Log of /trunk/finley/src

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Revision 3516 - Directory Listing
Modified Fri May 20 00:57:41 2011 UTC (9 years, 11 months ago) by gross

missing file

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Revision 3515 - Directory Listing
Modified Thu May 19 08:20:57 2011 UTC (9 years, 11 months ago) by gross

some first work for DiracFunctions

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Revision 3508 - Directory Listing
Modified Fri May 13 04:15:29 2011 UTC (9 years, 11 months ago) by lgao

Add Boomer AMG as a new preconditioner 
Can be used by .setPreconditioner(SolverOptions.BOOMERAMG)
and the following parallel coarsening method can be 
used together with Boomer AMG preconditioner: 
  .setCoarsening(SolverOptions.CIJP_FIXED_RANDOM_COARSENING)
  .setCoarsening(SolverOptions.CIJP_COARSENING)
  .setCoarsening(SolverOptions.FALGOUT_COARSENING)
  .setCoarsening(SolverOptions.PMIS_COARSENING)
  .setCoarsening(SolverOptions.HMIS_COARSENING)

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

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Revision 3490 - Directory Listing
Modified Wed Mar 30 02:24:33 2011 UTC (10 years ago) by caltinay

More gcc-4.6 fixes (mostly initialized-but-unused-var warnings)

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Revision 3454 - Directory Listing
Modified Tue Jan 25 04:00:29 2011 UTC (10 years, 2 months ago) by caltinay

Fixed some minor doxygen issues.

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Revision 3440 - Directory Listing
Modified Fri Jan 14 00:04:53 2011 UTC (10 years, 3 months ago) by gross

a second AMG interpolation implemented

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Revision 3402 - Directory Listing
Modified Tue Dec 7 07:36:12 2010 UTC (10 years, 4 months ago) by gross

AMG support now block size > 3 (requires clapack or MKL).

additional diagnostics for AMG 

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Revision 3400 - Directory Listing
Modified Mon Dec 6 02:23:07 2010 UTC (10 years, 4 months ago) by caltinay

Moved vtkCellType.h to weipa where it belongs now.

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Revision 3379 - Directory Listing
Modified Wed Nov 24 04:48:49 2010 UTC (10 years, 4 months ago) by gross

some clarification on lumping

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Revision 3355 - Directory Listing
Modified Tue Nov 16 06:35:06 2010 UTC (10 years, 5 months ago) by caltinay

Fixed building with boost < 1.40 by
- removing the saveVTK method from dudley's MeshAdapter completely
  (no point introducing it now when we are trying to get rid of it soon)
- adding a helper function to weipa's python layer which can be called from C++
  with older boost versions.

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Revision 3352 - Directory Listing
Modified Tue Nov 16 03:58:09 2010 UTC (10 years, 5 months ago) by gross

exposure of AMG options

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Revision 3349 - Directory Listing
Modified Mon Nov 15 05:09:56 2010 UTC (10 years, 5 months ago) by caltinay

escript now supports out-of-tree builds.
All build and test files are now created under a user-definable build_dir
directory.
This also fixes issue 291.
Removed most svn:ignore props since they are no longer required.

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Revision 3344 - Directory Listing
Modified Thu Nov 11 23:26:52 2010 UTC (10 years, 5 months ago) by caltinay

Phew!
-escript, finley, and dudley now uses weipa's saveVTK implementation
-moved tests from finley to weipa accordingly; dudley still to do
-rebaselined all test files
-fixed a few issues in weipa.saveVTK, e.g. saving metadata without schema
-added a deprecation warning to esys.escript.util.saveVTK
-todo: change doco, tests and other places to use weipa.saveVTK

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Revision 3317 - Directory Listing
Modified Thu Oct 28 00:50:41 2010 UTC (10 years, 5 months ago) by caltinay

Removed bogus mpi.h includes, replaced others by our esysUtils wrapper
and rearranged so that the wrapper always comes before netcdf which fixes
linking problems when disabling mpi on systems with netCDF 4.x.

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Revision 3312 - Directory Listing
Modified Tue Oct 26 07:54:58 2010 UTC (10 years, 5 months ago) by gross

last step for a clean up version of the AMG

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Revision 3286 - Directory Listing
Modified Tue Oct 19 00:36:27 2010 UTC (10 years, 6 months ago) by gross

small memory leak fixed.

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Revision 3283 - Directory Listing
Modified Mon Oct 18 22:39:28 2010 UTC (10 years, 6 months ago) by gross

AMG reengineered, BUG is Smoother fixed.

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Revision 3269 - Directory Listing
Modified Wed Oct 13 03:21:50 2010 UTC (10 years, 6 months ago) by jfenwick

Fixed some intel compiler warnings.
Put linearPDEs back the way it was and present a common interface for dudley and finley (as per Lutz)

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Revision 3259 - Directory Listing
Modified Mon Oct 11 01:48:14 2010 UTC (10 years, 6 months ago) by jfenwick

Merging dudley and scons updates from branches

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Revision 3181 - Directory Listing
Modified Tue Sep 14 05:01:00 2010 UTC (10 years, 7 months ago) by jfenwick

Fix to buggy recovery of colouring information.
Unfortunately unable to fix buggy spelling of colour.

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Revision 3111 - Directory Listing
Modified Thu Aug 26 06:49:42 2010 UTC (10 years, 7 months ago) by gross

some diagnostics for time step backtracing added

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Revision 3094 - Directory Listing
Modified Fri Aug 13 08:38:06 2010 UTC (10 years, 8 months ago) by gross

The MPI and sequational GAUSS_SEIDEL have been merged.
The couring and main diagonal pointer is now manged by the patternm which means that they are calculated once only even if the preconditioner is deleted.

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Revision 3078 - Directory Listing
Modified Tue Aug 3 03:12:16 2010 UTC (10 years, 8 months ago) by jfenwick

Switched the build_dir keyword param to variant_dir.
Should fix issue 525.

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Revision 3071 - Directory Listing
Modified Wed Jul 21 05:37:30 2010 UTC (10 years, 9 months ago) by gross

new darcy flux

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Revision 3051 - Directory Listing
Modified Tue Jun 29 00:45:49 2010 UTC (10 years, 9 months ago) by lgao

Hybrid MPI/OpenMP versioned Gauss_Seidel preconditioner is added. 
To use it, use "SolverOptions.GAUSS_SEIDEL_MPI" in python script. 

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Revision 2991 - Directory Listing
Modified Mon Mar 22 05:42:48 2010 UTC (11 years, 1 month ago) by gross

isub as private added

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Revision 2990 - Directory Listing
Modified Fri Mar 19 05:57:22 2010 UTC (11 years, 1 month ago) by gross

some prints removed.

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Revision 2989 - Directory Listing
Modified Thu Mar 18 01:45:55 2010 UTC (11 years, 1 month ago) by gross

- bug in error handling in the case of lumped mass matrix fixed.
- switched back to rowsum lumping as there are problems with HRZ lumping for order 2 

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Revision 2988 - Directory Listing
Modified Tue Mar 16 06:14:30 2010 UTC (11 years, 1 month ago) by gross

C-level lumping switched on

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Revision 2987 - Directory Listing
Modified Tue Mar 16 01:32:43 2010 UTC (11 years, 1 month ago) by gross

FCT solver rewritten

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Revision 2940 - Directory Listing
Modified Fri Feb 19 00:38:45 2010 UTC (11 years, 2 months ago) by caltinay

Minor potential optimization: prefer empty() over size()==0.

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Revision 2934 - Directory Listing
Modified Fri Feb 12 05:09:06 2010 UTC (11 years, 2 months ago) by gross

gmsh reader supports second order recs and hex now

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Revision 2898 - Directory Listing
Modified Mon Feb 1 01:23:46 2010 UTC (11 years, 2 months ago) by caltinay

Reverted the move of system_dep.h since it didn't solve the problem nicely.
Created a wrapper class for the needed functionality instead.

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Revision 2897 - Directory Listing
Modified Mon Feb 1 01:22:50 2010 UTC (11 years, 2 months ago) by lgao

Fix the Parmetis problem related with Mantis issue 0000480. 
In case there is any node with no vertex, Parmetis will not
be used and a message will be printed. 

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Revision 2895 - Directory Listing
Modified Fri Jan 29 04:58:16 2010 UTC (11 years, 2 months ago) by caltinay

Moved finley's system_dep.h file up to the C level to be able to export two
functions that are used by the dataexporter. Changed include paths and C++
style comments accordingly.

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Revision 2881 - Directory Listing
Modified Thu Jan 28 02:03:15 2010 UTC (11 years, 2 months ago) by jfenwick

Don't panic.
Updating copyright stamps

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Revision 2856 - Directory Listing
Modified Mon Jan 18 04:14:37 2010 UTC (11 years, 3 months ago) by gross

FunctionSpaces provide now some information about their approximation order.

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Revision 2850 - Directory Listing
Modified Fri Jan 15 07:14:25 2010 UTC (11 years, 3 months ago) by gross

the powerlaw is working again. tests are switched on again.

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Revision 2842 - Directory Listing
Modified Thu Jan 14 05:42:02 2010 UTC (11 years, 3 months ago) by caltinay

Changed domain::dump() to write out NodeDistribution & DofDistribution even if
the current process has 0 nodes.

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Revision 2828 - Directory Listing
Modified Tue Dec 22 01:24:40 2009 UTC (11 years, 3 months ago) by artak

Smoother for AMG now can be selected from python. Now only Jacobi and Gauss-Seidel are available as smoothers.

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Revision 2816 - Directory Listing
Modified Thu Dec 10 02:09:43 2009 UTC (11 years, 4 months ago) by artak

Standard coarsening is added to options list.

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Revision 2814 - Directory Listing
Modified Tue Dec 8 01:50:29 2009 UTC (11 years, 4 months ago) by caltinay

Removed minor code duplication.

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Revision 2779 - Directory Listing
Modified Thu Nov 26 03:51:15 2009 UTC (11 years, 4 months ago) by caltinay

Fixed more instances of garbage=cstring+integer errors (d'oh!)

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Revision 2778 - Directory Listing
Modified Thu Nov 26 01:50:30 2009 UTC (11 years, 4 months ago) by caltinay

Fixed unintended pointer arithmetic with c-strings in MeshAdapter::dump() and
shortened error messages while being at it.

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Revision 2770 - Directory Listing
Modified Wed Nov 25 01:24:51 2009 UTC (11 years, 4 months ago) by jfenwick

Removed buffer implementation of Lazy.
Removed supporting Alloc/Free Sample buffer calls.

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Revision 2760 - Directory Listing
Modified Thu Nov 19 05:22:45 2009 UTC (11 years, 5 months ago) by artak

The first version of the new AMG preconditioner. It need a lot of polishing for efficiency. Old AMG now called AMLI preconditioner.

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Revision 2756 - Directory Listing
Modified Thu Nov 19 00:40:02 2009 UTC (11 years, 5 months ago) by gross

missing file added.

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Revision 2755 - Directory Listing
Modified Wed Nov 18 23:19:32 2009 UTC (11 years, 5 months ago) by caltinay

Reverted changes to Mesh_read from last commit. They break compilation with
MPI and seem unintentional.

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Revision 2754 - Directory Listing
Modified Wed Nov 18 07:44:26 2009 UTC (11 years, 5 months ago) by gross

tests for macro elements in saveVTK added.

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Revision 2752 - Directory Listing
Modified Wed Nov 18 06:01:18 2009 UTC (11 years, 5 months ago) by caltinay

Fixed compilation error in mesh reader when using MPI.

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Revision 2751 - Directory Listing
Modified Wed Nov 18 00:30:47 2009 UTC (11 years, 5 months ago) by caltinay

Removed stray forward declaration.

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Revision 2750 - Directory Listing
Modified Tue Nov 17 23:39:20 2009 UTC (11 years, 5 months ago) by caltinay

Fixed some compilation errors with OpenMP introduced in last commit.

