Log of /trunk

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Revision 7031 - Directory Listing
Modified Tue Nov 17 23:44:30 2020 UTC (3 months, 1 week ago) by aellery

Bug fix. Escript now compiles with boost numpy support in Ubuntu 18.04 bionic

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Revision 7030 - Directory Listing
Modified Tue Nov 17 09:30:11 2020 UTC (3 months, 1 week ago) by uqaeller

bug fix

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Revision 7029 - Directory Listing
Modified Tue Nov 17 06:50:01 2020 UTC (3 months, 1 week ago) by aellery

Fixed bug that prevented escript from compiling with boost numpy

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Revision 7027 - Directory Listing
Modified Fri Aug 7 05:26:26 2020 UTC (6 months, 2 weeks ago) by uqaeller

Merged in most of Mark's work

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Revision 7025 - Directory Listing
Modified Thu Aug 6 23:40:52 2020 UTC (6 months, 2 weeks ago) by uqaeller

-Release 5.6
-Fixed a bug that prevented the userguide from building
-Updated the Trilinos config information in the install guide

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Revision 7024 - Directory Listing
Modified Thu Aug 6 01:19:48 2020 UTC (6 months, 2 weeks ago) by uqaeller

Temporarily disabled MUMPS in SConstruct as it will not be supported in version 5.6.

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Revision 7023 - Directory Listing
Modified Wed Aug 5 04:02:31 2020 UTC (6 months, 2 weeks ago) by uqaeller

Updated the docker build for the newest release of Trilinos.

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Revision 7022 - Directory Listing
Modified Tue Aug 4 04:52:33 2020 UTC (6 months, 3 weeks ago) by uqaeller

Updated the Ubuntu section of the install guide.

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Revision 7021 - Directory Listing
Modified Tue Aug 4 02:46:15 2020 UTC (6 months, 3 weeks ago) by uqaeller

Added a scons template and build script for Anaconda 3.

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Revision 7020 - Directory Listing
Modified Mon Aug 3 04:34:45 2020 UTC (6 months, 3 weeks ago) by uqaeller

Updated the flatpak build.

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Revision 7011 - Directory Listing
Modified Wed Jul 22 04:13:34 2020 UTC (7 months ago) by uqaeller

Prototype for the builtin MUMPS solver.

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Revision 7010 - Directory Listing
Modified Mon Jul 20 23:27:34 2020 UTC (7 months ago) by uqaeller

Bug fix

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Revision 7009 - Directory Listing
Modified Wed Jul 15 03:31:39 2020 UTC (7 months, 1 week ago) by uqaeller

Fixed broken tests.

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Revision 7008 - Directory Listing
Modified Mon Jul 13 04:08:04 2020 UTC (7 months, 1 week ago) by gross

code cleaned!

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Revision 7007 - Directory Listing
Modified Mon Jul 13 02:47:49 2020 UTC (7 months, 1 week ago) by gross

E components added

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Revision 7006 - Directory Listing
Modified Sat Jul 11 00:42:17 2020 UTC (7 months, 2 weeks ago) by aellery

copyWithData tests.

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Revision 7005 - Directory Listing
Modified Sat Jul 11 00:20:49 2020 UTC (7 months, 2 weeks ago) by aellery

Fixed a number of broken tests.

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Revision 7004 - Directory Listing
Modified Thu Jul 9 05:00:17 2020 UTC (7 months, 2 weeks ago) by aellery

The version of Trilinos on github has both the experimental headers and the non-experimental headers for Tpetra. I've modified dependencies.py to select the non-experimental code first, if it is present.

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Revision 7003 - Directory Listing
Modified Thu Jul 9 03:43:41 2020 UTC (7 months, 2 weeks ago) by aellery

- Fixed undocumented bug in which the tests in run_symbolic.py
- Added tests for copyWithMask

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Revision 7002 - Directory Listing
Modified Tue Jul 7 02:27:30 2020 UTC (7 months, 2 weeks ago) by aellery

-Updated the trilinos section of the install guide
-Added sympy to hadFeature
-Fixed an undocumented bug in which the sympy tests would run even though escript was built without sympy support

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Revision 7001 - Directory Listing
Modified Thu Jul 2 05:30:59 2020 UTC (7 months, 3 weeks ago) by aellery

A new and improved version of copyWithMask. 

New documentation and testing in the next commit.

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Revision 7000 - Directory Listing
Modified Tue Jun 30 06:25:47 2020 UTC (7 months, 3 weeks ago) by aellery

-Fixed bug 519 (escript would not compile with Boost 1.73.0 due to deprecated headers)
-Changed saveDataCSV so that only one MPI process writes output at a time
-Solved undocumented bug in the build program that was causing an error (when reading the version of OPENMPI)

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Revision 6999 - Directory Listing
Modified Mon Jun 22 23:54:32 2020 UTC (8 months ago) by uqaeller

Added more information to setSolverMethod in escriptcpp.cpp

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Revision 6998 - Directory Listing
Modified Mon Jun 22 05:49:29 2020 UTC (8 months ago) by uqaeller

Added MKL_PARDISO to the solver options section of the user guide

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Revision 6997 - Directory Listing
Modified Tue Jun 16 03:57:47 2020 UTC (8 months, 1 week ago) by uqaeller

-Fixed undocumented bug that prevented escript from compiling with the latest version of Trilinos (briefly, the Trilinos code in dependencies.py would find the header files for the experimental version of Tpetra BlockCrsMatrix when it did not exist.)
-Added a second Trilinos cmake script to the install guide. The install guide now has two Trilinos build scripts, one of which configures Trilinos to build with MPI support and one to build without MPI support. 

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Revision 6996 - Directory Listing
Modified Tue Jun 16 00:23:06 2020 UTC (8 months, 1 week ago) by uqaeller

Added missing special method (__repr__) to Data.

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Revision 6995 - Directory Listing
Modified Mon Jun 15 06:01:07 2020 UTC (8 months, 1 week ago) by uqaeller

Fixed a number of broken tests.

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Revision 6994 - Directory Listing
Modified Fri Jun 12 04:33:39 2020 UTC (8 months, 1 week ago) by uqaeller

-Fixed bug in run_seismic_app
-Added a test to Solveroptions to make sure that Trilinos libraries are available when the user selects them

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Revision 6993 - Directory Listing
Modified Fri Jun 12 01:21:26 2020 UTC (8 months, 2 weeks ago) by uqaeller

Fixed broken app unit tests.

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Revision 6992 - Directory Listing
Modified Wed Jun 10 09:21:46 2020 UTC (8 months, 2 weeks ago) by gross

fixes for minimizer

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Revision 6991 - Directory Listing
Modified Tue Jun 9 09:18:18 2020 UTC (8 months, 2 weeks ago) by gross

some fixes to minimize

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Revision 6990 - Directory Listing
Modified Tue Jun 9 03:28:26 2020 UTC (8 months, 2 weeks ago) by uqaeller

Modified Data to always print a summary when the user calls str(Data)

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Revision 6989 - Directory Listing
Modified Tue Jun 9 01:55:04 2020 UTC (8 months, 2 weeks ago) by uqaeller

Increased the number of iterations in some of the inversion examples, to guarantee convergence.

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Revision 6988 - Directory Listing
Modified Mon Jun 8 08:12:59 2020 UTC (8 months, 2 weeks ago) by gross

log message under MPI fixed

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Revision 6987 - Directory Listing
Modified Mon Jun 8 07:23:54 2020 UTC (8 months, 2 weeks ago) by gross

complex solver on dudley

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Revision 6986 - Directory Listing
Modified Mon Jun 8 07:15:37 2020 UTC (8 months, 2 weeks ago) by gross

mkl testing

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Revision 6985 - Directory Listing
Modified Mon Jun 8 06:57:18 2020 UTC (8 months, 2 weeks ago) by gross

umfpack testing added

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Revision 6984 - Directory Listing
Modified Mon Jun 8 06:46:33 2020 UTC (8 months, 2 weeks ago) by uqaeller

- Added a section of unit testing to the install guide
- Fixed a bug in the unit test for getConnections (for Dudley)
- Temporarily commented out numpyToData in escriptcpp.cpp because it was breaking the tests

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Revision 6983 - Directory Listing
Modified Mon Jun 8 06:02:17 2020 UTC (8 months, 2 weeks ago) by gross

direct solver tests for Dudley added

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Revision 6982 - Directory Listing
Modified Mon Jun 8 05:55:15 2020 UTC (8 months, 2 weeks ago) by gross

tests for complex PDEs in Pipley added

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Revision 6981 - Directory Listing
Modified Mon Jun 8 05:31:08 2020 UTC (8 months, 2 weeks ago) by gross

more direct solver testing

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Revision 6980 - Directory Listing
Modified Mon Jun 8 05:12:18 2020 UTC (8 months, 2 weeks ago) by gross

typo fixed

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Revision 6979 - Directory Listing
Modified Mon Jun 8 05:11:45 2020 UTC (8 months, 2 weeks ago) by gross

testing for direct added

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Revision 6978 - Directory Listing
Modified Mon Jun 8 05:03:44 2020 UTC (8 months, 2 weeks ago) by gross

test for direct trilinos added

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Revision 6977 - Directory Listing
Modified Mon Jun 8 05:01:20 2020 UTC (8 months, 2 weeks ago) by gross

test for direct trilinos added

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Revision 6976 - Directory Listing
Modified Mon Jun 8 04:45:42 2020 UTC (8 months, 2 weeks ago) by gross

test fixed

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Revision 6975 - Directory Listing
Modified Fri Jun 5 05:55:28 2020 UTC (8 months, 2 weeks ago) by gross

BFGS removed and testing fixed

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Revision 6974 - Directory Listing
Modified Thu Jun 4 10:00:14 2020 UTC (8 months, 3 weeks ago) by gross

testing for UMFPACK, MKL and complex PDEs added. In this first check in this is for finley only

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Revision 6973 - Directory Listing
Modified Thu Jun 4 06:55:57 2020 UTC (8 months, 3 weeks ago) by gross

test fixed

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Revision 6972 - Directory Listing
Modified Wed Jun 3 10:31:03 2020 UTC (8 months, 3 weeks ago) by gross

dependency on esys.escript removed

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Revision 6971 - Directory Listing
Modified Fri May 22 05:03:21 2020 UTC (9 months ago) by uqaeller

Prototype of numpyToData (currently working for Scalar data). Vector/Tensor version and updates to documentation will be in the next commit.

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Revision 6963 - Directory Listing
Modified Mon Apr 13 22:44:33 2020 UTC (10 months, 1 week ago) by uqaeller

More flatpak changes

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Revision 6962 - Directory Listing
Modified Mon Apr 13 22:43:18 2020 UTC (10 months, 1 week ago) by uqaeller

Updated the flatpak appdata file.

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Revision 6951 - Directory Listing
Modified Fri Feb 14 05:49:45 2020 UTC (12 months, 1 week ago) by uqaeller

- Added a deprecation warning and a bug warning to interpolateFromTable
- Changes to the dockerfile
- Changes to the Anaconda build

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Revision 6949 - Directory Listing
Modified Thu Feb 6 02:36:07 2020 UTC (12 months, 2 weeks ago) by uqaeller

Release version 5.5

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Revision 6948 - Directory Listing
Modified Wed Feb 5 07:41:00 2020 UTC (12 months, 2 weeks ago) by uqaeller

Updated finley read_gmsh (changes to msh 4.1 nodes section)

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Revision 6947 - Directory Listing
Modified Wed Feb 5 01:05:55 2020 UTC (12 months, 2 weeks ago) by uqaeller

- Fixed a bug in which the app unit tests were all failing due to import errors in testrunner
- Decreased the size of the mesh in run_dc_app.py so that the unit tests in run_dc_app do not require as much memory
- Added some test meshes for Finley readGmsh (that were missing from a previous commit)

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Revision 6946 - Directory Listing
Modified Tue Feb 4 06:01:05 2020 UTC (12 months, 3 weeks ago) by acodd

apps

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Revision 6945 - Directory Listing
Modified Sat Feb 1 02:13:14 2020 UTC (12 months, 3 weeks ago) by uqaeller

Modified the anaconda build script so that it will build with Python 3.0+. Previously the script only worked with Python 2.7.

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Revision 6944 - Directory Listing
Modified Thu Jan 30 03:39:44 2020 UTC (12 months, 3 weeks ago) by uqaeller

Updated the install guide.

Also, added in a new option (disable_boost_numpy) which enables a user to disable the boost_numpy libraries (on by default) during the build.

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Revision 6943 - Directory Listing
Modified Tue Jan 28 05:18:49 2020 UTC (12 months, 4 weeks ago) by acodd

apps and examples2

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Revision 6942 - Directory Listing
Modified Tue Jan 21 06:03:41 2020 UTC (13 months ago) by uqaeller

Fixed an undocumented bug in which the direct_PASO tests would run if escript was compiled with Trilinos (but without a direct solver for PASO).

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Revision 6941 - Directory Listing
Modified Tue Jan 21 04:28:16 2020 UTC (13 months ago) by uqaeller

- Updated the CREDITS file
- Fixed an undocumented bug in datamanager

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Revision 6940 - Directory Listing
Modified Mon Jan 20 23:45:45 2020 UTC (13 months ago) by uqaeller

Temporary fix to bug 496 (the sympy bug)

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Revision 6939 - Directory Listing
Modified Mon Jan 20 03:37:18 2020 UTC (13 months ago) by uqaeller

Updated the copyright header.

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Revision 6938 - Directory Listing
Modified Sun Jan 19 23:31:36 2020 UTC (13 months ago) by uqaeller

Removed applications folder.

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Revision 6937 - Directory Listing
Modified Fri Jan 17 03:50:13 2020 UTC (13 months, 1 week ago) by uqaeller

Fixed bug 500 and feature 479

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Revision 6936 - Directory Listing
Modified Wed Jan 15 00:05:28 2020 UTC (13 months, 1 week ago) by aellery

bug fixes

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Revision 6935 - Directory Listing
Modified Tue Jan 7 22:44:43 2020 UTC (13 months, 2 weeks ago) by uqaeller

Fixed a segmentation fault in finley readGmsh

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Revision 6934 - Directory Listing
Modified Wed Dec 18 02:37:35 2019 UTC (14 months, 1 week ago) by acodd

LBFGS comments

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Revision 6933 - Directory Listing
Modified Thu Dec 12 04:34:34 2019 UTC (14 months, 2 weeks ago) by acodd

lbfgs

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Revision 6932 - Directory Listing
Modified Thu Dec 12 02:48:08 2019 UTC (14 months, 2 weeks ago) by acodd

LBFGS comments

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Revision 6931 - Directory Listing
Modified Tue Dec 10 06:57:28 2019 UTC (14 months, 2 weeks ago) by aellery

fixed mistake in last commit

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Revision 6930 - Directory Listing
Modified Tue Dec 10 06:31:29 2019 UTC (14 months, 2 weeks ago) by aellery

More changes to finley readgmsh

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Revision 6929 - Directory Listing
Modified Tue Dec 10 02:20:07 2019 UTC (14 months, 2 weeks ago) by aellery

Improved version of readGmsh for Finley.

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Revision 6928 - Directory Listing
Modified Mon Dec 9 05:29:21 2019 UTC (14 months, 2 weeks ago) by acodd

more updates to userguide 

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Revision 6927 - Directory Listing
Modified Sun Dec 8 22:26:40 2019 UTC (14 months, 2 weeks ago) by acodd

user guide updates

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Revision 6926 - Directory Listing
Modified Fri Dec 6 02:07:43 2019 UTC (14 months, 2 weeks ago) by aellery

Fixed bug 499

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Revision 6925 - Directory Listing
Modified Tue Dec 3 06:44:43 2019 UTC (14 months, 3 weeks ago) by aellery

Added the ability to assemble lumped matrices with complex values using a linearPDE that was created from a Speckley Brick.

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Revision 6924 - Directory Listing
Modified Tue Dec 3 04:37:59 2019 UTC (14 months, 3 weeks ago) by aellery

Added a new assembler to Speckley that allows a user to assemble a lumped matrix with complex values on a Speckley Rectangle. Previously this was only possible for real values. This resolves bug 488 on redmine (Speckley segmentation bug).

The next commit will add similar functionality for Speckley Brick.

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Revision 6923 - Directory Listing
Modified Mon Dec 2 05:57:07 2019 UTC (14 months, 3 weeks ago) by aellery

- Amended the userguide to include ComplexScalar, ComplexVector etc.
- Fixed a bug in run_comm1 & run_comm4 (failure if escript was compiled without scipy)
- Temporarily removed the ability to interpolate from ReducedFunction to Function in dudley and finley

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Revision 6922 - Directory Listing
Modified Fri Nov 29 07:12:12 2019 UTC (14 months, 3 weeks ago) by aellery

Added a new function, ComplexData, that returns a complex Data object.

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Revision 6921 - Directory Listing
Modified Fri Nov 29 05:00:59 2019 UTC (14 months, 3 weeks ago) by aellery

Added complex versions of Scalar, Vector and Tensor (ComplexScalar, ComplexVector, ComplexTensor)

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Revision 6920 - Directory Listing
Modified Thu Nov 28 12:02:17 2019 UTC (14 months, 4 weeks ago) by aellery

Enable interpolation from ReducedFunction to Function in Dudley and Finley.

