Listing
Modified Fri May 11 01:31:29 2012 UTC (5 years, 1 month ago) by caltinay
Re-enable numpy header detection with python 2.


Revision 3895 - Directory Listing
Modified Mon Apr 16 00:09:42 2012 UTC (5 years, 2 months ago) by jfenwick
Adding some files which went missing in the merge


Revision 3894 - Directory Listing
Modified Wed Apr 11 03:13:15 2012 UTC (5 years, 2 months ago) by jfenwick
Still need to add notes to the install guide about Python3.


Revision 3893 - Directory Listing
Modified Wed Apr 11 01:40:10 2012 UTC (5 years, 2 months ago) by jfenwick
Pycad now generates scripts with floating points at 6 decimal places.
Tests have been ammended to match this.


Revision 3892 - Directory Listing
Modified Tue Apr 10 08:57:23 2012 UTC (5 years, 2 months ago) by jfenwick
Merged changes across from the attempt2 branch.
This version builds and passes python2 tests.
It also passes most python3 tests.




Revision 3887 - Directory Listing
Modified Thu Apr 5 03:14:59 2012 UTC (5 years, 2 months ago) by gross
low level system in AMG is created one only now.

Revision 3886 - Directory Listing
Modified Thu Apr 5 00:50:30 2012 UTC (5 years, 2 months ago) by gross
some minor problems with MPI AMG fixed.

Revision 3885 - Directory Listing
Modified Wed Apr 4 22:12:26 2012 UTC (5 years, 2 months ago) by gross
some fix in AMG

Revision 3884 - Directory Listing
Modified Wed Apr 4 04:55:43 2012 UTC (5 years, 2 months ago) by gross
some fix in AMG

Revision 3883 - Directory Listing
Modified Mon Mar 26 03:24:14 2012 UTC (5 years, 3 months ago) by caltinay
Modified dlopenflags in escript's init module so newer MKL libraries can
successfully load support libraries.


Revision 3882 - Directory Listing
Modified Thu Mar 22 02:15:57 2012 UTC (5 years, 3 months ago) by caltinay
Added another constraint for the numpy optimized array access: endianness.
The scipy netcdf reader gave me big endian data which resulted in garbage.
Can use the astype() method in python to convert.


Revision 3867 - Directory Listing
Modified Thu Mar 15 05:45:54 2012 UTC (5 years, 3 months ago) by caltinay
weipa treats shapes (1,) and (1,1) as scalars. Fixes bogus output in VTK writer.


Revision 3866 - Directory Listing
Modified Wed Mar 14 02:06:13 2012 UTC (5 years, 3 months ago) by caltinay
Use system silo on guineapig now.


Revision 3865 - Directory Listing
Modified Mon Mar 12 23:49:05 2012 UTC (5 years, 3 months ago) by caltinay
Re-enabled threaded MKL on epic.


Revision 3863 - Directory Listing
Modified Mon Mar 12 00:15:40 2012 UTC (5 years, 3 months ago) by gross
some debug prints removed

Revision 3861 - Directory Listing
Modified Fri Mar 9 02:06:29 2012 UTC (5 years, 3 months ago) by caltinay
Added options file that disables openMP and replaces the MKL library for savanna.


Revision 3853 - Directory Listing
Modified Thu Mar 1 07:25:03 2012 UTC (5 years, 3 months ago) by caltinay
Fixed hybrid mode when using OpenMPI by adding --cpus-per-rank argument to
mpirun in the launcher. Updated epic options file accordingly.


Revision 3852 - Directory Listing
Modified Thu Mar 1 05:34:52 2012 UTC (5 years, 3 months ago) by jfenwick
Correcting some indent errors


Revision 3851 - Directory Listing
Modified Wed Feb 29 05:23:30 2012 UTC (5 years, 3 months ago) by jfenwick
Start of cross-compile build for py3

Revision 3850 - Directory Listing
Modified Tue Feb 28 06:04:42 2012 UTC (5 years, 3 months ago) by caltinay
Support for CSC in ripley.


Revision 3843 - Directory Listing
Modified Mon Feb 27 05:50:58 2012 UTC (5 years, 4 months ago) by caltinay
Updated epic options, disabled OpenMP until problems solved.


Revision 3842 - Directory Listing
Modified Mon Feb 27 04:19:16 2012 UTC (5 years, 4 months ago) by caltinay
Updated savanna libraries and compiler version.


