Log of /5.2

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Revision 6691 - Directory Listing
Modified Mon Jun 25 02:28:12 2018 UTC (4 years, 7 months ago) by jfenwick
Copied from: trunk revision 6690

Prep for 5.2

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Revision 6690 - Directory Listing
Modified Mon Jun 25 02:10:43 2018 UTC (4 years, 7 months ago) by jfenwick
Original Path: trunk

Adding Adam

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Revision 6689 - Directory Listing
Modified Mon Jun 25 01:31:43 2018 UTC (4 years, 7 months ago) by jfenwick
Original Path: trunk

Added Ander

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Revision 6688 - Directory Listing
Modified Mon Jun 25 01:31:06 2018 UTC (4 years, 7 months ago) by jfenwick
Original Path: trunk

Added slightly more doco on lazy

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Revision 6687 - Directory Listing
Modified Sun Jun 17 23:36:56 2018 UTC (4 years, 7 months ago) by aellery
Original Path: trunk

Added a footnote to the start of the linearPDEs chapter of the userguide that describes the linear PDE using nabla notation.

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Revision 6686 - Directory Listing
Modified Thu Jun 14 04:01:43 2018 UTC (4 years, 7 months ago) by aellery
Original Path: trunk

Fixed some minor typos

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Revision 6685 - Directory Listing
Modified Wed Jun 13 09:32:12 2018 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

fixed filename.

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Revision 6684 - Directory Listing
Modified Wed Jun 13 04:48:44 2018 UTC (4 years, 7 months ago) by jfenwick
Original Path: trunk

ncLong is deprecated

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Revision 6683 - Directory Listing
Modified Tue Jun 12 01:00:29 2018 UTC (4 years, 7 months ago) by jfenwick
Original Path: trunk

Remove MathJax replacement (this should be handled from options file now).

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Revision 6682 - Directory Listing
Modified Tue Jun 12 00:56:30 2018 UTC (4 years, 7 months ago) by jfenwick
Original Path: trunk

Can now specify mathjax path in options file.

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Revision 6681 - Directory Listing
Modified Mon Jun 11 05:40:04 2018 UTC (4 years, 7 months ago) by jfenwick
Original Path: trunk

Deal with overfull boxes

Scaled some of the compound figures to 95%

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Revision 6680 - Directory Listing
Modified Mon Jun 11 04:55:47 2018 UTC (4 years, 7 months ago) by jfenwick
Original Path: trunk

Correct case issue in cite to visit.
Split very long lines in .bib file

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Revision 6679 - Directory Listing
Modified Mon Jun 11 04:24:41 2018 UTC (4 years, 7 months ago) by jfenwick
Original Path: trunk

Latex fixes

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Revision 6678 - Directory Listing
Modified Mon Jun 11 04:05:30 2018 UTC (4 years, 7 months ago) by jfenwick
Original Path: trunk

Fixing overfull hboxes

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Revision 6677 - Directory Listing
Modified Mon Jun 11 01:04:45 2018 UTC (4 years, 7 months ago) by jfenwick
Original Path: trunk

Fix some BiBTex issues

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Revision 6676 - Directory Listing
Modified Mon May 21 00:34:56 2018 UTC (4 years, 8 months ago) by uqagarro
Original Path: trunk

New version with gradient test corrected

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Revision 6675 - Directory Listing
Modified Mon May 21 00:32:28 2018 UTC (4 years, 8 months ago) by uqagarro
Original Path: trunk

New version with gradient test corrected

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Revision 6674 - Directory Listing
Modified Sun May 20 23:15:00 2018 UTC (4 years, 8 months ago) by uqagarro
Original Path: trunk

Temporary last version of run_specialOnSpeckly.py until I correct the new version

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Revision 6673 - Directory Listing
Modified Thu May 17 03:31:29 2018 UTC (4 years, 8 months ago) by uqagarro
Original Path: trunk

Some bugs fixed regarded to r6670

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Revision 6672 - Directory Listing
Modified Thu May 17 01:58:32 2018 UTC (4 years, 8 months ago) by uqagarro
Original Path: trunk

Fixed some index swap bugs belonging to gradient calculus on Speckley.

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Revision 6671 - Directory Listing
Modified Thu May 17 01:55:18 2018 UTC (4 years, 8 months ago) by uqagarro
Original Path: trunk

A few testsadded on run_specialOnSpeckley covering gradient error on Speckley

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Revision 6670 - Directory Listing
Modified Mon Apr 30 03:03:17 2018 UTC (4 years, 9 months ago) by uqagarro
Original Path: trunk

Raising exception for worng q type on linearPDE call

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Revision 6669 - Directory Listing
Modified Sun Apr 29 23:40:55 2018 UTC (4 years, 9 months ago) by uqagarro
Original Path: trunk

Type error corrected

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Revision 6668 - Directory Listing
Modified Wed Apr 25 23:32:03 2018 UTC (4 years, 9 months ago) by uqagarro
Original Path: trunk

More tests checking diameter calculous on util.py

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Revision 6667 - Directory Listing
Modified Thu Apr 12 03:18:19 2018 UTC (4 years, 9 months ago) by uqagarro
Original Path: trunk

Fix some debugging left

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Revision 6666 - Directory Listing
Modified Thu Apr 12 02:32:20 2018 UTC (4 years, 9 months ago) by jfenwick
Original Path: trunk

actually fix the filename

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Revision 6665 - Directory Listing
Modified Thu Apr 12 02:01:08 2018 UTC (4 years, 9 months ago) by uqagarro
Original Path: trunk

typographic bug

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Revision 6664 - Directory Listing
Modified Thu Apr 12 01:42:02 2018 UTC (4 years, 9 months ago) by uqagarro
Original Path: trunk

Bug fixed on tensor_transposed_mult method. It failed when second element
rank was 2.

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Revision 6663 - Directory Listing
Modified Thu Apr 12 01:28:12 2018 UTC (4 years, 9 months ago) by jfenwick
Original Path: trunk

Stop using hardcoded filenames in example scripts

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Revision 6662 - Directory Listing
Modified Mon Apr 9 04:12:20 2018 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

Use py3 version of sphinx

Fixes #417

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Revision 6661 - Directory Listing
Modified Mon Apr 9 04:08:21 2018 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

Removing some from X import *

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Revision 6660 - Directory Listing
Modified Mon Apr 9 01:41:05 2018 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

some docstring fixes s

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Revision 6659 - Directory Listing
Modified Mon Apr 9 00:30:36 2018 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

symlink

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Revision 6658 - Directory Listing
Modified Mon Apr 9 00:29:43 2018 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

prepare for defaulting badger to py3

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Revision 6657 - Directory Listing
Modified Thu Mar 29 04:43:17 2018 UTC (4 years, 10 months ago) by uqagarro
Original Path: trunk

Added test for IncompressibleIsotropicFlowCartesianOnFinley
with higher NE

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Revision 6656 - Directory Listing
Modified Thu Mar 29 03:28:02 2018 UTC (4 years, 10 months ago) by uqagarro
Original Path: trunk

Increased max_correction_step=50->100 parameter on update method under 
IncompressibleIsotropicFlowCartesian class so that tolerance level is
reached on run_models.py on finley.

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Revision 6655 - Directory Listing
Modified Mon Mar 26 02:11:30 2018 UTC (4 years, 10 months ago) by uqagarro
Original Path: trunk

Added tests for Diameter type functions.
Corrected spelling error in call.

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Revision 6654 - Directory Listing
Modified Mon Mar 19 01:27:25 2018 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

Make sid include netcdf4 support by default

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Revision 6653 - Directory Listing
Modified Mon Mar 19 01:24:25 2018 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

Added netcdfv4 deps to install guide

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Revision 6652 - Directory Listing
Modified Wed Mar 14 08:22:11 2018 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

makeTagMap and skeleton test

The test is there and is hooked into Finley, Dudley and Ripley.
The test does not do enough.

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Revision 6651 - Directory Listing
Modified Wed Feb 7 02:12:08 2018 UTC (5 years ago) by jfenwick
Original Path: trunk

Make everyone sad by touching all the files

Copyright dates update

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Revision 6650 - Directory Listing
Modified Tue Jan 30 03:47:05 2018 UTC (5 years ago) by caltinay
Original Path: trunk

Fix for typeError in ripley::setDecompositionPolicy.

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Revision 6649 - Directory Listing
Modified Wed Jan 3 09:33:32 2018 UTC (5 years, 1 month ago) by gross
Original Path: trunk

minimizers: bug in tolerance setting fixed.

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Revision 6648 - Directory Listing
Modified Wed Dec 20 01:46:56 2017 UTC (5 years, 1 month ago) by jfenwick
Original Path: trunk

remove dependency on esysUtils

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Revision 6647 - Directory Listing
Modified Thu Dec 7 06:52:32 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Sphinxing continues

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Revision 6646 - Directory Listing
Modified Thu Dec 7 05:14:57 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

It continues

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Revision 6645 - Directory Listing
Modified Thu Dec 7 03:06:33 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Misc fixes

Including converting some :cvar : to :note: (because sphinx wants to
cross reference them)

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Revision 6644 - Directory Listing
Modified Thu Dec 7 03:03:47 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Don't generate doc for escriptcore.

It was confusing sphinx and anything in there is either exposed elsewhere
or is not necessary for public use

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Revision 6643 - Directory Listing
Modified Thu Dec 7 02:12:20 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Switching imports over

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Revision 6642 - Directory Listing
Modified Thu Dec 7 01:07:04 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

More import fixes

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Revision 6641 - Directory Listing
Modified Thu Dec 7 01:05:41 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

cleanup index page

So we don't list all the sub packages on the main index

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Revision 6640 - Directory Listing
Modified Thu Dec 7 01:04:21 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Fix some problems which my test install didn't find

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Revision 6639 - Directory Listing
Modified Wed Dec 6 07:29:25 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

more minor tweaks

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Revision 6638 - Directory Listing
Modified Wed Dec 6 06:28:41 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

More cleanup

This work consists of fixing formatting errors in doc strings
  and
converting from ... imports    into import ... as to reduce the namespace 
pollution which is confusing sphinx

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Revision 6637 - Directory Listing
Modified Wed Dec 6 02:21:12 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Fix some sphinx errors

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Revision 6636 - Directory Listing
Modified Tue Dec 5 05:03:43 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Switch doc generating to python3-sphinx.

This will probably create some breakages.
Upside is that doco is being generated properly again (if you use py3).

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Revision 6635 - Directory Listing
Modified Tue Dec 5 05:02:14 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Update badger's idea of which distro we are on

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Revision 6634 - Directory Listing
Modified Tue Dec 5 05:01:43 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Add a package docstring to escript

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Revision 6633 - Directory Listing
Modified Tue Nov 28 07:22:39 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

more spelling

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Revision 6632 - Directory Listing
Modified Tue Nov 28 06:35:15 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Spelling mistake in man page which lintian found

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Revision 6631 - Directory Listing
Modified Mon Nov 27 00:33:52 2017 UTC (5 years, 2 months ago) by caltinay
Original Path: trunk

see if our builds succeed with intel 2018.1...

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Revision 6630 - Directory Listing
Modified Fri Nov 24 03:22:29 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

check for sympy in the specified python rather than the one scons is using

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Revision 6629 - Directory Listing
Modified Thu Nov 23 11:05:06 2017 UTC (5 years, 2 months ago) by caltinay
Original Path: trunk

fixed typo.

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Revision 6628 - Directory Listing
Modified Thu Nov 23 06:02:01 2017 UTC (5 years, 2 months ago) by caltinay
Original Path: trunk

should fix the logic for #416...

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Revision 6627 - Directory Listing
Modified Thu Nov 23 05:45:58 2017 UTC (5 years, 2 months ago) by caltinay
Original Path: trunk

g++ 7 fixes for Wimplicit-fallthrough.