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Revision 6919 - Directory Listing
Modified Thu Nov 28 05:07:45 2019 UTC (14 months, 4 weeks ago) by aellery

Modified the install guide to include the python 3 versions of packages. Also, added python 3 versions of the options files.

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Revision 6918 - Directory Listing
Modified Mon Nov 25 07:18:01 2019 UTC (15 months ago) by aellery

Lumping is now set on by default when using Speckley.

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Revision 6917 - Directory Listing
Modified Sun Nov 24 23:45:51 2019 UTC (15 months ago) by aellery

Fixed bug.

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Revision 6916 - Directory Listing
Modified Fri Nov 22 23:07:43 2019 UTC (15 months ago) by aellery

Fixed bug in last commit.

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Revision 6915 - Directory Listing
Modified Fri Nov 22 07:03:42 2019 UTC (15 months ago) by aellery

Added the ability to integrate over Dirac Delta Data objects to Speckley.

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Revision 6914 - Directory Listing
Modified Fri Nov 22 05:55:37 2019 UTC (15 months ago) by aellery

Added the ability to integrate over Dirac Delta Data to Ripley

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Revision 6913 - Directory Listing
Modified Fri Nov 22 04:55:05 2019 UTC (15 months ago) by aellery

Added integration over Dirac Delta Data objects in Finley.

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Revision 6912 - Directory Listing
Modified Wed Nov 13 00:54:29 2019 UTC (15 months, 1 week ago) by aellery

Added getX() for Data objects.

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Revision 6911 - Directory Listing
Modified Mon Nov 11 05:09:19 2019 UTC (15 months, 2 weeks ago) by aellery

Updated the capybara and newton options files for Debian 10.

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Revision 6898 - Directory Listing
Modified Fri Oct 25 06:20:25 2019 UTC (16 months ago) by aellery

I have made some minor changes to make escript compatible with the newer versions of Trilinos.

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Revision 6892 - Directory Listing
Modified Tue Oct 15 04:55:57 2019 UTC (16 months, 1 week ago) by aellery

- Updated the jupyter dockerfile
- Fixed the problem that John was having with the examples

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Revision 6890 - Directory Listing
Modified Thu Oct 3 05:22:36 2019 UTC (16 months, 3 weeks ago) by aellery

- Updated the Jupyter docker file

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Revision 6887 - Directory Listing
Modified Mon Sep 16 01:38:50 2019 UTC (17 months, 1 week ago) by aellery

Bug fix (syntax)

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Revision 6886 - Directory Listing
Modified Sun Sep 15 23:11:45 2019 UTC (17 months, 1 week ago) by aellery

Bug fix, changes to docker-jupyter

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Revision 6885 - Directory Listing
Modified Wed Sep 11 05:44:23 2019 UTC (17 months, 2 weeks ago) by aellery

The people maintaining Trilinos have recently moved some of the Tpetra BlockCRSMatrix code from experimental to their main code base. This commit brings escript up to date with their changes.

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Revision 6884 - Directory Listing
Modified Tue Sep 10 05:20:46 2019 UTC (17 months, 2 weeks ago) by gross

partial TVTK interface fix

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Revision 6883 - Directory Listing
Modified Mon Sep 9 04:13:19 2019 UTC (17 months, 2 weeks ago) by aellery

Fixed bug in EscriptToTVTK

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Revision 6882 - Directory Listing
Modified Fri Aug 30 04:05:42 2019 UTC (17 months, 3 weeks ago) by aellery

Bug fix

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Revision 6881 - Directory Listing
Modified Wed Aug 28 02:51:14 2019 UTC (17 months, 4 weeks ago) by aellery

- Added a new function called convertToNumpy that converts a Data object to a numpy array (see the userguide for information)
- Fixed a bug in escriptToTVTK

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Revision 6880 - Directory Listing
Modified Thu Aug 22 23:24:06 2019 UTC (18 months ago) by aellery

Turned off the omp pragma in getNumpyX temporarily

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Revision 6879 - Directory Listing
Modified Thu Aug 22 06:47:24 2019 UTC (18 months ago) by aellery

Fixed undocumented bug.

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Revision 6878 - Directory Listing
Modified Thu Aug 15 06:03:17 2019 UTC (18 months, 1 week ago) by aellery

- Prototype of the EscriptToTVTK function in Weipa. 
- Moved the readthedocs yaml files to the tools folder

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Revision 6877 - Directory Listing
Modified Fri Aug 9 06:10:21 2019 UTC (18 months, 2 weeks ago) by aellery

Added some OMP pragmas to last commit

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Revision 6876 - Directory Listing
Modified Fri Aug 9 06:00:29 2019 UTC (18 months, 2 weeks ago) by aellery

Dudley and Finley now have a function, getTVTK, which returns two numpy arrays that contain the point information and connectivity information required by tVTK.

Example use:

domain=Rectangle(n0=10,n1=10)
points,connectivity = getTVTK(domain)

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Revision 6875 - Directory Listing
Modified Fri Aug 9 02:20:21 2019 UTC (18 months, 2 weeks ago) by aellery

Added a new function to finley and dudley, getConnectivityInfo, that returns a numpy array that contains the connectivity information for the mesh.

Example use:

import numpy
from esys.finley import *
domain=Rectangle(n0=10,n1=10)
info=domain.getConnectivityInfo()

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Revision 6874 - Directory Listing
Modified Wed Aug 7 06:14:59 2019 UTC (18 months, 2 weeks ago) by aellery

Fixed bug that caused the intel-mpi-py3-paso-long buildbot to fail

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Revision 6873 - Directory Listing
Modified Wed Aug 7 04:47:35 2019 UTC (18 months, 2 weeks ago) by aellery

Added tests for getNumpyX

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Revision 6872 - Directory Listing
Modified Tue Aug 6 07:31:34 2019 UTC (18 months, 2 weeks ago) by aellery

I have added a new function named getNumpyX which works the same as getX except that it returns a numpy ndarray instead of a Data object.

Example use:

import numpy
from esys.finley import Rectangle
domain=Rectangle(n0=10,n1=10)
numpyCoordinates=domain.getNumpyX()

I have also updated the userguide. I'm adding in some tests for this in the next commit.

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Revision 6871 - Directory Listing
Modified Tue Aug 6 00:15:46 2019 UTC (18 months, 2 weeks ago) by aellery

Fixed undocumented bug with the getNumpy function.

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Revision 6869 - Directory Listing
Modified Fri Aug 2 05:43:10 2019 UTC (18 months, 3 weeks ago) by gross

fix in whereZero

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Revision 6868 - Directory Listing
Modified Fri Aug 2 05:42:52 2019 UTC (18 months, 3 weeks ago) by gross

fix in whereZero

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Revision 6866 - Directory Listing
Modified Thu Aug 1 03:44:53 2019 UTC (18 months, 3 weeks ago) by aellery

Added options files for debian buster

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Revision 6865 - Directory Listing
Modified Mon Jul 29 04:21:24 2019 UTC (18 months, 4 weeks ago) by aellery

Added a readthedocs configuration file.

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Revision 6864 - Directory Listing
Modified Fri Jul 26 06:49:39 2019 UTC (19 months ago) by aellery

- Added anaconda to the install guide

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Revision 6852 - Directory Listing
Modified Thu Jul 18 02:21:48 2019 UTC (19 months, 1 week ago) by aellery

Changes to the anaconda build that bring it into line with the requirements of conda-forge on anaconda cloud.

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Revision 6851 - Directory Listing
Modified Tue Jul 9 03:07:07 2019 UTC (19 months, 2 weeks ago) by aellery

eScript version 5.4.

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Revision 6850 - Directory Listing
Modified Mon Jul 8 04:14:42 2019 UTC (19 months, 2 weeks ago) by aellery

Another change to the anaconda build

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Revision 6849 - Directory Listing
Modified Sun Jul 7 00:48:20 2019 UTC (19 months, 2 weeks ago) by aellery

Fixed a broken link in the linux Anaconda build

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Revision 6848 - Directory Listing
Modified Thu Jul 4 06:33:52 2019 UTC (19 months, 3 weeks ago) by aellery

Minor changes to the svn revision code in SConstruct.

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Revision 6847 - Directory Listing
Modified Thu Jul 4 04:46:42 2019 UTC (19 months, 3 weeks ago) by aellery

- Fixed bug from last commit
- Added a docker section to the install guide

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Revision 6846 - Directory Listing
Modified Wed Jul 3 07:22:58 2019 UTC (19 months, 3 weeks ago) by aellery

Temporarily turning off some of the preprocessor directives to fix a compilation bug that I introduced in the last commit.

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Revision 6845 - Directory Listing
Modified Wed Jul 3 06:03:14 2019 UTC (19 months, 3 weeks ago) by aellery

-Turned run_comm1.py back on
-Dudley can now read files using gmsh MSH4 format
-Activated a test in test_linearPDEs that was turned off.

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Revision 6844 - Directory Listing
Modified Mon Jul 1 05:32:01 2019 UTC (19 months, 3 weeks ago) by aellery

-It is now possible to load gmsh msh version 4.1 files using finley
-I have temporarily disabled the test run_comm1

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Revision 6843 - Directory Listing
Modified Tue Jun 25 01:13:21 2019 UTC (20 months ago) by aellery

eScript not prints a wanting during compilation if the version number is unknown.

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Revision 6842 - Directory Listing
Modified Thu Jun 20 05:16:13 2019 UTC (20 months ago) by aellery

-Fixed bug in minimizers testing
-Updated install guide for flatpak

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Revision 6841 - Directory Listing
Modified Thu Jun 20 03:44:37 2019 UTC (20 months, 1 week ago) by aellery

-Added (experimental) newton interpolation in minimizers.py. This code takes the values of alpha and phi(alpha) from all previous iterations, interpolates a polynomial through them using the Newton method, and finds a root to the interpolated polynomial using the newton method. I'm leaving this feature undocumented for the moment. To use it, set interpolationOrder==4 in LBFGS. 
-Changed the volume in the dockerbuild to /home/appuser

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Revision 6840 - Directory Listing
Modified Wed Jun 19 04:27:57 2019 UTC (20 months, 1 week ago) by aellery

More flatpak changes

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Revision 6839 - Directory Listing
Modified Mon Jun 17 06:30:37 2019 UTC (20 months, 1 week ago) by aellery

I wrote a new version of the interpolation function (in minimizers.py) that should be a little faster.

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Revision 6838 - Directory Listing
Modified Sun Jun 16 22:51:47 2019 UTC (20 months, 1 week ago) by aellery

Another change to the flatpak appdata

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Revision 6837 - Directory Listing
Modified Thu Jun 13 04:03:11 2019 UTC (20 months, 1 week ago) by aellery

Added a new test to run_minimizers.py that checks that the minimizer will converge for the different interpolation orders.

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Revision 6836 - Directory Listing
Modified Fri Jun 7 03:15:54 2019 UTC (20 months, 2 weeks ago) by aellery

Made some changes to the trilinos section of the install guide.

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Revision 6835 - Directory Listing
Modified Thu Jun 6 04:42:19 2019 UTC (20 months, 2 weeks ago) by aellery

Fixed bug that was causing test_symmetryOnIterative_System to fail on savanna.

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Revision 6834 - Directory Listing
Modified Thu Jun 6 02:32:48 2019 UTC (20 months, 3 weeks ago) by aellery

Another minor change

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Revision 6833 - Directory Listing
Modified Thu Jun 6 02:14:47 2019 UTC (20 months, 3 weeks ago) by aellery

Another minor bug fix

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Revision 6832 - Directory Listing
Modified Wed Jun 5 22:41:34 2019 UTC (20 months, 3 weeks ago) by aellery

Changed a test that was causing one of the buildbots to crash.

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Revision 6831 - Directory Listing
Modified Wed Jun 5 01:26:01 2019 UTC (20 months, 3 weeks ago) by aellery

Fixed another testing bug.

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Revision 6830 - Directory Listing
Modified Tue Jun 4 22:39:54 2019 UTC (20 months, 3 weeks ago) by aellery

Various bug fixes.

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Revision 6829 - Directory Listing
Modified Tue Jun 4 02:14:13 2019 UTC (20 months, 3 weeks ago) by aellery

Changes to savanna_options.py

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Revision 6828 - Directory Listing
Modified Mon Jun 3 22:56:03 2019 UTC (20 months, 3 weeks ago) by aellery

Temporarily disabling the default settings in solveroptions

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Revision 6827 - Directory Listing
Modified Mon Jun 3 04:48:42 2019 UTC (20 months, 3 weeks ago) by aellery

- Fixed bug that was causing some of the linear pde system test to crash for trilinos.
- Removed the remaining CUDA code from SConstruct and ripley
- Updated the flatpak appdata file following feedback from the guys who run flathub
- Some new files in the tools/flatpak folder

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Revision 6826 - Directory Listing
Modified Fri May 31 04:50:53 2019 UTC (20 months, 3 weeks ago) by aellery

I have disabled the tests test_DIRECT and test_DIRECT_System.

In their place, I have added four equivalent tests, namely
test_DIRECT_PASO
test_DIRECT_Trilinos
test_DIRECT_System_PASO
test_DIRECT_System_Trilinos

which are equivalent, which test both PASO and Trilinos.

---

Revision 6825 - Directory Listing
Modified Fri May 31 04:01:17 2019 UTC (20 months, 3 weeks ago) by aellery

Temporarily disable two tests. See bug 471 on redmine

---

Revision 6824 - Directory Listing
Modified Fri May 31 02:10:47 2019 UTC (20 months, 3 weeks ago) by aellery

Added a new flag that can be used to disable gmsh during a build. To build escript without gmsh, use the flag

use_gmsh=False

Gmsh is still enabled by default, if it is available.

---

Revision 6823 - Directory Listing
Modified Thu May 30 23:30:01 2019 UTC (20 months, 3 weeks ago) by aellery

Changing some file names.

---

Revision 6822 - Directory Listing
Modified Thu May 30 06:58:34 2019 UTC (20 months, 3 weeks ago) by aellery

-Added some new tests to test_linearPDEs.py
-Made some changes to the default solver settings
-Updated flatpak appdata file (changed licence information)
-Fixed bug in the trilinos dockerfile
-Fixed undocumented bug in escriptcpp.cpp (setDim)

---

Revision 6821 - Directory Listing
Modified Wed May 29 06:42:09 2019 UTC (20 months, 4 weeks ago) by aellery

Final version of the flatpak build files and logos. 

These build files have been uploaded to flathub and should be publicalyl available in a few days after the build has been reviewed by the flatpak maintainers.

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Revision 6820 - Directory Listing
Modified Tue May 28 03:46:50 2019 UTC (20 months, 4 weeks ago) by aellery

Fixed openMP bug in Trilinos

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Revision 6819 - Directory Listing
Modified Mon May 27 04:00:47 2019 UTC (21 months ago) by aellery

Fixed bug that was causing the buildbot intel-hyb-py3-trilinos-long to crash.

---

Revision 6818 - Directory Listing
Modified Sun May 26 10:57:45 2019 UTC (21 months ago) by aellery

1. Fixed the lid_driven_cavity.py bug
2. Added various files required by flathub (logo, appstream data, *.desktop file etc.)

---

Revision 6817 - Directory Listing
Modified Mon May 20 04:37:27 2019 UTC (21 months, 1 week ago) by aellery

Minor changes.

---

Revision 6816 - Directory Listing
Modified Mon May 20 04:30:14 2019 UTC (21 months, 1 week ago) by aellery

I accidently introduced a bug into TransportPDE when I rewrote the solver buddy. This bug has been fixed in this commit.

Briefly, prior to this commit, if escript was compiled with both Trilinos and PASO, the solver method would default to SO_METHOD_DIRECT_TRILINOS when solving a problem in 2D. When the testing code got up to the TransportPDE tests, it would switch the solver method to PASO. Unfortunately, the function mapEscriptOption in Options.cpp (which maps solver options for PASO) contains a switch that does not have this option (SO_METHOD_DIRECT_TRILINOS). This was the cause of the error. 

I have added a couple of lines to the switch in mapEscriptOption that maps SO_METHOD_DIRECT_TRILINOS to PASO_DIRECT so that if a user sets SO_METHOD_DIRECT_TRILINOS and then switches the solver to PASO, the code selects the PASO direct solver. The Tranpsort PDE tests are now working correctly.

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Revision 6815 - Directory Listing
Modified Fri May 10 06:04:03 2019 UTC (21 months, 2 weeks ago) by aellery

-BOOST_BYTE_ORDER has been deprecated. I have written some code to take this change into account
-Fixed a problem in the trilinoswrap code cause by the last commit

---

Revision 6814 - Directory Listing
Modified Thu May 9 00:53:01 2019 UTC (21 months, 2 weeks ago) by aellery

Fixed bug that was stopping the clang-ser-py3-paso-int buildbot from completing. 

The bug occurred because it is possible to build boost without boost numpy support. The old dependencies.py code incorrectly assumed that the boost numpy headers are always there. 