Revision 3841 - Directory Listing
Modified Mon Feb 27 04:18:53 2012 UTC (5 years, 4 months ago) by caltinay
Added support for OFFSET1 matrices in ripley.


Revision 3837 - Directory Listing
Modified Thu Feb 16 03:58:58 2012 UTC (5 years, 4 months ago) by caltinay
Test cleanup.


Revision 3836 - Directory Listing
Modified Thu Feb 16 03:17:18 2012 UTC (5 years, 4 months ago) by caltinay
Transport problem support for ripley.


Revision 3835 - Directory Listing
Modified Wed Feb 15 23:19:01 2012 UTC (5 years, 4 months ago) by gross
and another attempt to fix MPI compilation

Revision 3834 - Directory Listing
Modified Wed Feb 15 07:09:09 2012 UTC (5 years, 4 months ago) by gross
some declaration problems fixed 

Revision 3833 - Directory Listing
Modified Wed Feb 15 06:19:45 2012 UTC (5 years, 4 months ago) by lgao
Fix the merging problem for this file. 



Revision 3830 - Directory Listing
Modified Wed Feb 15 04:27:47 2012 UTC (5 years, 4 months ago) by lgao
Add comments for Smoother 



Revision 3829 - Directory Listing
Modified Wed Feb 15 03:33:08 2012 UTC (5 years, 4 months ago) by lgao
Fix warnings from another machine. 



Revision 3828 - Directory Listing
Modified Wed Feb 15 03:27:58 2012 UTC (5 years, 4 months ago) by lgao
Fix all warnings reported on guineapig.



Revision 3827 - Directory Listing
Modified Tue Feb 14 11:42:08 2012 UTC (5 years, 4 months ago) by lgao
 Merge branch "amg_from_3530" back into trunk.



Revision 3825 - Directory Listing
Modified Tue Feb 14 06:11:58 2012 UTC (5 years, 4 months ago) by gross
don't call MPI withing parallel regions

Revision 3824 - Directory Listing
Modified Tue Feb 14 01:22:16 2012 UTC (5 years, 4 months ago) by gross
fix for openmp

Revision 3823 - Directory Listing
Modified Mon Feb 13 08:09:32 2012 UTC (5 years, 4 months ago) by gross
some fixes for openmp/mpi compilation and linearNC can now handel constraints.

Revision 3822 - Directory Listing
Modified Mon Feb 13 06:22:06 2012 UTC (5 years, 4 months ago) by gross
Transport solver supports now constraints (except the linear CN)

Revision 3816 - Directory Listing
Modified Thu Feb 9 05:46:36 2012 UTC (5 years, 4 months ago) by caltinay
WrappedArray now honours the 'strides' field in the numpy array interface
and supports more data types. Fixes test failures on savanna which for some
reason did not surface on other machines.


Revision 3814 - Directory Listing
Modified Thu Feb 9 00:11:08 2012 UTC (5 years, 4 months ago) by caltinay
Changes to savanna options file to use intel 12 and numpy 1.6.1.


Revision 3808 - Directory Listing
Modified Mon Feb 6 06:17:47 2012 UTC (5 years, 4 months ago) by gross
some modifications to the test examples

Revision 3807 - Directory Listing
Modified Mon Feb 6 06:14:25 2012 UTC (5 years, 4 months ago) by gross
LINEAR_CRANK_NICOLSON solver added

Revision 3806 - Directory Listing
Modified Mon Feb 6 02:32:48 2012 UTC (5 years, 4 months ago) by caltinay
ripley::getSize() also returns circumcircle now.


Revision 3805 - Directory Listing
Modified Mon Feb 6 01:42:20 2012 UTC (5 years, 4 months ago) by gross
return circumcircle  now.

Revision 3804 - Directory Listing
Modified Mon Feb 6 00:48:22 2012 UTC (5 years, 4 months ago) by caltinay
Fixed utest.sh generator so tests can be run if the installation prefix is
not `pwd`


Revision 3803 - Directory Listing
Modified Fri Feb 3 06:16:30 2012 UTC (5 years, 4 months ago) by caltinay
Fixes to ripley unit test setup


Revision 3802 - Directory Listing
Modified Fri Feb 3 06:05:57 2012 UTC (5 years, 4 months ago) by caltinay
Quick fix for potential invalid memory access in paso.