Yes these are only comment changes but they are parsed, see
https://developers.redhat.com/blog/2017/03/10/wimplicit-fallthrough-in-gcc-7/

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Revision 6626 - Directory Listing
Modified Thu Nov 23 05:35:27 2017 UTC (5 years, 2 months ago) by caltinay
Original Path: trunk

Added missing break - caught by g++ 7.2

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Revision 6625 - Directory Listing
Modified Tue Nov 21 03:24:24 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

initial options for capybara

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Revision 6624 - Directory Listing
Modified Wed Nov 15 11:22:21 2017 UTC (5 years, 2 months ago) by caltinay
Original Path: trunk

Fixing idxtype long builds of finley.

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Revision 6623 - Directory Listing
Modified Thu Nov 9 02:26:55 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Building up options files for capybara.

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Revision 6622 - Directory Listing
Modified Thu Nov 9 02:24:15 2017 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Modify netcdf dependencies checks to look for the files actually being included.
(netcdfcpp.h or ncVar.h).

It turns out that behind the scenes that they both depend on netcdf.h, but it's a good idea in theory.

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Revision 6621 - Directory Listing
Modified Thu Nov 2 23:01:02 2017 UTC (5 years, 3 months ago) by jfenwick
Original Path: trunk

Report exceptions from saveCSV if the cause is locally known.

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Revision 6620 - Directory Listing
Modified Mon Aug 14 08:31:59 2017 UTC (5 years, 5 months ago) by gross
Original Path: trunk

gather function fixed.

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Revision 6619 - Directory Listing
Modified Thu Aug 3 05:41:09 2017 UTC (5 years, 6 months ago) by jfenwick
Original Path: trunk

Unicode causing a problem

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Revision 6618 - Directory Listing
Modified Wed Aug 2 07:38:37 2017 UTC (5 years, 6 months ago) by jfenwick
Original Path: trunk

Work on NetCDF4 inversion.

This does not work completely yet.

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Revision 6617 - Directory Listing
Modified Mon Jul 31 04:28:25 2017 UTC (5 years, 6 months ago) by caltinay
Original Path: trunk

added missing include.

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Revision 6616 - Directory Listing
Modified Thu Jul 27 23:42:51 2017 UTC (5 years, 6 months ago) by jfenwick
Original Path: trunk

Adding function to test what type of netcdf file we are looking at 

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Revision 6615 - Directory Listing
Modified Thu Jun 22 08:24:11 2017 UTC (5 years, 7 months ago) by jfenwick
Original Path: trunk

Fix final warning in #402

Initialise an uninitialised fd_set

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Revision 6614 - Directory Listing
Modified Thu Jun 22 06:37:41 2017 UTC (5 years, 7 months ago) by jfenwick
Original Path: trunk

Final tests for #269

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

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Revision 6613 - Directory Listing
Modified Tue Jun 20 10:09:18 2017 UTC (5 years, 7 months ago) by jfenwick
Original Path: trunk

Sigh

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Revision 6612 - Directory Listing
Modified Tue Jun 20 03:21:40 2017 UTC (5 years, 7 months ago) by jfenwick
Original Path: trunk

Merging changes from release branch

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Revision 6611 - Directory Listing
Modified Tue Jun 20 03:18:04 2017 UTC (5 years, 7 months ago) by jfenwick
Original Path: trunk

Removing to make way for more complete version from another branch.

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Revision 6610 - Directory Listing
Modified Fri Jun 9 07:26:10 2017 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

More work on the _Inf functions

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Revision 6609 - Directory Listing
Modified Thu Jun 8 07:08:54 2017 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

C++ functions Inf versions of the Nan replacement functions
No python interface or unit tests yet

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Revision 6600 - Directory Listing
Modified Tue Jun 6 07:49:33 2017 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

Missing file

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Revision 6592 - Directory Listing
Modified Mon Jun 5 02:15:01 2017 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

Some notes on trilinos

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Revision 6591 - Directory Listing
Modified Fri Jun 2 02:24:51 2017 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

Printing tagged Data now reports if tag is unused.

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

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Revision 6590 - Directory Listing
Modified Fri Jun 2 01:10:53 2017 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

Only summarise data if it is expanded

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Revision 6589 - Directory Listing
Modified Thu Jun 1 06:27:03 2017 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

Change list for 5.2.

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

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Revision 6588 - Directory Listing
Modified Thu Jun 1 01:25:24 2017 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

Describe mpi_no_host option

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Revision 6587 - Directory Listing
Modified Wed May 24 07:50:23 2017 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

Fix lazy related test failures.

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Revision 6586 - Directory Listing
Modified Tue May 23 07:00:19 2017 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

Fix broken symlinks in debian build

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

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Revision 6585 - Directory Listing
Modified Tue May 23 04:13:09 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

regenerated gradient tests for both real and complex data and moved them to a separate file.

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Revision 6584 - Directory Listing
Modified Tue May 23 01:15:08 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

typos fixed.

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Revision 6583 - Directory Listing
Modified Mon May 22 08:04:56 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Regenerated interpolation tests for both real and complex data.

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

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Revision 6582 - Directory Listing
Modified Sun May 21 09:43:12 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

fixed typo.

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Revision 6581 - Directory Listing
Modified Fri May 19 06:39:36 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Implement #412 - complex support for paso's coupler.

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

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Revision 6580 - Directory Listing
Modified Fri May 19 04:05:40 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Implemented complex dofToNodes in ripley which should fix the current segfaults.
NodesToDof still missing.

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

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Revision 6579 - Directory Listing
Modified Fri May 19 01:37:23 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Regenerated tests for integration for real & complex Data. Moved them into a
separate file which is included from the spatial functions tests so will be
picked up without changes by the domains.

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Revision 6578 - Directory Listing
Modified Wed May 17 04:16:40 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Complex interpolation in speckley.

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Revision 6577 - Directory Listing
Modified Wed May 17 02:34:45 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

complex integrals for speckley. Fixes #398

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Revision 6576 - Directory Listing
Modified Wed May 17 01:42:26 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Finished complex interpolation cases in dudley.

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Revision 6575 - Directory Listing
Modified Wed May 17 01:04:36 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

complex integration and interpolation in dudley.

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Revision 6574 - Directory Listing
Modified Wed May 17 00:53:31 2017 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

Don't call openmp function if you aren't in openmp

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Revision 6573 - Directory Listing
Modified Wed May 17 00:02:42 2017 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

Add mpi_no_host option

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

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Revision 6572 - Directory Listing
Modified Tue May 16 23:16:45 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

implementation of complex integrals in finley. (#398)

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Revision 6571 - Directory Listing
Modified Mon May 15 11:39:06 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Forgot to enable the code path.

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Revision 6570 - Directory Listing
Modified Mon May 15 11:23:29 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Complex interpolation in finley is complete.

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Revision 6569 - Directory Listing
Modified Mon May 15 10:17:13 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

complex element data interpolation in finley.

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Revision 6568 - Directory Listing
Modified Mon May 15 09:29:39 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Implemented remaining cases of complex nodal interpolation in finley.

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Revision 6567 - Directory Listing
Modified Mon May 15 07:33:56 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

This fixes #408 by implementing complex interpolation in finley from DOF to Nodes. The opposite direction is still missing.

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Revision 6566 - Directory Listing
Modified Mon May 15 05:03:56 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Implement complex interpolation in finley. This does not include Copy/AverageNodalData yet.

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Revision 6565 - Directory Listing
Modified Mon May 15 04:44:05 2017 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Preparation for complex interpolation in finley. Throws exception instead of crashing now.

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Revision 6559 - Directory Listing
Modified Wed May 10 06:21:29 2017 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

new test for tensor_transpose_mult

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Revision 6558 - Directory Listing
Modified Wed May 10 04:55:32 2017 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

Finish phase()

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

Fixes #385

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Revision 6557 - Directory Listing
Modified Tue May 9 01:22:56 2017 UTC (5 years, 9 months ago) by jfenwick
Original Path: trunk

Fix issue #409

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

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Revision 6556 - Directory Listing
Modified Mon May 8 02:42:09 2017 UTC (5 years, 9 months ago) by jfenwick
Original Path: trunk

Add compare tool.

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

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

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Revision 6555 - Directory Listing
Modified Sun May 7 11:44:34 2017 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

fixed minor typo.

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Revision 6554 - Directory Listing
Modified Wed May 3 01:15:37 2017 UTC (5 years, 9 months ago) by jfenwick
Original Path: trunk

Add a temporary work-around for #401.
Internally, tensor_transposed_mult(a,b) directly calls 
tensor_mult(a, tranpose(b)).

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

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

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Revision 6553 - Directory Listing
Modified Fri Apr 28 03:35:26 2017 UTC (5 years, 9 months ago) by jfenwick
Original Path: trunk

Fix some unused vars

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Revision 6552 - Directory Listing
Modified Wed Apr 26 02:33:23 2017 UTC (5 years, 9 months ago) by jfenwick
Original Path: trunk

Options for ferret

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Revision 6551 - Directory Listing
Modified Tue Apr 4 06:17:09 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

commenting some imports

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Revision 6550 - Directory Listing
Modified Tue Apr 4 05:34:33 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

minor tweaks

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Revision 6549 - Directory Listing
Modified Mon Mar 27 06:32:03 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Fixed various.

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

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Revision 6548 - Directory Listing
Modified Mon Mar 27 06:16:26 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Fix a missing complex->data conversion

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Revision 6547 - Directory Listing
Modified Mon Mar 27 06:15:05 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Dont assume a tensor product has a real result

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Revision 6546 - Directory Listing
Modified Mon Mar 27 00:00:49 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Add test for overloaded +

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

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Revision 6545 - Directory Listing
Modified Fri Mar 24 00:21:35 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Fixing the last commit.   (I did test it)

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Revision 6544 - Directory Listing
Modified Thu Mar 23 23:59:21 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Add two tests

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Revision 6543 - Directory Listing
Modified Thu Mar 23 06:33:16 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Adding eigenvalues_and_eigenvector test.

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

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Revision 6542 - Directory Listing
Modified Thu Mar 23 00:35:22 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Better version of earlier fix.

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

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

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Revision 6541 - Directory Listing
Modified Thu Mar 23 00:33:27 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Remove unused test category

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Revision 6540 - Directory Listing
Modified Wed Mar 22 06:50:34 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Fix nasty concurrency bug.

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

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Revision 6539 - Directory Listing
Modified Tue Mar 14 07:46:12 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Fix incorrect collapse behaviour

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

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Revision 6538 - Directory Listing
Modified Tue Mar 14 03:49:20 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Fix whereZero bugs

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

Reorder some declarations to stop the compiler complaining.

---

Revision 6537 - Directory Listing
Modified Tue Mar 14 00:01:31 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Add missing deepCopy cases

---

Revision 6536 - Directory Listing
Modified Mon Mar 13 06:30:35 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Bug fixes.