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Revision 2749 - Directory Listing
Modified Tue Nov 17 07:34:16 2009 UTC (11 years, 5 months ago) by gross

missing files.

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Revision 2748 - Directory Listing
Modified Tue Nov 17 07:32:59 2009 UTC (11 years, 5 months ago) by gross

Macro elements are implemented now. VTK writer for macro elements still needs testing.

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Revision 2744 - Directory Listing
Modified Mon Nov 16 23:45:55 2009 UTC (11 years, 5 months ago) by caltinay

SaveVTK: exponent could have 3 digits so reserve enough space.

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Revision 2743 - Directory Listing
Modified Mon Nov 16 05:28:47 2009 UTC (11 years, 5 months ago) by caltinay

Corrected memory allocation size for tensors in saveVTK. Fixes issue 460.

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Revision 2742 - Directory Listing
Modified Thu Nov 12 06:03:37 2009 UTC (11 years, 5 months ago) by jfenwick

Merging changes from the lapack branch.

The inverse() operation has been moved into c++. [No lazy support for this operation yet.]
Optional Lapack support has been added for matrices larger than 3x3. 
service0 is set to use mkl_lapack.

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Revision 2732 - Directory Listing
Modified Mon Oct 26 01:11:31 2009 UTC (11 years, 5 months ago) by jfenwick

Fixed segfault in debug+omp tests.
Cause:
  variable used in parallel section not declared shared.

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Revision 2722 - Directory Listing
Modified Fri Oct 16 06:45:01 2009 UTC (11 years, 6 months ago) by gross

First steps towards macro elements. at the monent a  macro element is identical to its counterpart of 2nd order.

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Revision 2644 - Directory Listing
Modified Wed Sep 2 04:14:03 2009 UTC (11 years, 7 months ago) by jfenwick

Add unit tests for saveDataCSV which should be ready for use now.
Keyword args are now output in sorted order.

Removed some unneeded functions.

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Revision 2642 - Directory Listing
Modified Tue Sep 1 04:15:50 2009 UTC (11 years, 7 months ago) by jfenwick

pre cleanup

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Revision 2641 - Directory Listing
Modified Mon Aug 31 07:41:49 2009 UTC (11 years, 7 months ago) by jfenwick

Fixed some of my stupids related to MPI compile errors.

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Revision 2640 - Directory Listing
Modified Mon Aug 31 06:22:10 2009 UTC (11 years, 7 months ago) by jfenwick

Adding getMPIComm

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Revision 2635 - Directory Listing
Modified Thu Aug 27 04:54:41 2009 UTC (11 years, 7 months ago) by jfenwick

A bunch of changes related to saveDataCSV.
[Not completed or unit tested yet]

Added saveDataCSV to util.py
AbstractDomain (and MeshAdapter) have a commonFunctionSpace method to 
take a group of FunctionSpaces and return something they can all be interpolated to.

Added pointToStream() in DataTypes to help print points.

added actsConstant() to data - required because DataConstant doesn't store samples the same way other Data do.

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Revision 2625 - Directory Listing
Modified Fri Aug 21 06:30:25 2009 UTC (11 years, 8 months ago) by jfenwick

Merging changes from new doco branch.
All docstrings are now in reStructured text.
A few email addresses have been fixes as well.

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Revision 2608 - Directory Listing
Modified Tue Aug 18 01:25:18 2009 UTC (11 years, 8 months ago) by jfenwick

Updating Lutz' email

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Revision 2596 - Directory Listing
Modified Thu Aug 6 03:09:03 2009 UTC (11 years, 8 months ago) by lgao

Add new diagnostic information: "net time" (the execution time of solver, excluding the setup time for solver and the execution time of preconditioner)

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Revision 2595 - Directory Listing
Modified Thu Aug 6 00:49:09 2009 UTC (11 years, 8 months ago) by gross

there was wrong test which triggered an excpetion in some cases where things were actually right

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Revision 2554 - Directory Listing
Modified Fri Jul 24 05:38:54 2009 UTC (11 years, 8 months ago) by gross

bug with MKL call fixed.

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Revision 2551 - Directory Listing
Modified Thu Jul 23 09:19:15 2009 UTC (11 years, 8 months ago) by gross

a problem with the sparse matrix unrolling fixed.

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Revision 2548 - Directory Listing
Modified Mon Jul 20 06:20:06 2009 UTC (11 years, 9 months ago) by jfenwick

Updating copyright notices

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Revision 2533 - Directory Listing
Modified Wed Jul 15 05:57:01 2009 UTC (11 years, 9 months ago) by gross

finley delivers now a status identifier of the mesh.

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Revision 2524 - Directory Listing
Modified Wed Jul 8 00:39:26 2009 UTC (11 years, 9 months ago) by artak

Minimum size of the coarsest level matrix option added to solver options

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Revision 2521 - Directory Listing
Modified Tue Jul 7 00:08:58 2009 UTC (11 years, 9 months ago) by jfenwick

Modified Lazy so that resolving a single sample uses the node cache method.
Fixed some doxygen problems.

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Revision 2519 - Directory Listing
Modified Mon Jul 6 00:43:08 2009 UTC (11 years, 9 months ago) by jfenwick

Correcting some doxygen errors

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Revision 2518 - Directory Listing
Modified Fri Jul 3 07:43:11 2009 UTC (11 years, 9 months ago) by gross

bug in setNewX fixed: now it is made sure that the FunctionSpace of the new coordinates is correct.

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Revision 2511 - Directory Listing
Modified Thu Jul 2 05:16:19 2009 UTC (11 years, 9 months ago) by gross

more openmp

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Revision 2487 - Directory Listing
Modified Tue Jun 23 04:26:07 2009 UTC (11 years, 9 months ago) by jfenwick

Fixed const-ness on some return values.
Null-Domain now reports tag one as being in use.

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Revision 2484 - Directory Listing
Modified Mon Jun 22 04:22:19 2009 UTC (11 years, 10 months ago) by gross

numarray removed from docu; Locator revised.

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Revision 2474 - Directory Listing
Modified Tue Jun 16 06:32:15 2009 UTC (11 years, 10 months ago) by gross

linearPDEs has is now using the SolverOptions class to talk to PASO

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Revision 2425 - Directory Listing
Modified Thu May 14 09:06:35 2009 UTC (11 years, 11 months ago) by gross

bug in getListOfTags fixed and some tested added

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Revision 2421 - Directory Listing
Modified Thu May 14 02:29:06 2009 UTC (11 years, 11 months ago) by gross

vtk writer supports now meta data and meta data schema

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Revision 2385 - Directory Listing
Modified Wed Apr 15 03:52:38 2009 UTC (12 years ago) by gross

two fixes dealing with zero samples under MPI

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Revision 2379 - Directory Listing
Modified Thu Apr 9 07:36:55 2009 UTC (12 years ago) by gross

type fixed.

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Revision 2368 - Directory Listing
Modified Mon Apr 6 05:05:35 2009 UTC (12 years ago) by gross

some fixes for MKL and Mpisize>1

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Revision 2358 - Directory Listing
Modified Wed Apr 1 22:25:24 2009 UTC (12 years ago) by gross

mpi is not really ready yet.

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Revision 2322 - Directory Listing
Modified Thu Mar 19 04:13:21 2009 UTC (12 years, 1 month ago) by gross

ops

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Revision 2320 - Directory Listing
Modified Thu Mar 19 03:40:16 2009 UTC (12 years, 1 month ago) by gross

some modifictaions to make sure that Mesh_merge.c Mesh_glueFaces.c Mesh_joinFaces.c reject to work under MPI

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Revision 2315 - Directory Listing
Modified Wed Mar 18 00:38:48 2009 UTC (12 years, 1 month ago) by gross

fixes for MPI

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Revision 2311 - Directory Listing
Modified Mon Mar 16 23:00:08 2009 UTC (12 years, 1 month ago) by jfenwick

Fixed a bug causing Mac crashes.

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Revision 2310 - Directory Listing
Modified Mon Mar 16 04:07:43 2009 UTC (12 years, 1 month ago) by gross

some modifications to the test to fix a problem cased by reordering in MPI

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Revision 2308 - Directory Listing
Modified Mon Mar 16 01:20:56 2009 UTC (12 years, 1 month ago) by gross

size_t may be 64 bits which is incompatible to MPI_INT. This problem is fixed by inserting a cast in Mesh_read.c. 
Moreover a fix has been added making sure that gmsh and triangle are executed on one processor only.

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Revision 2271 - Directory Listing
Modified Mon Feb 16 05:08:29 2009 UTC (12 years, 2 months ago) by jfenwick

Merging version 2269 to trunk

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Revision 2256 - Directory Listing
Modified Mon Feb 9 06:20:32 2009 UTC (12 years, 2 months ago) by jfenwick

Throw an exception if AbstractDomain::MPIBarrier is called (This shouldn't happen).
Added Barrier to saveVTK.
Replaced some misused keywords.

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Revision 2243 - Directory Listing
Modified Wed Feb 4 05:22:28 2009 UTC (12 years, 2 months ago) by gross

small bug fixed which could lead to a seg fault

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Revision 2197 - Directory Listing
Modified Thu Jan 8 05:49:16 2009 UTC (12 years, 3 months ago) by gross

modifications to the way cosntraints are handeled in the Transport problem

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Revision 2172 - Directory Listing
Modified Wed Dec 17 08:30:12 2008 UTC (12 years, 4 months ago) by phornby

Fixed some signed/unsigned comparisons occurin g via MAX(). 
They were harmless anyway.

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Revision 2156 - Directory Listing
Modified Mon Dec 15 05:09:02 2008 UTC (12 years, 4 months ago) by gross

some modifications to the iterative solver to make them easier to use. 
There are also improved versions of the Darcy flux solver and the incompressible solver.

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Revision 2151 - Directory Listing
Modified Wed Dec 10 06:34:25 2008 UTC (12 years, 4 months ago) by caltinay

Moved common functionality from saveDX/VTK into private method. May be used
for future save* methods.

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Revision 2150 - Directory Listing
Modified Wed Dec 10 05:57:12 2008 UTC (12 years, 4 months ago) by caltinay

Removed unnecessary "magic name length".

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Revision 2149 - Directory Listing
Modified Wed Dec 10 05:08:17 2008 UTC (12 years, 4 months ago) by caltinay

Fixed a typo in error message.

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Revision 2141 - Directory Listing
Modified Tue Dec 9 04:32:32 2008 UTC (12 years, 4 months ago) by caltinay

saveVTK: Reviewed and changed parts of this function due to several issues.
Confirmed that it's still working using finley/test/python/generate_dumps.py
(manually inserted saveVTK) with and without MPI on 1 and 4 processors.

Changes include:
- removed unnecessary USE_VTK check - we are not using any VTK functions
- fixed writing of Rec9 & Hex27 connectivity data in MPI mode
- fixed some cases where the file was not closed and memory was not freed
- replaced many instances of fprintf by fputs (simple strings)
- some minor optimizations by moving or initializing variables and combining
  if-clauses
- got rid of ~300 lines of code and switched to consistent indentation making
  the file a bit better readable

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Revision 2100 - Directory Listing
Modified Wed Nov 26 08:13:00 2008 UTC (12 years, 4 months ago) by gross

This commit cleans up the incompressible solver and adds a DarcyFlux solver in model module. 
Some documentation for both classes has been added.
The convection code is only linear at the moment.

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Revision 2094 - Directory Listing
Modified Tue Nov 25 05:45:41 2008 UTC (12 years, 4 months ago) by caltinay

saveVTK: Close the file even if error is set upon completion. Note that
in some places the function still returns without proper clean up but
this won't be fixed until the rewrite to avoid more mess in the code.

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Revision 2087 - Directory Listing
Modified Mon Nov 24 04:51:30 2008 UTC (12 years, 4 months ago) by jfenwick

Addressing mantis issue #221.
Interpolation.. and probeInterpolation.. now "work" for the NullDomain.
Work means throw a descriptive exception if you try to move into or out 
of the NullDomain.
The bad_cast exception related to this has been fixed.