Revision 3801 - Directory Listing
Modified Fri Feb 3 05:21:02 2012 UTC (5 years, 4 months ago) by caltinay
Fixed OpenMP bug in paso local AMG.


Revision 3800 - Directory Listing
Modified Fri Feb 3 01:18:06 2012 UTC (5 years, 4 months ago) by caltinay
Fixed integration with constant data on ripley.


Revision 3799 - Directory Listing
Modified Thu Feb 2 10:41:28 2012 UTC (5 years, 4 months ago) by gross
test for gradient of constant data added

Revision 3798 - Directory Listing
Modified Thu Feb 2 09:47:27 2012 UTC (5 years, 4 months ago) by gross
test for interpolation of constant data added

Revision 3797 - Directory Listing
Modified Thu Feb 2 09:28:59 2012 UTC (5 years, 4 months ago) by gross
test for integration of constant data added.

Revision 3796 - Directory Listing
Modified Thu Feb 2 06:26:15 2012 UTC (5 years, 4 months ago) by gross
typo in grad calculation fixed.

Revision 3795 - Directory Listing
Modified Thu Feb 2 05:54:34 2012 UTC (5 years, 4 months ago) by caltinay
Had to remove 'nowait' directive from PDE boundary conditions since all
4 (2D) / 8 (3D) values are updated the way it is implemented. This caused
race conditions when updating RHS.


Revision 3794 - Directory Listing
Modified Wed Feb 1 23:02:26 2012 UTC (5 years, 4 months ago) by gross
uninitialied variable fixed.

Revision 3793 - Directory Listing
Modified Wed Feb 1 07:39:43 2012 UTC (5 years, 4 months ago) by gross
new implementation of FCT solver with some modifications to the python interface

Revision 3792 - Directory Listing
Modified Wed Feb 1 06:16:25 2012 UTC (5 years, 4 months ago) by caltinay
Merged ripley rectangular domain into trunk.


Revision 3788 - Directory Listing
Modified Mon Jan 30 04:41:33 2012 UTC (5 years, 4 months ago) by caltinay
Fixed showEscriptParams() which hasn't worked for 2 years or so.


Revision 3787 - Directory Listing
Modified Fri Jan 27 01:43:47 2012 UTC (5 years, 5 months ago) by caltinay
Changed test cases from y.interpolateTable(...x...) to x.interpolateTable(...y...)


Revision 3786 - Directory Listing
Modified Wed Jan 25 04:46:39 2012 UTC (5 years, 5 months ago) by jfenwick
Made 2D interpolation call consistant with 1D and 3D.
Doco updates later


Revision 3784 - Directory Listing
Modified Wed Jan 25 01:31:42 2012 UTC (5 years, 5 months ago) by caltinay
Implemented optimized copy from numpy in WrappedArray (#652).


Revision 3782 - Directory Listing
Modified Tue Jan 24 01:30:38 2012 UTC (5 years, 5 months ago) by caltinay
Another attempt to fix #649


Revision 3778 - Directory Listing
Modified Fri Jan 20 05:09:52 2012 UTC (5 years, 5 months ago) by gross
better error reporting from UMFPACK

Revision 3775 - Directory Listing
Modified Wed Jan 18 07:26:34 2012 UTC (5 years, 5 months ago) by jfenwick
Weipa updated


Revision 3774 - Directory Listing
Modified Wed Jan 18 06:29:34 2012 UTC (5 years, 5 months ago) by jfenwick
dudley, pasowrap, pycad


Revision 3772 - Directory Listing
Modified Wed Jan 18 04:19:33 2012 UTC (5 years, 5 months ago) by jfenwick
Converting finley directories


Revision 3771 - Directory Listing
Modified Wed Jan 18 02:30:48 2012 UTC (5 years, 5 months ago) by jfenwick
First stage of 2.6/3 conversion


Revision 3747 - Directory Listing
Modified Thu Dec 15 02:13:14 2011 UTC (5 years, 6 months ago) by gross
inconsistent notation fixed.

Revision 3739 - Directory Listing
Modified Tue Dec 13 00:48:26 2011 UTC (5 years, 6 months ago) by caltinay
Ok, the python wrappers do use esysUtils for the exception translator.
Anything else?


Revision 3738 - Directory Listing
Modified Tue Dec 13 00:37:55 2011 UTC (5 years, 6 months ago) by caltinay
Windoze: Fixed warning and linker error
Don't look for non-existing pasowrap tests.