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

---

Revision 6535 - Directory Listing
Modified Mon Mar 13 04:38:47 2017 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Fix sign and abs

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

---

Revision 6534 - Directory Listing
Modified Fri Mar 10 04:47:23 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Fix crash

---

Revision 6533 - Directory Listing
Modified Fri Mar 10 04:08:40 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Lazy fixes

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

---

Revision 6532 - Directory Listing
Modified Thu Mar 9 10:32:46 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

More option files

---

Revision 6531 - Directory Listing
Modified Thu Mar 9 04:43:36 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Add Xenial options

---

Revision 6530 - Directory Listing
Modified Thu Mar 9 01:31:15 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Noting dependency on legacy-netcdf for debian styles

---

Revision 6529 - Directory Listing
Modified Thu Mar 9 01:29:12 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Adding yakkety options

---

Revision 6528 - Directory Listing
Modified Wed Mar 8 05:07:31 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Remove AUTOLAZY fiddles

---

Revision 6527 - Directory Listing
Modified Wed Mar 8 05:05:17 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Correct error messages about anti-hermitian

---

Revision 6526 - Directory Listing
Modified Wed Mar 8 03:48:11 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Fix error in m_iscompl determination

---

Revision 6525 - Directory Listing
Modified Wed Mar 8 02:11:25 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Stray print removal

---

Revision 6524 - Directory Listing
Modified Wed Mar 8 02:08:04 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

"Reordering statements involving reference params" considered dangerous

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Revision 6523 - Directory Listing
Modified Tue Mar 7 06:50:34 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

UPDATE THE COPYRIGHT DATES

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Revision 6522 - Directory Listing
Modified Tue Mar 7 05:55:32 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Various

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

---

Revision 6521 - Directory Listing
Modified Tue Mar 7 04:24:20 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Merging clazy branch

---

Revision 6519 - Directory Listing
Modified Tue Mar 7 01:55:01 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Remove debug print

---

Revision 6515 - Directory Listing
Modified Mon Mar 6 01:54:53 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

More helpful exception message

---

Revision 6510 - Directory Listing
Modified Thu Mar 2 23:47:07 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Move my netcdf variable fiddles after the environment is recreated

---

Revision 6509 - Directory Listing
Modified Thu Mar 2 07:36:17 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

netcdf build option is now 3-state

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

---

Revision 6508 - Directory Listing
Modified Thu Mar 2 03:42:31 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Weipa netcdf update

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

Need to clean up scons options control

---

Revision 6507 - Directory Listing
Modified Wed Mar 1 06:19:04 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

More netcdf4 work

Still need to convert weipa

---

Revision 6506 - Directory Listing
Modified Tue Feb 28 03:58:20 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Work on new netcdf

---

Revision 6505 - Directory Listing
Modified Tue Feb 21 06:11:12 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Work on new netcdf interface

It passes unit tests ....

---

Revision 6504 - Directory Listing
Modified Tue Feb 21 01:00:17 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Helper function to open netcdf

---

Revision 6503 - Directory Listing
Modified Mon Feb 20 03:39:19 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

netcdf4 version of load

---

Revision 6502 - Directory Listing
Modified Mon Feb 20 03:38:46 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

hiding some variables

---

Revision 6501 - Directory Listing
Modified Mon Feb 20 03:36:51 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Removing debug vectors from debug builds since netcdfc++4 doesn\'t seem to like them

---

Revision 6500 - Directory Listing
Modified Fri Feb 17 04:54:25 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Forgot to check with MPI

---

Revision 6499 - Directory Listing
Modified Thu Feb 16 06:37:07 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Work towards netcdf4

---

Revision 6498 - Directory Listing
Modified Wed Feb 15 05:12:55 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

partial workaround of complex testing issue

---

Revision 6497 - Directory Listing
Modified Wed Feb 15 00:44:55 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Reader for netcdf classic headers.

---

Revision 6496 - Directory Listing
Modified Tue Feb 14 00:38:08 2017 UTC (5 years, 11 months ago) by gross
Original Path: trunk

bug to obtain function space fixed.

---

Revision 6495 - Directory Listing
Modified Fri Feb 10 08:16:28 2017 UTC (5 years, 11 months ago) by gross
Original Path: trunk

magnetic intensity added.

---

Revision 6494 - Directory Listing
Modified Thu Feb 9 23:28:53 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

This version seems to work

---

Revision 6493 - Directory Listing
Modified Thu Feb 9 23:23:37 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Added stdlocationisprefix option

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

---

Revision 6492 - Directory Listing
Modified Thu Feb 9 07:32:43 2017 UTC (5 years, 11 months ago) by gross
Original Path: trunk

new section in inversion guide

---

Revision 6491 - Directory Listing
Modified Thu Feb 9 02:04:18 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

fix name of macports boostio

---

Revision 6490 - Directory Listing
Modified Thu Feb 9 01:21:02 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

because Darwin different

---

Revision 6489 - Directory Listing
Modified Thu Feb 9 00:28:44 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

fix it

---

Revision 6488 - Directory Listing
Modified Wed Feb 8 23:55:10 2017 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Attempt to make python detection better

---

Revision 6487 - Directory Listing
Modified Tue Feb 7 00:51:09 2017 UTC (6 years ago) by caltinay
Original Path: trunk

fix typo.

---

Revision 6486 - Directory Listing
Modified Fri Jan 27 00:13:27 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Another case of allowing complex

---

Revision 6485 - Directory Listing
Modified Wed Jan 25 04:45:38 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Some more tests

---

Revision 6484 - Directory Listing
Modified Wed Jan 25 04:43:39 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

More helpful error message

---

Revision 6483 - Directory Listing
Modified Wed Jan 25 02:56:14 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Biting bullet and doing separate generator for matrix

---

Revision 6482 - Directory Listing
Modified Tue Jan 24 07:45:33 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

More tests

Still need to look at the MVp testing

---

Revision 6481 - Directory Listing
Modified Tue Jan 24 07:34:24 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Decree: Tensor products are not always real.

---

Revision 6480 - Directory Listing
Modified Tue Jan 24 05:01:31 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Test for outer

---

Revision 6479 - Directory Listing
Modified Mon Jan 23 11:33:19 2017 UTC (6 years ago) by caltinay
Original Path: trunk

Unbreak ripley Brick.

---

Revision 6478 - Directory Listing
Modified Mon Jan 23 10:15:02 2017 UTC (6 years ago) by caltinay
Original Path: trunk

Let ripley's auto decomposition deal with this test. For <=4 ranks this
now succeeds, let's see what happens on Savanna...

---

Revision 6477 - Directory Listing
Modified Mon Jan 23 10:13:13 2017 UTC (6 years ago) by caltinay
Original Path: trunk

Fixing default decomposition policy in ripley (ouch!).

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

---

Revision 6476 - Directory Listing
Modified Mon Jan 23 08:32:07 2017 UTC (6 years ago) by caltinay
Original Path: trunk

Fix test that was way too strict - obviously something in GDAL changed that
caused the failures when comparing data origin. But 7 digits are far too
many given the data is in meters.

---

Revision 6475 - Directory Listing
Modified Fri Jan 20 02:17:33 2017 UTC (6 years ago) by caltinay
Original Path: trunk

syncing savanna options with actual dev-deps module. We had switched to
intel 17 a while back.

---

Revision 6474 - Directory Listing
Modified Fri Jan 20 00:12:46 2017 UTC (6 years ago) by gross
Original Path: trunk

docstring updated.

---

Revision 6473 - Directory Listing
Modified Thu Jan 19 07:27:04 2017 UTC (6 years ago) by caltinay
Original Path: trunk

complex integrals for ripley - part of #398. This is not properly tested.
Trying to integrate complex Data on other domains now throws rather than segfaulting.

---

Revision 6472 - Directory Listing
Modified Thu Jan 19 00:39:08 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Fix failing unit tests

---

Revision 6471 - Directory Listing
Modified Wed Jan 18 06:09:47 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Make tuples acceptable to getRank and getShape

---

Revision 6470 - Directory Listing
Modified Wed Jan 18 05:37:05 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Initial tests binary operation

---

Revision 6469 - Directory Listing
Modified Tue Jan 17 07:45:36 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Add zeroed copy

---

Revision 6468 - Directory Listing
Modified Tue Jan 17 07:35:13 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

reductions no longer ignore tags with default values

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

---

Revision 6467 - Directory Listing
Modified Wed Jan 11 03:13:14 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Fix unit test failure

---

Revision 6466 - Directory Listing
Modified Wed Jan 11 01:52:56 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Now includes tests of all ops in the original test set

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

---

Revision 6465 - Directory Listing
Modified Wed Jan 11 01:28:23 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Fix bug in get_tagged
Adding test for eigenvalues - not currently testing the scalar input case

---

Revision 6464 - Directory Listing
Modified Wed Jan 11 00:00:46 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

More tests

Rename data_only to no_scalars [which is more accurate]

---

Revision 6463 - Directory Listing
Modified Tue Jan 10 22:46:54 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Fix test failures

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

---

Revision 6462 - Directory Listing
Modified Tue Jan 10 06:37:50 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

hermitian tests debug output

---

Revision 6461 - Directory Listing
Modified Tue Jan 10 06:29:51 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Stop (anit-)hermitian from using numpy.transpose

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

---

Revision 6460 - Directory Listing
Modified Tue Jan 10 04:54:19 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Correct docstring for antihermitian

---

Revision 6459 - Directory Listing
Modified Tue Jan 10 04:28:51 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Fix build failure and add test

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

---

Revision 6458 - Directory Listing
Modified Tue Jan 10 03:04:13 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

More debug and test for transpose

---

Revision 6457 - Directory Listing
Modified Tue Jan 10 02:05:39 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

More tests

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

Tests now check rank-4 cases.

---

Revision 6456 - Directory Listing
Modified Tue Jan 10 02:03:16 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Change in whereX semantics

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

---

Revision 6455 - Directory Listing
Modified Mon Jan 9 05:35:43 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Tests and fix to util.length

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

---

Revision 6454 - Directory Listing
Modified Mon Jan 9 04:19:59 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Have unary tests for the trig now

---

Revision 6453 - Directory Listing
Modified Mon Jan 9 03:17:00 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

More tests using the more general tester.

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

---

Revision 6452 - Directory Listing
Modified Sun Jan 8 21:41:36 2017 UTC (6 years ago) by jfenwick
Original Path: trunk

Adapt to moving openmpi library

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

---

Revision 6451 - Directory Listing
Modified Tue Dec 20 06:22:39 2016 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

Added '--mca io romio314' to guineapig options to get around a regression(?) in
OMPIO.
Basically it looks like current OpenMPI in Debian blocks when calling
MPI_File_write_shared from a subset of ranks only (which we do in a test).
My understanding of the spec is that this should not block as it's not a
collective operation and it certainly works with ROMIO and IntelMPI which is
why I think it may be a regression. This should probably be asked on the
OpenMPI mailing list. I have a test case if required.

---

Revision 6450 - Directory Listing
Modified Thu Dec 15 02:33:38 2016 UTC (6 years, 1 month ago) by jfenwick
Original Path: trunk

Starting work on the unary ops

---

Revision 6449 - Directory Listing
Modified Wed Dec 14 01:01:48 2016 UTC (6 years, 1 month ago) by jfenwick
Original Path: trunk

Removing references to the old util_reduction tests.
Note that this does weaken the ability to test domains which do not support
tagging because all types are tested together now.
However, if that becomes necessary, we can query the functionspace and 
not add tagged tests if it reports not supporting tagging.
At this point, more compact tests are more important.

---

Revision 6448 - Directory Listing
Modified Tue Dec 13 06:25:52 2016 UTC (6 years, 1 month ago) by jfenwick
Original Path: trunk

Switch over to new util tests.
Fix some bugs

---

Revision 6447 - Directory Listing
Modified Tue Dec 13 05:07:30 2016 UTC (6 years, 1 month ago) by jfenwick
Original Path: trunk

Reduction tests

---

Revision 6446 - Directory Listing
Modified Tue Dec 13 04:44:28 2016 UTC (6 years, 1 month ago) by jfenwick
Original Path: trunk

Enable NAN_CHECK for all builds.
If you don't support std::isnan, then you don't support c++11

---

Revision 6445 - Directory Listing
Modified Wed Dec 7 07:01:18 2016 UTC (6 years, 2 months ago) by jfenwick
Original Path: trunk

Make sure some of the test values are negative

---

Revision 6444 - Directory Listing
Modified Tue Dec 6 08:24:19 2016 UTC (6 years, 2 months ago) by jfenwick
Original Path: trunk

More progress

---

Revision 6443 - Directory Listing
Modified Mon Dec 5 23:28:02 2016 UTC (6 years, 2 months ago) by jfenwick
Original Path: trunk

Start on test restructure

---

Revision 6442 - Directory Listing
Modified Fri Dec 2 06:17:38 2016 UTC (6 years, 2 months ago) by gross
Original Path: trunk

some modifications VGL

---

Revision 6441 - Directory Listing
Modified Tue Nov 29 07:27:03 2016 UTC (6 years, 2 months ago) by gross
Original Path: trunk

arguments fixed

---

Revision 6440 - Directory Listing
Modified Tue Nov 29 07:26:33 2016 UTC (6 years, 2 months ago) by gross
Original Path: trunk

namespace problem fixed

---

Revision 6439 - Directory Listing
Modified Tue Nov 29 05:35:33 2016 UTC (6 years, 2 months ago) by jfenwick
Original Path: trunk

Adding a comment to explain what TestDomainTest is actually for.
Remove test_assemblage_* since all of those tests are covered by
test_assemblage [I'm sure Simon warned me about that].
Collapse the 3D2 parts which depended on them.
 Other than cleaning up, this should not change what is tested.

