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Revision 4814 - Directory Listing
Modified Fri Mar 28 04:31:02 2014 UTC (5 years 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 (5 years ago) by sshaw
moving away from shared pointers in domain components

Revision 4810 - Directory Listing
Modified Thu Mar 27 07:00:30 2014 UTC (5 years ago) by caltinay
Removed some obsolete checkPtr's. More to come...


Revision 4809 - Directory Listing
Modified Thu Mar 27 05:52:41 2014 UTC (5 years 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 (5 years ago) by caltinay
2 fixes to dirac points which fixes #240.


Revision 4806 - Directory Listing
Modified Thu Mar 27 03:03:13 2014 UTC (5 years 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 (5 years 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 (5 years 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 (5 years ago) by caltinay
paso::Coupler and paso::Connector.


Revision 4800 - Directory Listing
Modified Wed Mar 26 01:50:04 2014 UTC (5 years ago) by caltinay
paso::SystemMatrixPattern


Revision 4799 - Directory Listing
Modified Wed Mar 26 00:37:59 2014 UTC (5 years 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 (5 years ago) by caltinay
added missing const.


Revision 4797 - Directory Listing
Modified Mon Mar 24 05:42:42 2014 UTC (5 years 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 (5 years 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 (5 years ago) by jduplessis
adding symbolic to user guide, work in progress


Revision 4793 - Directory Listing
Modified Fri Mar 21 06:44:26 2014 UTC (5 years, 1 month 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 (5 years, 1 month ago) by jfenwick
make escriptcore/ visible

Revision 4791 - Directory Listing
Modified Fri Mar 21 03:32:56 2014 UTC (5 years, 1 month ago) by jduplessis
changed has_key to in for python 3

Revision 4789 - Directory Listing
Modified Fri Mar 21 00:30:32 2014 UTC (5 years, 1 month 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 (5 years, 1 month ago) by sshaw
fixed a broken numerical comparison

Revision 4787 - Directory Listing
Modified Fri Mar 21 00:08:15 2014 UTC (5 years, 1 month 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 (5 years, 1 month ago) by sshaw
fixed silly naming issue

Revision 4783 - Directory Listing
Modified Thu Mar 20 06:23:23 2014 UTC (5 years, 1 month ago) by sshaw
refactored linearPDE tests (removing repetition)

Revision 4782 - Directory Listing
Modified Thu Mar 20 05:16:16 2014 UTC (5 years, 1 month 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 (5 years, 1 month ago) by jduplessis
added test for preservation of data substitutions

Revision 4780 - Directory Listing
Modified Thu Mar 20 03:19:54 2014 UTC (5 years, 1 month ago) by sshaw
fixing a race condition in file tests

Revision 4779 - Directory Listing
Modified Thu Mar 20 01:52:49 2014 UTC (5 years, 1 month ago) by jfenwick
Temporarily adjusting magic numbers

Revision 4778 - Directory Listing
Modified Thu Mar 20 00:41:58 2014 UTC (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month ago) by caltinay
Removed some superfluous checks and typos.


Revision 4775 - Directory Listing
Modified Wed Mar 19 23:12:53 2014 UTC (5 years, 1 month 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 (5 years, 1 month ago) by sshaw
removing ridiculous remaining return

Revision 4771 - Directory Listing
Modified Wed Mar 19 04:22:37 2014 UTC (5 years, 1 month ago) by sshaw
fixed multiple ranks trying to unlink tempfiles

Revision 4770 - Directory Listing
Modified Wed Mar 19 03:48:43 2014 UTC (5 years, 1 month 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 (5 years, 1 month ago) by sshaw
added missing ifdefs for library presence

Revision 4768 - Directory Listing
Modified Wed Mar 19 02:51:33 2014 UTC (5 years, 1 month ago) by jduplessis
Removed commented for loops


Revision 4767 - Directory Listing
Modified Wed Mar 19 02:48:33 2014 UTC (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month ago) by gross
mapping test fixed

Revision 4761 - Directory Listing
Modified Tue Mar 18 00:25:55 2014 UTC (5 years, 1 month ago) by sshaw
fixed partially overridden class warnings with intel compiler

Revision 4760 - Directory Listing
Modified Mon Mar 17 23:48:37 2014 UTC (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month ago) by sshaw
added conflict test for ripley Brick

Revision 4754 - Directory Listing
Modified Mon Mar 17 02:51:12 2014 UTC (5 years, 1 month ago) by sshaw
now with 0% missing files!

Revision 4753 - Directory Listing
Modified Mon Mar 17 02:39:44 2014 UTC (5 years, 1 month 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 (5 years, 1 month ago) by sshaw
completed LameAssemblers

Revision 4749 - Directory Listing
Modified Fri Mar 14 03:05:07 2014 UTC (5 years, 1 month ago) by sshaw
making inversioncostfunctions python3 compatible

Revision 4748 - Directory Listing
Modified Fri Mar 14 00:30:51 2014 UTC (5 years, 1 month 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 (5 years, 1 month ago) by gross
first version of a FWI

Revision 4743 - Directory Listing
Modified Wed Mar 12 21:09:20 2014 UTC (5 years, 1 month ago) by gross
mapping for FWI added

Revision 4742 - Directory Listing
Modified Wed Mar 12 07:21:24 2014 UTC (5 years, 1 month ago) by jduplessis
updated setitem and getitem to preserve data substitutions


Revision 4741 - Directory Listing
Modified Wed Mar 12 03:31:10 2014 UTC (5 years, 1 month 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 (5 years, 1 month ago) by sshaw
exporting compression support to buildvars

Revision 4739 - Directory Listing
Modified Wed Mar 12 03:25:32 2014 UTC (5 years, 1 month ago) by sshaw
fixing test file filename mismatch

Revision 4738 - Directory Listing
Modified Wed Mar 12 01:32:36 2014 UTC (5 years, 1 month 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 (5 years, 1 month ago) by gross
missing file

Revision 4735 - Directory Listing
Modified Mon Mar 10 07:44:58 2014 UTC (5 years, 1 month ago) by sshaw
fixing/completing 2D lame assembler


Revision 4733 - Directory Listing
Modified Mon Mar 10 05:57:11 2014 UTC (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month ago) by jduplessis
renamed

Revision 4727 - Directory Listing
Modified Fri Mar 7 05:28:12 2014 UTC (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month ago) by jfenwick
Fixing strange casts.
Removed old methods.


Revision 4720 - Directory Listing
Modified Fri Feb 28 01:38:09 2014 UTC (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month ago) by sshaw
Added a missed include guard


Revision 4717 - Directory Listing
Modified Thu Feb 27 12:30:04 2014 UTC (5 years, 1 month ago) by jfenwick
Fix copy error from 3d down to 2d.



Revision 4716 - Directory Listing
Modified Thu Feb 27 11:02:55 2014 UTC (5 years, 1 month 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 (5 years, 1 month ago) by jfenwick
Fixing print statement

Revision 4714 - Directory Listing
Modified Thu Feb 27 05:04:15 2014 UTC (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month ago) by jfenwick
Another try at this test.



Revision 4710 - Directory Listing
Modified Mon Feb 24 03:41:06 2014 UTC (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month ago) by jduplessis
Removed rotation from ydirection test


Revision 4707 - Directory Listing
Modified Fri Feb 21 03:07:09 2014 UTC (5 years, 1 month ago) by jduplessis
Modified domain in tests


Revision 4706 - Directory Listing
Modified Fri Feb 21 02:39:58 2014 UTC (5 years, 1 month ago) by jfenwick
Some additional cleanup I missed


Revision 4705 - Directory Listing
Modified Fri Feb 21 02:36:15 2014 UTC (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month ago) by gross
some more work toward seismic data

Revision 4699 - Directory Listing
Modified Wed Feb 19 09:31:45 2014 UTC (5 years, 1 month 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 (5 years, 1 month ago) by gross
data sources support tags now

Revision 4697 - Directory Listing
Modified Wed Feb 19 08:03:56 2014 UTC (5 years, 1 month ago) by gross
data sources support tags now

Revision 4696 - Directory Listing
Modified Wed Feb 19 07:29:50 2014 UTC (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month ago) by sshaw
adding HTI support to 3D wave assembler

Revision 4692 - Directory Listing
Modified Wed Feb 19 05:26:55 2014 UTC (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month ago) by sshaw
adjusting porcupine config to use MPI by default

Revision 4689 - Directory Listing
Modified Wed Feb 19 05:13:17 2014 UTC (5 years, 1 month ago) by jfenwick
Give the unit test enough room


Revision 4688 - Directory Listing
Modified Wed Feb 19 03:18:58 2014 UTC (5 years, 1 month ago) by gross
acoustic forward problem + testing add

Revision 4687 - Directory Listing
Modified Wed Feb 19 00:03:29 2014 UTC (5 years, 1 month 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 months ago) by jduplessis
adding nonlinearpde test for ripley.


Revision 4682 - Directory Listing
Modified Mon Feb 17 05:24:14 2014 UTC (5 years, 2 months ago) by jduplessis


Revision 4681 - Directory Listing
Modified Mon Feb 17 04:05:11 2014 UTC (5 years, 2 months ago) by jduplessis


Revision 4680 - Directory Listing
Modified Mon Feb 17 04:04:40 2014 UTC (5 years, 2 months ago) by jduplessis
changed name


Revision 4679 - Directory Listing
Modified Mon Feb 17 04:02:56 2014 UTC (5 years, 2 months ago) by jduplessis
Changed name


Revision 4678 - Directory Listing
Modified Mon Feb 17 03:35:08 2014 UTC (5 years, 2 months ago) by jduplessis
adding ripley test for nlpde


Revision 4677 - Directory Listing
Modified Mon Feb 17 02:49:59 2014 UTC (5 years, 2 months ago) by jduplessis
adding nlpde tests


Revision 4676 - Directory Listing
Modified Mon Feb 17 02:41:15 2014 UTC (5 years, 2 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 (5 years, 2 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 (5 years, 2 months ago) by jfenwick
Not using GNU only getopt arguments

Revision 4673 - Directory Listing
Modified Thu Feb 13 08:14:11 2014 UTC (5 years, 2 months ago) by jfenwick
Ammended install doco for OSX

Revision 4672 - Directory Listing
Modified Thu Feb 13 01:10:29 2014 UTC (5 years, 2 months ago) by sshaw
compacted older style C comparison structure

Revision 4671 - Directory Listing
Modified Thu Feb 13 00:18:10 2014 UTC (5 years, 2 months ago) by jfenwick
Fixed another comparator which wasn't strict


Revision 4670 - Directory Listing
Modified Wed Feb 12 08:24:31 2014 UTC (5 years, 2 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 (5 years, 2 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 (5 years, 2 months ago) by jfenwick
Improvements but still needs more validation


Revision 4667 - Directory Listing
Modified Tue Feb 11 00:47:26 2014 UTC (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 months ago) by sshaw
more informative exception for unsupported error message

Revision 4660 - Directory Listing
Modified Fri Feb 7 03:08:49 2014 UTC (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 months ago) by gross
removed unwanted table

Revision 4655 - Directory Listing
Modified Thu Feb 6 04:15:42 2014 UTC (5 years, 2 months ago) by jfenwick
Reverting r4654

Revision 4654 - Directory Listing
Modified Wed Feb 5 06:55:35 2014 UTC (5 years, 2 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 (5 years, 2 months ago) by jfenwick
Made index chars unsigned to prevent warnings

Revision 4652 - Directory Listing
Modified Wed Feb 5 05:15:07 2014 UTC (5 years, 2 months ago) by jfenwick
Made index chars unsigned to prevent warnings

Revision 4651 - Directory Listing
Modified Wed Feb 5 05:00:34 2014 UTC (5 years, 2 months ago) by jfenwick
Fixed missing include

Revision 4650 - Directory Listing
Modified Wed Feb 5 04:16:01 2014 UTC (5 years, 2 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 (5 years, 2 months ago) by caltinay
Forgot something...


Revision 4648 - Directory Listing
Modified Wed Feb 5 02:03:08 2014 UTC (5 years, 2 months ago) by caltinay
Fix segfault reported in #57.


Revision 4647 - Directory Listing
Modified Mon Feb 3 03:29:43 2014 UTC (5 years, 2 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 (5 years, 2 months ago) by gross
some extensions to synthetic_sonicHTI.py

Revision 4645 - Directory Listing
Modified Mon Feb 3 00:06:24 2014 UTC (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 months ago) by gross
TTI fixes

Revision 4636 - Directory Listing
Modified Tue Jan 28 04:24:30 2014 UTC (5 years, 2 months ago) by sshaw
fixed more whitespace issues


Revision 4635 - Directory Listing
Modified Tue Jan 28 03:34:04 2014 UTC (5 years, 2 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 (5 years, 2 months ago) by jfenwick
Fixes to keep clang happy

Revision 4633 - Directory Listing
Modified Tue Jan 28 01:04:17 2014 UTC (5 years, 2 months ago) by caltinay
Fixed failure for lazy data when interpolating.


Revision 4632 - Directory Listing
Modified Tue Jan 28 00:22:53 2014 UTC (5 years, 2 months ago) by gross
missing file

Revision 4631 - Directory Listing
Modified Fri Jan 24 04:13:56 2014 UTC (5 years, 2 months ago) by gross
2d TTI added

Revision 4630 - Directory Listing
Modified Fri Jan 24 03:32:11 2014 UTC (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 months ago) by jduplessis
fixing error in comment


Revision 4626 - Directory Listing
Modified Wed Jan 22 06:07:34 2014 UTC (5 years, 2 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 (5 years, 2 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 (5 years, 2 months ago) by sshaw
removed some leftover debug prints

Revision 4623 - Directory Listing
Modified Fri Jan 17 05:53:17 2014 UTC (5 years, 3 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 (5 years, 3 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 (5 years, 3 months ago) by jfenwick
getSampleDataRO is now const

Revision 4620 - Directory Listing
Modified Thu Jan 16 03:17:20 2014 UTC (5 years, 3 months ago) by caltinay
py3 RuntimeError does not have 'message' member.


Revision 4619 - Directory Listing
Modified Thu Jan 16 02:10:26 2014 UTC (5 years, 3 months ago) by caltinay
updated gp py3 options.


Revision 4618 - Directory Listing
Modified Wed Jan 15 04:35:19 2014 UTC (5 years, 3 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 (5 years, 3 months ago) by caltinay
new name for boost library on guineapig


Revision 4616 - Directory Listing
Modified Tue Jan 14 22:57:47 2014 UTC (5 years, 3 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 (5 years, 3 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 (5 years, 3 months ago) by caltinay
Corrected a faulty test.


Revision 4613 - Directory Listing
Modified Mon Jan 13 01:09:01 2014 UTC (5 years, 3 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 (5 years, 3 months ago) by gross
modifications to sonic seismic

Revision 4611 - Directory Listing
Modified Mon Dec 23 04:03:00 2013 UTC (5 years, 3 months ago) by gross
scaling corrected

Revision 4610 - Directory Listing
Modified Mon Dec 23 00:01:23 2013 UTC (5 years, 3 months ago) by gross
exposed createAbsorbtionLayerFunction

Revision 4609 - Directory Listing
Modified Fri Dec 20 07:56:56 2013 UTC (5 years, 3 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 (5 years, 4 months ago) by sshaw
tiny grammar fix in user guide

Revision 4607 - Directory Listing
Modified Wed Dec 18 09:46:16 2013 UTC (5 years, 4 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 (5 years, 4 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 (5 years, 4 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 (5 years, 4 months ago) by sshaw
fixed tabs/space mix for python3

Revision 4603 - Directory Listing
Modified Wed Dec 18 02:24:32 2013 UTC (5 years, 4 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 (5 years, 4 months ago) by jfenwick
Fixed missing \


Revision 4601 - Directory Listing
Modified Tue Dec 17 23:37:08 2013 UTC (5 years, 4 months ago) by gross
downunder: self-demagnetization added as forward model. 



Revision 4600 - Directory Listing
Modified Tue Dec 17 04:28:40 2013 UTC (5 years, 4 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 (5 years, 4 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 (5 years, 4 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 (5 years, 4 months ago) by gross
unused variable fixed

Revision 4586 - Directory Listing
Modified Wed Dec 11 06:03:27 2013 UTC (5 years, 4 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 (5 years, 4 months ago) by sshaw
uint -> unsigned int

Revision 4584 - Directory Listing
Modified Wed Dec 11 04:24:15 2013 UTC (5 years, 4 months ago) by sshaw
more buildbot commit testing

Revision 4583 - Directory Listing
Modified Wed Dec 11 02:09:19 2013 UTC (5 years, 4 months ago) by jfenwick
deliberate error to test buildbot

Revision 4582 - Directory Listing
Modified Wed Dec 11 02:08:41 2013 UTC (5 years, 4 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 (5 years, 4 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 (5 years, 4 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 (5 years, 4 months ago) by sshaw
adding porcupine's scons options file

Revision 4578 - Directory Listing
Modified Tue Dec 10 04:07:51 2013 UTC (5 years, 4 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 (5 years, 4 months ago) by sshaw
Undoing unintended commit of omp wrapper removal

Revision 4576 - Directory Listing
Modified Mon Dec 9 23:35:30 2013 UTC (5 years, 4 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 (5 years, 4 months ago) by jfenwick
Some more work on this


Revision 4574 - Directory Listing
Modified Mon Dec 9 04:29:44 2013 UTC (5 years, 4 months ago) by gross
some corrections

Revision 4573 - Directory Listing
Modified Mon Dec 9 03:42:50 2013 UTC (5 years, 4 months ago) by gross
HTI added

Revision 4572 - Directory Listing
Modified Sun Dec 8 00:54:37 2013 UTC (5 years, 4 months ago) by jfenwick
Some work on rectangle random MPI

Revision 4571 - Directory Listing
Modified Fri Dec 6 02:47:14 2013 UTC (5 years, 4 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 (5 years, 4 months ago) by gross
strain convention corrected.

Revision 4569 - Directory Listing
Modified Fri Dec 6 02:21:12 2013 UTC (5 years, 4 months ago) by gross
some update

Revision 4568 - Directory Listing
Modified Thu Dec 5 23:13:26 2013 UTC (5 years, 4 months ago) by jfenwick
Package building files for saucy


Revision 4567 - Directory Listing
Modified Thu Dec 5 09:00:23 2013 UTC (5 years, 4 months ago) by jfenwick
Options file for ubuntu 13.10


Revision 4566 - Directory Listing
Modified Thu Dec 5 01:02:47 2013 UTC (5 years, 4 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 (5 years, 4 months ago) by gross
and another typo fixed.

Revision 4564 - Directory Listing
Modified Wed Dec 4 06:34:14 2013 UTC (5 years, 4 months ago) by gross
VTI wave added  

Revision 4563 - Directory Listing
Modified Wed Dec 4 06:30:59 2013 UTC (5 years, 4 months ago) by gross
typo fixed

Revision 4562 - Directory Listing
Modified Wed Dec 4 05:41:10 2013 UTC (5 years, 4 months ago) by gross
VTI wave added  

Revision 4561 - Directory Listing
Modified Wed Dec 4 05:19:32 2013 UTC (5 years, 4 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 (5 years, 4 months ago) by rschaa
Options file for ferret


Revision 4559 - Directory Listing
Modified Wed Dec 4 02:05:34 2013 UTC (5 years, 4 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 (5 years, 4 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 (5 years, 4 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 (5 years, 4 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 (5 years, 4 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 (5 years, 4 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 (5 years, 4 months ago) by gross
clarification on receiver array

Revision 4552 - Directory Listing
Modified Mon Dec 2 06:13:47 2013 UTC (5 years, 4 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 (5 years, 4 months ago) by sshaw
Fixed missing install keyword in instructions


Revision 4550 - Directory Listing
Modified Fri Nov 29 07:44:37 2013 UTC (5 years, 4 months ago) by gross
some modifications

Revision 4549 - Directory Listing
Modified Fri Nov 29 05:24:40 2013 UTC (5 years, 4 months ago) by gross
argument for lumping added.

Revision 4548 - Directory Listing
Modified Fri Nov 29 04:39:15 2013 UTC (5 years, 4 months ago) by gross
renamed file

Revision 4547 - Directory Listing
Modified Thu Nov 28 23:47:27 2013 UTC (5 years, 4 months ago) by jfenwick
Added msec unit


Revision 4546 - Directory Listing
Modified Thu Nov 28 05:30:48 2013 UTC (5 years, 4 months ago) by gross
sonic wave propagation added

Revision 4545 - Directory Listing
Modified Thu Nov 28 05:02:43 2013 UTC (5 years, 4 months ago) by gross
wave simulator base added

Revision 4544 - Directory Listing
Modified Thu Nov 28 04:01:46 2013 UTC (5 years, 4 months ago) by gross
wave simulator base added

Revision 4543 - Directory Listing
Modified Thu Nov 28 03:42:10 2013 UTC (5 years, 4 months ago) by gross
missing retirn statement added

Revision 4542 - Directory Listing
Modified Thu Nov 28 01:33:22 2013 UTC (5 years, 4 months ago) by jfenwick
Moving to new icc and associated modules.




Revision 4541 - Directory Listing
Modified Thu Nov 28 01:17:19 2013 UTC (5 years, 4 months ago) by gross
Ricker wavelet added

Revision 4540 - Directory Listing
Modified Thu Nov 28 01:06:10 2013 UTC (5 years, 4 months ago) by gross
segy writer added

Revision 4539 - Directory Listing
Modified Thu Nov 28 00:38:10 2013 UTC (5 years, 4 months ago) by gross
segy writer test added.

Revision 4538 - Directory Listing
Modified Thu Nov 28 00:37:48 2013 UTC (5 years, 4 months ago) by gross
segy writer added

Revision 4537 - Directory Listing
Modified Mon Nov 25 06:44:46 2013 UTC (5 years, 4 months ago) by gross
missing references and double labeling fixed.

Revision 4536 - Directory Listing
Modified Thu Nov 21 07:58:32 2013 UTC (5 years, 4 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 (5 years, 4 months ago) by gross
strong correlation joint inversion fixed.

Revision 4534 - Directory Listing
Modified Thu Nov 7 08:17:02 2013 UTC (5 years, 5 months ago) by gross
typo fixed

Revision 4533 - Directory Listing
Modified Thu Nov 7 04:56:11 2013 UTC (5 years, 5 months ago) by gross
typo fixed

Revision 4532 - Directory Listing
Modified Thu Nov 7 04:54:56 2013 UTC (5 years, 5 months ago) by gross
strongly coupled joint inversion added

Revision 4531 - Directory Listing
Modified Mon Nov 4 02:09:05 2013 UTC (5 years, 5 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 (5 years, 5 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 (5 years, 5 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 (5 years, 6 months ago) by caltinay
Added timeStepFormat option to saveESD (mantis 723).


Revision 4527 - Directory Listing
Modified Mon Sep 2 21:54:35 2013 UTC (5 years, 7 months ago) by jfenwick
use enums

Revision 4526 - Directory Listing
Modified Mon Sep 2 06:34:25 2013 UTC (5 years, 7 months ago) by jfenwick
Single rank rectangle randoms.


Revision 4525 - Directory Listing
Modified Fri Aug 30 09:14:35 2013 UTC (5 years, 7 months ago) by jfenwick
try this

Revision 4524 - Directory Listing
Modified Tue Aug 27 01:32:10 2013 UTC (5 years, 7 months ago) by jfenwick
Steube!!!!!


Revision 4523 - Directory Listing
Modified Mon Aug 26 23:04:07 2013 UTC (5 years, 7 months ago) by caltinay
New working raijin options.


Revision 4522 - Directory Listing
Modified Mon Aug 26 22:15:26 2013 UTC (5 years, 7 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 (5 years, 7 months ago) by jfenwick
Remove bool_t
Part of random.



Revision 4520 - Directory Listing
Modified Thu Aug 22 06:42:57 2013 UTC (5 years, 7 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 (5 years, 8 months ago) by caltinay
Initial raijin options file.


Revision 4518 - Directory Listing
Modified Tue Aug 13 01:49:59 2013 UTC (5 years, 8 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 (5 years, 8 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 (5 years, 8 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 (5 years, 8 months ago) by jfenwick
Intel compiler mutter grumble

Revision 4514 - Directory Listing
Modified Mon Aug 5 03:28:44 2013 UTC (5 years, 8 months ago) by jfenwick
Look at the MPI

Revision 4513 - Directory Listing
Modified Mon Aug 5 00:57:34 2013 UTC (5 years, 8 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 (5 years, 8 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 (5 years, 8 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 (5 years, 8 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 (5 years, 8 months ago) by jfenwick
Fixed paths for utest.sh


Revision 4508 - Directory Listing
Modified Wed Jul 24 04:23:22 2013 UTC (5 years, 8 months ago) by jfenwick
Moving to escriptcore

Revision 4507 - Directory Listing
Modified Wed Jul 24 02:50:22 2013 UTC (5 years, 8 months ago) by jfenwick
It begins

Revision 4506 - Directory Listing
Modified Wed Jul 24 01:28:42 2013 UTC (5 years, 8 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 (5 years, 8 months ago) by jfenwick
Hopefully addresses mantis721

Revision 4504 - Directory Listing
Modified Mon Jul 22 02:04:34 2013 UTC (5 years, 8 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 (5 years, 9 months ago) by caltinay
Skip new test with >1 rank.


Revision 4502 - Directory Listing
Modified Wed Jul 17 03:12:28 2013 UTC (5 years, 9 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 (5 years, 9 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 (5 years, 9 months ago) by caltinay
updated scons script


Revision 4499 - Directory Listing
Modified Tue Jul 16 05:42:19 2013 UTC (5 years, 9 months ago) by caltinay
finley: mainly const'ness fixes, some formatting.


Revision 4498 - Directory Listing
Modified Tue Jul 16 01:56:37 2013 UTC (5 years, 9 months ago) by caltinay
Another special case fix.


Revision 4497 - Directory Listing
Modified Mon Jul 15 23:32:28 2013 UTC (5 years, 9 months ago) by caltinay
Small fix for non-mpi build.


Revision 4496 - Directory Listing
Modified Mon Jul 15 06:53:44 2013 UTC (5 years, 9 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 (5 years, 9 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 (5 years, 9 months ago) by caltinay
Suppressions for savanna runs.


Revision 4493 - Directory Listing
Modified Wed Jul 3 06:32:11 2013 UTC (5 years, 9 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 (5 years, 9 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 (5 years, 9 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 (5 years, 9 months ago) by caltinay
More python suppressions from savanna.


Revision 4489 - Directory Listing
Modified Fri Jun 28 00:05:31 2013 UTC (5 years, 9 months 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 (5 years, 9 months 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 (5 years, 9 months ago) by caltinay
More leak fixes and suppression file additions.


Revision 4481 - Directory Listing
Modified Mon Jun 24 06:22:27 2013 UTC (5 years, 9 months ago) by caltinay
Hmm. That's a nasty undocumented "feature"...


Revision 4480 - Directory Listing
Modified Mon Jun 24 05:09:52 2013 UTC (5 years, 9 months 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 (5 years, 10 months ago) by caltinay
Missed a subtle fact about the stringstream constructor...


Revision 4478 - Directory Listing
Modified Thu Jun 20 06:34:02 2013 UTC (5 years, 10 months 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 (5 years, 10 months 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 (5 years, 10 months 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 (5 years, 10 months 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 (5 years, 10 months ago) by caltinay
Remove superfluous \label


Revision 4463 - Directory Listing
Modified Mon Jun 17 06:11:32 2013 UTC (5 years, 10 months ago) by gross
missing file

Revision 4462 - Directory Listing
Modified Mon Jun 17 04:12:06 2013 UTC (5 years, 10 months 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 (5 years, 10 months ago) by caltinay
small py3 fix.


Revision 4455 - Directory Listing
Modified Thu Jun 13 03:13:36 2013 UTC (5 years, 10 months 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 (5 years, 10 months ago) by caltinay
More "delete test output files after checking"


Revision 4451 - Directory Listing
Modified Thu Jun 13 01:38:56 2013 UTC (5 years, 10 months ago) by jfenwick
some pending changes on badger

Revision 4450 - Directory Listing
Modified Thu Jun 13 00:45:59 2013 UTC (5 years, 10 months 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 (5 years, 10 months ago) by jfenwick
Finishing off this end.


Revision 4448 - Directory Listing
Modified Wed Jun 12 23:05:12 2013 UTC (5 years, 10 months ago) by caltinay
Only one rank should delete file in tests.


Revision 4447 - Directory Listing
Modified Wed Jun 12 13:55:53 2013 UTC (5 years, 10 months ago) by caltinay
Clean up some generated test files.


Revision 4446 - Directory Listing
Modified Tue Jun 11 04:00:15 2013 UTC (5 years, 10 months ago) by caltinay
This should fix the py3 error...


Revision 4445 - Directory Listing
Modified Tue Jun 11 03:35:55 2013 UTC (5 years, 10 months 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 (5 years, 10 months ago) by caltinay
Converted IndexList to a std::list.


Revision 4443 - Directory Listing
Modified Mon Jun 10 04:50:27 2013 UTC (5 years, 10 months 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 (5 years, 10 months ago) by caltinay
cosmetic changes.


Revision 4441 - Directory Listing
Modified Fri Jun 7 02:23:49 2013 UTC (5 years, 10 months 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 (5 years, 10 months ago) by jfenwick
options files changes and install changes

Revision 4439 - Directory Listing
Modified Wed Jun 5 02:09:35 2013 UTC (5 years, 10 months ago) by jfenwick
some work on install doco

Revision 4438 - Directory Listing
Modified Tue Jun 4 09:00:50 2013 UTC (5 years, 10 months ago) by jfenwick
Some changes to packaging

Revision 4437 - Directory Listing
Modified Tue Jun 4 05:37:18 2013 UTC (5 years, 10 months 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 (5 years, 10 months ago) by caltinay
Tweak.


Revision 4435 - Directory Listing
Modified Mon Jun 3 04:27:57 2013 UTC (5 years, 10 months 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 (5 years, 10 months ago) by caltinay
tab-fixes and an indexing fix.


Revision 4433 - Directory Listing
Modified Fri May 31 12:09:58 2013 UTC (5 years, 10 months 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 (5 years, 10 months ago) by caltinay
updated sconscript file


Revision 4431 - Directory Listing
Modified Fri May 31 07:09:03 2013 UTC (5 years, 10 months ago) by caltinay
finley ElementFile is now a class...


Revision 4430 - Directory Listing
Modified Fri May 31 00:38:42 2013 UTC (5 years, 10 months 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 (5 years, 10 months 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 (5 years, 10 months 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 (5 years, 10 months ago) by jfenwick
Testing commit


Revision 4425 - Directory Listing
Modified Mon May 27 05:44:28 2013 UTC (5 years, 10 months ago) by caltinay
svn server test and finley stuff.


Revision 4424 - Directory Listing
Modified Mon May 27 04:48:31 2013 UTC (5 years, 10 months ago) by caltinay
SVN server test.


Revision 4423 - Directory Listing
Modified Mon May 27 04:38:59 2013 UTC (5 years, 10 months ago) by caltinay
finley bits.


Revision 4422 - Directory Listing
Modified Fri May 24 04:42:29 2013 UTC (5 years, 10 months ago) by caltinay
s/jacobeans/jacobians and other bits and pieces.


Revision 4421 - Directory Listing
Modified Tue May 21 05:16:39 2013 UTC (5 years, 10 months 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 (5 years, 11 months ago) by caltinay
Enabled metis on guineapig.


Revision 4419 - Directory Listing
Modified Mon May 20 05:03:35 2013 UTC (5 years, 11 months ago) by caltinay
Fixed a typo.


Revision 4418 - Directory Listing
Modified Mon May 20 04:08:16 2013 UTC (5 years, 11 months ago) by caltinay
Try...


Revision 4417 - Directory Listing
Modified Mon May 20 02:15:47 2013 UTC (5 years, 11 months ago) by caltinay
Retab regularizations.


Revision 4416 - Directory Listing
Modified Fri May 17 02:32:33 2013 UTC (5 years, 11 months ago) by jfenwick
Renaming a thing and adding some doco.

Revision 4415 - Directory Listing
Modified Fri May 17 00:33:02 2013 UTC (5 years, 11 months ago) by caltinay
Commented unused var to make compiler happy.


Revision 4414 - Directory Listing
Modified Thu May 16 05:37:32 2013 UTC (5 years, 11 months ago) by caltinay
Few more bits and pieces in finley.


Revision 4410 - Directory Listing
Modified Tue May 14 11:29:23 2013 UTC (5 years, 11 months ago) by caltinay
Oops, I saw this coming.


Revision 4408 - Directory Listing
Modified Tue May 14 06:58:43 2013 UTC (5 years, 11 months 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 (5 years, 11 months ago) by jfenwick
Added output function to arithmetic tuple

Revision 4406 - Directory Listing
Modified Tue May 14 02:54:09 2013 UTC (5 years, 11 months 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 (5 years, 11 months ago) by caltinay
Once again..


Revision 4404 - Directory Listing
Modified Sun May 12 23:25:10 2013 UTC (5 years, 11 months ago) by caltinay
Retab forwardmodels


Revision 4400 - Directory Listing
Modified Fri May 10 04:05:00 2013 UTC (5 years, 11 months 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 (5 years, 11 months ago) by jfenwick
just fiddling

Revision 4398 - Directory Listing
Modified Thu May 9 08:42:44 2013 UTC (5 years, 11 months 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 (5 years, 11 months 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 (5 years, 11 months 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 (5 years, 11 months 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 (5 years, 11 months 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 (5 years, 11 months ago) by caltinay
Correct indexing of forward models.


Revision 4392 - Directory Listing
Modified Mon May 6 02:18:33 2013 UTC (5 years, 11 months ago) by caltinay
More saveSilo checks.


Revision 4391 - Directory Listing
Modified Mon May 6 02:15:48 2013 UTC (5 years, 11 months 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 (5 years, 11 months ago) by caltinay
Fixed advertising of NetCdfData availability.


Revision 4389 - Directory Listing
Modified Mon May 6 01:52:05 2013 UTC (5 years, 11 months ago) by caltinay
retab coordinates.py


Revision 4388 - Directory Listing
Modified Thu May 2 01:55:08 2013 UTC (5 years, 11 months ago) by jfenwick
I need this

Revision 4387 - Directory Listing
Modified Thu May 2 00:46:49 2013 UTC (5 years, 11 months ago) by jfenwick
The future is now

Revision 4386 - Directory Listing
Modified Tue Apr 30 02:58:02 2013 UTC (5 years, 11 months ago) by jfenwick
Add missing [0]

Revision 4385 - Directory Listing
Modified Mon Apr 29 06:03:30 2013 UTC (5 years, 11 months ago) by jfenwick
It was bugging me

Revision 4384 - Directory Listing
Modified Sat Apr 27 05:09:37 2013 UTC (5 years, 11 months ago) by jfenwick
Partially complete new install instructions

Revision 4383 - Directory Listing
Modified Fri Apr 26 06:13:12 2013 UTC (5 years, 11 months ago) by jfenwick
Changes to install doco


Revision 4382 - Directory Listing
Modified Thu Apr 25 04:44:14 2013 UTC (5 years, 11 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 (5 years, 11 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 (5 years, 11 months ago) by jfenwick
Attempt to help windows

Revision 4379 - Directory Listing
Modified Wed Apr 24 20:31:19 2013 UTC (5 years, 11 months ago) by gross
more documentation on geodetic coordinates.

Revision 4378 - Directory Listing
Modified Wed Apr 24 06:21:42 2013 UTC (5 years, 11 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 (5 years, 11 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 (5 years, 11 months ago) by gross
domumentation update on coordinate systems - part I

Revision 4375 - Directory Listing
Modified Mon Apr 22 05:35:52 2013 UTC (5 years, 11 months ago) by caltinay
More ripley code cleaning/optimisation.


Revision 4374 - Directory Listing
Modified Mon Apr 22 03:21:48 2013 UTC (5 years, 11 months ago) by gross
some typo fixed.

Revision 4373 - Directory Listing
Modified Mon Apr 22 03:16:24 2013 UTC (5 years, 11 months ago) by gross
more on geodetic coordinates

Revision 4372 - Directory Listing
Modified Mon Apr 22 00:02:36 2013 UTC (5 years, 11 months ago) by caltinay
Retab...


Revision 4371 - Directory Listing
Modified Fri Apr 19 08:47:57 2013 UTC (6 years 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 (6 years 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 (6 years ago) by jfenwick
fix problems revealed on freebsd

Revision 4368 - Directory Listing
Modified Thu Apr 18 02:26:35 2013 UTC (6 years ago) by jfenwick
put back std::

Revision 4367 - Directory Listing
Modified Wed Apr 17 09:55:25 2013 UTC (6 years 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 (6 years ago) by caltinay
Be more careful with namespace & includes.


Revision 4365 - Directory Listing
Modified Wed Apr 17 03:46:22 2013 UTC (6 years ago) by caltinay
Skip tests for #ranks > 1 again.


Revision 4364 - Directory Listing
Modified Wed Apr 17 01:56:00 2013 UTC (6 years ago) by caltinay
Decorated some test cases.


Revision 4363 - Directory Listing
Modified Wed Apr 17 01:07:38 2013 UTC (6 years ago) by caltinay
retab coordinates.py.


Revision 4362 - Directory Listing
Modified Tue Apr 16 04:37:13 2013 UTC (6 years 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 (6 years ago) by jfenwick
beginnings of an option file for macports

Revision 4360 - Directory Listing
Modified Mon Apr 15 02:41:42 2013 UTC (6 years ago) by jfenwick
some mismatched memory ops

Revision 4359 - Directory Listing
Modified Fri Apr 12 04:54:20 2013 UTC (6 years ago) by gross
more on coordinate systems

Revision 4358 - Directory Listing
Modified Fri Apr 12 04:54:00 2013 UTC (6 years ago) by gross
more on coordinate systems

Revision 4357 - Directory Listing
Modified Thu Apr 11 06:07:14 2013 UTC (6 years ago) by caltinay
templated writeBinaryGrid and a bit of cleanup.


Revision 4356 - Directory Listing
Modified Tue Apr 9 00:15:59 2013 UTC (6 years ago) by caltinay
Retabbed file for py3 pleasure.


Revision 4355 - Directory Listing
Modified Fri Apr 5 07:25:02 2013 UTC (6 years ago) by jfenwick
start install guide overhall

Revision 4354 - Directory Listing
Modified Fri Apr 5 03:55:03 2013 UTC (6 years ago) by jfenwick
adding option files for distros

Revision 4353 - Directory Listing
Modified Fri Apr 5 00:14:35 2013 UTC (6 years 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 (6 years ago) by jfenwick


Revision 4349 - Directory Listing
Modified Wed Apr 3 09:37:54 2013 UTC (6 years ago) by gross
first contributions for geodeic coordinates

Revision 4348 - Directory Listing
Modified Tue Apr 2 07:15:43 2013 UTC (6 years 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 (6 years ago) by jfenwick
Fixed some const char* conversions


Revision 4346 - Directory Listing
Modified Tue Apr 2 04:46:45 2013 UTC (6 years 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 (6 years ago) by gross
fix potential at botttom added.

Revision 4343 - Directory Listing
Modified Wed Mar 27 06:44:36 2013 UTC (6 years ago) by gross
 

Revision 4342 - Directory Listing
Modified Tue Mar 26 02:31:41 2013 UTC (6 years 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 (6 years ago) by caltinay
GOCAD Voxet writer in weipa.


Revision 4340 - Directory Listing
Modified Fri Mar 22 04:38:36 2013 UTC (6 years 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 (6 years ago) by jfenwick
options file for all standalone builds

Revision 4337 - Directory Listing
Modified Fri Mar 22 00:05:25 2013 UTC (6 years 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 (6 years, 1 month 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 (6 years, 1 month ago) by caltinay
Removed stray print statement.


Revision 4323 - Directory Listing
Modified Tue Mar 19 00:17:36 2013 UTC (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month ago) by jfenwick
gracefully end if pyproj is not installed

Revision 4310 - Directory Listing
Modified Tue Mar 12 03:23:26 2013 UTC (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month ago) by caltinay
Added missing import.


Revision 4307 - Directory Listing
Modified Mon Mar 11 02:46:17 2013 UTC (6 years, 1 month ago) by azadeh
shake29->weasel


Revision 4306 - Directory Listing
Modified Mon Mar 11 02:36:55 2013 UTC (6 years, 1 month ago) by caltinay
python 3 compat.


Revision 4303 - Directory Listing
Modified Mon Mar 11 01:17:39 2013 UTC (6 years, 1 month ago) by caltinay
Enabled index in inversion doc. Eliminated some typos.


Revision 4301 - Directory Listing
Modified Mon Mar 11 00:52:31 2013 UTC (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month ago) by azadeh
changing Magnetic Images


Revision 4297 - Directory Listing
Modified Fri Mar 8 06:14:17 2013 UTC (6 years, 1 month 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 (6 years, 1 month ago) by caltinay
Oopsie


Revision 4295 - Directory Listing
Modified Fri Mar 8 04:42:01 2013 UTC (6 years, 1 month 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 (6 years, 1 month ago) by gross
text for magnetic inversion tutorial added.

Revision 4293 - Directory Listing
Modified Fri Mar 8 00:07:07 2013 UTC (6 years, 1 month ago) by jfenwick
fixing sneaky bug in grouptest

Revision 4292 - Directory Listing
Modified Thu Mar 7 22:39:32 2013 UTC (6 years, 1 month ago) by caltinay
Broken? It ain't broken ;-) Sorry Joel.


Revision 4290 - Directory Listing
Modified Thu Mar 7 07:04:29 2013 UTC (6 years, 1 month ago) by jfenwick
Ignore __pycache__ when generating sphinx docs

Revision 4289 - Directory Listing
Modified Thu Mar 7 07:02:59 2013 UTC (6 years, 1 month ago) by jfenwick
including inversion examples in bundles and tests

Revision 4288 - Directory Listing
Modified Thu Mar 7 06:35:14 2013 UTC (6 years, 1 month ago) by gross
some modifications clarifying the B field orientation

Revision 4287 - Directory Listing
Modified Thu Mar 7 05:26:44 2013 UTC (6 years, 1 month 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 (6 years, 1 month ago) by caltinay
Assorted spelling fixes.


Revision 4285 - Directory Listing
Modified Thu Mar 7 01:08:43 2013 UTC (6 years, 1 month ago) by caltinay
Corrected some spelling.


Revision 4284 - Directory Listing
Modified Thu Mar 7 00:43:48 2013 UTC (6 years, 1 month ago) by caltinay
Replaced dummy implementations by pure virtual methods.


Revision 4283 - Directory Listing
Modified Thu Mar 7 00:11:36 2013 UTC (6 years, 1 month ago) by caltinay
Minor epydoc fixes.


Revision 4282 - Directory Listing
Modified Wed Mar 6 08:33:59 2013 UTC (6 years, 1 month ago) by gross
first contribution for the magnetic cookbook.

Revision 4281 - Directory Listing
Modified Wed Mar 6 07:08:36 2013 UTC (6 years, 1 month ago) by gross
typo - sorry

Revision 4279 - Directory Listing
Modified Wed Mar 6 05:10:44 2013 UTC (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month ago) by caltinay
Small fix to example file.


Revision 4273 - Directory Listing
Modified Tue Mar 5 04:14:44 2013 UTC (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month ago) by caltinay
Some more work.


Revision 4268 - Directory Listing
Modified Mon Mar 4 00:41:08 2013 UTC (6 years, 1 month ago) by gross
some citation fixed.


Revision 4267 - Directory Listing
Modified Fri Mar 1 04:50:54 2013 UTC (6 years, 1 month 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 (6 years, 1 month ago) by caltinay
Deleted old data files.


Revision 4265 - Directory Listing
Modified Fri Mar 1 00:52:30 2013 UTC (6 years, 1 month ago) by jfenwick
because we arent using python 2.5 anymore

Revision 4264 - Directory Listing
Modified Thu Feb 28 11:32:57 2013 UTC (6 years, 1 month ago) by jfenwick
Trying

Revision 4263 - Directory Listing
Modified Thu Feb 28 05:59:04 2013 UTC (6 years, 1 month ago) by caltinay
No more xrange in downunder.


Revision 4262 - Directory Listing
Modified Thu Feb 28 05:49:11 2013 UTC (6 years, 1 month ago) by caltinay
removed use of xrange and hack.


Revision 4260 - Directory Listing
Modified Wed Feb 27 04:58:47 2013 UTC (6 years, 1 month 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 (6 years, 1 month ago) by azadeh
cookmagnetic


Revision 4258 - Directory Listing
Modified Wed Feb 27 03:50:08 2013 UTC (6 years, 1 month ago) by azadeh
cookmagnetic


Revision 4256 - Directory Listing
Modified Wed Feb 27 03:25:05 2013 UTC (6 years, 1 month ago) by azadeh
changing some magnetic result image names


Revision 4255 - Directory Listing
Modified Wed Feb 27 03:06:21 2013 UTC (6 years, 1 month 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 (6 years, 1 month ago) by azadeh
added joint result 


Revision 4253 - Directory Listing
Modified Wed Feb 27 02:55:32 2013 UTC (6 years, 1 month ago) by azadeh
removed joint result


Revision 4252 - Directory Listing
Modified Wed Feb 27 02:49:06 2013 UTC (6 years, 1 month ago) by azadeh
added magnetic inversion results


Revision 4251 - Directory Listing
Modified Wed Feb 27 02:47:10 2013 UTC (6 years, 1 month 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 (6 years, 1 month ago) by caltinay
Fix for joint example.


Revision 4249 - Directory Listing
Modified Tue Feb 26 01:01:59 2013 UTC (6 years, 1 month 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 (6 years, 1 month ago) by jfenwick
This should not trigger the build

Revision 4247 - Directory Listing
Modified Mon Feb 25 05:51:41 2013 UTC (6 years, 1 month ago) by jfenwick


Revision 4246 - Directory Listing
Modified Mon Feb 25 05:49:49 2013 UTC (6 years, 1 month ago) by jfenwick
still testing

Revision 4245 - Directory Listing
Modified Mon Feb 25 05:45:06 2013 UTC (6 years, 1 month ago) by jfenwick
again

Revision 4244 - Directory Listing
Modified Mon Feb 25 05:37:50 2013 UTC (6 years, 1 month 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 (6 years, 1 month ago) by jfenwick
For testing buildbot


Revision 4242 - Directory Listing
Modified Mon Feb 25 03:16:14 2013 UTC (6 years, 1 month 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 (6 years, 1 month ago) by jfenwick
Added py3 config

Revision 4240 - Directory Listing
Modified Fri Feb 22 01:51:19 2013 UTC (6 years, 1 month ago) by jfenwick
options file for a clang buildbot

Revision 4239 - Directory Listing
Modified Fri Feb 22 00:35:01 2013 UTC (6 years, 1 month ago) by caltinay
initialize utm zone in er mapper reader.