Revision 3737 - Directory Listing
Modified Tue Dec 13 00:04:39 2011 UTC (5 years, 6 months ago) by caltinay
Reordered and removed superfluous libraries from link lines. Hope W32 likes
that.


Revision 3736 - Directory Listing
Modified Mon Dec 12 01:26:51 2011 UTC (5 years, 6 months ago) by jfenwick
Fixed apparent multiple instances of Esys


Revision 3734 - Directory Listing
Modified Fri Dec 9 04:48:08 2011 UTC (5 years, 6 months ago) by caltinay
pycad kept creating temporary files. This should hopefully fix it.


Revision 3729 - Directory Listing
Modified Thu Dec 8 06:46:49 2011 UTC (5 years, 6 months ago) by jfenwick
Fixed mistake in Finley_Assemble_PDE and the dudley equivalent.

Cihan - you might want to look to see if Ripley is affected



Revision 3728 - Directory Listing
Modified Thu Dec 8 05:11:19 2011 UTC (5 years, 6 months ago) by jfenwick
Oops


Revision 3727 - Directory Listing
Modified Thu Dec 8 04:55:56 2011 UTC (5 years, 6 months ago) by jfenwick
More broken linkage


Revision 3726 - Directory Listing
Modified Thu Dec 8 04:35:52 2011 UTC (5 years, 6 months ago) by jfenwick
Fixing some broken linkage on windows


Revision 3723 - Directory Listing
Modified Wed Dec 7 05:59:04 2011 UTC (5 years, 6 months ago) by caltinay
Don't eat exceptions when using MPI with one rank.


Revision 3720 - Directory Listing
Modified Wed Dec 7 04:32:21 2011 UTC (5 years, 6 months ago) by caltinay
Fixed off-by-one error in FunctionSpace


Revision 3689 - Directory Listing
Modified Wed Nov 23 01:39:45 2011 UTC (5 years, 7 months ago) by gross
integration nodes fixed

Revision 3681 - Directory Listing
Modified Fri Nov 18 04:54:15 2011 UTC (5 years, 7 months ago) by caltinay
Moved implementation of getTransportTypeId() and getSystemMatrixTypeId() into
pasowrap.


Revision 3678 - Directory Listing
Modified Thu Nov 17 06:32:05 2011 UTC (5 years, 7 months ago) by jfenwick
Reversing other changes which made it in somehow


Revision 3677 - Directory Listing
Modified Thu Nov 17 04:01:12 2011 UTC (5 years, 7 months ago) by caltinay
Fixed order of libraries which makes static esysUtils work again.


Revision 3676 - Directory Listing
Modified Thu Nov 17 03:52:25 2011 UTC (5 years, 7 months ago) by jfenwick
Removed some debug text
Corrected some dudley where they should not have been.
Set savanna to build shared for now


Revision 3675 - Directory Listing
Modified Thu Nov 17 00:53:38 2011 UTC (5 years, 7 months ago) by jfenwick
pasowrap joins the trunk.


Revision 3667 - Directory Listing
Modified Tue Nov 15 23:29:23 2011 UTC (5 years, 7 months ago) by gross
better consistence of script and notation

Revision 3666 - Directory Listing
Modified Tue Nov 15 23:10:20 2011 UTC (5 years, 7 months ago) by gross
fix for https://mantis.esscc.uq.edu.au/view.php?id=647

Revision 3650 - Directory Listing
Modified Fri Nov 4 07:02:55 2011 UTC (5 years, 7 months ago) by gross
ode solver added

Revision 3649 - Directory Listing
Modified Fri Nov 4 04:35:15 2011 UTC (5 years, 7 months ago) by gross
gmsh reader understand name tags now.

Revision 3648 - Directory Listing
Modified Thu Nov 3 08:13:31 2011 UTC (5 years, 7 months ago) by gross
typos fixed

Revision 3647 - Directory Listing
Modified Tue Nov 1 23:33:18 2011 UTC (5 years, 7 months ago) by lgao
With this option file, unit tests finished successfully with the following order to load module: 

module load mpi/gcc/openmpi/1.4.3
module load python/2.6.7
module load boost/1.46.1-python-2.6
module load netcdf/4.0.1
module load scons/2.0.1-python-2.6
module load intel-compilers/11.1.075
module load intel-mkl/10.3.5.220
module load python-numpy/1.3.0-python-2.6
module load cppunit/1.12.1
module load python-matplotlib/0.98.5.3-python-2.6
module load hdf5/1.8.6
module load silo/4.7.2
module load hypre/2.0.0

HYPRE is loaded but not used yet since the installed hypre module on epic comes with static library only. 