---

Revision 6438 - Directory Listing
Modified Mon Nov 7 08:30:55 2016 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Remainder of this batch of default removing.

---

Revision 6437 - Directory Listing
Modified Mon Nov 7 04:20:32 2016 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Fix compile error introduced last time.
Fix more calls in Dudley

---

Revision 6436 - Directory Listing
Modified Mon Nov 7 01:28:47 2016 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Throw in some routines which don't support complex yet.
Fix some routines which rely on being able to get the entire 
vector by referencing relative to [0] (problem for lazy).
   This was addressed by adding a more explicit call.
Make calls to getSample?? pass explicit type parameter.

There is more to be done here.

---

Revision 6435 - Directory Listing
Modified Sat Nov 5 12:35:35 2016 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

fix for #387 in ripley - implementation of complex straightforward interpolations.

---

Revision 6434 - Directory Listing
Modified Sat Nov 5 12:16:07 2016 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Final pieces for #386: Complex gradients for Speckley 3D order 2-10. Removed workaround from escript.

---

Revision 6433 - Directory Listing
Modified Sat Nov 5 12:14:52 2016 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

#386: speckley complex gradients for 2D orders 3-10

---

Revision 6432 - Directory Listing
Modified Sat Nov 5 11:55:44 2016 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

#386 - complex gradient for speckley 2D.

---

Revision 6431 - Directory Listing
Modified Sat Nov 5 11:38:07 2016 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

#386: complex gradients for dudley.

---

Revision 6430 - Directory Listing
Modified Sat Nov 5 11:27:45 2016 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Part of #386 - complex gradients for finley.

---

Revision 6429 - Directory Listing
Modified Thu Nov 3 23:35:58 2016 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Part of #386 - complex gradient for ripley Brick.

---

Revision 6428 - Directory Listing
Modified Thu Nov 3 07:32:41 2016 UTC (6 years, 3 months ago) by gross
Original Path: trunk

workaround for Bug #389 removed

---

Revision 6427 - Directory Listing
Modified Thu Nov 3 07:32:38 2016 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Complex interpolation changes for ripley.
Needs better tests and removal of work-around once the other domains 
are done.

---

Revision 6426 - Directory Listing
Modified Thu Nov 3 05:07:00 2016 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Initial work on fixing the complex interpolation issue.
This is just Ripley::Rectangle others to follow

---

Revision 6425 - Directory Listing
Modified Thu Nov 3 03:34:29 2016 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Beginnings of interpolation fixes for complex.
I have not undone the python work-around because I still need to look
at the domains.
Starting with ripley

---

Revision 6424 - Directory Listing
Modified Thu Nov 3 02:13:09 2016 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Fixing copyWithMask to work with complex Data (issue #389)

---

Revision 6423 - Directory Listing
Modified Wed Nov 2 13:05:29 2016 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

prepare for complex gradients. Workaround in util.py still guards against badness.

---

Revision 6422 - Directory Listing
Modified Wed Nov 2 13:04:09 2016 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

and the accompanying header changes to the last commit...

---

Revision 6421 - Directory Listing
Modified Wed Nov 2 13:03:45 2016 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

implemented complex gradient for ripley 2D.

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

---

Revision 6420 - Directory Listing
Modified Wed Nov 2 06:35:58 2016 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Fix Scalar with complex

#392

---

Revision 6419 - Directory Listing
Modified Wed Nov 2 06:09:25 2016 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Fix segfault in slice assignment with complex.

Addresses issue #394

---

Revision 6418 - Directory Listing
Modified Wed Nov 2 05:04:51 2016 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Fix TensorX factories to allow passing a complex scalar.

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

---

Revision 6417 - Directory Listing
Modified Wed Nov 2 03:57:52 2016 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Fix setToZero

---

Revision 6416 - Directory Listing
Modified Wed Nov 2 03:01:53 2016 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Prevent saveDataCSV from being called with complex values

---

Revision 6415 - Directory Listing
Modified Wed Nov 2 02:46:34 2016 UTC (6 years, 3 months ago) by gross
Original Path: trunk

work around for bug #391 (right version now)

---

Revision 6414 - Directory Listing
Modified Wed Nov 2 02:44:31 2016 UTC (6 years, 3 months ago) by gross
Original Path: trunk

work around for bug #391

---

Revision 6413 - Directory Listing
Modified Wed Nov 2 02:31:11 2016 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Added untested .phase()  to Data.

---

Revision 6412 - Directory Listing
Modified Wed Nov 2 02:18:49 2016 UTC (6 years, 3 months ago) by gross
Original Path: trunk

work around for bug #390

---

Revision 6411 - Directory Listing
Modified Wed Nov 2 01:48:58 2016 UTC (6 years, 3 months ago) by gross
Original Path: trunk

work around for bug #386

---

Revision 6410 - Directory Listing
Modified Tue Nov 1 06:12:42 2016 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Very minor fix towards more repeatable builds

---

Revision 6409 - Directory Listing
Modified Thu Oct 27 07:35:14 2016 UTC (6 years, 3 months ago) by gross
Original Path: trunk

print statement removed

---

Revision 6408 - Directory Listing
Modified Thu Oct 27 03:29:59 2016 UTC (6 years, 3 months ago) by gross
Original Path: trunk

work around for  Bug #389

---

Revision 6407 - Directory Listing
Modified Wed Oct 19 03:13:45 2016 UTC (6 years, 3 months ago) by gross
Original Path: trunk

replaced complex argument by isComplex as complex is python keyword.

---

Revision 6406 - Directory Listing
Modified Wed Oct 19 02:16:52 2016 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

recording badgers trilinos options

---

Revision 6405 - Directory Listing
Modified Thu Oct 13 23:35:11 2016 UTC (6 years, 3 months ago) by gross
Original Path: trunk

interpolation from reduced to full for finley Function. needs more work

---

Revision 6404 - Directory Listing
Modified Thu Sep 22 05:37:56 2016 UTC (6 years, 4 months ago) by jfenwick
Original Path: trunk

Fixing the openmp options for icpc

---

Revision 6400 - Directory Listing
Modified Thu Sep 8 13:09:10 2016 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Should fix #381 - Trilinos support for periodic boundaries.

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

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

---

Revision 6399 - Directory Listing
Modified Wed Aug 3 00:21:25 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

fix warnings for paso-only build.

---

Revision 6398 - Directory Listing
Modified Tue Aug 2 12:39:07 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

update changelog.

---

Revision 6397 - Directory Listing
Modified Mon Aug 1 22:52:08 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

Implemented feature #281.

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

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Revision 6396 - Directory Listing
Modified Mon Aug 1 22:27:28 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

changed order of direct solver preference as the Trilinos MUMPS interface clearly has issues.

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Revision 6395 - Directory Listing
Modified Mon Aug 1 22:25:27 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

moving isDirectSolver() function to escript to correct solver library selection logic.

Also updated Ripley SystemMatrix overload with recent change.

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Revision 6394 - Directory Listing
Modified Mon Aug 1 22:00:00 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

Work towards solving #281 - added static member but unused at the moment.

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Revision 6393 - Directory Listing
Modified Mon Aug 1 06:20:09 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

Implement #379.

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

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Revision 6392 - Directory Listing
Modified Mon Aug 1 02:27:56 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

Implemented setting specific direct solver. Fixes #378

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Revision 6391 - Directory Listing
Modified Thu Jul 28 05:44:42 2016 UTC (6 years, 6 months ago) by jfenwick
Original Path: trunk

Removing instructions for installing from packages
Started changelog in user guide

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Revision 6390 - Directory Listing
Modified Wed Jul 27 07:46:27 2016 UTC (6 years, 6 months ago) by jfenwick
Original Path: trunk

Fiddling with changelog

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Revision 6389 - Directory Listing
Modified Wed Jul 27 07:39:57 2016 UTC (6 years, 6 months ago) by jfenwick
Original Path: trunk

Adding suitesparse to builddeps

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Revision 6388 - Directory Listing
Modified Wed Jul 27 04:57:45 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

add a way to modify solver options in simplesolve and use it to set
AMG block size so tests pass.

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Revision 6387 - Directory Listing
Modified Mon Jul 25 06:11:40 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

removed deprecated symbol, fixes #325

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Revision 6386 - Directory Listing
Modified Mon Jul 25 06:01:14 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

trying again to avoid mumps issue.

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Revision 6385 - Directory Listing
Modified Mon Jul 25 03:17:21 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

trying to fix remaining test failures which would have always failed but
only now are we actually running direct solvers under MPI...

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Revision 6384 - Directory Listing
Modified Mon Jul 25 02:49:01 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

modifying NE for ripley domain to circumvent Trilinos-MUMPS issue.

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

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Revision 6383 - Directory Listing
Modified Mon Jul 25 02:47:11 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

fixing parameter passing to Amesos2.

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Revision 6382 - Directory Listing
Modified Mon Jul 25 00:02:08 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

removing two duplicate tests.

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Revision 6381 - Directory Listing
Modified Fri Jul 22 09:12:46 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

changed some assertions so we get a better idea of values.

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

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Revision 6380 - Directory Listing
Modified Fri Jul 22 06:32:45 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

enable more tests that were skipped due to trilinos limitations.

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Revision 6379 - Directory Listing
Modified Fri Jul 22 06:31:38 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

fix indexing when adding to unrolled matrix...

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Revision 6378 - Directory Listing
Modified Fri Jul 22 06:05:44 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

added unroll flag to dudley and finley and enabled tests that were skipped
before.

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Revision 6377 - Directory Listing
Modified Fri Jul 22 05:49:14 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

add ILUT to the cases that require unrolling. Enable previously disabled tests
in ripley that now pass.
There are now bogus failures because the wrapper no longer throws for cases
that were not supported earlier. I can't fix that before changing finley and
dudley...

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Revision 6376 - Directory Listing
Modified Fri Jul 22 05:35:20 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

Woohoo! We can now 'unroll' Trilinos block matrices in order to get around the
limitations of Trilinos for solving block problems.
This commit adds the functionality to the wrapper and enables it for ripley.
dudley and finley will follow and I haven't enabled the tests yet.

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Revision 6375 - Directory Listing
Modified Fri Jul 22 00:27:31 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

finally, allow setting direct solver params from python.

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Revision 6374 - Directory Listing
Modified Thu Jul 21 05:00:24 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

Pass preconditioner options to Trilinos.

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Revision 6373 - Directory Listing
Modified Wed Jul 20 23:47:10 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

moved util method to separate header. Started setting options for preconditioners.

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Revision 6372 - Directory Listing
Modified Wed Jul 20 06:14:51 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

We can now pass Trilinos options through the SolverBuddy.

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

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Revision 6371 - Directory Listing
Modified Wed Jul 20 03:02:32 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

replicated the changes that keep factorization/problem for block matrices.

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Revision 6370 - Directory Listing
Modified Wed Jul 20 01:47:26 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

fix my launcher.

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Revision 6369 - Directory Listing
Modified Tue Jul 19 07:11:15 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

Trilinoswrap now keeps previously computed factorizations in case of
direct solver, and previously set 'problem' in case of iterative solver.

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

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

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Revision 6368 - Directory Listing
Modified Tue Jul 19 07:03:29 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

diagnostics reporting in block matrix wrapper.