Revision 4238 - Directory Listing
Modified Thu Feb 21 09:58:49 2013 UTC (6 years, 1 month ago) by jfenwick
fixed some relative imports and uses of xrange

Revision 4237 - Directory Listing
Modified Thu Feb 21 07:27:36 2013 UTC (6 years, 1 month 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 (6 years, 1 month ago) by jfenwick
Noted that saveDX and saveVTK have been removed.


Revision 4235 - Directory Listing
Modified Thu Feb 21 04:05:53 2013 UTC (6 years, 1 month ago) by caltinay
small fix.


Revision 4234 - Directory Listing
Modified Thu Feb 21 04:00:31 2013 UTC (6 years, 1 month ago) by gross
typo fixed

Revision 4233 - Directory Listing
Modified Thu Feb 21 02:00:09 2013 UTC (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month ago) by caltinay
Removed some superfluous files.


Revision 4229 - Directory Listing
Modified Wed Feb 20 03:39:46 2013 UTC (6 years, 1 month ago) by azadeh
cookgravity


Revision 4228 - Directory Listing
Modified Wed Feb 20 03:34:07 2013 UTC (6 years, 1 month ago) by caltinay
Tweak & fix for data plotters


Revision 4227 - Directory Listing
Modified Wed Feb 20 03:10:50 2013 UTC (6 years, 1 month ago) by caltinay
ER Mapper data source updates.


Revision 4226 - Directory Listing
Modified Wed Feb 20 03:07:36 2013 UTC (6 years, 1 month ago) by caltinay
typo.


Revision 4225 - Directory Listing
Modified Wed Feb 20 02:45:09 2013 UTC (6 years, 1 month ago) by azadeh
moving images to figures folder


Revision 4224 - Directory Listing
Modified Wed Feb 20 02:34:18 2013 UTC (6 years, 1 month ago) by azadeh
changing images in cook gravity


Revision 4223 - Directory Listing
Modified Wed Feb 20 01:47:26 2013 UTC (6 years, 1 month ago) by caltinay
$#@%%^@(!


Revision 4222 - Directory Listing
Modified Wed Feb 20 01:27:40 2013 UTC (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month ago) by caltinay
Report if pyproj is available.


Revision 4215 - Directory Listing
Modified Tue Feb 19 02:52:40 2013 UTC (6 years, 1 month ago) by azadeh
adding gravity coarse data


Revision 4214 - Directory Listing
Modified Tue Feb 19 02:42:43 2013 UTC (6 years, 1 month 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 (6 years, 1 month ago) by caltinay
Some cleanup and more consistent logging.


Revision 4212 - Directory Listing
Modified Tue Feb 19 00:11:28 2013 UTC (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month ago) by jfenwick
Added suggests for new libraries used by downunder.


Revision 4209 - Directory Listing
Modified Mon Feb 18 06:00:56 2013 UTC (6 years, 2 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 (6 years, 2 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 (6 years, 2 months ago) by azadeh
adding bar for gravity image


Revision 4206 - Directory Listing
Modified Sun Feb 17 23:32:07 2013 UTC (6 years, 2 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 (6 years, 2 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 (6 years, 2 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 (6 years, 2 months ago) by gross
Clarification of file names.

Revision 4202 - Directory Listing
Modified Thu Feb 14 06:53:41 2013 UTC (6 years, 2 months ago) by gross
Some adjustments to the sturture and naming

Revision 4201 - Directory Listing
Modified Thu Feb 14 06:40:01 2013 UTC (6 years, 2 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 (6 years, 2 months ago) by azadeh
adding content folder to show input files


Revision 4199 - Directory Listing
Modified Wed Feb 13 08:39:05 2013 UTC (6 years, 2 months ago) by gross
more in the inversion cook-book

Revision 4198 - Directory Listing
Modified Wed Feb 13 06:49:10 2013 UTC (6 years, 2 months ago) by gross
name adjustments and remove unused files

Revision 4197 - Directory Listing
Modified Wed Feb 13 05:53:19 2013 UTC (6 years, 2 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 (6 years, 2 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 (6 years, 2 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 (6 years, 2 months ago) by azadeh
Fixing some naming clashes

Revision 4193 - Directory Listing
Modified Tue Feb 12 00:59:49 2013 UTC (6 years, 2 months ago) by azadeh
reference


Revision 4192 - Directory Listing
Modified Tue Feb 12 00:28:47 2013 UTC (6 years, 2 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 (6 years, 2 months ago) by gross
more on gravity cook book

Revision 4190 - Directory Listing
Modified Mon Feb 11 05:10:00 2013 UTC (6 years, 2 months ago) by gross
unit gal added

Revision 4189 - Directory Listing
Modified Mon Feb 11 04:17:00 2013 UTC (6 years, 2 months ago) by gross
some images added

Revision 4188 - Directory Listing
Modified Mon Feb 11 01:51:22 2013 UTC (6 years, 2 months ago) by caltinay
Removed unneeded (large) result files.


Revision 4187 - Directory Listing
Modified Mon Feb 11 01:05:10 2013 UTC (6 years, 2 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 (6 years, 2 months ago) by azadeh
adding gravity plots with different Mu


Revision 4185 - Directory Listing
Modified Fri Feb 8 09:06:21 2013 UTC (6 years, 2 months ago) by gross
modifications to cookbook

Revision 4184 - Directory Listing
Modified Fri Feb 8 04:33:48 2013 UTC (6 years, 2 months ago) by azadeh
new images in cookgravity


Revision 4183 - Directory Listing
Modified Mon Feb 4 02:58:02 2013 UTC (6 years, 2 months ago) by azadeh
joint result image updated


Revision 4182 - Directory Listing
Modified Fri Feb 1 02:29:53 2013 UTC (6 years, 2 months ago) by caltinay
Revised Intro/Overview text.


Revision 4181 - Directory Listing
Modified Fri Feb 1 02:16:56 2013 UTC (6 years, 2 months ago) by azadeh
cook joint


Revision 4180 - Directory Listing
Modified Thu Jan 31 04:58:16 2013 UTC (6 years, 2 months ago) by azadeh
updating


Revision 4179 - Directory Listing
Modified Thu Jan 31 04:30:50 2013 UTC (6 years, 2 months ago) by caltinay
More doco.


Revision 4178 - Directory Listing
Modified Thu Jan 31 03:18:56 2013 UTC (6 years, 2 months ago) by caltinay
Some more doco.


Revision 4177 - Directory Listing
Modified Thu Jan 31 02:23:02 2013 UTC (6 years, 2 months ago) by azadeh
cook joint and magnetic


Revision 4176 - Directory Listing
Modified Wed Jan 30 05:30:30 2013 UTC (6 years, 2 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 (6 years, 2 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 (6 years, 2 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 (6 years, 2 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 (6 years, 2 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 (6 years, 2 months ago) by jfenwick
Release title and dep fix

Revision 4167 - Directory Listing
Modified Fri Jan 25 05:21:30 2013 UTC (6 years, 2 months ago) by jfenwick
fixes for doco for earlier releases

Revision 4166 - Directory Listing
Modified Fri Jan 25 04:18:45 2013 UTC (6 years, 2 months ago) by azadeh
gravity


Revision 4165 - Directory Listing
Modified Fri Jan 25 01:07:57 2013 UTC (6 years, 2 months ago) by azadeh
joint


Revision 4164 - Directory Listing
Modified Thu Jan 24 05:34:13 2013 UTC (6 years, 2 months ago) by caltinay
netcdf data source description.


Revision 4163 - Directory Listing
Modified Thu Jan 24 05:03:48 2013 UTC (6 years, 2 months ago) by azadeh
changing


Revision 4162 - Directory Listing
Modified Thu Jan 24 03:53:19 2013 UTC (6 years, 2 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 (6 years, 2 months ago) by azadeh
modifying 


Revision 4160 - Directory Listing
Modified Thu Jan 24 00:13:32 2013 UTC (6 years, 2 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 (6 years, 2 months ago) by azadeh
dding magnetic images


Revision 4158 - Directory Listing
Modified Wed Jan 23 07:02:21 2013 UTC (6 years, 2 months ago) by caltinay
Write output even when max iterations reached.


Revision 4157 - Directory Listing
Modified Wed Jan 23 03:52:07 2013 UTC (6 years, 2 months ago) by caltinay
added magnetic netcdf example (no data yet).


Revision 4156 - Directory Listing
Modified Wed Jan 23 03:45:14 2013 UTC (6 years, 2 months ago) by azadeh
changes in document


Revision 4155 - Directory Listing
Modified Wed Jan 23 00:05:03 2013 UTC (6 years, 2 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 (6 years, 2 months ago) by jfenwick
Round 1 of copyright fixes

Revision 4153 - Directory Listing
Modified Tue Jan 22 01:57:50 2013 UTC (6 years, 2 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 (6 years, 2 months ago) by caltinay
Moved figures to subdirectory.


Revision 4151 - Directory Listing
Modified Tue Jan 22 00:23:39 2013 UTC (6 years, 2 months ago) by azadeh
update joint and magnetic cookbook.


Revision 4150 - Directory Listing
Modified Mon Jan 21 04:14:24 2013 UTC (6 years, 2 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 (6 years, 2 months ago) by caltinay
Checkpoint - DomainBuilder documented.


Revision 4148 - Directory Listing
Modified Mon Jan 21 01:04:20 2013 UTC (6 years, 2 months ago) by caltinay
Updated netcdf gravity inversion example.


Revision 4147 - Directory Listing
Modified Fri Jan 18 03:35:15 2013 UTC (6 years, 3 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 (6 years, 3 months ago) by gross
some remarks on the class dependency added.

Revision 4145 - Directory Listing
Modified Fri Jan 18 00:51:49 2013 UTC (6 years, 3 months ago) by caltinay
Checkpoint.


Revision 4144 - Directory Listing
Modified Fri Jan 18 00:34:21 2013 UTC (6 years, 3 months ago) by gross
new diagrams

Revision 4143 - Directory Listing
Modified Thu Jan 17 08:48:47 2013 UTC (6 years, 3 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 (6 years, 3 months ago) by gross
documentation of inversion cost function added

Revision 4141 - Directory Listing
Modified Tue Jan 15 04:11:12 2013 UTC (6 years, 3 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 (6 years, 3 months ago) by caltinay
Updated example inversion files.


Revision 4139 - Directory Listing
Modified Tue Jan 15 00:13:28 2013 UTC (6 years, 3 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 (6 years, 3 months ago) by gross
some rearrangement of part II

Revision 4137 - Directory Listing
Modified Mon Jan 14 22:59:13 2013 UTC (6 years, 3 months ago) by caltinay
Disabled another test.


Revision 4136 - Directory Listing
Modified Mon Jan 14 05:20:34 2013 UTC (6 years, 3 months ago) by caltinay
clarifications about cartesian domain


Revision 4135 - Directory Listing
Modified Mon Jan 14 04:54:14 2013 UTC (6 years, 3 months ago) by caltinay
Fixed test file.


Revision 4134 - Directory Listing
Modified Sun Jan 13 23:24:35 2013 UTC (6 years, 3 months ago) by caltinay
Removed failing test.


Revision 4133 - Directory Listing
Modified Fri Jan 11 06:41:10 2013 UTC (6 years, 3 months ago) by gross
some documentation on Inversion Cost function added.

Revision 4132 - Directory Listing
Modified Fri Jan 11 05:46:49 2013 UTC (6 years, 3 months ago) by caltinay
Range of epydoc fixes.


Revision 4131 - Directory Listing
Modified Fri Jan 11 03:54:16 2013 UTC (6 years, 3 months ago) by gross
documentaion of inversion driver API added.

Revision 4130 - Directory Listing
Modified Thu Jan 10 03:38:17 2013 UTC (6 years, 3 months ago) by caltinay
Do not end document after chapter :-)


Revision 4129 - Directory Listing
Modified Thu Jan 10 03:30:45 2013 UTC (6 years, 3 months ago) by caltinay
Fixed small typo


Revision 4128 - Directory Listing
Modified Thu Jan 10 02:04:08 2013 UTC (6 years, 3 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 (6 years, 3 months ago) by azadeh
add documentation for gravity.


Revision 4126 - Directory Listing
Modified Tue Jan 8 02:37:48 2013 UTC (6 years, 3 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 (6 years, 3 months ago) by gross
some fixes in the inversion set-up

Revision 4124 - Directory Listing
Modified Fri Dec 21 01:35:43 2012 UTC (6 years, 3 months ago) by gross
joint inversion added

Revision 4123 - Directory Listing
Modified Thu Dec 20 23:47:55 2012 UTC (6 years, 3 months ago) by gross
small fix

Revision 4122 - Directory Listing
Modified Thu Dec 20 05:42:35 2012 UTC (6 years, 3 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 (6 years, 4 months ago) by gross
changes to the boundary conditions.

Revision 4120 - Directory Listing
Modified Tue Dec 18 04:49:37 2012 UTC (6 years, 4 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 (6 years, 4 months ago) by gross
some adjustments to the documentation

Revision 4118 - Directory Listing
Modified Mon Dec 17 00:50:47 2012 UTC (6 years, 4 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 (6 years, 4 months ago) by gross
some adjustments with names

Revision 4116 - Directory Listing
Modified Fri Dec 14 07:21:14 2012 UTC (6 years, 4 months ago) by gross
tests for oscillatory data added.

Revision 4115 - Directory Listing
Modified Fri Dec 14 04:48:48 2012 UTC (6 years, 4 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 (6 years, 4 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 (6 years, 4 months ago) by caltinay
shake29 options file.


Revision 4112 - Directory Listing
Modified Fri Dec 14 01:51:30 2012 UTC (6 years, 4 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 (6 years, 4 months ago) by jfenwick
Fixed the genrst script to be executable

Revision 4110 - Directory Listing
Modified Fri Dec 14 01:21:33 2012 UTC (6 years, 4 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 (6 years, 4 months ago) by caltinay
Fixed tests.


Revision 4108 - Directory Listing
Modified Thu Dec 13 06:38:11 2012 UTC (6 years, 4 months ago) by caltinay
Changed methods to add padding areas.


Revision 4107 - Directory Listing
Modified Thu Dec 13 05:54:03 2012 UTC (6 years, 4 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 (6 years, 4 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 (6 years, 4 months ago) by caltinay
Updated test to reflect interface changes.


Revision 4104 - Directory Listing
Modified Thu Dec 13 03:30:23 2012 UTC (6 years, 4 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 (6 years, 4 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 (6 years, 4 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 (6 years, 4 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 (6 years, 4 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 (6 years, 4 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 (6 years, 4 months ago) by caltinay
Unbroke my breakage.


Revision 4097 - Directory Listing
Modified Fri Dec 7 01:18:35 2012 UTC (6 years, 4 months ago) by caltinay
Minor edits.


Revision 4096 - Directory Listing
Modified Thu Dec 6 04:05:29 2012 UTC (6 years, 4 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 (6 years, 4 months ago) by caltinay
A bit of doco cleanup.


Revision 4094 - Directory Listing
Modified Mon Dec 3 23:28:38 2012 UTC (6 years, 4 months ago) by caltinay
Fixed typo.


Revision 4093 - Directory Listing
Modified Fri Nov 30 04:52:01 2012 UTC (6 years, 4 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 (6 years, 4 months ago) by caltinay
Minor change. Test commit.


Revision 4091 - Directory Listing
Modified Mon Nov 26 10:27:29 2012 UTC (6 years, 4 months ago) by gross
Some terminology introduced and magnetic inversion corrected.

Revision 4090 - Directory Listing
Modified Mon Nov 26 03:51:04 2012 UTC (6 years, 4 months ago) by caltinay
Savanna tweaks.


Revision 4089 - Directory Listing
Modified Fri Nov 23 04:41:54 2012 UTC (6 years, 4 months ago) by caltinay
Switch to new toolchain on Savanna.


Revision 4088 - Directory Listing
Modified Thu Nov 22 23:31:37 2012 UTC (6 years, 4 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 (6 years, 4 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 (6 years, 4 months ago) by jfenwick
Doco for 1D interpolation [resolves #631]

Revision 4085 - Directory Listing
Modified Tue Nov 20 07:04:11 2012 UTC (6 years, 4 months ago) by jfenwick
nonuniformInterolate and Slope added.
Doco later


Revision 4084 - Directory Listing
Modified Tue Nov 20 06:22:07 2012 UTC (6 years, 4 months ago) by jfenwick
Adding some linebreaks

Revision 4083 - Directory Listing
Modified Mon Nov 19 22:19:42 2012 UTC (6 years, 4 months ago) by caltinay
removed manually set weights from scripts.


Revision 4082 - Directory Listing
Modified Mon Nov 19 06:16:06 2012 UTC (6 years, 5 months ago) by jfenwick
Minor changes to install doco

Revision 4081 - Directory Listing
Modified Mon Nov 19 02:35:18 2012 UTC (6 years, 5 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 (6 years, 5 months ago) by jfenwick
Epydoc fixes


Revision 4079 - Directory Listing
Modified Fri Nov 16 07:59:01 2012 UTC (6 years, 5 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 (6 years, 5 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 (6 years, 5 months ago) by caltinay
Minor change.


Revision 4076 - Directory Listing
Modified Thu Nov 15 03:45:24 2012 UTC (6 years, 5 months ago) by gross
    def getDirectionalDerivative(self, m, d, grad_m):
        

Revision 4075 - Directory Listing
Modified Thu Nov 15 03:31:37 2012 UTC (6 years, 5 months ago) by gross
missing latex files

Revision 4074 - Directory Listing
Modified Thu Nov 15 03:30:59 2012 UTC (6 years, 5 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 (6 years, 5 months ago) by jfenwick
Fixing doco build error


Revision 4072 - Directory Listing
Modified Thu Nov 15 01:58:35 2012 UTC (6 years, 5 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 (6 years, 5 months ago) by gross
small fix

Revision 4070 - Directory Listing
Modified Tue Nov 13 07:55:22 2012 UTC (6 years, 5 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 (6 years, 5 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 (6 years, 5 months ago) by vboros
Small corrections to the magnetic forward model



Revision 4067 - Directory Listing
Modified Mon Nov 12 07:35:14 2012 UTC (6 years, 5 months ago) by vboros
Magnetostatics background added



Revision 4066 - Directory Listing
Modified Mon Nov 12 06:18:47 2012 UTC (6 years, 5 months ago) by jfenwick
renaming wheezyoptions file

Revision 4065 - Directory Listing
Modified Mon Nov 12 04:47:32 2012 UTC (6 years, 5 months ago) by jfenwick
Trying without uml

Revision 4064 - Directory Listing
Modified Fri Nov 9 07:25:14 2012 UTC (6 years, 5 months ago) by jfenwick
Tweaks

Revision 4063 - Directory Listing
Modified Fri Nov 9 06:15:00 2012 UTC (6 years, 5 months ago) by caltinay
Fixed a typo in method description.


Revision 4062 - Directory Listing
Modified Fri Nov 9 04:53:08 2012 UTC (6 years, 5 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 (6 years, 5 months ago) by caltinay
Updated data source test cases.


Revision 4060 - Directory Listing
Modified Fri Nov 9 03:50:19 2012 UTC (6 years, 5 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 (6 years, 5 months ago) by jfenwick
Start of substitution for rules


Revision 4058 - Directory Listing
Modified Fri Nov 2 06:47:06 2012 UTC (6 years, 5 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 (6 years, 5 months ago) by caltinay
toc/hyperref fixes for inversion pdf.


Revision 4056 - Directory Listing
Modified Thu Nov 1 07:20:38 2012 UTC (6 years, 5 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 (6 years, 5 months ago) by gross
Renaming of filenames

Revision 4054 - Directory Listing
Modified Wed Oct 31 23:27:57 2012 UTC (6 years, 5 months ago) by gross
prilimary checkin 

Revision 4053 - Directory Listing
Modified Wed Oct 31 07:27:35 2012 UTC (6 years, 5 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 (6 years, 5 months ago) by gross
missing references added (mantis id=683)

Revision 4051 - Directory Listing
Modified Wed Oct 31 03:40:47 2012 UTC (6 years, 5 months ago) by caltinay
Split inversion cookbook into two parts...


Revision 4050 - Directory Listing
Modified Wed Oct 31 01:01:24 2012 UTC (6 years, 5 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 (6 years, 5 months ago) by caltinay
Fixed typos.


Revision 4048 - Directory Listing
Modified Tue Oct 30 21:54:15 2012 UTC (6 years, 5 months ago) by gross
fixed modification in the DataSource creator

Revision 4047 - Directory Listing
Modified Tue Oct 30 09:10:07 2012 UTC (6 years, 5 months ago) by gross
More on magnetic inversion

Revision 4046 - Directory Listing
Modified Tue Oct 30 04:43:25 2012 UTC (6 years, 5 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 (6 years, 5 months ago) by caltinay
Imported inversion cookbook.


Revision 4044 - Directory Listing
Modified Tue Oct 30 03:35:17 2012 UTC (6 years, 5 months ago) by caltinay
Some doco fixes for downunder.


Revision 4043 - Directory Listing
Modified Tue Oct 30 03:34:43 2012 UTC (6 years, 5 months ago) by caltinay
Compile fixes for install guide.


Revision 4042 - Directory Listing
Modified Mon Oct 29 05:55:58 2012 UTC (6 years, 5 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 (6 years, 5 months ago) by caltinay
Fixed a typo


Revision 4040 - Directory Listing
Modified Sun Oct 28 22:37:45 2012 UTC (6 years, 5 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 (6 years, 5 months ago) by gross
magnetic inversion added

Revision 4038 - Directory Listing
Modified Fri Oct 26 04:47:25 2012 UTC (6 years, 5 months ago) by jfenwick
Minor fix to control file

Revision 4037 - Directory Listing
Modified Fri Oct 26 03:04:30 2012 UTC (6 years, 5 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 (6 years, 5 months ago) by caltinay
Added saveVTK tests for ripley domains.


Revision 4035 - Directory Listing
Modified Thu Oct 25 03:10:14 2012 UTC (6 years, 5 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 (6 years, 5 months ago) by caltinay
Fixes to inversion. Using resetRightHandSideCoefficients() now.


Revision 4033 - Directory Listing
Modified Wed Oct 24 08:14:41 2012 UTC (6 years, 5 months ago) by gross
some typos fixed.

Revision 4032 - Directory Listing
Modified Wed Oct 24 08:06:15 2012 UTC (6 years, 5 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 (6 years, 5 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 (6 years, 5 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 (6 years, 5 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 (6 years, 5 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 (6 years, 5 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 (6 years, 5 months ago) by gross
missing file

Revision 4025 - Directory Listing
Modified Mon Oct 22 08:18:47 2012 UTC (6 years, 5 months ago) by gross
 linearPDE.resetRightHandSideCoefficients has been implemented and tested.

Revision 4024 - Directory Listing
Modified Mon Oct 22 06:11:29 2012 UTC (6 years, 5 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 (6 years, 6 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 (6 years, 6 months ago) by caltinay
Fixed checks in ripley::addPDEToRHS().


Revision 4021 - Directory Listing
Modified Mon Oct 15 02:31:00 2012 UTC (6 years, 6 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 (6 years, 6 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 (6 years, 6 months ago) by jfenwick
More tabbing errors,
range/xrange
...

Revision 4018 - Directory Listing
Modified Thu Oct 11 04:43:39 2012 UTC (6 years, 6 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 (6 years, 6 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 (6 years, 6 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 (6 years, 6 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 (6 years, 6 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 (6 years, 6 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 (6 years, 6 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 (6 years, 6 months ago) by caltinay
Updated test reference file.


Revision 4010 - Directory Listing
Modified Tue Oct 2 06:57:11 2012 UTC (6 years, 6 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 (6 years, 6 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 (6 years, 6 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 (6 years, 6 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 (6 years, 6 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 (6 years, 6 months ago) by caltinay
test fixes, doco updates, annoyance removals.


Revision 4004 - Directory Listing
Modified Fri Sep 28 04:45:25 2012 UTC (6 years, 6 months ago) by caltinay
don't use escript.escript.Data...


Revision 4003 - Directory Listing
Modified Fri Sep 28 00:20:01 2012 UTC (6 years, 6 months ago) by jfenwick
Load balancing on unit tests

Revision 4002 - Directory Listing
Modified Fri Sep 28 00:16:56 2012 UTC (6 years, 6 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 (6 years, 6 months ago) by caltinay
Removed obsolete files.


Revision 4000 - Directory Listing
Modified Thu Sep 27 01:32:07 2012 UTC (6 years, 6 months ago) by caltinay
s/escript/escore/


Revision 3999 - Directory Listing
Modified Thu Sep 27 01:31:07 2012 UTC (6 years, 6 months ago) by jfenwick
Splitting tests


Revision 3998 - Directory Listing
Modified Thu Sep 27 01:17:28 2012 UTC (6 years, 6 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 (6 years, 6 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 (6 years, 6 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 (6 years, 6 months ago) by jfenwick
More module fiddles

Revision 3994 - Directory Listing
Modified Wed Sep 26 07:38:38 2012 UTC (6 years, 6 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 (6 years, 6 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 (6 years, 6 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 (6 years, 6 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 (6 years, 6 months ago) by caltinay
First set of assorted epydoc fixes/additions.


Revision 3989 - Directory Listing
Modified Tue Sep 25 02:21:54 2012 UTC (6 years, 6 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 (6 years, 6 months ago) by caltinay
Scale coordinates if pyproj is not available


Revision 3987 - Directory Listing
Modified Sun Sep 23 23:24:37 2012 UTC (6 years, 6 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 (6 years, 6 months ago) by caltinay
Added explicit cast to make osx happy.


Revision 3985 - Directory Listing
Modified Fri Sep 21 06:44:17 2012 UTC (6 years, 6 months ago) by caltinay
Unit test for ER Mapper reader.


Revision 3984 - Directory Listing
Modified Fri Sep 21 06:41:54 2012 UTC (6 years, 6 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 (6 years, 6 months ago) by caltinay
Use ReducedFunction for data sources.


Revision 3982 - Directory Listing
Modified Fri Sep 21 03:23:22 2012 UTC (6 years, 6 months ago) by jfenwick
More edits + removing pyvisi from trunk


Revision 3981 - Directory Listing
Modified Fri Sep 21 02:47:54 2012 UTC (6 years, 6 months ago) by jfenwick
First pass of updating copyright notices

Revision 3980 - Directory Listing
Modified Fri Sep 21 01:55:39 2012 UTC (6 years, 6 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 (6 years, 6 months ago) by caltinay
Fixed tests under MPI.


Revision 3978 - Directory Listing
Modified Thu Sep 20 04:36:17 2012 UTC (6 years, 6 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 (6 years, 6 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 (6 years, 6 months ago) by caltinay
fixed python-2.7'ism.


Revision 3975 - Directory Listing
Modified Thu Sep 20 01:54:06 2012 UTC (6 years, 6 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 (6 years, 7 months ago) by caltinay
Can now constrain sides of domain.


Revision 3971 - Directory Listing
Modified Wed Sep 19 02:55:35 2012 UTC (6 years, 7 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 (6 years, 7 months ago) by jfenwick
More install doc fixes


Revision 3969 - Directory Listing
Modified Tue Sep 18 05:34:38 2012 UTC (6 years, 7 months ago) by jfenwick
Removing reference to nose


Revision 3968 - Directory Listing
Modified Mon Sep 17 06:30:02 2012 UTC (6 years, 7 months ago) by jfenwick
Starting updates to the install guide


Revision 3967 - Directory Listing
Modified Mon Sep 17 04:02:58 2012 UTC (6 years, 7 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 (6 years, 7 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 (6 years, 7 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 (6 years, 7 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 (6 years, 7 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 (6 years, 7 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 (6 years, 7 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 (6 years, 7 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 (6 years, 7 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 (6 years, 7 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 (6 years, 7 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 (6 years, 7 months ago) by caltinay
Fixes to netcdf reader for inversions.


Revision 3955 - Directory Listing
Modified Tue Sep 4 01:44:41 2012 UTC (6 years, 7 months ago) by caltinay
Added CentOS 6 vm options file.


Revision 3954 - Directory Listing
Modified Tue Sep 4 01:43:58 2012 UTC (6 years, 7 months ago) by caltinay
Fixed an issue with incompatible nose.


Revision 3953 - Directory Listing
Modified Mon Sep 3 00:57:12 2012 UTC (6 years, 7 months ago) by caltinay
Some test output adjustments.


Revision 3952 - Directory Listing
Modified Sun Sep 2 23:42:25 2012 UTC (6 years, 7 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 (6 years, 7 months ago) by caltinay
Fixed tests with python versions <2.7.


Revision 3950 - Directory Listing
Modified Fri Aug 24 06:10:02 2012 UTC (6 years, 7 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 (6 years, 7 months ago) by caltinay
Added tests for mappings.


Revision 3948 - Directory Listing
Modified Fri Aug 24 01:01:34 2012 UTC (6 years, 7 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 (6 years, 7 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 (6 years, 7 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 (6 years, 7 months ago) by jfenwick
Changing utest behaviour for MPI


Revision 3944 - Directory Listing
Modified Mon Aug 20 02:11:22 2012 UTC (6 years, 8 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 (6 years, 8 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 (6 years, 8 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 (6 years, 8 months ago) by jfenwick
Some more test disabling


Revision 3940 - Directory Listing
Modified Thu Jul 26 05:54:58 2012 UTC (6 years, 8 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 (6 years, 8 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 (6 years, 9 months ago) by jfenwick
Added unit test for tagreader


Revision 3931 - Directory Listing
Modified Tue Jul 10 00:39:09 2012 UTC (6 years, 9 months ago) by jfenwick
Fixing spelling


Revision 3928 - Directory Listing
Modified Mon Jul 9 23:23:43 2012 UTC (6 years, 9 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 (6 years, 9 months ago) by jfenwick
Avoid warning


Revision 3923 - Directory Listing
Modified Mon Jul 9 05:12:12 2012 UTC (6 years, 9 months ago) by jfenwick
Fixing build error.


Revision 3922 - Directory Listing
Modified Mon Jul 9 02:19:51 2012 UTC (6 years, 9 months ago) by jfenwick
Adds setvalue to locator
Addresses mantis #531


Revision 3921 - Directory Listing
Modified Thu Jul 5 05:02:49 2012 UTC (6 years, 9 months ago) by jfenwick
Fix build error


Revision 3920 - Directory Listing
Modified Thu Jul 5 03:42:30 2012 UTC (6 years, 9 months ago) by jfenwick
Copied over tagname reading stuff from finley


Revision 3919 - Directory Listing
Modified Thu Jul 5 03:12:02 2012 UTC (6 years, 9 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 (6 years, 9 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 (6 years, 9 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 (6 years, 9 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 (6 years, 9 months ago) by caltinay
Added declspecs for all ripley classes.


Revision 3914 - Directory Listing
Modified Wed Jun 20 04:51:47 2012 UTC (6 years, 10 months 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 (6 years, 10 months 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 (6 years, 10 months 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 (6 years, 10 months ago) by jfenwick
Copyright changes

Revision 3910 - Directory Listing
Modified Thu Jun 14 00:45:03 2012 UTC (6 years, 10 months ago) by gross
Small bug fixed.

Revision 3909 - Directory Listing
Modified Wed Jun 13 07:03:06 2012 UTC (6 years, 10 months ago) by gross
darcy solver removes hydrostatic pressure from problem now

Revision 3908 - Directory Listing
Modified Wed Jun 13 05:43:45 2012 UTC (6 years, 10 months 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 (6 years, 10 months 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 (6 years, 10 months ago) by jfenwick
Disable AMG on MPI builds


Revision 3905 - Directory Listing
Modified Tue Jun 5 08:33:41 2012 UTC (6 years, 10 months ago) by gross
length scale changed

Revision 3904 - Directory Listing
Modified Tue Jun 5 08:30:24 2012 UTC (6 years, 10 months ago) by gross
incorrect macro element argument removed

Revision 3903 - Directory Listing
Modified Tue Jun 5 08:26:20 2012 UTC (6 years, 10 months ago) by gross
offset removed: not clear why this was there

Revision 3901 - Directory Listing
Modified Wed May 23 08:09:45 2012 UTC (6 years, 10 months 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 (6 years, 11 months ago) by jfenwick
correcting example

Revision 3896 - Directory Listing
Modified Fri May 11 01:31:29 2012 UTC (6 years, 11 months ago) by caltinay
Re-enable numpy header detection with python 2.


Revision 3895 - Directory Listing
Modified Mon Apr 16 00:09:42 2012 UTC (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years ago) by gross
some minor problems with MPI AMG fixed.

Revision 3885 - Directory Listing
Modified Wed Apr 4 22:12:26 2012 UTC (7 years ago) by gross
some fix in AMG

Revision 3884 - Directory Listing
Modified Wed Apr 4 04:55:43 2012 UTC (7 years ago) by gross
some fix in AMG

Revision 3883 - Directory Listing
Modified Mon Mar 26 03:24:14 2012 UTC (7 years 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 (7 years 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 (7 years, 1 month 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 (7 years, 1 month ago) by caltinay
Use system silo on guineapig now.


Revision 3865 - Directory Listing
Modified Mon Mar 12 23:49:05 2012 UTC (7 years, 1 month ago) by caltinay
Re-enabled threaded MKL on epic.


Revision 3863 - Directory Listing
Modified Mon Mar 12 00:15:40 2012 UTC (7 years, 1 month ago) by gross
some debug prints removed

Revision 3861 - Directory Listing
Modified Fri Mar 9 02:06:29 2012 UTC (7 years, 1 month 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 (7 years, 1 month 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 (7 years, 1 month ago) by jfenwick
Correcting some indent errors


Revision 3851 - Directory Listing
Modified Wed Feb 29 05:23:30 2012 UTC (7 years, 1 month ago) by jfenwick
Start of cross-compile build for py3

Revision 3850 - Directory Listing
Modified Tue Feb 28 06:04:42 2012 UTC (7 years, 1 month ago) by caltinay
Support for CSC in ripley.


Revision 3843 - Directory Listing
Modified Mon Feb 27 05:50:58 2012 UTC (7 years, 1 month ago) by caltinay
Updated epic options, disabled OpenMP until problems solved.


Revision 3842 - Directory Listing
Modified Mon Feb 27 04:19:16 2012 UTC (7 years, 1 month ago) by caltinay
Updated savanna libraries and compiler version.


Revision 3841 - Directory Listing
Modified Mon Feb 27 04:18:53 2012 UTC (7 years, 1 month ago) by caltinay
Added support for OFFSET1 matrices in ripley.


Revision 3837 - Directory Listing
Modified Thu Feb 16 03:58:58 2012 UTC (7 years, 2 months ago) by caltinay
Test cleanup.


Revision 3836 - Directory Listing
Modified Thu Feb 16 03:17:18 2012 UTC (7 years, 2 months ago) by caltinay
Transport problem support for ripley.


Revision 3835 - Directory Listing
Modified Wed Feb 15 23:19:01 2012 UTC (7 years, 2 months ago) by gross
and another attempt to fix MPI compilation

Revision 3834 - Directory Listing
Modified Wed Feb 15 07:09:09 2012 UTC (7 years, 2 months ago) by gross
some declaration problems fixed 

Revision 3833 - Directory Listing
Modified Wed Feb 15 06:19:45 2012 UTC (7 years, 2 months ago) by lgao
Fix the merging problem for this file. 



Revision 3830 - Directory Listing
Modified Wed Feb 15 04:27:47 2012 UTC (7 years, 2 months ago) by lgao
Add comments for Smoother 



Revision 3829 - Directory Listing
Modified Wed Feb 15 03:33:08 2012 UTC (7 years, 2 months ago) by lgao
Fix warnings from another machine. 



Revision 3828 - Directory Listing
Modified Wed Feb 15 03:27:58 2012 UTC (7 years, 2 months ago) by lgao
Fix all warnings reported on guineapig.



Revision 3827 - Directory Listing
Modified Tue Feb 14 11:42:08 2012 UTC (7 years, 2 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 (7 years, 2 months ago) by gross
don't call MPI withing parallel regions

Revision 3824 - Directory Listing
Modified Tue Feb 14 01:22:16 2012 UTC (7 years, 2 months ago) by gross
fix for openmp

Revision 3823 - Directory Listing
Modified Mon Feb 13 08:09:32 2012 UTC (7 years, 2 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 (7 years, 2 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 (7 years, 2 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 (7 years, 2 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 (7 years, 2 months ago) by gross
some modifications to the test examples

Revision 3807 - Directory Listing
Modified Mon Feb 6 06:14:25 2012 UTC (7 years, 2 months ago) by gross
LINEAR_CRANK_NICOLSON solver added

Revision 3806 - Directory Listing
Modified Mon Feb 6 02:32:48 2012 UTC (7 years, 2 months ago) by caltinay
ripley::getSize() also returns circumcircle now.


Revision 3805 - Directory Listing
Modified Mon Feb 6 01:42:20 2012 UTC (7 years, 2 months ago) by gross
return circumcircle  now.

Revision 3804 - Directory Listing
Modified Mon Feb 6 00:48:22 2012 UTC (7 years, 2 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 (7 years, 2 months ago) by caltinay
Fixes to ripley unit test setup


Revision 3802 - Directory Listing
Modified Fri Feb 3 06:05:57 2012 UTC (7 years, 2 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 (7 years, 2 months ago) by caltinay
Fixed OpenMP bug in paso local AMG.


Revision 3800 - Directory Listing
Modified Fri Feb 3 01:18:06 2012 UTC (7 years, 2 months ago) by caltinay
Fixed integration with constant data on ripley.


Revision 3799 - Directory Listing
Modified Thu Feb 2 10:41:28 2012 UTC (7 years, 2 months ago) by gross
test for gradient of constant data added

Revision 3798 - Directory Listing
Modified Thu Feb 2 09:47:27 2012 UTC (7 years, 2 months ago) by gross
test for interpolation of constant data added

Revision 3797 - Directory Listing
Modified Thu Feb 2 09:28:59 2012 UTC (7 years, 2 months ago) by gross
test for integration of constant data added.

Revision 3796 - Directory Listing
Modified Thu Feb 2 06:26:15 2012 UTC (7 years, 2 months ago) by gross
typo in grad calculation fixed.

Revision 3795 - Directory Listing
Modified Thu Feb 2 05:54:34 2012 UTC (7 years, 2 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 (7 years, 2 months ago) by gross
uninitialied variable fixed.

Revision 3793 - Directory Listing
Modified Wed Feb 1 07:39:43 2012 UTC (7 years, 2 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 (7 years, 2 months ago) by caltinay
Merged ripley rectangular domain into trunk.


Revision 3788 - Directory Listing
Modified Mon Jan 30 04:41:33 2012 UTC (7 years, 2 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 (7 years, 2 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 (7 years, 2 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 (7 years, 2 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 (7 years, 2 months ago) by caltinay
Another attempt to fix #649


Revision 3778 - Directory Listing
Modified Fri Jan 20 05:09:52 2012 UTC (7 years, 3 months ago) by gross
better error reporting from UMFPACK

Revision 3775 - Directory Listing
Modified Wed Jan 18 07:26:34 2012 UTC (7 years, 3 months ago) by jfenwick
Weipa updated


Revision 3774 - Directory Listing
Modified Wed Jan 18 06:29:34 2012 UTC (7 years, 3 months ago) by jfenwick
dudley, pasowrap, pycad


Revision 3772 - Directory Listing
Modified Wed Jan 18 04:19:33 2012 UTC (7 years, 3 months ago) by jfenwick
Converting finley directories


Revision 3771 - Directory Listing
Modified Wed Jan 18 02:30:48 2012 UTC (7 years, 3 months ago) by jfenwick
First stage of 2.6/3 conversion


Revision 3747 - Directory Listing
Modified Thu Dec 15 02:13:14 2011 UTC (7 years, 4 months ago) by gross
inconsistent notation fixed.

Revision 3739 - Directory Listing
Modified Tue Dec 13 00:48:26 2011 UTC (7 years, 4 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 (7 years, 4 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 (7 years, 4 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 (7 years, 4 months ago) by jfenwick
Fixed apparent multiple instances of Esys


Revision 3734 - Directory Listing
Modified Fri Dec 9 04:48:08 2011 UTC (7 years, 4 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 (7 years, 4 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 (7 years, 4 months ago) by jfenwick
Oops


Revision 3727 - Directory Listing
Modified Thu Dec 8 04:55:56 2011 UTC (7 years, 4 months ago) by jfenwick
More broken linkage


Revision 3726 - Directory Listing
Modified Thu Dec 8 04:35:52 2011 UTC (7 years, 4 months ago) by jfenwick
Fixing some broken linkage on windows


Revision 3723 - Directory Listing
Modified Wed Dec 7 05:59:04 2011 UTC (7 years, 4 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 (7 years, 4 months ago) by caltinay
Fixed off-by-one error in FunctionSpace


Revision 3689 - Directory Listing
Modified Wed Nov 23 01:39:45 2011 UTC (7 years, 4 months ago) by gross
integration nodes fixed

Revision 3681 - Directory Listing
Modified Fri Nov 18 04:54:15 2011 UTC (7 years, 5 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 (7 years, 5 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 (7 years, 5 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 (7 years, 5 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 (7 years, 5 months ago) by jfenwick
pasowrap joins the trunk.


Revision 3667 - Directory Listing
Modified Tue Nov 15 23:29:23 2011 UTC (7 years, 5 months ago) by gross
better consistence of script and notation

Revision 3666 - Directory Listing
Modified Tue Nov 15 23:10:20 2011 UTC (7 years, 5 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 (7 years, 5 months ago) by gross
ode solver added

Revision 3649 - Directory Listing
Modified Fri Nov 4 04:35:15 2011 UTC (7 years, 5 months ago) by gross
gmsh reader understand name tags now.

Revision 3648 - Directory Listing
Modified Thu Nov 3 08:13:31 2011 UTC (7 years, 5 months ago) by gross
typos fixed

Revision 3647 - Directory Listing
Modified Tue Nov 1 23:33:18 2011 UTC (7 years, 5 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 (7 years, 5 months ago) by lgao
working option file on epic



Revision 3645 - Directory Listing
Modified Fri Oct 28 00:11:30 2011 UTC (7 years, 5 months ago) by caltinay
Fixed typos.


Revision 3644 - Directory Listing
Modified Thu Oct 27 06:42:56 2011 UTC (7 years, 5 months ago) by gross
hint to add surface items in pycad

Revision 3643 - Directory Listing
Modified Thu Oct 27 06:23:16 2011 UTC (7 years, 5 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 (7 years, 5 months ago) by caltinay
Assorted spelling/comment fixes in paso.


Revision 3641 - Directory Listing
Modified Thu Oct 27 02:16:12 2011 UTC (7 years, 5 months ago) by gross
more work on the assemblage

Revision 3639 - Directory Listing
Modified Tue Oct 25 02:13:26 2011 UTC (7 years, 5 months ago) by caltinay
Assorted spelling fixes in finley C.


Revision 3637 - Directory Listing
Modified Fri Oct 21 04:29:33 2011 UTC (7 years, 6 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 (7 years, 6 months ago) by caltinay
Fixed minor issues.


Revision 3630 - Directory Listing
Modified Wed Oct 19 03:04:53 2011 UTC (7 years, 6 months ago) by gross
minor fix to dary flux

Revision 3629 - Directory Listing
Modified Wed Oct 19 03:04:27 2011 UTC (7 years, 6 months ago) by gross
darcy example added

Revision 3628 - Directory Listing
Modified Wed Oct 19 02:09:36 2011 UTC (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 months ago) by gross
missing argument in gmsh reader documentation added

Revision 3624 - Directory Listing
Modified Wed Oct 12 07:58:25 2011 UTC (7 years, 6 months ago) by gross
changes for epic.ivec.org

Revision 3623 - Directory Listing
Modified Tue Oct 11 03:59:40 2011 UTC (7 years, 6 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 (7 years, 6 months ago) by trankine
Epic.ivec.org scons build template

Revision 3620 - Directory Listing
Modified Wed Oct 5 06:06:14 2011 UTC (7 years, 6 months ago) by gross
bug fixed

Revision 3619 - Directory Listing
Modified Wed Oct 5 03:53:34 2011 UTC (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 7 months ago) by caltinay
Fixed double/float warning.


Revision 3606 - Directory Listing
Modified Mon Sep 19 16:26:51 2011 UTC (7 years, 7 months ago) by trankine
Trial nosetests runner tests for better integration

Revision 3605 - Directory Listing
Modified Mon Sep 19 07:47:23 2011 UTC (7 years, 7 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 (7 years, 7 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 (7 years, 7 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 (7 years, 7 months ago) by caltinay
Fix scons checks on windows


Revision 3601 - Directory Listing
Modified Mon Sep 19 01:21:33 2011 UTC (7 years, 7 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 (7 years, 7 months ago) by trankine
Updating cgisrv3 options for external cppunit

Revision 3599 - Directory Listing
Modified Fri Sep 16 01:34:46 2011 UTC (7 years, 7 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 (7 years, 7 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 (7 years, 7 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 (7 years, 7 months ago) by caltinay
Deleted some obsolete options files.


Revision 3595 - Directory Listing
Modified Thu Sep 15 05:56:47 2011 UTC (7 years, 7 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 (7 years, 7 months ago) by caltinay
Added missing declspecs in paso. Thanks Terry.


Revision 3589 - Directory Listing
Modified Mon Sep 12 03:25:25 2011 UTC (7 years, 7 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 (7 years, 7 months ago) by gross
Typo fixed.

Revision 3586 - Directory Listing
Modified Fri Sep 9 04:02:29 2011 UTC (7 years, 7 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 (7 years, 7 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 (7 years, 7 months ago) by jfenwick
Removing Locator.setValue for now


Revision 3583 - Directory Listing
Modified Tue Sep 6 04:27:59 2011 UTC (7 years, 7 months ago) by caltinay
Updated shake75 options file.


Revision 3582 - Directory Listing
Modified Tue Sep 6 02:02:17 2011 UTC (7 years, 7 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 (7 years, 7 months ago) by gross
Used python 2.7 syntax. Sorry!