Revision 3646 - Directory Listing
Modified Fri Oct 28 05:20:38 2011 UTC (5 years, 8 months ago) by lgao
working option file on epic



Revision 3645 - Directory Listing
Modified Fri Oct 28 00:11:30 2011 UTC (5 years, 8 months ago) by caltinay
Fixed typos.


Revision 3644 - Directory Listing
Modified Thu Oct 27 06:42:56 2011 UTC (5 years, 8 months ago) by gross
hint to add surface items in pycad

Revision 3643 - Directory Listing
Modified Thu Oct 27 06:23:16 2011 UTC (5 years, 8 months ago) by caltinay
Updated savanna options file. We're now using silo 4.8, netcdf 4.1.1 and boost 1.42 on savanna.


Revision 3642 - Directory Listing
Modified Thu Oct 27 03:41:51 2011 UTC (5 years, 8 months ago) by caltinay
Assorted spelling/comment fixes in paso.


Revision 3641 - Directory Listing
Modified Thu Oct 27 02:16:12 2011 UTC (5 years, 8 months ago) by gross
more work on the assemblage

Revision 3639 - Directory Listing
Modified Tue Oct 25 02:13:26 2011 UTC (5 years, 8 months ago) by caltinay
Assorted spelling fixes in finley C.


Revision 3637 - Directory Listing
Modified Fri Oct 21 04:29:33 2011 UTC (5 years, 8 months ago) by caltinay
Fixed memory leaks in loadMesh() for dudley and finley.


Revision 3635 - Directory Listing
Modified Fri Oct 21 00:26:01 2011 UTC (5 years, 8 months ago) by caltinay
Fixed minor issues.


Revision 3630 - Directory Listing
Modified Wed Oct 19 03:04:53 2011 UTC (5 years, 8 months ago) by gross
minor fix to dary flux

Revision 3629 - Directory Listing
Modified Wed Oct 19 03:04:27 2011 UTC (5 years, 8 months ago) by gross
darcy example added

Revision 3628 - Directory Listing
Modified Wed Oct 19 02:09:36 2011 UTC (5 years, 8 months ago) by caltinay
Prepend our libraries instead of appending. This should fix HYPRE link
issue on epic.


Revision 3627 - Directory Listing
Modified Fri Oct 14 13:54:49 2011 UTC (5 years, 8 months ago) by caltinay
Reverted some changes that slipped in and caused the Silo writer to not behave.


Revision 3626 - Directory Listing
Modified Fri Oct 14 02:34:55 2011 UTC (5 years, 8 months ago) by gross
Silo and cppunit added for epic (there is still a problem with hypre)

Revision 3625 - Directory Listing
Modified Thu Oct 13 01:54:27 2011 UTC (5 years, 8 months ago) by gross
missing argument in gmsh reader documentation added

Revision 3624 - Directory Listing
Modified Wed Oct 12 07:58:25 2011 UTC (5 years, 8 months ago) by gross
changes for epic.ivec.org

Revision 3623 - Directory Listing
Modified Tue Oct 11 03:59:40 2011 UTC (5 years, 8 months ago) by caltinay
Added option to enable/disable saving of mesh data in weipa.
Now defaults to false since it's mainly for debugging.
Fixes #640.


Revision 3622 - Directory Listing
Modified Thu Oct 6 08:06:41 2011 UTC (5 years, 8 months ago) by trankine
Epic.ivec.org scons build template

Revision 3620 - Directory Listing
Modified Wed Oct 5 06:06:14 2011 UTC (5 years, 8 months ago) by gross
bug fixed

Revision 3619 - Directory Listing
Modified Wed Oct 5 03:53:34 2011 UTC (5 years, 8 months ago) by gross
some rescaling of permeability in the darcy solver added

Revision 3618 - Directory Listing
Modified Fri Sep 30 04:07:09 2011 UTC (5 years, 8 months ago) by jfenwick
Allowed 'no' as an mpi type.
Allowed SVN_VERSION to be specified from the command line.
TO BE USED ONLY FOR RELEASE PURPOSES where you do not have a .svn checkout


Revision 3616 - Directory Listing
Modified Fri Sep 30 00:56:37 2011 UTC (5 years, 8 months ago) by jfenwick
Center a table that I noticed and use upquote package to stop LaTeX from
mucking about with ' in python code.