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Revision 6367 - Directory Listing
Modified Tue Jul 19 04:56:16 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

SolverBuddy: overload updateDiagnostics so we can call it from C++ - not ideal
but quick fix before a revamp of the whole class.
TrilinosMatrix: update solver diagnostics for time, residual and num iter.
RipleyMatrix: don't copy the SolverBuddy so the diags are actually returned.

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Revision 6366 - Directory Listing
Modified Mon Jul 18 23:16:50 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

allow oversubscribe on guineapig for gmsh mpi invocation.

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Revision 6365 - Directory Listing
Modified Mon Jul 18 11:23:09 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

remove -host arg on guineapig to avoid the new openmpi behaviour. We
probably need a bit more logic to fix this properly and more generally.

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Revision 6364 - Directory Listing
Modified Mon Jul 18 02:25:04 2016 UTC (6 years, 6 months ago) by jfenwick
Original Path: trunk

Force shorter trees to get lazy testing done in reasonable time

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Revision 6363 - Directory Listing
Modified Tue Jul 12 06:23:40 2016 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

update solver diagnostics for cusp solvers.

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Revision 6362 - Directory Listing
Modified Thu Jul 7 03:12:06 2016 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Doesn't fix any major problem bit closes #370

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

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Revision 6361 - Directory Listing
Modified Wed Jul 6 04:10:30 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

change solver tolerance for joint inversion test which takes too long with Lazy.

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Revision 6360 - Directory Listing
Modified Wed Jul 6 03:02:30 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

complex finley contact elements.

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Revision 6359 - Directory Listing
Modified Wed Jul 6 02:44:18 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

finley complex dirac.

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Revision 6358 - Directory Listing
Modified Wed Jul 6 02:38:10 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

complex finley 3D PDE systems.

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Revision 6357 - Directory Listing
Modified Wed Jul 6 02:24:03 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

complex finley 2D PDE systems.

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Revision 6356 - Directory Listing
Modified Wed Jul 6 01:53:11 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

complex finley single 3D PDEs.

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Revision 6355 - Directory Listing
Modified Wed Jul 6 01:03:10 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

fix compile without trilinos and add support for 2D complex single PDEs to finley.

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Revision 6354 - Directory Listing
Modified Wed Jul 6 00:24:29 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

first step for complex PDEs in finley.

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Revision 6353 - Directory Listing
Modified Tue Jul 5 06:36:20 2016 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Another attempt to fix #372

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Revision 6352 - Directory Listing
Modified Tue Jul 5 05:53:49 2016 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Fixing summary for complex data

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Revision 6351 - Directory Listing
Modified Tue Jul 5 05:47:29 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

dudley complex dirac.

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Revision 6350 - Directory Listing
Modified Tue Jul 5 05:42:37 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

complex dudley 3D PDE systems.

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Revision 6349 - Directory Listing
Modified Tue Jul 5 05:33:02 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

complex dudley 2D systems.

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Revision 6348 - Directory Listing
Modified Tue Jul 5 05:31:48 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

interrogate coefficient for value type rather than PDE.

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

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Revision 6347 - Directory Listing
Modified Tue Jul 5 04:50:14 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

complex support for dudley 3D single PDEs.

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Revision 6346 - Directory Listing
Modified Mon Jul 4 07:27:36 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

oops, sorry.

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Revision 6345 - Directory Listing
Modified Mon Jul 4 05:32:05 2016 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Converting minGlobalDataPoint and maxGlobalDataPoint to internal_
That way people should not be using it and we can get rid of #5

Fixed a minor error in an error message.

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Revision 6344 - Directory Listing
Modified Mon Jul 4 03:19:25 2016 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Fix #372
Add some minimal testing
Change some references to "view"

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Revision 6343 - Directory Listing
Modified Mon Jul 4 02:11:54 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

implemented complex-valued 2D single PDE solves with dudley.

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Revision 6342 - Directory Listing
Modified Mon Jul 4 01:27:07 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

enable complex PDE solves in 3D with ripley.

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Revision 6341 - Directory Listing
Modified Sun Jul 3 23:56:33 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

fixing type for smoother argument.

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Revision 6340 - Directory Listing
Modified Fri Jul 1 12:58:45 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

Final piece of the puzzle: enable nullifyRowsAndCols for complex matrices.

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

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

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Revision 6339 - Directory Listing
Modified Fri Jul 1 12:56:43 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

(2.1) use the right type for solution vector.

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Revision 6338 - Directory Listing
Modified Fri Jul 1 12:42:35 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

(5) this is the first big one -

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

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Revision 6337 - Directory Listing
Modified Fri Jul 1 12:38:18 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

(4) add complex argument to LinearProblem, LinearPDE and PDECoef.

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Revision 6336 - Directory Listing
Modified Fri Jul 1 12:37:05 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

(3) add isComplex & setComplex to solver options.

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Revision 6335 - Directory Listing
Modified Fri Jul 1 12:36:22 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

(2) use the right type to initialize Data object for mat-vec mult.

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Revision 6334 - Directory Listing
Modified Fri Jul 1 12:35:42 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

The next few commits will start introducing complex-valued PDEs to escript.

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

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Revision 6333 - Directory Listing
Modified Fri Jul 1 03:58:43 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

write some more features into buildvars.

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Revision 6332 - Directory Listing
Modified Thu Jun 30 09:32:40 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

missed one.

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Revision 6331 - Directory Listing
Modified Thu Jun 30 09:31:06 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

fixing unreachable code warnings issued by nvcc.

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Revision 6330 - Directory Listing
Modified Sat Jun 25 11:36:26 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

added missing x.

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Revision 6329 - Directory Listing
Modified Fri Jun 24 04:19:10 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

*sigh* add another barrier for file writer test - still not convinced openMPI
behaves properly.

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Revision 6328 - Directory Listing
Modified Fri Jun 24 00:36:00 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

try again - store exception in another var to avoid it becoming out of context.

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Revision 6327 - Directory Listing
Modified Thu Jun 23 21:42:45 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

tweak solver tolerance for all trilinos order 2 pde's in finley

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Revision 6326 - Directory Listing
Modified Thu Jun 23 10:32:39 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

more Amesos2 skips.

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Revision 6325 - Directory Listing
Modified Thu Jun 23 09:12:54 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

oops, these tests use pde systems so can't use Amesos2 yet.

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Revision 6324 - Directory Listing
Modified Thu Jun 23 06:26:22 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

fix.

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Revision 6323 - Directory Listing
Modified Thu Jun 23 06:05:23 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

skip ILUT block tests with trilinos.

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Revision 6322 - Directory Listing
Modified Thu Jun 23 05:56:49 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

don't reference e before assignment.

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Revision 6321 - Directory Listing
Modified Thu Jun 23 05:38:50 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

feature #3: this should fix up remaining tests that only checked paso_direct.
I also moved paso_direct to 'hasFeature' as it's a boolean...

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Revision 6320 - Directory Listing
Modified Thu Jun 23 05:22:01 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

i broke it.

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Revision 6319 - Directory Listing
Modified Thu Jun 23 05:01:39 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

remove Super LU from everywhere, we never supported it and never will directly.

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Revision 6318 - Directory Listing
Modified Thu Jun 23 04:58:46 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

remove pastix from everywhere. We never supported it and never will directly.

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Revision 6317 - Directory Listing
Modified Thu Jun 23 04:48:29 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

parts for feature #3 - automatically choose trilinos if:
1) package == default
2) method == direct
3) trilinos available
4) mpi size > 1

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Revision 6316 - Directory Listing
Modified Thu Jun 23 04:25:56 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

update tests, we now support pde systems with trilinos.

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Revision 6315 - Directory Listing
Modified Wed Jun 22 03:59:33 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

lookin' good so unskip more tests.

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Revision 6314 - Directory Listing
Modified Tue Jun 21 23:27:35 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

set mat error tolerance for LSQR as well.

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Revision 6313 - Directory Listing
Modified Tue Jun 21 22:58:20 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

forgot to change a line.

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Revision 6312 - Directory Listing
Modified Tue Jun 21 06:51:27 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

re-enable MueLu with long-index builds. There are only a few tweaks required
in Trilinos which I have done locally so if the tests pass we can go from
there.

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Revision 6311 - Directory Listing
Modified Tue Jun 21 06:41:55 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

lots of noise due to reformatting but mainly added braces around parallel
loops within switch so nvcc doesn't choke.

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Revision 6310 - Directory Listing
Modified Tue Jun 21 04:18:28 2016 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Bringing in some changes from debian

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Revision 6309 - Directory Listing
Modified Tue Jun 21 01:15:15 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

updated mole py3 options.

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Revision 6308 - Directory Listing
Modified Mon Jun 20 01:59:34 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

trying to fix remaining trilinos errors.

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Revision 6307 - Directory Listing
Modified Sun Jun 19 11:05:47 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

fixing order of expressions in nlpde so Lsup works in MPI.
Also only do the lsup's if required (debug output).

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Revision 6306 - Directory Listing
Modified Sat Jun 18 13:26:00 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

fix test

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Revision 6305 - Directory Listing
Modified Sat Jun 18 11:11:30 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

suppress sympy warning with py3

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Revision 6304 - Directory Listing
Modified Sat Jun 18 11:00:33 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

tweak.

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Revision 6303 - Directory Listing
Modified Sat Jun 18 10:53:18 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

changed default value for ILUT drop tolerance and fixed a typo.

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Revision 6302 - Directory Listing
Modified Fri Jun 17 09:27:13 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

off-by-one errors.

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Revision 6301 - Directory Listing
Modified Fri Jun 17 07:45:23 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

yes

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Revision 6300 - Directory Listing
Modified Fri Jun 17 07:03:44 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

another attempt to fix the logic.

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Revision 6299 - Directory Listing
Modified Fri Jun 17 05:53:58 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

fix paso direct solver detection logic in tests.

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Revision 6298 - Directory Listing
Modified Fri Jun 17 04:00:35 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

type fixes in debug mode and savanna lib reference fix.

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Revision 6297 - Directory Listing
Modified Fri Jun 17 00:05:11 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

make lazy-related config options tristate variables.

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Revision 6296 - Directory Listing
Modified Thu Jun 16 23:58:54 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

don't claim to have paso direct solvers without paso.
Fix tests accordingly as well.

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Revision 6295 - Directory Listing
Modified Thu Jun 16 23:53:23 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

mara options update.

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Revision 6294 - Directory Listing
Modified Thu Jun 16 10:35:10 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

added default trilinos options to savanna.

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Revision 6293 - Directory Listing
Modified Thu Jun 16 08:34:17 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

more test fixes.

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Revision 6292 - Directory Listing
Modified Thu Jun 16 06:18:23 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

fix for non-mpi build. this time tested.

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Revision 6291 - Directory Listing
Modified Thu Jun 16 05:47:55 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

advertise if escript was built with long indices as this means we can't run
MueLu (AMG) tests. Increased number of GS sweeps for a test that hangs again.

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Revision 6290 - Directory Listing
Modified Thu Jun 16 01:49:20 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

attempt to fix non-mpi build. not tested.

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Revision 6289 - Directory Listing
Modified Wed Jun 15 22:43:24 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

ILUT does not appear to work with Trilinos block matrices

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Revision 6288 - Directory Listing
Modified Wed Jun 15 13:23:14 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

starting to move savanna to py3 toolchain.

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Revision 6287 - Directory Listing
Modified Wed Jun 15 06:33:57 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

add c++11 flag to all compilers by default.

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Revision 6286 - Directory Listing
Modified Wed Jun 15 06:21:00 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

added trilinos options (not actually installed yet).

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Revision 6285 - Directory Listing
Modified Wed Jun 15 06:19:18 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

new mole options. There doesn't seem to be a boost-python3 yet so
the py3 builds will fail.

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Revision 6284 - Directory Listing
Modified Wed Jun 15 06:05:20 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

newton changes for buildbot.

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Revision 6283 - Directory Listing
Modified Wed Jun 15 05:58:34 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

Preparing for buildbot changes.

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Revision 6282 - Directory Listing
Modified Tue Jun 14 04:54:01 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

changes to finley tests. See last few commits for details.