---

Revision 6813 - Directory Listing
Modified Wed May 8 07:01:14 2019 UTC (21 months, 2 weeks ago) by aellery

-Fix for bug 464 (Missing Trilinos header file due to deprecation)
-Fix for the bug that was stopping the gnu-omp-py3-paso-long buildbot from completing
-Update to trilinos documentation in the install guide

---

Revision 6812 - Directory Listing
Modified Fri May 3 00:36:47 2019 UTC (21 months, 3 weeks ago) by aellery

Another silo fix

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Revision 6811 - Directory Listing
Modified Thu May 2 12:35:51 2019 UTC (21 months, 3 weeks ago) by aellery

Fixed bad commit

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Revision 6810 - Directory Listing
Modified Wed May 1 07:03:46 2019 UTC (21 months, 3 weeks ago) by aellery

Fixed undocumented bug: unit testing would attempt to run silo tests, even when escript was compiled without support for silo.

---

Revision 6809 - Directory Listing
Modified Tue Apr 30 06:40:36 2019 UTC (21 months, 3 weeks ago) by aellery

-Fixed bug in the linux anaconda build script.
-Updated the trilinos section of the install guide.

---

Revision 6808 - Directory Listing
Modified Tue Apr 30 03:20:28 2019 UTC (21 months, 3 weeks ago) by aellery

bug fix

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Revision 6807 - Directory Listing
Modified Thu Apr 18 04:19:40 2019 UTC (22 months, 1 week ago) by aellery

Update to the Ubuntu section of the install guide.

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Revision 6806 - Directory Listing
Modified Fri Apr 12 09:39:17 2019 UTC (22 months, 2 weeks ago) by aellery

Fixed a bug in the anaconda build. 

Also, escript now now be installed / uninstalled inside Anaconda using the commands

conda install -c aellery escript
conda uninstall escript

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Revision 6805 - Directory Listing
Modified Tue Apr 9 08:02:10 2019 UTC (22 months, 2 weeks ago) by aellery

Added a script to build escript in Anaconda.

---

Revision 6804 - Directory Listing
Modified Thu Apr 4 07:37:16 2019 UTC (22 months, 3 weeks ago) by aellery

This commit:
1. Updated the trilinos install information in the install guide
2. Fixed a bug in the escript dockerfile. Also, added MKL and MKL_PARDISO to the trilinos build.

---

Revision 6803 - Directory Listing
Modified Mon Apr 1 04:08:47 2019 UTC (22 months, 3 weeks ago) by aellery

Fix for bug 465 (naming of documentation file).

Now, when the documentation is built, scons will label the install guide as install.r[revision].pdf where [revision] is the revision in the subversion repository.

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Revision 6802 - Directory Listing
Modified Fri Mar 29 09:58:24 2019 UTC (22 months, 4 weeks ago) by aellery

I have created an (experimental) docker container with escript. It is now possible to install escript using the command:

docker run aellery/esys.escript.5.3

The first time this is run, docker will download and install escript on the machine. Afterwards, this command just runs escript without downloading anything. I have not tested it yet, but this should also work on Windows docker, which means that we now have a build of escript that runs on Windows 10.

If everyone is happy with the build in this container and cannot find any bugs, I will set up an official escript account on docker-hub and reupload the build there. (I'll pick an appropriate account name so that the install command is something like "docker run esys/escript.5.3".)

This commit contains:
1. An updated install guide
2. A much more impressive escript dockerfile that build escripts with both PASO (umfpack) and Trilinos (Cholmod, MUMPS, scaLAPACK, Suitesparse and SuperLU).

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Revision 6801 - Directory Listing
Modified Wed Mar 27 06:12:08 2019 UTC (23 months ago) by aellery

1. Modified the flatpak json file to bring in in line with the standards required by flathub.
2. Some changes to the install guide.
3. Modified docker_trilinos to build stretch-slim (instead of sid) and install cmake from stretch-backports.

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Revision 6800 - Directory Listing
Modified Tue Mar 26 13:28:32 2019 UTC (23 months ago) by aellery

Added (experimental) Dockerfiles for escript.

---

Revision 6799 - Directory Listing
Modified Mon Mar 25 05:53:58 2019 UTC (23 months ago) by aellery

I have rewritten the solverbuddy. Briefly:

1. The remaining AMG code has been removed from PASO.
2. If Trilinos is available, escript will now use it by default.
3. eScript will use a direct solver by default, (if one is available,) when solving 2 dimensional problems and an iterative solver, by default, when solving 3 dimensional problems. This can be changed by a user by manually specifying which solver to use.
4. There is a new option available, setHermitian(), that allows a user to specify when a coefficient matrix is Hermitian.
5. Symmetry information is always passed onto the Trilinos solver when this information is relevant.
6. All tests have been updated, when relevant, to reflect these changes.
7. I fixed a couple of undocumented bugs.

---

Revision 6798 - Directory Listing
Modified Wed Mar 6 06:25:41 2019 UTC (23 months, 3 weeks ago) by aellery

Removed the natgrid references from the cookbook and changed calls to matplotlib.griddata to scipy.interpolate.griddata (as the matplotlib griddata function is deprecated). Also, updated the cookbook to reflect these changes.

This closes bug 448 (problems with calls to matplotlib griddata.)

---

Revision 6797 - Directory Listing
Modified Tue Mar 5 04:51:59 2019 UTC (23 months, 3 weeks ago) by aellery

Improved documentation for the escript subworld feature.

---

Revision 6796 - Directory Listing
Modified Mon Mar 4 01:56:25 2019 UTC (23 months, 3 weeks ago) by aellery

Updated the install guide.

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Revision 6795 - Directory Listing
Modified Sat Mar 2 04:47:23 2019 UTC (23 months, 3 weeks ago) by aellery

Added a script to flatpak that allows users to install python modules inside the flatpak sandbox.

---

Revision 6794 - Directory Listing
Modified Tue Feb 26 02:59:55 2019 UTC (23 months, 4 weeks ago) by aellery

Updated the flatpak manifest. 

Added a readme that describes how everything works. 

Updated the install.pdf with this new info.

---

Revision 6793 - Directory Listing
Modified Fri Feb 22 02:16:34 2019 UTC (2 years ago) by aellery

Fixed bug in the flatpak build script.

---

Revision 6792 - Directory Listing
Modified Wed Feb 20 06:36:53 2019 UTC (2 years ago) by aellery

I've put together a flatpak of escript to make it easier for end users to install it on their machines. To easily install escript on any linux distro, install flatpak and flatpak-builder from a repository and then type

flatpak-builder [some build directory] [path to escript.json]

where escript.json is the file I have uploaded in this commit. Note that this will require flatpak version 1.2.0 or higher, so if you want to try this out on debian you will need to install flatpak and flatpak-builder from stretch-backports. Then to run, type

flatpak-builder --run [some build directory] [path to escript.json] run-escript

I have not uploaded this to flathub yet as I am still testing it for bugs.

---

Revision 6791 - Directory Listing
Modified Mon Feb 11 05:42:06 2019 UTC (2 years ago) by aellery

Made some changes to prevent errors when using the latest version of the clang compiler (7.0.1)

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Revision 6790 - Directory Listing
Modified Sun Feb 10 23:26:34 2019 UTC (2 years ago) by aellery

Temporarily undoing previous commit to fix a problem with one of the buildbots

---

Revision 6789 - Directory Listing
Modified Fri Feb 8 06:43:46 2019 UTC (2 years ago) by aellery

Bringing the files in localdebian up to date.

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Revision 6788 - Directory Listing
Modified Fri Feb 8 04:46:42 2019 UTC (2 years ago) by aellery

Added compiler flags for clang++ to SConstruct. 

---

Revision 6787 - Directory Listing
Modified Mon Feb 4 01:41:55 2019 UTC (2 years ago) by aellery

eScripts now compiles successfully with the anaconda python interpreter.

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Revision 6786 - Directory Listing
Modified Fri Feb 1 06:30:43 2019 UTC (2 years ago) by aellery

eScripts now compiles on gcc version 8.2.

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Revision 6785 - Directory Listing
Modified Thu Jan 31 03:06:03 2019 UTC (2 years ago) by aellery

The buildbot intel-hyb-py3-trilinos-long was failing to compile because it could not locate the trilinos header files (on savanna). This problem has occurred due to a bug in the scons CheckCXXHeader() function. I have rewritten dependencies.py so that it checks for the existence of these libraries using the python function os.path.isfile() instead.

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Revision 6784 - Directory Listing
Modified Thu Jan 31 00:20:32 2019 UTC (2 years ago) by aellery

Minor changes.

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Revision 6783 - Directory Listing
Modified Wed Jan 30 23:52:36 2019 UTC (2 years ago) by aellery

Fixed bug 433.

---

Revision 6782 - Directory Listing
Modified Wed Jan 30 06:38:11 2019 UTC (2 years ago) by aellery

Temporary fix to bug 433. Trilinos will now solve for the Hessian matrix used by the LBFGS algorithm in inversions.py using GMRES instead of CG.

---

Revision 6781 - Directory Listing
Modified Mon Jan 28 22:31:05 2019 UTC (2 years ago) by aellery

Removed PAPI from SConstruct and dependencies.py

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Revision 6780 - Directory Listing
Modified Fri Jan 25 00:02:24 2019 UTC (2 years, 1 month ago) by aellery

Fixed undocumented bug that was preventing the sphinx documentation from building (due to a Python magic number error).

Also, I have modified the sid options files to help escript find the location of the openmpi header files. 

---

Revision 6779 - Directory Listing
Modified Thu Jan 24 02:26:40 2019 UTC (2 years, 1 month ago) by aellery

eScripts now displays more information about the Trilinos libraries during compilation.

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Revision 6778 - Directory Listing
Modified Mon Jan 21 00:33:18 2019 UTC (2 years, 1 month ago) by aellery

Adding version 4 c++ to netcdf build depd

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Revision 6777 - Directory Listing
Modified Mon Jan 21 00:23:07 2019 UTC (2 years, 1 month ago) by aellery

Use debians version of control

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Revision 6776 - Directory Listing
Modified Wed Jan 16 00:57:22 2019 UTC (2 years, 1 month ago) by aellery

Fixed bug 457 (escript would not run on Quoll with more than 6 threads)

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Revision 6775 - Directory Listing
Modified Tue Jan 15 02:24:03 2019 UTC (2 years, 1 month ago) by jfenwick

This should work

---

Revision 6774 - Directory Listing
Modified Fri Jan 11 01:04:51 2019 UTC (2 years, 1 month ago) by aellery

The order of the interpolation used by the linesearch is now 1 by default. If using cubic interpolation, a user can control the final test by setting the parameters tol_df and tol_sm. 

:param interpolationOrder: the order of the interpolation used (1, 2 or 3)
:param tol_df: if using the cubic interpolation, the new value of alpha must 
:               differ from the previous value by at least this much
:param tol_sm: if using the cubic interpolation, the new value of alpha must
:               not be less than tol_sm*(alpha_{i-1})

---

Revision 6773 - Directory Listing
Modified Thu Jan 10 01:28:28 2019 UTC (2 years, 1 month ago) by aellery

Fixed minor bug in cubic interpolate.

---

Revision 6772 - Directory Listing
Modified Wed Jan 9 22:58:20 2019 UTC (2 years, 1 month ago) by aellery

A user can now manually set the order of the interpolation used in the line search in the LBFGS and BFGS minimizers. Example usage:

solver=MinimizerLBFGS()
solver.setOptions(interpolationOrder=1)

Accepted values for interpolationOrder are 1, 2 and 3.

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Revision 6771 - Directory Listing
Modified Wed Jan 9 05:31:41 2019 UTC (2 years, 1 month ago) by aellery

Updated the list of changes in the userguide

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Revision 6770 - Directory Listing
Modified Wed Jan 9 04:47:56 2019 UTC (2 years, 1 month ago) by aellery

Fixed the bug that was causing the buildbot intel-mpi-py3-paso-long to fail

---

Revision 6769 - Directory Listing
Modified Mon Jan 7 23:59:00 2019 UTC (2 years, 1 month ago) by aellery

I have rewritten the interpolation algorithm in the zoom function in minimizers.py. This new algorithm uses quadratic interpolation on the first step and cubic interpolation on subsequent steps. Unlike the prior version it does not require any additional function evaluations.

In case anybody is curious, the if statements in quadinterpolate and cubicinterpolate account for the following scenarios in which the algorithm could fail:
72: The user has passed alpha_lo and alpha_hi on the incorrect order
76: The user is approximating the derivative of the function phi using finite differences
80: The minimum of the interpolated quadratic is outside of the domain
85: The user has passed alpha_lo and alpha_hi in the incorrect order
87: Duplicate point (alpha_lo = 0 so that phi(alpha_lo) = phi(0))
95: The answer is going to be complex, which will cause PASO to break (this shouldn't happen unless the user does something silly. I have only included this for completeness)
99: It is possible that multiple roots lie in the domain. This finds the larger of the two that is less than alpha_hi.
100: The minimum of the interpolated cubic is outside of the domain
102: This is a safeguard to ensure that the new value of alpha is not too close to the last value and isn't too much smaller than the last value.

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Revision 6768 - Directory Listing
Modified Fri Jan 4 03:48:42 2019 UTC (2 years, 1 month ago) by aellery

Fixed the broken test run_gravity.py.

This code seems to be working, but with the new version of minimizers.py the gravity inversion is a little slower to converge than it was before. Slightly increasing the maximum number of solver iterations solved the problem.

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Revision 6767 - Directory Listing
Modified Fri Jan 4 02:48:53 2019 UTC (2 years, 1 month ago) by aellery

Fixed a minor typo in inversions.py that was causing gravmag_netcdf.py to break.

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Revision 6766 - Directory Listing
Modified Fri Jan 4 01:31:39 2019 UTC (2 years, 1 month ago) by aellery

I have fixed the bug that was causing the tests run_gravity.py and run_inversion_gravmag_2d.py to fail on the buildbot gnu-omp-py3-paso-long.

The interpolation function I coded for minimizers.py finds the minimum of a parabola that goes through the points phi(alpha_lo) and phi(alpha_hi) and whose gradient matches phi(alpha) at alpha_lo. Occasionally the minimum of this function lies outside of the domain [alpha_lo, alpha_hi] and, when this occurs, the line search function breaks down. The interpolation function now checks that the minimum is within the interval and if it is not it falls back on the bisection method.

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Revision 6765 - Directory Listing
Modified Thu Jan 3 01:15:12 2019 UTC (2 years, 1 month ago) by aellery

I have fixed a broken test (run_minimizers.TestMinimizerNLCG)

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Revision 6764 - Directory Listing
Modified Wed Jan 2 07:09:09 2019 UTC (2 years, 1 month ago) by aellery

I have added quadratic interpolation to the zoom function in minimisers.py.

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Revision 6763 - Directory Listing
Modified Fri Dec 21 16:15:51 2018 UTC (2 years, 2 months ago) by gross

inversin fixed.

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Revision 6762 - Directory Listing
Modified Fri Dec 21 15:56:13 2018 UTC (2 years, 2 months ago) by gross

failing test fixed

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Revision 6761 - Directory Listing
Modified Thu Dec 20 01:54:55 2018 UTC (2 years, 2 months ago) by aellery

Undoing mistake.

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Revision 6760 - Directory Listing
Modified Thu Dec 20 01:42:59 2018 UTC (2 years, 2 months ago) by aellery

Minor changes to dudley/Mesh_readGmsh.cpp

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Revision 6759 - Directory Listing
Modified Wed Dec 19 23:10:41 2018 UTC (2 years, 2 months ago) by aellery

eScripts has a new feature! Dudley can now load gmsh MSH4.0 files!

Also, I fixed a bug in finley Mesh_readGmsh.cpp.

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Revision 6758 - Directory Listing
Modified Fri Dec 14 20:45:13 2018 UTC (2 years, 2 months ago) by gross

Some Major fixes in the BFGS for long standing bugs: line serach and zoom are returning gradient consistent with args and Jx which fixes a uncurable break down in some cases, more messages are printed, restart is not resetting alpha, args are now consistent.

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Revision 6757 - Directory Listing
Modified Fri Dec 14 05:53:07 2018 UTC (2 years, 2 months ago) by aellery

eScripts has a new feature!

Finley can now read gmsh 4.0 msh files!

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Revision 6756 - Directory Listing
Modified Thu Nov 29 07:23:43 2018 UTC (2 years, 2 months ago) by aellery

Temporarily undoing last commit.

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Revision 6755 - Directory Listing
Modified Thu Nov 29 01:40:36 2018 UTC (2 years, 2 months ago) by aellery

A large number of the tests in doc/examples were creating files during the testing phase and then not deleting them afterwards. I have gone through these tests and added some code to do a clean up once each test is done.

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Revision 6754 - Directory Listing
Modified Wed Nov 21 06:54:51 2018 UTC (2 years, 3 months ago) by aellery

Lutz - I have finished removing the algebraic multigrid stuff from PASO. 

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Revision 6753 - Directory Listing
Modified Wed Nov 21 06:02:04 2018 UTC (2 years, 3 months ago) by aellery

Updated the Fedora installation instructions in the installation guide.

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Revision 6752 - Directory Listing
Modified Wed Nov 21 04:49:54 2018 UTC (2 years, 3 months ago) by aellery

Updated the install guide for centOS version 7.0.

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Revision 6751 - Directory Listing
Modified Wed Nov 21 02:35:29 2018 UTC (2 years, 3 months ago) by aellery

Fixed support bug 443 (escripts would not compile on openSUSE).