Fixes #632


Revision 3607 - Directory Listing
Modified Mon Sep 19 22:08:24 2011 UTC (5 years, 9 months ago) by caltinay
Fixed double/float warning.


Revision 3606 - Directory Listing
Modified Mon Sep 19 16:26:51 2011 UTC (5 years, 9 months ago) by trankine
Trial nosetests runner tests for better integration

Revision 3605 - Directory Listing
Modified Mon Sep 19 07:47:23 2011 UTC (5 years, 9 months ago) by trankine
cppunit actually does do the install step in the msvc project files and does put the build products where scons can find them.

Revision 3604 - Directory Listing
Modified Mon Sep 19 04:47:53 2011 UTC (5 years, 9 months ago) by caltinay
Changed detection of pdflatex since some versions of scons require .ltx or
.latex file extensions when pdflatex is not available.
Also added cleanup of utest.sh and buildvars file.


Revision 3603 - Directory Listing
Modified Mon Sep 19 03:42:53 2011 UTC (5 years, 9 months ago) by caltinay
Fixed some unused var errors in non-mpi build.


Revision 3602 - Directory Listing
Modified Mon Sep 19 02:38:11 2011 UTC (5 years, 9 months ago) by caltinay
Fix scons checks on windows


Revision 3601 - Directory Listing
Modified Mon Sep 19 01:21:33 2011 UTC (5 years, 9 months ago) by trankine
Updating cgisrv3 options for external cppunit - because I cant see brackets.

Revision 3600 - Directory Listing
Modified Mon Sep 19 00:58:15 2011 UTC (5 years, 9 months ago) by trankine
Updating cgisrv3 options for external cppunit

Revision 3599 - Directory Listing
Modified Fri Sep 16 01:34:46 2011 UTC (5 years, 9 months ago) by caltinay
Updated install guide to mention external CppUnit dependency for unit tests.


Revision 3598 - Directory Listing
Modified Fri Sep 16 01:01:17 2011 UTC (5 years, 9 months ago) by caltinay
New config option build_shared (which replaces share_paso & share_esysUtils).
Also enabled building escriptreader library on Windows which should now
work in both shared and static mode.


Revision 3597 - Directory Listing
Modified Thu Sep 15 06:03:17 2011 UTC (5 years, 9 months ago) by caltinay
Switching to external cppunit:
-removed tools/CppUnitTest
-updated scons script and files
-updated tests to changed API
-updated readme

Bumped scons options file version to 201. Additions:
-cppunit*
-boomeramg*
-vsl_random



Revision 3596 - Directory Listing
Modified Thu Sep 15 05:58:15 2011 UTC (5 years, 9 months ago) by caltinay
Deleted some obsolete options files.


Revision 3595 - Directory Listing
Modified Thu Sep 15 05:56:47 2011 UTC (5 years, 9 months ago) by caltinay
Skip some more gmsh-dependend tests if gmsh is not available.


Revision 3594 - Directory Listing
Modified Thu Sep 15 00:45:04 2011 UTC (5 years, 9 months ago) by caltinay
Added missing declspecs in paso. Thanks Terry.


Revision 3589 - Directory Listing
Modified Mon Sep 12 03:25:25 2011 UTC (5 years, 9 months ago) by gross
This fixes the bug 616. Problem was that the Coupler used the pattern of original rather than unrolled pattern.

Revision 3588 - Directory Listing
Modified Mon Sep 12 01:53:17 2011 UTC (5 years, 9 months ago) by gross
Typo fixed.

Revision 3586 - Directory Listing
Modified Fri Sep 9 04:02:29 2011 UTC (5 years, 9 months ago) by caltinay
run_domainreaders now passes some parameters to the constructors so
kwargs is tested to be working. Addresses #578.


Revision 3585 - Directory Listing
Modified Wed Sep 7 06:16:08 2011 UTC (5 years, 9 months ago) by caltinay
Fix for #582: Determine if gmsh was compiled with MPI support and use
MPI_Comm_spawn to invoke it if necessary.