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Revision 6281 - Directory Listing
Modified Tue Jun 14 02:42:32 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

Changes to dudley tests. See last commit.
The main things are: separated all test classes that were inheriting from more
than one base class. Also switched to a glob in SConscript as some tests files
were not even in the list to be run.

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Revision 6280 - Directory Listing
Modified Tue Jun 14 02:39:13 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

BIG FAT MAJOR OOPS!
It looks like some of our tests have never actually run because something
goes wrong when a test class inherits from multiple test classes in escript.
Dudley never supported contact elements, yet only some of the tests were marked
as skipped. Symfuncs refers to self.RES_TOL which was never defined.

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

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Revision 6279 - Directory Listing
Modified Mon Jun 13 07:05:21 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

this should fix most of the remaining trilinos test failures.

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Revision 6278 - Directory Listing
Modified Mon Jun 13 06:39:59 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

trilinos-based interpolation from DOF->ReducedNodes in finley.

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Revision 6277 - Directory Listing
Modified Mon Jun 13 06:18:44 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

implemented trilinos-based interpolation from red. DOF -> reducedNodes in finley.
Replaced some assertTrue's by more specific tests for more useful output.

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Revision 6276 - Directory Listing
Modified Mon Jun 13 05:27:47 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

get around the fact that we're overriding cxx_extra on the command line.

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Revision 6275 - Directory Listing
Modified Mon Jun 13 03:28:07 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

missing dependency?

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Revision 6274 - Directory Listing
Modified Mon Jun 13 02:02:34 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

another one.

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Revision 6273 - Directory Listing
Modified Mon Jun 13 01:01:53 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

same as last one.

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Revision 6272 - Directory Listing
Modified Mon Jun 13 01:00:49 2016 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

don't sys.exit if there is no pyproj.

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Revision 6271 - Directory Listing
Modified Thu Jun 9 04:30:10 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

work around the fact that closing a MPI shared file does not always
have barrier semantics.

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Revision 6270 - Directory Listing
Modified Thu Jun 9 00:46:11 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

added preliminary tinaroo options

---

Revision 6269 - Directory Listing
Modified Wed Jun 8 04:29:26 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fix intel warnings

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Revision 6268 - Directory Listing
Modified Wed Jun 8 02:14:17 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

use configured python in launcher

---

Revision 6267 - Directory Listing
Modified Wed Jun 8 01:57:48 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

Fixing test that appears to depend on filesystem type/MPI implementation.

---

Revision 6266 - Directory Listing
Modified Fri Jun 3 12:00:02 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

avoid the oversubscribing issue by disabling cpu binding on guineapig.

---

Revision 6265 - Directory Listing
Modified Fri Jun 3 06:31:31 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

update to guineapig options file. We now inherit from sid.

---

Revision 6264 - Directory Listing
Modified Fri Jun 3 06:23:10 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fixing last dudley failures with trilinos. MueLu is not compatible with
block matrices yet so skip those tests. On the other hand we can now run
AMG tests with >1 rank.

---

Revision 6263 - Directory Listing
Modified Fri Jun 3 06:03:20 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fixing another shared pointer race condition by caching a value.

---

Revision 6262 - Directory Listing
Modified Fri Jun 3 05:14:55 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fix some tests with trilinos.
We now support direct solvers with mpi but not with pde systems.

---

Revision 6261 - Directory Listing
Modified Fri Jun 3 05:13:03 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fixed shared ptr race in dudley. Store pointer to matrix rather than
shared ptr when assembling PDE. This could be considered part of #365

---

Revision 6260 - Directory Listing
Modified Fri Jun 3 04:15:26 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

modify solver tolerance for trilinos for some tests.
Paso's Jacobi seems to do a better job.

---

Revision 6259 - Directory Listing
Modified Fri Jun 3 03:07:20 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

do not require Zoltan2.

---

Revision 6258 - Directory Listing
Modified Fri Jun 3 00:34:00 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

ditto for assertAlmostEquals

---

Revision 6257 - Directory Listing
Modified Fri Jun 3 00:30:37 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

s/assertEquals/assertEqual/g since the former is deprecated.

---

Revision 6256 - Directory Listing
Modified Thu Jun 2 23:03:48 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

added missing requireWrite().

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Revision 6255 - Directory Listing
Modified Thu Jun 2 06:52:06 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

modified build summary so we save some space and make clear what solvers
are available.

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Revision 6254 - Directory Listing
Modified Thu Jun 2 05:22:41 2016 UTC (6 years, 8 months ago) by jfenwick
Original Path: trunk

Standards bump

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Revision 6253 - Directory Listing
Modified Thu Jun 2 05:04:41 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

...final?

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Revision 6252 - Directory Listing
Modified Thu Jun 2 05:02:50 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

brrr, they switched from reporting via stderr to stdout...

---

Revision 6251 - Directory Listing
Modified Thu Jun 2 04:58:45 2016 UTC (6 years, 8 months ago) by jfenwick
Original Path: trunk

Hoping to make lintian happier

---

Revision 6250 - Directory Listing
Modified Thu Jun 2 04:44:29 2016 UTC (6 years, 8 months ago) by jfenwick
Original Path: trunk

Change the ssh agent to use when there is no ssh.
Since this situation only arises in debian testing in chroots,
I think it is ok not to expose this as a configuration option.

---

Revision 6249 - Directory Listing
Modified Thu Jun 2 04:37:00 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fixes #368 - if this is openmpi try to get the version to determine default
options.

---

Revision 6248 - Directory Listing
Modified Thu Jun 2 04:13:21 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

more scons changes:
- replaced p.stdout.read... by p.communicate as recommended by doco
- moved python lib name enquiry logic from options file into dependencies.py
- reporting python version in summary now.

---

Revision 6247 - Directory Listing
Modified Thu Jun 2 02:35:41 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

Another change that may break things...
- added new TristateVariable to scons
- use it only for lapack for now whose value now defaults to 'auto', i.e.
   if mkl is installed, use it, otherwise try to link with atlas, all
   unless longindices is True.
- updated options files accordingly.

---

Revision 6246 - Directory Listing
Modified Thu Jun 2 00:47:54 2016 UTC (6 years, 8 months ago) by jfenwick
Original Path: trunk

Let's try this

---

Revision 6245 - Directory Listing
Modified Thu Jun 2 00:35:02 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

do not override launcher on guineapig - py3 tests failed because we used
mpirun for a non-mpi build and ran gmsh twice in a row.

---

Revision 6244 - Directory Listing
Modified Wed Jun 1 10:41:29 2016 UTC (6 years, 8 months ago) by jfenwick
Original Path: trunk

Fixing imports after options file changes

---

Revision 6243 - Directory Listing
Modified Wed Jun 1 09:50:18 2016 UTC (6 years, 8 months ago) by jfenwick
Original Path: trunk

move overlord path setting to cxx_extra after options file changes

---

Revision 6242 - Directory Listing
Modified Wed Jun 1 07:57:06 2016 UTC (6 years, 8 months ago) by jfenwick
Original Path: trunk

Try to get build testing working

---

Revision 6241 - Directory Listing
Modified Wed Jun 1 06:00:06 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

**Warning, this may break your build**
- Bumped required options version to 203 - new options for trilinos, paso, weipa
- scons/templates/README_FIRST is now the file that explains all the options,
  added comment to README but need to change install guide still.
- removed some obsolete options files
- removed most comments from template files, they now refer to README_FIRST
- removed usepython3 option as we now determine this based on python version
  string.
- enabled use of numpy.h with python 3 (last commit should have fixed the
  issues)

---

Revision 6240 - Directory Listing
Modified Wed Jun 1 05:52:38 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

WrappedArray is now compatible with python 3, i.e. we can now use numpy.h
with python 3.

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Revision 6239 - Directory Listing
Modified Wed Jun 1 01:34:54 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

intialize sin_zero to be on the safe side (CID 99655)

---

Revision 6238 - Directory Listing
Modified Wed Jun 1 01:24:29 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fixing coverity-detected leaks CID 99614,99615

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Revision 6237 - Directory Listing
Modified Wed Jun 1 01:17:10 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fixing coverity-detected leak CID 99603

---

Revision 6236 - Directory Listing
Modified Wed Jun 1 01:09:03 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fixing coverity-detected leaks CID 115857,115858.

---

Revision 6235 - Directory Listing
Modified Wed Jun 1 01:05:29 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fixing coverity-detected leaks CID 115859,115860,115861.

---

Revision 6234 - Directory Listing
Modified Wed Jun 1 01:00:21 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fixing coverity-detected leaks CID 115863,115864,115865.

---

Revision 6233 - Directory Listing
Modified Mon May 30 23:45:53 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

i broke the other end. Hope this fixes it.

---

Revision 6232 - Directory Listing
Modified Mon May 30 04:21:28 2016 UTC (6 years, 8 months ago) by jfenwick
Original Path: trunk

Other changes to match the previous commit.

---

Revision 6231 - Directory Listing
Modified Mon May 30 03:50:37 2016 UTC (6 years, 8 months ago) by jfenwick
Original Path: trunk

I don't think we need this (and debian points out that it doesn't have a copyright notice).

---

Revision 6230 - Directory Listing
Modified Sun May 29 10:46:41 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

unfortunately we need to skip this test now when both escript and gmsh
is built with MPI. Another solution would be to add another function to
gmshrunner for merging meshes and call it instead of subprocess.call(...)

---

Revision 6229 - Directory Listing
Modified Sun May 29 10:42:41 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

how on earth did we miss this before??!

---

Revision 6228 - Directory Listing
Modified Sat May 28 10:21:18 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

non-mpi is a thing

---

Revision 6227 - Directory Listing
Modified Fri May 27 09:59:21 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

change to a cppunit assertion which currently fails on guineapig to make it
output a sane error.

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

---

Revision 6226 - Directory Listing
Modified Fri May 27 02:55:38 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fix modellib test to use feature checker for gmsh.

---

Revision 6225 - Directory Listing
Modified Fri May 27 01:47:50 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fixed deprecation warning

---

Revision 6224 - Directory Listing
Modified Thu May 26 06:33:37 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fix newton options file.

---

Revision 6223 - Directory Listing
Modified Thu May 26 01:06:02 2016 UTC (6 years, 8 months ago) by jfenwick
Original Path: trunk

Fixes to itest.sh and extract tests

---

Revision 6222 - Directory Listing
Modified Wed May 25 23:36:21 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

updated gp options for stretch.

---

Revision 6221 - Directory Listing
Modified Wed May 25 12:26:50 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

don't use MueLu with index type long - lapack is incompatible.

---

Revision 6220 - Directory Listing
Modified Wed May 25 09:48:35 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

add some colour to my compiler errors

---

Revision 6219 - Directory Listing
Modified Wed May 25 07:00:28 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

skip paso test in finley without paso and fix assemble parameter issue
without paso.

---

Revision 6218 - Directory Listing
Modified Mon May 23 13:42:19 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fixed typo.

---

Revision 6217 - Directory Listing
Modified Mon May 23 06:57:40 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

increase GS sweeps once more.

---

Revision 6216 - Directory Listing
Modified Mon May 23 06:52:32 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

trying to support 2nd order elements in finley with trilinos. WIP

---

Revision 6215 - Directory Listing
Modified Mon May 23 02:58:03 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

trilinos-based DOF->node interpolation in finley. Not complete yet.

---

Revision 6214 - Directory Listing
Modified Fri May 20 07:04:31 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

implemented trilinos interpolation from DOF->nodes in dudley.

---

Revision 6213 - Directory Listing
Modified Fri May 20 04:32:25 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

can now interpolate multi-component Data objects from DOF -> nodes with
trilinos in ripley.

---

Revision 6212 - Directory Listing
Modified Tue May 17 00:52:16 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

typo with trilinos.

---

Revision 6211 - Directory Listing
Modified Mon May 16 11:48:02 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

guard slave-only functions in readgmsh to avoid unused func warnings in
non-MPI builds.