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Revision 6750 - Directory Listing
Modified Wed Nov 21 02:31:55 2018 UTC (2 years, 3 months ago) by caltinay

Fix soname so we can build with boost 1.67 (debian #914141).

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Revision 6749 - Directory Listing
Modified Fri Nov 16 02:02:41 2018 UTC (2 years, 3 months ago) by aellery

Fixed minor error in last commit.

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Revision 6748 - Directory Listing
Modified Thu Nov 15 23:50:51 2018 UTC (2 years, 3 months ago) by aellery

Fixed bug 450 (saveSilo tests were failing).

The tests were failing on meerkat because Python could not locate the example mesh files when WEIPA_WORKDIR was undefined. This is similar to the problem that was causing the dudley test run_inputOutput.py to fail.

While debugging, I noticed that the saveSilo test script was creating a lot of files and then not deleting them after the tests had run. I have changed a couple of lines to fix this.

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Revision 6747 - Directory Listing
Modified Mon Nov 12 04:19:02 2018 UTC (2 years, 3 months ago) by caltinay

This should prevent the lockups we are seeing when forking to run gmsh.

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Revision 6746 - Directory Listing
Modified Mon Nov 12 02:30:30 2018 UTC (2 years, 3 months ago) by caltinay

netCDF 4 requires new style nc4 format with Int64 datatypes.

This will break loading new dumps with previous escript versions.

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Revision 6745 - Directory Listing
Modified Mon Nov 12 02:00:20 2018 UTC (2 years, 3 months ago) by caltinay

more gcc 8 fixes.

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Revision 6744 - Directory Listing
Modified Mon Nov 12 01:28:36 2018 UTC (2 years, 3 months ago) by caltinay

gcc 8 fixes.

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Revision 6743 - Directory Listing
Modified Mon Nov 12 01:03:04 2018 UTC (2 years, 3 months ago) by aellery

I believe that the openMP test fails on several of the buildbots because the environment variables FINLEY_WORKDIR and DUDLEY_WORKDIR are not defined. I have updated dudley/test/python/run_inputOutput.py and finley/test/python/run_inputOutput.py so that when FINLEY_WORKDIR and DUDLEY_WORKDIR are undefined they default to the test directory.

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Revision 6742 - Directory Listing
Modified Sat Nov 10 00:24:20 2018 UTC (2 years, 3 months ago) by aellery

I have removed all boomer_amg options from the scons templates README_FIRST file and have added in a description of the option "insane".

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Revision 6741 - Directory Listing
Modified Fri Nov 9 05:25:29 2018 UTC (2 years, 3 months ago) by aellery

Fixed bug 430 (voxet_reader not using proper tmp files)

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Revision 6740 - Directory Listing
Modified Fri Nov 9 00:31:37 2018 UTC (2 years, 3 months ago) by aellery

Updated the trilinos section of the install guide.

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Revision 6739 - Directory Listing
Modified Wed Nov 7 23:58:41 2018 UTC (2 years, 3 months ago) by aellery

I have removed support for boomerAMG from eScript. Specific changes are:

i) I have removed the definition of the variables "boomeramg", "boomeramg_prefix" and "boomeramg_libs" from SConstruct as well as the boomerAMG section of dependencies.py. Similarly, I have removed the boomerAMG section of paso/src/SConscript. Also, I have removed boomeramg from the report that scons prints out after compilation.
ii) I have removed the enum SO_PRECONDITIONER_BOOMERAMG from escriptcpp.cpp 
iii) I have removed the enum SO_PRECONDITIONER_BOOMERAMG from escriptcore/src/SolverOptions.h and have updated a few comments.
iv) I have removed the case for SO_PRECONDITIONER_BOOMERAMG from the switches in SolverBuddy::getSummary(), SolverBuddy::getName() and SolverBuddy::setPreconditioner() in SolverOptions.cpp
v) In paso/src/Preconditioner.h, I have redefined the structure Preconditioner_AMG_Root so that it does not include a pointer to a Preconditioner_BoomerAMG.
vi) I have updated a couple of files in paso (AMG.cpp, AMG_Root.cpp) to reflect the changes in this structure (specifically, the fact that prec->boomeramg is now meaningless).
vii) I have removed a preprocessor directive in paso/src/Options.h (#define PASO_BOOMERAMG 60) and have updated paso/src/Options.cpp to reflect this change by removing this case from several switches.
viii) The files paso/src/BOOMERAMG.h and paso/src/BOOMERAMG.cpp have been removed from the latest commit.

On meerkat, with these changes, escripts compiles without any problems.

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Revision 6738 - Directory Listing
Modified Fri Nov 2 04:49:38 2018 UTC (2 years, 3 months ago) by aellery

Fixed another minor testing bug in dudley and finley.

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Revision 6737 - Directory Listing
Modified Fri Nov 2 04:05:47 2018 UTC (2 years, 3 months ago) by aellery

Fixed bug in downunder test run_dcforward.py

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Revision 6736 - Directory Listing
Modified Thu Nov 1 23:50:29 2018 UTC (2 years, 3 months ago) by aellery

Minor bug fixes.

I fixed several errors that were preventing eScripts from compiling (on Debian Stretch) when CUDA was enabled.

A set of problems arose due to a preprocessor directive starting on line 869 of RipleyDomain.cpp that the compiler only includes in the specific case where CUDA is enabled but MPI is not. Specifically:
(i) the switch statement inside this directive did not explicitly handle several values of the enum variables in escript/SolverOptions.h and had no default case. As a result the compiler was bouncing back an error. I have resolved this issue by adding a default case to the statement.
(ii) the if statement following the switch in this preprocessor directive set the variable "package" to a non-existent enum "SO_PACKAGE_DEFAULT" which I believe is a typo for "SO_DEFAULT".

I have also fixed:
(iii) The file ripley_UnitTest.cpp was trying to include the nonexistent file "escript/Esys_MPI.h" instead of "escript/EsysMPI.h", causing the compiler to bounce back an error.

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Revision 6735 - Directory Listing
Modified Wed Oct 31 23:59:03 2018 UTC (2 years, 3 months ago) by aellery

Minor bug fix.

eScripts was not compiling correctly when PAPI was enabled because performance.cpp in paso does not contain a declaration of PasoException. I have added a single line to the top of this file that points the compiler towards PasoException.h. This has resolved the error.

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Revision 6734 - Directory Listing
Modified Tue Oct 30 04:54:56 2018 UTC (2 years, 3 months ago) by aellery

 
eScripts has a new feature!
 
I have fixed the speckley::Brick ownSample function. It is now possible to save speckley Bricks in CSV format using saveDataCSV().

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Revision 6733 - Directory Listing
Modified Tue Oct 30 00:26:26 2018 UTC (2 years, 3 months ago) by aellery

I have identified and fixed the bug that was causing the dudley test run_inputOutput.py and the finley test run_inputOutput.py to fail.

This error occured because the environment variables DUDLEY_TEST_DATA and FINLEY_TEST_DATA were not defined. As a result, the test script was trying to load files from a directory that didn't exist, causing the functions readGmsh and readMesh to bounce back an error. I have modified these tests so that when DUDLEY_TEST_DATA and FINLEY_TEST_DATA are undefined, the script defaults to the correct directory. This has fixed the error and the test now runs to completion.

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Revision 6732 - Directory Listing
Modified Fri Oct 26 04:29:41 2018 UTC (2 years, 4 months ago) by aellery

Fixed bug 249 (SaveVTK return value unchecked in tests, not exceptions).

I have changed saveVTK to a void function that throws an exception whenever something goes wrong. I have also updated the tests in weipa/test/EscriptDatasetTestCase.cpp to take these exceptions into account when calling on saveVTK. All of the weipa tests for saveVTK now perform the proper checks and run to completion without any problems.

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Revision 6731 - Directory Listing
Modified Thu Oct 25 23:37:33 2018 UTC (2 years, 4 months ago) by aellery

Fixed bug #317 (remove deprecated functions and params in seismic.py).

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Revision 6730 - Directory Listing
Modified Thu Oct 25 00:50:20 2018 UTC (2 years, 4 months ago) by aellery

I have changed the sorting algoritm in run_comm4.py to a quicksort.

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Revision 6729 - Directory Listing
Modified Wed Oct 24 23:17:17 2018 UTC (2 years, 4 months ago) by aellery

Fixed the bug that was causing the downunder/test/python/run_comm4.py test to fail.

The cause of the error was a call to numpy.InterpolatedUnivariateSpline on line 626. This function returns an error if the values in the array x are not strictly increasing. I have added a couple of loops (lines 589-610) that sort this array and delete any duplicate entries. This has fixed the error and the test now runs to completion.

I have also changed a line in seismic.py that was causing a different test to crash (doc/examples/synthetic_HTI.py). This error was caused because python could not locate a function.

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Revision 6728 - Directory Listing
Modified Wed Oct 24 06:28:21 2018 UTC (2 years, 4 months ago) by aellery

Fixed an undocumented bug that was causing the tests in doc/examples/inversion/synthetic_HTI.py and doc/examples/inversion/synthetic_VTI.py to crash.

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Revision 6727 - Directory Listing
Modified Fri Oct 12 03:21:27 2018 UTC (2 years, 4 months ago) by aellery

Fixed bug 87

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Revision 6726 - Directory Listing
Modified Mon Oct 8 04:44:29 2018 UTC (2 years, 4 months ago) by aellery

Fixed bug #435 (compile warnings under clang++).

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Revision 6725 - Directory Listing
Modified Thu Oct 4 06:47:39 2018 UTC (2 years, 4 months ago) by aellery

Fixed bug 444

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Revision 6724 - Directory Listing
Modified Tue Oct 2 00:24:45 2018 UTC (2 years, 4 months ago) by aellery

I have added a temporary fix to bug 444 (speckley ownsample has not been implemented). Using this fix, a user can run saveDataCSV on a speckley rectangle or brick. At the moment, however, it will only run using a single MPI process. I will code a more permanent solution that utilises multiple MPI processes asap.

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Revision 6723 - Directory Listing
Modified Thu Sep 27 00:17:09 2018 UTC (2 years, 4 months ago) by aellery

eScripts currently fails to compile on django builder intel-mpi-py3-paso-long as the compiler settings are incorrect. I have changed the settings in SConstruct to fix this.

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Revision 6722 - Directory Listing
Modified Thu Sep 27 00:00:06 2018 UTC (2 years, 4 months ago) by aellery

eScripts has a new feature!

Added enhancement #420 on RedMine. Scons will not run a sanity check if you pass the option "insane=True". I.e. if you run the command

scons insane=True

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Revision 6721 - Directory Listing
Modified Wed Sep 26 05:58:38 2018 UTC (2 years, 5 months ago) by aellery

getNumpy now supports complex Data. I have also added a new section to the documentation (3.2.11) that describes how the getNumpy function works.

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Revision 6720 - Directory Listing
Modified Wed Sep 26 02:02:45 2018 UTC (2 years, 5 months ago) by aellery

getNumpy now returns named structured arrays.

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Revision 6719 - Directory Listing
Modified Tue Sep 25 02:53:15 2018 UTC (2 years, 5 months ago) by aellery

I have modified getNumpy so that it no longer accepts Data objects that contain complex numbers, due to a bug.

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Revision 6718 - Directory Listing
Modified Mon Sep 24 00:50:08 2018 UTC (2 years, 5 months ago) by aellery

eScripts has a new Feature!


If multiple Data objects are passed to getNumpy then getNumpy will return multiple numpy ndarrays. Example usage:
a = Scalar(1.0, Function(domain))
b = Vector([2.0,2.0], ContinuousFunction(domain))
a,b = getNumpy(a=a,b=b)

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Revision 6717 - Directory Listing
Modified Fri Sep 21 04:32:52 2018 UTC (2 years, 5 months ago) by aellery

Fixed the boost numpy linker bug.

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Revision 6716 - Directory Listing
Modified Fri Sep 21 02:51:37 2018 UTC (2 years, 5 months ago) by aellery

Bug fix.

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Revision 6715 - Directory Listing
Modified Tue Sep 4 23:38:18 2018 UTC (2 years, 5 months ago) by aellery

Minor bug fix

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Revision 6714 - Directory Listing
Modified Thu Aug 30 02:08:54 2018 UTC (2 years, 5 months ago) by aellery

escripts currently does not compile properly with boost version 1.63 or higher as it cannot locate the boost python numpy module. I have updated the code to temporarily deactive getNumpy until this is fixed.

To compile with getNumpy, point the compiler to the missing library then change line 277 of site_scons/dependencies.py to read:

if boostversion >= 106300:

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Revision 6713 - Directory Listing
Modified Wed Aug 29 03:11:52 2018 UTC (2 years, 5 months ago) by aellery

getNumpy now supports complex numbers.

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Revision 6712 - Directory Listing
Modified Wed Aug 29 00:02:21 2018 UTC (2 years, 5 months ago) by aellery

eScripts has a new feature!!!


When compiled with boost version 1.63 or higher, the command getNumpy( [data] ) will return a numpy ndarray containing the values in the data object [data]. The code is optimised to use MPI. Please note that at the moment the code does not support masks or complex numbers.

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Revision 6711 - Directory Listing
Modified Mon Aug 20 01:37:23 2018 UTC (2 years, 6 months ago) by aellery

Fixed bug 441. (Removed the work-around for the issues caused in the Locator function by bug 391)

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Revision 6710 - Directory Listing
Modified Fri Aug 17 05:53:03 2018 UTC (2 years, 6 months ago) by aellery

Updated the userguide to reflect changes made in revision 6709 (added feature 500)

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Revision 6709 - Directory Listing
Modified Fri Aug 17 04:56:51 2018 UTC (2 years, 6 months ago) by aellery

Escript now has a new feature!

saveDataCSV will now write the reference id of the node or element as the first column of the output CSV file when the user calls on it using the flag "refid=True".

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Revision 6708 - Directory Listing
Modified Wed Aug 15 04:30:31 2018 UTC (2 years, 6 months ago) by aellery

Fixed bug 391. Data.getTupleForGlobalDataPoint now works for complex data.

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Revision 6707 - Directory Listing
Modified Mon Aug 13 22:51:29 2018 UTC (2 years, 6 months ago) by aellery

saveDataCSV now works correctly.

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Revision 6706 - Directory Listing
Modified Mon Aug 6 02:44:09 2018 UTC (2 years, 6 months ago) by caltinay

Fixing Werror=catch-value with gcc 8.

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Revision 6702 - Directory Listing
Modified Tue Jun 26 20:48:32 2018 UTC (2 years, 8 months ago) by gross

UFRN building added

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Revision 6698 - Directory Listing
Modified Tue Jun 26 00:32:19 2018 UTC (2 years, 8 months ago) by jfenwick

Update testing information for OSX

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Revision 6690 - Directory Listing
Modified Mon Jun 25 02:10:43 2018 UTC (2 years, 8 months ago) by jfenwick

Adding Adam

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Revision 6689 - Directory Listing
Modified Mon Jun 25 01:31:43 2018 UTC (2 years, 8 months ago) by jfenwick

Added Ander

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Revision 6688 - Directory Listing
Modified Mon Jun 25 01:31:06 2018 UTC (2 years, 8 months ago) by jfenwick

Added slightly more doco on lazy

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Revision 6687 - Directory Listing
Modified Sun Jun 17 23:36:56 2018 UTC (2 years, 8 months ago) by aellery

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 (2 years, 8 months ago) by aellery

Fixed some minor typos

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Revision 6685 - Directory Listing
Modified Wed Jun 13 09:32:12 2018 UTC (2 years, 8 months ago) by caltinay

fixed filename.