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Revision 2078 - Directory Listing
Modified Thu Nov 20 16:10:10 2008 UTC (12 years, 5 months ago) by phornby

Two changes.

1. Move blocktimer from escript to esysUtils.
2. Make it possible to link to paso as a DLL or .so.

Should have no effect on 'nix's

In respect of 1., blocktimer had begun to spring up everywhere, so
for the moment I thought it best to move it to the only other library that
pops up all over the place.

In respect of 2., paso needed to be a DLL in order to use the windows intelc /fast
option, which does aggressive multi-file optimisations. Even in its current form, it either
vectorises or parallelises  hundreds more loops in the esys system than appear in the pragmas.

In achieving 2. I have not been too delicate in adding

PASO_DLL_API

declarations to the .h files in paso/src. Only toward the end of the process of
the conversion, when the number of linker errors dropped below 20, say, did I choosy about what
functions in a header I declared PASO_DLL_API. As a result, there are likely to be many routines
declared as external functions symbols that are in fact internal to the paso DLL. 
Why is this an issue?  It prevents the intelc compiler from getting aggressive on the paso module.
With pain there is sometimes gain. At least all the DLL rules in windows give good
(non-microsoft) compiler writers a chance to really shine.

So, if you should see a PASO_DLL_API on a function in a paso header file,
and think to yourself, "that function is only called in paso, why export it?", then feel free to
delete the PASO_DLL_API export declaration.

Here's hoping for no breakage.....

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Revision 2076 - Directory Listing
Modified Thu Nov 20 12:34:17 2008 UTC (12 years, 5 months ago) by phornby

I may get into trouble for this.
boost-python 1.34 does have a docstring_options class,
but does not have a 3 argument constructor for
it. So the test has been modified to 


#if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)

If you wish to make things more delicate, one can define a 2 argument construction
of docopt just for 1.34 (with an #elif). Probably not worth the effort frankly.

Hope that this has not broken anything for anyone else. The SVN logs suggest this is a
little fragile.....

Also, please be aware that much of our chemistry interface code, that we wish to use with
escript, makes extensive use of boost python.
Having two different boost versions mucking with the python interpreter sounds
like a really bad idea, I'm sure you'll agree.
The problem is that it is not a simple task for us to build new versions of boost-python
on all our platforms. Consequently, it would be nice to be informed when you guys
intend to upgrade a support library of this nature so that we can plan and allocate
resources to keep up.

Cheers.

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Revision 2069 - Directory Listing
Modified Thu Nov 20 09:13:19 2008 UTC (12 years, 5 months ago) by phornby

Another ElementTypeId TypeId=NoType; fix.

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Revision 2064 - Directory Listing
Modified Thu Nov 20 04:06:34 2008 UTC (12 years, 5 months ago) by jfenwick

docstring_options was added in boost 1.34 - macro'd it out if you are 
compiling earlier than that.

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Revision 2061 - Directory Listing
Modified Wed Nov 19 03:40:21 2008 UTC (12 years, 5 months ago) by jfenwick

Fixing some warnings from epydoc.
Disabled c++ signatures in python docstrings.
Removed references to Bruce in epydoc and the users guide.

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Revision 2059 - Directory Listing
Modified Mon Nov 17 22:57:50 2008 UTC (12 years, 5 months ago) by gross

changes as suggested by phornby

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Revision 2052 - Directory Listing
Modified Mon Nov 17 11:15:07 2008 UTC (12 years, 5 months ago) by phornby

MALLOC_CHUNK -> malloc_chunk in case there is a name-space
collision with a macro at some time in the future.

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Revision 2041 - Directory Listing
Modified Sat Nov 15 12:45:15 2008 UTC (12 years, 5 months ago) by phornby

ESYS_STATIC_LIB no longer needs to be defined in SConscript files.

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Revision 2034 - Directory Listing
Modified Thu Nov 13 03:03:42 2008 UTC (12 years, 5 months ago) by artak

variable <set> is initilized to get rid of compiler warnning errors. finley/src/Quadrature.c

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Revision 2033 - Directory Listing
Modified Wed Nov 12 08:14:11 2008 UTC (12 years, 5 months ago) by phornby

As in the last message, add an extra CPPDEFINE to py_local_wrapper_env

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Revision 2031 - Directory Listing
Modified Wed Nov 12 08:02:33 2008 UTC (12 years, 5 months ago) by phornby

Need finer control than INTERFACE_STATIC_LIB could exert. Now there is a
XXX_STATIC_LIB for each lib.

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Revision 2030 - Directory Listing
Modified Wed Nov 12 07:34:08 2008 UTC (12 years, 5 months ago) by phornby

Fix the undef'fing of _DLL_API in windows case.

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Revision 2029 - Directory Listing
Modified Wed Nov 12 07:27:05 2008 UTC (12 years, 5 months ago) by phornby

Test a more elegant way of handling XXX_DLL_API macros.

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Revision 2027 - Directory Listing
Modified Tue Nov 11 02:52:24 2008 UTC (12 years, 5 months ago) by phornby

Ensure ESCRIPT_EXPORTS is defined only while compiling escript on windows.
A similar comment applies to FINLEY_EXPORTS.

SConstruct:
Fixed a comment.
reformatted the Export() call, and added IS_WINDOWS_PLATFORM to the exports.

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Revision 2025 - Directory Listing
Modified Tue Nov 11 00:18:33 2008 UTC (12 years, 5 months ago) by jfenwick

__const on some strings

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Revision 2019 - Directory Listing
Modified Mon Nov 10 13:49:00 2008 UTC (12 years, 5 months ago) by phornby

Yet another concerted effort to handle missing macro arguments
in a portable way.

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Revision 2018 - Directory Listing
Modified Mon Nov 10 13:31:43 2008 UTC (12 years, 5 months ago) by phornby

Only import mathimf.h on win32 with intelc. Allow others to use the
standard math.h

change the #ifndef const -> #ifndef __const (oops!!)

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Revision 1991 - Directory Listing
Modified Fri Nov 7 04:32:38 2008 UTC (12 years, 5 months ago) by caltinay

finley: Constify two variables.

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Revision 1990 - Directory Listing
Modified Fri Nov 7 04:19:07 2008 UTC (12 years, 5 months ago) by ksteube

Changes to avoid compiler warnings
Finley files now pass -Wall on gcc 4.3.2
	saveVTK.c: replaced printf(string) with printf("%s", string)
	MeshAdapterFactory.cpp: moved a few lines to avoid possible use of uninitialized vars
	MeshAdapter.cpp: initialized ncdims in mesh dump
There is still a warning from a boost include file

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Revision 1986 - Directory Listing
Modified Thu Nov 6 23:33:14 2008 UTC (12 years, 5 months ago) by jfenwick

Warning removal

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Revision 1985 - Directory Listing
Modified Thu Nov 6 22:13:54 2008 UTC (12 years, 5 months ago) by caltinay

finley: Fixed compiler warnings (uninitialized vars). This is only a temporary hack. At a later stage this beast will be rewritten...

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Revision 1981 - Directory Listing
Modified Thu Nov 6 05:27:33 2008 UTC (12 years, 5 months ago) by jfenwick

More warning removal.

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Revision 1942 - Directory Listing
Modified Wed Oct 29 03:29:35 2008 UTC (12 years, 5 months ago) by phornby

remove unused rtmp var.

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Revision 1920 - Directory Listing
Modified Thu Oct 23 10:05:27 2008 UTC (12 years, 5 months ago) by phornby

remove unused vars.

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Revision 1919 - Directory Listing
Modified Thu Oct 23 10:03:10 2008 UTC (12 years, 5 months ago) by phornby

Remove un-used vars introduced by my _WIN32 compilation branch. This is a checkin to allow a test of both compilation brabches.

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Revision 1912 - Directory Listing
Modified Thu Oct 23 05:08:31 2008 UTC (12 years, 5 months ago) by ksteube

Finished wrapper script by setting PATH.

The wrapper script reproduces the environment of the person who built
the software + values specified in his hostname_options.py file.  A
user can run a python script without setting any environment variables
or loading any SGI modules.

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Revision 1907 - Directory Listing
Modified Wed Oct 22 11:41:18 2008 UTC (12 years, 5 months ago) by phornby

Mesh_read.c - remove a debug printout introduced by me (oops).

Pattern_coupling.c - remove declaration of naib where it was not used, and remove naib frpm
omp pragmas where it was not declared, and not used.

Apparently cognac.ivec.org did not like this??

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Revision 1900 - Directory Listing
Modified Mon Oct 20 07:33:42 2008 UTC (12 years, 6 months ago) by phornby

Fake commit to sync with my windows machine.

Fix looks like like it worked on Dedbian. Thanks.

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Revision 1896 - Directory Listing
Modified Sun Oct 19 23:16:21 2008 UTC (12 years, 6 months ago) by gross

small fixes.

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Revision 1893 - Directory Listing
Modified Fri Oct 17 09:59:39 2008 UTC (12 years, 6 months ago) by gross

brakets in SCAN error detection were missing.

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Revision 1887 - Directory Listing
Modified Wed Oct 15 03:26:25 2008 UTC (12 years, 6 months ago) by ksteube

Fixed two typos that stopped the test suite from running.

Also, gcc 4.3.2 issued several warnings not seen before:
ignoring the return value of fscanf and using the wrong format
with printf.

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Revision 1877 - Directory Listing
Modified Tue Oct 14 02:58:39 2008 UTC (12 years, 6 months ago) by ksteube

convection.py checkpointing uses mkdir/rmdir, and under MPI there
was a race condition.

mkdir needs to be run on only one CPU and then a barrier to prevent
working processors from using the directory before it exists.

Added methods domain.MPIBarrier and domain.onMasterProcessor() to
implement this technique.

A more general solution might be possible in the future.

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Revision 1876 - Directory Listing
Modified Mon Oct 13 10:19:17 2008 UTC (12 years, 6 months ago) by phornby

ftell lies on windows, so there is a win32 branch that reads the tag lines char by char.

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Revision 1872 - Directory Listing
Modified Mon Oct 13 00:18:55 2008 UTC (12 years, 6 months ago) by jfenwick

Closing the moreshared branch

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Revision 1866 - Directory Listing
Modified Thu Oct 9 04:01:06 2008 UTC (12 years, 6 months ago) by ksteube

Repair to saveVTK similar to revision 1677 (there we got the number of offsets correct
and in this revision we got the number of types correct).
In case of MPI > 1 do not run saveDX tests since saveDX is not MPI parallel.

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Revision 1859 - Directory Listing
Modified Wed Oct 8 03:03:37 2008 UTC (12 years, 6 months ago) by gross

first version of testing for transport solver.

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Revision 1854 - Directory Listing
Modified Tue Oct 7 01:38:55 2008 UTC (12 years, 6 months ago) by ksteube

local_NE0 typo

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Revision 1847 - Directory Listing
Modified Fri Oct 3 06:45:34 2008 UTC (12 years, 6 months ago) by phornby

OK, these get the blahcpp.so names correct now.

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Revision 1845 - Directory Listing
Modified Fri Oct 3 05:23:47 2008 UTC (12 years, 6 months ago) by gross

some naming problem for the installation of escriptcpp and finleycpp. Apparently this came is trough some mofifications in windows

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Revision 1840 - Directory Listing
Modified Fri Oct 3 03:16:11 2008 UTC (12 years, 6 months ago) by phornby

These now install the correct .pyd files on windows.