---

Revision 6210 - Directory Listing
Modified Mon May 16 08:42:05 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

more test adjustments.

---

Revision 6209 - Directory Listing
Modified Mon May 16 04:32:21 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fixed typo.

---

Revision 6208 - Directory Listing
Modified Mon May 16 02:17:37 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

rebaseline test meshes.

---

Revision 6207 - Directory Listing
Modified Mon May 16 00:49:48 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

merged finley Mesh and MeshAdapter into FinleyDomain.

---

Revision 6206 - Directory Listing
Modified Sun May 15 12:18:58 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fix test.

---

Revision 6205 - Directory Listing
Modified Sun May 15 09:40:50 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

minor changes to sync dudley and finley.

---

Revision 6204 - Directory Listing
Modified Thu May 12 23:05:56 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

fixed types for index type long.

---

Revision 6203 - Directory Listing
Modified Wed May 11 06:13:51 2016 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

dudley: merged Mesh and MeshAdapter into DudleyDomain to finally remove the
now unnecessary indirection. If all builders are happy we can do the same
for finley.

---

Revision 6202 - Directory Listing
Modified Thu May 5 04:47:09 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

slightly better error messages on test failure in pdetools.

---

Revision 6201 - Directory Listing
Modified Thu May 5 04:32:02 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

re-increase num GS sweeps in test now that it succeeds with paso. Trilinos
requires this

---

Revision 6200 - Directory Listing
Modified Wed May 4 23:57:49 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

paso: allow saving to matrix market with >1 rank by collecting matrix on master.

---

Revision 6199 - Directory Listing
Modified Wed May 4 23:56:52 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

addresses #366. Gauss-Seidel sweeps now only use the main block of the
system matrix.

---

Revision 6198 - Directory Listing
Modified Wed May 4 06:17:49 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

resetting number of GS sweeps to 1 in MINRES test. See bug #366

---

Revision 6197 - Directory Listing
Modified Fri Apr 29 14:02:32 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

moved Distribution struct to escript and updated domains accordingly.
We can now build the full escript suite without paso (-:

---

Revision 6196 - Directory Listing
Modified Thu Apr 28 03:38:25 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

It looks like there is an issue with paso's GAUSS-SEIDEL and parallel domains
where some ranks have no element, or similar(?)
Getting around this in the unit tests now by optimizing domain distribution,
obviously that only works with parmetis. Alternative would be to use slightly
larger test domains.

---

Revision 6195 - Directory Listing
Modified Thu Apr 28 01:10:46 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

more tweaking.

---

Revision 6194 - Directory Listing
Modified Wed Apr 27 23:46:30 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

lowering number of GS sweeps again to see if intel-hybrid likes it.

---

Revision 6193 - Directory Listing
Modified Wed Apr 27 06:11:40 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

preparations for paso-less dudley.

---

Revision 6192 - Directory Listing
Modified Wed Apr 27 05:53:11 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

moved createRandomVector from distribution to AMG, the only place it is
needed. This is in preparation for moving the lightweight Distribution
struct to escript so it can be used without paso.

---

Revision 6191 - Directory Listing
Modified Wed Apr 27 05:24:32 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

use omp reduction operator now that we don't care about gcc 4.4.

---

Revision 6190 - Directory Listing
Modified Wed Apr 27 05:23:15 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

moved numPositives from paso::Distribution to paso::util.

---

Revision 6189 - Directory Listing
Modified Wed Apr 27 03:39:21 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

PRES20 is synonymous with GMRES and ILU0 with RILU in trilinos for now until
we have the proper options in place.

---

Revision 6188 - Directory Listing
Modified Wed Apr 27 03:38:10 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

silence trilinos matrix constructors and remove unneeded code as the devs
confirmed we don't need resumeFill/fillComplete for block matrices.

---

Revision 6187 - Directory Listing
Modified Wed Apr 27 03:36:18 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

don't test REC_ILU which has never been supported (and paso silently fell
back to Jacobi). Test ILUT instead which is not supported by paso either but
Trilinos.

---

Revision 6186 - Directory Listing
Modified Wed Apr 27 01:34:39 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

fixed typo for block matrices.

---

Revision 6185 - Directory Listing
Modified Wed Apr 27 01:34:17 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

only run paso tests when paso is installed - for now in ripley.

---

Revision 6184 - Directory Listing
Modified Wed Apr 27 01:30:57 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

more fixes to weipa readerlib build

---

Revision 6183 - Directory Listing
Modified Wed Apr 27 00:09:32 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

fix weipa readerlib build.

---

Revision 6182 - Directory Listing
Modified Tue Apr 26 06:31:51 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

rather than skipping pde system tests with trilinos we now expect failures,
which actually translate to quite a few unexpected successes.
There is still a threading issue somewhere...

---

Revision 6181 - Directory Listing
Modified Tue Apr 26 06:16:15 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

added support for (experimental) block matrices in Trilinos.
They appear to be much slower and only a limited number of
solvers/preconditioners are supported but it's a start.
Test updates pending.

---

Revision 6180 - Directory Listing
Modified Sat Apr 16 04:53:19 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

fix escriptreader dependencies

---

Revision 6179 - Directory Listing
Modified Fri Apr 15 12:48:58 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

ditto.

---

Revision 6178 - Directory Listing
Modified Fri Apr 15 10:43:52 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

missed these.

---

Revision 6177 - Directory Listing
Modified Fri Apr 15 08:26:07 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

fixed typo

---

Revision 6176 - Directory Listing
Modified Fri Apr 15 07:10:51 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

fix OMP race conditions in trilinos matrix.

---

Revision 6175 - Directory Listing
Modified Fri Apr 15 06:59:14 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

make sure to copy python lists rather than adding on or PrependUnique is
useless.

---

Revision 6174 - Directory Listing
Modified Fri Apr 15 03:41:03 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

Some reorganisation of EscriptParams and related changes.
We now distinguish between modifiable parameters and build features.
To interrogate the latter use:
escript::hasFeature()  [ python: escript.hasFeature() ]
and
escript::listFeatures() [ python: escript.listFeatures() ]

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

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

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

---

Revision 6173 - Directory Listing
Modified Thu Apr 14 05:56:55 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

moved reference to JMPI down to Coupler.

---

Revision 6172 - Directory Listing
Modified Thu Apr 14 05:15:27 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

type change in paso.

---

Revision 6171 - Directory Listing
Modified Wed Apr 13 13:39:08 2016 UTC (6 years, 9 months ago) by jfenwick
Original Path: trunk

adding tests to tagged versions

---

Revision 6170 - Directory Listing
Modified Wed Apr 13 07:46:34 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

moved common code to base class in ripley and implemented single-component
dofToNodes with trilinos.

---

Revision 6169 - Directory Listing
Modified Wed Apr 13 05:24:45 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

ripley now builds without paso but dof2nodes is currently unimplemented then.

---

Revision 6168 - Directory Listing
Modified Wed Apr 13 03:08:12 2016 UTC (6 years, 9 months ago) by jfenwick
Original Path: trunk

Making Lazy and the rest of escript use the same operator enumeration

---

Revision 6167 - Directory Listing
Modified Tue Apr 12 09:34:03 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

forgot to commit.

---

Revision 6166 - Directory Listing
Modified Tue Apr 12 06:51:37 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

Starting to make Paso optional in ripley.

---

Revision 6165 - Directory Listing
Modified Mon Apr 11 10:25:51 2016 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

limit number of elements in speckley test.

---

Revision 6164 - Directory Listing
Modified Mon Apr 11 06:06:43 2016 UTC (6 years, 9 months ago) by jfenwick
Original Path: trunk

Test fixes and more tests

---

Revision 6163 - Directory Listing
Modified Sun Apr 10 23:44:11 2016 UTC (6 years, 9 months ago) by jfenwick
Original Path: trunk

Fix to prevent complex tests running with lazy.

---

Revision 6162 - Directory Listing
Modified Fri Apr 8 09:46:26 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

Data() constructor fix.

---

Revision 6161 - Directory Listing
Modified Fri Apr 8 06:57:08 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

report filename in error message.

---

Revision 6160 - Directory Listing
Modified Fri Apr 8 06:24:27 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Bump standards version to see what happens

---

Revision 6159 - Directory Listing
Modified Fri Apr 8 06:22:04 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Non-backwards compatible change!

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

Adds some additional tests for complex.

---

Revision 6158 - Directory Listing
Modified Fri Apr 8 05:00:26 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

create test directory. This was always failing but buildbot only now
stops to report this.

---

Revision 6157 - Directory Listing
Modified Fri Apr 8 04:43:52 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

fixed savanna options file for noomp.

---

Revision 6156 - Directory Listing
Modified Fri Apr 8 04:39:55 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

index type fix.

---

Revision 6155 - Directory Listing
Modified Fri Apr 8 00:48:28 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

index type long fixes in weipa. Weipa does not support long but converts
at the moment...

---

Revision 6154 - Directory Listing
Modified Thu Apr 7 02:52:30 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Complex fixes and a small number of tests

---

Revision 6153 - Directory Listing
Modified Thu Apr 7 00:35:31 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

no-op - remove parmetis line from netwon options.

---

Revision 6152 - Directory Listing
Modified Thu Apr 7 00:33:51 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

we should now properly catch segfaults when testing.

---

Revision 6151 - Directory Listing
Modified Wed Apr 6 23:44:46 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Remove getsubst

---

Revision 6150 - Directory Listing
Modified Wed Apr 6 23:44:12 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

fix newton options file.

---

Revision 6149 - Directory Listing
Modified Wed Apr 6 23:36:42 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

fix a typo introduced in r6144. Buildbot reported success since then but
was actually segfaulting!!

---

Revision 6148 - Directory Listing
Modified Wed Apr 6 10:28:13 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

fix savanna options file and make sure libraries get added once only.

---

Revision 6147 - Directory Listing
Modified Wed Apr 6 07:57:22 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Complex changes

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

---

Revision 6146 - Directory Listing
Modified Wed Apr 6 07:10:59 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

add lib path for trilinos.

---

Revision 6145 - Directory Listing
Modified Wed Apr 6 06:28:57 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

now refraining from adding all libraries to all targets. So we don't link
unnecessary libraries, e.g. escript does not need parmetis etc...

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Revision 6144 - Directory Listing
Modified Wed Apr 6 05:25:13 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

last round of namespacing defines.

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Revision 6143 - Directory Listing
Modified Wed Apr 6 03:59:15 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

try to fix another warning.

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Revision 6142 - Directory Listing
Modified Wed Apr 6 03:57:28 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

two fixes.

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Revision 6141 - Directory Listing
Modified Wed Apr 6 03:51:30 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

more namespacing of defines.

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Revision 6140 - Directory Listing
Modified Wed Apr 6 03:17:31 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Eigenvectors for _some_ complex cases

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

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Revision 6139 - Directory Listing
Modified Wed Apr 6 02:58:19 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

fix for scons versions < 2.4

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Revision 6138 - Directory Listing
Modified Wed Apr 6 02:10:10 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

starting to 'namespace' our way too generic defines...

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Revision 6137 - Directory Listing
Modified Wed Apr 6 01:57:52 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

new configure check for working complex std::acos

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Revision 6136 - Directory Listing
Modified Wed Apr 6 01:45:53 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Swap axes for complex

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Revision 6135 - Directory Listing
Modified Wed Apr 6 01:07:38 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

transpose for complex

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Revision 6134 - Directory Listing
Modified Wed Apr 6 00:48:07 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

trace for non-constant data

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Revision 6133 - Directory Listing
Modified Wed Apr 6 00:33:10 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

trace() now supports complex

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Revision 6132 - Directory Listing
Modified Wed Apr 6 00:14:03 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

don't skip test with #ranks=1 and fix it (readGmsh).

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Revision 6131 - Directory Listing
Modified Tue Apr 5 23:55:59 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Bug fix and test for complex NaN replacement

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Revision 6130 - Directory Listing
Modified Tue Apr 5 07:05:01 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

more index_t != int fixes in dudley and finley. Both compile now with index
type long. Weipa doesn't.