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Revision 6684 - Directory Listing
Modified Wed Jun 13 04:48:44 2018 UTC (2 years, 8 months ago) by jfenwick

ncLong is deprecated

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Revision 6683 - Directory Listing
Modified Tue Jun 12 01:00:29 2018 UTC (2 years, 8 months ago) by jfenwick

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 (2 years, 8 months ago) by jfenwick

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 (2 years, 8 months ago) by jfenwick

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 (2 years, 8 months ago) by jfenwick

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 (2 years, 8 months ago) by jfenwick

Latex fixes

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Revision 6678 - Directory Listing
Modified Mon Jun 11 04:05:30 2018 UTC (2 years, 8 months ago) by jfenwick

Fixing overfull hboxes

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Revision 6677 - Directory Listing
Modified Mon Jun 11 01:04:45 2018 UTC (2 years, 8 months ago) by jfenwick

Fix some BiBTex issues

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Revision 6676 - Directory Listing
Modified Mon May 21 00:34:56 2018 UTC (2 years, 9 months ago) by uqagarro

New version with gradient test corrected

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Revision 6675 - Directory Listing
Modified Mon May 21 00:32:28 2018 UTC (2 years, 9 months ago) by uqagarro

New version with gradient test corrected

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Revision 6674 - Directory Listing
Modified Sun May 20 23:15:00 2018 UTC (2 years, 9 months ago) by uqagarro

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 (2 years, 9 months ago) by uqagarro

Some bugs fixed regarded to r6670

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Revision 6672 - Directory Listing
Modified Thu May 17 01:58:32 2018 UTC (2 years, 9 months ago) by uqagarro

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 (2 years, 9 months ago) by uqagarro

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 (2 years, 9 months ago) by uqagarro

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 (2 years, 9 months ago) by uqagarro

Type error corrected

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Revision 6668 - Directory Listing
Modified Wed Apr 25 23:32:03 2018 UTC (2 years, 10 months ago) by uqagarro

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 (2 years, 10 months ago) by uqagarro

Fix some debugging left

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Revision 6666 - Directory Listing
Modified Thu Apr 12 02:32:20 2018 UTC (2 years, 10 months ago) by jfenwick

actually fix the filename

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Revision 6665 - Directory Listing
Modified Thu Apr 12 02:01:08 2018 UTC (2 years, 10 months ago) by uqagarro

typographic bug

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Revision 6664 - Directory Listing
Modified Thu Apr 12 01:42:02 2018 UTC (2 years, 10 months ago) by uqagarro

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 (2 years, 10 months ago) by jfenwick

Stop using hardcoded filenames in example scripts

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Revision 6662 - Directory Listing
Modified Mon Apr 9 04:12:20 2018 UTC (2 years, 10 months ago) by jfenwick

Use py3 version of sphinx

Fixes #417

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Revision 6661 - Directory Listing
Modified Mon Apr 9 04:08:21 2018 UTC (2 years, 10 months ago) by jfenwick

Removing some from X import *

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Revision 6660 - Directory Listing
Modified Mon Apr 9 01:41:05 2018 UTC (2 years, 10 months ago) by jfenwick

some docstring fixes s

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Revision 6659 - Directory Listing
Modified Mon Apr 9 00:30:36 2018 UTC (2 years, 10 months ago) by jfenwick

symlink

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Revision 6658 - Directory Listing
Modified Mon Apr 9 00:29:43 2018 UTC (2 years, 10 months ago) by jfenwick

prepare for defaulting badger to py3

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Revision 6657 - Directory Listing
Modified Thu Mar 29 04:43:17 2018 UTC (2 years, 10 months ago) by uqagarro

Added test for IncompressibleIsotropicFlowCartesianOnFinley
with higher NE

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Revision 6656 - Directory Listing
Modified Thu Mar 29 03:28:02 2018 UTC (2 years, 10 months ago) by uqagarro

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 (2 years, 11 months ago) by uqagarro

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 (2 years, 11 months ago) by jfenwick

Make sid include netcdf4 support by default

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Revision 6653 - Directory Listing
Modified Mon Mar 19 01:24:25 2018 UTC (2 years, 11 months ago) by jfenwick

Added netcdfv4 deps to install guide

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Revision 6652 - Directory Listing
Modified Wed Mar 14 08:22:11 2018 UTC (2 years, 11 months ago) by jfenwick

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 (3 years ago) by jfenwick

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 (3 years ago) by caltinay

Fix for typeError in ripley::setDecompositionPolicy.

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

minimizers: bug in tolerance setting fixed.

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Revision 6648 - Directory Listing
Modified Wed Dec 20 01:46:56 2017 UTC (3 years, 2 months ago) by jfenwick

remove dependency on esysUtils

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Revision 6647 - Directory Listing
Modified Thu Dec 7 06:52:32 2017 UTC (3 years, 2 months ago) by jfenwick

Sphinxing continues

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Revision 6646 - Directory Listing
Modified Thu Dec 7 05:14:57 2017 UTC (3 years, 2 months ago) by jfenwick

It continues

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Revision 6645 - Directory Listing
Modified Thu Dec 7 03:06:33 2017 UTC (3 years, 2 months ago) by jfenwick

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 (3 years, 2 months ago) by jfenwick

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 (3 years, 2 months ago) by jfenwick

Switching imports over

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Revision 6642 - Directory Listing
Modified Thu Dec 7 01:07:04 2017 UTC (3 years, 2 months ago) by jfenwick

More import fixes

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Revision 6641 - Directory Listing
Modified Thu Dec 7 01:05:41 2017 UTC (3 years, 2 months ago) by jfenwick

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 (3 years, 2 months ago) by jfenwick

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 (3 years, 2 months ago) by jfenwick

more minor tweaks

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Revision 6638 - Directory Listing
Modified Wed Dec 6 06:28:41 2017 UTC (3 years, 2 months ago) by jfenwick

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 (3 years, 2 months ago) by jfenwick

Fix some sphinx errors

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Revision 6636 - Directory Listing
Modified Tue Dec 5 05:03:43 2017 UTC (3 years, 2 months ago) by jfenwick

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 (3 years, 2 months ago) by jfenwick

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 (3 years, 2 months ago) by jfenwick

Add a package docstring to escript

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Revision 6633 - Directory Listing
Modified Tue Nov 28 07:22:39 2017 UTC (3 years, 2 months ago) by jfenwick

more spelling

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Revision 6632 - Directory Listing
Modified Tue Nov 28 06:35:15 2017 UTC (3 years, 2 months ago) by jfenwick

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 (3 years, 2 months ago) by caltinay

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 (3 years, 3 months ago) by jfenwick

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 (3 years, 3 months ago) by caltinay

fixed typo.

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Revision 6628 - Directory Listing
Modified Thu Nov 23 06:02:01 2017 UTC (3 years, 3 months ago) by caltinay

should fix the logic for #416...

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Revision 6627 - Directory Listing
Modified Thu Nov 23 05:45:58 2017 UTC (3 years, 3 months ago) by caltinay

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 (3 years, 3 months ago) by caltinay

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 (3 years, 3 months ago) by jfenwick

initial options for capybara

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Revision 6624 - Directory Listing
Modified Wed Nov 15 11:22:21 2017 UTC (3 years, 3 months ago) by caltinay

Fixing idxtype long builds of finley.

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Revision 6623 - Directory Listing
Modified Thu Nov 9 02:26:55 2017 UTC (3 years, 3 months ago) by jfenwick

Building up options files for capybara.

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Revision 6622 - Directory Listing
Modified Thu Nov 9 02:24:15 2017 UTC (3 years, 3 months ago) by jfenwick

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 (3 years, 3 months ago) by jfenwick

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 (3 years, 6 months ago) by gross

gather function fixed.

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

Unicode causing a problem

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Revision 6618 - Directory Listing
Modified Wed Aug 2 07:38:37 2017 UTC (3 years, 6 months ago) by jfenwick

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 (3 years, 6 months ago) by caltinay

added missing include.

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Revision 6616 - Directory Listing
Modified Thu Jul 27 23:42:51 2017 UTC (3 years, 6 months ago) by jfenwick

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 (3 years, 8 months ago) by jfenwick

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 (3 years, 8 months ago) by jfenwick

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 (3 years, 8 months ago) by jfenwick

Sigh

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Revision 6612 - Directory Listing
Modified Tue Jun 20 03:21:40 2017 UTC (3 years, 8 months ago) by jfenwick

Merging changes from release branch

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Revision 6611 - Directory Listing
Modified Tue Jun 20 03:18:04 2017 UTC (3 years, 8 months ago) by jfenwick

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 (3 years, 8 months ago) by jfenwick

More work on the _Inf functions

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Revision 6609 - Directory Listing
Modified Thu Jun 8 07:08:54 2017 UTC (3 years, 8 months ago) by jfenwick

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 (3 years, 8 months ago) by jfenwick

Missing file

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Revision 6592 - Directory Listing
Modified Mon Jun 5 02:15:01 2017 UTC (3 years, 8 months ago) by jfenwick

Some notes on trilinos

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Revision 6591 - Directory Listing
Modified Fri Jun 2 02:24:51 2017 UTC (3 years, 8 months ago) by jfenwick

Printing tagged Data now reports if tag is unused.

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

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Revision 6590 - Directory Listing
Modified Fri Jun 2 01:10:53 2017 UTC (3 years, 8 months ago) by jfenwick

Only summarise data if it is expanded

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Revision 6589 - Directory Listing
Modified Thu Jun 1 06:27:03 2017 UTC (3 years, 8 months ago) by jfenwick

Change list for 5.2.

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

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Revision 6588 - Directory Listing
Modified Thu Jun 1 01:25:24 2017 UTC (3 years, 8 months ago) by jfenwick

Describe mpi_no_host option

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Revision 6587 - Directory Listing
Modified Wed May 24 07:50:23 2017 UTC (3 years, 9 months ago) by jfenwick

Fix lazy related test failures.

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Revision 6586 - Directory Listing
Modified Tue May 23 07:00:19 2017 UTC (3 years, 9 months ago) by jfenwick

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 (3 years, 9 months ago) by caltinay

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 (3 years, 9 months ago) by caltinay

typos fixed.

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Revision 6583 - Directory Listing
Modified Mon May 22 08:04:56 2017 UTC (3 years, 9 months ago) by caltinay

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 (3 years, 9 months ago) by caltinay

fixed typo.

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Revision 6581 - Directory Listing
Modified Fri May 19 06:39:36 2017 UTC (3 years, 9 months ago) by caltinay

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 (3 years, 9 months ago) by caltinay

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

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

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Revision 6579 - Directory Listing
Modified Fri May 19 01:37:23 2017 UTC (3 years, 9 months ago) by caltinay

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

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Revision 6578 - Directory Listing
Modified Wed May 17 04:16:40 2017 UTC (3 years, 9 months ago) by caltinay

Complex interpolation in speckley.

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Revision 6577 - Directory Listing
Modified Wed May 17 02:34:45 2017 UTC (3 years, 9 months ago) by caltinay

complex integrals for speckley. Fixes #398

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Revision 6576 - Directory Listing
Modified Wed May 17 01:42:26 2017 UTC (3 years, 9 months ago) by caltinay

Finished complex interpolation cases in dudley.

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Revision 6575 - Directory Listing
Modified Wed May 17 01:04:36 2017 UTC (3 years, 9 months ago) by caltinay

complex integration and interpolation in dudley.

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Revision 6574 - Directory Listing
Modified Wed May 17 00:53:31 2017 UTC (3 years, 9 months ago) by jfenwick

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 (3 years, 9 months ago) by jfenwick

Add mpi_no_host option

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

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Revision 6572 - Directory Listing
Modified Tue May 16 23:16:45 2017 UTC (3 years, 9 months ago) by caltinay

implementation of complex integrals in finley. (#398)

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Revision 6571 - Directory Listing
Modified Mon May 15 11:39:06 2017 UTC (3 years, 9 months ago) by caltinay

Forgot to enable the code path.

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Revision 6570 - Directory Listing
Modified Mon May 15 11:23:29 2017 UTC (3 years, 9 months ago) by caltinay

Complex interpolation in finley is complete.

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Revision 6569 - Directory Listing
Modified Mon May 15 10:17:13 2017 UTC (3 years, 9 months ago) by caltinay

complex element data interpolation in finley.

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Revision 6568 - Directory Listing
Modified Mon May 15 09:29:39 2017 UTC (3 years, 9 months ago) by caltinay

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 (3 years, 9 months ago) by caltinay

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 (3 years, 9 months ago) by caltinay

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 (3 years, 9 months ago) by caltinay

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 (3 years, 9 months ago) by jfenwick

new test for tensor_transpose_mult

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Revision 6558 - Directory Listing
Modified Wed May 10 04:55:32 2017 UTC (3 years, 9 months ago) by jfenwick

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 (3 years, 9 months ago) by jfenwick

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 (3 years, 9 months ago) by jfenwick

Add compare tool.

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

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

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Revision 6555 - Directory Listing
Modified Sun May 7 11:44:34 2017 UTC (3 years, 9 months ago) by caltinay

fixed minor typo.

---

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

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

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

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

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Revision 6553 - Directory Listing
Modified Fri Apr 28 03:35:26 2017 UTC (3 years, 9 months ago) by jfenwick

Fix some unused vars

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Revision 6552 - Directory Listing
Modified Wed Apr 26 02:33:23 2017 UTC (3 years, 10 months ago) by jfenwick

Options for ferret

---

Revision 6551 - Directory Listing
Modified Tue Apr 4 06:17:09 2017 UTC (3 years, 10 months ago) by jfenwick

commenting some imports

---

Revision 6550 - Directory Listing
Modified Tue Apr 4 05:34:33 2017 UTC (3 years, 10 months ago) by jfenwick

minor tweaks

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Revision 6549 - Directory Listing
Modified Mon Mar 27 06:32:03 2017 UTC (3 years, 11 months ago) by jfenwick

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 (3 years, 11 months ago) by jfenwick

Fix a missing complex->data conversion

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Revision 6547 - Directory Listing
Modified Mon Mar 27 06:15:05 2017 UTC (3 years, 11 months ago) by jfenwick

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 (3 years, 11 months ago) by jfenwick

Add test for overloaded +

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

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Revision 6545 - Directory Listing
Modified Fri Mar 24 00:21:35 2017 UTC (3 years, 11 months ago) by jfenwick

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 (3 years, 11 months ago) by jfenwick

Add two tests

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Revision 6543 - Directory Listing
Modified Thu Mar 23 06:33:16 2017 UTC (3 years, 11 months ago) by jfenwick

Adding eigenvalues_and_eigenvector test.

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

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Revision 6542 - Directory Listing
Modified Thu Mar 23 00:35:22 2017 UTC (3 years, 11 months ago) by jfenwick

Better version of earlier fix.

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

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

---

Revision 6541 - Directory Listing
Modified Thu Mar 23 00:33:27 2017 UTC (3 years, 11 months ago) by jfenwick

Remove unused test category

---

Revision 6540 - Directory Listing
Modified Wed Mar 22 06:50:34 2017 UTC (3 years, 11 months ago) by jfenwick

Fix nasty concurrency bug.

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

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Revision 6539 - Directory Listing
Modified Tue Mar 14 07:46:12 2017 UTC (3 years, 11 months ago) by jfenwick

Fix incorrect collapse behaviour

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

---

Revision 6538 - Directory Listing
Modified Tue Mar 14 03:49:20 2017 UTC (3 years, 11 months ago) by jfenwick

Fix whereZero bugs

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

Reorder some declarations to stop the compiler complaining.

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Revision 6537 - Directory Listing
Modified Tue Mar 14 00:01:31 2017 UTC (3 years, 11 months ago) by jfenwick

Add missing deepCopy cases

---

Revision 6536 - Directory Listing
Modified Mon Mar 13 06:30:35 2017 UTC (3 years, 11 months ago) by jfenwick

Bug fixes.

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

---

Revision 6535 - Directory Listing
Modified Mon Mar 13 04:38:47 2017 UTC (3 years, 11 months ago) by jfenwick

Fix sign and abs

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

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Revision 6534 - Directory Listing
Modified Fri Mar 10 04:47:23 2017 UTC (3 years, 11 months ago) by jfenwick

Fix crash

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Revision 6533 - Directory Listing
Modified Fri Mar 10 04:08:40 2017 UTC (3 years, 11 months ago) by jfenwick

Lazy fixes

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

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Revision 6532 - Directory Listing
Modified Thu Mar 9 10:32:46 2017 UTC (3 years, 11 months ago) by jfenwick

More option files

---

Revision 6531 - Directory Listing
Modified Thu Mar 9 04:43:36 2017 UTC (3 years, 11 months ago) by jfenwick

Add Xenial options

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Revision 6530 - Directory Listing
Modified Thu Mar 9 01:31:15 2017 UTC (3 years, 11 months ago) by jfenwick

Noting dependency on legacy-netcdf for debian styles

---

Revision 6529 - Directory Listing
Modified Thu Mar 9 01:29:12 2017 UTC (3 years, 11 months ago) by jfenwick

Adding yakkety options

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Revision 6528 - Directory Listing
Modified Wed Mar 8 05:07:31 2017 UTC (3 years, 11 months ago) by jfenwick

Remove AUTOLAZY fiddles

---

Revision 6527 - Directory Listing
Modified Wed Mar 8 05:05:17 2017 UTC (3 years, 11 months ago) by jfenwick

Correct error messages about anti-hermitian

---

Revision 6526 - Directory Listing
Modified Wed Mar 8 03:48:11 2017 UTC (3 years, 11 months ago) by jfenwick

Fix error in m_iscompl determination

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Revision 6525 - Directory Listing
Modified Wed Mar 8 02:11:25 2017 UTC (3 years, 11 months ago) by jfenwick

Stray print removal

---

Revision 6524 - Directory Listing
Modified Wed Mar 8 02:08:04 2017 UTC (3 years, 11 months ago) by jfenwick

"Reordering statements involving reference params" considered dangerous

---

Revision 6523 - Directory Listing
Modified Tue Mar 7 06:50:34 2017 UTC (3 years, 11 months ago) by jfenwick

UPDATE THE COPYRIGHT DATES

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Revision 6522 - Directory Listing
Modified Tue Mar 7 05:55:32 2017 UTC (3 years, 11 months ago) by jfenwick

Various

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

---

Revision 6521 - Directory Listing
Modified Tue Mar 7 04:24:20 2017 UTC (3 years, 11 months ago) by jfenwick

Merging clazy branch

---

Revision 6519 - Directory Listing
Modified Tue Mar 7 01:55:01 2017 UTC (3 years, 11 months ago) by jfenwick

Remove debug print

---

Revision 6515 - Directory Listing
Modified Mon Mar 6 01:54:53 2017 UTC (3 years, 11 months ago) by jfenwick

More helpful exception message

---

Revision 6510 - Directory Listing
Modified Thu Mar 2 23:47:07 2017 UTC (3 years, 11 months ago) by jfenwick

Move my netcdf variable fiddles after the environment is recreated

---

Revision 6509 - Directory Listing
Modified Thu Mar 2 07:36:17 2017 UTC (3 years, 11 months ago) by jfenwick

netcdf build option is now 3-state

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

---

Revision 6508 - Directory Listing
Modified Thu Mar 2 03:42:31 2017 UTC (3 years, 11 months ago) by jfenwick

Weipa netcdf update

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

Need to clean up scons options control

---

Revision 6507 - Directory Listing
Modified Wed Mar 1 06:19:04 2017 UTC (3 years, 11 months ago) by jfenwick

More netcdf4 work

Still need to convert weipa

---

Revision 6506 - Directory Listing
Modified Tue Feb 28 03:58:20 2017 UTC (3 years, 11 months ago) by jfenwick

Work on new netcdf

---

Revision 6505 - Directory Listing
Modified Tue Feb 21 06:11:12 2017 UTC (4 years ago) by jfenwick

Work on new netcdf interface

It passes unit tests ....