Revision 3584 - Directory Listing
Modified Tue Sep 6 11:08:34 2011 UTC (5 years, 9 months ago) by jfenwick
Removing Locator.setValue for now


Revision 3583 - Directory Listing
Modified Tue Sep 6 04:27:59 2011 UTC (5 years, 9 months ago) by caltinay
Updated shake75 options file.


Revision 3582 - Directory Listing
Modified Tue Sep 6 02:02:17 2011 UTC (5 years, 9 months ago) by gross
some clarification of the documentation on the Stokes solver.

Revision 3581 - Directory Listing
Modified Tue Sep 6 00:52:58 2011 UTC (5 years, 9 months ago) by gross
Used python 2.7 syntax. Sorry!

Revision 3580 - Directory Listing
Modified Tue Sep 6 00:31:35 2011 UTC (5 years, 9 months ago) by gross
error handeling for python compilation improved.

Revision 3579 - Directory Listing
Modified Mon Sep 5 23:25:01 2011 UTC (5 years, 9 months ago) by jfenwick
Stopping unit test from failing until I can get it working


Revision 3578 - Directory Listing
Modified Mon Sep 5 23:18:45 2011 UTC (5 years, 9 months ago) by gross
Missing dependence added (?) and typo in test files fixed.

Revision 3577 - Directory Listing
Modified Mon Sep 5 08:22:52 2011 UTC (5 years, 9 months ago) by gross
getFLux fixed and tests added.


Revision 3576 - Directory Listing
Modified Mon Sep 5 06:33:20 2011 UTC (5 years, 9 months ago) by caltinay
Fixed two more instances of macro-dependent unused vars.


Revision 3575 - Directory Listing
Modified Fri Sep 2 08:31:08 2011 UTC (5 years, 9 months ago) by jfenwick
Fixing bug I introduced with the last commit


Revision 3574 - Directory Listing
Modified Fri Sep 2 07:19:31 2011 UTC (5 years, 9 months ago) by jfenwick
Added setValue to locator.
Some unit tests added but they aren't being triggered for some reason


Revision 3573 - Directory Listing
Modified Fri Sep 2 05:51:02 2011 UTC (5 years, 9 months ago) by jfenwick
Added more comprehensible doco about 3D interpolation.
Also fixed a bug but this may break code which previously used 3D interpolation.

This fixes mantis #581


Revision 3572 - Directory Listing
Modified Thu Sep 1 07:54:42 2011 UTC (5 years, 9 months ago) by jfenwick
Comment out a non-existant function from the Finley interface and (hopefully)
fix mantis bug #623


Revision 3571 - Directory Listing
Modified Thu Sep 1 03:53:23 2011 UTC (5 years, 9 months ago) by gross
LinearSolver option RILU has been removed from the documentation it is not supported yet.

Revision 3570 - Directory Listing
Modified Thu Sep 1 03:11:26 2011 UTC (5 years, 9 months ago) by jfenwick
Fixed some bib entries, changed visit script in guide to use " instead of '.
Reworded a sentence.


Revision 3569 - Directory Listing
Modified Thu Sep 1 02:42:36 2011 UTC (5 years, 9 months ago) by gross
Darcy flow solver and docu reviewed. Coupled solvers have been removed.


Revision 3568 - Directory Listing
Modified Tue Aug 30 08:23:24 2011 UTC (5 years, 9 months ago) by gross
darcy flux documentation updated.

Revision 3567 - Directory Listing
Modified Tue Aug 30 07:55:02 2011 UTC (5 years, 9 months ago) by gross
FIXME and TODO fixed.

Revision 3566 - Directory Listing
Modified Tue Aug 30 07:37:55 2011 UTC (5 years, 9 months ago) by gross
small fix to units

Revision 3565 - Directory Listing
Modified Mon Aug 29 10:28:57 2011 UTC (5 years, 9 months ago) by jfenwick
surely it will accept this one


Revision 3564 - Directory Listing
Modified Mon Aug 29 09:09:30 2011 UTC (5 years, 9 months ago) by jfenwick
In case windows is case sensitive


Revision 3563 - Directory Listing
Modified Mon Aug 29 04:26:46 2011 UTC (5 years, 9 months ago) by jfenwick
Another try to fix the windows issue


Revision 3562 - Directory Listing
Modified Mon Aug 29 03:31:13 2011 UTC (5 years, 9 months ago) by jfenwick
Removed DLL export from non-exported methods


Revision 3561 - Directory Listing
Modified Mon Aug 29 02:51:05 2011 UTC (5 years, 9 months ago) by jfenwick
Attempt to fix windows problem


Revision 3560 - Directory Listing
Modified Mon Aug 29 01:10:42 2011 UTC (5 years, 9 months ago) by gross
lf missing in buildvars print

Revision 3559 - Directory Listing
Modified Fri Aug 26 07:47:27 2011 UTC (5 years, 10 months ago) by jfenwick
Silence some warnings unused var warnings under gcc.