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Revision 6129 - Directory Listing
Modified Tue Apr 5 06:12:25 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

rebaseline.

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Revision 6128 - Directory Listing
Modified Tue Apr 5 05:19:48 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Hopefully fix OSX problem.

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Revision 6127 - Directory Listing
Modified Tue Apr 5 04:39:31 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Rename nonsymmetric to antisymmetric in tests

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Revision 6126 - Directory Listing
Modified Tue Apr 5 04:29:41 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

more index_t != int fixes in dudley.

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Revision 6125 - Directory Listing
Modified Tue Apr 5 04:12:13 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Fix incorrect behaviour of anti-symmetric for scalars.

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

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Revision 6124 - Directory Listing
Modified Tue Apr 5 03:23:12 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

Fixing python module build on OS X. Added PythonModule builder so we do this generically now.

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Revision 6123 - Directory Listing
Modified Mon Apr 4 06:24:25 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Fixes to debian build

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Revision 6122 - Directory Listing
Modified Mon Apr 4 04:15:50 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

two fixes for long int build.

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Revision 6121 - Directory Listing
Modified Mon Apr 4 03:47:52 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

fix dudley test.

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Revision 6120 - Directory Listing
Modified Mon Apr 4 01:33:51 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

guilty as charged.

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Revision 6119 - Directory Listing
Modified Sun Apr 3 23:36:59 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

merging trilinos branch to trunk.
We can now build with trilinos and use it instead of paso for single PDEs.
There are some more things to be done...

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Revision 6114 - Directory Listing
Modified Fri Apr 1 03:37:52 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

symmetric and antisymmetric now support complex

Also a number of methods are renamed from nonsymmetric

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Revision 6113 - Directory Listing
Modified Fri Apr 1 00:22:23 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

trying to fix deb build.

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Revision 6112 - Directory Listing
Modified Thu Mar 31 09:40:10 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Relicense all the things!

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Revision 6110 - Directory Listing
Modified Thu Mar 31 06:31:03 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Rename nonsymetric to antisymmetric.

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

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Revision 6107 - Directory Listing
Modified Thu Mar 31 00:47:21 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Use tags in test

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Revision 6103 - Directory Listing
Modified Wed Mar 30 05:01:49 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Add variable to control using replacement acos on broken OSX

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Revision 6102 - Directory Listing
Modified Wed Mar 30 05:00:20 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Add some missing functions.

There may be others

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Revision 6099 - Directory Listing
Modified Tue Mar 29 03:50:14 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Don't expect an exception is we aren't doing that check.

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Revision 6098 - Directory Listing
Modified Tue Mar 29 02:21:44 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Remove "within object" checks for sharing from normal codepath

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

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Revision 6097 - Directory Listing
Modified Sun Mar 27 03:31:00 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Tricky race condition hidden in duplicate code

Not sure now why I needed two paths for this.

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Revision 6096 - Directory Listing
Modified Sun Mar 27 03:30:14 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Don\'t know why the other builders didn't need this

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Revision 6095 - Directory Listing
Modified Sat Mar 26 03:06:30 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Fixing remaining examples

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Revision 6094 - Directory Listing
Modified Fri Mar 25 14:19:11 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Fix more tests.  Note needed to change example to add another import.

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

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Revision 6093 - Directory Listing
Modified Thu Mar 24 07:18:55 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Removing unintended inclusions in __all__ for esys.escript

Patched some unit tests which were affected.

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Revision 6092 - Directory Listing
Modified Thu Mar 24 05:43:00 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Adding some complex versions to ops.

And some tests but not enough yet

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Revision 6091 - Directory Listing
Modified Thu Mar 24 04:52:53 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Fix race condition in checking for sharing.

Bit tricky to find this one.

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Revision 6088 - Directory Listing
Modified Wed Mar 23 00:44:58 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Removing old shared tracking

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Revision 6087 - Directory Listing
Modified Tue Mar 22 22:32:12 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Fixing tests

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Revision 6086 - Directory Listing
Modified Tue Mar 22 09:54:51 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Trying to switch over to using shared_ptr.use_count()

Let's see how the buildbot likes it

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Revision 6084 - Directory Listing
Modified Tue Mar 22 04:23:02 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Renaming headers for (hopefully) easier understanding

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Revision 6083 - Directory Listing
Modified Tue Mar 22 03:30:18 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Removing the DataMaths namespace

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Revision 6082 - Directory Listing
Modified Tue Mar 22 02:57:49 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

More cleanup

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

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Revision 6078 - Directory Listing
Modified Mon Mar 21 06:02:29 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

please keep third-party includes after our own to avoid reintroducing
the "python has to be first" issue.

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Revision 6077 - Directory Listing
Modified Mon Mar 21 06:00:21 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Compile error fix.

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

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Revision 6076 - Directory Listing
Modified Fri Mar 18 12:06:46 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Fixing some namespaces and includes

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Revision 6075 - Directory Listing
Modified Fri Mar 18 06:30:04 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

More code removal and test fixing.

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

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Revision 6074 - Directory Listing
Modified Fri Mar 18 02:42:48 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Starting to remove dead code.

DataAlgorithmAdapter is only used by the code which tests it.

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Revision 6073 - Directory Listing
Modified Thu Mar 17 03:30:53 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

sigh use the correct version of abs()

Added test to detect this particular break again.

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Revision 6072 - Directory Listing
Modified Thu Mar 17 00:34:01 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Remove horrible debug output

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Revision 6071 - Directory Listing
Modified Wed Mar 16 07:07:05 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

More test fixes. Better error message on TestDomain.

That throw should probably be an assert though

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Revision 6070 - Directory Listing
Modified Wed Mar 16 07:05:32 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Ensure that objects with no samples do not contribute to inf and sup.

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Revision 6069 - Directory Listing
Modified Wed Mar 16 04:30:40 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Passes a few more tests.

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

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Revision 6068 - Directory Listing
Modified Wed Mar 16 03:37:43 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Remove some tests which expect illegal index lookups to throw.

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

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Revision 6067 - Directory Listing
Modified Wed Mar 16 02:47:38 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

Back to having a single ESYS_ASSERT macro BUT when built with MPI we
are now merely printing the error message and calling MPI_Abort on COMM_WORLD.
My understanding is that this should work on subworlds as well as all
processes are part of COMM_WORLD...

Addresses #362

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Revision 6066 - Directory Listing
Modified Tue Mar 15 06:42:55 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Code path conversions.

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

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Revision 6065 - Directory Listing
Modified Tue Mar 15 06:29:38 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

A bit of a hack.

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

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Revision 6064 - Directory Listing
Modified Mon Mar 14 01:06:18 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Data::hasNoSamples()  now actually looks at how many samples we have.

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Revision 6063 - Directory Listing
Modified Mon Mar 14 00:50:44 2016 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Fix to prevent new codepath from trying to act on locally empty data.

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

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Revision 6061 - Directory Listing
Modified Fri Mar 11 04:40:28 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

Undoing the switch to use MPI-aware assert in Data.h because some
functions are only called from a subset of ranks which would then
cause definite hangs due to the error reduction operation. We need
to find a better way of dealing with this.

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Revision 6060 - Directory Listing
Modified Fri Mar 11 02:51:26 2016 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

added an MPI-aware version of ESYS_ASSERT and replaced suitable places.
This will not fix the current buildbot hang as that is within a block
where we don't have a JMPI intance.

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Revision 6057 - Directory Listing
Modified Thu Mar 10 06:00:58 2016 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

Well it passes my tests

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Revision 6056 - Directory Listing
Modified Thu Mar 10 04:29:53 2016 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

Small fix - hard to find

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Revision 6050 - Directory Listing
Modified Wed Mar 9 22:44:52 2016 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

make it compile on savanna again.

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Revision 6048 - Directory Listing
Modified Wed Mar 9 07:34:47 2016 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

Relocating binaryDataOp to Data.cpp

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Revision 6047 - Directory Listing
Modified Wed Mar 9 07:25:42 2016 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

Removing code some code not used by new path

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Revision 6046 - Directory Listing
Modified Wed Mar 9 07:05:48 2016 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

More pruning and switching

All self-update operations use the new path

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Revision 6045 - Directory Listing
Modified Wed Mar 9 06:28:47 2016 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

Adding more operations to the alternate binary codepath

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Revision 6044 - Directory Listing
Modified Wed Mar 9 05:57:27 2016 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

next try to fix the getopts issue.

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Revision 6043 - Directory Listing
Modified Wed Mar 9 04:44:10 2016 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

Making a macro

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Revision 6042 - Directory Listing
Modified Wed Mar 9 04:30:36 2016 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

Preliminary to lazy cleanup


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

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Revision 6041 - Directory Listing
Modified Wed Mar 9 03:48:05 2016 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

the -- appears to break parsing properly...

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Revision 6039 - Directory Listing
Modified Wed Mar 9 01:56:34 2016 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

Enable alternate path.

Let's see what the buildbot thinks of it.

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Revision 6038 - Directory Listing
Modified Wed Mar 9 01:32:00 2016 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

Bug fixes and function for unary ops.

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

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Revision 6037 - Directory Listing
Modified Wed Mar 9 01:28:53 2016 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

It turns out that explict can be helpful.

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Revision 6036 - Directory Listing
Modified Wed Mar 9 00:41:26 2016 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

grr, another revert.

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Revision 6035 - Directory Listing
Modified Wed Mar 9 00:39:20 2016 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

reverted accidental commit of SConstruct.

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Revision 6034 - Directory Listing
Modified Wed Mar 9 00:37:57 2016 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

a few changes to GroupTest / utest:
GroupTest class now takes a name parameter that is used as (shell) function
name in utest for the test group.
By default all tests are run as before but one can now do:
./utest.sh build '-t2' escriptcpp
to only run the escript c++ unit tests.
Also tweaked a couple things so utest.sh does now work with dash.

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Revision 6033 - Directory Listing
Modified Wed Mar 9 00:13:29 2016 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

More tests for addition

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Revision 6032 - Directory Listing
Modified Tue Mar 8 10:02:26 2016 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

hmm, I thought we're using globs...

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Revision 6031 - Directory Listing
Modified Tue Mar 8 06:27:14 2016 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

added a generic baseclass for PDE solver tests which is used by all domains.
Renamed test files to prepare for Trilinos merge at some point.

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Revision 6029 - Directory Listing
Modified Mon Mar 7 11:16:41 2016 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

increase domain size. Not entirely sure why we get spurious runtime errors
only for this test case but we shall see...

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Revision 6028 - Directory Listing
Modified Mon Mar 7 05:55:01 2016 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

Modify TestDomain to generate correct coordinates in MPI.

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

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Revision 6027 - Directory Listing
Modified Mon Mar 7 03:01:22 2016 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

fix for serial.

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Revision 6026 - Directory Listing
Modified Mon Mar 7 01:58:51 2016 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

Fixes #361 - bug in readGmsh + MPI reading nodes
Also fixes another related issue reading elements with a certain number of ranks

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Revision 6025 - Directory Listing
Modified Fri Mar 4 05:47:57 2016 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

Added more tests for + operator.

This time we test inplace updates

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Revision 6024 - Directory Listing
Modified Fri Mar 4 04:14:27 2016 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

Fixing testing.

Pulling alernative binary op skeleton.

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Revision 6023 - Directory Listing
Modified Fri Mar 4 01:38:00 2016 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

clear error code when restarting solver!

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Revision 6022 - Directory Listing
Modified Fri Mar 4 00:02:44 2016 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

Additional test for various combinations of Data

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

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Revision 6021 - Directory Listing
Modified Thu Mar 3 23:56:55 2016 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

fix for non-MPI builds.

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Revision 6020 - Directory Listing
Modified Thu Mar 3 23:51:14 2016 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

This should fix current test failures with Multiresolution domains.
The assumption that all ranks have the same number of DOF does not hold for
these domains but the distribution vector did not reflect that.