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Revision 1839 - Directory Listing
Modified Fri Oct 3 02:06:00 2008 UTC (12 years, 6 months ago) by phornby

temporary fix to get run_tests working

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Revision 1823 - Directory Listing
Modified Wed Oct 1 05:56:05 2008 UTC (12 years, 6 months ago) by artak

GS preconditioner now works for block_size 2 and 3 as well. Sweep parameter introdiced, but not working yet

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Revision 1819 - Directory Listing
Modified Tue Sep 30 05:58:06 2008 UTC (12 years, 6 months ago) by artak

Firs version of symmetric Gauss-Seidel preconditioner with coloring

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Revision 1818 - Directory Listing
Modified Tue Sep 30 04:09:13 2008 UTC (12 years, 6 months ago) by gross

chnaged the wrong line

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Revision 1816 - Directory Listing
Modified Tue Sep 30 03:40:51 2008 UTC (12 years, 6 months ago) by gross

bug with MPI fixed (relevant for cases of n0 and n1 < num processors)

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Revision 1814 - Directory Listing
Modified Tue Sep 30 00:21:21 2008 UTC (12 years, 6 months ago) by gross

Contact elements have the right tyoe now.

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Revision 1811 - Directory Listing
Modified Thu Sep 25 23:11:13 2008 UTC (12 years, 6 months ago) by ksteube

Copyright updated in all files

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Revision 1807 - Directory Listing
Modified Thu Sep 25 01:04:51 2008 UTC (12 years, 6 months ago) by ksteube

The new MPI parallel ReadMesh is now the default after having passed
all tests both with and without MPI.
If you have been using ReadMesh you should notice no difference.
If you were using ReadMeshMPI then change to ReadMesh.

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Revision 1804 - Directory Listing
Modified Wed Sep 24 07:52:19 2008 UTC (12 years, 6 months ago) by gross

a robister version of the upwinding scheme

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Revision 1802 - Directory Listing
Modified Tue Sep 23 01:03:29 2008 UTC (12 years, 6 months ago) by jfenwick

Added canTag methods to FunctionSpace and AbstractDomain (and its 
offspring).
This checks to see if the domain supports tags for the given type of 
function space.

Constructors for DataTagged now throw exceptions if you attempt to make 
a DataTagged with a FunctionSpace which does not support tags.
To allow the default constructor to work, NullDomain has a single 
functioncode which "supports" tagging.

Fixed a bug in DataTagged::toString and DataTypes::pointToString.

Added FunctionSpace::getListOfTagsSTL.

algorithm(DataTagged, BinaryFunction) in DataAlgorithm now only 
processes tags known to be in use.
This fixes mantis issue #0000186.

Added comment to Data.h intro warning about holding references if the 
underlying DataAbstract changes.

_python_ unit tests have been updated to test TaggedData with invalid 
FunctionSpaces and to give the correct answers to Lsup etc.

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Revision 1801 - Directory Listing
Modified Fri Sep 19 01:37:09 2008 UTC (12 years, 7 months ago) by ksteube

Fixed serialization of I/O for MPI...code didn't compile without MPI

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Revision 1800 - Directory Listing
Modified Thu Sep 18 05:28:20 2008 UTC (12 years, 7 months ago) by ksteube

Serialized parallel I/O when writing mesh or data to NetCDF file on multiple MPI processors.
Added domain method getMPIComm() to complement getMPISize() and getMPIRank().

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Revision 1796 - Directory Listing
Modified Wed Sep 17 01:45:46 2008 UTC (12 years, 7 months ago) by jfenwick

Merged noarrayview branch onto trunk.

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Revision 1787 - Directory Listing
Modified Mon Sep 15 01:36:34 2008 UTC (12 years, 7 months ago) by artak

MINRES solver is added to escript. Additional 16 tests are added to run_simplesolve for MINRES and TFQMR solvers

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Revision 1777 - Directory Listing
Modified Tue Sep 9 06:39:37 2008 UTC (12 years, 7 months ago) by ksteube

Implemented Lutz fix for MPI mesh dump/load using NetCDF

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Revision 1776 - Directory Listing
Modified Tue Sep 9 06:03:53 2008 UTC (12 years, 7 months ago) by ksteube

Cleared away some debugging prints

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Revision 1774 - Directory Listing
Modified Tue Sep 9 03:50:45 2008 UTC (12 years, 7 months ago) by gross

bug: unitialized values

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Revision 1771 - Directory Listing
Modified Mon Sep 8 22:47:55 2008 UTC (12 years, 7 months ago) by ksteube

Removed failing test until we fix a bug.
Fixed several compiler warnings.

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Revision 1770 - Directory Listing
Modified Mon Sep 8 06:58:47 2008 UTC (12 years, 7 months ago) by ksteube

Detects an array reference out of bounds when running run_inputOutput.py

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Revision 1766 - Directory Listing
Modified Mon Sep 8 02:51:14 2008 UTC (12 years, 7 months ago) by gross

code formatting

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Revision 1765 - Directory Listing
Modified Mon Sep 8 02:49:57 2008 UTC (12 years, 7 months ago) by gross

some fixes for the case of empty processor

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Revision 1764 - Directory Listing
Modified Mon Sep 8 02:48:26 2008 UTC (12 years, 7 months ago) by gross

type for the non mpi case fixed.

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Revision 1763 - Directory Listing
Modified Mon Sep 8 02:47:55 2008 UTC (12 years, 7 months ago) by gross

more code formatting

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Revision 1762 - Directory Listing
Modified Mon Sep 8 02:42:39 2008 UTC (12 years, 7 months ago) by gross

some formatting

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Revision 1760 - Directory Listing
Modified Mon Sep 8 02:35:56 2008 UTC (12 years, 7 months ago) by gross

some renaming of variables to clarify what is going on

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Revision 1755 - Directory Listing
Modified Mon Sep 8 01:34:40 2008 UTC (12 years, 7 months ago) by ksteube

Added new field to NetCDF dump of mesh

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Revision 1754 - Directory Listing
Modified Sun Sep 7 22:07:26 2008 UTC (12 years, 7 months ago) by ksteube

Added new test suite run_inputOutput.py to systematically test I/O.
Can determine if two domains are same with Fourier analysis.
Added new method getNumDataPointsGlobal to return number of DPs of a distributed mesh.
Reading of tags in ReadMeshMPI failed occasionally, should be more robust now.

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Revision 1753 - Directory Listing
Modified Sun Sep 7 22:01:23 2008 UTC (12 years, 7 months ago) by ksteube

Test suite fails due to missing arg in call to Finley_Mesh_createMappings.
Added NULL arg, but still need to find proper fix as loadMesh does not work.

Adjusted SConstruct to delete pythonMPI if not compiled for MPI.

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Revision 1750 - Directory Listing
Modified Wed Sep 3 23:09:29 2008 UTC (12 years, 7 months ago) by gross

small bug fixed

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Revision 1749 - Directory Listing
Modified Wed Sep 3 07:25:01 2008 UTC (12 years, 7 months ago) by gross

fixes a problem with the saveVTK writing under mpi

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Revision 1748 - Directory Listing
Modified Wed Sep 3 06:10:39 2008 UTC (12 years, 7 months ago) by ksteube

MPI parallelism for Data().dump and load.  Use multiple NetCDF
files, one file per MPI process

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Revision 1745 - Directory Listing
Modified Wed Sep 3 00:41:24 2008 UTC (12 years, 7 months ago) by ksteube

MPI mesh_read was crashing if tags not present

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Revision 1744 - Directory Listing
Modified Tue Sep 2 07:39:18 2008 UTC (12 years, 7 months ago) by ksteube

Can now read and MPI distribute a finley mesh including the tags.

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Revision 1743 - Directory Listing
Modified Tue Sep 2 00:54:05 2008 UTC (12 years, 7 months ago) by ksteube

Avoid crash due to zero-length writes in MPI_File_write_ordered.
Write a space instead of empty string.
The space will be at the end of a line and cause no problem.

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Revision 1741 - Directory Listing
Modified Mon Sep 1 04:06:41 2008 UTC (12 years, 7 months ago) by gross

VTK writer supports HEX27 and REC9 now.

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Revision 1740 - Directory Listing
Modified Fri Aug 29 06:23:11 2008 UTC (12 years, 7 months ago) by gross

and some fixes for the GMSH reader

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Revision 1739 - Directory Listing
Modified Fri Aug 29 06:19:53 2008 UTC (12 years, 7 months ago) by gross

Fix in the MPI mesh reader: Owner need to be set.

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Revision 1738 - Directory Listing
Modified Fri Aug 29 05:06:45 2008 UTC (12 years, 7 months ago) by gross

some changes improving the robustness for MPI if the elements/processor is small

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Revision 1736 - Directory Listing
Modified Fri Aug 29 02:23:16 2008 UTC (12 years, 7 months ago) by gross

This fixes a problem which is typically arising when using reduced order
with MPI and a "small" number of elements per processor. In this case it
can happen that the couple matrix is not using all entries sent to the
processor. The old implementations assumed that the indices will cover
the entire input. This assumption has been removed.

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Revision 1735 - Directory Listing
Modified Fri Aug 29 00:18:26 2008 UTC (12 years, 7 months ago) by gross

This fixes a bug in the callculation of communication tables in
particular for the data to be send away. The problem was that the
previously used method based on the idea to use the elements stored on a
processor to decide what to send away is not suitable for the reduced
DOF. Now each processor sends a list of the DOFs it is expecting to its
naighbours. 

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Revision 1733 - Directory Listing
Modified Thu Aug 28 01:46:07 2008 UTC (12 years, 7 months ago) by gross

bug fix: if the numer of elements to be generated suppose to be zero
still face elements and nodes are generated. this is fixed now.

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Revision 1732 - Directory Listing
Modified Wed Aug 27 05:47:03 2008 UTC (12 years, 7 months ago) by ksteube

MPI read of finley mesh file working except for a bug related to mesh_prepare

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Revision 1725 - Directory Listing
Modified Tue Aug 26 03:31:49 2008 UTC (12 years, 7 months ago) by ksteube

MPI read of .fly mesh file: fixed bug in message size while fanning out elements

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Revision 1723 - Directory Listing
Modified Fri Aug 22 04:24:19 2008 UTC (12 years, 7 months ago) by gross

some unnecessary code removed.

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Revision 1722 - Directory Listing
Modified Fri Aug 22 04:20:30 2008 UTC (12 years, 7 months ago) by gross

The CSR matrix patters handed ober to ParMetis may not containn the main diagonal entry. 
This revisison is fixing the problem.

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Revision 1720 - Directory Listing
Modified Fri Aug 22 00:24:35 2008 UTC (12 years, 8 months ago) by gross

PARAMETIS macro renamed to USE_PARAMETIS as set by scons

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Revision 1716 - Directory Listing
Modified Thu Aug 21 05:03:49 2008 UTC (12 years, 8 months ago) by gross

getListOfTags method added to FunctionSpace class

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Revision 1713 - Directory Listing
Modified Wed Aug 20 07:03:45 2008 UTC (12 years, 8 months ago) by ksteube

MPI read of mesh.fly: reduced memory requirements

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Revision 1707 - Directory Listing
Modified Thu Aug 14 06:38:14 2008 UTC (12 years, 8 months ago) by ksteube

Fixed nightly tests for savanna (no longer running in PBS cause can't
compile on compute node).
Modified domain.print_mesh_info() to tell how many elements are owned by
a node and how many are in the overlap.
Instrumented the preconditioner step.

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Revision 1705 - Directory Listing
Modified Thu Aug 14 05:56:40 2008 UTC (12 years, 8 months ago) by ksteube

Branch scons-dev is hereby closed.
Some parts of scons scripts have been re-written.

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Revision 1703 - Directory Listing
Modified Thu Aug 14 05:34:25 2008 UTC (12 years, 8 months ago) by artak

TFQMR solver is added to PASO solver. It is not parallelised yet.

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Revision 1677 - Directory Listing
Modified Mon Jul 28 06:36:19 2008 UTC (12 years, 8 months ago) by gross

bug in the MPI version of saveVTK fixed

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Revision 1669 - Directory Listing
Modified Thu Jul 24 01:10:04 2008 UTC (12 years, 8 months ago) by gross

A problem with VTK writer and MPI is fixed: Apparently MPI_file_open does not "delete" the file  which has the effect that 
if less date are written into the file as the file contained when opened bits of the previous containt remains in the file. This problem is fixed
by deleting the file if it exists before open it with MPI. The additional function Paso_existFile needed to be added as there is no standart C 
function to test the exists of a file.