Revision 3580 - Directory Listing
Modified Tue Sep 6 00:31:35 2011 UTC (7 years, 7 months ago) by gross
error handeling for python compilation improved.

Revision 3579 - Directory Listing
Modified Mon Sep 5 23:25:01 2011 UTC (7 years, 7 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 (7 years, 7 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 (7 years, 7 months ago) by gross
getFLux fixed and tests added.


Revision 3576 - Directory Listing
Modified Mon Sep 5 06:33:20 2011 UTC (7 years, 7 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 (7 years, 7 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 (7 years, 7 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 (7 years, 7 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 (7 years, 7 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 (7 years, 7 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 (7 years, 7 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 (7 years, 7 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 (7 years, 7 months ago) by gross
darcy flux documentation updated.

Revision 3567 - Directory Listing
Modified Tue Aug 30 07:55:02 2011 UTC (7 years, 7 months ago) by gross
FIXME and TODO fixed.

Revision 3566 - Directory Listing
Modified Tue Aug 30 07:37:55 2011 UTC (7 years, 7 months ago) by gross
small fix to units

Revision 3565 - Directory Listing
Modified Mon Aug 29 10:28:57 2011 UTC (7 years, 7 months ago) by jfenwick
surely it will accept this one


Revision 3564 - Directory Listing
Modified Mon Aug 29 09:09:30 2011 UTC (7 years, 7 months ago) by jfenwick
In case windows is case sensitive


Revision 3563 - Directory Listing
Modified Mon Aug 29 04:26:46 2011 UTC (7 years, 7 months ago) by jfenwick
Another try to fix the windows issue


Revision 3562 - Directory Listing
Modified Mon Aug 29 03:31:13 2011 UTC (7 years, 7 months ago) by jfenwick
Removed DLL export from non-exported methods


Revision 3561 - Directory Listing
Modified Mon Aug 29 02:51:05 2011 UTC (7 years, 7 months ago) by jfenwick
Attempt to fix windows problem


Revision 3560 - Directory Listing
Modified Mon Aug 29 01:10:42 2011 UTC (7 years, 7 months ago) by gross
lf missing in buildvars print

Revision 3559 - Directory Listing
Modified Fri Aug 26 07:47:27 2011 UTC (7 years, 7 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 (7 years, 7 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 (7 years, 7 months ago) by jfenwick
Fixed icc problem


Revision 3551 - Directory Listing
Modified Fri Aug 19 03:53:41 2011 UTC (7 years, 8 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 (7 years, 8 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 (7 years, 8 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 (7 years, 8 months ago) by jfenwick
Fixing badger options


Revision 3547 - Directory Listing
Modified Tue Aug 2 04:24:09 2011 UTC (7 years, 8 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 (7 years, 8 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 (7 years, 8 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 (7 years, 8 months ago) by jfenwick
Temporary fix to get windows to compile


Revision 3543 - Directory Listing
Modified Fri Jul 22 06:58:03 2011 UTC (7 years, 8 months ago) by gross
and the generator script

Revision 3542 - Directory Listing
Modified Fri Jul 22 06:57:41 2011 UTC (7 years, 8 months ago) by gross
first attempts toward a multi grid solver

Revision 3541 - Directory Listing
Modified Fri Jul 22 03:21:06 2011 UTC (7 years, 8 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 (7 years, 9 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 (7 years, 10 months 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 (7 years, 10 months ago) by gross


Revision 3527 - Directory Listing
Modified Tue May 24 06:59:20 2011 UTC (7 years, 10 months ago) by gross
modifications to the coal seam gas 

Revision 3526 - Directory Listing
Modified Tue May 24 05:01:46 2011 UTC (7 years, 10 months ago) by gross
coal code uses nodal wells now

Revision 3525 - Directory Listing
Modified Tue May 24 04:04:58 2011 UTC (7 years, 10 months ago) by gross
and more typos fixed.

Revision 3524 - Directory Listing
Modified Tue May 24 02:23:00 2011 UTC (7 years, 10 months ago) by gross
typo fixed.

Revision 3523 - Directory Listing
Modified Tue May 24 02:03:37 2011 UTC (7 years, 10 months ago) by caltinay
Fixed declaration order (register const) for gcc-4.6


Revision 3522 - Directory Listing
Modified Tue May 24 00:57:58 2011 UTC (7 years, 10 months ago) by gross
(almost) full support for Point elements

Revision 3521 - Directory Listing
Modified Mon May 23 07:23:02 2011 UTC (7 years, 10 months ago) by gross
typo fixed

Revision 3520 - Directory Listing
Modified Mon May 23 06:24:30 2011 UTC (7 years, 10 months ago) by gross
some fixes for to point interpolation

Revision 3519 - Directory Listing
Modified Mon May 23 05:55:47 2011 UTC (7 years, 10 months ago) by gross
compiler fixes

Revision 3516 - Directory Listing
Modified Fri May 20 00:57:41 2011 UTC (7 years, 11 months ago) by gross
missing file

Revision 3515 - Directory Listing
Modified Thu May 19 08:20:57 2011 UTC (7 years, 11 months ago) by gross
some first work for DiracFunctions

Revision 3514 - Directory Listing
Modified Thu May 19 04:48:34 2011 UTC (7 years, 11 months ago) by caltinay
Fixed __truediv__ and added __rtruediv__ for new python division operator.


Revision 3513 - Directory Listing
Modified Thu May 19 04:45:19 2011 UTC (7 years, 11 months ago) by lgao
When "werror" is set to True, scons build will complains about compilation failure of some boost "multi-array" test case. This causes recently unit-tests failures. So I set "werror" back to False before someone who has the knowledge fixes the problem.



Revision 3511 - Directory Listing
Modified Tue May 17 23:56:13 2011 UTC (7 years, 11 months ago) by lgao
Fixed the scons build problem in case MPI is not in use (this 
is the reason why unit tests failed to execute properly for the
past several days).



Revision 3510 - Directory Listing
Modified Fri May 13 06:09:49 2011 UTC (7 years, 11 months ago) by gross
some fixes for the compilation without BOOMERAMG

Revision 3508 - Directory Listing
Modified Fri May 13 04:15:29 2011 UTC (7 years, 11 months ago) by lgao
Add Boomer AMG as a new preconditioner 
Can be used by .setPreconditioner(SolverOptions.BOOMERAMG)
and the following parallel coarsening method can be 
used together with Boomer AMG preconditioner: 
  .setCoarsening(SolverOptions.CIJP_FIXED_RANDOM_COARSENING)
  .setCoarsening(SolverOptions.CIJP_COARSENING)
  .setCoarsening(SolverOptions.FALGOUT_COARSENING)
  .setCoarsening(SolverOptions.PMIS_COARSENING)
  .setCoarsening(SolverOptions.HMIS_COARSENING)

Note that Boomer AMG is only available when MPI is enabled.  



Revision 3506 - Directory Listing
Modified Wed May 11 01:59:45 2011 UTC (7 years, 11 months ago) by jfenwick
Use VSL if MKLRANDOM is defined.
Use different seeds for different ranks/threads.
Use different seeds for successive calls with no seed given.


Revision 3505 - Directory Listing
Modified Fri Apr 29 07:09:45 2011 UTC (7 years, 11 months ago) by jfenwick
arithmetic operations now return NotImplemented if they don't know what to do.
Fixes mantis issue #54


Revision 3504 - Directory Listing
Modified Thu Apr 28 12:55:05 2011 UTC (7 years, 11 months ago) by jfenwick
Move arithmetic ops into explicitly named methods

Revision 3503 - Directory Listing
Modified Thu Apr 28 06:55:30 2011 UTC (7 years, 11 months ago) by gross
missing file

Revision 3502 - Directory Listing
Modified Thu Apr 28 05:06:24 2011 UTC (7 years, 11 months ago) by gross
Darcy flow solver is now supporting 4 solvers

Revision 3501 - Directory Listing
Modified Wed Apr 13 04:07:53 2011 UTC (8 years ago) by gross


Revision 3500 - Directory Listing
Modified Mon Apr 11 03:09:06 2011 UTC (8 years ago) by gross
GMRES solver for new DarcyFlux solver added

Revision 3499 - Directory Listing
Modified Fri Apr 8 00:14:35 2011 UTC (8 years ago) by gross


Revision 3498 - Directory Listing
Modified Thu Apr 7 01:12:59 2011 UTC (8 years ago) by lgao
Two modifications to OpenMP versioned AMG: 
(1) in RungeStueben Search: 
    * use a smaller panel to reduce the searching time for an unkown with
      the largest lambda value;
    * fix the mistakes made in this function (Two places where set S is 
      expected, not set S^T).
(2) while construct the coarse level matrix A_C:
      A_C = P^T (A P) where A is the fine level matrix and P is the 
      interpolation operator. Since we've already had the tranpose of P
      when we process "A_temp = A P", the performance of matrix product 
      can be improved when we use P^T for the calculation of A_temp.



Revision 3497 - Directory Listing
Modified Wed Apr 6 06:11:56 2011 UTC (8 years ago) by gross


Revision 3494 - Directory Listing
Modified Tue Apr 5 04:12:08 2011 UTC (8 years ago) by gross
more coal seam gas

Revision 3490 - Directory Listing
Modified Wed Mar 30 02:24:33 2011 UTC (8 years ago) by caltinay
More gcc-4.6 fixes (mostly initialized-but-unused-var warnings)


Revision 3489 - Directory Listing
Modified Wed Mar 30 00:46:04 2011 UTC (8 years ago) by caltinay
Fixed a few warnings emitted by gcc-4.6.


Revision 3487 - Directory Listing
Modified Mon Mar 28 03:44:22 2011 UTC (8 years ago) by gross
some compile fixes

Revision 3486 - Directory Listing
Modified Sun Mar 27 22:27:45 2011 UTC (8 years ago) by gross
bug in eigenvector calculation fixed (see mantis=594)

Revision 3485 - Directory Listing
Modified Thu Mar 24 22:44:40 2011 UTC (8 years ago) by gross
some compile fixes

Revision 3484 - Directory Listing
Modified Thu Mar 24 05:42:07 2011 UTC (8 years ago) by gross
some work on coal gas

Revision 3483 - Directory Listing
Modified Wed Mar 23 04:18:35 2011 UTC (8 years ago) by gross
Ops: AMG MPI chould not be called yet.

Revision 3482 - Directory Listing
Modified Wed Mar 23 04:06:52 2011 UTC (8 years ago) by gross
some work on AMG MPI

Revision 3481 - Directory Listing
Modified Wed Mar 23 04:05:58 2011 UTC (8 years ago) by gross


Revision 3480 - Directory Listing
Modified Wed Mar 23 04:03:39 2011 UTC (8 years ago) by gross


Revision 3479 - Directory Listing
Modified Wed Mar 23 04:03:22 2011 UTC (8 years ago) by gross


Revision 3478 - Directory Listing
Modified Wed Mar 23 04:02:39 2011 UTC (8 years ago) by gross
coal gas stuff


Revision 3475 - Directory Listing
Modified Thu Mar 17 00:28:08 2011 UTC (8 years, 1 month ago) by caltinay
Removed an obsolete file.


Revision 3470 - Directory Listing
Modified Mon Mar 14 03:50:49 2011 UTC (8 years, 1 month ago) by caltinay
Fix for mantis issue 591 (added __truediv__ methods to Data class).



Revision 3469 - Directory Listing
Modified Tue Feb 22 06:39:16 2011 UTC (8 years, 1 month ago) by jfenwick
Fix docstring in dudley

Revision 3468 - Directory Listing
Modified Tue Feb 22 06:38:57 2011 UTC (8 years, 1 month ago) by jfenwick
Made constructors more efficient.
Only has a very minor affect on performance

Revision 3467 - Directory Listing
Modified Tue Feb 8 09:31:46 2011 UTC (8 years, 2 months ago) by caltinay
Fixed unit test after last change.


Revision 3466 - Directory Listing
Modified Tue Feb 8 05:16:21 2011 UTC (8 years, 2 months ago) by caltinay
Added TEMP and friends to the list of env vars exported by scons.
Modified pycad's gmsh command line since the mesh filename may also contain
spaces.


Revision 3465 - Directory Listing
Modified Tue Feb 8 00:11:15 2011 UTC (8 years, 2 months ago) by caltinay
Use the subprocess module within pycad's Triangle.


Revision 3464 - Directory Listing
Modified Mon Feb 7 05:17:11 2011 UTC (8 years, 2 months ago) by caltinay
Use the subprocess module with argument list to run gmsh from pycad to avoid
having to deal with spaces in path names.


Revision 3463 - Directory Listing
Modified Mon Feb 7 02:09:57 2011 UTC (8 years, 2 months ago) by caltinay
Check for gmsh in main SConstruct file and skip tests that depend on it when
the executable is not found.


Revision 3462 - Directory Listing
Modified Mon Feb 7 02:01:50 2011 UTC (8 years, 2 months ago) by caltinay
Removed debug output.


Revision 3461 - Directory Listing
Modified Sun Feb 6 23:33:37 2011 UTC (8 years, 2 months ago) by caltinay
Re-enabled silo on savanna as well.


Revision 3460 - Directory Listing
Modified Sun Feb 6 23:24:22 2011 UTC (8 years, 2 months ago) by jfenwick
Re-enabling MPI on savanna


Revision 3459 - Directory Listing
Modified Wed Feb 2 01:54:45 2011 UTC (8 years, 2 months ago) by caltinay
Patch from Terry to fix compilation on Windows with MKL enabled.


Revision 3458 - Directory Listing
Modified Mon Jan 31 07:06:42 2011 UTC (8 years, 2 months ago) by gross
more on AMG under MPI

Revision 3457 - Directory Listing
Modified Thu Jan 27 01:38:17 2011 UTC (8 years, 2 months ago) by caltinay
Added missing cookbook figures from Anthony.


Revision 3456 - Directory Listing
Modified Tue Jan 25 08:20:02 2011 UTC (8 years, 2 months ago) by gross
segfault fixed

Revision 3455 - Directory Listing
Modified Tue Jan 25 04:23:17 2011 UTC (8 years, 2 months ago) by gross
some compilation fixes

Revision 3454 - Directory Listing
Modified Tue Jan 25 04:00:29 2011 UTC (8 years, 2 months ago) by caltinay
Fixed some minor doxygen issues.


Revision 3453 - Directory Listing
Modified Tue Jan 25 03:59:30 2011 UTC (8 years, 2 months ago) by caltinay
Disabled C99 extensions on guineapig again.


Revision 3452 - Directory Listing
Modified Tue Jan 25 01:53:57 2011 UTC (8 years, 2 months ago) by caltinay
Fixed building cookbook, including toc (scons scans for keywords in the tex
files but not in .cls as it seems).
Also fixed a few epydoc warnings and typos.



Revision 3451 - Directory Listing
Modified Sun Jan 23 23:11:01 2011 UTC (8 years, 2 months ago) by gross
compilation fixes

Revision 3450 - Directory Listing
Modified Fri Jan 21 06:39:56 2011 UTC (8 years, 2 months ago) by gross
more compilation fixing

Revision 3449 - Directory Listing
Modified Fri Jan 21 05:48:15 2011 UTC (8 years, 2 months ago) by gross
compile problem in AMG fixed.

Revision 3448 - Directory Listing
Modified Fri Jan 21 04:38:54 2011 UTC (8 years, 2 months ago) by ahallam
Quick final changes to cookbook to accomodate example10c problem. 'So long and thanks for all the fish.'

Revision 3447 - Directory Listing
Modified Fri Jan 21 04:33:42 2011 UTC (8 years, 2 months ago) by ahallam
example10c removed from testing as it is not in the cookbook.

Revision 3446 - Directory Listing
Modified Thu Jan 20 06:47:07 2011 UTC (8 years, 3 months ago) by gross
and more work toward AMG MPI

Revision 3445 - Directory Listing
Modified Wed Jan 19 06:02:15 2011 UTC (8 years, 3 months ago) by gross
more work towards MPI AMG

Revision 3444 - Directory Listing
Modified Tue Jan 18 23:17:27 2011 UTC (8 years, 3 months ago) by gross
run_domainreaders.py can only be run for MPI ranks = 1 as gmsh does not support MPI yet

Revision 3443 - Directory Listing
Modified Tue Jan 18 05:38:48 2011 UTC (8 years, 3 months ago) by gross
test for AMG fixed. New test set guarantees SPD stiffness matrix. Previously this was not guaranteed and could lead to singular coarse level matrices (which cause MKL based runs to fail)

Revision 3442 - Directory Listing
Modified Tue Jan 18 01:47:36 2011 UTC (8 years, 3 months ago) by gross
 emeregncy

Revision 3441 - Directory Listing
Modified Fri Jan 14 01:09:09 2011 UTC (8 years, 3 months ago) by gross
clarifiaction of function names as a first step towards a MPI version of AMG

Revision 3440 - Directory Listing
Modified Fri Jan 14 00:04:53 2011 UTC (8 years, 3 months ago) by gross
a second AMG interpolation implemented

Revision 3439 - Directory Listing
Modified Fri Jan 14 00:04:01 2011 UTC (8 years, 3 months ago) by gross
some modifications to fix the cook examples runs for testing

Revision 3438 - Directory Listing
Modified Thu Jan 13 23:24:50 2011 UTC (8 years, 3 months ago) by gross
mesh size reduced

Revision 3437 - Directory Listing
Modified Mon Jan 10 05:05:15 2011 UTC (8 years, 3 months ago) by plaub
Fixed test for new default arguments


Revision 3436 - Directory Listing
Modified Mon Jan 10 02:06:07 2011 UTC (8 years, 3 months ago) by plaub
Added/modified AMG tests:

  - "self.failUnless(...)" became "self.assertTrue(...)"
    because fail* is soon to be deprecated,
  - fixed logical error in self.assertTrue argument,
  - added another test, 'testSquare'.

Added some print statements to AMG.c in verbose mode to
identify which of the stopping conditions were fulfilled.

Changed default AMG parameters for 'setNumPreSweeps' and 
'setNumPostSweeps' to 1 (huge speed improvment).

P.S Beware of bugs in the above code; I have only proved 
it correct, not tried it... Jokes!



Revision 3435 - Directory Listing
Modified Fri Jan 7 03:40:39 2011 UTC (8 years, 3 months ago) by gross
initial value changed

Revision 3434 - Directory Listing
Modified Fri Jan 7 03:35:58 2011 UTC (8 years, 3 months ago) by gross
initial value changed

Revision 3433 - Directory Listing
Modified Fri Jan 7 02:39:05 2011 UTC (8 years, 3 months ago) by gross
initial value changed

Revision 3432 - Directory Listing
Modified Fri Jan 7 01:32:07 2011 UTC (8 years, 3 months ago) by jfenwick
Made import statements a bit more specific to clean up the epydoc

Revision 3431 - Directory Listing
Modified Fri Jan 7 01:19:21 2011 UTC (8 years, 3 months ago) by gross
redundant setMinCoarseMatrixSparsity removed.

Revision 3430 - Directory Listing
Modified Thu Jan 6 09:09:19 2011 UTC (8 years, 3 months ago) by gross
import order is critical

Revision 3429 - Directory Listing
Modified Thu Jan 6 07:40:01 2011 UTC (8 years, 3 months ago) by gross
SAMESIGN macro added

Revision 3428 - Directory Listing
Modified Thu Jan 6 01:12:36 2011 UTC (8 years, 3 months ago) by jfenwick
Fixed errors (and space/tabs) in geometry.py
Added unit tests


Revision 3427 - Directory Listing
Modified Thu Jan 6 00:11:45 2011 UTC (8 years, 3 months ago) by ahallam
Missing script.

Revision 3426 - Directory Listing
Modified Wed Jan 5 02:51:35 2011 UTC (8 years, 3 months ago) by ahallam
Added new example tests.

Revision 3425 - Directory Listing
Modified Wed Jan 5 02:50:38 2011 UTC (8 years, 3 months ago) by ahallam
Added new example tests.

Revision 3424 - Directory Listing
Modified Wed Jan 5 00:24:46 2011 UTC (8 years, 3 months ago) by gross
memory leak in UMFPACK interface fixed

Revision 3423 - Directory Listing
Modified Thu Dec 16 04:24:13 2010 UTC (8 years, 4 months ago) by jfenwick
Fix a typo in geometry.py


Revision 3422 - Directory Listing
Modified Mon Dec 13 23:27:47 2010 UTC (8 years, 4 months ago) by caltinay
Updated shake75 options file to use visit 2.2


Revision 3421 - Directory Listing
Modified Mon Dec 13 23:15:01 2010 UTC (8 years, 4 months ago) by artak
semi-colon is missing

Revision 3417 - Directory Listing
Modified Sun Dec 12 23:40:27 2010 UTC (8 years, 4 months ago) by artak
Treat warnings as errors is disabled.

Revision 3412 - Directory Listing
Modified Fri Dec 10 02:03:49 2010 UTC (8 years, 4 months ago) by gross
some fixes for MKL lapack

Revision 3411 - Directory Listing
Modified Thu Dec 9 22:42:02 2010 UTC (8 years, 4 months ago) by gross
some cleaning

Revision 3410 - Directory Listing
Modified Thu Dec 9 07:02:52 2010 UTC (8 years, 4 months ago) by ahallam
Minor changes to cookbook, gravity example.

Revision 3409 - Directory Listing
Modified Thu Dec 9 07:01:23 2010 UTC (8 years, 4 months ago) by ahallam
minor changes to examples before holiday.

Revision 3407 - Directory Listing
Modified Wed Dec 8 05:16:08 2010 UTC (8 years, 4 months ago) by jfenwick
Obsolete


Revision 3406 - Directory Listing
Modified Wed Dec 8 01:09:37 2010 UTC (8 years, 4 months ago) by ahallam
Updates to cookbook documentation for release.

Revision 3405 - Directory Listing
Modified Wed Dec 8 01:09:06 2010 UTC (8 years, 4 months ago) by ahallam
Changes to example09 for memory footprint. One change too help wording in layer_cake function. example09b removed from testing. Not for impending release.

Revision 3404 - Directory Listing
Modified Tue Dec 7 10:24:32 2010 UTC (8 years, 4 months ago) by gross
missing file

Revision 3403 - Directory Listing
Modified Tue Dec 7 08:13:51 2010 UTC (8 years, 4 months ago) by gross
some small fixes

Revision 3402 - Directory Listing
Modified Tue Dec 7 07:36:12 2010 UTC (8 years, 4 months ago) by gross
AMG support now block size > 3 (requires clapack or MKL).

additional diagnostics for AMG 



Revision 3400 - Directory Listing
Modified Mon Dec 6 02:23:07 2010 UTC (8 years, 4 months ago) by caltinay
Moved vtkCellType.h to weipa where it belongs now.


Revision 3399 - Directory Listing
Modified Mon Dec 6 02:02:16 2010 UTC (8 years, 4 months ago) by caltinay
Updated VTK files to reflect changes to the writer.


Revision 3398 - Directory Listing
Modified Mon Dec 6 00:02:33 2010 UTC (8 years, 4 months ago) by caltinay
Fixed the quad mask in a very specific case and changed saveVTK to write a
specific value for unused nodes instead of the first one which breaks unit
tests depending on the number of ranks used.
Still need to rebaseline some VTK files so the tests pass.


Revision 3397 - Directory Listing
Modified Sun Dec 5 22:46:25 2010 UTC (8 years, 4 months ago) by caltinay
Fixed an issue in saveVTK/Silo.


Revision 3396 - Directory Listing
Modified Fri Dec 3 08:24:16 2010 UTC (8 years, 4 months ago) by gross
wrong pointer handed

Revision 3395 - Directory Listing
Modified Fri Dec 3 06:30:35 2010 UTC (8 years, 4 months ago) by gross
small correction

Revision 3394 - Directory Listing
Modified Fri Dec 3 06:07:08 2010 UTC (8 years, 4 months ago) by jfenwick
Nasty hack to dodge a linking issue for serial builds on savanna


Revision 3393 - Directory Listing
Modified Fri Dec 3 04:14:56 2010 UTC (8 years, 4 months ago) by caltinay
shake24 (darwin) needs -L/usr/lib to pull correct gcc library.
The python library path was also not entirely correct - fixed.


Revision 3392 - Directory Listing
Modified Thu Dec 2 03:26:29 2010 UTC (8 years, 4 months ago) by ahallam
Updates to cookbook. Includes new section on variable meshing. To be reviewed.

Revision 3391 - Directory Listing
Modified Thu Dec 2 02:25:53 2010 UTC (8 years, 4 months ago) by gross
seg fault fixed.

Revision 3390 - Directory Listing
Modified Thu Dec 2 00:34:37 2010 UTC (8 years, 4 months ago) by jfenwick
RandomData added


Revision 3389 - Directory Listing
Modified Wed Dec 1 23:03:35 2010 UTC (8 years, 4 months ago) by ahallam
Some changes to the cookbook examples. Starting Inversion experimentation.

Revision 3388 - Directory Listing
Modified Mon Nov 29 06:07:07 2010 UTC (8 years, 4 months ago) by caltinay
Added quotes around some variables to fix running scripts located in a
directory whose name contains spaces.


Revision 3387 - Directory Listing
Modified Thu Nov 25 07:09:23 2010 UTC (8 years, 4 months ago) by caltinay
Fixed some annoying typos.


Revision 3386 - Directory Listing
Modified Thu Nov 25 05:05:50 2010 UTC (8 years, 4 months ago) by caltinay
scons choked on the newlines within the parameter list. Fixed.


Revision 3385 - Directory Listing
Modified Thu Nov 25 04:41:33 2010 UTC (8 years, 4 months ago) by ahallam
Updates to cookbook, something is wrong with the sconstruct though

Revision 3384 - Directory Listing
Modified Thu Nov 25 03:28:01 2010 UTC (8 years, 4 months ago) by ahallam
Cookbook lumping updates.

Revision 3383 - Directory Listing
Modified Thu Nov 25 02:17:51 2010 UTC (8 years, 4 months ago) by caltinay
Fixed some typos and added missing symlinks. 


Revision 3382 - Directory Listing
Modified Thu Nov 25 00:43:18 2010 UTC (8 years, 4 months ago) by jfenwick
I've added better credits for dev team.
There is a new page just before the contents page with current dev team 
and a more detailed list in the user guide appendix.

Please check this and let me know if you think there are errors or 
omissions.

Also fixed a typo.
Removed reference to python style files we no longer use from the 
license file.



Revision 3381 - Directory Listing
Modified Wed Nov 24 23:37:55 2010 UTC (8 years, 4 months ago) by ahallam
Proofing of lumping.tex

Revision 3380 - Directory Listing
Modified Wed Nov 24 05:03:25 2010 UTC (8 years, 4 months ago) by gross
update to change list

Revision 3379 - Directory Listing
Modified Wed Nov 24 04:48:49 2010 UTC (8 years, 4 months ago) by gross
some clarification on lumping

Revision 3378 - Directory Listing
Modified Tue Nov 23 05:09:25 2010 UTC (8 years, 4 months ago) by caltinay
Pass dictionary of data objects to EscriptDataset as kwargs in DataManager.


Revision 3377 - Directory Listing
Modified Tue Nov 23 02:01:20 2010 UTC (8 years, 4 months ago) by caltinay
Removed empty esys, include and lib directories since the install prefix is
variable now. Don't shoot me for this if this hurts.


Revision 3376 - Directory Listing
Modified Tue Nov 23 01:56:20 2010 UTC (8 years, 4 months ago) by caltinay
Invoke run-escript instead of escript in runTest.


Revision 3375 - Directory Listing
Modified Tue Nov 23 00:37:23 2010 UTC (8 years, 4 months ago) by jfenwick
Fix to unit tests


Revision 3374 - Directory Listing
Modified Tue Nov 23 00:30:20 2010 UTC (8 years, 4 months ago) by ahallam
Fixes to example scripts.

Revision 3373 - Directory Listing
Modified Tue Nov 23 00:29:07 2010 UTC (8 years, 4 months ago) by ahallam
New figures.

Revision 3372 - Directory Listing
Modified Mon Nov 22 23:10:03 2010 UTC (8 years, 4 months ago) by caltinay
Added missing import to fix unit test


Revision 3371 - Directory Listing
Modified Mon Nov 22 06:13:47 2010 UTC (8 years, 4 months ago) by caltinay
Sort data objects by name before passing them to the EscriptDataset object.
This addresses #537.


Revision 3370 - Directory Listing
Modified Sun Nov 21 23:22:25 2010 UTC (8 years, 4 months ago) by ahallam
Rearranged figures for release.

Revision 3369 - Directory Listing
Modified Fri Nov 19 06:26:11 2010 UTC (8 years, 5 months ago) by gross
matrix balance introduced in paso

Revision 3368 - Directory Listing
Modified Fri Nov 19 05:59:46 2010 UTC (8 years, 5 months ago) by jfenwick
3d interpolateTable support.
New more generic interface for table interpolation.
tests and doco updated

Revision 3367 - Directory Listing
Modified Fri Nov 19 02:07:25 2010 UTC (8 years, 5 months ago) by caltinay
added quick intro to visualization with VisIt and fixed a file reference.


Revision 3366 - Directory Listing
Modified Thu Nov 18 23:41:42 2010 UTC (8 years, 5 months ago) by caltinay
esys.weipa Python interface documentation.


Revision 3365 - Directory Listing
Modified Thu Nov 18 10:49:40 2010 UTC (8 years, 5 months ago) by caltinay
Fixed compilation without VisIt.


Revision 3364 - Directory Listing
Modified Thu Nov 18 05:51:44 2010 UTC (8 years, 5 months ago) by caltinay
Expose visitInitialize and visitPublishData through the python interface.


Revision 3363 - Directory Listing
Modified Thu Nov 18 05:49:45 2010 UTC (8 years, 5 months ago) by caltinay
Catch some corner cases in weipa's VisIt controller to make it more foolproof
and allow reinitialization.


Revision 3362 - Directory Listing
Modified Thu Nov 18 04:59:44 2010 UTC (8 years, 5 months ago) by caltinay
Made the VisIt interface less verbose in non-debug mode and removed unused
includes.


Revision 3361 - Directory Listing
Modified Thu Nov 18 01:56:36 2010 UTC (8 years, 5 months ago) by caltinay
Minor enhancement.


Revision 3360 - Directory Listing
Modified Thu Nov 18 00:20:21 2010 UTC (8 years, 5 months ago) by jfenwick
Fix some epydoc errors
Fixed issue 564
removed minimize.py since it hasn't worked in who knows how long

Revision 3359 - Directory Listing
Modified Wed Nov 17 23:32:36 2010 UTC (8 years, 5 months ago) by jfenwick
Fixing problem with ./utest.sh including full build path


Revision 3358 - Directory Listing
Modified Wed Nov 17 08:02:32 2010 UTC (8 years, 5 months ago) by gross
a more flexiblae version of safeDiv

Revision 3357 - Directory Listing
Modified Wed Nov 17 06:21:37 2010 UTC (8 years, 5 months ago) by caltinay
Fixed a crash when loading data from netCDF files.


Revision 3356 - Directory Listing
Modified Wed Nov 17 05:27:47 2010 UTC (8 years, 5 months ago) by caltinay
Finley type Finley_Tri3Face_Contact is no longer untested within weipa.


Revision 3355 - Directory Listing
Modified Tue Nov 16 06:35:06 2010 UTC (8 years, 5 months ago) by caltinay
Fixed building with boost < 1.40 by
- removing the saveVTK method from dudley's MeshAdapter completely
  (no point introducing it now when we are trying to get rid of it soon)
- adding a helper function to weipa's python layer which can be called from C++
  with older boost versions.



Revision 3354 - Directory Listing
Modified Tue Nov 16 04:48:09 2010 UTC (8 years, 5 months ago) by jfenwick
Fix problem with superclass init


Revision 3353 - Directory Listing
Modified Tue Nov 16 04:32:40 2010 UTC (8 years, 5 months ago) by gross
some clarification on AMG in the documentation

Revision 3352 - Directory Listing
Modified Tue Nov 16 03:58:09 2010 UTC (8 years, 5 months ago) by gross
exposure of AMG options

Revision 3351 - Directory Listing
Modified Tue Nov 16 02:39:40 2010 UTC (8 years, 5 months ago) by gross
modified approach for AMG coarsning using a panel

Revision 3350 - Directory Listing
Modified Mon Nov 15 05:14:43 2010 UTC (8 years, 5 months ago) by caltinay
Fixed MSVC90 file as per Gordon's report.


Revision 3349 - Directory Listing
Modified Mon Nov 15 05:09:56 2010 UTC (8 years, 5 months ago) by caltinay
escript now supports out-of-tree builds.
All build and test files are now created under a user-definable build_dir
directory.
This also fixes issue 291.
Removed most svn:ignore props since they are no longer required.


Revision 3348 - Directory Listing
Modified Fri Nov 12 05:55:50 2010 UTC (8 years, 5 months ago) by caltinay
Added weipa import statements to the relevant parts in user guide and cookbook.
Documented the deprecation of esys.escript.saveVTK in the changes chapter.


Revision 3347 - Directory Listing
Modified Fri Nov 12 04:58:27 2010 UTC (8 years, 5 months ago) by caltinay
-Do not compare mesh variables (like owner, color etc) in the saveVTK tests
since they depend on the number of ranks.
-Fixed a problem where ranks without data samples can't know whether a
reduced mesh is to be used or not.


Revision 3346 - Directory Listing
Modified Fri Nov 12 01:19:02 2010 UTC (8 years, 5 months ago) by caltinay
Replaced usage of esys.escript.util.saveVTK by weipa.saveVTK in all python
scripts.


Revision 3345 - Directory Listing
Modified Thu Nov 11 23:51:45 2010 UTC (8 years, 5 months ago) by caltinay
Moved dudley saveVTK tests to weipa and removed unneeded files.


Revision 3344 - Directory Listing
Modified Thu Nov 11 23:26:52 2010 UTC (8 years, 5 months ago) by caltinay
Phew!
-escript, finley, and dudley now uses weipa's saveVTK implementation
-moved tests from finley to weipa accordingly; dudley still to do
-rebaselined all test files
-fixed a few issues in weipa.saveVTK, e.g. saving metadata without schema
-added a deprecation warning to esys.escript.util.saveVTK
-todo: change doco, tests and other places to use weipa.saveVTK



Revision 3343 - Directory Listing
Modified Wed Nov 10 02:01:29 2010 UTC (8 years, 5 months ago) by jfenwick
Rename users guide to user.pdf from guide.pdf to match the conventions 
we follow with the other files.

Corrected the description of Einstein convention from "convenient"
to "compact". 


Revision 3342 - Directory Listing
Modified Tue Nov 9 03:41:58 2010 UTC (8 years, 5 months ago) by caltinay
Fixed interpolation for Line3Macro elements in weipa.


Revision 3341 - Directory Listing
Modified Mon Nov 8 21:34:01 2010 UTC (8 years, 5 months ago) by caltinay
Renamed MS options file.


Revision 3340 - Directory Listing
Modified Mon Nov 8 01:25:58 2010 UTC (8 years, 5 months ago) by jfenwick
Relax python version check.
Only checks X.Y not X.Y.Z
Fixes mantis #556


Revision 3339 - Directory Listing
Modified Fri Nov 5 05:30:31 2010 UTC (8 years, 5 months ago) by jfenwick
Fixed more package clashing problems.
Package install.pdf not install.tex
Changed title on most documents to esys-Escript except for the cookbook coz I like ti that way.

Revision 3338 - Directory Listing
Modified Fri Nov 5 03:50:51 2010 UTC (8 years, 5 months ago) by jfenwick
Remove old name for man page to prevent clash with erlang.
Changed default library to link for boost to boost_python-mt



Revision 3337 - Directory Listing
Modified Fri Nov 5 03:20:19 2010 UTC (8 years, 5 months ago) by jfenwick
Work around weird scons behaviour


Revision 3336 - Directory Listing
Modified Fri Nov 5 00:28:44 2010 UTC (8 years, 5 months ago) by jfenwick
Fixed bib entry


Revision 3335 - Directory Listing
Modified Wed Nov 3 05:02:57 2010 UTC (8 years, 5 months ago) by jfenwick
Fix the launcher so that it can give an environment even if buildvars is not present.
Environment now includes scons for standalone builds.
Fixes and cleanup for the install documentation.
scons TEMPLATES updated to define the optionfile version by default.

...mumble
   finley no longer imports escript into the default namespace
...

Revision 3334 - Directory Listing
Modified Wed Nov 3 00:46:56 2010 UTC (8 years, 5 months ago) by jfenwick
Added 3.2 to changes page

Revision 3333 - Directory Listing
Modified Mon Nov 1 06:08:05 2010 UTC (8 years, 5 months ago) by caltinay
Updated lapack paths on guineapig.


Revision 3332 - Directory Listing
Modified Mon Nov 1 05:26:55 2010 UTC (8 years, 5 months ago) by jfenwick
Copy run-escript over for a prefix install.
Fixes mantis issue: 551

Revision 3331 - Directory Listing
Modified Mon Nov 1 05:21:18 2010 UTC (8 years, 5 months ago) by caltinay
Appendix done. Fixed some overfull hboxes.


Revision 3330 - Directory Listing
Modified Mon Nov 1 04:29:09 2010 UTC (8 years, 5 months ago) by caltinay
Finished user's guide chapters up to Appendix.


Revision 3329 - Directory Listing
Modified Fri Oct 29 05:55:55 2010 UTC (8 years, 5 months ago) by caltinay
Faultsystems2d. not finished yet.


Revision 3328 - Directory Listing
Modified Fri Oct 29 02:21:42 2010 UTC (8 years, 5 months ago) by caltinay
Fixed script filename


Revision 3327 - Directory Listing
Modified Fri Oct 29 02:08:37 2010 UTC (8 years, 5 months ago) by gross
missing omp function added.

Revision 3326 - Directory Listing
Modified Fri Oct 29 00:45:32 2010 UTC (8 years, 5 months ago) by caltinay
6.2 Darcy Flux. Note that I commented the gravity flow subsection since it's
not written.


Revision 3325 - Directory Listing
Modified Fri Oct 29 00:30:51 2010 UTC (8 years, 5 months ago) by caltinay
Section 6.1.


Revision 3324 - Directory Listing
Modified Thu Oct 28 23:43:09 2010 UTC (8 years, 5 months ago) by caltinay
Finished pycad chapter 5, regenerated eps files


Revision 3323 - Directory Listing
Modified Thu Oct 28 09:53:46 2010 UTC (8 years, 5 months ago) by gross
some openmp fizes.

Revision 3322 - Directory Listing
Modified Thu Oct 28 05:26:37 2010 UTC (8 years, 5 months ago) by jfenwick
Adapt install guide to new style.
Simplify package building scripts to autodetect necessary info and build control file automatically.


Revision 3321 - Directory Listing
Modified Thu Oct 28 05:02:41 2010 UTC (8 years, 5 months ago) by gross
a problem with surface orientation fixed.

Revision 3320 - Directory Listing
Modified Thu Oct 28 03:29:51 2010 UTC (8 years, 5 months ago) by caltinay
This fixes the scons warning about not finding the Intel top dir on Savanna.


Revision 3319 - Directory Listing
Modified Thu Oct 28 03:14:27 2010 UTC (8 years, 5 months ago) by caltinay
export PATH to scons when creating environment so tools in non-default
locations such as latex on savanna are found.


Revision 3318 - Directory Listing
Modified Thu Oct 28 01:05:36 2010 UTC (8 years, 5 months ago) by caltinay
This should fix building paso without OpenMP.


Revision 3317 - Directory Listing
Modified Thu Oct 28 00:50:41 2010 UTC (8 years, 5 months ago) by caltinay
Removed bogus mpi.h includes, replaced others by our esysUtils wrapper
and rearranged so that the wrapper always comes before netcdf which fixes
linking problems when disabling mpi on systems with netCDF 4.x.


Revision 3316 - Directory Listing
Modified Wed Oct 27 01:43:21 2010 UTC (8 years, 5 months ago) by caltinay
Finished Chapter 4, added missing bibliography entries for Trilinos and SuperLU


Revision 3315 - Directory Listing
Modified Wed Oct 27 01:20:27 2010 UTC (8 years, 5 months ago) by gross
bug in sparse matrixmatrix fixed.

Revision 3314 - Directory Listing
Modified Tue Oct 26 22:22:20 2010 UTC (8 years, 5 months ago) by gross
output removed/leaned up

Revision 3313 - Directory Listing
Modified Tue Oct 26 22:00:09 2010 UTC (8 years, 5 months ago) by gross
some print statements removed

Revision 3312 - Directory Listing
Modified Tue Oct 26 07:54:58 2010 UTC (8 years, 5 months ago) by gross
last step for a clean up version of the AMG

Revision 3311 - Directory Listing
Modified Tue Oct 26 05:43:25 2010 UTC (8 years, 5 months ago) by jfenwick
Added raggedbottom to last page before appendix.
Condensed the latex picture figures a bit


Revision 3310 - Directory Listing
Modified Tue Oct 26 03:58:17 2010 UTC (8 years, 5 months ago) by jfenwick
Fixed some pdf bookmarks and added the index package


Revision 3309 - Directory Listing
Modified Tue Oct 26 03:56:26 2010 UTC (8 years, 5 months ago) by caltinay
Updated escript section with added DataManager reference.


Revision 3308 - Directory Listing
Modified Tue Oct 26 03:24:54 2010 UTC (8 years, 5 months ago) by jfenwick
Moved listing and class up a level.
Removed hackscore from cookbook.
Made cookbook use the new stuff - removed old stuff

Revision 3307 - Directory Listing
Modified Tue Oct 26 01:19:19 2010 UTC (8 years, 5 months ago) by caltinay
Put index back in and added link to index and biblio to the TOC.


Revision 3306 - Directory Listing
Modified Mon Oct 25 05:09:13 2010 UTC (8 years, 5 months ago) by caltinay
Commented declaremodule and modulesynopsis.


Revision 3305 - Directory Listing
Modified Mon Oct 25 05:04:22 2010 UTC (8 years, 5 months ago) by jfenwick
Fancy shuffling


Revision 3304 - Directory Listing
Modified Mon Oct 25 04:43:48 2010 UTC (8 years, 5 months ago) by caltinay
Disabled building html user's guide - it doesn't read the class file properly
and the PDF now supports links.


Revision 3303 - Directory Listing
Modified Mon Oct 25 04:33:31 2010 UTC (8 years, 5 months ago) by gross
more clean up work on the AMG

Revision 3302 - Directory Listing
Modified Mon Oct 25 01:50:07 2010 UTC (8 years, 5 months ago) by jfenwick
Fixed appendix so hyperref generates links properly

Revision 3301 - Directory Listing
Modified Mon Oct 25 01:27:54 2010 UTC (8 years, 5 months ago) by jfenwick
Modified layout of descriptions.
Fixed some overfull hboxes

Revision 3300 - Directory Listing
Modified Mon Oct 25 00:22:14 2010 UTC (8 years, 5 months ago) by jfenwick
Some text fixes


Revision 3299 - Directory Listing
Modified Sun Oct 24 23:44:18 2010 UTC (8 years, 5 months ago) by gross
some fixes

Revision 3298 - Directory Listing
Modified Fri Oct 22 06:49:04 2010 UTC (8 years, 5 months ago) by caltinay


Revision 3297 - Directory Listing
Modified Fri Oct 22 05:47:37 2010 UTC (8 years, 5 months ago) by caltinay
small fix


Revision 3296 - Directory Listing
Modified Fri Oct 22 02:53:24 2010 UTC (8 years, 5 months ago) by caltinay
hackscore removal.


Revision 3295 - Directory Listing
Modified Fri Oct 22 01:56:02 2010 UTC (8 years, 5 months ago) by jfenwick


Revision 3294 - Directory Listing
Modified Fri Oct 22 01:15:56 2010 UTC (8 years, 5 months ago) by jfenwick
Tweaks


Revision 3293 - Directory Listing
Modified Thu Oct 21 23:18:32 2010 UTC (8 years, 5 months ago) by caltinay
user's guide builds again with new class file. The cleanup can commence...


Revision 3292 - Directory Listing
Modified Thu Oct 21 05:02:49 2010 UTC (8 years, 6 months ago) by jfenwick
Adding the class file


Revision 3291 - Directory Listing
Modified Thu Oct 21 00:37:42 2010 UTC (8 years, 6 months ago) by caltinay
Work on user's guide up to section 3.2 (exclusive), including some text on
new DataManager class.
Also reworked a couple of images.
This should be the last commit of the guide before changes to the latex class.


Revision 3290 - Directory Listing
Modified Wed Oct 20 08:31:56 2010 UTC (8 years, 6 months ago) by gross
small fixes

Revision 3289 - Directory Listing
Modified Wed Oct 20 07:07:11 2010 UTC (8 years, 6 months ago) by gross
missing factor fixed.

Revision 3288 - Directory Listing
Modified Tue Oct 19 01:08:31 2010 UTC (8 years, 6 months ago) by caltinay
Corrections to user guide sections 1.5 and 1.6.
Converted backgrounds of the very complex stokes flow eps files by raster
images leaving the vectors untouched so the change is barely visible but
makes loading the PDF page some orders of magnitude faster.


Revision 3287 - Directory Listing
Modified Tue Oct 19 00:42:22 2010 UTC (8 years, 6 months ago) by gross
complaint from valgrind about an uninitialized value fixed (no impact on result)

Revision 3286 - Directory Listing
Modified Tue Oct 19 00:36:27 2010 UTC (8 years, 6 months ago) by gross
small memory leak fixed.

Revision 3285 - Directory Listing
Modified Tue Oct 19 00:28:00 2010 UTC (8 years, 6 months ago) by gross
bug in initialization step fixed.

Revision 3284 - Directory Listing
Modified Mon Oct 18 23:48:04 2010 UTC (8 years, 6 months ago) by gross
old AMLI code collected in a single file. It does not compile and should be merged with RecILU

Revision 3283 - Directory Listing
Modified Mon Oct 18 22:39:28 2010 UTC (8 years, 6 months ago) by gross
AMG reengineered, BUG is Smoother fixed.



Revision 3282 - Directory Listing
Modified Fri Oct 15 06:59:32 2010 UTC (8 years, 6 months ago) by caltinay
Don't build guide_pdf when only guide_html was requested.


Revision 3281 - Directory Listing
Modified Fri Oct 15 06:52:34 2010 UTC (8 years, 6 months ago) by caltinay
latex2html doesn't like './' in graphicspath, so removed it.