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Revision 6504 - Directory Listing
Modified Tue Feb 21 01:00:17 2017 UTC (4 years ago) by jfenwick

Helper function to open netcdf

---

Revision 6503 - Directory Listing
Modified Mon Feb 20 03:39:19 2017 UTC (4 years ago) by jfenwick

netcdf4 version of load

---

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

hiding some variables

---

Revision 6501 - Directory Listing
Modified Mon Feb 20 03:36:51 2017 UTC (4 years ago) by jfenwick

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

---

Revision 6500 - Directory Listing
Modified Fri Feb 17 04:54:25 2017 UTC (4 years ago) by jfenwick

Forgot to check with MPI

---

Revision 6499 - Directory Listing
Modified Thu Feb 16 06:37:07 2017 UTC (4 years ago) by jfenwick

Work towards netcdf4

---

Revision 6498 - Directory Listing
Modified Wed Feb 15 05:12:55 2017 UTC (4 years ago) by jfenwick

partial workaround of complex testing issue

---

Revision 6497 - Directory Listing
Modified Wed Feb 15 00:44:55 2017 UTC (4 years ago) by jfenwick

Reader for netcdf classic headers.

---

Revision 6496 - Directory Listing
Modified Tue Feb 14 00:38:08 2017 UTC (4 years ago) by gross

bug to obtain function space fixed.

---

Revision 6495 - Directory Listing
Modified Fri Feb 10 08:16:28 2017 UTC (4 years ago) by gross

magnetic intensity added.

---

Revision 6494 - Directory Listing
Modified Thu Feb 9 23:28:53 2017 UTC (4 years ago) by jfenwick

This version seems to work

---

Revision 6493 - Directory Listing
Modified Thu Feb 9 23:23:37 2017 UTC (4 years ago) by jfenwick

Added stdlocationisprefix option

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

---

Revision 6492 - Directory Listing
Modified Thu Feb 9 07:32:43 2017 UTC (4 years ago) by gross

new section in inversion guide

---

Revision 6491 - Directory Listing
Modified Thu Feb 9 02:04:18 2017 UTC (4 years ago) by jfenwick

fix name of macports boostio

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Revision 6490 - Directory Listing
Modified Thu Feb 9 01:21:02 2017 UTC (4 years ago) by jfenwick

because Darwin different

---

Revision 6489 - Directory Listing
Modified Thu Feb 9 00:28:44 2017 UTC (4 years ago) by jfenwick

fix it

---

Revision 6488 - Directory Listing
Modified Wed Feb 8 23:55:10 2017 UTC (4 years ago) by jfenwick

Attempt to make python detection better

---

Revision 6487 - Directory Listing
Modified Tue Feb 7 00:51:09 2017 UTC (4 years ago) by caltinay

fix typo.

---

Revision 6486 - Directory Listing
Modified Fri Jan 27 00:13:27 2017 UTC (4 years ago) by jfenwick

Another case of allowing complex

---

Revision 6485 - Directory Listing
Modified Wed Jan 25 04:45:38 2017 UTC (4 years, 1 month ago) by jfenwick

Some more tests

---

Revision 6484 - Directory Listing
Modified Wed Jan 25 04:43:39 2017 UTC (4 years, 1 month ago) by jfenwick

More helpful error message

---

Revision 6483 - Directory Listing
Modified Wed Jan 25 02:56:14 2017 UTC (4 years, 1 month ago) by jfenwick

Biting bullet and doing separate generator for matrix

---

Revision 6482 - Directory Listing
Modified Tue Jan 24 07:45:33 2017 UTC (4 years, 1 month ago) by jfenwick

More tests

Still need to look at the MVp testing

---

Revision 6481 - Directory Listing
Modified Tue Jan 24 07:34:24 2017 UTC (4 years, 1 month ago) by jfenwick

Decree: Tensor products are not always real.

---

Revision 6480 - Directory Listing
Modified Tue Jan 24 05:01:31 2017 UTC (4 years, 1 month ago) by jfenwick

Test for outer

---

Revision 6479 - Directory Listing
Modified Mon Jan 23 11:33:19 2017 UTC (4 years, 1 month ago) by caltinay

Unbreak ripley Brick.

---

Revision 6478 - Directory Listing
Modified Mon Jan 23 10:15:02 2017 UTC (4 years, 1 month ago) by caltinay

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

---

Revision 6477 - Directory Listing
Modified Mon Jan 23 10:13:13 2017 UTC (4 years, 1 month ago) by caltinay

Fixing default decomposition policy in ripley (ouch!).

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

---

Revision 6476 - Directory Listing
Modified Mon Jan 23 08:32:07 2017 UTC (4 years, 1 month ago) by caltinay

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

---

Revision 6475 - Directory Listing
Modified Fri Jan 20 02:17:33 2017 UTC (4 years, 1 month ago) by caltinay

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

---

Revision 6474 - Directory Listing
Modified Fri Jan 20 00:12:46 2017 UTC (4 years, 1 month ago) by gross

docstring updated.

---

Revision 6473 - Directory Listing
Modified Thu Jan 19 07:27:04 2017 UTC (4 years, 1 month ago) by caltinay

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

---

Revision 6472 - Directory Listing
Modified Thu Jan 19 00:39:08 2017 UTC (4 years, 1 month ago) by jfenwick

Fix failing unit tests

---

Revision 6471 - Directory Listing
Modified Wed Jan 18 06:09:47 2017 UTC (4 years, 1 month ago) by jfenwick

Make tuples acceptable to getRank and getShape

---

Revision 6470 - Directory Listing
Modified Wed Jan 18 05:37:05 2017 UTC (4 years, 1 month ago) by jfenwick

Initial tests binary operation

---

Revision 6469 - Directory Listing
Modified Tue Jan 17 07:45:36 2017 UTC (4 years, 1 month ago) by jfenwick

Add zeroed copy

---

Revision 6468 - Directory Listing
Modified Tue Jan 17 07:35:13 2017 UTC (4 years, 1 month ago) by jfenwick

reductions no longer ignore tags with default values

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

---

Revision 6467 - Directory Listing
Modified Wed Jan 11 03:13:14 2017 UTC (4 years, 1 month ago) by jfenwick

Fix unit test failure

---

Revision 6466 - Directory Listing
Modified Wed Jan 11 01:52:56 2017 UTC (4 years, 1 month ago) by jfenwick

Now includes tests of all ops in the original test set

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

---

Revision 6465 - Directory Listing
Modified Wed Jan 11 01:28:23 2017 UTC (4 years, 1 month ago) by jfenwick

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

---

Revision 6464 - Directory Listing
Modified Wed Jan 11 00:00:46 2017 UTC (4 years, 1 month ago) by jfenwick

More tests

Rename data_only to no_scalars [which is more accurate]

---

Revision 6463 - Directory Listing
Modified Tue Jan 10 22:46:54 2017 UTC (4 years, 1 month ago) by jfenwick

Fix test failures

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

---

Revision 6462 - Directory Listing
Modified Tue Jan 10 06:37:50 2017 UTC (4 years, 1 month ago) by jfenwick

hermitian tests debug output

---

Revision 6461 - Directory Listing
Modified Tue Jan 10 06:29:51 2017 UTC (4 years, 1 month ago) by jfenwick

Stop (anit-)hermitian from using numpy.transpose

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

---

Revision 6460 - Directory Listing
Modified Tue Jan 10 04:54:19 2017 UTC (4 years, 1 month ago) by jfenwick

Correct docstring for antihermitian

---

Revision 6459 - Directory Listing
Modified Tue Jan 10 04:28:51 2017 UTC (4 years, 1 month ago) by jfenwick

Fix build failure and add test

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

---

Revision 6458 - Directory Listing
Modified Tue Jan 10 03:04:13 2017 UTC (4 years, 1 month ago) by jfenwick

More debug and test for transpose

---

Revision 6457 - Directory Listing
Modified Tue Jan 10 02:05:39 2017 UTC (4 years, 1 month ago) by jfenwick

More tests

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

Tests now check rank-4 cases.

---

Revision 6456 - Directory Listing
Modified Tue Jan 10 02:03:16 2017 UTC (4 years, 1 month ago) by jfenwick

Change in whereX semantics

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

---

Revision 6455 - Directory Listing
Modified Mon Jan 9 05:35:43 2017 UTC (4 years, 1 month ago) by jfenwick

Tests and fix to util.length

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

---

Revision 6454 - Directory Listing
Modified Mon Jan 9 04:19:59 2017 UTC (4 years, 1 month ago) by jfenwick

Have unary tests for the trig now

---

Revision 6453 - Directory Listing
Modified Mon Jan 9 03:17:00 2017 UTC (4 years, 1 month ago) by jfenwick

More tests using the more general tester.

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

---

Revision 6452 - Directory Listing
Modified Sun Jan 8 21:41:36 2017 UTC (4 years, 1 month ago) by jfenwick

Adapt to moving openmpi library

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

---

Revision 6451 - Directory Listing
Modified Tue Dec 20 06:22:39 2016 UTC (4 years, 2 months ago) by caltinay

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

---

Revision 6450 - Directory Listing
Modified Thu Dec 15 02:33:38 2016 UTC (4 years, 2 months ago) by jfenwick

Starting work on the unary ops

---

Revision 6449 - Directory Listing
Modified Wed Dec 14 01:01:48 2016 UTC (4 years, 2 months ago) by jfenwick

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

---

Revision 6448 - Directory Listing
Modified Tue Dec 13 06:25:52 2016 UTC (4 years, 2 months ago) by jfenwick

Switch over to new util tests.
Fix some bugs

---

Revision 6447 - Directory Listing
Modified Tue Dec 13 05:07:30 2016 UTC (4 years, 2 months ago) by jfenwick

Reduction tests

---

Revision 6446 - Directory Listing
Modified Tue Dec 13 04:44:28 2016 UTC (4 years, 2 months ago) by jfenwick

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

---

Revision 6445 - Directory Listing
Modified Wed Dec 7 07:01:18 2016 UTC (4 years, 2 months ago) by jfenwick

Make sure some of the test values are negative

---

Revision 6444 - Directory Listing
Modified Tue Dec 6 08:24:19 2016 UTC (4 years, 2 months ago) by jfenwick

More progress

---

Revision 6443 - Directory Listing
Modified Mon Dec 5 23:28:02 2016 UTC (4 years, 2 months ago) by jfenwick

Start on test restructure

---

Revision 6442 - Directory Listing
Modified Fri Dec 2 06:17:38 2016 UTC (4 years, 2 months ago) by gross

some modifications VGL

---

Revision 6441 - Directory Listing
Modified Tue Nov 29 07:27:03 2016 UTC (4 years, 2 months ago) by gross

arguments fixed

---

Revision 6440 - Directory Listing
Modified Tue Nov 29 07:26:33 2016 UTC (4 years, 2 months ago) by gross

namespace problem fixed

---

Revision 6439 - Directory Listing
Modified Tue Nov 29 05:35:33 2016 UTC (4 years, 2 months ago) by jfenwick

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

---

Revision 6438 - Directory Listing
Modified Mon Nov 7 08:30:55 2016 UTC (4 years, 3 months ago) by jfenwick

Remainder of this batch of default removing.

---

Revision 6437 - Directory Listing
Modified Mon Nov 7 04:20:32 2016 UTC (4 years, 3 months ago) by jfenwick

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

---

Revision 6436 - Directory Listing
Modified Mon Nov 7 01:28:47 2016 UTC (4 years, 3 months ago) by jfenwick

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

There is more to be done here.

---

Revision 6435 - Directory Listing
Modified Sat Nov 5 12:35:35 2016 UTC (4 years, 3 months ago) by caltinay

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

---

Revision 6434 - Directory Listing
Modified Sat Nov 5 12:16:07 2016 UTC (4 years, 3 months ago) by caltinay

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

---

Revision 6433 - Directory Listing
Modified Sat Nov 5 12:14:52 2016 UTC (4 years, 3 months ago) by caltinay

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

---

Revision 6432 - Directory Listing
Modified Sat Nov 5 11:55:44 2016 UTC (4 years, 3 months ago) by caltinay

#386 - complex gradient for speckley 2D.

---

Revision 6431 - Directory Listing
Modified Sat Nov 5 11:38:07 2016 UTC (4 years, 3 months ago) by caltinay

#386: complex gradients for dudley.

---

Revision 6430 - Directory Listing
Modified Sat Nov 5 11:27:45 2016 UTC (4 years, 3 months ago) by caltinay

Part of #386 - complex gradients for finley.

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Revision 6429 - Directory Listing
Modified Thu Nov 3 23:35:58 2016 UTC (4 years, 3 months ago) by caltinay

Part of #386 - complex gradient for ripley Brick.

---

Revision 6428 - Directory Listing
Modified Thu Nov 3 07:32:41 2016 UTC (4 years, 3 months ago) by gross

workaround for Bug #389 removed

---

Revision 6427 - Directory Listing
Modified Thu Nov 3 07:32:38 2016 UTC (4 years, 3 months ago) by jfenwick

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

---

Revision 6426 - Directory Listing
Modified Thu Nov 3 05:07:00 2016 UTC (4 years, 3 months ago) by jfenwick

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

---

Revision 6425 - Directory Listing
Modified Thu Nov 3 03:34:29 2016 UTC (4 years, 3 months ago) by jfenwick

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

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Revision 6424 - Directory Listing
Modified Thu Nov 3 02:13:09 2016 UTC (4 years, 3 months ago) by jfenwick

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

---

Revision 6423 - Directory Listing
Modified Wed Nov 2 13:05:29 2016 UTC (4 years, 3 months ago) by caltinay

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

---

Revision 6422 - Directory Listing
Modified Wed Nov 2 13:04:09 2016 UTC (4 years, 3 months ago) by caltinay

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

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Revision 6421 - Directory Listing
Modified Wed Nov 2 13:03:45 2016 UTC (4 years, 3 months ago) by caltinay

implemented complex gradient for ripley 2D.

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

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Revision 6420 - Directory Listing
Modified Wed Nov 2 06:35:58 2016 UTC (4 years, 3 months ago) by jfenwick

Fix Scalar with complex

#392

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Revision 6419 - Directory Listing
Modified Wed Nov 2 06:09:25 2016 UTC (4 years, 3 months ago) by jfenwick

Fix segfault in slice assignment with complex.

Addresses issue #394

---

Revision 6418 - Directory Listing
Modified Wed Nov 2 05:04:51 2016 UTC (4 years, 3 months ago) by jfenwick

Fix TensorX factories to allow passing a complex scalar.

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

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Revision 6417 - Directory Listing
Modified Wed Nov 2 03:57:52 2016 UTC (4 years, 3 months ago) by jfenwick

Fix setToZero

---

Revision 6416 - Directory Listing
Modified Wed Nov 2 03:01:53 2016 UTC (4 years, 3 months ago) by jfenwick

Prevent saveDataCSV from being called with complex values

---

Revision 6415 - Directory Listing
Modified Wed Nov 2 02:46:34 2016 UTC (4 years, 3 months ago) by gross

work around for bug #391 (right version now)

---

Revision 6414 - Directory Listing
Modified Wed Nov 2 02:44:31 2016 UTC (4 years, 3 months ago) by gross

work around for bug #391

---

Revision 6413 - Directory Listing
Modified Wed Nov 2 02:31:11 2016 UTC (4 years, 3 months ago) by jfenwick

Added untested .phase()  to Data.

---

Revision 6412 - Directory Listing
Modified Wed Nov 2 02:18:49 2016 UTC (4 years, 3 months ago) by gross

work around for bug #390

---

Revision 6411 - Directory Listing
Modified Wed Nov 2 01:48:58 2016 UTC (4 years, 3 months ago) by gross

work around for bug #386

---

Revision 6410 - Directory Listing
Modified Tue Nov 1 06:12:42 2016 UTC (4 years, 3 months ago) by jfenwick

Very minor fix towards more repeatable builds

---

Revision 6409 - Directory Listing
Modified Thu Oct 27 07:35:14 2016 UTC (4 years, 3 months ago) by gross

print statement removed

---

Revision 6408 - Directory Listing
Modified Thu Oct 27 03:29:59 2016 UTC (4 years, 3 months ago) by gross

work around for  Bug #389

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Revision 6407 - Directory Listing
Modified Wed Oct 19 03:13:45 2016 UTC (4 years, 4 months ago) by gross

replaced complex argument by isComplex as complex is python keyword.