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Revision 1665 - Directory Listing
Modified Wed Jul 23 03:23:03 2008 UTC (12 years, 8 months ago) by gross

bug in the MPI version of saveVTK fixed

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Revision 1664 - Directory Listing
Modified Tue Jul 22 03:41:38 2008 UTC (12 years, 9 months ago) by ksteube

Install() on Mac OS was naming shared libs file.dylib...not OK for our
libraries for python calling C++ (escriptcpp.so and finleycpp.so).
This is because python's dlopen() calls only look for .so files.

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Revision 1660 - Directory Listing
Modified Mon Jul 21 03:23:46 2008 UTC (12 years, 9 months ago) by ksteube

Some variables were not declared as a result of recent cleanup

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Revision 1650 - Directory Listing
Modified Tue Jul 15 08:58:22 2008 UTC (12 years, 9 months ago) by phornby

more care with m_t and diagS needed in the pragmas.

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Revision 1649 - Directory Listing
Modified Tue Jul 15 08:41:02 2008 UTC (12 years, 9 months ago) by phornby

Make operator=() on exception non-virtual. Should silence the Altix compiler.
However, if an exception is cast to another parent type, and
operator=() is called when the exception so cast is an l-value in the assignment,
an "incomplete" assignment will occur, copying only the parent class members of the 
l-value in the assignmnet.

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Revision 1646 - Directory Listing
Modified Tue Jul 15 05:27:39 2008 UTC (12 years, 9 months ago) by phornby

Unused vars due to the #if 0's in the code.

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Revision 1645 - Directory Listing
Modified Tue Jul 15 05:26:38 2008 UTC (12 years, 9 months ago) by phornby

unused vars.

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Revision 1639 - Directory Listing
Modified Mon Jul 14 08:55:25 2008 UTC (12 years, 9 months ago) by gross

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Revision 1637 - Directory Listing
Modified Mon Jul 14 05:34:59 2008 UTC (12 years, 9 months ago) by ksteube

Resolved some compiler warnings
Changed blocktimer to not use strdup, intead malloc and strcpy

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Revision 1634 - Directory Listing
Modified Sat Jul 12 09:08:33 2008 UTC (12 years, 9 months ago) by phornby

linux_gcc_eg_options.py:
remove the std99 option, it is no longer needed as the code compiles without
C 1999 extension (need for these extensions elinminated in windows port).
Turn on all warnings except unknown pragmas. Should catch a lot of stuff.

SConstruct:
Impassioned plea

system_dep.h:
Add the standard incantation for dealing with const declarations
in C code called from C and C++

blocktimer:
Get the calling interface right for C code called from C and C++
and use __const as defined in system_dep.h
(Should be re-factored into compiler_dep.h file).

MeshAdapterFactory.cpp:
Since we have (effectively) no control over netCDF policy,
cast const char *'s to char *'s

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Revision 1632 - Directory Listing
Modified Sat Jul 12 07:17:50 2008 UTC (12 years, 9 months ago) by trankine

compiling with netcdf on revealed an unused var.

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Revision 1628 - Directory Listing
Modified Fri Jul 11 13:12:46 2008 UTC (12 years, 9 months ago) by phornby

Merge in /branches/windows_from_1456_trunk_1620_merged_in branch.

You will find a preserved pre-merge trunk in tags under tags/trunk_at_1625.
That will be useful for diffing & checking on my stupidity.

Here is a list of the conflicts and their resolution at this
point in time.


=================================================================================
(LLWS == looks like white space).

finley/src/Assemble_addToSystemMatrix.c - resolve to branch - unused var. may be wrong.....
finley/src/CPPAdapter/SystemMatrixAdapter.cpp - resolve to branch - LLWS
finley/src/CPPAdapter/MeshAdapter.cpp - resolve to branch - LLWS
paso/src/PCG.c - resolve to branch - unused var fixes.
paso/src/SolverFCT.c - resolve to branch - LLWS
paso/src/FGMRES.c - resolve to branch - LLWS
paso/src/Common.h - resolve to trunk version. It's omp.h's include... not sure it's needed,
but for the sake of saftey.....
paso/src/Functions.c - resolve to branch version, indentation/tab removal and return error
on bad unimplemented Paso_FunctionCall.
paso/src/SolverFCT_solve.c - resolve to branch version, unused vars
paso/src/SparseMatrix_MatrixVector.c - resolve to branch version, unused vars.
escript/src/Utils.cpp - resloved to branch, needs WinSock2.h
escript/src/DataExpanded.cpp - resolved to branch version - LLWS
escript/src/DataFactory.cpp - resolve to branch version
=================================================================================

This currently passes tests on linux (debian), but is not checked on windows or Altix yet.

This checkin is to make a trunk I can check out for windows to do tests on it.

Known outstanding problem is in the operator=() method of exceptions
causing warning messages on the intel compilers.

May the God of doughnuts have mercy on my soul.

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Revision 1574 - Directory Listing
Modified Mon May 26 13:59:58 2008 UTC (12 years, 10 months ago) by gross

some modifications that may help to speed up compilation

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Revision 1572 - Directory Listing
Modified Mon May 26 12:50:56 2008 UTC (12 years, 10 months ago) by gross

some openmp problems in PCG fixed.

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Revision 1568 - Directory Listing
Modified Sat May 24 03:15:08 2008 UTC (12 years, 10 months ago) by ksteube

Some testing on ac.apac.edu.au, more work needed
New pyvisi example offscreen.py for offscreen rendering

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Revision 1564 - Directory Listing
Modified Thu May 22 09:31:33 2008 UTC (12 years, 11 months ago) by gross

some openmp dynamic scheduling for MVM.

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Revision 1562 - Directory Listing
Modified Wed May 21 13:04:40 2008 UTC (12 years, 11 months ago) by gross

The algebraic upwinding with MPI. The case of boundary constraint needs still some attention. 

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Revision 1552 - Directory Listing
Modified Thu May 8 08:52:41 2008 UTC (12 years, 11 months ago) by gross

some changes to make the implementatiopn of a upwind MPI version easier

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Revision 1513 - Directory Listing
Modified Tue Apr 15 08:47:57 2008 UTC (13 years ago) by gross

pragma ivdep removed. icc produced wrong code.

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Revision 1476 - Directory Listing
Modified Mon Apr 7 23:38:50 2008 UTC (13 years ago) by gross

Jacobian-free Newton method added to Paso

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Revision 1464 - Directory Listing
Modified Tue Apr 1 23:27:09 2008 UTC (13 years ago) by gross

bug for interpoltion from reduced solution to elements in MPI fixed.

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Revision 1459 - Directory Listing
Modified Thu Mar 27 01:49:10 2008 UTC (13 years ago) by ksteube

Implemented ParMETIS for mesh partition optimization under MPI.
Documented optimize=True in User Guide for Brick() and Rectangle().

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Revision 1455 - Directory Listing
Modified Thu Feb 28 17:19:44 2008 UTC (13 years, 1 month ago) by phornby

Merge of branches/windows_from_1431_trunk.

Revamp of the exception system.
Fix unused vars and signed/unsigned comparisons.
defined a macro THROW(ARG) in the system_dep.h's to
deal with the expectations of declarations on different architectures.

Details in the logs of branches/windows_from_1431_trunk.

pre-merge snapshot of the trunk in tags/trunk_at_1452

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Revision 1428 - Directory Listing
Modified Wed Feb 27 08:07:11 2008 UTC (13 years, 1 month ago) by trankine

Merge changes from windows port branch to test build on *nix not broken.

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Revision 1417 - Directory Listing
Modified Mon Feb 25 04:45:48 2008 UTC (13 years, 1 month ago) by gross

some more work on the transport solver.

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Revision 1414 - Directory Listing
Modified Thu Feb 14 10:01:43 2008 UTC (13 years, 2 months ago) by gross

a first verion of a Stokes solver

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Revision 1407 - Directory Listing
Modified Mon Feb 4 06:45:48 2008 UTC (13 years, 2 months ago) by gross

new upwinding algorithm (still fails)

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Revision 1402 - Directory Listing
Modified Thu Jan 31 00:17:49 2008 UTC (13 years, 2 months ago) by ksteube

now implemented to read/fan out elements

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Revision 1388 - Directory Listing
Modified Fri Jan 11 07:45:58 2008 UTC (13 years, 3 months ago) by trankine

And get the *(&(*&(* name right

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Revision 1387 - Directory Listing
Modified Fri Jan 11 07:45:26 2008 UTC (13 years, 3 months ago) by trankine
Original Path: temp/finley/src

Restore the trunk that existed before the windows changes were committed to the (now moved to branches) old trunk.

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Revision 1384 - Directory Listing
Modified Fri Jan 11 02:29:38 2008 UTC (13 years, 3 months ago) by phornby
Original Path: temp_trunk_copy/finley/src

Make a temp copy of the trunk before checking in the windows changes

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Revision 1382 - Directory Listing
Modified Thu Jan 10 00:21:22 2008 UTC (13 years, 3 months ago) by gross

some tests got deactivated. they are back now.

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Revision 1377 - Directory Listing
Modified Wed Jan 9 03:45:59 2008 UTC (13 years, 3 months ago) by gross

Some code was moved around to slow down the bustling intel compiler v10.

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Revision 1376 - Directory Listing
Modified Wed Jan 9 01:38:18 2008 UTC (13 years, 3 months ago) by gross

inserted sys.exit(1) into the tests so scons can detect the failure of the test. 
A similar statement has been removed from an earlier as it produces problems on 64bit Linux. Previously exit(0) was called in case of success but now this is not done in order to avoid a fatal end of the program. in the case of an error in the test there could be a fatal error so but I guess that this not really a problem.

PS: the fact that signal 0 was returned even for the case of an error lead to the illusion that all tests have been completed successfully.

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Revision 1375 - Directory Listing
Modified Wed Jan 9 00:15:05 2008 UTC (13 years, 3 months ago) by gross

bug in interpolation at reduced face elements fixed.

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Revision 1370 - Directory Listing
Modified Wed Jan 2 09:21:43 2008 UTC (13 years, 3 months ago) by gross

explicit upwinding scheme added.

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Revision 1367 - Directory Listing
Modified Wed Dec 19 02:45:07 2007 UTC (13 years, 4 months ago) by gross

finley can now assemble a transport problem.

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Revision 1366 - Directory Listing
Modified Tue Dec 18 05:49:17 2007 UTC (13 years, 4 months ago) by gross

finley can create a TransportProblem now

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Revision 1365 - Directory Listing
Modified Mon Dec 17 07:28:23 2007 UTC (13 years, 4 months ago) by gross

some cosmetics.

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Revision 1364 - Directory Listing
Modified Mon Dec 17 07:22:45 2007 UTC (13 years, 4 months ago) by gross

finley interface to paso's transport solver added.

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Revision 1361 - Directory Listing
Modified Fri Dec 14 09:26:51 2007 UTC (13 years, 4 months ago) by gross

first steps towards a flux controlled transport solver.

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Revision 1360 - Directory Listing
Modified Thu Dec 13 05:05:00 2007 UTC (13 years, 4 months ago) by ksteube

Partial implementation of ReadMeshMPI.
Will eventually replace ReadMesh but for now has a different name.

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Revision 1359 - Directory Listing
Modified Wed Dec 5 03:42:09 2007 UTC (13 years, 4 months ago) by gross

debug print removed.

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Revision 1358 - Directory Listing
Modified Wed Dec 5 03:41:06 2007 UTC (13 years, 4 months ago) by gross

setTaggedValue works now for expanded data.