Revision 3280 - Directory Listing
Modified Fri Oct 15 05:11:11 2010 UTC (8 years, 6 months ago) by caltinay
Corrections to 1.4 of the user's guide.


Revision 3279 - Directory Listing
Modified Fri Oct 15 04:02:06 2010 UTC (8 years, 6 months ago) by caltinay
Some corrections to 1.3 of user's guide and defined graphicspath globally.


Revision 3278 - Directory Listing
Modified Fri Oct 15 02:00:45 2010 UTC (8 years, 6 months ago) by caltinay
Updated section 1.2 of user's guide.


Revision 3277 - Directory Listing
Modified Fri Oct 15 01:06:24 2010 UTC (8 years, 6 months ago) by caltinay
This should keep scons happy on systems without pdflatex issuing a warning
to the user. Also updated all other doc sconscript files to use a global
release_dir prefix so we can easily move the files somewhere else if req'd.


Revision 3276 - Directory Listing
Modified Thu Oct 14 21:38:05 2010 UTC (8 years, 6 months ago) by gross
new damage solver

Revision 3275 - Directory Listing
Modified Thu Oct 14 06:15:27 2010 UTC (8 years, 6 months ago) by gross
As it turns out the tangential operator implementation is not a good idea.
This a check in to save the last version of this approach before starting using a different method.



Revision 3274 - Directory Listing
Modified Thu Oct 14 06:14:30 2010 UTC (8 years, 6 months ago) by caltinay
Some initial corrections to the user's guide.


Revision 3273 - Directory Listing
Modified Thu Oct 14 05:44:08 2010 UTC (8 years, 6 months ago) by caltinay
Fixed guide_html dependencies so the pages are really rebuilt when source
files change.


Revision 3272 - Directory Listing
Modified Thu Oct 14 04:02:06 2010 UTC (8 years, 6 months ago) by caltinay
Similar to last commit but for cookbook. Can't test since cookbook doesn't
build at the moment.


Revision 3271 - Directory Listing
Modified Thu Oct 14 02:16:00 2010 UTC (8 years, 6 months ago) by caltinay
-use existing scons pdflatex target for user's guide
-create temporary files in build directory rather than source directory
-make latex less verbose if verbosity option is off
This fixes #291 for user's guide.


Revision 3270 - Directory Listing
Modified Thu Oct 14 00:30:11 2010 UTC (8 years, 6 months ago) by caltinay
added -dEPSCrop option to ps2pdf so graphics are cropped as expected.


Revision 3269 - Directory Listing
Modified Wed Oct 13 03:21:50 2010 UTC (8 years, 6 months ago) by jfenwick
Fixed some intel compiler warnings.
Put linearPDEs back the way it was and present a common interface for dudley and finley (as per Lutz)


Revision 3268 - Directory Listing
Modified Wed Oct 13 02:16:23 2010 UTC (8 years, 6 months ago) by caltinay
Do not ignore unknown options since the warnings are not easily visible,
bail out instead.


Revision 3267 - Directory Listing
Modified Wed Oct 13 02:12:06 2010 UTC (8 years, 6 months ago) by caltinay
Renamed restarts.py to datamanager.py, added a method to explicitly set the
domain without adding data. Calling export() without domain/data will now
output a warning. Some additional cleanup.


Revision 3266 - Directory Listing
Modified Wed Oct 13 00:32:46 2010 UTC (8 years, 6 months ago) by caltinay
Disable MPI on shake24 due to conflicting installations in default locations.


Revision 3265 - Directory Listing
Modified Tue Oct 12 04:42:03 2010 UTC (8 years, 6 months ago) by caltinay
Updated relevant sections in install guide to reflect scons option changes.
Standalone section needs to be updated before the release.


Revision 3264 - Directory Listing
Modified Tue Oct 12 04:40:06 2010 UTC (8 years, 6 months ago) by jfenwick
Minor changes to avoid optimiser bug in intel-10


Revision 3263 - Directory Listing
Modified Tue Oct 12 01:16:21 2010 UTC (8 years, 6 months ago) by caltinay
Updated convection script to use escript DataManager.


Revision 3262 - Directory Listing
Modified Mon Oct 11 07:19:40 2010 UTC (8 years, 6 months ago) by gross
header file include added

Revision 3261 - Directory Listing
Modified Mon Oct 11 04:25:42 2010 UTC (8 years, 6 months ago) by jfenwick
Disable some unit tests for dudley until I can fix MPI failures


Revision 3260 - Directory Listing
Modified Mon Oct 11 03:41:35 2010 UTC (8 years, 6 months ago) by jfenwick
Removing dead files


Revision 3259 - Directory Listing
Modified Mon Oct 11 01:48:14 2010 UTC (8 years, 6 months ago) by jfenwick
Merging dudley and scons updates from branches


Revision 3250 - Directory Listing
Modified Thu Oct 7 01:49:18 2010 UTC (8 years, 6 months ago) by caltinay
Fixed a declaration/definition mismatch.


Revision 3245 - Directory Listing
Modified Tue Oct 5 23:17:56 2010 UTC (8 years, 6 months ago) by jfenwick
Removing out of date scripts


Revision 3233 - Directory Listing
Modified Mon Oct 4 00:54:26 2010 UTC (8 years, 6 months ago) by jfenwick
Fixed build error


Revision 3232 - Directory Listing
Modified Fri Oct 1 02:08:38 2010 UTC (8 years, 6 months ago) by ahallam
Updates to cookbook, new chapter DC Resis and IP. Using new packages hyperref, natbib

Revision 3222 - Directory Listing
Modified Wed Sep 29 03:55:44 2010 UTC (8 years, 6 months ago) by caltinay
This should make windoze happy.


Revision 3209 - Directory Listing
Modified Mon Sep 27 01:54:46 2010 UTC (8 years, 6 months ago) by caltinay
Added missing libraries to escriptconvert.


Revision 3208 - Directory Listing
Modified Sun Sep 26 23:31:17 2010 UTC (8 years, 6 months ago) by jfenwick
List tests as not working with MPI


Revision 3201 - Directory Listing
Modified Thu Sep 23 06:54:18 2010 UTC (8 years, 6 months ago) by gross
bug in meanValue fixed.

Revision 3200 - Directory Listing
Modified Thu Sep 23 06:53:36 2010 UTC (8 years, 6 months ago) by gross
more damage

Revision 3195 - Directory Listing
Modified Wed Sep 22 00:28:04 2010 UTC (8 years, 6 months ago) by ahallam
Shortened runtime of cookbook examples to aid testing.

Revision 3194 - Directory Listing
Modified Tue Sep 21 09:14:56 2010 UTC (8 years, 6 months ago) by gross
missing files

Revision 3193 - Directory Listing
Modified Tue Sep 21 06:56:44 2010 UTC (8 years, 6 months ago) by gross
more clean up in AMG

Revision 3192 - Directory Listing
Modified Fri Sep 17 04:02:57 2010 UTC (8 years, 7 months ago) by caltinay
- weipa's saveVTK will now save multiple files if the data objects to write are
  not on the same mesh.
- the save* methods now also add the appropriate file extension if not already
  supplied


Revision 3191 - Directory Listing
Modified Fri Sep 17 00:44:20 2010 UTC (8 years, 7 months ago) by caltinay
Use consistent naming for domain, mesh and 'chunks'


Revision 3190 - Directory Listing
Modified Thu Sep 16 23:29:09 2010 UTC (8 years, 7 months ago) by jfenwick
Disable some cookbook examples until we can get issues sorted out


Revision 3188 - Directory Listing
Modified Thu Sep 16 04:36:38 2010 UTC (8 years, 7 months ago) by caltinay
Fixed deletion of old restart directories with a checkpoint freq>1.


Revision 3186 - Directory Listing
Modified Thu Sep 16 01:23:53 2010 UTC (8 years, 7 months ago) by caltinay
Added checkpoint frequency setting to DataManager so that visualisation files
can be created independent of restart files. Also removed the overhead of
creating an EscriptDataset instance for the restart-only case.



Revision 3185 - Directory Listing
Modified Thu Sep 16 00:30:09 2010 UTC (8 years, 7 months ago) by caltinay
Weipa now supports initialization from DataConstant instances.


Revision 3183 - Directory Listing
Modified Tue Sep 14 23:09:59 2010 UTC (8 years, 7 months ago) by jfenwick
Adding timing information to unit tests.


Revision 3182 - Directory Listing
Modified Tue Sep 14 06:05:55 2010 UTC (8 years, 7 months ago) by jfenwick
Temporarily removing example8c from unit testing.
It seems to lock the test - or it runs for rediculous timeframes.


Revision 3181 - Directory Listing
Modified Tue Sep 14 05:01:00 2010 UTC (8 years, 7 months ago) by jfenwick
Fix to buggy recovery of colouring information.
Unfortunately unable to fix buggy spelling of colour.


Revision 3180 - Directory Listing
Modified Tue Sep 14 03:39:55 2010 UTC (8 years, 7 months ago) by gross
some fixes for the case that no direc solver is available.

Revision 3179 - Directory Listing
Modified Tue Sep 14 01:55:24 2010 UTC (8 years, 7 months ago) by gross
typo fixed

Revision 3178 - Directory Listing
Modified Tue Sep 14 00:31:59 2010 UTC (8 years, 7 months ago) by caltinay
Corrected check for python version in launcher, added a function get_buildvar
for convenience.


Revision 3177 - Directory Listing
Modified Mon Sep 13 10:30:24 2010 UTC (8 years, 7 months ago) by gross
running vresion

Revision 3176 - Directory Listing
Modified Sat Sep 11 01:09:54 2010 UTC (8 years, 7 months ago) by caltinay
Maybe this will finally make the Mac happy.


Revision 3175 - Directory Listing
Modified Fri Sep 10 09:03:38 2010 UTC (8 years, 7 months ago) by gross
intial checkin 

Revision 3174 - Directory Listing
Modified Fri Sep 10 03:55:18 2010 UTC (8 years, 7 months ago) by caltinay
Enabled debian's lapack on shake75.


Revision 3168 - Directory Listing
Modified Wed Sep 8 23:01:25 2010 UTC (8 years, 7 months ago) by ahallam
Missing *.png

Revision 3167 - Directory Listing
Modified Wed Sep 8 03:24:29 2010 UTC (8 years, 7 months ago) by caltinay
Only run pyvisi tests if VTK was enabled at configuration time.


Revision 3166 - Directory Listing
Modified Tue Sep 7 23:47:06 2010 UTC (8 years, 7 months ago) by ahallam
Fix doc build error. I will add the figure when I come in tomorrow and turn Darra on.


Revision 3165 - Directory Listing
Modified Tue Sep 7 09:15:16 2010 UTC (8 years, 7 months ago) by caltinay
Next attempt at fixing mac test failure.


Revision 3164 - Directory Listing
Modified Tue Sep 7 09:10:09 2010 UTC (8 years, 7 months ago) by caltinay
Do not use VTK on guineapig - pyvisi is deprecated anyway.


Revision 3162 - Directory Listing
Modified Tue Sep 7 05:29:32 2010 UTC (8 years, 7 months ago) by jfenwick
Changes to match packages in the debian repo.
Also got rid of lib/pyversion


Revision 3160 - Directory Listing
Modified Mon Sep 6 09:17:28 2010 UTC (8 years, 7 months ago) by gross
bug fixed in RILU and test modified.

Revision 3159 - Directory Listing
Modified Mon Sep 6 06:59:31 2010 UTC (8 years, 7 months ago) by gross
AMG is using now a simpler interface to the Smoothers.

Revision 3158 - Directory Listing
Modified Mon Sep 6 06:09:11 2010 UTC (8 years, 7 months ago) by gross
GS and Jacobi are now used through the same interface.

Revision 3154 - Directory Listing
Modified Sun Sep 5 22:49:51 2010 UTC (8 years, 7 months ago) by caltinay
Possible fix for mac linker error.


Revision 3153 - Directory Listing
Modified Sun Sep 5 01:31:49 2010 UTC (8 years, 7 months ago) by ahallam
Updates to cookbook. Fixes to SWP and new Gravitational Potential

Revision 3151 - Directory Listing
Modified Fri Sep 3 05:46:12 2010 UTC (8 years, 7 months ago) by caltinay
More weipa tests including saveVTK.


Revision 3150 - Directory Listing
Modified Fri Sep 3 05:40:27 2010 UTC (8 years, 7 months ago) by caltinay
Removed executable prop from non-executables.


Revision 3148 - Directory Listing
Modified Fri Sep 3 02:09:47 2010 UTC (8 years, 7 months ago) by jfenwick
Another attempt to patch the X issue


Revision 3147 - Directory Listing
Modified Fri Sep 3 02:03:05 2010 UTC (8 years, 7 months ago) by caltinay
Don't clear domain on error. Moved adding Metadata-tags to the C++ level.


Revision 3146 - Directory Listing
Modified Fri Sep 3 01:29:21 2010 UTC (8 years, 7 months ago) by caltinay
Properly initialise data centering variable.


Revision 3143 - Directory Listing
Modified Fri Sep 3 00:31:55 2010 UTC (8 years, 7 months ago) by caltinay
-Moved finley specifics into weipa subclasses
-EscriptDataset is now the only weipa class exported in Windows
-Some weipa code cleanup



Revision 3142 - Directory Listing
Modified Thu Sep 2 23:58:47 2010 UTC (8 years, 7 months ago) by jfenwick
Trying to fix X problem


Revision 3140 - Directory Listing
Modified Thu Sep 2 07:26:43 2010 UTC (8 years, 7 months ago) by gross
a more robust version of MINRES (really?)

Revision 3139 - Directory Listing
Modified Thu Sep 2 06:37:43 2010 UTC (8 years, 7 months ago) by caltinay
Fixed a typo.


Revision 3135 - Directory Listing
Modified Thu Sep 2 03:28:39 2010 UTC (8 years, 7 months ago) by ahallam
Updates to cookbook scripts. Gravitation Examples.

Revision 3133 - Directory Listing
Modified Thu Sep 2 02:04:29 2010 UTC (8 years, 7 months ago) by caltinay
Added methods to set mesh labels and units to DataManager.


Revision 3132 - Directory Listing
Modified Thu Sep 2 01:48:31 2010 UTC (8 years, 7 months ago) by caltinay
Removed unused variable.


Revision 3131 - Directory Listing
Modified Thu Sep 2 01:40:47 2010 UTC (8 years, 7 months ago) by caltinay
DataManager now uses Python magic to figure out how to load the domain without
hardcoding anything finley-specific.


Revision 3129 - Directory Listing
Modified Wed Sep 1 07:58:23 2010 UTC (8 years, 7 months ago) by caltinay
Fixed unit test.


Revision 3128 - Directory Listing
Modified Wed Sep 1 03:54:09 2010 UTC (8 years, 7 months ago) by caltinay
-Added mesh axis label/unit and variable unit support to weipa's Silo writer
-Created EscriptDataset python wrapper
-Some code cleanup and a ghost zone fix for the VisIt interface


Revision 3125 - Directory Listing
Modified Tue Aug 31 05:37:30 2010 UTC (8 years, 7 months ago) by gross
more code cleaning

Revision 3121 - Directory Listing
Modified Mon Aug 30 23:12:58 2010 UTC (8 years, 7 months ago) by gross
missing file

Revision 3120 - Directory Listing
Modified Mon Aug 30 10:48:00 2010 UTC (8 years, 7 months ago) by gross
first iteration on Paso code clean up

Revision 3116 - Directory Listing
Modified Mon Aug 30 00:54:52 2010 UTC (8 years, 7 months ago) by caltinay
Prepared weipa to use Silo's HDF5 driver & compression which performs better
than the default PDB. Code is disabled though because NetCDF 4 is currently
interfering (Unidata has been contacted). Added a note about this.


Revision 3113 - Directory Listing
Modified Fri Aug 27 04:04:56 2010 UTC (8 years, 7 months ago) by caltinay
Fixed commit from rev.2867 which broke the ability to specify script parameters.


Revision 3112 - Directory Listing
Modified Thu Aug 26 07:10:36 2010 UTC (8 years, 7 months ago) by gross
missing include added.

Revision 3111 - Directory Listing
Modified Thu Aug 26 06:49:42 2010 UTC (8 years, 7 months ago) by gross
some diagnostics for time step backtracing added

Revision 3110 - Directory Listing
Modified Thu Aug 26 05:42:18 2010 UTC (8 years, 7 months ago) by caltinay
Fixed a typo.


Revision 3109 - Directory Listing
Modified Thu Aug 26 04:33:18 2010 UTC (8 years, 7 months ago) by caltinay
Added accessor for the simulation cycle and log which directory was used to
restart.


Revision 3108 - Directory Listing
Modified Thu Aug 26 03:43:05 2010 UTC (8 years, 7 months ago) by caltinay
More weipa tests.


Revision 3107 - Directory Listing
Modified Thu Aug 26 03:41:28 2010 UTC (8 years, 7 months ago) by caltinay
Removed ugly #defines in favour of a class.


Revision 3106 - Directory Listing
Modified Wed Aug 25 08:15:38 2010 UTC (8 years, 7 months ago) by caltinay
Fixed export when 'work_dir' is set to sth other than the current dir.


Revision 3105 - Directory Listing
Modified Wed Aug 25 04:37:52 2010 UTC (8 years, 7 months ago) by gross
bug fixed in the Gauss Seidel

Revision 3104 - Directory Listing
Modified Wed Aug 25 00:53:25 2010 UTC (8 years, 7 months ago) by caltinay
Set up initial test suite files for weipa and some basic preliminary tests.


Revision 3103 - Directory Listing
Modified Tue Aug 24 07:01:33 2010 UTC (8 years, 7 months ago) by gross
test fix

Revision 3102 - Directory Listing
Modified Tue Aug 24 06:14:21 2010 UTC (8 years, 7 months ago) by caltinay
Inject the DataManager class to the escript namespace.


Revision 3101 - Directory Listing
Modified Tue Aug 24 06:08:12 2010 UTC (8 years, 7 months ago) by caltinay
weipa's saveVTK now stores metadata schema & string as expected.


Revision 3100 - Directory Listing
Modified Mon Aug 23 09:31:09 2010 UTC (8 years, 7 months ago) by gross
bug in ILU0 fixed.

Revision 3099 - Directory Listing
Modified Sun Aug 22 04:35:15 2010 UTC (8 years, 7 months ago) by ahallam
Gravitational Potential Example- Needs some tuning.

Revision 3098 - Directory Listing
Modified Fri Aug 20 08:08:27 2010 UTC (8 years, 8 months ago) by gross
fix to the GaussSeidel

Revision 3097 - Directory Listing
Modified Fri Aug 20 04:59:12 2010 UTC (8 years, 8 months ago) by gross
some modifications to the GaussSeidel

Revision 3096 - Directory Listing
Modified Thu Aug 19 01:40:52 2010 UTC (8 years, 8 months ago) by caltinay
-New VisIt simulation control interface in weipa (uses VisIt's simv2)
-Rewrote restarts.py to be a more generic data manager for restarts and exports
-Removed weipa python file since the functionality is now handled by restarts.py


Revision 3095 - Directory Listing
Modified Tue Aug 17 03:42:31 2010 UTC (8 years, 8 months ago) by caltinay
Fixed building libescriptreader for the VisIt plugin.


Revision 3094 - Directory Listing
Modified Fri Aug 13 08:38:06 2010 UTC (8 years, 8 months ago) by gross
The MPI and sequational GAUSS_SEIDEL have been merged.
The couring and main diagonal pointer is now manged by the patternm which means that they are calculated once only even if the preconditioner is deleted.




Revision 3093 - Directory Listing
Modified Fri Aug 13 08:07:45 2010 UTC (8 years, 8 months ago) by gross
problem with no MPI compilation fixed

Revision 3092 - Directory Listing
Modified Fri Aug 13 07:55:03 2010 UTC (8 years, 8 months ago) by caltinay
Added getDataFlat() which will be used by the VisIt simulation interface


Revision 3091 - Directory Listing
Modified Fri Aug 13 07:47:57 2010 UTC (8 years, 8 months ago) by caltinay
-fixed cleanup on error when invoking escriptconvert in parallel
-fixed saving VTK files on one rank if data was loaded in chunks
-cleaned up EscriptDataset and split a couple of methods


Revision 3089 - Directory Listing
Modified Mon Aug 9 07:20:58 2010 UTC (8 years, 8 months ago) by ahallam
Updates to example scripts - should now be working except for example09b.py which needs more memory.

Revision 3084 - Directory Listing
Modified Wed Aug 4 03:26:50 2010 UTC (8 years, 8 months ago) by gross
small bug fixed.

Revision 3083 - Directory Listing
Modified Tue Aug 3 06:34:35 2010 UTC (8 years, 8 months ago) by caltinay
Updated some svn:ignore props.


Revision 3081 - Directory Listing
Modified Tue Aug 3 05:36:42 2010 UTC (8 years, 8 months ago) by gross
a light restart manager added.

Revision 3078 - Directory Listing
Modified Tue Aug 3 03:12:16 2010 UTC (8 years, 8 months ago) by jfenwick
Switched the build_dir keyword param to variant_dir.
Should fix issue 525.



Revision 3077 - Directory Listing
Modified Mon Aug 2 23:01:14 2010 UTC (8 years, 8 months ago) by jfenwick
Fix my error


Revision 3076 - Directory Listing
Modified Mon Aug 2 05:21:40 2010 UTC (8 years, 8 months ago) by jfenwick
Removing hardcoded savanna from the SConstruct file.


Revision 3075 - Directory Listing
Modified Wed Jul 28 02:51:20 2010 UTC (8 years, 8 months ago) by ahallam
Updates to cookbook example. Lumping turned off for order 2 models until bug resolves.

Revision 3074 - Directory Listing
Modified Tue Jul 27 01:47:45 2010 UTC (8 years, 8 months ago) by gross
tolerance for PCG relaxed.

Revision 3073 - Directory Listing
Modified Mon Jul 26 06:10:50 2010 UTC (8 years, 8 months ago) by jfenwick
Rename files to fix build problem


Revision 3072 - Directory Listing
Modified Fri Jul 23 07:10:03 2010 UTC (8 years, 8 months ago) by gross
wrong file

Revision 3071 - Directory Listing
Modified Wed Jul 21 05:37:30 2010 UTC (8 years, 9 months ago) by gross
new darcy flux

Revision 3070 - Directory Listing
Modified Wed Jul 21 04:09:58 2010 UTC (8 years, 9 months ago) by jfenwick
Fixord


Revision 3069 - Directory Listing
Modified Wed Jul 21 03:24:48 2010 UTC (8 years, 9 months ago) by ahallam
Updates to layer cake and cookbook as well as examples.

Revision 3068 - Directory Listing
Modified Mon Jul 19 00:43:31 2010 UTC (8 years, 9 months ago) by ahallam
Missing Figures

Revision 3067 - Directory Listing
Modified Mon Jul 19 00:40:37 2010 UTC (8 years, 9 months ago) by ahallam
Cookbook Updates - Chapter 9 - New figures.

Revision 3066 - Directory Listing
Modified Sun Jul 18 23:32:07 2010 UTC (8 years, 9 months ago) by ahallam
Missing Picture causing errors.

Revision 3065 - Directory Listing
Modified Thu Jul 15 02:59:27 2010 UTC (8 years, 9 months ago) by ahallam
Updates to newer examples.

Revision 3064 - Directory Listing
Modified Thu Jul 15 02:58:23 2010 UTC (8 years, 9 months ago) by ahallam
Updates to cookbook with fixed images and new chaper for 3d seismic model. New chapter is now added.

Revision 3063 - Directory Listing
Modified Thu Jul 15 02:57:46 2010 UTC (8 years, 9 months ago) by ahallam
Updates to cookbook with fixed images and new chaper for 3d seismic model.

Revision 3062 - Directory Listing
Modified Wed Jul 14 00:18:30 2010 UTC (8 years, 9 months ago) by ahallam
Joels suggested changes for naming conventions. The function is now located in esys.pycad.extras as layer_cake.

Revision 3061 - Directory Listing
Modified Tue Jul 13 23:34:10 2010 UTC (8 years, 9 months ago) by ahallam
function LayerCake fixed is now under esys.pycad.layer_cake

Revision 3060 - Directory Listing
Modified Tue Jul 13 00:55:09 2010 UTC (8 years, 9 months ago) by ahallam
Adding layer cake builder to pycad

Revision 3059 - Directory Listing
Modified Tue Jul 6 03:31:48 2010 UTC (8 years, 9 months ago) by jfenwick
Fix error message in launcher. Allow non-data objects to be passed to condEval

Revision 3058 - Directory Listing
Modified Tue Jul 6 02:13:14 2010 UTC (8 years, 9 months ago) by ahallam


Revision 3057 - Directory Listing
Modified Tue Jul 6 02:10:59 2010 UTC (8 years, 9 months ago) by ahallam


Revision 3056 - Directory Listing
Modified Mon Jul 5 00:07:16 2010 UTC (8 years, 9 months ago) by jfenwick
Have the escript launcher check the PBS_NODEFILE variable for hosts.


Revision 3055 - Directory Listing
Modified Sun Jul 4 21:52:36 2010 UTC (8 years, 9 months ago) by ahallam
3d wave equation and ABC

Revision 3054 - Directory Listing
Modified Wed Jun 30 02:22:25 2010 UTC (8 years, 9 months ago) by ahallam
Missing Figures...

Revision 3053 - Directory Listing
Modified Tue Jun 29 01:31:31 2010 UTC (8 years, 9 months ago) by jfenwick
Fixes to deal with new savanna configuration.
Blocking out missing images.


Revision 3052 - Directory Listing
Modified Tue Jun 29 00:57:45 2010 UTC (8 years, 9 months ago) by lgao
Revert the commit of this options file made by my last commit for Gauss-Seidel. 



Revision 3051 - Directory Listing
Modified Tue Jun 29 00:45:49 2010 UTC (8 years, 9 months ago) by lgao
Hybrid MPI/OpenMP versioned Gauss_Seidel preconditioner is added. 
To use it, use "SolverOptions.GAUSS_SEIDEL_MPI" in python script. 



Revision 3050 - Directory Listing
Modified Sun Jun 27 22:54:12 2010 UTC (8 years, 9 months ago) by jfenwick
Visual studio 2008 (v9.0) with Microsoft MPI libraries.
Courtesy of Gordon German.


Revision 3047 - Directory Listing
Modified Thu Jun 24 00:33:05 2010 UTC (8 years, 9 months ago) by jfenwick
Adding user name to tmpfiles.
Changing name of cluster options file to savanna from service0


Revision 3046 - Directory Listing
Modified Tue Jun 22 08:01:55 2010 UTC (8 years, 9 months ago) by gross
some examples for a simple subduction model

Revision 3045 - Directory Listing
Modified Fri Jun 18 06:38:18 2010 UTC (8 years, 10 months ago) by lgao
Enable MKL and Lapack (the unit test problem has been fixed after Artak's commit). 



Revision 3044 - Directory Listing
Modified Fri Jun 18 04:48:47 2010 UTC (8 years, 10 months ago) by artak
Put back

Revision 3043 - Directory Listing
Modified Fri Jun 18 04:45:14 2010 UTC (8 years, 10 months ago) by artak
Problem with latest MKL should be fixed now. The problem was solving unrolled block matrix with MKL.

Revision 3042 - Directory Listing
Modified Fri Jun 18 04:01:43 2010 UTC (8 years, 10 months ago) by lgao
Disable Lapack to disable MKL.



Revision 3041 - Directory Listing
Modified Fri Jun 18 04:01:40 2010 UTC (8 years, 10 months ago) by artak
Should be faster with openmp. Some ROW-COL conversion.

Revision 3040 - Directory Listing
Modified Fri Jun 18 03:05:17 2010 UTC (8 years, 10 months ago) by lgao
Using lastest MKL library and set "usemkl=no" before the
problem with MKL in unit tests is solved ("maximum number 
of iteration step reached" for test_***_AMG_System). 



Revision 3039 - Directory Listing
Modified Tue Jun 15 07:21:56 2010 UTC (8 years, 10 months ago) by caltinay
Fix the NetCDF 4.1 issue (hopefully) - MPICH and IntelMPI have the required
definition.


Revision 3038 - Directory Listing
Modified Tue Jun 15 07:08:46 2010 UTC (8 years, 10 months ago) by lgao
Update the path to Intel-mpi 4.0.0.027



Revision 3037 - Directory Listing
Modified Mon Jun 14 00:59:30 2010 UTC (8 years, 10 months ago) by caltinay
Renamed escriptexport to weipa. Fixes #475.


Revision 3036 - Directory Listing
Modified Mon Jun 14 00:13:18 2010 UTC (8 years, 10 months ago) by caltinay
Fixed compilation with MPI and NetCDF 4.1. Removed obsolete options file.


Revision 3035 - Directory Listing
Modified Thu Jun 10 01:48:41 2010 UTC (8 years, 10 months ago) by jfenwick
Lazy node support for conditional evaluation.
It should be a complete operation now.


Revision 3034 - Directory Listing
Modified Wed Jun 9 03:24:23 2010 UTC (8 years, 10 months ago) by jfenwick
Adding unit tests for condEval


Revision 3033 - Directory Listing
Modified Wed Jun 2 10:17:00 2010 UTC (8 years, 10 months ago) by gross
fix for overflow

Revision 3032 - Directory Listing
Modified Mon May 31 02:58:15 2010 UTC (8 years, 10 months ago) by jfenwick
Add work around for windows not liking chained X::Y::Z.
TestDomain now supports tags and getX.
This is to allow testing for some features without invoking finley


Revision 3031 - Directory Listing
Modified Thu May 27 04:04:33 2010 UTC (8 years, 10 months ago) by jfenwick
Adding condEval function to Data.
Unit tests and a different name to follow.

Revision 3030 - Directory Listing
Modified Fri May 21 05:25:20 2010 UTC (8 years, 11 months ago) by lgao
Update savanna_options file to use the correct silo module.



Revision 3029 - Directory Listing
Modified Fri May 21 02:01:37 2010 UTC (8 years, 11 months ago) by ahallam
small updates and work on seismic code

Revision 3028 - Directory Listing
Modified Thu May 13 03:41:27 2010 UTC (8 years, 11 months ago) by gross
a new test problem (doesn't use unit testing)

Revision 3027 - Directory Listing
Modified Wed May 12 05:26:09 2010 UTC (8 years, 11 months ago) by gross
some little fixes in an old script

Revision 3026 - Directory Listing
Modified Mon May 10 06:23:49 2010 UTC (8 years, 11 months ago) by gross
some fix for omp

Revision 3025 - Directory Listing
Modified Thu May 6 01:20:46 2010 UTC (8 years, 11 months ago) by ahallam
Updates to wave equation examples. Pressure wave examples should be completed now. Working on seismic wave examples. Cookbook chapter for pressure wave examples also added.

Revision 3024 - Directory Listing
Modified Wed May 5 01:12:32 2010 UTC (8 years, 11 months ago) by jfenwick
Some savanna fixes but not complete


Revision 3023 - Directory Listing
Modified Wed May 5 01:00:16 2010 UTC (8 years, 11 months ago) by lgao
Option file update for machine "sunzi".


Revision 3022 - Directory Listing
Modified Wed May 5 00:14:45 2010 UTC (8 years, 11 months ago) by gross
typo fixed.


Revision 3021 - Directory Listing
Modified Tue May 4 10:14:12 2010 UTC (8 years, 11 months ago) by gross
MPI problem fixed.

Revision 3020 - Directory Listing
Modified Tue May 4 09:10:03 2010 UTC (8 years, 11 months ago) by gross
reactive solver added

Revision 3019 - Directory Listing
Modified Fri Apr 30 06:10:37 2010 UTC (8 years, 11 months ago) by jfenwick
adding Lin options

Revision 3018 - Directory Listing
Modified Thu Apr 29 21:35:24 2010 UTC (8 years, 11 months ago) by gross
some stupid lines removed

Revision 3017 - Directory Listing
Modified Thu Apr 29 03:40:12 2010 UTC (8 years, 11 months ago) by artak
Some AMLI for systems fixes

Revision 3016 - Directory Listing
Modified Wed Apr 28 05:28:44 2010 UTC (8 years, 11 months ago) by artak
firstprivate added for OpenMP

Revision 3015 - Directory Listing
Modified Wed Apr 28 05:06:26 2010 UTC (8 years, 11 months ago) by artak
OpenMP commented out for now

Revision 3014 - Directory Listing
Modified Wed Apr 28 04:05:21 2010 UTC (8 years, 11 months ago) by gross
a more stable handling of divergence in the CN or BE

Revision 3013 - Directory Listing
Modified Wed Apr 28 03:47:51 2010 UTC (8 years, 11 months ago) by artak
Block separation part commented out for AMG preconditioner

Revision 3012 - Directory Listing
Modified Wed Apr 28 03:39:22 2010 UTC (8 years, 11 months ago) by lgao
Fix the MPI compilation bug.



Revision 3011 - Directory Listing
Modified Wed Apr 28 02:21:23 2010 UTC (8 years, 11 months ago) by artak
New method added for unrolling System matrix. Direct solver now uses unrolled copy of the AMG matrix.

Revision 3010 - Directory Listing
Modified Tue Apr 27 05:10:46 2010 UTC (8 years, 11 months ago) by artak
Preparation for AMG on Systems without cut using frobenius norm

Revision 3009 - Directory Listing
Modified Thu Apr 22 11:17:42 2010 UTC (8 years, 11 months ago) by gross
another MPI problem fixed

Revision 3008 - Directory Listing
Modified Thu Apr 22 10:19:20 2010 UTC (8 years, 11 months ago) by gross
MPI problem fixed

Revision 3007 - Directory Listing
Modified Thu Apr 22 09:08:36 2010 UTC (8 years, 11 months ago) by gross
typo for MPI cse fixed

Revision 3006 - Directory Listing
Modified Thu Apr 22 08:31:28 2010 UTC (8 years, 11 months ago) by gross
local_norm_w removed

Revision 3005 - Directory Listing
Modified Thu Apr 22 05:59:31 2010 UTC (8 years, 11 months ago) by gross
early call of setPreconditioner in FCT solver removed.

Revision 3004 - Directory Listing
Modified Wed Apr 14 05:27:30 2010 UTC (9 years ago) by ahallam
Sampling theorem, stability requirements, Laplacian discussion, Pressure wave PDE

Revision 3003 - Directory Listing
Modified Wed Apr 7 02:29:57 2010 UTC (9 years ago) by ahallam
Pressure wave working, accelleration example, new entries to cookbook for example 7.

Revision 3002 - Directory Listing
Modified Wed Apr 7 02:25:45 2010 UTC (9 years ago) by gross
gmsh now supports the Mesh.SubdivisionAlgorithm and Mesh.Algorithm3D option.
The Mesh.Algorithm, Mesh.Smoothing, Mesh.Optimization options are now set in the
.geo file rather than in the command line.






Revision 3001 - Directory Listing
Modified Wed Mar 31 04:29:10 2010 UTC (9 years ago) by ahallam
Pressue wave problem, looking at sampling theorem, and Crank-Nicolson

Revision 3000 - Directory Listing
Modified Tue Mar 30 03:10:13 2010 UTC (9 years ago) by lgao
Gauss_Seidel preconditioner is now SPD. 



Revision 2999 - Directory Listing
Modified Fri Mar 26 00:00:39 2010 UTC (9 years ago) by artak
NE set to 10 elemennt, because 6 is too small for mpi=8 job.

Revision 2998 - Directory Listing
Modified Wed Mar 24 04:00:20 2010 UTC (9 years ago) by artak
More openMP corrections

Revision 2997 - Directory Listing
Modified Wed Mar 24 01:46:33 2010 UTC (9 years ago) by artak
Some openMP corrections

Revision 2996 - Directory Listing
Modified Tue Mar 23 06:24:09 2010 UTC (9 years ago) by artak
Tests are added for GAUSS_SEIDEL

Revision 2995 - Directory Listing
Modified Tue Mar 23 06:14:26 2010 UTC (9 years ago) by artak
AMG levels maximum set 5

Revision 2994 - Directory Listing
Modified Tue Mar 23 06:13:14 2010 UTC (9 years ago) by artak
AMG levels maximum set 5

Revision 2993 - Directory Listing
Modified Tue Mar 23 04:29:30 2010 UTC (9 years ago) by artak
Some optimization on GAUSS_SEIDEL sweeps.

Revision 2992 - Directory Listing
Modified Tue Mar 23 04:16:28 2010 UTC (9 years ago) by artak
Sweeps bug is fixed and some more comments added about how sweeps computed

Revision 2991 - Directory Listing
Modified Mon Mar 22 05:42:48 2010 UTC (9 years, 1 month ago) by gross
isub as private added

Revision 2990 - Directory Listing
Modified Fri Mar 19 05:57:22 2010 UTC (9 years, 1 month ago) by gross
some prints removed.

Revision 2989 - Directory Listing
Modified Thu Mar 18 01:45:55 2010 UTC (9 years, 1 month ago) by gross
- bug in error handling in the case of lumped mass matrix fixed.
- switched back to rowsum lumping as there are problems with HRZ lumping for order 2 



Revision 2988 - Directory Listing
Modified Tue Mar 16 06:14:30 2010 UTC (9 years, 1 month ago) by gross
C-level lumping switched on

Revision 2987 - Directory Listing
Modified Tue Mar 16 01:32:43 2010 UTC (9 years, 1 month ago) by gross
FCT solver rewritten

Revision 2982 - Directory Listing
Modified Wed Mar 10 04:27:47 2010 UTC (9 years, 1 month ago) by caltinay
Some minor corrections to the cookbook (mainly word repetitions and typos).


Revision 2980 - Directory Listing
Modified Tue Mar 9 03:50:58 2010 UTC (9 years, 1 month ago) by artak
minor change to fix latest bug

Revision 2979 - Directory Listing
Modified Tue Mar 9 02:54:32 2010 UTC (9 years, 1 month ago) by ahallam
cookbook review final final 3.1 - artak and tony corrections

Revision 2978 - Directory Listing
Modified Tue Mar 9 02:11:07 2010 UTC (9 years, 1 month ago) by artak
minor

Revision 2977 - Directory Listing
Modified Tue Mar 9 00:33:28 2010 UTC (9 years, 1 month ago) by ahallam
cookbook review final 3.1

Revision 2976 - Directory Listing
Modified Mon Mar 8 01:18:33 2010 UTC (9 years, 1 month ago) by artak
Lame equation is corrected. Options for using smoother in AMG is added. A book on AMG is cited for standard coarsening. 

Revision 2975 - Directory Listing
Modified Thu Mar 4 05:44:12 2010 UTC (9 years, 1 month ago) by ahallam
Cookbook modifications Review -> Not quite finished yet.
New figure.

Revision 2974 - Directory Listing
Modified Thu Mar 4 03:09:35 2010 UTC (9 years, 1 month ago) by artak
forgot to skip example06.py as well

Revision 2973 - Directory Listing
Modified Thu Mar 4 03:07:22 2010 UTC (9 years, 1 month ago) by artak
example05c.py is not tested if matplotlib library version is too old, where quiver() does not support angle parameter.

Revision 2972 - Directory Listing
Modified Thu Mar 4 01:33:38 2010 UTC (9 years, 1 month ago) by artak
DONE. Einstain Summation Convention (ESC, what an irony, reminds me ESC button) is removed from cookbook as it is not used anywhere in the cookbook.

Revision 2971 - Directory Listing
Modified Wed Mar 3 23:19:00 2010 UTC (9 years, 1 month ago) by jfenwick
I hate voodoo.
Putting pdfinfo directive in two places in the cookbook header so that
both versions of evince get the right title.


Revision 2970 - Directory Listing
Modified Wed Mar 3 05:23:50 2010 UTC (9 years, 1 month ago) by jfenwick
Fix out of date comment


Revision 2969 - Directory Listing
Modified Wed Mar 3 04:27:00 2010 UTC (9 years, 1 month ago) by artak
reached Chapter 4

Revision 2968 - Directory Listing
Modified Wed Mar 3 04:02:30 2010 UTC (9 years, 1 month ago) by caltinay
Updated service0 & shake75 options to use cxx_extra


Revision 2967 - Directory Listing
Modified Wed Mar 3 03:50:46 2010 UTC (9 years, 1 month ago) by caltinay
scons now understands cc_extra and cxx_extra. The former applies only to the
C compiler, the latter to the C++ compiler which fixes #510.


Revision 2966 - Directory Listing
Modified Wed Mar 3 03:19:39 2010 UTC (9 years, 1 month ago) by jfenwick
Fixing non-ansi compliant code


Revision 2965 - Directory Listing
Modified Wed Mar 3 01:53:41 2010 UTC (9 years, 1 month ago) by jfenwick
Added MPI aware MIS


Revision 2964 - Directory Listing
Modified Wed Mar 3 01:21:09 2010 UTC (9 years, 1 month ago) by artak
up to Chapter 3

Revision 2963 - Directory Listing
Modified Wed Mar 3 01:10:11 2010 UTC (9 years, 1 month ago) by artak
up to section 2.1.9

Revision 2962 - Directory Listing
Modified Wed Mar 3 01:03:56 2010 UTC (9 years, 1 month ago) by gross
bar as unit added

Revision 2961 - Directory Listing
Modified Wed Mar 3 00:56:59 2010 UTC (9 years, 1 month ago) by jfenwick
Hacking cookbook


Revision 2960 - Directory Listing
Modified Tue Mar 2 07:54:11 2010 UTC (9 years, 1 month ago) by gross
new DarcyFlux solver

Revision 2959 - Directory Listing
Modified Tue Mar 2 06:27:17 2010 UTC (9 years, 1 month ago) by artak
more corrections on exmaple 1, up to section 2.1.5

Revision 2958 - Directory Listing
Modified Tue Mar 2 06:00:39 2010 UTC (9 years, 1 month ago) by artak
more corrections on exmaple 1, up to section 2.1.5

Revision 2957 - Directory Listing
Modified Tue Mar 2 01:28:19 2010 UTC (9 years, 1 month ago) by artak
more corrections

Revision 2956 - Directory Listing
Modified Mon Mar 1 01:31:59 2010 UTC (9 years, 1 month ago) by artak
First corrections: NEEDS MORE AND MORE...

Revision 2955 - Directory Listing
Modified Mon Mar 1 00:54:37 2010 UTC (9 years, 1 month ago) by jfenwick
Fix hackscore error


Revision 2954 - Directory Listing
Modified Fri Feb 26 06:09:47 2010 UTC (9 years, 1 month ago) by gross
bug introduced by a smart programmer to the Locator has been fixed?


Revision 2953 - Directory Listing
Modified Thu Feb 25 10:00:23 2010 UTC (9 years, 1 month ago) by gross
final touch to the naming in the cookbook

Revision 2952 - Directory Listing
Modified Thu Feb 25 09:52:10 2010 UTC (9 years, 1 month ago) by gross
even more renaming in the cookbook

Revision 2951 - Directory Listing
Modified Thu Feb 25 07:43:40 2010 UTC (9 years, 1 month ago) by gross
more renaming in the cookbook

Revision 2950 - Directory Listing
Modified Thu Feb 25 07:33:16 2010 UTC (9 years, 1 month ago) by gross
more renames in the cookbook.

Revision 2949 - Directory Listing
Modified Thu Feb 25 05:23:11 2010 UTC (9 years, 1 month ago) by gross
renaming examples part 1

Revision 2948 - Directory Listing
Modified Thu Feb 25 04:54:30 2010 UTC (9 years, 1 month ago) by gross
a new almost completed version of the cookbook

Revision 2944 - Directory Listing
Modified Tue Feb 23 23:51:20 2010 UTC (9 years, 1 month ago) by jfenwick
Fix latex markup in pdf title.
It turns out \pdfinfo must come after \maketitle if you don't want the
latex version of the title.

This behaviour does not happen in evince 2.22.2 (standard in lenny) but does
happen in more recent versions.



Revision 2943 - Directory Listing
Modified Tue Feb 23 01:49:27 2010 UTC (9 years, 1 month ago) by artak
VTK as a required package is removed from cookbook

Revision 2942 - Directory Listing
Modified Mon Feb 22 05:43:44 2010 UTC (9 years, 1 month ago) by caltinay
Fixed a small typo in the cookbook abstract.


Revision 2941 - Directory Listing
Modified Mon Feb 22 05:17:43 2010 UTC (9 years, 1 month ago) by caltinay
saveESD now doesn't store the absolute path to the files in the ESD file so
the whole dataset can be moved easily.


Revision 2940 - Directory Listing
Modified Fri Feb 19 00:38:45 2010 UTC (9 years, 2 months ago) by caltinay
Minor potential optimization: prefer empty() over size()==0.


Revision 2939 - Directory Listing
Modified Thu Feb 18 04:16:59 2010 UTC (9 years, 2 months ago) by gross
some print statements removed.

Revision 2938 - Directory Listing
Modified Thu Feb 18 00:24:35 2010 UTC (9 years, 2 months ago) by caltinay
saveESD: Add a warning about the experimental status of ESD.
Save the ESD file within the data directory.


Revision 2937 - Directory Listing
Modified Tue Feb 16 00:01:52 2010 UTC (9 years, 2 months ago) by caltinay
Corrected an MPI datatype


Revision 2936 - Directory Listing
Modified Mon Feb 15 03:29:53 2010 UTC (9 years, 2 months ago) by gross
some clarification added.

Revision 2935 - Directory Listing
Modified Mon Feb 15 03:15:59 2010 UTC (9 years, 2 months ago) by gross
pycad support 3D transfinite meshing now.

Revision 2934 - Directory Listing
Modified Fri Feb 12 05:09:06 2010 UTC (9 years, 2 months ago) by gross
gmsh reader supports second order recs and hex now

Revision 2933 - Directory Listing
Modified Tue Feb 9 03:27:37 2010 UTC (9 years, 2 months ago) by gross
test for positivity of initial solution in transport solver has been switched on again

Revision 2932 - Directory Listing
Modified Mon Feb 8 06:48:19 2010 UTC (9 years, 2 months ago) by gross
printfs removed.