---

Revision 6406 - Directory Listing
Modified Wed Oct 19 02:16:52 2016 UTC (4 years, 4 months ago) by jfenwick

recording badgers trilinos options

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Revision 6405 - Directory Listing
Modified Thu Oct 13 23:35:11 2016 UTC (4 years, 4 months ago) by gross

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

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Revision 6404 - Directory Listing
Modified Thu Sep 22 05:37:56 2016 UTC (4 years, 5 months ago) by jfenwick

Fixing the openmp options for icpc

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Revision 6400 - Directory Listing
Modified Thu Sep 8 13:09:10 2016 UTC (4 years, 5 months ago) by caltinay

Should fix #381 - Trilinos support for periodic boundaries.

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

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

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Revision 6399 - Directory Listing
Modified Wed Aug 3 00:21:25 2016 UTC (4 years, 6 months ago) by caltinay

fix warnings for paso-only build.

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Revision 6398 - Directory Listing
Modified Tue Aug 2 12:39:07 2016 UTC (4 years, 6 months ago) by caltinay

update changelog.

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Revision 6397 - Directory Listing
Modified Mon Aug 1 22:52:08 2016 UTC (4 years, 6 months ago) by caltinay

Implemented feature #281.

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

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Revision 6396 - Directory Listing
Modified Mon Aug 1 22:27:28 2016 UTC (4 years, 6 months ago) by caltinay

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 (4 years, 6 months ago) by caltinay

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 (4 years, 6 months ago) by caltinay

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 (4 years, 6 months ago) by caltinay

Implement #379.

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

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Revision 6392 - Directory Listing
Modified Mon Aug 1 02:27:56 2016 UTC (4 years, 6 months ago) by caltinay

Implemented setting specific direct solver. Fixes #378

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Revision 6391 - Directory Listing
Modified Thu Jul 28 05:44:42 2016 UTC (4 years, 6 months ago) by jfenwick

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 (4 years, 7 months ago) by jfenwick

Fiddling with changelog

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Revision 6389 - Directory Listing
Modified Wed Jul 27 07:39:57 2016 UTC (4 years, 7 months ago) by jfenwick

Adding suitesparse to builddeps

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Revision 6388 - Directory Listing
Modified Wed Jul 27 04:57:45 2016 UTC (4 years, 7 months ago) by caltinay

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 (4 years, 7 months ago) by caltinay

removed deprecated symbol, fixes #325

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Revision 6386 - Directory Listing
Modified Mon Jul 25 06:01:14 2016 UTC (4 years, 7 months ago) by caltinay

trying again to avoid mumps issue.

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Revision 6385 - Directory Listing
Modified Mon Jul 25 03:17:21 2016 UTC (4 years, 7 months ago) by caltinay

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

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Revision 6384 - Directory Listing
Modified Mon Jul 25 02:49:01 2016 UTC (4 years, 7 months ago) by caltinay

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

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

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Revision 6383 - Directory Listing
Modified Mon Jul 25 02:47:11 2016 UTC (4 years, 7 months ago) by caltinay

fixing parameter passing to Amesos2.

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Revision 6382 - Directory Listing
Modified Mon Jul 25 00:02:08 2016 UTC (4 years, 7 months ago) by caltinay

removing two duplicate tests.

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Revision 6381 - Directory Listing
Modified Fri Jul 22 09:12:46 2016 UTC (4 years, 7 months ago) by caltinay

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

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

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Revision 6380 - Directory Listing
Modified Fri Jul 22 06:32:45 2016 UTC (4 years, 7 months ago) by caltinay

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 (4 years, 7 months ago) by caltinay

fix indexing when adding to unrolled matrix...

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Revision 6378 - Directory Listing
Modified Fri Jul 22 06:05:44 2016 UTC (4 years, 7 months ago) by caltinay

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 (4 years, 7 months ago) by caltinay

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

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Revision 6376 - Directory Listing
Modified Fri Jul 22 05:35:20 2016 UTC (4 years, 7 months ago) by caltinay

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

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Revision 6375 - Directory Listing
Modified Fri Jul 22 00:27:31 2016 UTC (4 years, 7 months ago) by caltinay

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 (4 years, 7 months ago) by caltinay

Pass preconditioner options to Trilinos.

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Revision 6373 - Directory Listing
Modified Wed Jul 20 23:47:10 2016 UTC (4 years, 7 months ago) by caltinay

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 (4 years, 7 months ago) by caltinay

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 (4 years, 7 months ago) by caltinay

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 (4 years, 7 months ago) by caltinay

fix my launcher.

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Revision 6369 - Directory Listing
Modified Tue Jul 19 07:11:15 2016 UTC (4 years, 7 months ago) by caltinay

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

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

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

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Revision 6368 - Directory Listing
Modified Tue Jul 19 07:03:29 2016 UTC (4 years, 7 months ago) by caltinay

diagnostics reporting in block matrix wrapper.

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Revision 6367 - Directory Listing
Modified Tue Jul 19 04:56:16 2016 UTC (4 years, 7 months ago) by caltinay

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

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Revision 6366 - Directory Listing
Modified Mon Jul 18 23:16:50 2016 UTC (4 years, 7 months ago) by caltinay

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 (4 years, 7 months ago) by caltinay

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

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Revision 6364 - Directory Listing
Modified Mon Jul 18 02:25:04 2016 UTC (4 years, 7 months ago) by jfenwick

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 (4 years, 7 months ago) by caltinay

update solver diagnostics for cusp solvers.

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Revision 6362 - Directory Listing
Modified Thu Jul 7 03:12:06 2016 UTC (4 years, 7 months ago) by jfenwick

Doesn't fix any major problem bit closes #370

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

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Revision 6361 - Directory Listing
Modified Wed Jul 6 04:10:30 2016 UTC (4 years, 7 months ago) by caltinay

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 (4 years, 7 months ago) by caltinay

complex finley contact elements.

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Revision 6359 - Directory Listing
Modified Wed Jul 6 02:44:18 2016 UTC (4 years, 7 months ago) by caltinay

finley complex dirac.

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Revision 6358 - Directory Listing
Modified Wed Jul 6 02:38:10 2016 UTC (4 years, 7 months ago) by caltinay

complex finley 3D PDE systems.

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Revision 6357 - Directory Listing
Modified Wed Jul 6 02:24:03 2016 UTC (4 years, 7 months ago) by caltinay

complex finley 2D PDE systems.

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Revision 6356 - Directory Listing
Modified Wed Jul 6 01:53:11 2016 UTC (4 years, 7 months ago) by caltinay

complex finley single 3D PDEs.

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Revision 6355 - Directory Listing
Modified Wed Jul 6 01:03:10 2016 UTC (4 years, 7 months ago) by caltinay

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 (4 years, 7 months ago) by caltinay

first step for complex PDEs in finley.

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Revision 6353 - Directory Listing
Modified Tue Jul 5 06:36:20 2016 UTC (4 years, 7 months ago) by jfenwick

Another attempt to fix #372

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Revision 6352 - Directory Listing
Modified Tue Jul 5 05:53:49 2016 UTC (4 years, 7 months ago) by jfenwick

Fixing summary for complex data

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Revision 6351 - Directory Listing
Modified Tue Jul 5 05:47:29 2016 UTC (4 years, 7 months ago) by caltinay

dudley complex dirac.

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Revision 6350 - Directory Listing
Modified Tue Jul 5 05:42:37 2016 UTC (4 years, 7 months ago) by caltinay

complex dudley 3D PDE systems.

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Revision 6349 - Directory Listing
Modified Tue Jul 5 05:33:02 2016 UTC (4 years, 7 months ago) by caltinay

complex dudley 2D systems.

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Revision 6348 - Directory Listing
Modified Tue Jul 5 05:31:48 2016 UTC (4 years, 7 months ago) by caltinay

interrogate coefficient for value type rather than PDE.

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

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Revision 6347 - Directory Listing
Modified Tue Jul 5 04:50:14 2016 UTC (4 years, 7 months ago) by caltinay

complex support for dudley 3D single PDEs.

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

oops, sorry.

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

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

Fixed a minor error in an error message.

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

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 (4 years, 7 months ago) by caltinay

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 (4 years, 7 months ago) by caltinay

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 (4 years, 7 months ago) by caltinay

fixing type for smoother argument.

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Revision 6340 - Directory Listing
Modified Fri Jul 1 12:58:45 2016 UTC (4 years, 7 months ago) by caltinay

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

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

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

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Revision 6339 - Directory Listing
Modified Fri Jul 1 12:56:43 2016 UTC (4 years, 7 months ago) by caltinay

(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 (4 years, 7 months ago) by caltinay

(5) this is the first big one -

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

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Revision 6337 - Directory Listing
Modified Fri Jul 1 12:38:18 2016 UTC (4 years, 7 months ago) by caltinay

(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 (4 years, 7 months ago) by caltinay

(3) add isComplex & setComplex to solver options.

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Revision 6335 - Directory Listing
Modified Fri Jul 1 12:36:22 2016 UTC (4 years, 7 months ago) by caltinay

(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 (4 years, 7 months ago) by caltinay

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

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

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Revision 6333 - Directory Listing
Modified Fri Jul 1 03:58:43 2016 UTC (4 years, 7 months ago) by caltinay

write some more features into buildvars.

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Revision 6332 - Directory Listing
Modified Thu Jun 30 09:32:40 2016 UTC (4 years, 7 months ago) by caltinay

missed one.

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Revision 6331 - Directory Listing
Modified Thu Jun 30 09:31:06 2016 UTC (4 years, 7 months ago) by caltinay

fixing unreachable code warnings issued by nvcc.

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Revision 6330 - Directory Listing
Modified Sat Jun 25 11:36:26 2016 UTC (4 years, 8 months ago) by caltinay

added missing x.

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Revision 6329 - Directory Listing
Modified Fri Jun 24 04:19:10 2016 UTC (4 years, 8 months ago) by caltinay

*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 (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

more Amesos2 skips.

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Revision 6325 - Directory Listing
Modified Thu Jun 23 09:12:54 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

fix.

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Revision 6323 - Directory Listing
Modified Thu Jun 23 06:05:23 2016 UTC (4 years, 8 months ago) by caltinay

skip ILUT block tests with trilinos.

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Revision 6322 - Directory Listing
Modified Thu Jun 23 05:56:49 2016 UTC (4 years, 8 months ago) by caltinay

don't reference e before assignment.

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Revision 6321 - Directory Listing
Modified Thu Jun 23 05:38:50 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6320 - Directory Listing
Modified Thu Jun 23 05:22:01 2016 UTC (4 years, 8 months ago) by caltinay

i broke it.

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Revision 6319 - Directory Listing
Modified Thu Jun 23 05:01:39 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

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

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Revision 6316 - Directory Listing
Modified Thu Jun 23 04:25:56 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

lookin' good so unskip more tests.

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Revision 6314 - Directory Listing
Modified Tue Jun 21 23:27:35 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

forgot to change a line.

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Revision 6312 - Directory Listing
Modified Tue Jun 21 06:51:27 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6311 - Directory Listing
Modified Tue Jun 21 06:41:55 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by jfenwick

Bringing in some changes from debian

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Revision 6309 - Directory Listing
Modified Tue Jun 21 01:15:15 2016 UTC (4 years, 8 months ago) by caltinay

updated mole py3 options.

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Revision 6308 - Directory Listing
Modified Mon Jun 20 01:59:34 2016 UTC (4 years, 8 months ago) by caltinay

trying to fix remaining trilinos errors.

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Revision 6307 - Directory Listing
Modified Sun Jun 19 11:05:47 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

fix test

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Revision 6305 - Directory Listing
Modified Sat Jun 18 11:11:30 2016 UTC (4 years, 8 months ago) by caltinay

suppress sympy warning with py3

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Revision 6304 - Directory Listing
Modified Sat Jun 18 11:00:33 2016 UTC (4 years, 8 months ago) by caltinay

tweak.

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Revision 6303 - Directory Listing
Modified Sat Jun 18 10:53:18 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

off-by-one errors.

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Revision 6301 - Directory Listing
Modified Fri Jun 17 07:45:23 2016 UTC (4 years, 8 months ago) by caltinay

yes

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Revision 6300 - Directory Listing
Modified Fri Jun 17 07:03:44 2016 UTC (4 years, 8 months ago) by caltinay

another attempt to fix the logic.

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Revision 6299 - Directory Listing
Modified Fri Jun 17 05:53:58 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

make lazy-related config options tristate variables.

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Revision 6296 - Directory Listing
Modified Thu Jun 16 23:58:54 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

mara options update.

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Revision 6294 - Directory Listing
Modified Thu Jun 16 10:35:10 2016 UTC (4 years, 8 months ago) by caltinay

added default trilinos options to savanna.

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Revision 6293 - Directory Listing
Modified Thu Jun 16 08:34:17 2016 UTC (4 years, 8 months ago) by caltinay

more test fixes.

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Revision 6292 - Directory Listing
Modified Thu Jun 16 06:18:23 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

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

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Revision 6290 - Directory Listing
Modified Thu Jun 16 01:49:20 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

starting to move savanna to py3 toolchain.

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Revision 6287 - Directory Listing
Modified Wed Jun 15 06:33:57 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

added trilinos options (not actually installed yet).

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Revision 6285 - Directory Listing
Modified Wed Jun 15 06:19:18 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

newton changes for buildbot.

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Revision 6283 - Directory Listing
Modified Wed Jun 15 05:58:34 2016 UTC (4 years, 8 months ago) by caltinay

Preparing for buildbot changes.

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Revision 6282 - Directory Listing
Modified Tue Jun 14 04:54:01 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

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

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Revision 6280 - Directory Listing
Modified Tue Jun 14 02:39:13 2016 UTC (4 years, 8 months ago) by caltinay

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

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

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Revision 6279 - Directory Listing
Modified Mon Jun 13 07:05:21 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

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

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Revision 6276 - Directory Listing
Modified Mon Jun 13 05:27:47 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

missing dependency?

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Revision 6274 - Directory Listing
Modified Mon Jun 13 02:02:34 2016 UTC (4 years, 8 months ago) by caltinay

another one.

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Revision 6273 - Directory Listing
Modified Mon Jun 13 01:01:53 2016 UTC (4 years, 8 months ago) by caltinay

same as last one.

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Revision 6272 - Directory Listing
Modified Mon Jun 13 01:00:49 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

added preliminary tinaroo options

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Revision 6269 - Directory Listing
Modified Wed Jun 8 04:29:26 2016 UTC (4 years, 8 months ago) by caltinay

fix intel warnings

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Revision 6268 - Directory Listing
Modified Wed Jun 8 02:14:17 2016 UTC (4 years, 8 months ago) by caltinay

use configured python in launcher

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Revision 6267 - Directory Listing
Modified Wed Jun 8 01:57:48 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6266 - Directory Listing
Modified Fri Jun 3 12:00:02 2016 UTC (4 years, 8 months ago) by caltinay

avoid the oversubscribing issue by disabling cpu binding on guineapig.

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Revision 6265 - Directory Listing
Modified Fri Jun 3 06:31:31 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6264 - Directory Listing
Modified Fri Jun 3 06:23:10 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6263 - Directory Listing
Modified Fri Jun 3 06:03:20 2016 UTC (4 years, 8 months ago) by caltinay

fixing another shared pointer race condition by caching a value.

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Revision 6262 - Directory Listing
Modified Fri Jun 3 05:14:55 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6261 - Directory Listing
Modified Fri Jun 3 05:13:03 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6260 - Directory Listing
Modified Fri Jun 3 04:15:26 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6259 - Directory Listing
Modified Fri Jun 3 03:07:20 2016 UTC (4 years, 8 months ago) by caltinay

do not require Zoltan2.

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Revision 6258 - Directory Listing
Modified Fri Jun 3 00:34:00 2016 UTC (4 years, 8 months ago) by caltinay

ditto for assertAlmostEquals

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Revision 6257 - Directory Listing
Modified Fri Jun 3 00:30:37 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6256 - Directory Listing
Modified Thu Jun 2 23:03:48 2016 UTC (4 years, 8 months ago) by caltinay

added missing requireWrite().

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Revision 6255 - Directory Listing
Modified Thu Jun 2 06:52:06 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by jfenwick

Standards bump

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Revision 6253 - Directory Listing
Modified Thu Jun 2 05:04:41 2016 UTC (4 years, 8 months ago) by caltinay

...final?