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Revision 1353 - Directory Listing
Modified Thu Nov 22 06:05:35 2007 UTC (13 years, 5 months ago) by matt

Reversed the removal of blocktimer code. This needs to be fixed properly for
the Windows stuff to work.

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Revision 1352 - Directory Listing
Modified Thu Nov 22 03:43:28 2007 UTC (13 years, 5 months ago) by matt

Removed blocktimer code from Finley_Assemble_PDE().

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Revision 1347 - Directory Listing
Modified Fri Nov 16 05:37:07 2007 UTC (13 years, 5 months ago) by ksteube

Completed mesh.dump(file) and mesh=LoadMesh(file) by adding TagMap and
implementing MPI parallelism.
Now allocating ElementFile for ContactElements even if there are none.
Removed file Mesh_dump.c since dump/loadMesh are in CPPAdapter/MeshAdapter*.cpp.

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Revision 1346 - Directory Listing
Modified Wed Nov 14 22:48:12 2007 UTC (13 years, 5 months ago) by ksteube

dump/LoadMesh methods work except for TagMap, Point elements probably OK but are untested.

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Revision 1345 - Directory Listing
Modified Wed Nov 14 07:53:34 2007 UTC (13 years, 5 months ago) by ksteube

Created LoadMesh to read a mesh from a distributed NetCDF file.
Can read nodes but not elements yet.

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Revision 1344 - Directory Listing
Modified Wed Nov 14 04:28:25 2007 UTC (13 years, 5 months ago) by ksteube

Now using TMPMEMFREE but still thrashes memory for very large mesh.
Future solution will be to use NetCDF subsetting and less temp memory.

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Revision 1343 - Directory Listing
Modified Wed Nov 14 02:48:02 2007 UTC (13 years, 5 months ago) by ksteube

First cut implementation of mesh.dump() using NetCDF.  TagMap not
saved yet.  The code for Points probably works but has not been tested.

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Revision 1342 - Directory Listing
Modified Thu Nov 8 23:56:58 2007 UTC (13 years, 5 months ago) by gross

improvements on integration schemes for tets and tris: double precision (not all), higher orders

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Revision 1340 - Directory Listing
Modified Thu Nov 8 06:24:43 2007 UTC (13 years, 5 months ago) by ksteube

Fixed create a local labeling of the DOFs

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Revision 1339 - Directory Listing
Modified Wed Nov 7 01:53:12 2007 UTC (13 years, 5 months ago) by ksteube

Modified scons target release_src to include lib/ and include/ since
their presence is required for a build.  Modified
mydomain.print_mesh_info(True) to include more useful info about a
distributed domain.  Added mypde.getOperator().print_matrix_info(True)
to tell about a distributed matrix.

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Revision 1338 - Directory Listing
Modified Mon Nov 5 06:32:29 2007 UTC (13 years, 5 months ago) by gross

bug in the selection of the order of the output mesh fixed.

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Revision 1335 - Directory Listing
Modified Fri Nov 2 05:54:25 2007 UTC (13 years, 5 months ago) by gross

color ranges were not initialized.

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Revision 1326 - Directory Listing
Modified Mon Oct 1 08:10:41 2007 UTC (13 years, 6 months ago) by ksteube

Implemented domain.print_mesh_info() so we can see the distribution of elements & nodes.
Implemented -DBOUNDS_CHECK to catch an error with periodicN=True.

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Revision 1322 - Directory Listing
Modified Thu Sep 27 04:40:43 2007 UTC (13 years, 6 months ago) by ksteube

Code now compiles and runs on cyclone.hpcu.uq.edu.au.
Had to remove intelc from the SConstruct, but didn't commit that change.
Changed a couple C++ comments to C comments.

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Revision 1317 - Directory Listing
Modified Tue Sep 25 03:41:48 2007 UTC (13 years, 6 months ago) by ksteube

yet another file copied from MPI branch to trunk

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Revision 1315 - Directory Listing
Modified Tue Sep 25 02:41:13 2007 UTC (13 years, 6 months ago) by ksteube

Copied more files from MPI branch to trunk

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Revision 1313 - Directory Listing
Modified Tue Sep 25 01:44:26 2007 UTC (13 years, 6 months ago) by ksteube

Copied a handful of files from trunk-mpi-branch into trunk

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Revision 1312 - Directory Listing
Modified Mon Sep 24 06:18:44 2007 UTC (13 years, 6 months ago) by ksteube

The MPI branch is hereby closed. All future work should be in trunk.

Previously in revision 1295 I merged the latest changes to trunk into trunk-mpi-branch.
In this revision I copied all files from trunk-mpi-branch over the corresponding
trunk files. I did not use 'svn merge', it was a copy.

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Revision 1235 - Directory Listing
Modified Mon Aug 13 00:25:29 2007 UTC (13 years, 8 months ago) by phornby

Started the removal of IS_WINDOWS_PLATFORM, and now insis that the windows options file be kept up to date, and be complete.

boost_libs -> boost_lib.

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Revision 1221 - Directory Listing
Modified Fri Aug 3 00:27:20 2007 UTC (13 years, 8 months ago) by ksteube

Disabled HRZ lumping until the tests pass

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Revision 1220 - Directory Listing
Modified Thu Aug 2 04:46:20 2007 UTC (13 years, 8 months ago) by btully

Included HRZ lumping scheme for the LUMPED solver.

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Revision 1204 - Directory Listing
Modified Sat Jun 23 11:43:12 2007 UTC (13 years, 9 months ago) by gross

a frame for an improved lumping procedure added.

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Revision 1198 - Directory Listing
Modified Tue Jun 19 00:24:29 2007 UTC (13 years, 10 months ago) by btully

Updated Rec9 Shape Functions.
Included a new definition for Hex27 Reference Element and associated Shape Functions.

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Revision 1179 - Directory Listing
Modified Wed May 30 05:10:02 2007 UTC (13 years, 10 months ago) by gross

some debug print outs removed.

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Revision 1178 - Directory Listing
Modified Wed May 30 05:03:17 2007 UTC (13 years, 10 months ago) by gross

bug in visualization interface test fixed.

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Revision 1177 - Directory Listing
Modified Wed May 30 05:01:29 2007 UTC (13 years, 10 months ago) by gross

debug print out removed.

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Revision 1171 - Directory Listing
Modified Fri May 25 06:55:05 2007 UTC (13 years, 10 months ago) by gross

some modifications to the tests to consider the new integration schemes for tri and tet

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Revision 1170 - Directory Listing
Modified Fri May 25 05:24:57 2007 UTC (13 years, 10 months ago) by btully

Added new methods for integration of Tri's and Tet's For Order 2 and 3.
NB: There is a conflict in the testing of the getNormal() function. On consultation with Lutz, we have concluded this is an issue with the test rather than the new methods.

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Revision 1163 - Directory Listing
Modified Wed May 23 23:56:39 2007 UTC (13 years, 10 months ago) by gross

import of DISPLAY environment variable into scons ENV added. This is required to run pyvisi tests under XGL

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Revision 1157 - Directory Listing
Modified Mon May 21 06:45:52 2007 UTC (13 years, 11 months ago) by gross

ops, wrong name

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Revision 1156 - Directory Listing
Modified Mon May 21 06:45:14 2007 UTC (13 years, 11 months ago) by gross

node label optimization

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Revision 1141 - Directory Listing
Modified Tue May 15 04:24:51 2007 UTC (13 years, 11 months ago) by gross

Some changes to make things run on windows. There is still a problem with netcdf an long file names on windows but there is the suspicion that this is a bigger problem related to boost (compiler options). In fact runs with large numbers of iteration/time steps tend to create seg faults. 

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Revision 1139 - Directory Listing
Modified Mon May 14 05:12:53 2007 UTC (13 years, 11 months ago) by ksteube

Finished renaming of boost_lib to boost_libs and boost_lib_path to boost_libs_path.

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Revision 1137 - Directory Listing
Modified Thu May 10 08:11:31 2007 UTC (13 years, 11 months ago) by gross

This version passes the tests on windows except for 

   * vtk
   * netCDF

The version needs to be tested on altix and linux

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Revision 1134 - Directory Listing
Modified Wed May 9 01:44:04 2007 UTC (13 years, 11 months ago) by gross

fixed a bag in the extra bits to make the ordering unique. This does not effect the correctness of the result but makes sure that the results are independent from the sorting algorithm.

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Revision 1133 - Directory Listing
Modified Tue May 8 07:19:33 2007 UTC (13 years, 11 months ago) by gross

Changes needed for windows. This still does not work on and has not run on linux and the altix. 
 
There are a few changes in names in the scons script, in particular _libs is used rather than _lib and _libs is always a list. By default on windows MSVC is used. The location of python is at C:\Program Files\python<version>, boost at C:\Program Files\boost and netcdf at C:\Program Files\netcdf. 

 

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Revision 1116 - Directory Listing
Modified Mon Apr 23 03:36:34 2007 UTC (14 years ago) by gross

Interporpolation from full to reduced integration order added.

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Revision 1107 - Directory Listing
Modified Thu Apr 19 02:14:18 2007 UTC (14 years ago) by gross

Small bug in ReadMeh call fixed.
Test for typ of verbose argument in pdetools.SaddlePointSolver added.

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Revision 1092 - Directory Listing
Modified Fri Apr 13 03:39:49 2007 UTC (14 years ago) by gross

the useless profilinf for data.cpp removed (doDebug=yes should work again)
and a small bug in the gmsh reader fixed.

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Revision 1080 - Directory Listing
Modified Wed Apr 11 06:07:30 2007 UTC (14 years ago) by gross

small typo fixed.

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Revision 1072 - Directory Listing
Modified Thu Mar 29 06:44:30 2007 UTC (14 years ago) by gross

PDE assemblage for reduced integration order + tests added.

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Revision 1064 - Directory Listing
Modified Tue Mar 27 06:21:02 2007 UTC (14 years ago) by gross

test for reduced integration order for grad, interpolate and integrate added.
Bug shown by the tests have been fixed.

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Revision 1062 - Directory Listing
Modified Mon Mar 26 06:17:53 2007 UTC (14 years ago) by gross

reduced integration schemes are implemented now for grad, integrate, etc. Tests still to be added.

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Revision 1059 - Directory Listing
Modified Fri Mar 23 11:01:53 2007 UTC (14 years, 1 month ago) by gross

first steps toward reduced element integration order. The escript bit is done but the finley part still needs work.

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Revision 1049 - Directory Listing
Modified Tue Mar 20 03:00:18 2007 UTC (14 years, 1 month ago) by gross

bandwidth optimizer has been moved back (Lutz: switch on your brain.
)

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Revision 1048 - Directory Listing
Modified Tue Mar 20 02:59:14 2007 UTC (14 years, 1 month ago) by gross

bandwidth optimizer has been moved.

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Revision 1044 - Directory Listing
Modified Mon Mar 19 07:29:31 2007 UTC (14 years, 1 month ago) by gross

clear name tagging is supported now.

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Revision 1030 - Directory Listing
Modified Wed Mar 14 05:14:44 2007 UTC (14 years, 1 month ago) by phornby

Assemble_CopyElementData.c - resolve with my local edits.
Mesh_saveVTK.c - remove debug print.
DataArrayView.h - remove dllim/export declarations on template functions.

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Revision 1028 - Directory Listing
Modified Wed Mar 14 00:15:24 2007 UTC (14 years, 1 month ago) by gross

modifications to be compliant with _WIN32. The substitutes for asinh, acosh, atanh are still missing (erf will through an exception)

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Revision 1022 - Directory Listing
Modified Tue Mar 13 02:25:53 2007 UTC (14 years, 1 month ago) by phornby

Now define the destructors for all the Exceptions (sorry guys & gals).

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Revision 1020 - Directory Listing
Modified Mon Mar 12 10:12:36 2007 UTC (14 years, 1 month ago) by phornby

Added explicit destructors to all Exception classes.

Fixed an ifdef in TestCase.cpp

Made the conditional definition of M_PI in LocalOps.h
depend only on M_PI being undefined.