Revision 2931 - Directory Listing
Modified Mon Feb 8 06:45:41 2010 UTC (9 years, 2 months ago) by gross
more changes on the cookbook

Revision 2930 - Directory Listing
Modified Mon Feb 8 06:25:43 2010 UTC (9 years, 2 months ago) by caltinay
escriptconvert can now convert both to Silo and VTK and is thus built by
default


Revision 2929 - Directory Listing
Modified Mon Feb 8 05:13:27 2010 UTC (9 years, 2 months ago) by caltinay
Implemented mantis issue 464 in dataexporter: better resolution for Tri6 and
Tet10 elements via point-in-triangle and point-in-tetrahedron tests.


Revision 2926 - Directory Listing
Modified Thu Feb 4 23:13:53 2010 UTC (9 years, 2 months ago) by jfenwick
Attempting to fix a problem with windows linking in the ironically named INKNOWWHATIMDOING section


Revision 2925 - Directory Listing
Modified Thu Feb 4 23:12:34 2010 UTC (9 years, 2 months ago) by jfenwick
Update savanna to build c99 style



Revision 2924 - Directory Listing
Modified Thu Feb 4 05:30:53 2010 UTC (9 years, 2 months ago) by trankine
* windows specific "we cant work out autolink" workaround
http://old.nabble.com/boost-1.41-and-autolink-%28maybe-the-wrong-list%29-td27040284.html

Revision 2923 - Directory Listing
Modified Thu Feb 4 04:05:36 2010 UTC (9 years, 2 months ago) by jfenwick
Bringing non-release specific things from stage3.1 r2922 back to trunk


Revision 2919 - Directory Listing
Modified Thu Feb 4 00:53:58 2010 UTC (9 years, 2 months ago) by caltinay
Took over Macro element handling from finley.saveVTK.


Revision 2918 - Directory Listing
Modified Thu Feb 4 00:53:37 2010 UTC (9 years, 2 months ago) by caltinay
Quick fix for Windows scons problem due to the same files being compiled twice
in the same directory. Visit plugin is not for Windows anyway so disabled it
there.


Revision 2917 - Directory Listing
Modified Wed Feb 3 06:19:50 2010 UTC (9 years, 2 months ago) by caltinay
Fix for the fix ;-) The dataexporter is used in a context where HAVE_MPI is set
but mpi not initialised -> have to check for mpiSize.


Revision 2915 - Directory Listing
Modified Wed Feb 3 05:55:16 2010 UTC (9 years, 2 months ago) by gross
uninitialised variable error for non-mpi case fixed.

Revision 2914 - Directory Listing
Modified Wed Feb 3 05:38:12 2010 UTC (9 years, 2 months ago) by gross
missing import added.

Revision 2913 - Directory Listing
Modified Wed Feb 3 04:30:46 2010 UTC (9 years, 2 months ago) by gross
type fixed

Revision 2912 - Directory Listing
Modified Wed Feb 3 03:31:24 2010 UTC (9 years, 2 months ago) by gross
some missing functions

Revision 2911 - Directory Listing
Modified Wed Feb 3 03:30:40 2010 UTC (9 years, 2 months ago) by jfenwick
Changed name of launcher and rotated figure correctly.


Revision 2910 - Directory Listing
Modified Wed Feb 3 03:22:31 2010 UTC (9 years, 2 months ago) by caltinay
Added a libescriptreader.a target which does not depend on escript or finley
at runtime. This will be used for the VisIt plugin so is not built by default.


Revision 2907 - Directory Listing
Modified Wed Feb 3 01:39:15 2010 UTC (9 years, 2 months ago) by gross
needdirs replaced by mkDir from esys.escript

Revision 2906 - Directory Listing
Modified Tue Feb 2 05:26:03 2010 UTC (9 years, 2 months ago) by gross
some minor :-) fix.

Revision 2905 - Directory Listing
Modified Tue Feb 2 04:26:42 2010 UTC (9 years, 2 months ago) by gross
some missing files.

Revision 2904 - Directory Listing
Modified Tue Feb 2 04:21:52 2010 UTC (9 years, 2 months ago) by gross
more revision on cookbook: example 1 and 2 have been swapped.

Revision 2903 - Directory Listing
Modified Tue Feb 2 00:20:52 2010 UTC (9 years, 2 months ago) by lgao
Switch to MKL 10.2.2.025 on service0.



Revision 2902 - Directory Listing
Modified Mon Feb 1 23:53:16 2010 UTC (9 years, 2 months ago) by lgao
Switch to Parmetis 3.1.1 on service0.



Revision 2900 - Directory Listing
Modified Mon Feb 1 06:05:38 2010 UTC (9 years, 2 months ago) by caltinay
Switch to Silo 4.7.2 on service0 (bug fix release).


Revision 2899 - Directory Listing
Modified Mon Feb 1 01:55:53 2010 UTC (9 years, 2 months ago) by caltinay
Added missing declspec to FileSavers.


Revision 2898 - Directory Listing
Modified Mon Feb 1 01:23:46 2010 UTC (9 years, 2 months ago) by caltinay
Reverted the move of system_dep.h since it didn't solve the problem nicely.
Created a wrapper class for the needed functionality instead.


Revision 2897 - Directory Listing
Modified Mon Feb 1 01:22:50 2010 UTC (9 years, 2 months ago) by lgao
Fix the Parmetis problem related with Mantis issue 0000480. 
In case there is any node with no vertex, Parmetis will not
be used and a message will be printed. 




Revision 2896 - Directory Listing
Modified Sun Jan 31 22:17:22 2010 UTC (9 years, 2 months ago) by caltinay
Added missing extern C for finley include.


Revision 2895 - Directory Listing
Modified Fri Jan 29 04:58:16 2010 UTC (9 years, 2 months ago) by caltinay
Moved finley's system_dep.h file up to the C level to be able to export two
functions that are used by the dataexporter. Changed include paths and C++
style comments accordingly.


Revision 2893 - Directory Listing
Modified Fri Jan 29 03:41:33 2010 UTC (9 years, 2 months ago) by caltinay
Link to esysUtils to be able to use escript exceptions.


Revision 2891 - Directory Listing
Modified Fri Jan 29 00:26:07 2010 UTC (9 years, 2 months ago) by caltinay
Fix for ambiguous call to sqrt...


Revision 2890 - Directory Listing
Modified Fri Jan 29 00:22:39 2010 UTC (9 years, 2 months ago) by caltinay
Oh, apparently a 'defect in the standard' and VC++ didn't like it. Hopefully,
this should fix it.


Revision 2888 - Directory Listing
Modified Fri Jan 29 00:07:00 2010 UTC (9 years, 2 months ago) by caltinay
Looks like netcdf.hh doesn't exist on Windows so changed to netcdfcpp.h.


Revision 2887 - Directory Listing
Modified Thu Jan 28 05:49:09 2010 UTC (9 years, 2 months ago) by caltinay
Fixed a compile issue with MPI.


Revision 2886 - Directory Listing
Modified Thu Jan 28 05:39:23 2010 UTC (9 years, 2 months ago) by caltinay
New version of saveVTK within dataexporter. Not pythonised yet since it needs
more testing and release 3.1 will not ship dataexporter.


Revision 2884 - Directory Listing
Modified Thu Jan 28 05:00:59 2010 UTC (9 years, 2 months ago) by jfenwick
Updated various nan checks to consider the windows _isnan

The default compiler flags have changed as well.
+ intel will now take -std=c99 instead of -ansi
+ gcc has -ansi removed which means it defaults to gnu99

We could have set gcc to -std=c99 as well but that gives a 
warning on g++ which gets converted into an error by our
pedantic warning.

Rationale:
We need something more than ansi to get proper nan handling.
- We currently don't have any code which does not comply with ansi
  but the nan checks don't work.

Impact:
If we want our code to still be able to compile on older compilers
(at reduced functionality) we need to be careful not to introduce other
c99-isms.
If we don't care, then it's time for some celebratory // comments.



Revision 2883 - Directory Listing
Modified Thu Jan 28 02:28:27 2010 UTC (9 years, 2 months ago) by caltinay
Switch to gcc 4.4 on guineapig


Revision 2882 - Directory Listing
Modified Thu Jan 28 02:27:49 2010 UTC (9 years, 2 months ago) by caltinay
Scons now allows to specify which C & C++ compiler to use via cc and cxx
variables. Fixes mantis # 485.


Revision 2881 - Directory Listing
Modified Thu Jan 28 02:03:15 2010 UTC (9 years, 2 months ago) by jfenwick
Don't panic.
Updating copyright stamps


Revision 2880 - Directory Listing
Modified Thu Jan 28 01:21:30 2010 UTC (9 years, 2 months ago) by caltinay
Better resolution for Hex27 & Rec9 data in dataexporter (mantis #486).
Saved Silo data resolution is now equal to finley.SaveVTK generated data in
all cases.


Revision 2879 - Directory Listing
Modified Thu Jan 28 01:00:26 2010 UTC (9 years, 2 months ago) by jfenwick
Move definition of build_platform on t.poulet suggestion.
Redefine the IS_NAN macro to replace versions commented as
'This does not work'
If you are not compiling with a c99 compliant compiler you will not 
recognise nulls but this seems to be the best we can do right now 
without checking for explicit bit patterns.


Revision 2878 - Directory Listing
Modified Thu Jan 28 00:59:30 2010 UTC (9 years, 2 months ago) by gross
more work on cookbook review

Revision 2877 - Directory Listing
Modified Thu Jan 28 00:28:45 2010 UTC (9 years, 2 months ago) by caltinay
Fixes to Silo writer: Multivars for tensors are now correct even with empty
ranks.


Revision 2875 - Directory Listing
Modified Wed Jan 27 04:09:24 2010 UTC (9 years, 2 months ago) by jfenwick
Updated version string to something which won't keep changing


Revision 2873 - Directory Listing
Modified Wed Jan 27 01:09:33 2010 UTC (9 years, 2 months ago) by caltinay
Fix for mantis #480 when parmetis is off.


Revision 2872 - Directory Listing
Modified Wed Jan 27 00:59:58 2010 UTC (9 years, 2 months ago) by artak
/home/ changed to /Users/ for mac

Revision 2870 - Directory Listing
Modified Mon Jan 25 08:34:15 2010 UTC (9 years, 2 months ago) by gross
more review on the cookbook.

Revision 2869 - Directory Listing
Modified Mon Jan 25 05:11:28 2010 UTC (9 years, 2 months ago) by gross
back to the old version. The last checkin was a mistake.

Revision 2868 - Directory Listing
Modified Mon Jan 25 04:44:45 2010 UTC (9 years, 2 months ago) by artak
Some fixes for 3.1 release. Notes about Snow Leopard is added and installing from ports removed.

Revision 2867 - Directory Listing
Modified Fri Jan 22 06:28:02 2010 UTC (9 years, 2 months ago) by gross
now option -i is used if no script is given

Revision 2866 - Directory Listing
Modified Fri Jan 22 05:38:56 2010 UTC (9 years, 2 months ago) by gross
small fix for the case n=1 under mpi

Revision 2865 - Directory Listing
Modified Fri Jan 22 03:19:32 2010 UTC (9 years, 2 months ago) by gross
launcher for MPI supports now -i option (see mantis 361)

Revision 2864 - Directory Listing
Modified Fri Jan 22 03:09:55 2010 UTC (9 years, 2 months ago) by gross
projector added to users guide

Revision 2863 - Directory Listing
Modified Thu Jan 21 07:18:37 2010 UTC (9 years, 2 months ago) by gross
fix for mantis 454

Revision 2862 - Directory Listing
Modified Thu Jan 21 04:45:39 2010 UTC (9 years, 2 months ago) by gross
more review in the cookbook

Revision 2861 - Directory Listing
Modified Wed Jan 20 02:47:42 2010 UTC (9 years, 3 months ago) by gross
some modification to the cookbook

Revision 2860 - Directory Listing
Modified Tue Jan 19 05:25:39 2010 UTC (9 years, 3 months ago) by gross
prints removed.

Revision 2859 - Directory Listing
Modified Tue Jan 19 05:21:50 2010 UTC (9 years, 3 months ago) by gross
a work around for gcc 4.4 added.

Revision 2858 - Directory Listing
Modified Tue Jan 19 01:07:52 2010 UTC (9 years, 3 months ago) by gross
small fixes with the reduced solution for the transport problem

Revision 2857 - Directory Listing
Modified Mon Jan 18 07:44:42 2010 UTC (9 years, 3 months ago) by gross
test for ApproximationOrder added and Transport type problem now choose reduced when necessary only.

Revision 2856 - Directory Listing
Modified Mon Jan 18 04:14:37 2010 UTC (9 years, 3 months ago) by gross
FunctionSpaces provide now some information about their approximation order.

Revision 2855 - Directory Listing
Modified Mon Jan 18 03:39:29 2010 UTC (9 years, 3 months ago) by jfenwick
Fixed


Revision 2854 - Directory Listing
Modified Mon Jan 18 01:54:04 2010 UTC (9 years, 3 months ago) by caltinay
Fixed a compile error and removed unneeded member.


Revision 2853 - Directory Listing
Modified Mon Jan 18 01:46:05 2010 UTC (9 years, 3 months ago) by caltinay
Do not attempt to read node file data if #nodes=0.


Revision 2852 - Directory Listing
Modified Mon Jan 18 00:22:23 2010 UTC (9 years, 3 months ago) by jfenwick
Fix MPI issue in toString.
Fixes unit tet failure in myfistrscript.py


Revision 2851 - Directory Listing
Modified Fri Jan 15 07:37:47 2010 UTC (9 years, 3 months ago) by gross
typos fixed.


Revision 2850 - Directory Listing
Modified Fri Jan 15 07:14:25 2010 UTC (9 years, 3 months ago) by gross
the powerlaw is working again. tests are switched on again.

Revision 2849 - Directory Listing
Modified Fri Jan 15 03:45:52 2010 UTC (9 years, 3 months ago) by caltinay
Oops...


Revision 2848 - Directory Listing
Modified Fri Jan 15 03:44:44 2010 UTC (9 years, 3 months ago) by caltinay
Removed unneeded member and initialised some others in the constructor.


Revision 2847 - Directory Listing
Modified Fri Jan 15 03:35:05 2010 UTC (9 years, 3 months ago) by caltinay
Improved error handling when using MPI and fixed Silo output when not all
ranks contribute to a data variable.


Revision 2846 - Directory Listing
Modified Fri Jan 15 03:16:08 2010 UTC (9 years, 3 months ago) by caltinay
removeGhostNodes is broken and unnecessary anyway so removed.


Revision 2845 - Directory Listing
Modified Fri Jan 15 03:10:42 2010 UTC (9 years, 3 months ago) by caltinay
escriptconvert passes MPI communicator to EscriptDataset now so files are
read/written in parallel.


Revision 2844 - Directory Listing
Modified Fri Jan 15 00:23:39 2010 UTC (9 years, 3 months ago) by jfenwick
Fixed some options to deal with silo errors.


Revision 2843 - Directory Listing
Modified Thu Jan 14 05:51:28 2010 UTC (9 years, 3 months ago) by gross
new compressible solver

Revision 2842 - Directory Listing
Modified Thu Jan 14 05:42:02 2010 UTC (9 years, 3 months ago) by caltinay
Changed domain::dump() to write out NodeDistribution & DofDistribution even if
the current process has 0 nodes.


Revision 2841 - Directory Listing
Modified Thu Jan 14 01:02:56 2010 UTC (9 years, 3 months ago) by jfenwick
Unit tests for 2838 and adding setTags variant which takes a string instead of a tag num.



Revision 2840 - Directory Listing
Modified Thu Jan 14 01:00:15 2010 UTC (9 years, 3 months ago) by caltinay
Enabled Silo on guineapig


Revision 2839 - Directory Listing
Modified Wed Jan 13 23:34:49 2010 UTC (9 years, 3 months ago) by artak
minor compiliation problem under MKL is fixed.

Revision 2838 - Directory Listing
Modified Wed Jan 13 06:01:03 2010 UTC (9 years, 3 months ago) by jfenwick
Vector, Tensor, Tensor3, Tensor4 can now take a (nested) sequence for 
their initial value.



Revision 2837 - Directory Listing
Modified Wed Jan 13 01:28:23 2010 UTC (9 years, 3 months ago) by caltinay
Added missing import statement.


Revision 2836 - Directory Listing
Modified Mon Jan 11 01:41:29 2010 UTC (9 years, 3 months ago) by artak
minor adjustments

Revision 2835 - Directory Listing
Modified Mon Jan 11 01:23:52 2010 UTC (9 years, 3 months ago) by artak
Default smoother set to Gauss-Seidel. This one more robust than jacobi, but jacobi is faster.

Revision 2834 - Directory Listing
Modified Thu Jan 7 06:06:56 2010 UTC (9 years, 3 months ago) by caltinay
Reduced elements are now handled separate from the main elements within the
data exporter. This simplifies usage considerably.


Revision 2833 - Directory Listing
Modified Thu Jan 7 05:44:46 2010 UTC (9 years, 3 months ago) by artak
minor openmp fix

Revision 2832 - Directory Listing
Modified Thu Jan 7 05:16:50 2010 UTC (9 years, 3 months ago) by artak
minor

Revision 2831 - Directory Listing
Modified Thu Jan 7 05:08:19 2010 UTC (9 years, 3 months ago) by artak
Splitting can be read from file. This is useful for testing.

Revision 2830 - Directory Listing
Modified Thu Jan 7 04:49:55 2010 UTC (9 years, 3 months ago) by caltinay
saveSilo now passes MPI communicator to data exporter.


Revision 2829 - Directory Listing
Modified Wed Jan 6 02:51:31 2010 UTC (9 years, 3 months ago) by ahallam
minor updates to cookbook

Revision 2828 - Directory Listing
Modified Tue Dec 22 01:24:40 2009 UTC (9 years, 3 months ago) by artak
Smoother for AMG now can be selected from python. Now only Jacobi and Gauss-Seidel are available as smoothers.

Revision 2827 - Directory Listing
Modified Fri Dec 18 03:41:09 2009 UTC (9 years, 4 months ago) by jfenwick
There is now a mechanism to pass a C function into escript and invoke it on each datapoint with:

applyBinaryCFunction

Warning in order to use this function your escript must be compiled with 
scons ...  iknowwhatimdoing=yes

---------------------
Because this code relies on casts that the C standard does not allow some code has been moved into Dodgy{.h .cpp}

Scons files have been modified to treat these files specially [Warnings are not errors for these files.]

Revision 2826 - Directory Listing
Modified Fri Dec 18 01:33:35 2009 UTC (9 years, 4 months ago) by artak
MINRES anf TFQMR add initioal guess. Tolerance for both solvers changed. However tolerance computaion needs to be more involved than it is now to avoid unnecessary very small tolerances.

Revision 2825 - Directory Listing
Modified Thu Dec 17 00:10:06 2009 UTC (9 years, 4 months ago) by jfenwick
More fixes to resolveGroup


Revision 2824 - Directory Listing
Modified Wed Dec 16 01:22:56 2009 UTC (9 years, 4 months ago) by jfenwick
ResolveGroup fixed so it actually resolves groups.
Children, when you iterate backwards remember its i>=0 not i>0


Revision 2822 - Directory Listing
Modified Mon Dec 14 03:10:16 2009 UTC (9 years, 4 months ago) by caltinay
dataexporter: Ensure that NetCDF files created using N ranks are only loaded
when mpi size equals N or 1.


Revision 2821 - Directory Listing
Modified Fri Dec 11 07:00:35 2009 UTC (9 years, 4 months ago) by caltinay
EscriptDataset takes an optional communicator now.


Revision 2820 - Directory Listing
Modified Thu Dec 10 05:03:11 2009 UTC (9 years, 4 months ago) by artak
Paso Testing tools now can select coarseing.The builld_PasoTests target is also added to scons. 

Revision 2819 - Directory Listing
Modified Thu Dec 10 04:12:35 2009 UTC (9 years, 4 months ago) by caltinay
Added include to make badger happy. Hope everyone's happy now.


Revision 2818 - Directory Listing
Modified Thu Dec 10 04:10:16 2009 UTC (9 years, 4 months ago) by caltinay
dataexporter links against escript now to make the Mac happy.


Revision 2817 - Directory Listing
Modified Thu Dec 10 02:12:33 2009 UTC (9 years, 4 months ago) by artak
test is added for selecting standard coarsening.

Revision 2816 - Directory Listing
Modified Thu Dec 10 02:09:43 2009 UTC (9 years, 4 months ago) by artak
Standard coarsening is added to options list.

Revision 2815 - Directory Listing
Modified Tue Dec 8 08:15:19 2009 UTC (9 years, 4 months ago) by gross
this fixes a problem of element distribution attribute for lines

Revision 2814 - Directory Listing
Modified Tue Dec 8 01:50:29 2009 UTC (9 years, 4 months ago) by caltinay
Removed minor code duplication.


Revision 2813 - Directory Listing
Modified Tue Dec 8 00:30:13 2009 UTC (9 years, 4 months ago) by caltinay
Added missing include.


Revision 2812 - Directory Listing
Modified Tue Dec 8 00:12:07 2009 UTC (9 years, 4 months ago) by caltinay
Implemented saveSilo within a new dataexporter module. If Silo is not available
at compile time the function throws. Ultimately, saveVTK will be moved here as
well.


Revision 2811 - Directory Listing
Modified Mon Dec 7 05:57:16 2009 UTC (9 years, 4 months ago) by caltinay
Fixed compilation when silo is not used.


Revision 2810 - Directory Listing
Modified Mon Dec 7 04:13:49 2009 UTC (9 years, 4 months ago) by caltinay
Reincarnation of the escriptreader as a more flexible escriptexport library:
 - can be initialised with instances of escript::Data and Finley_Mesh
 - is now MPI aware at the EscriptDataset level including Silo writer
 - now uses boost shared pointers
The lib is currently only used by the escriptconvert tool but this is going to
change...


Revision 2809 - Directory Listing
Modified Mon Dec 7 03:39:37 2009 UTC (9 years, 4 months ago) by jfenwick
TestDomain now divides the total number of samples between ranks rather 
than putting all samples on all ranks.


Revision 2808 - Directory Listing
Modified Mon Dec 7 00:26:45 2009 UTC (9 years, 4 months ago) by artak
default coarseneing is Ruge-Stueben.

Revision 2807 - Directory Listing
Modified Mon Dec 7 00:02:55 2009 UTC (9 years, 4 months ago) by artak
Post and pre smoothing parameters are added for AMLI. Little bit reengineering according to Axelson's original AMLI paper.

Revision 2806 - Directory Listing
Modified Fri Dec 4 06:46:13 2009 UTC (9 years, 4 months ago) by caltinay
bin/escript:
 - bail out early if buildvars is not around
 - quote variables to avoid syntax errors
 - some work towards POSIX compliance (s/==/=/ in string comparisons)
 - escript -V was still spitting out 'pre2.0' -> changed to pre4.0
 - fixed minor typos


Revision 2805 - Directory Listing
Modified Fri Dec 4 05:21:31 2009 UTC (9 years, 4 months ago) by artak
minor

Revision 2804 - Directory Listing
Modified Fri Dec 4 02:06:51 2009 UTC (9 years, 4 months ago) by artak
Some memory and code optimizations in updateWeights method.

Revision 2803 - Directory Listing
Modified Thu Dec 3 05:35:20 2009 UTC (9 years, 4 months ago) by artak
Parameters are added for post and pre smoothing. Now user can choose number of pre and post smoothing steps in AMG (e.g. setNumPreSweeps(5)). 

Revision 2802 - Directory Listing
Modified Thu Dec 3 01:51:55 2009 UTC (9 years, 4 months ago) by artak
Aggressive coarsening is implemented. Removes more elements but adds more iteration steps.

Revision 2801 - Directory Listing
Modified Thu Dec 3 01:45:48 2009 UTC (9 years, 4 months ago) by ahallam
Final updates to first 3 chapters of cookbook before moving on to linear elastic wave equation examples.

Revision 2800 - Directory Listing
Modified Thu Dec 3 01:45:12 2009 UTC (9 years, 4 months ago) by ahallam
Getting rid of unneeded directories

Revision 2799 - Directory Listing
Modified Thu Dec 3 01:35:08 2009 UTC (9 years, 4 months ago) by jfenwick
resolveGroup function added to python.
Unit tests for resolveGroup, resolve and delay.

Revision 2798 - Directory Listing
Modified Thu Dec 3 01:02:47 2009 UTC (9 years, 4 months ago) by caltinay
Use system NetCDF on guineapig.


Revision 2797 - Directory Listing
Modified Wed Dec 2 23:30:21 2009 UTC (9 years, 4 months ago) by caltinay
Changed NetCDF include path - this should enable netcdf on guineapig.


Revision 2796 - Directory Listing
Modified Wed Dec 2 05:02:43 2009 UTC (9 years, 4 months ago) by caltinay
null-commit to trigger buildbot


Revision 2795 - Directory Listing
Modified Wed Dec 2 02:39:23 2009 UTC (9 years, 4 months ago) by jfenwick
Removed node limit on lazy expressions.
The parameter LAZY_STR_FMT {0,1,2}  controls how lazy expressions are printed.
0 gives default output
1 gives a tree form.
2 just prints depth

Revision 2794 - Directory Listing
Modified Wed Dec 2 00:43:17 2009 UTC (9 years, 4 months ago) by gross
returning to the older version.

Revision 2793 - Directory Listing
Modified Tue Dec 1 06:10:10 2009 UTC (9 years, 4 months ago) by gross
some new util functions

Revision 2792 - Directory Listing
Modified Tue Dec 1 05:02:18 2009 UTC (9 years, 4 months ago) by jfenwick
Oops.
matrixInverse now checks MPI to see if any other ranks raised exceptions.

Revision 2791 - Directory Listing
Modified Tue Dec 1 03:36:36 2009 UTC (9 years, 4 months ago) by jfenwick
Added expression depth to toString for LazyData.


Revision 2790 - Directory Listing
Modified Sun Nov 29 23:57:45 2009 UTC (9 years, 4 months ago) by jfenwick
Fix scons file for unit tests.


Revision 2789 - Directory Listing
Modified Fri Nov 27 05:40:25 2009 UTC (9 years, 4 months ago) by caltinay
Removed unused variable from OpenMP block.
Fixes compilation error with gcc 4.3.


Revision 2788 - Directory Listing
Modified Fri Nov 27 05:23:14 2009 UTC (9 years, 4 months ago) by jfenwick
Go back to version 10


Revision 2787 - Directory Listing
Modified Fri Nov 27 05:03:09 2009 UTC (9 years, 4 months ago) by jfenwick
Worked around icc11 problem in table interpolate.
Best guess is that a stackframe was getting mauled somehow.



Revision 2786 - Directory Listing
Modified Fri Nov 27 01:07:28 2009 UTC (9 years, 4 months ago) by caltinay
Fixed a little typo.


Revision 2785 - Directory Listing
Modified Thu Nov 26 05:17:40 2009 UTC (9 years, 4 months ago) by lgao
Minor fix for unused variables



Revision 2784 - Directory Listing
Modified Thu Nov 26 05:09:14 2009 UTC (9 years, 4 months ago) by artak
More performance tunning. Sparsity check is added. If Coarse level matrix is denser than 1% then stop.

Revision 2783 - Directory Listing
Modified Thu Nov 26 05:07:33 2009 UTC (9 years, 4 months ago) by lgao
process C_TensorBinaryOperation at the level of a whole sample rather than 
each datapoint when an Expanded data is operating with a Constant data. This
could improve the efficiency of the non-lazy version escipt. 



Revision 2782 - Directory Listing
Modified Thu Nov 26 04:42:29 2009 UTC (9 years, 4 months ago) by caltinay
Added missing var declaration.


Revision 2781 - Directory Listing
Modified Thu Nov 26 04:12:11 2009 UTC (9 years, 4 months ago) by jfenwick
Some additional info from Thomas

Revision 2780 - Directory Listing
Modified Thu Nov 26 03:54:24 2009 UTC (9 years, 4 months ago) by jfenwick
Put the windows instructions back in.
Put more detail in the MPI hints.

Revision 2779 - Directory Listing
Modified Thu Nov 26 03:51:15 2009 UTC (9 years, 4 months ago) by caltinay
Fixed more instances of garbage=cstring+integer errors (d'oh!)


Revision 2778 - Directory Listing
Modified Thu Nov 26 01:50:30 2009 UTC (9 years, 4 months ago) by caltinay
Fixed unintended pointer arithmetic with c-strings in MeshAdapter::dump() and
shortened error messages while being at it.


Revision 2777 - Directory Listing
Modified Thu Nov 26 01:06:00 2009 UTC (9 years, 4 months ago) by jfenwick
Added the LAZY_STACK_PROF #define for Lazy.
If enabled lazy will print the (roughly) maximum stack used by any openmp 
thread over the course of this session.


Revision 2776 - Directory Listing
Modified Wed Nov 25 23:41:16 2009 UTC (9 years, 4 months ago) by jfenwick
Switching tests which read gmsh to not run under MPI


Revision 2775 - Directory Listing
Modified Wed Nov 25 05:01:43 2009 UTC (9 years, 4 months ago) by ahallam
minor updates to cookbook; new python syntax highlighting

Revision 2774 - Directory Listing
Modified Wed Nov 25 04:24:03 2009 UTC (9 years, 4 months ago) by artak
#ifndef changed to #ifdef in makeNaN

Revision 2773 - Directory Listing
Modified Wed Nov 25 04:02:01 2009 UTC (9 years, 4 months ago) by jfenwick
Hadn't realised isnan was a macro.
Checking for it rather than FP_NAN


Revision 2772 - Directory Listing
Modified Wed Nov 25 02:02:50 2009 UTC (9 years, 4 months ago) by ahallam
Fixed auto build error for heatrefraction_mesher002.py

Added clear figure line for run_heatrefraction.py process.

Revision 2771 - Directory Listing
Modified Wed Nov 25 01:38:49 2009 UTC (9 years, 4 months ago) by jfenwick
Fix


Revision 2770 - Directory Listing
Modified Wed Nov 25 01:24:51 2009 UTC (9 years, 4 months ago) by jfenwick
Removed buffer implementation of Lazy.
Removed supporting Alloc/Free Sample buffer calls.

Revision 2769 - Directory Listing
Modified Tue Nov 24 00:36:22 2009 UTC (9 years, 4 months ago) by jfenwick
Unit tests for NaN handling

Revision 2768 - Directory Listing
Modified Mon Nov 23 23:56:14 2009 UTC (9 years, 4 months ago) by jfenwick
Dodge problem in NoPDE class


Revision 2767 - Directory Listing
Modified Mon Nov 23 06:00:37 2009 UTC (9 years, 4 months ago) by artak
More openmp calls are added,escpecialy in arg_max method.

Revision 2766 - Directory Listing
Modified Mon Nov 23 05:10:53 2009 UTC (9 years, 4 months ago) by jfenwick
inf, sup and Lsup now correctly handle +-infinity.
They also will return NaN if any part of their input is NaN.

This will break unit tests since it exposes the hidden bug (#447 in mantis)

This code relies on the ability to test for NaNs.
To do this it makes use of macros and functions from C99.
If you do not have a C99 compiler, then you will probably get the old behaviour.
That is, you won't know when you have NaNs.


Also did minor tweak to saveDataCSV doco.

Revision 2765 - Directory Listing
Modified Fri Nov 20 01:49:19 2009 UTC (9 years, 5 months ago) by artak
First steps toward efficiency. Coarsening process is improved. Some profiling tools are added.

Revision 2764 - Directory Listing
Modified Thu Nov 19 23:48:05 2009 UTC (9 years, 5 months ago) by artak
Some openMP calls are removed.

Revision 2763 - Directory Listing
Modified Thu Nov 19 06:28:03 2009 UTC (9 years, 5 months ago) by lgao
Minor fix to my previous commit.




Revision 2762 - Directory Listing
Modified Thu Nov 19 06:24:44 2009 UTC (9 years, 5 months ago) by lgao
fix the compilation problem I introduced for Non-MPI build due
to my last commit for Data::toString().



Revision 2761 - Directory Listing
Modified Thu Nov 19 06:11:07 2009 UTC (9 years, 5 months ago) by artak
AMLI preconditioner (previously called  AMG)

Revision 2760 - Directory Listing
Modified Thu Nov 19 05:22:45 2009 UTC (9 years, 5 months ago) by artak
The first version of the new AMG preconditioner. It need a lot of polishing for efficiency. Old AMG now called AMLI preconditioner.

Revision 2759 - Directory Listing
Modified Thu Nov 19 05:19:47 2009 UTC (9 years, 5 months ago) by artak
methods needed for the new AMG preconditioner

Revision 2758 - Directory Listing
Modified Thu Nov 19 04:21:55 2009 UTC (9 years, 5 months ago) by caltinay
Added missing imports. all_tests still fails though due to other problems.


Revision 2757 - Directory Listing
Modified Thu Nov 19 01:04:57 2009 UTC (9 years, 5 months ago) by lgao
Solve the print statement problem for MPI program (matis issue 465). 



Revision 2756 - Directory Listing
Modified Thu Nov 19 00:40:02 2009 UTC (9 years, 5 months ago) by gross
missing file added.

Revision 2755 - Directory Listing
Modified Wed Nov 18 23:19:32 2009 UTC (9 years, 5 months ago) by caltinay
Reverted changes to Mesh_read from last commit. They break compilation with
MPI and seem unintentional.


Revision 2754 - Directory Listing
Modified Wed Nov 18 07:44:26 2009 UTC (9 years, 5 months ago) by gross
tests for macro elements in saveVTK added.

Revision 2753 - Directory Listing
Modified Wed Nov 18 06:06:50 2009 UTC (9 years, 5 months ago) by lgao
fix bugs in minGlobalDataPoint() and maxGlobalDataPoint()



Revision 2752 - Directory Listing
Modified Wed Nov 18 06:01:18 2009 UTC (9 years, 5 months ago) by caltinay
Fixed compilation error in mesh reader when using MPI.


Revision 2751 - Directory Listing
Modified Wed Nov 18 00:30:47 2009 UTC (9 years, 5 months ago) by caltinay
Removed stray forward declaration.


Revision 2750 - Directory Listing
Modified Tue Nov 17 23:39:20 2009 UTC (9 years, 5 months ago) by caltinay
Fixed some compilation errors with OpenMP introduced in last commit.


Revision 2749 - Directory Listing
Modified Tue Nov 17 07:34:16 2009 UTC (9 years, 5 months ago) by gross
missing files.

Revision 2748 - Directory Listing
Modified Tue Nov 17 07:32:59 2009 UTC (9 years, 5 months ago) by gross
Macro elements are implemented now. VTK writer for macro elements still needs testing.

Revision 2747 - Directory Listing
Modified Tue Nov 17 05:19:59 2009 UTC (9 years, 5 months ago) by lgao
Minor rivision to minGlobalDataPoint()



Revision 2746 - Directory Listing
Modified Tue Nov 17 05:13:51 2009 UTC (9 years, 5 months ago) by lgao
Fix the error in minGlobalDataPoint() and maxGlobalDataPoint() due to 
the fact that the number of samples on one MPI rank could be 0. Therefore,
not every MPI rank has valid min/max data point. 



Revision 2745 - Directory Listing
Modified Tue Nov 17 04:23:02 2009 UTC (9 years, 5 months ago) by jfenwick
Added getInfLocator and getSupLocator to pdetools.
This means if you want to use them, you will need to import them.
These methods return a locator to a point with the smallest/largest value.

Added resolve() and delay() to utils.
Now you can do things like:

d=delay(v)
..
..
z=resolve(d+1)



Revision 2744 - Directory Listing
Modified Mon Nov 16 23:45:55 2009 UTC (9 years, 5 months ago) by caltinay
SaveVTK: exponent could have 3 digits so reserve enough space.


Revision 2743 - Directory Listing
Modified Mon Nov 16 05:28:47 2009 UTC (9 years, 5 months ago) by caltinay
Corrected memory allocation size for tensors in saveVTK. Fixes issue 460.


Revision 2742 - Directory Listing
Modified Thu Nov 12 06:03:37 2009 UTC (9 years, 5 months ago) by jfenwick
Merging changes from the lapack branch.

The inverse() operation has been moved into c++. [No lazy support for this operation yet.]
Optional Lapack support has been added for matrices larger than 3x3. 
service0 is set to use mkl_lapack.




Revision 2738 - Directory Listing
Modified Fri Nov 6 05:33:13 2009 UTC (9 years, 5 months ago) by jfenwick
Taipan and DataVector use size_type (currently long) internally to talk 
about sizes.
[A lot more work needs to be done on this].
Exceptions now give nicer messages and output the problematic numbers.

Some minor doco errors fixed.

escript.util.mkDir
Now checks to see if the pathname already exists as a non-directory.
On suggestion from slanger it now calls makedirs.




Revision 2737 - Directory Listing
Modified Tue Nov 3 00:44:00 2009 UTC (9 years, 5 months ago) by jfenwick
icc will now record compiler options in libraries.
escriptParams now has a pretty printer option for lazy expressions.

Revision 2736 - Directory Listing
Modified Mon Nov 2 04:15:27 2009 UTC (9 years, 5 months ago) by caltinay
Fixed a couple of typos.


Revision 2735 - Directory Listing
Modified Mon Nov 2 02:03:24 2009 UTC (9 years, 5 months ago) by jfenwick
Fixed bug where calling minval() reintroduced laziness after it had been removed.


Revision 2734 - Directory Listing
Modified Fri Oct 30 05:39:48 2009 UTC (9 years, 5 months ago) by jfenwick
Fixed bug in lazy maxval and minval


Revision 2733 - Directory Listing
Modified Mon Oct 26 02:05:11 2009 UTC (9 years, 5 months ago) by caltinay
escriptreader: added debug flag to configure.ac


Revision 2732 - Directory Listing
Modified Mon Oct 26 01:11:31 2009 UTC (9 years, 5 months ago) by jfenwick
Fixed segfault in debug+omp tests.
Cause:
  variable used in parallel section not declared shared.



Revision 2731 - Directory Listing
Modified Thu Oct 22 04:17:21 2009 UTC (9 years, 5 months ago) by trankine
* Added xe.ivec.org options file as reminder for David Schibeci [dschibeci@ccg.murdoch.edu.au]

Revision 2730 - Directory Listing
Modified Thu Oct 22 01:50:27 2009 UTC (9 years, 5 months ago) by artak
order member variable added to the tests.

Revision 2729 - Directory Listing
Modified Thu Oct 22 01:45:28 2009 UTC (9 years, 5 months ago) by jfenwick
UMFPack and MPI added to guineapig options.
Defaults for omp and mpi removed from SConstruct.


Revision 2728 - Directory Listing
Modified Thu Oct 22 00:13:10 2009 UTC (9 years, 5 months ago) by artak
minor

Revision 2727 - Directory Listing
Modified Wed Oct 21 23:56:23 2009 UTC (9 years, 5 months ago) by jfenwick
Added guineapig options


Revision 2726 - Directory Listing
Modified Wed Oct 21 23:50:05 2009 UTC (9 years, 5 months ago) by artak
New diagonal dominancy based algorithm is added. The coarseneng strategy is changed.

Revision 2725 - Directory Listing
Modified Wed Oct 21 23:44:06 2009 UTC (9 years, 5 months ago) by artak
AMG unit tests are disabled for 2-nd order elements.

Revision 2724 - Directory Listing
Modified Sun Oct 18 23:50:18 2009 UTC (9 years, 6 months ago) by jfenwick
And again


Revision 2723 - Directory Listing
Modified Sun Oct 18 23:44:37 2009 UTC (9 years, 6 months ago) by jfenwick
Use correct types for MPI op parameters


Revision 2722 - Directory Listing
Modified Fri Oct 16 06:45:01 2009 UTC (9 years, 6 months ago) by gross
First steps towards macro elements. at the monent a  macro element is identical to its counterpart of 2nd order.





Revision 2721 - Directory Listing
Modified Fri Oct 16 05:40:12 2009 UTC (9 years, 6 months ago) by jfenwick
minval and maxval are now lazy operations (they weren't before).
Whether or not Lsup, sup and inf resolve their arguments before computing answers is controlled by the escriptParam 'RESOLVE_COLLECTIVE'.
Note: integrate() still forces a resolve.

Added some unit tests for operations which weren't tested before.
Added deepcopy implementations for lazy operations which got missed somehow.

Revision 2720 - Directory Listing
Modified Wed Oct 14 23:43:21 2009 UTC (9 years, 6 months ago) by gross
missing modules added

Revision 2719 - Directory Listing
Modified Wed Oct 14 06:38:03 2009 UTC (9 years, 6 months ago) by gross
a new Stokes solver added

Revision 2718 - Directory Listing
Modified Wed Oct 14 04:03:27 2009 UTC (9 years, 6 months ago) by gross
syntax errors fixed.

Revision 2717 - Directory Listing
Modified Wed Oct 14 03:41:20 2009 UTC (9 years, 6 months ago) by gross
implements https://mantis.esscc.uq.edu.au/view.php?id=426

Revision 2716 - Directory Listing
Modified Tue Oct 13 04:58:08 2009 UTC (9 years, 6 months ago) by jfenwick
Small mod - process C_Tensor??Operation on ExpandedData as a whole 
sample rather than a datapoint at a time.
This is just to bring Non-Lazy into line with Lazy.


Revision 2715 - Directory Listing
Modified Sun Oct 11 23:29:56 2009 UTC (9 years, 6 months ago) by lgao
change back to use Intel MPI (avoid the MPT+MKL problem).



Revision 2714 - Directory Listing
Modified Wed Oct 7 23:29:19 2009 UTC (9 years, 6 months ago) by gross
typo in check fixed.

Revision 2713 - Directory Listing
Modified Wed Oct 7 00:35:06 2009 UTC (9 years, 6 months ago) by jfenwick
Fixes for windows.
Copied from Thomas Poulet


Revision 2712 - Directory Listing
Modified Wed Oct 7 00:22:43 2009 UTC (9 years, 6 months ago) by artak
MKL made default direct solver for AMG

Revision 2711 - Directory Listing
Modified Tue Oct 6 04:43:41 2009 UTC (9 years, 6 months ago) by artak
Little restructuring for solving memory bug in MKL_free process and making sure LDU factorzation done only once.

Revision 2710 - Directory Listing
Modified Mon Oct 5 23:15:04 2009 UTC (9 years, 6 months ago) by jfenwick
Change to error output requested by Thomas Poulet


Revision 2709 - Directory Listing
Modified Mon Oct 5 06:11:58 2009 UTC (9 years, 6 months ago) by artak
Paso_MKL1 put back again

Revision 2708 - Directory Listing
Modified Mon Oct 5 05:59:08 2009 UTC (9 years, 6 months ago) by artak
The n_F==n condition with potentially uninitialized value is fixed.

Revision 2707 - Directory Listing
Modified Fri Oct 2 05:02:59 2009 UTC (9 years, 6 months ago) by artak
some unnecessary lines are removed

Revision 2706 - Directory Listing
Modified Fri Oct 2 02:15:04 2009 UTC (9 years, 6 months ago) by jfenwick
Perhaps this will stop the cookbook from hating me.



Revision 2705 - Directory Listing
Modified Thu Oct 1 23:21:10 2009 UTC (9 years, 6 months ago) by artak
Some openMP codes in AMG systems are removed for testing.

Revision 2704 - Directory Listing
Modified Thu Oct 1 05:38:33 2009 UTC (9 years, 6 months ago) by artak
some clarity in the notations REMOVED changes IN_SET

Revision 2703 - Directory Listing
Modified Thu Oct 1 01:22:36 2009 UTC (9 years, 6 months ago) by jfenwick
Added calls to MPI_Abort to the pythonMPI wrappers.
Now if an uncaught exception is raised on any of the nodes, the whole world should be brought down. I've tested this on a barrier and it works.
One consequence of this is that you should not call sys.exit(2) but we don't recommend using sys.exit anyway.




Revision 2702 - Directory Listing
Modified Wed Sep 30 23:54:17 2009 UTC (9 years, 6 months ago) by artak
UMFPACK is enabled for savanna

Revision 2701 - Directory Listing
Modified Wed Sep 30 23:21:08 2009 UTC (9 years, 6 months ago) by artak
MKL test lines are removed 

Revision 2700 - Directory Listing
Modified Wed Sep 30 08:28:55 2009 UTC (9 years, 6 months ago) by gross
pycad test fixed.

Revision 2699 - Directory Listing
Modified Wed Sep 30 05:43:20 2009 UTC (9 years, 6 months ago) by artak
Direct solver switched to UMFPACK, till problem with MKL solved. When all unknows are eliminated then we switch to Jacobi preconditiner.

Revision 2698 - Directory Listing
Modified Wed Sep 30 01:46:31 2009 UTC (9 years, 6 months ago) by jfenwick
Removing extension from some image filenames


Revision 2697 - Directory Listing
Modified Wed Sep 30 01:29:22 2009 UTC (9 years, 6 months ago) by jfenwick
Trying to get cookbook scripts passing.
Split cblib in two to avoid importing pylab in scripts which
don't otheriwse need it.



Revision 2696 - Directory Listing
Modified Wed Sep 30 00:36:05 2009 UTC (9 years, 6 months ago) by lgao
change service0_options.py to use MPT 1.24



Revision 2695 - Directory Listing
Modified Tue Sep 29 06:29:12 2009 UTC (9 years, 6 months ago) by gross
pycad passes on more infromation from gmsh now.

Revision 2694 - Directory Listing
Modified Tue Sep 29 06:00:44 2009 UTC (9 years, 6 months ago) by gross
some hint on how to access gmsh error messages added.

Revision 2693 - Directory Listing
Modified Tue Sep 29 05:47:45 2009 UTC (9 years, 6 months ago) by artak
sorry python Indentation Error, fixed 

Revision 2692 - Directory Listing
Modified Tue Sep 29 05:35:31 2009 UTC (9 years, 6 months ago) by artak
minor typo

Revision 2691 - Directory Listing
Modified Tue Sep 29 05:30:27 2009 UTC (9 years, 6 months ago) by artak
Projector class had getSolverOptions(), but was returning null, so changed to return correct solver options.

Revision 2690 - Directory Listing
Modified Tue Sep 29 05:23:41 2009 UTC (9 years, 6 months ago) by gross
some description on gmsh reader added.