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Revision 6252 - Directory Listing
Modified Thu Jun 2 05:02:50 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6251 - Directory Listing
Modified Thu Jun 2 04:58:45 2016 UTC (4 years, 8 months ago) by jfenwick

Hoping to make lintian happier

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Revision 6250 - Directory Listing
Modified Thu Jun 2 04:44:29 2016 UTC (4 years, 8 months ago) by jfenwick

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

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Revision 6249 - Directory Listing
Modified Thu Jun 2 04:37:00 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6248 - Directory Listing
Modified Thu Jun 2 04:13:21 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6247 - Directory Listing
Modified Thu Jun 2 02:35:41 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6246 - Directory Listing
Modified Thu Jun 2 00:47:54 2016 UTC (4 years, 8 months ago) by jfenwick

Let's try this

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Revision 6245 - Directory Listing
Modified Thu Jun 2 00:35:02 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6244 - Directory Listing
Modified Wed Jun 1 10:41:29 2016 UTC (4 years, 8 months ago) by jfenwick

Fixing imports after options file changes

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Revision 6243 - Directory Listing
Modified Wed Jun 1 09:50:18 2016 UTC (4 years, 8 months ago) by jfenwick

move overlord path setting to cxx_extra after options file changes

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Revision 6242 - Directory Listing
Modified Wed Jun 1 07:57:06 2016 UTC (4 years, 8 months ago) by jfenwick

Try to get build testing working

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Revision 6241 - Directory Listing
Modified Wed Jun 1 06:00:06 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6240 - Directory Listing
Modified Wed Jun 1 05:52:38 2016 UTC (4 years, 8 months ago) by caltinay

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 (4 years, 8 months ago) by caltinay

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

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Revision 6238 - Directory Listing
Modified Wed Jun 1 01:24:29 2016 UTC (4 years, 8 months ago) by caltinay

fixing coverity-detected leaks CID 99614,99615

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Revision 6237 - Directory Listing
Modified Wed Jun 1 01:17:10 2016 UTC (4 years, 8 months ago) by caltinay

fixing coverity-detected leak CID 99603

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Revision 6236 - Directory Listing
Modified Wed Jun 1 01:09:03 2016 UTC (4 years, 8 months ago) by caltinay

fixing coverity-detected leaks CID 115857,115858.

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Revision 6235 - Directory Listing
Modified Wed Jun 1 01:05:29 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6234 - Directory Listing
Modified Wed Jun 1 01:00:21 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6233 - Directory Listing
Modified Mon May 30 23:45:53 2016 UTC (4 years, 8 months ago) by caltinay

i broke the other end. Hope this fixes it.

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Revision 6232 - Directory Listing
Modified Mon May 30 04:21:28 2016 UTC (4 years, 8 months ago) by jfenwick

Other changes to match the previous commit.

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Revision 6231 - Directory Listing
Modified Mon May 30 03:50:37 2016 UTC (4 years, 8 months ago) by jfenwick

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

---

Revision 6230 - Directory Listing
Modified Sun May 29 10:46:41 2016 UTC (4 years, 8 months ago) by caltinay

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

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Revision 6229 - Directory Listing
Modified Sun May 29 10:42:41 2016 UTC (4 years, 8 months ago) by caltinay

how on earth did we miss this before??!

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Revision 6228 - Directory Listing
Modified Sat May 28 10:21:18 2016 UTC (4 years, 8 months ago) by caltinay

non-mpi is a thing

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Revision 6227 - Directory Listing
Modified Fri May 27 09:59:21 2016 UTC (4 years, 9 months ago) by caltinay

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

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

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Revision 6226 - Directory Listing
Modified Fri May 27 02:55:38 2016 UTC (4 years, 9 months ago) by caltinay

fix modellib test to use feature checker for gmsh.

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Revision 6225 - Directory Listing
Modified Fri May 27 01:47:50 2016 UTC (4 years, 9 months ago) by caltinay

fixed deprecation warning

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Revision 6224 - Directory Listing
Modified Thu May 26 06:33:37 2016 UTC (4 years, 9 months ago) by caltinay

fix newton options file.

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Revision 6223 - Directory Listing
Modified Thu May 26 01:06:02 2016 UTC (4 years, 9 months ago) by jfenwick

Fixes to itest.sh and extract tests

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Revision 6222 - Directory Listing
Modified Wed May 25 23:36:21 2016 UTC (4 years, 9 months ago) by caltinay

updated gp options for stretch.

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Revision 6221 - Directory Listing
Modified Wed May 25 12:26:50 2016 UTC (4 years, 9 months ago) by caltinay

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

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Revision 6220 - Directory Listing
Modified Wed May 25 09:48:35 2016 UTC (4 years, 9 months ago) by caltinay

add some colour to my compiler errors

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Revision 6219 - Directory Listing
Modified Wed May 25 07:00:28 2016 UTC (4 years, 9 months ago) by caltinay

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

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Revision 6218 - Directory Listing
Modified Mon May 23 13:42:19 2016 UTC (4 years, 9 months ago) by caltinay

fixed typo.

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Revision 6217 - Directory Listing
Modified Mon May 23 06:57:40 2016 UTC (4 years, 9 months ago) by caltinay

increase GS sweeps once more.

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Revision 6216 - Directory Listing
Modified Mon May 23 06:52:32 2016 UTC (4 years, 9 months ago) by caltinay

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

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Revision 6215 - Directory Listing
Modified Mon May 23 02:58:03 2016 UTC (4 years, 9 months ago) by caltinay

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

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Revision 6214 - Directory Listing
Modified Fri May 20 07:04:31 2016 UTC (4 years, 9 months ago) by caltinay

implemented trilinos interpolation from DOF->nodes in dudley.

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Revision 6213 - Directory Listing
Modified Fri May 20 04:32:25 2016 UTC (4 years, 9 months ago) by caltinay

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

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Revision 6212 - Directory Listing
Modified Tue May 17 00:52:16 2016 UTC (4 years, 9 months ago) by caltinay

typo with trilinos.

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Revision 6211 - Directory Listing
Modified Mon May 16 11:48:02 2016 UTC (4 years, 9 months ago) by caltinay

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

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Revision 6210 - Directory Listing
Modified Mon May 16 08:42:05 2016 UTC (4 years, 9 months ago) by caltinay

more test adjustments.

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Revision 6209 - Directory Listing
Modified Mon May 16 04:32:21 2016 UTC (4 years, 9 months ago) by caltinay

fixed typo.

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Revision 6208 - Directory Listing
Modified Mon May 16 02:17:37 2016 UTC (4 years, 9 months ago) by caltinay

rebaseline test meshes.

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Revision 6207 - Directory Listing
Modified Mon May 16 00:49:48 2016 UTC (4 years, 9 months ago) by caltinay

merged finley Mesh and MeshAdapter into FinleyDomain.

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Revision 6206 - Directory Listing
Modified Sun May 15 12:18:58 2016 UTC (4 years, 9 months ago) by caltinay

fix test.

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Revision 6205 - Directory Listing
Modified Sun May 15 09:40:50 2016 UTC (4 years, 9 months ago) by caltinay

minor changes to sync dudley and finley.

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Revision 6204 - Directory Listing
Modified Thu May 12 23:05:56 2016 UTC (4 years, 9 months ago) by caltinay

fixed types for index type long.

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Revision 6203 - Directory Listing
Modified Wed May 11 06:13:51 2016 UTC (4 years, 9 months ago) by caltinay

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

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Revision 6202 - Directory Listing
Modified Thu May 5 04:47:09 2016 UTC (4 years, 9 months ago) by caltinay

slightly better error messages on test failure in pdetools.

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Revision 6201 - Directory Listing
Modified Thu May 5 04:32:02 2016 UTC (4 years, 9 months ago) by caltinay

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

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

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

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

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

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

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

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Revision 6197 - Directory Listing
Modified Fri Apr 29 14:02:32 2016 UTC (4 years, 9 months ago) by caltinay

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

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Revision 6196 - Directory Listing
Modified Thu Apr 28 03:38:25 2016 UTC (4 years, 9 months ago) by caltinay

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

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Revision 6195 - Directory Listing
Modified Thu Apr 28 01:10:46 2016 UTC (4 years, 9 months ago) by caltinay

more tweaking.

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Revision 6194 - Directory Listing
Modified Wed Apr 27 23:46:30 2016 UTC (4 years, 9 months ago) by caltinay

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

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Revision 6193 - Directory Listing
Modified Wed Apr 27 06:11:40 2016 UTC (4 years, 10 months ago) by caltinay

preparations for paso-less dudley.

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Revision 6192 - Directory Listing
Modified Wed Apr 27 05:53:11 2016 UTC (4 years, 10 months ago) by caltinay

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

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Revision 6191 - Directory Listing
Modified Wed Apr 27 05:24:32 2016 UTC (4 years, 10 months ago) by caltinay

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

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Revision 6190 - Directory Listing
Modified Wed Apr 27 05:23:15 2016 UTC (4 years, 10 months ago) by caltinay

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

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Revision 6189 - Directory Listing
Modified Wed Apr 27 03:39:21 2016 UTC (4 years, 10 months ago) by caltinay

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

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Revision 6188 - Directory Listing
Modified Wed Apr 27 03:38:10 2016 UTC (4 years, 10 months ago) by caltinay

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

---

Revision 6187 - Directory Listing
Modified Wed Apr 27 03:36:18 2016 UTC (4 years, 10 months ago) by caltinay

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

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Revision 6186 - Directory Listing
Modified Wed Apr 27 01:34:39 2016 UTC (4 years, 10 months ago) by caltinay

fixed typo for block matrices.

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Revision 6185 - Directory Listing
Modified Wed Apr 27 01:34:17 2016 UTC (4 years, 10 months ago) by caltinay

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

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Revision 6184 - Directory Listing
Modified Wed Apr 27 01:30:57 2016 UTC (4 years, 10 months ago) by caltinay

more fixes to weipa readerlib build

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Revision 6183 - Directory Listing
Modified Wed Apr 27 00:09:32 2016 UTC (4 years, 10 months ago) by caltinay

fix weipa readerlib build.

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Revision 6182 - Directory Listing
Modified Tue Apr 26 06:31:51 2016 UTC (4 years, 10 months ago) by caltinay

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

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Revision 6181 - Directory Listing
Modified Tue Apr 26 06:16:15 2016 UTC (4 years, 10 months ago) by caltinay

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

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Revision 6180 - Directory Listing
Modified Sat Apr 16 04:53:19 2016 UTC (4 years, 10 months ago) by caltinay

fix escriptreader dependencies

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Revision 6179 - Directory Listing
Modified Fri Apr 15 12:48:58 2016 UTC (4 years, 10 months ago) by caltinay

ditto.

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Revision 6178 - Directory Listing
Modified Fri Apr 15 10:43:52 2016 UTC (4 years, 10 months ago) by caltinay

missed these.

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Revision 6177 - Directory Listing
Modified Fri Apr 15 08:26:07 2016 UTC (4 years, 10 months ago) by caltinay

fixed typo

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Revision 6176 - Directory Listing
Modified Fri Apr 15 07:10:51 2016 UTC (4 years, 10 months ago) by caltinay

fix OMP race conditions in trilinos matrix.

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Revision 6175 - Directory Listing
Modified Fri Apr 15 06:59:14 2016 UTC (4 years, 10 months ago) by caltinay

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

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Revision 6174 - Directory Listing
Modified Fri Apr 15 03:41:03 2016 UTC (4 years, 10 months ago) by caltinay

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

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

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

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

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Revision 6173 - Directory Listing
Modified Thu Apr 14 05:56:55 2016 UTC (4 years, 10 months ago) by caltinay

moved reference to JMPI down to Coupler.

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Revision 6172 - Directory Listing
Modified Thu Apr 14 05:15:27 2016 UTC (4 years, 10 months ago) by caltinay

type change in paso.

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Revision 6171 - Directory Listing
Modified Wed Apr 13 13:39:08 2016 UTC (4 years, 10 months ago) by jfenwick

adding tests to tagged versions

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Revision 6170 - Directory Listing
Modified Wed Apr 13 07:46:34 2016 UTC (4 years, 10 months ago) by caltinay

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

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Revision 6169 - Directory Listing
Modified Wed Apr 13 05:24:45 2016 UTC (4 years, 10 months ago) by caltinay

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

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Revision 6168 - Directory Listing
Modified Wed Apr 13 03:08:12 2016 UTC (4 years, 10 months ago) by jfenwick

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

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Revision 6167 - Directory Listing
Modified Tue Apr 12 09:34:03 2016 UTC (4 years, 10 months ago) by caltinay

forgot to commit.

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Revision 6166 - Directory Listing
Modified Tue Apr 12 06:51:37 2016 UTC (4 years, 10 months ago) by caltinay

Starting to make Paso optional in ripley.

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Revision 6165 - Directory Listing
Modified Mon Apr 11 10:25:51 2016 UTC (4 years, 10 months ago) by caltinay

limit number of elements in speckley test.

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Revision 6164 - Directory Listing
Modified Mon Apr 11 06:06:43 2016 UTC (4 years, 10 months ago) by jfenwick

Test fixes and more tests

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Revision 6163 - Directory Listing
Modified Sun Apr 10 23:44:11 2016 UTC (4 years, 10 months ago) by jfenwick

Fix to prevent complex tests running with lazy.

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Revision 6162 - Directory Listing
Modified Fri Apr 8 09:46:26 2016 UTC (4 years, 10 months ago) by caltinay

Data() constructor fix.

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Revision 6161 - Directory Listing
Modified Fri Apr 8 06:57:08 2016 UTC (4 years, 10 months ago) by caltinay

report filename in error message.

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Revision 6160 - Directory Listing
Modified Fri Apr 8 06:24:27 2016 UTC (4 years, 10 months ago) by jfenwick

Bump standards version to see what happens

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Revision 6159 - Directory Listing
Modified Fri Apr 8 06:22:04 2016 UTC (4 years, 10 months ago) by jfenwick

Non-backwards compatible change!

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

Adds some additional tests for complex.

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Revision 6158 - Directory Listing
Modified Fri Apr 8 05:00:26 2016 UTC (4 years, 10 months ago) by caltinay

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

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Revision 6157 - Directory Listing
Modified Fri Apr 8 04:43:52 2016 UTC (4 years, 10 months ago) by caltinay

fixed savanna options file for noomp.

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Revision 6156 - Directory Listing
Modified Fri Apr 8 04:39:55 2016 UTC (4 years, 10 months ago) by caltinay

index type fix.

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Revision 6155 - Directory Listing
Modified Fri Apr 8 00:48:28 2016 UTC (4 years, 10 months ago) by caltinay

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

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Revision 6154 - Directory Listing
Modified Thu Apr 7 02:52:30 2016 UTC (4 years, 10 months ago) by jfenwick

Complex fixes and a small number of tests

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Revision 6153 - Directory Listing
Modified Thu Apr 7 00:35:31 2016 UTC (4 years, 10 months ago) by caltinay

no-op - remove parmetis line from netwon options.

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Revision 6152 - Directory Listing
Modified Thu Apr 7 00:33:51 2016 UTC (4 years, 10 months ago) by caltinay

we should now properly catch segfaults when testing.

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Revision 6151 - Directory Listing
Modified Wed Apr 6 23:44:46 2016 UTC (4 years, 10 months ago) by jfenwick

Remove getsubst

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Revision 6150 - Directory Listing
Modified Wed Apr 6 23:44:12 2016 UTC (4 years, 10 months ago) by caltinay

fix newton options file.

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Revision 6149 - Directory Listing
Modified Wed Apr 6 23:36:42 2016 UTC (4 years, 10 months ago) by caltinay

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

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Revision 6148 - Directory Listing
Modified Wed Apr 6 10:28:13 2016 UTC (4 years, 10 months ago) by caltinay

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

---

Revision 6147 - Directory Listing
Modified Wed Apr 6 07:57:22 2016 UTC (4 years, 10 months ago) by jfenwick

Complex changes

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

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Revision 6146 - Directory Listing
Modified Wed Apr 6 07:10:59 2016 UTC (4 years, 10 months ago) by caltinay

add lib path for trilinos.

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Revision 6145 - Directory Listing
Modified Wed Apr 6 06:28:57 2016 UTC (4 years, 10 months ago) by caltinay

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

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Revision 6144 - Directory Listing
Modified Wed Apr 6 05:25:13 2016 UTC (4 years, 10 months ago) by caltinay

last round of namespacing defines.

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Revision 6143 - Directory Listing
Modified Wed Apr 6 03:59:15 2016 UTC (4 years, 10 months ago) by caltinay

try to fix another warning.

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Revision 6142 - Directory Listing
Modified Wed Apr 6 03:57:28 2016 UTC (4 years, 10 months ago) by caltinay

two fixes.

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Revision 6141 - Directory Listing
Modified Wed Apr 6 03:51:30 2016 UTC (4 years, 10 months ago) by caltinay

more namespacing of defines.

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Revision 6140 - Directory Listing
Modified Wed Apr 6 03:17:31 2016 UTC (4 years, 10 months ago) by jfenwick

Eigenvectors for _some_ complex cases

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

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Revision 6139 - Directory Listing
Modified Wed Apr 6 02:58:19 2016 UTC (4 years, 10 months ago) by caltinay

fix for scons versions < 2.4

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Revision 6138 - Directory Listing
Modified Wed Apr 6 02:10:10 2016 UTC (4 years, 10 months ago) by caltinay

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 (4 years, 10 months ago) by caltinay

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 (4 years, 10 months ago) by jfenwick

Swap axes for complex

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Revision 6135 - Directory Listing
Modified Wed Apr 6 01:07:38 2016 UTC (4 years, 10 months ago) by jfenwick

transpose for complex

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Revision 6134 - Directory Listing
Modified Wed Apr 6 00:48:07 2016 UTC (4 years, 10 months ago) by jfenwick

trace for non-constant data

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Revision 6133 - Directory Listing
Modified Wed Apr 6 00:33:10 2016 UTC (4 years, 10 months ago) by jfenwick

trace() now supports complex

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Revision 6132 - Directory Listing
Modified Wed Apr 6 00:14:03 2016 UTC (4 years, 10 months ago) by caltinay

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 (4 years, 10 months ago) by jfenwick

Bug fix and test for complex NaN replacement