Replace dynamically dimensioned arrays in DataFactory & DataTagged with malloc.

sort() method of list does not take a named argument
(despite the manual's claims to the contary).

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Revision 1003 - Directory Listing
Modified Thu Mar 1 01:53:37 2007 UTC (14 years, 1 month ago) by gross

small fix on the finley gmsh reader for the case of no face elements.

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Revision 997 - Directory Listing
Modified Mon Feb 26 06:31:45 2007 UTC (14 years, 1 month ago) by gross

small small fixes in modellib

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Revision 971 - Directory Listing
Modified Wed Feb 14 04:40:49 2007 UTC (14 years, 2 months ago) by ksteube

Had to undo commit to new MPI branch. The changes went into the original and
not the branch. The files committed here are exactly the same as revision 969.

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Revision 969 - Directory Listing
Modified Tue Feb 13 23:02:23 2007 UTC (14 years, 2 months ago) by ksteube

Parallelization using MPI for solution of implicit problems.

Parallelization for explicit problems has already been accomplished in
the main SVN branch.

This is incomplete and is not ready for use.

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Revision 967 - Directory Listing
Modified Tue Feb 13 09:40:12 2007 UTC (14 years, 2 months ago) by gross

dump and load of expanded data via netCDF added. some test are still missing.

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Revision 964 - Directory Listing
Modified Tue Feb 13 05:10:26 2007 UTC (14 years, 2 months ago) by gross

The set/getRefVal functions of Data objects have been removed (mainly to avoid later problems with MPI).
Moreover, a faster access to the reference id of samples has been introduced. I don't think that anybody will
profit form this at this stage but it will allow a faster dump of data objects.

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Revision 960 - Directory Listing
Modified Tue Feb 13 01:39:05 2007 UTC (14 years, 2 months ago) by gross

typo in file name fixed

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Revision 959 - Directory Listing
Modified Tue Feb 13 01:38:39 2007 UTC (14 years, 2 months ago) by gross

typo in file name fixed

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Revision 940 - Directory Listing
Modified Mon Jan 29 00:09:08 2007 UTC (14 years, 2 months ago) by gross

ivdep removed as it produces wrong results with OPenMP

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Revision 939 - Directory Listing
Modified Thu Jan 25 04:23:38 2007 UTC (14 years, 2 months ago) by gross

bug in finley mesh reader fixed

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Revision 935 - Directory Listing
Modified Tue Jan 23 09:53:10 2007 UTC (14 years, 2 months ago) by gross

a missing file

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Revision 934 - Directory Listing
Modified Tue Jan 23 09:52:45 2007 UTC (14 years, 2 months ago) by gross

gmsh file reader for finley

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Revision 903 - Directory Listing
Modified Fri Nov 17 01:59:49 2006 UTC (14 years, 5 months ago) by gross

bug with tagged data in vtk and dx writer fixed

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Revision 888 - Directory Listing
Modified Tue Nov 7 08:31:26 2006 UTC (14 years, 5 months ago) by gross

Problem in Mesh_findMatchingFaces.c fixed:
default tolerance in python interface was set too tight.

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Revision 855 - Directory Listing
Modified Fri Sep 22 09:30:06 2006 UTC (14 years, 7 months ago) by gross

some tests for triangle meshes added

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Revision 853 - Directory Listing
Modified Wed Sep 20 05:56:36 2006 UTC (14 years, 7 months ago) by gross

some performance problems wit openmp fixed.

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Revision 850 - Directory Listing
Modified Sun Sep 17 23:27:00 2006 UTC (14 years, 7 months ago) by gross

some problems with vtk writer fixed

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Revision 818 - Directory Listing
Modified Sun Aug 27 11:10:34 2006 UTC (14 years, 7 months ago) by dhawcroft

saveVTK fixes

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Revision 817 - Directory Listing
Modified Sat Aug 26 03:08:52 2006 UTC (14 years, 7 months ago) by ksteube

Can now compile and run with MPI on shake71

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Revision 812 - Directory Listing
Modified Thu Aug 17 05:49:59 2006 UTC (14 years, 8 months ago) by dhawcroft

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Revision 808 - Directory Listing
Modified Fri Aug 11 01:25:16 2006 UTC (14 years, 8 months ago) by ksteube

Can now build escript and use doxygen on shake71

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Revision 806 - Directory Listing
Modified Thu Aug 10 11:58:52 2006 UTC (14 years, 8 months ago) by gross

Interface to the direct solver library UMLPACK is no implemented.

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Revision 799 - Directory Listing
Modified Mon Aug 7 23:30:53 2006 UTC (14 years, 8 months ago) by ksteube

Moved a #pragma to modify the appropriate line

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Revision 798 - Directory Listing
Modified Fri Aug 4 01:05:36 2006 UTC (14 years, 8 months ago) by gross

Reimplementation of the assemblage with persistent jacobeans.
There are also a few changes to the tests which has now
dramatically reduced the memory demand.

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Revision 796 - Directory Listing
Modified Mon Jul 31 06:16:17 2006 UTC (14 years, 8 months ago) by dhawcroft

much faster parallel saveVTK
needs testers, don't be shy

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Revision 794 - Directory Listing
Modified Sun Jul 30 03:45:01 2006 UTC (14 years, 8 months ago) by dhawcroft

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Revision 793 - Directory Listing
Modified Sat Jul 29 19:40:22 2006 UTC (14 years, 8 months ago) by dhawcroft

Preliminary MPI version of saveVTK. Needs testers. Works for point data and should work for cell centered data.

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Revision 788 - Directory Listing
Modified Wed Jul 26 05:12:15 2006 UTC (14 years, 8 months ago) by bcumming

small corrections to code in previous commit, and some header files that
should have been included in the last commit.

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Revision 787 - Directory Listing
Modified Wed Jul 26 01:46:45 2006 UTC (14 years, 8 months ago) by bcumming

MPI update
Each element (normal elements, faceElements, ContactElements and points)
are now assigned a unique global id to streamline per-element
calculations and file IO of element data.

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Revision 783 - Directory Listing
Modified Tue Jul 18 01:32:50 2006 UTC (14 years, 9 months ago) by gross

coordinates, element size and normals returned by corresponding
FunctionSpace mesthods are now protected against updates. So 
+=, -=, *=, /=, setTaggedValue, fillFromNumArray will through an
excpetion.

The FunctionSpace class does nut buffer the oordinates, element size and
normals yet.

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Revision 782 - Directory Listing
Modified Tue Jul 18 00:47:47 2006 UTC (14 years, 9 months ago) by bcumming

Large number of changes to Finley for meshing in MPI.

- optimisation and neatening up of rectcanglular mesh generation code
- first and second order 1D, 2D and 3D rectangular meshes are now
  available in finley and escript using MPI.
- reduced meshes now generated in MPI, and interpolation to and from 
  reduced data types now supported.  

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Revision 781 - Directory Listing
Modified Fri Jul 14 08:47:38 2006 UTC (14 years, 9 months ago) by gross

grad functions linked into the persistent jacobean scheme

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Revision 779 - Directory Listing
Modified Fri Jul 14 07:41:31 2006 UTC (14 years, 9 months ago) by woo409

+ Updated compilation options for Cognac to squeeze out a bit more performance
+ Now compiles using the Intel Math headers (mathimf.h) rather than plain math.h on both Win32 and Linux platforms when using the Intel compiler. Gives a small boost to performance on Altix and is essential on Windows

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Revision 777 - Directory Listing
Modified Wed Jul 12 08:54:45 2006 UTC (14 years, 9 months ago) by gross

integration with persistent jacobeans is running now

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Revision 776 - Directory Listing
Modified Wed Jul 12 00:07:31 2006 UTC (14 years, 9 months ago) by gross

basic code for persistence of jacobeans added. routines are not called yet

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Revision 767 - Directory Listing
Modified Fri Jun 30 07:29:08 2006 UTC (14 years, 9 months ago) by gross

new FunctionSpace method setTags added

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Revision 765 - Directory Listing
Modified Fri Jun 30 06:37:11 2006 UTC (14 years, 9 months ago) by gross

The test for the contact normal has been modified to take in cosideration the fact that the normal is unique up to the factor +/-1. 
Now the test checks the kllength of the normal for 1 and the angle to the reference normal.

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Revision 763 - Directory Listing
Modified Fri Jun 30 05:52:31 2006 UTC (14 years, 9 months ago) by gross

some modification in the element reordering which should solve some problems 
caused by the fact that qsort may handels == items differently on different platform.

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Revision 759 - Directory Listing
Modified Thu Jun 29 01:53:23 2006 UTC (14 years, 9 months ago) by bcumming

- added directory pythonMPI to the source tree. this directory contains
  the c++ wrapper that is used to run python scripts in parallel for the
  MPI version of escript/finley
- updated the SConstruct and ./scons/ess_options.py for conditional MPI
  compilation. To compile the MPI version on ESS uncomment the #define
  PASO_MPI in ./paso/src/Paso.h and add the command line option
  useMPI=yes when running scons.
- fixed a compile time error in the MPI build in  
  finley/src/CPPAdapter/MeshAdapterFactory.cpp 
     

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Revision 757 - Directory Listing
Modified Mon Jun 26 13:12:56 2006 UTC (14 years, 9 months ago) by woo409

+ Merge of intelc_win32 branch (revision 741:755) with trunk. Tested on iVEC altix (run_tests and py_tests all pass)

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Revision 751 - Directory Listing
Modified Mon Jun 26 01:46:34 2006 UTC (14 years, 9 months ago) by bcumming

Changes relating to the MPI version of escript
The standard OpenMP version of escript is unchanged

- updated data types (Finley_Mesh, Finley_NodeFile, etc) to store meshes
  over multiple MPI processes.
- added CommBuffer code in Paso for communication of Data associated
  with distributed meshes
- updates in Finley and Escript to support distributed data and operations
  on distributed data (such as interpolation).
- construction of RHS in MPI, so that simple explicit schemes (such as
  /docs/examples/wave.py without IO and the Locator) can run in MPI.
- updated mesh generation for first order line, rectangle and brick
  meshes and second order line meshes in MPI.        
- small changes to trunk/SConstruct and trunk/scons/ess_options.py to
  build the MPI version, these changes are turned off by default.

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Revision 731 - Directory Listing
Modified Mon May 15 04:09:52 2006 UTC (14 years, 11 months ago) by bcumming

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Revision 730 - Directory Listing
Modified Mon May 15 04:03:49 2006 UTC (14 years, 11 months ago) by bcumming

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Revision 727 - Directory Listing
Modified Fri May 12 06:31:06 2006 UTC (14 years, 11 months ago) by gross

In case of an error in paso a seg fault occured. this was caused by
inproper deallocation of memory in this case. this problem is fixed now.

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Revision 707 - Directory Listing
Modified Wed Apr 12 23:58:02 2006 UTC (15 years ago) by gross

latex build documentation is working now

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Revision 700 - Directory Listing
Modified Thu Apr 6 00:13:40 2006 UTC (15 years ago) by gross

A few changes in the build mechanism and the file structure so scons can build release tar files:

  * paso/src/Solver has been moved to paso/src 
  * all test_.py are now run_.py files and are assumed to be passing python tests. they can run by 
    scons py_tests and are part of the release test set
  * escript/py_src/test_ are moved to escript/test/python and are installed in to the build directory 
    (rather then the PYTHONPATH).
  * all py files in test/python which don't start with run_ or test_ are now 'local_py_tests'. they are installed i
    by not run automatically.
  * CppUnitTest is now treated as a escript module (against previous decisions).
  * scons realse builds nor tar/zip files with relvant source code (src and tests in seperate files)

the python tests don't pass yet due to path problems.

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Revision 687 - Directory Listing
Modified Mon Mar 27 22:17:32 2006 UTC (15 years ago) by gross

small fixes

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Revision 682 - Directory Listing
Modified Mon Mar 27 02:43:09 2006 UTC (15 years ago) by robwdcock

+ NEW BUILD SYSTEM

This commit contains the new build system with cross-platform support.
Most things work are before though you can have more control.