Revision 2689 - Directory Listing
Modified Tue Sep 29 05:22:51 2009 UTC (9 years, 6 months ago) by artak
getSolverOptionsDiv was returning Pressure options instead of Div equation options

Revision 2688 - Directory Listing
Modified Tue Sep 29 05:19:43 2009 UTC (9 years, 6 months ago) by artak
changes to default threshold values

Revision 2687 - Directory Listing
Modified Tue Sep 29 04:23:10 2009 UTC (9 years, 6 months ago) by caltinay
libescriptreader: fixed a path problem when using autotools to build


Revision 2686 - Directory Listing
Modified Tue Sep 29 03:39:36 2009 UTC (9 years, 6 months ago) by artak
 changes the default thresold, bug fixes in RS coupling and extra checks added in Solver 

Revision 2685 - Directory Listing
Modified Tue Sep 29 02:22:30 2009 UTC (9 years, 6 months ago) by gross
these files are not needed

Revision 2684 - Directory Listing
Modified Tue Sep 29 02:21:11 2009 UTC (9 years, 6 months ago) by gross
added missing file

Revision 2683 - Directory Listing
Modified Tue Sep 29 02:20:22 2009 UTC (9 years, 6 months ago) by gross
documentation for pycad added.

Revision 2681 - Directory Listing
Modified Thu Sep 24 03:04:04 2009 UTC (9 years, 6 months ago) by ahallam
proof reading and review of cookbook, minor changes only + updated depth profiles to cb from last week

Revision 2680 - Directory Listing
Modified Thu Sep 24 00:40:07 2009 UTC (9 years, 6 months ago) by caltinay
Updated service0 options file to use Silo 4.7 on Savanna


Revision 2679 - Directory Listing
Modified Thu Sep 24 00:36:57 2009 UTC (9 years, 6 months ago) by caltinay
Updated shake75 options file


Revision 2678 - Directory Listing
Modified Wed Sep 23 23:54:16 2009 UTC (9 years, 6 months ago) by jfenwick
Some fixes for compile errors for gcc_testing_version


Revision 2677 - Directory Listing
Modified Tue Sep 22 00:48:00 2009 UTC (9 years, 6 months ago) by jfenwick
Removed stuff in user guide about needing to make table larger to allow
boundary points.
The table interpolation is now OMP parallel.



Revision 2676 - Directory Listing
Modified Mon Sep 21 08:06:37 2009 UTC (9 years, 6 months ago) by gross
FaultSystem: MaxValue and MinValue return now a Locator. This makes it possible to extract values of from other data objects at the location of the min/max value

Revision 2675 - Directory Listing
Modified Mon Sep 21 02:32:17 2009 UTC (9 years, 6 months ago) by gross
getMinValue added to the fault system.

Revision 2674 - Directory Listing
Modified Mon Sep 21 00:37:18 2009 UTC (9 years, 6 months ago) by jfenwick
Base matplotlib tests on version number.
This will stop the Mac trying to run some tests it can't execute.


Revision 2673 - Directory Listing
Modified Fri Sep 18 05:33:10 2009 UTC (9 years, 7 months ago) by jfenwick
Some fixes to interpolation


Revision 2672 - Directory Listing
Modified Fri Sep 18 01:46:47 2009 UTC (9 years, 7 months ago) by ahallam
Heat refraction updates : alex's downhole profiles

Revision 2671 - Directory Listing
Modified Thu Sep 17 06:37:22 2009 UTC (9 years, 7 months ago) by gross
missing offset added in interpolation table

Revision 2670 - Directory Listing
Modified Thu Sep 17 06:17:57 2009 UTC (9 years, 7 months ago) by artak
Bug that made MPI tests to fail is fixed.

Revision 2669 - Directory Listing
Modified Thu Sep 17 06:01:30 2009 UTC (9 years, 7 months ago) by jfenwick
Added a bunch of valgrind supressions. Hopefully this will make it more useful.

Asking for an offset on a DataConstant containing no samples no longer fails under debug builds.
I've disabled the sample and dataPoint bounds checks since they don't make sense on DataConstant.

Revision 2668 - Directory Listing
Modified Thu Sep 17 04:04:09 2009 UTC (9 years, 7 months ago) by gross
some clarification in the table interpolation

Revision 2667 - Directory Listing
Modified Thu Sep 17 01:49:11 2009 UTC (9 years, 7 months ago) by jfenwick
Renamed the main cookbook tex file to match our convention.
Replaced doc/cookbook/figures/heatrefraction002contqu.pdf with
a version which is actually pdf. However it needs to be regnerated since
it it sideways.

The examples have had their copyright notices fixed (dates were too early).
sb2.py has been removed since it uses pyvisi.

scons will now build the cookbook as parts of a docs build.
Also in reposnse to :
scons cookbook_pdf



Revision 2666 - Directory Listing
Modified Thu Sep 17 00:10:00 2009 UTC (9 years, 7 months ago) by artak
OpenMP bug fixed and more openMP code added for cutting blocks.

Revision 2665 - Directory Listing
Modified Wed Sep 16 02:56:02 2009 UTC (9 years, 7 months ago) by gross
clarification in the fault depth vector

Revision 2664 - Directory Listing
Modified Wed Sep 16 01:06:50 2009 UTC (9 years, 7 months ago) by artak
Extra check is added for AMG levels. If coursening proccess does not eliminate at least 30% from the fine Matrix then it does not make sense to continue to the next level.

Revision 2663 - Directory Listing
Modified Tue Sep 15 06:04:44 2009 UTC (9 years, 7 months ago) by gross
finally there is a 3D version for the fault system class

Revision 2662 - Directory Listing
Modified Tue Sep 15 03:05:23 2009 UTC (9 years, 7 months ago) by artak
Migrating to block_sizes greather than 3 made easy.

Revision 2661 - Directory Listing
Modified Fri Sep 11 00:59:59 2009 UTC (9 years, 7 months ago) by artak
Finially unit tests for AMG preconditioner for single equations as well as for systems. Minor bug in AMG is also fixed

Revision 2660 - Directory Listing
Modified Thu Sep 10 04:26:39 2009 UTC (9 years, 7 months ago) by artak
minor

Revision 2659 - Directory Listing
Modified Thu Sep 10 03:54:50 2009 UTC (9 years, 7 months ago) by artak
first attempt of AMG on blocks

Revision 2658 - Directory Listing
Modified Thu Sep 10 02:58:44 2009 UTC (9 years, 7 months ago) by ahallam
Updates to all files scripts to support MPI testing proceedure. Updates to cookbook, new section on functino spaces/domains (needs work). Finalising first 3 chapters for editing.

Revision 2657 - Directory Listing
Modified Thu Sep 10 00:58:19 2009 UTC (9 years, 7 months ago) by jfenwick
Fixed some spelling errors.
Added text about parallel vis.


Revision 2656 - Directory Listing
Modified Wed Sep 9 23:47:10 2009 UTC (9 years, 7 months ago) by jfenwick
Fixing doco compile bug


Revision 2655 - Directory Listing
Modified Tue Sep 8 23:31:32 2009 UTC (9 years, 7 months ago) by gross
a comma is missing.

Revision 2654 - Directory Listing
Modified Tue Sep 8 07:11:12 2009 UTC (9 years, 7 months ago) by gross
2D fault systems are now working. 3D still needs work.

Revision 2653 - Directory Listing
Modified Tue Sep 8 04:26:30 2009 UTC (9 years, 7 months ago) by jfenwick
Fix bug in maxGlobalDataPoint and minGlobalDataPoint.
They now give the correct answers and the datapoint ids returned are globally
correct.

Removed some #defines from before COW
Removed hasNoSamples() - I don't trust myself to use that properly let alone anybody else.



Revision 2652 - Directory Listing
Modified Mon Sep 7 05:04:45 2009 UTC (9 years, 7 months ago) by artak
Paso_Pattern_coup changed to Paso_Pattern_YS for making clear that it refers to YAIR-SHAPIRA coarsenenig.

Revision 2651 - Directory Listing
Modified Mon Sep 7 03:39:45 2009 UTC (9 years, 7 months ago) by jfenwick
Fixed latex compile error.
Fixed some overful hboxes


Revision 2650 - Directory Listing
Modified Mon Sep 7 03:38:50 2009 UTC (9 years, 7 months ago) by jfenwick
Reducing the concentration of stupid.


Revision 2649 - Directory Listing
Modified Mon Sep 7 03:33:55 2009 UTC (9 years, 7 months ago) by gross
Some small fixes in FaultSystem

Revision 2648 - Directory Listing
Modified Mon Sep 7 00:06:15 2009 UTC (9 years, 7 months ago) by jfenwick
ecording some changes related to Anthony's cookbook.
These tests still do not run.

test_heatref.py is the current problem.
Current problems include:
undefined symbols
a dependence on X somehow.

I've already addressed the matplotlib X thing somewhere else.
Find and apply.



Revision 2647 - Directory Listing
Modified Fri Sep 4 05:25:25 2009 UTC (9 years, 7 months ago) by gross
fault system add. There is still an example for the usage missing.

Revision 2646 - Directory Listing
Modified Fri Sep 4 00:13:00 2009 UTC (9 years, 7 months ago) by jfenwick
Unit tests and user doco for interpolation and saveCSV

Revision 2645 - Directory Listing
Modified Thu Sep 3 02:20:33 2009 UTC (9 years, 7 months ago) by ahallam
More revisions to cookbook, fixed cblib.py for Scons, new figures.

Revision 2644 - Directory Listing
Modified Wed Sep 2 04:14:03 2009 UTC (9 years, 7 months ago) by jfenwick
Add unit tests for saveDataCSV which should be ready for use now.
Keyword args are now output in sorted order.

Removed some unneeded functions.

Revision 2643 - Directory Listing
Modified Wed Sep 2 00:10:00 2009 UTC (9 years, 7 months ago) by artak
Saving sparse matrix used before for debuging is removed

Revision 2642 - Directory Listing
Modified Tue Sep 1 04:15:50 2009 UTC (9 years, 7 months ago) by jfenwick
pre cleanup

Revision 2641 - Directory Listing
Modified Mon Aug 31 07:41:49 2009 UTC (9 years, 7 months ago) by jfenwick
Fixed some of my stupids related to MPI compile errors.


Revision 2640 - Directory Listing
Modified Mon Aug 31 06:22:10 2009 UTC (9 years, 7 months ago) by jfenwick
Adding getMPIComm


Revision 2637 - Directory Listing
Modified Fri Aug 28 04:12:24 2009 UTC (9 years, 7 months ago) by jfenwick
saveDataCSV looks good but does not do MPI yet.
Also not unit tested.


Revision 2636 - Directory Listing
Modified Thu Aug 27 05:26:42 2009 UTC (9 years, 7 months ago) by jfenwick
Disabling cookbook example checks until we can fix them.


Revision 2635 - Directory Listing
Modified Thu Aug 27 04:54:41 2009 UTC (9 years, 7 months ago) by jfenwick
A bunch of changes related to saveDataCSV.
[Not completed or unit tested yet]

Added saveDataCSV to util.py
AbstractDomain (and MeshAdapter) have a commonFunctionSpace method to 
take a group of FunctionSpaces and return something they can all be interpolated to.

Added pointToStream() in DataTypes to help print points.

added actsConstant() to data - required because DataConstant doesn't store samples the same way other Data do.

Revision 2634 - Directory Listing
Modified Thu Aug 27 04:03:32 2009 UTC (9 years, 7 months ago) by ahallam
Updates to cookbook. Updates to scripts. Updates to figures. Working examples added to SCons. Data folder structure included minus data. More folder rejigging.

Revision 2633 - Directory Listing
Modified Wed Aug 26 22:21:52 2009 UTC (9 years, 7 months ago) by ahallam
Sorry second regigging

Revision 2632 - Directory Listing
Modified Wed Aug 26 22:18:19 2009 UTC (9 years, 7 months ago) by ahallam
Regigger of cookbook directory structure. Examlples->examples/cookbook TEXT->doc/cookbook Figures-> doc/cookbook/figures

Revision 2629 - Directory Listing
Modified Tue Aug 25 06:39:26 2009 UTC (9 years, 7 months ago) by trankine
Changes to work on Windows with boost 1.39.0. Using command separator &. Note: there are still 2 CheckFunc that fail (but can be bypassed as the rest of the build works). 

Revision 2628 - Directory Listing
Modified Tue Aug 25 03:50:00 2009 UTC (9 years, 7 months ago) by jfenwick
Fixed linkage on getTestDomainFunctionSpace.

added Data.interpolateTable to perform 2D interpolation.
It needs better unit tests though.

Revision 2627 - Directory Listing
Modified Mon Aug 24 01:57:34 2009 UTC (9 years, 7 months ago) by gross
some bugs in pycad fixed.


Revision 2626 - Directory Listing
Modified Mon Aug 24 00:48:31 2009 UTC (9 years, 7 months ago) by jfenwick
Making arg0 and arg params in C_GeneralTensorProduct non-optional.
[The using the default args caused an exception.]


Revision 2625 - Directory Listing
Modified Fri Aug 21 06:30:25 2009 UTC (9 years, 8 months ago) by jfenwick
Merging changes from new doco branch.
All docstrings are now in reStructured text.
A few email addresses have been fixes as well.

Revision 2620 - Directory Listing
Modified Thu Aug 20 06:24:00 2009 UTC (9 years, 8 months ago) by gross
some small additions to pycad to make life a bit easier.

Revision 2608 - Directory Listing
Modified Tue Aug 18 01:25:18 2009 UTC (9 years, 8 months ago) by jfenwick
Updating Lutz' email


Revision 2607 - Directory Listing
Modified Tue Aug 18 01:02:56 2009 UTC (9 years, 8 months ago) by jfenwick
Added getMPIWorldSum function to the esys.escript module.
This function takes an integer from each member of the MPIWorld.
This will hopefully address mantis issue 359

Added unit tests for most of the c++ free functions in the module.




Revision 2606 - Directory Listing
Modified Thu Aug 13 04:32:23 2009 UTC (9 years, 8 months ago) by ahallam
Updates to first chapter in cookbook -> approaching completion.
New figures added for model descriptions.
Scripts updated to use pylab/matplotlib and movie making scripts added for *.avi creation.
Still to finalise in chapter 1
- twodheatdiff model of intrusion
	-contouring

- heat refraction scripts and begin cookbook sections
	- pycad discussion
	- steady state pde discussion
	- quiver plot discussion

Revision 2605 - Directory Listing
Modified Wed Aug 12 22:30:47 2009 UTC (9 years, 8 months ago) by gross
some changes to the cook book

Revision 2604 - Directory Listing
Modified Wed Aug 12 01:21:46 2009 UTC (9 years, 8 months ago) by jfenwick
The prefix option for building escript now works correctly.
This fixes mantis issue #362.


Revision 2603 - Directory Listing
Modified Wed Aug 12 00:44:35 2009 UTC (9 years, 8 months ago) by jfenwick
Compute nodes will now read the correct options file and use the correct compiler.
I have added env_export to the service0 options file.
Use this if there are variables from the calling environment which need to be passed through scons. (In this case the INTEL_LICENSE_FILE variable).

There are still some issues with icpc linking.


Revision 2602 - Directory Listing
Modified Tue Aug 11 00:38:42 2009 UTC (9 years, 8 months ago) by jfenwick
Merging changes made for release3.0 back to trunk.

Revision 2600 - Directory Listing
Modified Fri Aug 7 04:47:49 2009 UTC (9 years, 8 months ago) by jfenwick
Using the 'agg' backend in matplotlib to avoid reference to the X Display.


Revision 2599 - Directory Listing
Modified Fri Aug 7 00:16:02 2009 UTC (9 years, 8 months ago) by caltinay
saveESD: added option to save mesh at each timestep if required.


Revision 2598 - Directory Listing
Modified Thu Aug 6 03:47:56 2009 UTC (9 years, 8 months ago) by gross
small fix in ReversedCurve clas

Revision 2597 - Directory Listing
Modified Thu Aug 6 03:30:09 2009 UTC (9 years, 8 months ago) by ahallam
Updates to: cookbook documentation; heat refraction problems; mencoder investigation for *.png animation

Revision 2596 - Directory Listing
Modified Thu Aug 6 03:09:03 2009 UTC (9 years, 8 months ago) by lgao
Add new diagnostic information: "net time" (the execution time of solver, excluding the setup time for solver and the execution time of preconditioner)



Revision 2595 - Directory Listing
Modified Thu Aug 6 00:49:09 2009 UTC (9 years, 8 months ago) by gross
there was wrong test which triggered an excpetion in some cases where things were actually right

Revision 2594 - Directory Listing
Modified Thu Aug 6 00:47:48 2009 UTC (9 years, 8 months ago) by gross
change to the default value for toListOfTuples

Revision 2592 - Directory Listing
Modified Thu Aug 6 00:43:19 2009 UTC (9 years, 8 months ago) by gross
additional tests for the Locator

Revision 2589 - Directory Listing
Modified Wed Aug 5 23:06:35 2009 UTC (9 years, 8 months ago) by ahallam


Revision 2588 - Directory Listing
Modified Wed Aug 5 22:42:36 2009 UTC (9 years, 8 months ago) by ahallam
Heat diffraction initial committal 2 weeks work.

Revision 2583 - Directory Listing
Modified Wed Aug 5 01:49:56 2009 UTC (9 years, 8 months ago) by jfenwick
Minor fixes

Revision 2581 - Directory Listing
Modified Wed Aug 5 01:11:33 2009 UTC (9 years, 8 months ago) by jfenwick
Fixed unit test for missing matplotlib case.


Revision 2580 - Directory Listing
Modified Tue Aug 4 08:24:12 2009 UTC (9 years, 8 months ago) by gross
another example for the usage of matplot lib added to users guide.

Revision 2578 - Directory Listing
Modified Tue Aug 4 04:05:36 2009 UTC (9 years, 8 months ago) by jfenwick
Fixed problem with unit tests

Revision 2575 - Directory Listing
Modified Mon Aug 3 23:38:33 2009 UTC (9 years, 8 months ago) by jfenwick
Fixed some grammar note about Lenny not working.


Revision 2574 - Directory Listing
Modified Mon Aug 3 09:09:20 2009 UTC (9 years, 8 months ago) by gross
matplotlib description added to usersguide

Revision 2573 - Directory Listing
Modified Mon Aug 3 04:30:09 2009 UTC (9 years, 8 months ago) by gross
some more fixes on solver options.

Revision 2568 - Directory Listing
Modified Fri Jul 31 05:37:41 2009 UTC (9 years, 8 months ago) by jfenwick
Updated install guide to include the correct version of python.
Updated Mac build instructions not to use numarray or frameworks.
Removed (commented out) references to MacPorts in the Mac instructions.
- These need to be updated and Artak isn't here.

Removed (commented out) references to windows in the install guide.
CSIRO won't have a windows release ready yet. 



Revision 2567 - Directory Listing
Modified Fri Jul 31 01:17:37 2009 UTC (9 years, 8 months ago) by jfenwick
Added example options file for Mac


Revision 2566 - Directory Listing
Modified Wed Jul 29 01:39:16 2009 UTC (9 years, 8 months ago) by artak
AMG on systems not supported yet exeption is added

Revision 2565 - Directory Listing
Modified Tue Jul 28 05:50:15 2009 UTC (9 years, 8 months ago) by artak
stopping criteria is slightly changed.

Revision 2564 - Directory Listing
Modified Tue Jul 28 04:46:38 2009 UTC (9 years, 8 months ago) by gross
reduced PDE solutions added to topography

Revision 2563 - Directory Listing
Modified Tue Jul 28 03:50:45 2009 UTC (9 years, 8 months ago) by gross
reengineered version of the mountain class so it becomes easier to use for the convection code

Revision 2562 - Directory Listing
Modified Tue Jul 28 01:25:12 2009 UTC (9 years, 8 months ago) by artak
inplace bugs are fixed

Revision 2561 - Directory Listing
Modified Mon Jul 27 07:38:45 2009 UTC (9 years, 8 months ago) by gross
small bug in the calculation of the errors fixed.

Revision 2560 - Directory Listing
Modified Mon Jul 27 07:38:00 2009 UTC (9 years, 8 months ago) by gross
a test for unique PropertySet name added.

Revision 2559 - Directory Listing
Modified Mon Jul 27 05:19:21 2009 UTC (9 years, 8 months ago) by artak
typo: MaxIter changed IterMax

Revision 2558 - Directory Listing
Modified Mon Jul 27 05:03:32 2009 UTC (9 years, 8 months ago) by gross
a table added showing the available solver options for finley paso.

Revision 2557 - Directory Listing
Modified Mon Jul 27 04:46:37 2009 UTC (9 years, 8 months ago) by artak
minor comments changed

Revision 2556 - Directory Listing
Modified Mon Jul 27 02:05:20 2009 UTC (9 years, 8 months ago) by artak
memory leack fixed

Revision 2555 - Directory Listing
Modified Mon Jul 27 01:50:16 2009 UTC (9 years, 8 months ago) by artak
Pattern_free for Aggregiation coarsening is added.

Revision 2554 - Directory Listing
Modified Fri Jul 24 05:38:54 2009 UTC (9 years, 8 months ago) by gross
bug with MKL call fixed.

Revision 2553 - Directory Listing
Modified Fri Jul 24 01:30:14 2009 UTC (9 years, 8 months ago) by jfenwick
Added another citation.


Revision 2552 - Directory Listing
Modified Fri Jul 24 00:42:10 2009 UTC (9 years, 8 months ago) by artak
openmp change 

Revision 2551 - Directory Listing
Modified Thu Jul 23 09:19:15 2009 UTC (9 years, 8 months ago) by gross
a problem with the sparse matrix unrolling fixed.

Revision 2550 - Directory Listing
Modified Tue Jul 21 03:36:13 2009 UTC (9 years, 9 months ago) by gross
AMG throws an error now if block size not 1

Revision 2549 - Directory Listing
Modified Mon Jul 20 06:43:47 2009 UTC (9 years, 9 months ago) by jfenwick
Remainder of copyright date fixes

Revision 2548 - Directory Listing
Modified Mon Jul 20 06:20:06 2009 UTC (9 years, 9 months ago) by jfenwick
Updating copyright notices

Revision 2547 - Directory Listing
Modified Mon Jul 20 05:50:46 2009 UTC (9 years, 9 months ago) by caltinay
More work on the install guide.


Revision 2546 - Directory Listing
Modified Mon Jul 20 05:35:08 2009 UTC (9 years, 9 months ago) by jfenwick
Updated builddeb script to include the architecture in the package filename.
(the architecture is also written into the control file).
Modified dependencies to not include VTK.
Added python-matplotlib as a "Recomends" dependency.

This means we can build 64bit debs now.

Revision 2545 - Directory Listing
Modified Mon Jul 20 04:54:57 2009 UTC (9 years, 9 months ago) by caltinay
Install guide: fixed a minor typo


Revision 2544 - Directory Listing
Modified Mon Jul 20 04:50:38 2009 UTC (9 years, 9 months ago) by caltinay
Enable building doxygen docs for the escriptreader library.


Revision 2543 - Directory Listing
Modified Mon Jul 20 04:38:21 2009 UTC (9 years, 9 months ago) by caltinay
Install guide: fixed latex compilation due to incompatible hyperref package.


Revision 2542 - Directory Listing
Modified Mon Jul 20 04:18:27 2009 UTC (9 years, 9 months ago) by jfenwick
Importing esys.pyvisi now generates a warning.

Revision 2541 - Directory Listing
Modified Mon Jul 20 00:25:55 2009 UTC (9 years, 9 months ago) by jfenwick
Added matplotlib to the stand-alone path.
Removed VTK


Revision 2540 - Directory Listing
Modified Mon Jul 20 00:09:55 2009 UTC (9 years, 9 months ago) by jfenwick
Deprecating pyvisi in the user guide.

Revision 2539 - Directory Listing
Modified Sat Jul 18 02:47:34 2009 UTC (9 years, 9 months ago) by artak
the line added in RS for symetricity brings factorization failure in heatedblock example 

Revision 2538 - Directory Listing
Modified Fri Jul 17 06:24:15 2009 UTC (9 years, 9 months ago) by caltinay
Install guide: Reworked introduction and enabled hyperref package


Revision 2537 - Directory Listing
Modified Fri Jul 17 05:50:35 2009 UTC (9 years, 9 months ago) by jfenwick
Operation_make_pyvisi_go_away: Stage 1 of PI

Removing pyvisi example files.


Revision 2536 - Directory Listing
Modified Thu Jul 16 23:53:07 2009 UTC (9 years, 9 months ago) by caltinay
installguide: Fixed typos, minor semantics, repetitions and whitespace issues.


Revision 2535 - Directory Listing
Modified Thu Jul 16 23:39:58 2009 UTC (9 years, 9 months ago) by gross
LinearPDE is now updating stiffness matrix and right hand side even only geometry is modified. fix for 333

Revision 2534 - Directory Listing
Modified Thu Jul 16 06:49:19 2009 UTC (9 years, 9 months ago) by caltinay
Changed examples, tests and tutorials to save VTK files as .vtu instead .xml.
Visit doesn't know what to do with xml's and vtu is the proper extension
anyway.


Revision 2533 - Directory Listing
Modified Wed Jul 15 05:57:01 2009 UTC (9 years, 9 months ago) by gross
finley delivers now a status identifier of the mesh.

Revision 2532 - Directory Listing
Modified Fri Jul 10 01:13:44 2009 UTC (9 years, 9 months ago) by caltinay
libescriptreader: fixed a typo in configure script and added missing lib
to Makefile.


Revision 2531 - Directory Listing
Modified Thu Jul 9 23:56:57 2009 UTC (9 years, 9 months ago) by jfenwick
Setting always build on the api_epydoc target as a quick work around

Revision 2530 - Directory Listing
Modified Thu Jul 9 06:08:44 2009 UTC (9 years, 9 months ago) by jfenwick
Some changes relating to install from source.


Revision 2529 - Directory Listing
Modified Thu Jul 9 06:06:35 2009 UTC (9 years, 9 months ago) by jfenwick
Some changes to the install guide.
More work to do.

Revision 2528 - Directory Listing
Modified Wed Jul 8 23:27:49 2009 UTC (9 years, 9 months ago) by jfenwick
Added stand-alone example options file for install instructions.



Revision 2527 - Directory Listing
Modified Wed Jul 8 07:04:35 2009 UTC (9 years, 9 months ago) by lgao
endof line added.

Revision 2526 - Directory Listing
Modified Wed Jul 8 05:52:06 2009 UTC (9 years, 9 months ago) by caltinay
util: Updated saveESD to allow saving of time series. Combined with an update
of the visit plugin this fixes issue 325.


Revision 2525 - Directory Listing
Modified Wed Jul 8 03:41:15 2009 UTC (9 years, 9 months ago) by caltinay
libescriptreader: Added 'timestep increment' option to allow time series files
to be named like file.0, file.10, file.20 etc.


Revision 2524 - Directory Listing
Modified Wed Jul 8 00:39:26 2009 UTC (9 years, 9 months ago) by artak
Minimum size of the coarsest level matrix option added to solver options

Revision 2523 - Directory Listing
Modified Wed Jul 8 00:07:36 2009 UTC (9 years, 9 months ago) by jfenwick
Fixed bug in MPI form of mkDir


Revision 2522 - Directory Listing
Modified Tue Jul 7 06:17:47 2009 UTC (9 years, 9 months ago) by jfenwick
Split test_util_spatial_functions.py into three python files (it had three classes in it).
This reduces memory required to compile down to about 600Mb each as opposed to >1Gb.

This should not affect the tests performed.

Revision 2521 - Directory Listing
Modified Tue Jul 7 00:08:58 2009 UTC (9 years, 9 months ago) by jfenwick
Modified Lazy so that resolving a single sample uses the node cache method.
Fixed some doxygen problems.

Revision 2520 - Directory Listing
Modified Mon Jul 6 03:13:11 2009 UTC (9 years, 9 months ago) by artak
AMG now takes as an input Paso_options for selecting coarsenening algorithm and treshold variable.

Revision 2519 - Directory Listing
Modified Mon Jul 6 00:43:08 2009 UTC (9 years, 9 months ago) by jfenwick
Correcting some doxygen errors

Revision 2518 - Directory Listing
Modified Fri Jul 3 07:43:11 2009 UTC (9 years, 9 months ago) by gross
bug in setNewX fixed: now it is made sure that the FunctionSpace of the new coordinates is correct.

Revision 2517 - Directory Listing
Modified Fri Jul 3 05:27:45 2009 UTC (9 years, 9 months ago) by jfenwick
Fixed bug in Locator


Revision 2516 - Directory Listing
Modified Fri Jul 3 02:51:05 2009 UTC (9 years, 9 months ago) by gross
files are not needed anymore.


Revision 2515 - Directory Listing
Modified Fri Jul 3 00:59:05 2009 UTC (9 years, 9 months ago) by gross
missing files for documentation

Revision 2514 - Directory Listing
Modified Fri Jul 3 00:57:45 2009 UTC (9 years, 9 months ago) by jfenwick
Fixed compile warning on Mac



Revision 2513 - Directory Listing
Modified Thu Jul 2 08:42:11 2009 UTC (9 years, 9 months ago) by gross
some fixes in wave.py example

Revision 2512 - Directory Listing
Modified Thu Jul 2 05:34:14 2009 UTC (9 years, 9 months ago) by jfenwick
Made the warnings against linking gomp a bit more detailed.
Commented out gomp from the linux sample.

Revision 2511 - Directory Listing
Modified Thu Jul 2 05:16:19 2009 UTC (9 years, 9 months ago) by gross
more openmp

Revision 2510 - Directory Listing
Modified Thu Jul 2 05:15:59 2009 UTC (9 years, 9 months ago) by gross
fix for INTELMPI

Revision 2509 - Directory Listing
Modified Thu Jul 2 04:51:51 2009 UTC (9 years, 9 months ago) by artak
Now one can choose coarsening method from python for AMG. Some commented lines are removed.

Revision 2508 - Directory Listing
Modified Thu Jul 2 04:33:25 2009 UTC (9 years, 9 months ago) by jfenwick
Ensured that example files are copied with build_py_tests rather than py_tests.
This means that:
build_full
will set up all the files ready for utest.sh

Revision 2507 - Directory Listing
Modified Thu Jul 2 03:14:35 2009 UTC (9 years, 9 months ago) by artak
some profiling tools added

Revision 2506 - Directory Listing
Modified Thu Jul 2 01:23:30 2009 UTC (9 years, 9 months ago) by jfenwick
Fix to allow binary unit tests to run.
Note: I have only fixed the non-windows systems and I don't know if they
have the same problem.

Diagnosis of the utest problems continues.



Revision 2505 - Directory Listing
Modified Thu Jul 2 00:46:53 2009 UTC (9 years, 9 months ago) by lgao
adding config file for Lin's machine



Revision 2504 - Directory Listing
Modified Wed Jul 1 07:27:17 2009 UTC (9 years, 9 months ago) by jfenwick
First stage of fix to utest.sh


Revision 2503 - Directory Listing
Modified Wed Jul 1 05:05:08 2009 UTC (9 years, 9 months ago) by jfenwick
Fixing doc build so examples tar and zip are built properly.
Fixed image filenames in user guide.

Please do not put extensions on image files.



Revision 2502 - Directory Listing
Modified Tue Jun 30 05:49:22 2009 UTC (9 years, 9 months ago) by gross
tests for examples added. utest is not working yet.

Revision 2501 - Directory Listing
Modified Tue Jun 30 04:43:01 2009 UTC (9 years, 9 months ago) by jfenwick
Caching now works.
Number of levels and nodes permitted in a lazy expression has increased to 70 and 15000.

Revision 2500 - Directory Listing
Modified Tue Jun 30 00:42:38 2009 UTC (9 years, 9 months ago) by jfenwick
Experimental per node cache for lazy evaluation is now available via the 
LAZY_NODE_STORAGE #define 
It's a bit slower and larger for small problems but a bit faster and 
smaller for large (drucker prager) problems.


Revision 2499 - Directory Listing
Modified Mon Jun 29 04:31:00 2009 UTC (9 years, 9 months ago) by gross
new stand

Revision 2498 - Directory Listing
Modified Mon Jun 29 04:25:23 2009 UTC (9 years, 9 months ago) by gross
new function MaskFromTag

Revision 2497 - Directory Listing
Modified Mon Jun 29 00:04:45 2009 UTC (9 years, 9 months ago) by jfenwick
Calling resolve now replaces resolved expression with an identity node.


Revision 2496 - Directory Listing
Modified Fri Jun 26 06:09:47 2009 UTC (9 years, 9 months ago) by jfenwick
Added lazy version of swapaxes operation.

Revision 2495 - Directory Listing
Modified Fri Jun 26 03:39:21 2009 UTC (9 years, 9 months ago) by ahallam
Many revisions to Head Diff Documentation, One grammar correction to user guide.

Revision 2494 - Directory Listing
Modified Thu Jun 25 05:00:57 2009 UTC (9 years, 9 months ago) by ahallam
Many updates to onedheatdiff in example and documentation. Still in need of some TLC however.

Revision 2493 - Directory Listing
Modified Thu Jun 25 02:58:52 2009 UTC (9 years, 9 months ago) by jfenwick
Taipan now prints an error message if new[] throws.
Note, the exception is rethrown after the message is printed.


Revision 2492 - Directory Listing
Modified Wed Jun 24 01:28:57 2009 UTC (9 years, 9 months ago) by gross
MPI_DOUBLE changed to MPI_INT as lowProc is int

Revision 2491 - Directory Listing
Modified Wed Jun 24 00:03:08 2009 UTC (9 years, 9 months ago) by gross
some modifications to the OPENMPI launcher.

Revision 2490 - Directory Listing
Modified Tue Jun 23 06:02:26 2009 UTC (9 years, 9 months ago) by artak
adjusting to new Paso_Options.

Revision 2489 - Directory Listing
Modified Tue Jun 23 06:00:25 2009 UTC (9 years, 9 months ago) by artak
void *solver; is added to Paso_SpaseMatrix struct. Paso_MKL will need this.

Revision 2488 - Directory Listing
Modified Tue Jun 23 05:56:33 2009 UTC (9 years, 9 months ago) by artak
Paso_MKL1 supports Paso_SparseMatrix type with offset1

Revision 2487 - Directory Listing
Modified Tue Jun 23 04:26:07 2009 UTC (9 years, 9 months ago) by jfenwick
Fixed const-ness on some return values.
Null-Domain now reports tag one as being in use.

Revision 2486 - Directory Listing
Modified Tue Jun 23 03:38:54 2009 UTC (9 years, 9 months ago) by gross
a bit more info are printed for the DarcyFlux now.

Revision 2485 - Directory Listing
Modified Mon Jun 22 07:27:31 2009 UTC (9 years, 9 months ago) by jfenwick
Added unit test file.


Revision 2484 - Directory Listing
Modified Mon Jun 22 04:22:19 2009 UTC (9 years, 9 months ago) by gross
numarray removed from docu; Locator revised.

Revision 2483 - Directory Listing
Modified Mon Jun 22 03:33:43 2009 UTC (9 years, 9 months ago) by jfenwick
And Joel closes the barn door.


Revision 2482 - Directory Listing
Modified Fri Jun 19 05:56:20 2009 UTC (9 years, 10 months ago) by jfenwick
Added run_data_access.py to unit tests - tests things like toListOfTuples.
Corrected some doco comments.
Added TestDomain class to escript.
This should allow more testing without resorting to finley.

Revision 2481 - Directory Listing
Modified Fri Jun 19 04:29:06 2009 UTC (9 years, 10 months ago) by jfenwick
Corrected a comment and fixed more bugs in the bulk copyFromArrayToOffset method.

Revision 2480 - Directory Listing
Modified Fri Jun 19 03:35:14 2009 UTC (9 years, 10 months ago) by gross
test fixed.

Revision 2479 - Directory Listing
Modified Thu Jun 18 06:50:37 2009 UTC (9 years, 10 months ago) by gross
paso returns now some diagnostics. SCSL has been removed.


Revision 2478 - Directory Listing
Modified Thu Jun 18 06:20:57 2009 UTC (9 years, 10 months ago) by jfenwick
Fixed bug when creating scalar expanded data.
Fixed some comments and moved a variable into anonymous namespace

Revision 2477 - Directory Listing
Modified Wed Jun 17 06:22:15 2009 UTC (9 years, 10 months ago) by gross
modification to the cookbook

Revision 2476 - Directory Listing
Modified Wed Jun 17 04:42:13 2009 UTC (9 years, 10 months ago) by jfenwick
Added maxGlobalDataPoint.
Not currently unit tested.

Revision 2475 - Directory Listing
Modified Wed Jun 17 01:48:46 2009 UTC (9 years, 10 months ago) by artak
AMG now takes into account new SolverOptions class, namely one can select coarsening algorithms from python. Not all options are included into AMG, this will be implemented later on.

Revision 2474 - Directory Listing
Modified Tue Jun 16 06:32:15 2009 UTC (9 years, 10 months ago) by gross
linearPDEs has is now using the SolverOptions class to talk to PASO

Revision 2473 - Directory Listing
Modified Mon Jun 15 02:21:07 2009 UTC (9 years, 10 months ago) by jfenwick
Change logging functions so I don't get confused about what they do.
Added parameter to name the log file if called directly.

Revision 2472 - Directory Listing
Modified Thu Jun 11 23:33:47 2009 UTC (9 years, 10 months ago) by jfenwick
Added new params to control auto resolving for lazy data

Revision 2471 - Directory Listing
Modified Thu Jun 11 23:33:06 2009 UTC (9 years, 10 months ago) by jfenwick
Fixed extract of ndarray from xml to properly return booleans.
Modified some strings which had numarray:: in them

Revision 2470 - Directory Listing
Modified Thu Jun 11 08:32:32 2009 UTC (9 years, 10 months ago) by gross
SolverOption class added. It is not linked with anything.

Revision 2469 - Directory Listing
Modified Thu Jun 11 04:52:14 2009 UTC (9 years, 10 months ago) by ahallam
Week 11: Close to finishing wave equation, looking at adding friction to wave equation.

Revision 2468 - Directory Listing
Modified Thu Jun 11 02:55:51 2009 UTC (9 years, 10 months ago) by gross
some more work toward numpy

Revision 2467 - Directory Listing
Modified Tue Jun 9 23:12:04 2009 UTC (9 years, 10 months ago) by jfenwick
Fixed a missing file.


Revision 2466 - Directory Listing
Modified Tue Jun 9 05:02:56 2009 UTC (9 years, 10 months ago) by jfenwick
Fixed build from source instructions for linux to include offscreen rendering by default!

Revision 2465 - Directory Listing
Modified Tue Jun 9 05:01:36 2009 UTC (9 years, 10 months ago) by jfenwick
Changed the default behaviour of Data::toListOfTuples() so that scalars are returned in tuples.
This is to match the behaviour of getTupleForDataPoint.

Revision 2464 - Directory Listing
Modified Tue Jun 9 04:14:07 2009 UTC (9 years, 10 months ago) by artak
updated to use openmpi

Revision 2463 - Directory Listing
Modified Tue Jun 9 03:51:23 2009 UTC (9 years, 10 months ago) by jfenwick
Added an svn-ignore, added changes and references section to user guide.

Revision 2462 - Directory Listing
Modified Fri Jun 5 06:04:01 2009 UTC (9 years, 10 months ago) by jfenwick
Modified wrapper script to correctly point at numpy in standalone builds.
Updated build from source doco for linux to take numpy into account.
Also removed backticks in favour of $()  - it should be the same but latex won't eat them

Revision 2461 - Directory Listing
Modified Fri Jun 5 05:06:31 2009 UTC (9 years, 10 months ago) by jfenwick
Trying to presize a list to reduce runtime of toListOfTuples


Revision 2460 - Directory Listing
Modified Fri Jun 5 05:04:45 2009 UTC (9 years, 10 months ago) by ahallam
Week 10:
Continued work on wave equation and tutorial write up.

Revision 2459 - Directory Listing
Modified Thu Jun 4 06:17:54 2009 UTC (9 years, 10 months ago) by jfenwick
Removed some commented out code.
Added toListOfTuples to the DataObject.

Revision 2458 - Directory Listing
Modified Wed Jun 3 06:18:21 2009 UTC (9 years, 10 months ago) by jfenwick
Various numarray erasures


Revision 2456 - Directory Listing
Modified Wed Jun 3 03:54:25 2009 UTC (9 years, 10 months ago) by jfenwick
Switching savanna scons to use python-2.6.2 and boost-1.39


Revision 2455 - Directory Listing
Modified Wed Jun 3 03:29:07 2009 UTC (9 years, 10 months ago) by jfenwick
Merging changes from numpy branch.


Revision 2450 - Directory Listing
Modified Tue Jun 2 01:22:11 2009 UTC (9 years, 10 months ago) by artak
First version of 'greedy' algorithm for Ruge Stuben and Aggregiation.

Revision 2448 - Directory Listing
Modified Fri May 29 04:47:48 2009 UTC (9 years, 10 months ago) by ahallam
Week 9: implemented cosine taper for wave function, need to work on direct method without lumping, wave propagation velocity is still not correct

Revision 2447 - Directory Listing
Modified Fri May 29 04:32:53 2009 UTC (9 years, 10 months ago) by artak
minor

Revision 2446 - Directory Listing
Modified Fri May 29 04:24:01 2009 UTC (9 years, 10 months ago) by gross
same adjustment of nameing

Revision 2445 - Directory Listing
Modified Fri May 29 03:23:25 2009 UTC (9 years, 10 months ago) by gross
some improvement on convection which ios now working again

Revision 2444 - Directory Listing
Modified Fri May 29 01:51:28 2009 UTC (9 years, 10 months ago) by ahallam


Revision 2443 - Directory Listing
Modified Fri May 29 01:44:22 2009 UTC (9 years, 10 months ago) by ahallam
Fixing some things

Revision 2442 - Directory Listing
Modified Fri May 29 00:39:44 2009 UTC (9 years, 10 months ago) by artak
Some bugs are fixed.

Revision 2440 - Directory Listing
Modified Wed May 27 08:45:55 2009 UTC (9 years, 10 months ago) by gross
convection works now again.

Revision 2439 - Directory Listing
Modified Tue May 26 04:34:21 2009 UTC (9 years, 10 months ago) by artak
AMG now works with blocksize 3. Logical block sizes replaced with real block size before starting AMG. But this happens only when we use AMG as a preconditioner.

Revision 2438 - Directory Listing
Modified Tue May 26 02:26:52 2009 UTC (9 years, 10 months ago) by gross
new version of power law (blame Hans)

Revision 2436 - Directory Listing
Modified Mon May 25 05:05:00 2009 UTC (9 years, 10 months ago) by jfenwick
A fix for escript not compiling on boost 1.39.


Revision 2434 - Directory Listing
Modified Thu May 21 07:59:53 2009 UTC (9 years, 11 months ago) by ahallam
Week 8: Still working on seismic wave propagation. Need to come up with a smooth source function next week. All TEXT files up to date.

Revision 2433 - Directory Listing
Modified Wed May 20 08:43:43 2009 UTC (9 years, 11 months ago) by gross
some documentation on power law added

Revision 2432 - Directory Listing
Modified Wed May 20 06:06:20 2009 UTC (9 years, 11 months ago) by gross
power law and incompressible flow is running now

Revision 2431 - Directory Listing
Modified Wed May 20 03:39:57 2009 UTC (9 years, 11 months ago) by jfenwick
Added at the request of Dian.


Revision 2430 - Directory Listing
Modified Wed May 20 03:20:57 2009 UTC (9 years, 11 months ago) by jfenwick
Use Variables class instead of Options in scons versions which support 
it.


Revision 2429 - Directory Listing
Modified Tue May 19 10:04:54 2009 UTC (9 years, 11 months ago) by gross
pycad allows noe to set the number of elements per line and the generation of quadrilateral elements over serfaces.

Revision 2428 - Directory Listing
Modified Tue May 19 04:04:11 2009 UTC (9 years, 11 months ago) by gross
problem for python2.4 fixed: IOError has no attribute message.

Revision 2427 - Directory Listing
Modified Fri May 15 04:29:01 2009 UTC (9 years, 11 months ago) by ahallam
Week 7: Work done on wave problem.

Revision 2426 - Directory Listing
Modified Fri May 15 04:28:31 2009 UTC (9 years, 11 months ago) by ahallam
Week 7: Work done on wave problem.

Revision 2425 - Directory Listing
Modified Thu May 14 09:06:35 2009 UTC (9 years, 11 months ago) by gross
bug in getListOfTags fixed and some tested added

Revision 2424 - Directory Listing
Modified Thu May 14 05:15:47 2009 UTC (9 years, 11 months ago) by gross
small bug fixed.

Revision 2423 - Directory Listing
Modified Thu May 14 05:02:20 2009 UTC (9 years, 11 months ago) by gross
* handling LD_LIBRARY_PATH for Windows (that only uses PATH)
* passing PATH env var in mpi call for Windows

Revision 2422 - Directory Listing
Modified Thu May 14 03:17:28 2009 UTC (9 years, 11 months ago) by gross
bug in testing saveVTK fixed

Revision 2421 - Directory Listing
Modified Thu May 14 02:29:06 2009 UTC (9 years, 11 months ago) by gross
vtk writer supports now meta data and meta data schema

Revision 2420 - Directory Listing
Modified Thu May 14 02:28:58 2009 UTC (9 years, 11 months ago) by gross
vtk writer supports now meta data and meta data schema

Revision 2419 - Directory Listing
Modified Thu May 14 01:56:18 2009 UTC (9 years, 11 months ago) by jfenwick
Use os.path.join instead of os.sep in tests
If you can read this message it means svn commit mails are working again.
... Or you are looking at the logs

Revision 2418 - Directory Listing
Modified Wed May 13 08:36:04 2009 UTC (9 years, 11 months ago) by gross
redirect stdout to NULL instead of /dev/null for Windows

Revision 2417 - Directory Listing
Modified Wed May 13 08:18:47 2009 UTC (9 years, 11 months ago) by gross
some remarks on load and dump added to the users guide.

Revision 2416 - Directory Listing
Modified Wed May 13 06:03:59 2009 UTC (9 years, 11 months ago) by gross
* fix Windows MPI case: export system variables
* define ESCRIPT_NUM_PROC and ESCRIPT_NUM_NODES
* cleanup using os.path.join()

Revision 2415 - Directory Listing
Modified Wed May 13 02:48:39 2009 UTC (9 years, 11 months ago) by gross
FileWriter added: this class takes care of writing data which are global in MPI to a file. It is recommended to use this class rather then the build in open as it takes care of the case of many processors.

Revision 2414 - Directory Listing
Modified Tue May 12 03:33:49 2009 UTC (9 years, 11 months ago) by gross
added flags (commented out) to compile MPI version on Windows (Visual Studio 2003) using MPICH2

Revision 2413 - Directory Listing
Modified Tue May 12 01:26:20 2009 UTC (9 years, 11 months ago) by artak
There was a bug in computing logical_block_size. It was always returning 0.