Revision 3558 - Directory Listing
Modified Fri Aug 26 06:09:02 2011 UTC (5 years, 10 months ago) by jfenwick
Merged changes from dirac.
Now the only way to add diracPoints is to use the constructor


Revision 3552 - Directory Listing
Modified Mon Aug 22 00:05:17 2011 UTC (5 years, 10 months ago) by jfenwick
Fixed icc problem


Revision 3551 - Directory Listing
Modified Fri Aug 19 03:53:41 2011 UTC (5 years, 10 months ago) by jfenwick
Changing unit test calls to use non deprecated forms (python2.7)
fixes bug #568


Revision 3550 - Directory Listing
Modified Fri Aug 19 01:51:35 2011 UTC (5 years, 10 months ago) by jfenwick
Switching from rand() to boost::random for non-VSL randoms


Revision 3549 - Directory Listing
Modified Tue Aug 9 06:40:06 2011 UTC (5 years, 10 months ago) by jfenwick
Fix for issue #617
A couple of extra tests to make sure it doesn't happen again


Revision 3548 - Directory Listing
Modified Tue Aug 9 04:00:27 2011 UTC (5 years, 10 months ago) by jfenwick
Fixing badger options


Revision 3547 - Directory Listing
Modified Tue Aug 2 04:24:09 2011 UTC (5 years, 10 months ago) by lgao
Set "lapack" to "mkl" before the mantis bug 0000616 is solved. 



Revision 3546 - Directory Listing
Modified Thu Jul 28 01:32:20 2011 UTC (5 years, 11 months ago) by jfenwick
Replaced 'and' with && since windows doesn't seem to understand it


Revision 3545 - Directory Listing
Modified Wed Jul 27 06:29:09 2011 UTC (5 years, 11 months ago) by lgao
Turn off VSL for random data before the MKL library link line problem has been solved. 



Revision 3544 - Directory Listing
Modified Wed Jul 27 06:19:10 2011 UTC (5 years, 11 months ago) by jfenwick
Temporary fix to get windows to compile


Revision 3543 - Directory Listing
Modified Fri Jul 22 06:58:03 2011 UTC (5 years, 11 months ago) by gross
and the generator script

Revision 3542 - Directory Listing
Modified Fri Jul 22 06:57:41 2011 UTC (5 years, 11 months ago) by gross
first attempts toward a multi grid solver

Revision 3541 - Directory Listing
Modified Fri Jul 22 03:21:06 2011 UTC (5 years, 11 months ago) by trankine
migration to system maintained dependancies (not per build). will allow multi builders

Revision 3538 - Directory Listing
Modified Mon Jul 4 00:13:02 2011 UTC (5 years, 11 months ago) by jfenwick
Added paper with current dev team to the references section.


Revision 3529 - Directory Listing
Modified Thu May 26 00:36:10 2011 UTC (6 years, 1 month ago) by caltinay
Re-enable VisIt and Silo on savanna and use gcc-4.6 on shake75.


Revision 3528 - Directory Listing
Modified Tue May 24 07:02:08 2011 UTC (6 years, 1 month ago) by gross


Revision 3527 - Directory Listing
Modified Tue May 24 06:59:20 2011 UTC (6 years, 1 month ago) by gross
modifications to the coal seam gas 

Revision 3526 - Directory Listing
Modified Tue May 24 05:01:46 2011 UTC (6 years, 1 month ago) by gross
coal code uses nodal wells now

Revision 3525 - Directory Listing
Modified Tue May 24 04:04:58 2011 UTC (6 years, 1 month ago) by gross
and more typos fixed.

Revision 3524 - Directory Listing
Modified Tue May 24 02:23:00 2011 UTC (6 years, 1 month ago) by gross
typo fixed.

Revision 3523 - Directory Listing
Modified Tue May 24 02:03:37 2011 UTC (6 years, 1 month ago) by caltinay
Fixed declaration order (register const) for gcc-4.6


Revision 3522 - Directory Listing
Modified