ENVIRONMENT settings have changed:
+ You no longer require LD_LIBRARY_PATH or PYTHONPATH to point to the
esysroot for building and testing performed via scons
+ ACcESS altix users: It is recommended you change your modules to load
the latest intel compiler and other libraries required by boost to match
the setup in svn (you can override). The correct modules are as follows

module load intel_cc.9.0.026
export
MODULEPATH=${MODULEPATH}:/data/raid2/toolspp4/modulefiles/gcc-3.3.6
module load boost/1.33.0/python-2.4.1
module load python/2.4.1
module load numarray/1.3.3

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Revision 626 - Directory Listing
Modified Thu Mar 23 02:16:36 2006 UTC (15 years, 1 month ago) by elspeth

Copyright information inserted

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Revision 618 - Directory Listing
Modified Wed Mar 22 04:02:38 2006 UTC (15 years, 1 month ago) by gross

mmio moced to paso

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Revision 616 - Directory Listing
Modified Wed Mar 22 02:46:56 2006 UTC (15 years, 1 month ago) by elspeth

Copyright added to more source files.

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Revision 584 - Directory Listing
Modified Thu Mar 9 23:03:38 2006 UTC (15 years, 1 month ago) by gross

eigenvalues: compiles and passes tests on altix now

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Revision 552 - Directory Listing
Modified Wed Feb 22 03:18:07 2006 UTC (15 years, 1 month ago) by gross

and more work on saving the element jacobians (please don;t look at the code)

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Revision 547 - Directory Listing
Modified Tue Feb 21 06:10:54 2006 UTC (15 years, 2 months ago) by gross

solution and reduced solution can have reference numbers now!

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Revision 532 - Directory Listing
Modified Wed Feb 15 09:45:53 2006 UTC (15 years, 2 months ago) by gross

first steps towards the reuse of the element jacobians

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Revision 484 - Directory Listing
Modified Thu Feb 2 02:12:08 2006 UTC (15 years, 2 months ago) by jgs

add remainder of includes to SConscript includes install

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Revision 481 - Directory Listing
Modified Wed Feb 1 05:57:50 2006 UTC (15 years, 2 months ago) by jgs

add mechanism to install .h files to inc directories
(still need to specify full lists of .h files to install)

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Revision 480 - Directory Listing
Modified Wed Feb 1 05:15:12 2006 UTC (15 years, 2 months ago) by jgs

rationalise #includes and forward declarations

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Revision 474 - Directory Listing
Modified Mon Jan 30 04:23:44 2006 UTC (15 years, 2 months ago) by jgs

restructure escript source tree
move src/Data/* -> src
remove inc
modify #includes and cpppath settings accordingly

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Revision 472 - Directory Listing
Modified Fri Jan 27 01:50:59 2006 UTC (15 years, 2 months ago) by jgs

rationalise all #includes

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Revision 471 - Directory Listing
Modified Fri Jan 27 01:33:02 2006 UTC (15 years, 2 months ago) by jgs

reorganise finley src tree to remove inc dir and src/finley directory

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Revision 468 - Directory Listing
Modified Wed Jan 25 06:50:39 2006 UTC (15 years, 2 months ago) by jgs

reorganised esysUtils to remove inc directory

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Revision 467 - Directory Listing
Modified Wed Jan 25 05:43:46 2006 UTC (15 years, 2 months ago) by jgs

adjustments to includes to allow for new paso src tree structure

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Revision 449 - Directory Listing
Modified Mon Jan 23 03:48:51 2006 UTC (15 years, 2 months ago) by jgs

finley source directories now merged into one directory: src/finley

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Revision 430 - Directory Listing
Modified Wed Jan 11 06:40:50 2006 UTC (15 years, 3 months ago) by gross

ILU has been replicated is called RILU (recursive ILU) now. ILU will now be reimplemented.

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Revision 425 - Directory Listing
Modified Tue Jan 10 04:10:39 2006 UTC (15 years, 3 months ago) by gross

The sparse solver can be called by paso now. 

the building has been change to reduce some code redundancy:
now all scons SCscripts are importing scons/esys_options.py which
imports platform specific settings. 

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Revision 416 - Directory Listing
Modified Wed Jan 4 05:38:35 2006 UTC (15 years, 3 months ago) by gross

changes in Paso have been worked in

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Revision 402 - Directory Listing
Modified Thu Dec 22 22:46:54 2005 UTC (15 years, 3 months ago) by gross

cut of for small values

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Revision 352 - Directory Listing
Modified Wed Dec 14 02:21:37 2005 UTC (15 years, 4 months ago) by jgs

turns out Install() targets should also be made Default()
targets if you want them to actually reliably work!

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Revision 288 - Directory Listing
Modified Fri Dec 2 01:55:04 2005 UTC (15 years, 4 months ago) by jgs

now automatically build unit tests as required based on dependencies
between unit tests and libraries

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Revision 277 - Directory Listing
Modified Wed Nov 30 04:52:39 2005 UTC (15 years, 4 months ago) by jgs

explicitly define dependencies between modules

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Revision 273 - Directory Listing
Modified Wed Nov 30 03:30:40 2005 UTC (15 years, 4 months ago) by gross

cast to float added. this avoids problems with very small values

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Revision 272 - Directory Listing
Modified Wed Nov 30 03:30:30 2005 UTC (15 years, 4 months ago) by gross

cast to float added. this avoids problems with very small coodinates.

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Revision 271 - Directory Listing
Modified Wed Nov 30 03:27:30 2005 UTC (15 years, 4 months ago) by gross

cast to float added. this avoids problems with very small values

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Revision 223 - Directory Listing
Modified Thu Nov 24 23:12:13 2005 UTC (15 years, 4 months ago) by jgs

pass in cc/cxx settings from config file

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Revision 204 - Directory Listing
Modified Wed Nov 23 04:43:51 2005 UTC (15 years, 4 months ago) by jgs

revised scons files to account for new finley source tree structure

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Revision 203 - Directory Listing
Modified Wed Nov 23 04:36:15 2005 UTC (15 years, 4 months ago) by jgs

adjust include file names to allow for new finley source tree structure

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Revision 202 - Directory Listing
Modified Wed Nov 23 04:18:39 2005 UTC (15 years, 4 months ago) by jgs

scons builds will now take place in parallel "finley" src dir

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Revision 201 - Directory Listing
Modified Wed Nov 23 04:10:21 2005 UTC (15 years, 4 months ago) by jgs

copy finleyC and CPPAdapter to finley and finley/CPPAdapter to
facilitate scons builds

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Revision 192 - Directory Listing
Modified Mon Nov 21 04:52:14 2005 UTC (15 years, 5 months ago) by jgs

pass in top level install directory for finley/escript/bruce/paso
libraries when building via top level scons script

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Revision 191 - Directory Listing
Modified Mon Nov 21 04:10:12 2005 UTC (15 years, 5 months ago) by jgs

push platform dependent compiler flags and include directories up to library level scons files - these will eventually be brought in from external config files

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Revision 190 - Directory Listing
Modified Mon Nov 21 03:27:42 2005 UTC (15 years, 5 months ago) by jgs

pass in value for esysroot and use this to determine include file locations

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Revision 188 - Directory Listing
Modified Mon Nov 21 01:20:26 2005 UTC (15 years, 5 months ago) by jgs

explicitly add -fpic option to all compiler options lists
to ensure relocatable code is generated

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Revision 182 - Directory Listing
Modified Fri Nov 18 05:07:36 2005 UTC (15 years, 5 months ago) by jgs

first draft of config/construct files for finleyC/finleycpp libraries

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Revision 155 - Directory Listing
Modified Wed Nov 9 02:02:19 2005 UTC (15 years, 5 months ago) by jgs

move all directories from trunk/esys2 into trunk and remove esys2

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Revision 153 - Directory Listing
Modified Tue Oct 25 01:51:20 2005 UTC (15 years, 5 months ago) by jgs
Original Path: trunk/esys2/finley/src

Merge of development branch dev-02 back to main trunk on 2005-10-25

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Revision 150 - Directory Listing
Modified Thu Sep 15 03:44:45 2005 UTC (15 years, 7 months ago) by jgs
Original Path: trunk/esys2/finley/src

Merge of development branch dev-02 back to main trunk on 2005-09-15

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Revision 149 - Directory Listing
Modified Thu Sep 1 03:31:39 2005 UTC (15 years, 7 months ago) by jgs
Original Path: trunk/esys2/finley/src

Merge of development branch dev-02 back to main trunk on 2005-09-01

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Revision 148 - Directory Listing
Modified Tue Aug 23 01:24:31 2005 UTC (15 years, 8 months ago) by jgs
Original Path: trunk/esys2/finley/src

Merge of development branch dev-02 back to main trunk on 2005-08-23

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Revision 147 - Directory Listing
Modified Fri Aug 12 01:45:47 2005 UTC (15 years, 8 months ago) by jgs
Original Path: trunk/esys2/finley/src

erge of development branch dev-02 back to main trunk on 2005-08-12

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Revision 126 - Directory Listing
Modified Fri Jul 22 03:53:08 2005 UTC (15 years, 9 months ago) by jgs
Original Path: trunk/esys2/finley/src

Merge of development branch back to main trunk on 2005-07-22

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Revision 123 - Directory Listing
Modified Fri Jul 8 04:08:13 2005 UTC (15 years, 9 months ago) by jgs
Original Path: trunk/esys2/finley/src

Merge of development branch back to main trunk on 2005-07-08

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Revision 122 - Directory Listing
Modified Thu Jun 9 05:38:05 2005 UTC (15 years, 10 months ago) by jgs
Original Path: trunk/esys2/finley/src

Merge of development branch back to main trunk on 2005-06-09

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Revision 121 - Directory Listing
Modified Fri May 6 04:26:16 2005 UTC (15 years, 11 months ago) by jgs
Original Path: trunk/esys2/finley/src

Merge of development branch back to main trunk on 2005-05-06

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Revision 117 - Directory Listing
Modified Fri Apr 1 05:48:57 2005 UTC (16 years ago) by jgs
Original Path: trunk/esys2/finley/src

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Revision 115 - Directory Listing
Modified Fri Mar 4 07:12:47 2005 UTC (16 years, 1 month ago) by jgs
Original Path: trunk/esys2/finley/src

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Revision 113 - Directory Listing
Modified Mon Feb 28 07:06:33 2005 UTC (16 years, 1 month ago) by jgs
Original Path: trunk/esys2/finley/src

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Revision 110 - Directory Listing
Modified Mon Feb 14 04:14:42 2005 UTC (16 years, 2 months ago) by jgs
Original Path: trunk/esys2/finley/src

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Revision 108 - Directory Listing
Modified Thu Jan 27 06:21:59 2005 UTC (16 years, 2 months ago) by jgs
Original Path: trunk/esys2/finley/src

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Revision 104 - Directory Listing
Modified Fri Dec 17 07:43:12 2004 UTC (16 years, 4 months ago) by jgs
Original Path: trunk/esys2/finley/src

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Revision 102 - Directory Listing
Modified Wed Dec 15 07:08:39 2004 UTC (16 years, 4 months ago) by jgs
Original Path: trunk/esys2/finley/src

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Revision 100 - Directory Listing
Modified Wed Dec 15 03:48:48 2004 UTC (16 years, 4 months ago) by jgs
Original Path: trunk/esys2/finley/src

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Revision 97 - Directory Listing
Modified Tue Dec 14 05:39:33 2004 UTC (16 years, 4 months ago) by jgs
Original Path: trunk/esys2/finley/src

*** empty log message ***

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Revision 82 - Directory Listing
Added Tue Oct 26 06:53:54 2004 UTC (16 years, 5 months ago) by jgs
Original Path: trunk/esys2/finley/src

Initial revision