Revision 2412 - Directory Listing
Modified Fri May 8 04:27:17 2009 UTC (9 years, 11 months ago) by jfenwick
Clean up cookbook-
Cleaned up the svn:ignore
removed some latex intermediate files


Revision 2411 - Directory Listing
Modified Fri May 8 03:13:15 2009 UTC (9 years, 11 months ago) by ahallam
Week 6 I think?? Started work on 2d wave solution, want to change from verlet according to lutz. Have semi finished heat diffusion but is ready for review and further modification in the future. Added new sections to first chapter, may or may not be needed but added as a reminder anyway.

Revision 2409 - Directory Listing
Modified Tue May 5 06:22:11 2009 UTC (9 years, 11 months ago) by jfenwick
bin/escript is now under version control.
The wrapper template is no longer used.
Extraneous output doc removed from scons during build.

note: finleypython is no longer built (it was deprecated anyway).

Revision 2405 - Directory Listing
Modified Wed Apr 29 23:57:38 2009 UTC (9 years, 11 months ago) by jfenwick
Another attempt at building the doco.
--transform is not supported by savanna's tar


Revision 2404 - Directory Listing
Modified Wed Apr 29 06:53:36 2009 UTC (9 years, 11 months ago) by gross
documentation for units added.

Revision 2403 - Directory Listing
Modified Wed Apr 29 06:08:18 2009 UTC (9 years, 11 months ago) by gross
units support Celsius, Farenheit and kelvin now

Revision 2402 - Directory Listing
Modified Wed Apr 29 06:02:21 2009 UTC (9 years, 11 months ago) by jfenwick
Fixing the build of example tar and zip files so they don't have full 
paths.


Revision 2401 - Directory Listing
Modified Wed Apr 29 04:23:07 2009 UTC (9 years, 11 months ago) by ahallam
End Week 5:
Renamed *.tex files to more logical, changed to chapter format as HEAT_DIFFUSION.tex
Editted and Reviewed text portion and some python scripts for heat diffusion.
Looking to push for finalisation on heat diffusion in the next couple of week to begin next modelling problem/Chapter.

Revision 2399 - Directory Listing
Modified Tue Apr 28 12:04:34 2009 UTC (9 years, 11 months ago) by gross
some improvements on units

Revision 2398 - Directory Listing
Modified Tue Apr 28 04:41:53 2009 UTC (9 years, 11 months ago) by gross
first version of units in escript




Revision 2397 - Directory Listing
Modified Fri Apr 24 04:24:28 2009 UTC (9 years, 11 months ago) by ahallam
End Week 4, Finalised 1D examples, need work on text but script ok.
Begining of 2D example builds on 1D. Script semi-finalised, text to complete.

Revision 2394 - Directory Listing
Modified Fri Apr 17 01:32:30 2009 UTC (10 years ago) by caltinay
Updated shake75 options file.


Revision 2393 - Directory Listing
Modified Thu Apr 16 04:24:07 2009 UTC (10 years ago) by ahallam
End Day Commit
Working on onedheatdiff_var001

Revision 2392 - Directory Listing
Modified Thu Apr 16 01:53:23 2009 UTC (10 years ago) by ahallam
Initial Commital of CookBook to SVN
Has 2.5 Weeks work and semi completed first heat diffusion tutorial

Revision 2391 - Directory Listing
Modified Thu Apr 16 01:08:57 2009 UTC (10 years ago) by jfenwick
Minor tweak to title page.
Better handling of alternative names in SConstruct.


Revision 2390 - Directory Listing
Modified Wed Apr 15 06:46:42 2009 UTC (10 years ago) by gross
some minor fixes.

Revision 2389 - Directory Listing
Modified Wed Apr 15 06:46:01 2009 UTC (10 years ago) by gross
some minor fixes.

Revision 2388 - Directory Listing
Modified Wed Apr 15 06:21:25 2009 UTC (10 years ago) by jfenwick
scons files executed on compute nodes will use the config file for the service node (when we get the other issues 
sorted).


Revision 2387 - Directory Listing
Modified Wed Apr 15 05:05:27 2009 UTC (10 years ago) by jfenwick
Changed the figure eps->pdf to use a builder to make hypothetical windows doc building easier.

Revision 2386 - Directory Listing
Modified Wed Apr 15 03:54:25 2009 UTC (10 years ago) by gross
some minor fixes

Revision 2385 - Directory Listing
Modified Wed Apr 15 03:52:38 2009 UTC (10 years ago) by gross
two fixes dealing with zero samples under MPI

Revision 2384 - Directory Listing
Modified Wed Apr 15 00:17:20 2009 UTC (10 years ago) by jfenwick
Added getDataRW to DataC

Revision 2383 - Directory Listing
Modified Tue Apr 14 03:53:56 2009 UTC (10 years ago) by artak
-h parameter added for help

Revision 2382 - Directory Listing
Modified Tue Apr 14 03:48:22 2009 UTC (10 years ago) by artak
Testing environment now mor flexible. Added a lot of options.

Revision 2381 - Directory Listing
Modified Tue Apr 14 03:46:59 2009 UTC (10 years ago) by artak
Ruge Stuben and Aggregiation is added for testing performance of AMG solver.

Revision 2380 - Directory Listing
Modified Tue Apr 14 03:23:29 2009 UTC (10 years ago) by artak
minor typo

Revision 2379 - Directory Listing
Modified Thu Apr 9 07:36:55 2009 UTC (10 years ago) by gross
type fixed.

Revision 2378 - Directory Listing
Modified Thu Apr 9 01:09:08 2009 UTC (10 years ago) by jfenwick
Added warning when openmp params are specified by escript was build without openmp.
escript now reports the number of threads requested. 


Revision 2377 - Directory Listing
Modified Wed Apr 8 07:57:55 2009 UTC (10 years ago) by gross
a namespace  problem in pycad fixed.

Revision 2376 - Directory Listing
Modified Tue Apr 7 06:21:31 2009 UTC (10 years ago) by gross
output form others than the master process can now be switched off (stderr is still redirected to master)

Revision 2375 - Directory Listing
Modified Tue Apr 7 04:41:28 2009 UTC (10 years ago) by gross
MPI hints added

Revision 2374 - Directory Listing
Modified Tue Apr 7 00:26:49 2009 UTC (10 years ago) by jfenwick
Modified utest to use the wrapper script.


Revision 2373 - Directory Listing
Modified Mon Apr 6 23:49:31 2009 UTC (10 years ago) by jfenwick
Minor spelling and man page tweaks.


Revision 2372 - Directory Listing
Modified Mon Apr 6 23:36:15 2009 UTC (10 years ago) by gross
changes to the urls

Revision 2371 - Directory Listing
Modified Mon Apr 6 11:48:32 2009 UTC (10 years ago) by gross
missing  citations and references added

Revision 2370 - Directory Listing
Modified Mon Apr 6 06:41:49 2009 UTC (10 years ago) by gross
some modifications to docu for MPI

Revision 2369 - Directory Listing
Modified Mon Apr 6 05:32:12 2009 UTC (10 years ago) by gross
some fixed for mpich2

Revision 2368 - Directory Listing
Modified Mon Apr 6 05:05:35 2009 UTC (10 years ago) by gross
some fixes for MKL and Mpisize>1

Revision 2367 - Directory Listing
Modified Mon Apr 6 04:51:49 2009 UTC (10 years ago) by jfenwick
Added version number to deb files.
Fixed tests to check for ppmtompeg before running

Revision 2366 - Directory Listing
Modified Mon Apr 6 03:10:55 2009 UTC (10 years ago) by gross
starter for MPICH and MPICH2 add

Revision 2365 - Directory Listing
Modified Mon Apr 6 01:25:25 2009 UTC (10 years ago) by gross
all tests passed under scons on 4 mpi processes with  openmpi on shake34

Revision 2364 - Directory Listing
Modified Fri Apr 3 08:06:30 2009 UTC (10 years ago) by gross
MPI intel works now for the escript wrapper.

Revision 2363 - Directory Listing
Modified Fri Apr 3 03:56:19 2009 UTC (10 years ago) by gross
scons should now be able to run tests under MPI and OpenMP

Revision 2362 - Directory Listing
Modified Fri Apr 3 02:41:14 2009 UTC (10 years ago) by gross
escript wrapper does not use Compiled.with.*

Revision 2361 - Directory Listing
Modified Fri Apr 3 00:37:25 2009 UTC (10 years ago) by jfenwick
Hopefully fixing the bad figures.
It turns out latex2html can not handle the optional angle= param in 
\includegraphics


Revision 2360 - Directory Listing
Modified Thu Apr 2 04:12:12 2009 UTC (10 years ago) by artak
AMG now checks how many elemens left. if n_F<500, then it does not coursen further.

Revision 2359 - Directory Listing
Modified Thu Apr 2 03:50:33 2009 UTC (10 years ago) by jfenwick
Moved man page for easier testing.
Modified the wrapper script to take into account debian packaging.
This setting is recorded in the escript wrapper automatically by the package building script.

Revision 2358 - Directory Listing
Modified Wed Apr 1 22:25:24 2009 UTC (10 years ago) by gross
mpi is not really ready yet.

Revision 2357 - Directory Listing
Modified Wed Apr 1 06:01:56 2009 UTC (10 years ago) by gross
fixes to run escript command with SGI MPT

Revision 2356 - Directory Listing
Modified Wed Apr 1 04:46:22 2009 UTC (10 years ago) by gross
more on escript command.

Revision 2355 - Directory Listing
Modified Wed Apr 1 04:08:28 2009 UTC (10 years ago) by gross
intel MPI added.

Revision 2354 - Directory Listing
Modified Wed Apr 1 04:01:58 2009 UTC (10 years ago) by gross
some modifications to the Darcy flux solver to make it faster and more robust.

Revision 2353 - Directory Listing
Modified Wed Apr 1 01:49:47 2009 UTC (10 years ago) by artak
AMG levels parameter moved to options file. Now one can set how many levels AMG will go in SetDefauls. Default value is 3.

Revision 2352 - Directory Listing
Modified Wed Apr 1 01:15:15 2009 UTC (10 years ago) by jfenwick
Updated doco to reflect changed env variables


Revision 2351 - Directory Listing
Modified Tue Mar 31 08:26:41 2009 UTC (10 years ago) by gross
some fixes in the transport solver

Revision 2350 - Directory Listing
Modified Tue Mar 31 08:26:05 2009 UTC (10 years ago) by gross
more escript wrapper stuff

Revision 2349 - Directory Listing
Modified Mon Mar 30 08:14:23 2009 UTC (10 years ago) by gross
first version of escript command: no MPI support yet.

Revision 2348 - Directory Listing
Modified Mon Mar 30 06:27:14 2009 UTC (10 years ago) by gross
obsolet

Revision 2347 - Directory Listing
Modified Mon Mar 30 06:07:47 2009 UTC (10 years ago) by jfenwick
Added windows notes to install guide.


Revision 2346 - Directory Listing
Modified Mon Mar 30 05:05:44 2009 UTC (10 years ago) by jfenwick
Added instructions to test installations.


Revision 2345 - Directory Listing
Modified Mon Mar 30 04:44:06 2009 UTC (10 years ago) by jfenwick
Added proper man page (with formatting and everything).
Updated package description.


Revision 2344 - Directory Listing
Modified Mon Mar 30 02:13:58 2009 UTC (10 years ago) by jfenwick
Change __url__ to launchpad site


Revision 2343 - Directory Listing
Modified Mon Mar 30 01:34:45 2009 UTC (10 years ago) by jfenwick
Added -b option to wrapper script. For the running of non-python 
binaries.


Revision 2342 - Directory Listing
Modified Sun Mar 29 23:28:55 2009 UTC (10 years ago) by jfenwick
No comment.


Revision 2341 - Directory Listing
Modified Fri Mar 27 05:40:56 2009 UTC (10 years ago) by jfenwick


Revision 2340 - Directory Listing
Modified Fri Mar 27 05:32:05 2009 UTC (10 years ago) by jfenwick
And again

Revision 2339 - Directory Listing
Modified Fri Mar 27 05:14:55 2009 UTC (10 years ago) by jfenwick
Fixing a bug preventing docs from building

Revision 2338 - Directory Listing
Modified Fri Mar 27 05:01:49 2009 UTC (10 years ago) by jfenwick
Added vars for mpi_flavour
Output correct version into the user guide

Revision 2337 - Directory Listing
Modified Thu Mar 26 07:07:42 2009 UTC (10 years ago) by gross
Transport class uses now useBackwardEuler rather than the mysterious theta.

Revision 2336 - Directory Listing
Modified Thu Mar 26 06:09:20 2009 UTC (10 years ago) by jfenwick
Fixed title for pdf builds.
All the peices build now. (There are still issues with Figure 1.7 in the html version).

Revision 2335 - Directory Listing
Modified Thu Mar 26 04:33:44 2009 UTC (10 years ago) by jfenwick
The user guide now builds under pdflatex (if you have converted the figures). Unfortunately, it has a really ugly title.

Revision 2334 - Directory Listing
Modified Thu Mar 26 03:05:33 2009 UTC (10 years ago) by jfenwick
Getting install guide to build.


Revision 2333 - Directory Listing
Modified Wed Mar 25 02:15:11 2009 UTC (10 years ago) by jfenwick
Minor format tweaks.
All relevant info from the twiki install page now copied.
(Except INSTALL.SGI_ICE)


Revision 2332 - Directory Listing
Modified Tue Mar 24 01:13:08 2009 UTC (10 years ago) by jfenwick
Added new options to the escript wrapper.
This populates all the variables described in the documentation but does 
not necessarily do anything with them.

Fixed minor typo in doco.


Revision 2331 - Directory Listing
Modified Mon Mar 23 01:18:21 2009 UTC (10 years ago) by jfenwick
Updated the escript execution section.
Added a few references.

Revision 2330 - Directory Listing
Modified Mon Mar 23 01:18:03 2009 UTC (10 years ago) by artak
RILU changed to Jacobi in accordance with mantis bug reported a while ago

Revision 2329 - Directory Listing
Modified Mon Mar 23 00:42:57 2009 UTC (10 years ago) by artak
minor

Revision 2328 - Directory Listing
Modified Fri Mar 20 03:40:56 2009 UTC (10 years, 1 month ago) by artak
Added a section on installing using Macports. in srclinux.tex $ replaced by $

Revision 2327 - Directory Listing
Modified Thu Mar 19 06:01:26 2009 UTC (10 years, 1 month ago) by artak
Mac OS X development tools instructions are added.

Revision 2326 - Directory Listing
Modified Thu Mar 19 05:34:00 2009 UTC (10 years, 1 month ago) by artak
Instructions on how to install on Mac from source.

Revision 2325 - Directory Listing
Modified Thu Mar 19 05:32:13 2009 UTC (10 years, 1 month ago) by gross
tests for Lame equation added.

Revision 2324 - Directory Listing
Modified Thu Mar 19 04:35:30 2009 UTC (10 years, 1 month ago) by jfenwick
Fixed some non-portable paths in SConstruct.
Added section links for compiling only escript.

Revision 2323 - Directory Listing
Modified Thu Mar 19 04:23:32 2009 UTC (10 years, 1 month ago) by gross
test for Helmholtz added

Revision 2322 - Directory Listing
Modified Thu Mar 19 04:13:21 2009 UTC (10 years, 1 month ago) by gross
ops

Revision 2321 - Directory Listing
Modified Thu Mar 19 04:08:59 2009 UTC (10 years, 1 month ago) by artak
Mac instructions for binary bundle.

Revision 2320 - Directory Listing
Modified Thu Mar 19 03:40:16 2009 UTC (10 years, 1 month ago) by gross
some modifictaions to make sure that Mesh_merge.c Mesh_glueFaces.c Mesh_joinFaces.c reject to work under MPI

Revision 2319 - Directory Listing
Modified Thu Mar 19 03:19:41 2009 UTC (10 years, 1 month ago) by gross
some more work on tests on MPI

Revision 2318 - Directory Listing
Modified Thu Mar 19 03:18:11 2009 UTC (10 years, 1 month ago) by gross
more on MPI in the users guide.

Revision 2317 - Directory Listing
Modified Thu Mar 19 01:48:00 2009 UTC (10 years, 1 month ago) by jfenwick
Adding Content.


Revision 2316 - Directory Listing
Modified Thu Mar 19 01:22:15 2009 UTC (10 years, 1 month ago) by gross
some documentation on the escript wrapper added.

Revision 2315 - Directory Listing
Modified Wed Mar 18 00:38:48 2009 UTC (10 years, 1 month ago) by gross
fixes for MPI

Revision 2314 - Directory Listing
Modified Tue Mar 17 04:16:24 2009 UTC (10 years, 1 month ago) by gross
proper error handling for ppn2mpeg execution added.



Revision 2313 - Directory Listing
Modified Tue Mar 17 03:41:17 2009 UTC (10 years, 1 month ago) by gross
pyvisi is now rejecting to work under MPI with more than 1 processor. Tests for this configuration are dropped now.




Revision 2312 - Directory Listing
Modified Tue Mar 17 01:42:02 2009 UTC (10 years, 1 month ago) by jfenwick
Made the standalone setup a bit more generic.


Revision 2311 - Directory Listing
Modified Mon Mar 16 23:00:08 2009 UTC (10 years, 1 month ago) by jfenwick
Fixed a bug causing Mac crashes.


Revision 2310 - Directory Listing
Modified Mon Mar 16 04:07:43 2009 UTC (10 years, 1 month ago) by gross
some modifications to the test to fix a problem cased by reordering in MPI



Revision 2309 - Directory Listing
Modified Mon Mar 16 02:42:13 2009 UTC (10 years, 1 month ago) by caltinay
Fixed a typo affecting OpenMP usage.


Revision 2308 - Directory Listing
Modified Mon Mar 16 01:20:56 2009 UTC (10 years, 1 month ago) by gross
size_t may be 64 bits which is incompatible to MPI_INT. This problem is fixed by inserting a cast in Mesh_read.c. 
Moreover a fix has been added making sure that gmsh and triangle are executed on one processor only.




Revision 2307 - Directory Listing
Modified Mon Mar 16 00:38:09 2009 UTC (10 years, 1 month ago) by artak
some clean up. RS and Aggregiation are removed.

Revision 2306 - Directory Listing
Modified Mon Mar 16 00:23:57 2009 UTC (10 years, 1 month ago) by artak
verbose added

Revision 2305 - Directory Listing
Modified Mon Mar 16 00:19:41 2009 UTC (10 years, 1 month ago) by artak
verbose option is added

Revision 2304 - Directory Listing
Modified Fri Mar 13 03:17:24 2009 UTC (10 years, 1 month ago) by gross
a more robust way of doing whereZero and whereNotZero.

Revision 2303 - Directory Listing
Modified Fri Mar 13 01:34:36 2009 UTC (10 years, 1 month ago) by artak
This was the troublemaker for test failures on both MAC and Debian. I think numarry has a bug in memory managment. So we removed some numarray.array related lines in _givapp function and tests pass again.

Revision 2302 - Directory Listing
Modified Thu Mar 12 04:40:03 2009 UTC (10 years, 1 month ago) by jfenwick
Debian/ubuntu package now includes the user guide and the python doco (but not the c++) as well as the examples.tar.gz.
A file called buildvars is now written to the lib directory.
It contains some configuration things I can easily get in python.

Feel free to add additional ones.

Revision 2301 - Directory Listing
Modified Thu Mar 12 01:35:26 2009 UTC (10 years, 1 month ago) by gross
test for power law added

Revision 2300 - Directory Listing
Modified Wed Mar 11 08:17:57 2009 UTC (10 years, 1 month ago) by gross
a power law model. tests still need to be added and needs to be linked with an incompressible solver.

Revision 2299 - Directory Listing
Modified Wed Mar 11 03:14:41 2009 UTC (10 years, 1 month ago) by jfenwick
Modified script template to explcitly require bash (because of the 
bash-ism I'm using).
Wrapper script also sets up environment for standalone builds if the 
STANDALONE variable is set.

utest.sh will now be generated with executable bit set.


Revision 2298 - Directory Listing
Modified Sun Mar 8 23:45:29 2009 UTC (10 years, 1 month ago) by jfenwick
wrapper script construction does not record callers environment.

Revision 2297 - Directory Listing
Modified Fri Mar 6 04:46:14 2009 UTC (10 years, 1 month ago) by jfenwick
SConstruct now records the version of python used to build.
The wrapper script now checks (where possible) and exits with a warning 
if the versions do not match.


Revision 2296 - Directory Listing
Modified Thu Mar 5 05:47:34 2009 UTC (10 years, 1 month ago) by jfenwick
The escript wrapper now determines ESCRIPT_ROOT based on the position of the 
script rather than the value inserted at compile time.
This is one step towards making binary releases less tied to a known location.

SConstruct now keeps escript root at the front of LD_LIBRARY_PATH and PYTHONPATH

The wrapper script now accepts a -e arguement.
This doesn't actually run anything but outputs a set of exports which one can 
eval to give you the same environment as the wrapper.



Revision 2295 - Directory Listing
Modified Wed Mar 4 05:18:28 2009 UTC (10 years, 1 month ago) by jfenwick
Modified SConstruct to be smarter about when it puts /boost on the end 
of paths.


Revision 2294 - Directory Listing
Modified Mon Mar 2 03:44:27 2009 UTC (10 years, 1 month ago) by jfenwick
Added instructions on how to install debian package to the install guide.
Wrapper script generation now produces two scripts (escript and finleypython).
The two are identical - eventually we will remove finleypython.

Modified the wrapper script so it will print a message and start the python interpreter if you don't specify a script.

Revision 2293 - Directory Listing
Modified Fri Feb 27 05:34:51 2009 UTC (10 years, 1 month ago) by jfenwick
Cleaned up the dependencies.
The builddeb script puts fewer libraries in escript/lib and doesn't depend on dev packages on g++.

Revision 2292 - Directory Listing
Modified Fri Feb 27 02:07:43 2009 UTC (10 years, 1 month ago) by jfenwick
Disabling default use of OpenMP in SConstruct.
I have set the option in service0_options so savanna should build as before.

If you are expecting OpenMP by default on any other machine please adjust your options files accordingly.



Revision 2291 - Directory Listing
Modified Fri Feb 27 01:53:06 2009 UTC (10 years, 1 month ago) by jfenwick
Added scripts and such for building debian packages against Debian/Lenny.
Some things like the man page and the package description need some work but the packages produced appear to work.

If people are going to produce .debs please read read the packaging/lenny/README_developers_this_means_you

file.



Revision 2290 - Directory Listing
Modified Thu Feb 26 06:38:16 2009 UTC (10 years, 1 month ago) by jfenwick
Some minor changes to doco before I mess about with packaging.

Revision 2289 - Directory Listing
Modified Wed Feb 25 03:38:59 2009 UTC (10 years, 1 month ago) by jfenwick
Main compilation page copied from twiki.

Revision 2288 - Directory Listing
Modified Tue Feb 24 06:11:48 2009 UTC (10 years, 1 month ago) by gross
a new idea for the sacling factor

Revision 2287 - Directory Listing
Modified Tue Feb 24 04:29:17 2009 UTC (10 years, 1 month ago) by jfenwick
Added skeleton of install guide.
Removed some files which come in the standard texlive distro anyway.
Updated README_LICENSE to list python tex styles.

Revision 2286 - Directory Listing
Modified Mon Feb 23 02:50:06 2009 UTC (10 years, 1 month ago) by jfenwick
Added build_full target. This will build escript, the unit test binaries 
and compile all the python files.
This should be called before using utest.sh.

Added gcc openmp params for badger


Revision 2285 - Directory Listing
Modified Fri Feb 20 06:02:30 2009 UTC (10 years, 1 month ago) by jfenwick
Modified the escript python module.
If the escriptExitProfiling environment variable is set, then the 
contents of the status file from /proc will be copied to memescript.pid

This means we can log fun things like peak memory usage.

This only works on linux systems recent enough to have the status file.



Revision 2284 - Directory Listing
Modified Fri Feb 20 02:10:59 2009 UTC (10 years, 1 month ago) by gross
soem small fixes.

Revision 2283 - Directory Listing
Modified Fri Feb 20 01:08:21 2009 UTC (10 years, 1 month ago) by jfenwick
doxygen doco now correctly reports global project revsion number.
link to epydoc is now via a relative URL (avoids the problem of nightly doxygen pointing at out of date release epydoc).

Revision 2282 - Directory Listing
Modified Thu Feb 19 06:30:19 2009 UTC (10 years, 2 months ago) by jfenwick
setTaggedValueByName now throws if the tag name does not exist.
The documentation says this is what happens - now the code matches the doco.
This resolves issue 238

Revision 2281 - Directory Listing
Modified Thu Feb 19 05:36:38 2009 UTC (10 years, 2 months ago) by artak
minor comments are added

Revision 2280 - Directory Listing
Modified Thu Feb 19 03:34:35 2009 UTC (10 years, 2 months ago) by artak
Some statistics changed in solver.c. In AMG stopping criteria now depend on levels specified. In loadMM conditions on pivot and lval reformulated to avoid numerical overflow.

Revision 2279 - Directory Listing
Modified Tue Feb 17 10:51:12 2009 UTC (10 years, 2 months ago) by gross
mofification of the weighting factor

Revision 2278 - Directory Listing
Modified Tue Feb 17 07:39:16 2009 UTC (10 years, 2 months ago) by gross
for some reason my gcc version requires NL at the end of the source files.

Revision 2277 - Directory Listing
Modified Tue Feb 17 07:38:07 2009 UTC (10 years, 2 months ago) by gross
type fixed

Revision 2276 - Directory Listing
Modified Tue Feb 17 06:21:31 2009 UTC (10 years, 2 months ago) by jfenwick
utest.sh now builds correctly for Macintosh.
It turns out if you really want to differentiate between Mac and Linux, 
you should use platform not os.


Revision 2275 - Directory Listing
Modified Tue Feb 17 04:25:08 2009 UTC (10 years, 2 months ago) by artak
Extra tests are added for checking the quality of the solution from Jacobi and AMG.

Revision 2274 - Directory Listing
Modified Tue Feb 17 04:20:29 2009 UTC (10 years, 2 months ago) by artak
Bug fixed with type overflowing, namely in q_sort pivot and rval variables now unsigned long instead of int. Extra check is added to avoid this in the future.

Revision 2273 - Directory Listing
Modified Tue Feb 17 01:22:48 2009 UTC (10 years, 2 months ago) by jfenwick
Added compile flags to turn autolazy on and off.
These are for testing purposes only.


Revision 2272 - Directory Listing
Modified Mon Feb 16 23:40:03 2009 UTC (10 years, 2 months ago) by jfenwick
Stop icpc on savanna warning about ignoring namespaces.


Revision 2271 - Directory Listing
Modified Mon Feb 16 05:08:29 2009 UTC (10 years, 2 months ago) by jfenwick
Merging version 2269 to trunk


Revision 2269 - Directory Listing
Modified Fri Feb 13 03:55:28 2009 UTC (10 years, 2 months ago) by jfenwick
Updating prepare.py


Revision 2268 - Directory Listing
Modified Fri Feb 13 01:23:42 2009 UTC (10 years, 2 months ago) by jfenwick
Tweaking environment


Revision 2267 - Directory Listing
Modified Thu Feb 12 06:18:45 2009 UTC (10 years, 2 months ago) by gross
weighting factor introduced.

Revision 2265 - Directory Listing
Modified Wed Feb 11 07:46:07 2009 UTC (10 years, 2 months ago) by gross
somehow the fix of the test did not make it into the repository.

Revision 2264 - Directory Listing
Modified Wed Feb 11 06:48:28 2009 UTC (10 years, 2 months ago) by gross
a new darcy flux solver.

Revision 2263 - Directory Listing
Modified Wed Feb 11 03:56:47 2009 UTC (10 years, 2 months ago) by gross
test for gmsh command line generation fixed (didn't know that there is such a test)

Revision 2262 - Directory Listing
Modified Wed Feb 11 01:58:06 2009 UTC (10 years, 2 months ago) by jfenwick
Create missing directory in script.


Revision 2261 - Directory Listing
Modified Tue Feb 10 08:38:53 2009 UTC (10 years, 2 months ago) by gross
GMRES supports prconditioning from the right now.

Revision 2260 - Directory Listing
Modified Tue Feb 10 04:50:10 2009 UTC (10 years, 2 months ago) by jfenwick
That should be the last of the copyWithMask related errors.



Revision 2259 - Directory Listing
Modified Tue Feb 10 01:49:44 2009 UTC (10 years, 2 months ago) by jfenwick
Fixes errors due to feeding scalars and vectors into the same call to maximum.


Revision 2258 - Directory Listing
Modified Tue Feb 10 00:27:44 2009 UTC (10 years, 2 months ago) by jfenwick
Making directories required for pyvisi tests


Revision 2257 - Directory Listing
Modified Mon Feb 9 07:06:00 2009 UTC (10 years, 2 months ago) by gross
test can now deal with contact elements

Revision 2256 - Directory Listing
Modified Mon Feb 9 06:20:32 2009 UTC (10 years, 2 months ago) by jfenwick
Throw an exception if AbstractDomain::MPIBarrier is called (This shouldn't happen).
Added Barrier to saveVTK.
Replaced some misused keywords.


Revision 2255 - Directory Listing
Modified Mon Feb 9 06:10:13 2009 UTC (10 years, 2 months ago) by gross
problem in maximum fixed.

Revision 2254 - Directory Listing
Modified Sun Feb 8 23:40:22 2009 UTC (10 years, 2 months ago) by jfenwick
All these commits are because I am working with something which processes a clean checkout.


Revision 2253 - Directory Listing
Modified Sun Feb 8 23:35:28 2009 UTC (10 years, 2 months ago) by jfenwick
Fixing incorrect user info


Revision 2252 - Directory Listing
Modified Fri Feb 6 07:51:28 2009 UTC (10 years, 2 months ago) by gross
some notes for the kelvin model added. Implementation is still missing

Revision 2251 - Directory Listing
Modified Fri Feb 6 06:50:39 2009 UTC (10 years, 2 months ago) by gross
new compressible flow solver

Revision 2250 - Directory Listing
Modified Fri Feb 6 06:25:21 2009 UTC (10 years, 2 months ago) by jfenwick
Looking good.


Revision 2249 - Directory Listing
Modified Fri Feb 6 00:11:51 2009 UTC (10 years, 2 months ago) by jfenwick
Fixed some pathing issues.


Revision 2248 - Directory Listing
Modified Thu Feb 5 23:24:04 2009 UTC (10 years, 2 months ago) by gross
small fixes to gmsh command generation

Revision 2247 - Directory Listing
Modified Thu Feb 5 07:39:20 2009 UTC (10 years, 2 months ago) by gross
output control fixed.

Revision 2246 - Directory Listing
Modified Thu Feb 5 06:04:55 2009 UTC (10 years, 2 months ago) by jfenwick
Made some changes to the way copyWithMask works.


Revision 2245 - Directory Listing
Modified Wed Feb 4 06:27:59 2009 UTC (10 years, 2 months ago) by gross
renaming to make _GMRESm visibale

Revision 2244 - Directory Listing
Modified Wed Feb 4 06:27:34 2009 UTC (10 years, 2 months ago) by gross
fix for openmp

Revision 2243 - Directory Listing
Modified Wed Feb 4 05:22:28 2009 UTC (10 years, 2 months ago) by gross
small bug fixed which could lead to a seg fault

Revision 2242 - Directory Listing
Modified Wed Feb 4 05:04:20 2009 UTC (10 years, 2 months ago) by jfenwick
Development continues on unit test framework


Revision 2241 - Directory Listing
Modified Wed Feb 4 03:34:57 2009 UTC (10 years, 2 months ago) by artak
correct openmp options for MAC

Revision 2240 - Directory Listing
Modified Wed Feb 4 01:17:06 2009 UTC (10 years, 2 months ago) by artak
Some statistical print outs are added in solver and loadMM to Paso_SparseMatrix method is added

Revision 2239 - Directory Listing
Modified Wed Feb 4 00:42:46 2009 UTC (10 years, 2 months ago) by jfenwick
Added pyvisi and c++ unit tests to build of utest.sh

Revision 2238 - Directory Listing
Modified Tue Feb 3 06:17:34 2009 UTC (10 years, 2 months ago) by gross
gmsh does not support curveture based meshing optin anymore

Revision 2237 - Directory Listing
Modified Tue Feb 3 06:14:19 2009 UTC (10 years, 2 months ago) by gross
better method to du clipping

Revision 2236 - Directory Listing
Modified Tue Feb 3 06:13:50 2009 UTC (10 years, 2 months ago) by gross
switch to relative tolerance in face detection

Revision 2235 - Directory Listing
Modified Tue Feb 3 01:47:47 2009 UTC (10 years, 2 months ago) by jfenwick
Added support for generating non-scons test scripts

Revision 2234 - Directory Listing
Modified Mon Feb 2 05:30:30 2009 UTC (10 years, 2 months ago) by artak
two new tests for Mountains class are added.

Revision 2232 - Directory Listing
Modified Fri Jan 30 05:24:02 2009 UTC (10 years, 2 months ago) by jfenwick
Ooops need this one too.


Revision 2231 - Directory Listing
Modified Fri Jan 30 05:16:05 2009 UTC (10 years, 2 months ago) by jfenwick
Modified scons files to compile c++ unit tests with the same options used to compile the libraries.


Revision 2211 - Directory Listing
Modified Tue Jan 13 03:52:13 2009 UTC (10 years, 3 months ago) by artak
Example of a usage of Mountains class.

Revision 2210 - Directory Listing
Modified Tue Jan 13 03:49:47 2009 UTC (10 years, 3 months ago) by artak
First version of the mountains class.

Revision 2208 - Directory Listing
Modified Mon Jan 12 06:37:07 2009 UTC (10 years, 3 months ago) by gross
more work on the dary solver 



Revision 2206 - Directory Listing
Modified Fri Jan 9 03:50:29 2009 UTC (10 years, 3 months ago) by caltinay
Added some more doxygen docu to escriptreader classes.


Revision 2204 - Directory Listing
Modified Fri Jan 9 01:33:39 2009 UTC (10 years, 3 months ago) by caltinay
Fixed a little doxygen typo in the hyperlink.


Revision 2201 - Directory Listing
Modified Fri Jan 9 00:45:44 2009 UTC (10 years, 3 months ago) by caltinay
Avoid NULL reference.


Revision 2200 - Directory Listing
Modified Thu Jan 8 23:55:40 2009 UTC (10 years, 3 months ago) by jfenwick
Fixed python string substitution in error messages for trace and transpose.
Added tests for invalid axis offsets for trace on the c++ side.

Revision 2199 - Directory Listing
Modified Thu Jan 8 06:10:52 2009 UTC (10 years, 3 months ago) by jfenwick
Misc fixes:
Added some svn:ignore properties for output files that were cluttering things up.

Lazy fixes:
Fixed shape calculations for TRACE and TRANSPOSE for rank>2.
Adjusted unit test accordingly.

As a Temporary change to DataC.cpp to test for lazy data in DataC's expanded check.
This is wrong but would only affect people using lazy data.
The proper fix will come when the numarray removal code moves over from the branch.

Made tensor product AUTOLAZY capable.
Fixed some bugs resolving tensor products (incorrect offsets in buffers).
Macro'd some stray couts.

- It appears that AUTOLAZY now passes all unit tests.
- It will not be _really_ safe for general use until I can add COW. 
- (Everything's better with COW)

Revision 2198 - Directory Listing
Modified Thu Jan 8 05:59:21 2009 UTC (10 years, 3 months ago) by gross
bug with OPENMP fixed.



Revision 2197 - Directory Listing
Modified Thu Jan 8 05:49:16 2009 UTC (10 years, 3 months ago) by gross
modifications to the way cosntraints are handeled in the Transport problem



Revision 2196 - Directory Listing
Modified Wed Jan 7 06:14:59 2009 UTC (10 years, 3 months ago) by caltinay
As harsh as it sounds: removed obsolete friendship between DataVar and Mesh.
Updated and added documentation to some more methods.


Revision 2195 - Directory Listing
Modified Wed Jan 7 04:13:52 2009 UTC (10 years, 3 months ago) by jfenwick
Fixed a bug in lazy evaluation of Tensor Products.
Added / to end of boost path


Revision 2194 - Directory Listing
Modified Tue Jan 6 01:23:37 2009 UTC (10 years, 3 months ago) by caltinay
escript2silo: Allow different meshes for different timesteps.
escriptreader: Fixed segfaults for some error conditions.



Revision 2193 - Directory Listing
Modified Mon Jan 5 04:29:06 2009 UTC (10 years, 3 months ago) by lgraham
Edited Stokes flow and Level Set tutorials (grammar etc.)


Revision 2192 - Directory Listing
Modified Mon Jan 5 02:41:34 2009 UTC (10 years, 3 months ago) by lgraham
Edited Stokes flow tutorial


Revision 2191 - Directory Listing
Modified Mon Jan 5 00:30:15 2009 UTC (10 years, 3 months ago) by lgraham
Included a tutorial on fluid flow, using the StokesProblemCartesian class


Revision 2190 - Directory Listing
Modified Wed Dec 24 02:04:16 2008 UTC (10 years, 3 months ago) by caltinay
escriptreader: write special mesh variables into a "subdirectory" in the Silo
file. That way, "real" variables are better visible.



Revision 2189 - Directory Listing
Modified Tue Dec 23 04:24:37 2008 UTC (10 years, 3 months ago) by caltinay
Changed generate_dumps script to use saveESD().



Revision 2188 - Directory Listing
Modified Tue Dec 23 04:24:03 2008 UTC (10 years, 3 months ago) by caltinay
Implemented new utility function saveESD() which takes care of dumping the
given data objects with their domain and creates an ESD file containing the
required information. This obsoletes the necessity to use esdcreate for single
timestep datasets.


Revision 2187 - Directory Listing
Modified Tue Dec 23 04:13:15 2008 UTC (10 years, 3 months ago) by caltinay
Moved escriptreader related classes into own namespace.


Revision 2186 - Directory Listing
Modified Tue Dec 23 03:31:18 2008 UTC (10 years, 3 months ago) by caltinay
escript2silo was linked to libescriptreader using its relative path. Fixed that
by using a separate environment for the tools.


Revision 2185 - Directory Listing
Modified Mon Dec 22 04:41:03 2008 UTC (10 years, 3 months ago) by caltinay
Updated savanna scons file to pick up Silo library.


Revision 2184 - Directory Listing
Modified Mon Dec 22 04:27:26 2008 UTC (10 years, 3 months ago) by caltinay
Scons'ified escriptreader library and tools. Added checks and options for the
Silo library which is required for escript2silo and optional for the library.
Updated shake75 options file.


Revision 2183 - Directory Listing
Modified Fri Dec 19 03:52:50 2008 UTC (10 years, 4 months ago) by caltinay
Added escriptreader library with tools. For more information refer to README
file or wait for user documentation.


Revision 2182 - Directory Listing
Modified Thu Dec 18 03:30:17 2008 UTC (10 years, 4 months ago) by caltinay
Fixed some more typos


Revision 2181 - Directory Listing
Modified Thu Dec 18 00:58:48 2008 UTC (10 years, 4 months ago) by caltinay
Fixed two typos in bibliography


Revision 2180 - Directory Listing
Modified Thu Dec 18 00:30:25 2008 UTC (10 years, 4 months ago) by caltinay
Assorted spelling, grammar, whitespace and copy/paste error fixes (Part 3).
With boost 1.37 all epydoc warnings are gone now.
This commit should be a no-op.


Revision 2179 - Directory Listing
Modified Thu Dec 18 00:23:55 2008 UTC (10 years, 4 months ago) by caltinay
Fixed compilation with boost 1.37 (namespace clash).


Revision 2178 - Directory Listing
Modified Thu Dec 18 00:08:58 2008 UTC (10 years, 4 months ago) by artak
AMG coupling parameter added to options file.

Revision 2177 - Directory Listing
Modified Wed Dec 17 23:51:23 2008 UTC (10 years, 4 months ago) by jfenwick
used unused variable.
Added support for limiting the size of lazy expression trees.
500,000 seems a bit high

Revision 2172 - Directory Listing
Modified Wed Dec 17 08:30:12 2008 UTC (10 years, 4 months ago) by phornby
Fixed some signed/unsigned comparisons occurin g via MAX(). 
They were harmless anyway.

Revision 2171 - Directory Listing
Modified Wed Dec 17 08:21:29 2008 UTC (10 years, 4 months ago) by phornby
Unitary minus applied to unsigned returns unsigned error fixed
lines 1124 & 1142. Probably not what was intended......

Revision 2170 - Directory Listing
Modified Wed Dec 17 06:16:43 2008 UTC (10 years, 4 months ago) by jfenwick
Another unit test fix


Revision 2169 - Directory Listing
Modified Wed Dec 17 03:08:58 2008 UTC (10 years, 4 months ago) by caltinay
Assorted spelling, grammar, whitespace and copy/paste error fixes (Part 2).
All epydoc warnings for these files have been fixed.
This commit should be a no-op.


Revision 2168 - Directory Listing
Modified Wed Dec 17 00:50:37 2008 UTC (10 years, 4 months ago) by artak
methods are added for loading right-hand-side from MM format

Revision 2167 - Directory Listing
Modified Tue Dec 16 23:31:05 2008 UTC (10 years, 4 months ago) by jfenwick
Adjust tests for changes to number of buffers required.
Prevent cpp unit test from failing.

Revision 2166 - Directory Listing
Modified Tue Dec 16 06:08:02 2008 UTC (10 years, 4 months ago) by jfenwick
Fixed a bug related to lazy trace

Revision 2165 - Directory Listing
Modified Tue Dec 16 05:32:43 2008 UTC (10 years, 4 months ago) by artak
testing level as a parameter added

Revision 2164 - Directory Listing
Modified Tue Dec 16 04:00:23 2008 UTC (10 years, 4 months ago) by artak
escript library added

Revision 2163 - Directory Listing
Modified Tue Dec 16 03:55:06 2008 UTC (10 years, 4 months ago) by artak
minor

Revision 2162 - Directory Listing
Modified Tue Dec 16 03:51:27 2008 UTC (10 years, 4 months ago) by artak
Unused variable removed

Revision 2161 - Directory Listing
Modified Tue Dec 16 03:31:00 2008 UTC (10 years, 4 months ago) by artak
Paso Testing target is added.

Revision 2160 - Directory Listing
Modified Tue Dec 16 03:29:54 2008 UTC (10 years, 4 months ago) by artak
Testing envirounment for PASO

Revision 2159 - Directory Listing
Modified Tue Dec 16 03:27:16 2008 UTC (10 years, 4 months ago) by artak
Numerous bags are fixed for loading MatrixMarket files.

Revision 2158 - Directory Listing
Modified Mon Dec 15 07:17:47 2008 UTC (10 years, 4 months ago) by caltinay
Assorted spelling, grammar, whitespace and copy/paste error fixes (Part 1).
This commit should be a no-op.


Revision 2157 - Directory Listing
Modified Mon Dec 15 06:05:58 2008 UTC (10 years, 4 months ago) by jfenwick
Some lazy fixes to the symmetric operation.

Revision 2156 - Directory Listing
Modified Mon Dec 15 05:09:02 2008 UTC (10 years, 4 months ago) by gross
some modifications to the iterative solver to make them easier to use. 
There are also improved versions of the Darcy flux solver and the incompressible solver.



Revision 2155 - Directory Listing
Modified Mon Dec 15 04:12:58 2008 UTC (10 years, 4 months ago) by jfenwick
Test


Revision 2154 - Directory Listing
Modified Mon Dec 15 01:50:56 2008 UTC (10 years, 4 months ago) by trankine
* added include based on Joel's advice. Build now working on win32. unit tests not run yet...

Revision 2153 - Directory Listing
Modified Fri Dec 12 00:18:18 2008 UTC (10 years, 4 months ago) by jfenwick
Fixed a bug related to lazy tensor product.

Revision 2152 - Directory Listing
Modified Thu Dec 11 04:26:42 2008 UTC (10 years, 4 months ago) by jfenwick
Fixed some errors related to lazy processing of scalars.
AutoLazy passes more unit tests before failing.

Revision 2151 - Directory Listing
Modified Wed Dec 10 06:34:25 2008 UTC (10 years, 4 months ago) by caltinay
Moved common functionality from saveDX/VTK into private method. May be used
for future save* methods.


Revision 2150 - Directory Listing
Modified Wed Dec 10 05:57:12 2008 UTC (10 years, 4 months ago) by caltinay
Removed unnecessary "magic name length".


Revision 2149 - Directory Listing
Modified Wed Dec 10 05:08:17 2008 UTC (10 years, 4 months ago) by caltinay
Fixed a typo in error message.


Revision 2148 - Directory Listing
Modified Wed Dec 10 04:57:35 2008 UTC (10 years, 4 months ago) by lgraham
Updated the LevelSet class section in the Models chapter. The section is contained in a .tex file at the moment to avoid conflict.


Revision 2147 - Directory Listing
Modified Wed Dec 10 04:41:26 2008 UTC (10 years, 4 months ago) by jfenwick
Made some changes to c++ unit tests to accomodate AUTOLAZY.
whereZero and whereNonZero can now work with lazy data.
There are some double frees if AUTOLAZY is turned on so don't use it yet.

Revision 2146 - Directory Listing
Modified Wed Dec 10 02:59:46 2008 UTC (10 years, 4 months ago) by jfenwick
Replaced duplicate code in Data with macro calls.
Added AUTOLAZY parameter (defaults to off for now.)

Revision 2144 - Directory Listing
Modified Wed Dec 10 00:31:03 2008 UTC (10 years, 4 months ago) by artak
Some bugs are fixed: FSCANF_CHECK is returned NULL does not matter what. There are still some issues with ..._loadMM.

Revision 2142 - Directory Listing
Modified Tue Dec 9 06:22:57 2008 UTC (10 years, 4 months ago) by jfenwick
Added showEscriptParams to output a list of available params.


Revision 2141 - Directory Listing
Modified Tue Dec 9 04:32:32 2008 UTC (10 years, 4 months ago) by caltinay
saveVTK: Reviewed and changed parts of this function due to several issues.
Confirmed that it's still working using finley/test/python/generate_dumps.py
(manually inserted saveVTK) with and without MPI on 1 and 4 processors.

Changes include:
- removed unnecessary USE_VTK check - we are not using any VTK functions
- fixed writing of Rec9 & Hex27 connectivity data in MPI mode
- fixed some cases where the file was not closed and memory was not freed
- replaced many instances of fprintf by fputs (simple strings)
- some minor optimizations by moving or initializing variables and combining
  if-clauses
- got rid of ~300 lines of code and switched to consistent indentation making
  the file a bit better readable



Revision 2138 - Directory Listing
Modified Mon Dec 8 02:27:07 2008 UTC (10 years, 4 months ago) by lgraham
starting a section for the Level Set class in the Models chapter.


Revision 2132 - Directory Listing
Modified Fri Dec 5 00:18:06 2008 UTC (10 years, 4 months ago) by jfenwick
So its not just the Mac that needed -Wno-strict-aliasing



Revision 2131 - Directory Listing
Modified Thu Dec 4 06:09:50 2008 UTC (10 years, 4 months ago) by artak
Openmp bug is fixed in Paso_cum_sum and some printouts removed from Solver_AMG

Revision 2130 - Directory Listing
Modified Thu Dec 4 05:56:45 2008 UTC (10 years, 4 months ago) by jfenwick
Modifications to keep both the mac and linux happy.


Revision 2129 - Directory Listing
Modified Thu Dec 4 03:53:02 2008 UTC (10 years, 4 months ago) by lgraham
Added RT2D.py python script for levelset tutorial to examples directory.


Revision 2128 - Directory Listing
Modified Thu Dec 4 03:48:22 2008 UTC (10 years, 4 months ago) by lgraham
Added description of Rayleigh-Taylor instability python script, and a note on visualising the output with visit.


Revision 2127 - Directory Listing
Modified Thu Dec 4 03:42:45 2008 UTC (10 years, 4 months ago) by lgraham
added figures of simulation output for Rayleigh-Taylor instability; produced by visIt 


Revision 2126 - Directory Listing
Modified Thu Dec 4 00:13:03 2008 UTC (10 years, 4 months ago) by ksteube
fixed a logic mess I had made in Paso_MPIInfo_noError()


Revision 2125 - Directory Listing
Modified Wed Dec 3 09:13:10 2008 UTC (10 years, 4 months ago) by phornby
Just the usual signed/unsigned mismatch corrections. Should be harmless.
this checkin is to propagate the changes to other platforms for testing.

Revision 2123 - Directory Listing
Modified Wed Dec 3 03:26:02 2008 UTC (10 years, 4 months ago) by gross
typo fixed

Revision 2122 - Directory Listing
Modified Wed Dec 3 02:52:28 2008 UTC (10 years, 4 months ago) by artak
Codition is added in the corsening process to avoid rows with very small row sum.

Revision 2121 - Directory Listing
Modified Wed Dec 3 00:25:08 2008 UTC (10 years, 4 months ago) by jfenwick
Removing pdf from repository.

Revision 2120 - Directory Listing
Modified Tue Dec 2 06:21:49 2008 UTC (10 years, 4 months ago) by lgraham
Added Rayleigh-Taylor instability code into users guide


Revision 2115 - Directory Listing
Modified Tue Dec 2 01:21:07 2008 UTC (10 years, 4 months ago) by lgraham
Added in theory of the reinitialisation procedure for the level set method.



Revision 2114 - Directory Listing
Modified Tue Dec 2 01:16:25 2008 UTC (10 years, 4 months ago) by ksteube
a new script to create a source distribution file


Revision 2113 - Directory Listing
Modified Mon Dec 1 06:27:14 2008 UTC (10 years, 4 months ago) by artak
Temporary solution for nusty rows: a condition added 

Revision 2112 - Directory Listing
Modified Mon Dec 1 02:53:58 2008 UTC (10 years, 4 months ago) by artak
Uses Jacobi as a smoother and beats any preconditioner in 2D(for some problems) where number of elemens in one direction is more that 200

Revision 2110 - Directory Listing
Modified Fri Nov 28 05:55:00 2008 UTC (10 years, 4 months ago) by ksteube
Fixed nightly documentation.
Removed time command from wrapper. I thought it was standard UNIX but
somebody's system didn't have it, so I removed it.


Revision 2109 - Directory Listing
Modified Fri Nov 28 05:09:36 2008 UTC (10 years, 4 months ago) by jfenwick
An attempt at a license file.


Revision 2108 - Directory Listing
Modified Fri Nov 28 05:09:23 2008 UTC (10 years, 4 months ago) by gross
some minor changes to PCG and some extra suspicious characters.

Revision 2107 - Directory Listing
Modified Fri Nov 28 04:39:07 2008 UTC (10 years, 4 months ago) by artak
Current version of AMG uses ILU for relaxation, however it is not stable when schur matrix becames more denser. For example it is not stable for -e paramenter is more 400 in 2D for convection problem 

Revision 2106 - Directory Listing
Modified Fri Nov 28 04:31:23 2008 UTC (10 years, 4 months ago) by jfenwick
Removing files which are unused/old/not-distributable.

Revision 2105 - Directory Listing
Modified Fri Nov 28 01:52:12 2008 UTC (10 years, 4 months ago) by jfenwick
Data::copySelf() now returns an object instead of a pointer.
Fixed a bug in copyFromArray relating to expanded data.

Revision 2104 - Directory Listing
Modified Thu Nov 27 05:36:47 2008 UTC (10 years, 4 months ago) by jfenwick
Fixed non-compilage.
Removed mysterious t and t! from output.

Revision 2102 - Directory Listing
Modified Thu Nov 27 00:32:33 2008 UTC (10 years, 4 months ago) by jfenwick
Fixed wrapper script to OpenMP can run without invoking mpi.


Revision 2101 - Directory Listing
Modified Wed Nov 26 08:29:08 2008 UTC (10 years, 4 months ago) by gross
UMF link check activated. BLAS check stil fails.

Revision 2100 - Directory Listing
Modified Wed Nov 26 08:13:00 2008 UTC (10 years, 4 months ago) by gross
This commit cleans up the incompressible solver and adds a DarcyFlux solver in model module. 
Some documentation for both classes has been added.
The convection code is only linear at the moment.




Revision 2098 - Directory Listing
Modified Tue Nov 25 12:04:36 2008 UTC (10 years, 4 months ago) by phornby
Fix unsigned/signed comparison.

Revision 2097 - Directory Listing
Modified Tue Nov 25 12:03:29 2008 UTC (10 years, 4 months ago) by phornby
moved the code

#ifndef __const
# if (defined __STDC__ && __STDC__) || defined __cplusplus
#  define __const	const
# else
#  define __const
# endif
#endif

from escript/src/system_dep.h to esysUtils/src/system_dep.h, just for blocktimer's sake.


Revision 2096 - Directory Listing
Modified Tue Nov 25 10:29:27 2008 UTC (10 years, 4 months ago) by phornby
Starting from the recent reversion:

1. Leave __del__ alone.
2. mkstemp() actually opens the file it creates, only to be opened again in getMeshHandler(), so add an os.close() straight after the mkstemp()'s
3. in getMeshHandler(), close the script file immediately when finished with it instead of doing something non-local in __del__.

Untested on 'nix's at this point. Commit is for testing purposes.


Revision 2094 - Directory Listing
Modified Tue Nov 25 05:45:41 2008 UTC (10 years, 4 months ago) by caltinay
saveVTK: Close the file even if error is set upon completion. Note that
in some places the function still returns without proper clean up but
this won't be fixed until the rewrite to avoid more mess in the code.


Revision 2092 - Directory Listing
Modified Tue Nov 25 04:18:17 2008 UTC (10 years, 4 months ago) by jfenwick
Added macro to disable debug output from Lazy Data.

Revision 2091 - Directory Listing
Modified Tue Nov 25 03:26:51 2008 UTC (10 years, 4 months ago) by ksteube
Updates for running epydoc and creating examples_zipfile


Revision 2090 - Directory Listing
Modified Mon Nov 24 06:41:08 2008 UTC (10 years, 4 months ago) by ksteube
Reverted pycad/py_src/gmsh.py to before revision 1904.
A change had been made to the way the geo file was opened.


Revision 2089 - Directory Listing
Modified Mon Nov 24 06:07:29 2008 UTC (10 years, 4 months ago) by jfenwick
Resolve mantis issue 216.

Removed the asAbstractContinuousDomain(X) member which did not take cast 
failure into account.
Rewrote the few places where it was used.




Revision 2088 - Directory Listing
Modified Mon Nov 24 05:39:38 2008 UTC (10 years, 4 months ago) by caltinay
pycad: Added missing 'self' scope


Revision 2087 - Directory Listing
Modified Mon Nov 24 04:51:30 2008 UTC (10 years, 4 months ago) by jfenwick
Addressing mantis issue #221.
Interpolation.. and probeInterpolation.. now "work" for the NullDomain.
Work means throw a descriptive exception if you try to move into or out 
of the NullDomain.
The bad_cast exception related to this has been fixed.



Revision 2086 - Directory Listing
Modified Mon Nov 24 02:38:50 2008 UTC (10 years, 4 months ago) by jfenwick
Added checks in C_GeneralTensorProduct (Data:: and Delayed forms) as 
well as the DataAbstract Constructor to prevent Objects with Rank>4 
being created.

Moved the relevant #define into systemdep.

Removed some comments.


Revision 2085 - Directory Listing
Modified Mon Nov 24 00:45:48 2008 UTC (10 years, 4 months ago) by jfenwick
Added c++ unit tests for new operations.
Added resolve to some operations in Data


Revision 2084 - Directory Listing
Modified Fri Nov 21 05:20:42 2008 UTC (10 years, 4 months ago) by jfenwick
Fixed a warning in cpp unit tests under dodebug
Pointed the url for python doco at shake200 rather than iservo.
Added support for trace and transpose to LazyData.
Fixed bug in trace to initialise running totals.

Revision 2083 - Directory Listing
Modified Fri Nov 21 01:46:31 2008 UTC (10 years, 4 months ago) by caltinay
Same "fix" as before for unused fp_out and fp_err.


Revision 2082 - Directory Listing
Modified Fri Nov 21 01:46:05 2008 UTC (10 years, 4 months ago) by caltinay
Removed unused variable.


Revision 2081 - Directory Listing
Modified Fri Nov 21 01:28:31 2008 UTC (10 years, 4 months ago) by caltinay
escript/Data: Another fix for parallel var initialization. Also, the (error) return value of MPI_Gather was not used. I applied the same 'hack' as in other places in the file, namely declaring the variable beforehand but still ignoring the return value :-/


Revision 2080 - Directory Listing
Modified Fri Nov 21 01:20:14 2008 UTC (10 years, 4 months ago) by caltinay
paso/SchurComplement: Fixed variable initialization for OpenMP parallelization.


Revision 2079 - Directory Listing
Modified Fri Nov 21 01:04:56 2008 UTC (10 years, 4 months ago) by artak
Changed comment operator from // to /* */, because it does not compile in our C standart

Revision 2078 - Directory Listing
Modified Thu Nov 20 16:10:10 2008 UTC (10 years, 5 months ago) by phornby
Two changes.

1. Move blocktimer from escript to esysUtils.
2. Make it possible to link to paso as a DLL or .so.

Should have no effect on 'nix's

In respect of 1., blocktimer had begun to spring up everywhere, so
for the moment I thought it best to move it to the only other library that
pops up all over the place.

In respect of 2., paso needed to be a DLL in order to use the windows intelc /fast
option, which does aggressive multi-file optimisations. Even in its current form, it either
vectorises or parallelises  hundreds more loops in the esys system than appear in the pragmas.

In achieving 2. I have not been too delicate in adding

PASO_DLL_API

declarations to the .h files in paso/src. Only toward the end of the process of
the conversion, when the number of linker errors dropped below 20, say, did I choosy about what
functions in a header I declared PASO_DLL_API. As a result, there are likely to be many routines
declared as external functions symbols that are in fact internal to the paso DLL. 
Why is this an issue?  It prevents the intelc compiler from getting aggressive on the paso module.
With pain there is sometimes gain. At least all the DLL rules in windows give good
(non-microsoft) compiler writers a chance to really shine.

So, if you should see a PASO_DLL_API on a function in a paso header file,
and think to yourself, "that function is only called in paso, why export it?", then feel free to
delete the PASO_DLL_API export declaration.

Here's hoping for no breakage.....

Revision 2076 - Directory Listing
Modified Thu Nov 20 12:34:17 2008 UTC (10 years, 5 months ago) by phornby

I may get into trouble for this.
boost-python 1.34 does have a docstring_options class,
but does not have a 3 argument constructor for
it. So the test has been modified to 


#if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)

If you wish to make things more delicate, one can define a 2 argument construction
of docopt just for 1.34 (with an #elif). Probably not worth the effort frankly.

Hope that this has not broken anything for anyone else. The SVN logs suggest this is a
little fragile.....

Also, please be aware that much of our chemistry interface code, that we wish to use with
escript, makes extensive use of boost python.
Having two different boost versions mucking with the python interpreter sounds
like a really bad idea, I'm sure you'll agree.
The problem is that it is not a simple task for us to build new versions of boost-python
on all our platforms. Consequently, it would be nice to be informed when you guys
intend to upgrade a support library of this nature so that we can plan and allocate
resources to keep up.

Cheers.



Revision 2074 - Directory Listing
Modified Thu Nov 20 11:02:07 2008 UTC (10 years, 5 months ago) by phornby
Nearly there with dll'ing paso.



Revision 2073 - Directory Listing
Modified Thu Nov 20 10:51:41 2008 UTC (10 years, 5 months ago) by phornby
Still working away at makeing paso sharable on windows.



Revision 2072 - Directory Listing
Modified Thu Nov 20 10:40:19 2008 UTC (10 years, 5 months ago) by phornby
More PASO_DLL_API declarations for externally called routines.



Revision 2071 - Directory Listing
Modified Thu Nov 20 10:29:56 2008 UTC (10 years, 5 months ago) by phornby
More preparation for making paso a dll.



Revision 2070 - Directory Listing
Modified Thu Nov 20 10:11:13 2008 UTC (10 years, 5 months ago) by phornby
Further preparation for sharable paso.



Revision 2069 - Directory Listing
Modified Thu Nov 20 09:13:19 2008 UTC (10 years, 5 months ago) by phornby
Another ElementTypeId TypeId=NoType; fix.

Revision 2068 - Directory Listing
Modified Thu Nov 20 09:11:01 2008 UTC (10 years, 5 months ago) by phornby
Interim commit getting paso ready for becoming a shared library.



Revision 2067 - Directory Listing
Modified Thu Nov 20 06:22:56 2008 UTC (10 years, 5 months ago) by caltinay
Moved 'make dir' operation to the correct spot and extended the number
of timesteps a bit.



Revision 2066 - Directory Listing
Modified Thu Nov 20 05:31:33 2008 UTC (10 years, 5 months ago) by jfenwick
Fixed Data::toString to look at the amount of data actually stored rather than the number of points in the domain.

Added support for GeneralTensorProduct to LazyData

Revision 2065 - Directory Listing
Modified Thu Nov 20 04:25:47 2008 UTC (10 years, 5 months ago) by jfenwick
Have the epydoc put its output in the correct place before anyone 
notices.


Revision 2064 - Directory Listing
Modified Thu Nov 20 04:06:34 2008 UTC (10 years, 5 months ago) by jfenwick
docstring_options was added in boost 1.34 - macro'd it out if you are 
compiling earlier than that.


Revision 2063 - Directory Listing
Modified Wed Nov 19 04:59:43 2008 UTC (10 years, 5 months ago) by jfenwick
- Removed some deprecated directories.
- Removed the pythfilter script for converting python doco into c++ stubs. The license was unspecified and we don't use it.
- Suppressed long long warnings on gcc (the Mac complained).
- svn:ignored Mac library suffixes in lib directory

Revision 2062 - Directory Listing
Modified Wed Nov 19 04:32:13 2008 UTC (10 years, 5 months ago) by jfenwick
Fixed api_epydoc so that it actually rebuilds the doco when required.

Revision 2061 - Directory Listing
Modified Wed Nov 19 03:40:21 2008 UTC (10 years, 5 months ago) by jfenwick
Fixing some warnings from epydoc.
Disabled c++ signatures in python docstrings.
Removed references to Bruce in epydoc and the users guide.

Revision 2060 - Directory Listing
Modified Tue Nov 18 00:18:08 2008 UTC (10 years, 5 months ago) by jfenwick
Okay, so -isystem on the whole /usr/include directory appears to prevent 
compiling.  I suspect this might be something about changing the 
priority of includes.

Fixed.



Revision 2059 - Directory Listing
Modified Mon Nov 17 22:57:50 2008 UTC (10 years, 5 months ago) by gross
changes as suggested by phornby

Revision 2058 - Directory Listing
Modified Mon Nov 17 13:35:10 2008 UTC (10 years, 5 months ago) by phornby
Added (as comment for the moment) very aggressive intelc optimisation.
Also add options (as comments) to compile esysUtis and paso as DLL's so
I can eventually use the /fast option on the intelc compiler.

Revision 2057 - Directory Listing
Modified Mon Nov 17 13:30:46 2008 UTC (10 years, 5 months ago) by phornby
Prepare this file for the possibility of dynamic linkage.

SVN is doing something weird to me... I'm sure I committed this change already...

Revision 2056 - Directory Listing
Modified Mon Nov 17 13:27:55 2008 UTC (10 years, 5 months ago) by phornby
Prepare this file for the possibility of dynamic linkage.

Revision 2055 - Directory Listing
Modified Mon Nov 17 13:26:40 2008 UTC (10 years, 5 months ago) by phornby
I have found that windows intelc /Qiop option,
which performs multi-file loop parallisation and vectorisation,
taking account of all the information in a single .obj file that it generates,
will get it's second phase link action right if it is linking
to DLL's rather than statically linking. This and other SConscripts
have been modified to take account of the options that select a static
or dynamic library.

Revision 2054 - Directory Listing
Modified Mon Nov 17 13:20:41 2008 UTC (10 years, 5 months ago) by phornby
Added the share_esysUtils and share_paso options
both defaulting to False, to allow finer control over
the nature of these libraries. Following log messages will explain.

Revision 2053 - Directory Listing
Modified Mon Nov 17 11:24:40 2008 UTC (10 years, 5 months ago) by phornby
Fix the test for erf() under intelc on windows to something more informative.

Revision 2052 - Directory Listing
Modified Mon Nov 17 11:15:07 2008 UTC (10 years, 5 months ago) by phornby
MALLOC_CHUNK -> malloc_chunk in case there is a name-space
collision with a macro at some time in the future.



Revision 2051 - Directory Listing
Modified Mon Nov 17 09:24:02 2008 UTC (10 years, 5 months ago) by phornby
Now add the erf() test back for windows under the intelc compiler.



Revision 2050 - Directory Listing
Modified Mon Nov 17 08:59:57 2008 UTC (10 years, 5 months ago) by phornby
OK, I have to include this file in the experiment
to use the intelc math library on windows.



Revision 2049 - Directory Listing
Modified Mon Nov 17 08:54:33 2008 UTC (10 years, 5 months ago) by phornby
A little refinement of what to leave out of UnaryFuncs.h
if using the intelc compiler on windows.



Revision 2048 - Directory Listing
Modified Mon Nov 17 08:46:00 2008 UTC (10 years, 5 months ago) by phornby
Experimental commit to move the code to a windows box
on the other side of a firewall. Purpose: add support for the
imploved intelc math library on windows.



Revision 2045 - Directory Listing
Modified Sat Nov 15 14:08:09 2008 UTC (10 years, 5 months ago) by phornby
Make the windows intel compiler work harder at un-rolling loops and inlining absolutely everything
it can.

Revision 2044 - Directory Listing
Modified Sat Nov 15 13:19:49 2008 UTC (10 years, 5 months ago) by phornby
Consolidate many of the icl speed options into the /Ox option.

Revision 2043 - Directory Listing
Modified Sat Nov 15 12:53:27 2008 UTC (10 years, 5 months ago) by phornby
Make the intel compiler work for its money.

Revision 2042 - Directory Listing
Modified Sat Nov 15 12:52:46 2008 UTC (10 years, 5 months ago) by phornby
Prevent Windows compilers from keeping their own program database file.
This allows the use of the -jn scons option on Windows.

Revision 2041 - Directory Listing
Modified Sat Nov 15 12:45:15 2008 UTC (10 years, 5 months ago) by phornby
ESYS_STATIC_LIB no longer needs to be defined in SConscript files.

Revision 2040 - Directory Listing
Modified Sat Nov 15 12:43:11 2008 UTC (10 years, 5 months ago) by phornby
Handle ESYS_STATIC_LIB more elegantly, and make it
a two-liner to turn it into a DLL if needed.

Revision 2039 - Directory Listing
Modified Sat Nov 15 09:15:46 2008 UTC (10 years, 5 months ago) by phornby
Remove the "const from the alpha argument of 
Paso_SystemMatrix_MatrixVector_CSR_OFFSET0()
in order to match it's declaration.

This is C, and the double is passed by value, so alpha is
by nature const. This is C code, not C++. The const keyword has no place in C.

Revision 2038 - Directory Listing
Modified Fri Nov 14 00:12:58 2008 UTC (10 years, 5 months ago) by ksteube
Change -isystem to point to boost_path and python_path instead of to /usr/include


Revision 2037 - Directory Listing
Modified Thu Nov 13 06:17:12 2008 UTC (10 years, 5 months ago) by jfenwick
Fixed some warnings in the unit tests.
Added support for symmetric and nonsymmetric operations on LazyData.

Revision 2036 - Directory Listing
Modified Thu Nov 13 04:35:06 2008 UTC (10 years, 5 months ago) by jfenwick
A fix to deal with boost1.34s badness


Revision 2035 - Directory Listing
Modified Thu Nov 13 03:16:09 2008 UTC (10 years, 5 months ago) by jfenwick
Putting poisson.py back


Revision 2034 - Directory Listing
Modified Thu Nov 13 03:03:42 2008 UTC (10 years, 5 months ago) by artak
variable <set> is initilized to get rid of compiler warnning errors. finley/src/Quadrature.c

Revision 2033 - Directory Listing
Modified Wed Nov 12 08:14:11 2008 UTC (10 years, 5 months ago) by phornby
As in the last message, add an extra CPPDEFINE to py_local_wrapper_env



Revision 2032 - Directory Listing
Modified Wed Nov 12 08:11:19 2008 UTC (10 years, 5 months ago) by phornby
Missed an extra additional CPPDEFINES for the py_wrapper_local_env.



Revision 2031 - Directory Listing
Modified Wed Nov 12 08:02:33 2008 UTC (10 years, 5 months ago) by phornby
Need finer control than INTERFACE_STATIC_LIB could exert. Now there is a
XXX_STATIC_LIB for each lib.



Revision 2030 - Directory Listing
Modified Wed Nov 12 07:34:08 2008 UTC (10 years, 5 months ago) by phornby
Fix the undef'fing of _DLL_API in windows case.



Revision 2029 - Directory Listing
Modified Wed Nov 12 07:27:05 2008 UTC (10 years, 5 months ago) by phornby
Test a more elegant way of handling XXX_DLL_API macros.



Revision 2028 - Directory Listing
Modified Tue Nov 11 03:07:59 2008 UTC (10 years, 5 months ago) by phornby
add the test for __const definition because recent changes
have broken the windows compile of paso.

Fingers crossed this does not break anything else.

Revision 2027 - Directory Listing
Modified Tue Nov 11 02:52:24 2008 UTC (10 years, 5 months ago) by phornby
Ensure ESCRIPT_EXPORTS is defined only while compiling escript on windows.
A similar comment applies to FINLEY_EXPORTS.

SConstruct:
Fixed a comment.
reformatted the Export() call, and added IS_WINDOWS_PLATFORM to the exports.

Revision 2026 - Directory Listing
Modified Tue Nov 11 01:56:54 2008 UTC (10 years, 5 months ago) by jfenwick
I have changed the default scons options for gcc to be much more picky about warnings.
By default warnings will be treated as errors; so a program with warnings won't compile.

If you need to turn this off, usewarnings=no will work.

The previous usepedantic oprtion is no longer turned on by default.

This should have no effect on any of the other compilers.
If anyone wants to jump in and supply sensible values for the fatalwarnings variable for their favourite compiler go ahead.

Revision 2025 - Directory Listing
Modified Tue Nov 11 00:18:33 2008 UTC (10 years, 5 months ago) by jfenwick
__const on some strings

Revision 2021 - Directory Listing
Modified Mon Nov 10 14:07:49 2008 UTC (10 years, 5 months ago) by phornby
Use the NO_ARG trick on the PROC_OP macro expansions.



Revision 2020 - Directory Listing
Modified Mon Nov 10 14:02:17 2008 UTC (10 years, 5 months ago) by phornby
THROW_ANY is dead. Pls read comments in esysUtils/src/system_dep.h



Revision 2019 - Directory Listing
Modified Mon Nov 10 13:49:00 2008 UTC (10 years, 5 months ago) by phornby
Yet another concerted effort to handle missing macro arguments
in a portable way.



Revision 2018 - Directory Listing
Modified Mon Nov 10 13:31:43 2008 UTC (10 years, 5 months ago) by phornby
Only import mathimf.h on win32 with intelc. Allow others to use the
standard math.h

change the #ifndef const -> #ifndef __const (oops!!)



Revision 2017 - Directory Listing
Modified Mon Nov 10 13:19:38 2008 UTC (10 years, 5 months ago) by phornby
Tighten the test for including mathimf.h to be windows specific.

Also another experiment in eliminating THROW_ANY

Revision 2014 - Directory Listing
Modified Mon Nov 10 12:44:51 2008 UTC (10 years, 5 months ago) by phornby
Refine the intelc compiler options, and link to the dll version of libguide.

Revision 2013 - Directory Listing
Modified Mon Nov 10 12:16:32 2008 UTC (10 years, 5 months ago) by phornby
Add the tools_names vars to control the compiler toolset scons uses
on windows platforms. (See cgisrv3_options.py for example of use).

Revision 2012 - Directory Listing
Modified Mon Nov 10 12:13:45 2008 UTC (10 years, 5 months ago) by phornby
Grew tired of having to edit SConstruct every time I changed from
MSVC to intelc. Added the tools_names option to allow control of tools
in the Environment call from the options file. This only applies to
the windows branch at present.

Revision 2011 - Directory Listing
Modified Mon Nov 10 10:54:38 2008 UTC (10 years, 5 months ago) by phornby
Commit this options file because cgisrv3 is to be the windows auto build and test machine.

Revision 2009 - Directory Listing
Modified Mon Nov 10 10:01:50 2008 UTC (10 years, 5 months ago) by phornby
Simplify the _del_ method's file closure and unlinking based upon mkstemp's advertised
behaviour.



Revision 2008 - Directory Listing
Modified Mon Nov 10 08:59:14 2008 UTC (10 years, 5 months ago) by phornby
Signed/unsigned comparisons eliminated (just loop variables, easy fix).

Revision 2007 - Directory Listing
Modified Mon Nov 10 06:34:11 2008 UTC (10 years, 5 months ago) by jfenwick
Added a private operator= to Taipan to prevent people from copying trying to copy instances.
Not that we have any of that.... but if someone ever tries, we'll be ready for them.

I have come to the conclusion that -Weffc++ is not usable for us. Its output is too noisy complaining about classes which we do not control.

Revision 2006 - Directory Listing
Modified Mon Nov 10 03:07:08 2008 UTC (10 years, 5 months ago) by jfenwick
Updating svn:ignore properties.


Revision 2005 - Directory Listing
Modified Mon Nov 10 01:21:39 2008 UTC (10 years, 5 months ago) by jfenwick
Bringing all changes across from schroedinger.
(Note this does not mean development is done, just that it will happen
on the trunk for now).
If anyone notices any problems please contact me.



Revision 1991 - Directory Listing
Modified Fri Nov 7 04:32:38 2008 UTC (10 years, 5 months ago) by caltinay
finley: Constify two variables.


Revision 1990 - Directory Listing
Modified Fri Nov 7 04:19:07 2008 UTC (10 years, 5 months ago) by ksteube
Changes to avoid compiler warnings
Finley files now pass -Wall on gcc 4.3.2
	saveVTK.c: replaced printf(string) with printf("%s", string)
	MeshAdapterFactory.cpp: moved a few lines to avoid possible use of uninitialized vars
	MeshAdapter.cpp: initialized ncdims in mesh dump
There is still a warning from a boost include file


Revision 1989 - Directory Listing
Modified Fri Nov 7 04:11:33 2008 UTC (10 years, 5 months ago) by caltinay
modellib: completely revised tsunami script.
-updated finley usage (due to changed interface)
-moved VTK stuff to one place making it easy to disable (and use dumps instead)
-removed dependency on non-existing data server - script now depends on saved coastline/bathymetry data files OR calls scripts to create the data on the fly.
-PDE and triangulation code is unchanged except indentation updates


Revision 1986 - Directory Listing
Modified Thu Nov 6 23:33:14 2008 UTC (10 years, 5 months ago) by jfenwick
Warning removal

Revision 1985 - Directory Listing
Modified Thu Nov 6 22:13:54 2008 UTC (10 years, 5 months ago) by caltinay
finley: Fixed compiler warnings (uninitialized vars). This is only a temporary hack. At a later stage this beast will be rewritten...


Revision 1984 - Directory Listing
Modified Thu Nov 6 22:10:28 2008 UTC (10 years, 5 months ago) by caltinay
Added shake75 build options file


Revision 1983 - Directory Listing
Modified Thu Nov 6 22:00:18 2008 UTC (10 years, 5 months ago) by caltinay
Paso: Fixed compilation with OpenMPI


Revision 1982 - Directory Listing
Modified Thu Nov 6 06:16:07 2008 UTC (10 years, 5 months ago) by ksteube
Changed options file for host shake71 to rodinia


Revision 1981 - Directory Listing
Modified Thu Nov 6 05:27:33 2008 UTC (10 years, 5 months ago) by jfenwick
More warning removal.


Revision 1980 - Directory Listing
Modified Thu Nov 6 04:45:08 2008 UTC (10 years, 5 months ago) by artak
sum variable is removed from #pragma

Revision 1979 - Directory Listing
Modified Thu Nov 6 04:29:58 2008 UTC (10 years, 5 months ago) by artak
warning removal

Revision 1978 - Directory Listing
Modified Thu Nov 6 04:21:23 2008 UTC (10 years, 5 months ago) by artak
MINRES, TFQMR, GS are added

Revision 1977 - Directory Listing
Modified Thu Nov 6 03:54:35 2008 UTC (10 years, 5 months ago) by jfenwick
More warning removal.

Revision 1976 - Directory Listing
Modified Thu Nov 6 03:14:52 2008 UTC (10 years, 5 months ago) by artak
unused variables are removed to get rid of compiler warnings

Revision 1975 - Directory Listing
Modified Thu Nov 6 03:07:02 2008 UTC (10 years, 5 months ago) by artak
Some variables are initialized to get rid of compiler warnings

Revision 1974 - Directory Listing
Modified Thu Nov 6 02:40:10 2008 UTC (10 years, 5 months ago) by jfenwick
Changing ZERO and ONE in Solver.h to PASO_ZERO and PASO_ONE.
Changed three static vars to #defines

Revision 1973 - Directory Listing
Modified Thu Nov 6 02:31:37 2008 UTC (10 years, 5 months ago) by lgraham
Tidied up the white space between the equations and fixed gramma in the Rayleigh-Taylor Instability (levelset) tutorial.
Will include Escript code soon.


Revision 1971 - Directory Listing
Modified Thu Nov 6 01:11:23 2008 UTC (10 years, 5 months ago) by artak
Some typos fixed. The rearagments of figure 1, and footnotes added to avoid confusion.

Revision 1967 - Directory Listing
Modified Wed Nov 5 08:49:39 2008 UTC (10 years, 5 months ago) by phornby
changerd __del__ to close the tmp file before attempting to unlink it. This is required on windows, and probably wise on all platforms.

Revision 1966 - Directory Listing
Modified Wed Nov 5 04:59:22 2008 UTC (10 years, 5 months ago) by jfenwick
Some more fixes to user guide.

Revision 1965 - Directory Listing
Modified Wed Nov 5 03:24:09 2008 UTC (10 years, 5 months ago) by caltinay
Fixed working directory of the seismic_wave example.


Revision 1964 - Directory Listing
Modified Wed Nov 5 03:21:31 2008 UTC (10 years, 5 months ago) by caltinay
user's guide: Reviewed and updated pyvisi documentation.


Revision 1963 - Directory Listing
Modified Wed Nov 5 03:20:24 2008 UTC (10 years, 5 months ago) by caltinay
user's guide: Fixed some typos.


Revision 1962 - Directory Listing
Modified Tue Nov 4 07:17:31 2008 UTC (10 years, 5 months ago) by gross
there is an offet missing when copy data to a data point.



Revision 1961 - Directory Listing
Modified Tue Nov 4 06:09:33 2008 UTC (10 years, 5 months ago) by caltinay
Pyvisi: Fixed wording/typos in readme file.


Revision 1960 - Directory Listing
Modified Tue Nov 4 05:50:41 2008 UTC (10 years, 5 months ago) by artak
some unsed variables are removed

Revision 1959 - Directory Listing
Modified Tue Nov 4 01:49:19 2008 UTC (10 years, 5 months ago) by jfenwick
More fixes to doco.

Revision 1958 - Directory Listing
Modified Mon Nov 3 23:47:16 2008 UTC (10 years, 5 months ago) by jfenwick
Fixed URL to python doc in guide_defs


Revision 1957 - Directory Listing
Modified Mon Nov 3 06:14:18 2008 UTC (10 years, 5 months ago) by jfenwick
Some fixes to user guide


Revision 1956 - Directory Listing
Modified Mon Nov 3 05:08:42 2008 UTC (10 years, 5 months ago) by gross
bug fixed.

Revision 1955 - Directory Listing
Modified Fri Oct 31 04:01:24 2008 UTC (10 years, 5 months ago) by jfenwick
Fixed some macros so they don't add extra spaces.
Switched from input to include for chapters for faster recompile.


Revision 1954 - Directory Listing
Modified Fri Oct 31 03:22:34 2008 UTC (10 years, 5 months ago) by artak
condition is added to check wheter row sum is ZERO and some new coarsening algorithm is also added

Revision 1953 - Directory Listing
Modified Thu Oct 30 07:01:11 2008 UTC (10 years, 5 months ago) by phornby
removed one signed/unsigned value comparison. The remaining one at line 863 is far more difficult to deal with.

Revision 1952 - Directory Listing
Modified Thu Oct 30 06:16:00 2008 UTC (10 years, 5 months ago) by jfenwick
Fixed /* in a comment.
The rank of a datapoint is now an unsigned int.


Revision 1946 - Directory Listing
Modified Wed Oct 29 05:48:53 2008 UTC (10 years, 5 months ago) by jfenwick
A cleanup of some of the problems I found doing a Wall compile.

Removed some commented out lines.
Swapped some member initialisers.
Removed virtual qualifiers from some methods in FunctionSpace.
Fixed some unused or (possibly) uninitialised variables.



Revision 1942 - Directory Listing
Modified Wed Oct 29 03:29:35 2008 UTC (10 years, 5 months ago) by phornby
remove unused rtmp var.

Revision 1941 - Directory Listing
Modified Tue Oct 28 07:51:49 2008 UTC (10 years, 5 months ago) by ksteube
Updated installation directions in the User Guide to simply
point to the instructions on the wiki, which I have already
updated extensively.


Revision 1940 - Directory Listing
Modified Tue Oct 28 03:50:01 2008 UTC (10 years, 5 months ago) by artak
get Gauss-Seidel factorization moved solverAMG to getAMG. Stopping criterium for corsening changed to depend to the number of unknowns left

Revision 1939 - Directory Listing
Modified Tue Oct 28 03:47:08 2008 UTC (10 years, 5 months ago) by artak
get Gauss-Seidel factorization moved solverAMG to getAMG. Stopping criterium for corsening changed to depend to the number of unknowns left

Revision 1937 - Directory Listing
Modified Tue Oct 28 01:26:55 2008 UTC (10 years, 5 months ago) by ksteube
Created a mid-sized test suite 'scalable_tests' as an alternative to 'all_tests'.
These run on small-ish systems and also on all 512 cores of Savanna.
Most features are covered, but it's better to use 'all_tests'.


Revision 1936 - Directory Listing
Modified Mon Oct 27 23:30:57 2008 UTC (10 years, 5 months ago) by artak
checks openMP for proper break usage

Revision 1934 - Directory Listing
Modified Mon Oct 27 05:03:12 2008 UTC (10 years, 5 months ago) by artak
some typos

Revision 1933 - Directory Listing
Modified Mon Oct 27 04:58:59 2008 UTC (10 years, 5 months ago) by artak
Gauss-Seidel which takes into acound initianl x

Revision 1932 - Directory Listing
Modified Mon Oct 27 04:15:00 2008 UTC (10 years, 5 months ago) by artak
one input parameter is added

Revision 1931 - Directory Listing
Modified Mon Oct 27 01:31:28 2008 UTC (10 years, 5 months ago) by artak
Direct solver is added to solve_AMG. It is now working but I guess need optimization.

Revision 1930 - Directory Listing
Modified Fri Oct 24 09:35:55 2008 UTC (10 years, 5 months ago) by phornby
revert to MS compiler for now.

Revision 1929 - Directory Listing
Modified Fri Oct 24 09:20:17 2008 UTC (10 years, 5 months ago) by phornby
abortive attempt to automate the choice of windows compiler based uponj the options file.

Revision 1928 - Directory Listing
Modified Fri Oct 24 08:20:23 2008 UTC (10 years, 5 months ago) by phornby
Pass 2 at getting openMP going on windows.
Problem is incompatible mathinf.h and system math.h at this point.

Revision 1927 - Directory Listing
Modified Fri Oct 24 06:24:49 2008 UTC (10 years, 5 months ago) by phornby
First cut at omp options for windows.

Revision 1923 - Directory Listing
Modified Thu Oct 23 12:53:39 2008 UTC (10 years, 5 months ago) by phornby
The calls to Finley routines turned out to be cut & past errors, easily fixed.



Revision 1921 - Directory Listing
Modified Thu Oct 23 11:32:24 2008 UTC (10 years, 5 months ago) by phornby
Jump through hoops to meet the OPENMP 2.5 restrictions on loop variables.
It's all ready for OPENMP 3.0 improvments, and should compile cleanly on other platforms.



Revision 1920 - Directory Listing
Modified Thu Oct 23 10:05:27 2008 UTC (10 years, 5 months ago) by phornby
remove unused vars.

Revision 1919 - Directory Listing
Modified Thu Oct 23 10:03:10 2008 UTC (10 years, 5 months ago) by phornby
Remove un-used vars introduced by my _WIN32 compilation branch. This is a checkin to allow a test of both compilation brabches.

Revision 1918 - Directory Listing
Modified Thu Oct 23 09:14:13 2008 UTC (10 years, 5 months ago) by phornby
fix a signed and unsigned integer comparison. As your meshes get larger, this type of error will bite.

Revision 1917 - Directory Listing
Modified Thu Oct 23 09:09:31 2008 UTC (10 years, 5 months ago) by phornby
Remove unused vars, do a bit of standardising of indentation, and use the new Pattern_coupling.h to eliminate some implicit function declarations in Solver_AMG.c

Revision 1916 - Directory Listing
Modified Thu Oct 23 08:51:36 2008 UTC (10 years, 5 months ago) by phornby
This is a fake commit, to note that

Finley_IndexList_insertIndex is being called from paso's Pattern.c.

I was under the impresssion that this was a violation of the module rule forbidding
paso from calling Finley code. I have not fixed this, since I am not the
best person to formulate the workaround. My immediate suggestion would be to move the
functionality into paso, and call it from Finley. However, I'm sure there is a better way.



Revision 1915 - Directory Listing
Modified Thu Oct 23 08:40:09 2008 UTC (10 years, 5 months ago) by phornby
As far as I can tell, just the new Pattern_coupling.h and Pattern_coupling.h
are all that's needed to compile Pattern_coupling.c



Revision 1914 - Directory Listing
Modified Thu Oct 23 08:31:22 2008 UTC (10 years, 5 months ago) by phornby
Adding include files back to keep Altix happy.



Revision 1913 - Directory Listing
Modified Thu Oct 23 08:27:33 2008 UTC (10 years, 5 months ago) by phornby
Create Pattern_coupling.h as there were too many modules that implicitly defined these
functions. This checkin is to test the minimum number of files this change allows me to
include to get Pattern_coupling.c to compile correctly on the Altix.



Revision 1912 - Directory Listing
Modified Thu Oct 23 05:08:31 2008 UTC (10 years, 5 months ago) by ksteube
Finished wrapper script by setting PATH.

The wrapper script reproduces the environment of the person who built
the software + values specified in his hostname_options.py file.  A
user can run a python script without setting any environment variables
or loading any SGI modules.


Revision 1909 - Directory Listing
Modified Thu Oct 23 01:47:50 2008 UTC (10 years, 5 months ago) by ksteube
Updated the wrapper script to set MPI_NUM_MEMORY_REGIONS=0 to avoid
bug where truncated messages are sent in hybrid runs under MPT MPI


Revision 1907 - Directory Listing
Modified Wed Oct 22 11:41:18 2008 UTC (10 years, 5 months ago) by phornby
Mesh_read.c - remove a debug printout introduced by me (oops).

Pattern_coupling.c - remove declaration of naib where it was not used, and remove naib frpm
omp pragmas where it was not declared, and not used.

Apparently cognac.ivec.org did not like this??



Revision 1906 - Directory Listing
Modified Wed Oct 22 08:48:32 2008 UTC (10 years, 5 months ago) by phornby
This file was pining for a final return at its end.



Revision 1905 - Directory Listing
Modified Wed Oct 22 08:40:05 2008 UTC (10 years, 5 months ago) by phornby
I did a lot of rationalising of the indentation, which looks like an alarming number of changes. I just got sick of my editor getting confused about what the indent was in this function as opposed to the last one I was working on.

The real mods. are trivial, arising from the fact that 'nix'es will write 1e-05 (say), while winblows will write 1e-005. This causes string comparisons that check the mesh file generation to fail. This, combined with the more pedantic behaviour of unlink() made pycad very fragile on windows. All fixed now.

Test on the 'nixes tonight.

May I ask for a hold off on the branch merge, Joel, till I get this stable on all platforms, and deal with the usual unused vars. that pop up from all the ifdefs?

  

Revision 1904 - Directory Listing
Modified Wed Oct 22 08:27:56 2008 UTC (10 years, 5 months ago) by phornby
This now passes on windows. The main issue was that __del__ was being called when there was no open script or mesh file??? Could not fathom why, but added an extra test in __del__ to make sure the files were actually open before closing & unlinking.  It may be better to deal with the opening, writing, closing, os.system call, and final unlinking of the script file in getMeshHandler(). That way all manipulations are local, and only the mesh file need be handled in a remote piece of code like __del__.

Not tested on Altix or linux yet.... get to that tonight.

Revision 1902 - Directory Listing
Modified Wed Oct 22 03:54:14 2008 UTC (10 years, 5 months ago) by artak
some bugs fixed in coresening methods

Revision 1900 - Directory Listing
Modified Mon Oct 20 07:33:42 2008 UTC (10 years, 6 months ago) by phornby
Fake commit to sync with my windows machine.

Fix looks like like it worked on Dedbian. Thanks.



Revision 1897 - Directory Listing
Modified Mon Oct 20 00:32:30 2008 UTC (10 years, 6 months ago) by jfenwick
Modified Data::toString() so it doesn't throw on DataEmpty.
Added setEscriptParamInt and getEscriptParamInt as free functions.
At the moment all they do is allow you to set the param TOO_MANY_LINES.
This is used to determine when printing a Data object will show you the 
points and when it will print a summary.

I've set the default value back to 80 lines.
If you need to see more lines use (in python):

setEscriptParamInt("TOO_MANY_LINES",80000)



Revision 1896 - Directory Listing
Modified Sun Oct 19 23:16:21 2008 UTC (10 years, 6 months ago) by gross
small fixes.

Revision 1895 - Directory Listing
Modified Sat Oct 18 11:06:38 2008 UTC (10 years, 6 months ago) by phornby
Remove the amalgamated test suite because it consumes too much resource on winblows

Revision 1894 - Directory Listing
Modified Sat Oct 18 11:00:08 2008 UTC (10 years, 6 months ago) by phornby
Break run_linearPDEsOnFinley.py into 3 separate test modules to avoid crashes on winblows

Revision 1893 - Directory Listing
Modified Fri Oct 17 09:59:39 2008 UTC (10 years, 6 months ago) by gross
brakets in SCAN error detection were missing.

Revision 1892 - Directory Listing
Modified Fri Oct 17 00:55:59 2008 UTC (10 years, 6 months ago) by artak
memory leak is fixed

Revision 1891 - Directory Listing
Modified Fri Oct 17 00:15:17 2008 UTC (10 years, 6 months ago) by artak
minor

Revision 1890 - Directory Listing
Modified Fri Oct 17 00:14:22 2008 UTC (10 years, 6 months ago) by artak
Current version of AMG. check levels for stoping applies presmoothing, but not ready yet

Revision 1887 - Directory Listing
Modified Wed Oct 15 03:26:25 2008 UTC (10 years, 6 months ago) by ksteube
Fixed two typos that stopped the test suite from running.

Also, gcc 4.3.2 issued several warnings not seen before:
ignoring the return value of fscanf and using the wrong format
with printf.


Revision 1883 - Directory Listing
Modified Tue Oct 14 04:46:27 2008 UTC (10 years, 6 months ago) by artak
< changed to >=

Revision 1882 - Directory Listing
Modified Tue Oct 14 04:39:02 2008 UTC (10 years, 6 months ago) by artak
minor

Revision 1881 - Directory Listing
Modified Tue Oct 14 04:34:09 2008 UTC (10 years, 6 months ago) by artak
pattern multiply, binary operation are added

Revision 1880 - Directory Listing
Modified Tue Oct 14 04:23:21 2008 UTC (10 years, 6 months ago) by caltinay
s/==/=/ in one more place in generate_dumps.py


Revision 1878 - Directory Listing
Modified Tue Oct 14 03:39:13 2008 UTC (10 years, 6 months ago) by gross
new version of JacobiFree Newton GMRES + test added.

Revision