[escript] Log of /branches/newcdf

Revision 5415 - Directory Listing
Modified Tue Dec 23 23:31:47 2014 UTC (4 years, 2 months ago) by jfenwick
Copied from: trunk revision 5414

For experiments with the new netcdf

Revision 5414 - Directory Listing
Modified Tue Dec 23 07:53:35 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Bump version to allow experiments to not clash

Revision 5413 - Directory Listing
Modified Tue Dec 23 07:17:43 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

First steps towards python3 packages.
Problems still to be resolved:
  doesn't remove cleanly (esys/__init__.pyc is created)

Need to test interactions between the new packages and the old package

Revision 5412 - Directory Listing
Modified Mon Dec 22 06:40:31 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Adding options files for jessie

Revision 5411 - Directory Listing
Modified Mon Dec 22 01:39:10 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Fixed py3 matplotlib detection. Converted a division for py3

Revision 5410 - Directory Listing
Modified Sun Dec 21 23:24:54 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Switching versions back to development and using a single reference file for version and date.

Revision 5408 - Directory Listing
Modified Thu Dec 18 03:54:12 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

fixing stuff

Revision 5407 - Directory Listing
Modified Thu Dec 18 02:48:24 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

release changes

Revision 5404 - Directory Listing
Modified Thu Dec 18 00:10:22 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

Disabled OMP binding by default because it interfers with mpi binding
- threads were all running on one core on guineapig.

Revision 5403 - Directory Listing
Modified Wed Dec 17 08:24:44 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

no need to bind procs on guineapig

Revision 5402 - Directory Listing
Modified Wed Dec 17 05:44:00 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

True location of runMPIProgram

Revision 5401 - Directory Listing
Modified Wed Dec 17 04:09:16 2014 UTC (4 years, 2 months ago) by jduplessis
Original Path: trunk

mpirank added

Revision 5400 - Directory Listing
Modified Wed Dec 17 02:59:38 2014 UTC (4 years, 2 months ago) by jduplessis
Original Path: trunk

added unlink

Revision 5399 - Directory Listing
Modified Wed Dec 17 02:53:58 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

commented obsolete test.

Revision 5398 - Directory Listing
Modified Wed Dec 17 02:51:41 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

#$@!#@$ typo

Revision 5397 - Directory Listing
Modified Wed Dec 17 01:35:43 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

new, single interface to gmsh in escriptcore used by pycad and downunder.

Revision 5394 - Directory Listing
Modified Wed Dec 17 00:11:29 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

made pycad tests accept some whitespace differences

Revision 5392 - Directory Listing
Modified Tue Dec 16 07:01:26 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

formatting fixes in gmsh design.

Revision 5391 - Directory Listing
Modified Tue Dec 16 06:59:58 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

report gmshpy availability

Revision 5384 - Directory Listing
Modified Tue Dec 16 01:33:35 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

added commented setOrderN() call to gmshpy.

Revision 5383 - Directory Listing
Modified Tue Dec 16 00:44:47 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

replacing dcresistivity gmsh runner with pycads

Revision 5382 - Directory Listing
Modified Tue Dec 16 00:42:01 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

fix for exit status being destroyed in serial gmsh execution

Revision 5381 - Directory Listing
Modified Tue Dec 16 00:40:47 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

simple fix for dudley's finley dependency

Revision 5378 - Directory Listing
Modified Mon Dec 15 23:48:54 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Adding boostrandom to requirements

Revision 5377 - Directory Listing
Modified Mon Dec 15 23:35:27 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Updating debian changelog

Revision 5376 - Directory Listing
Modified Mon Dec 15 23:20:01 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Broadening tolerance for utopic version

Revision 5375 - Directory Listing
Modified Mon Dec 15 23:16:39 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

removing mixed tabs and spaces for python3

Revision 5374 - Directory Listing
Modified Mon Dec 15 06:10:16 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

updated raijin options file.

Revision 5373 - Directory Listing
Modified Mon Dec 15 06:09:58 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

Fixing OMP build with icc13 on raijin.

Revision 5372 - Directory Listing
Modified Mon Dec 15 05:48:55 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

removing parallel section on map inserts

Revision 5371 - Directory Listing
Modified Mon Dec 15 05:46:14 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Adding subst for utopic

Revision 5370 - Directory Listing
Modified Mon Dec 15 05:25:42 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Fix debian rules to account for different way to generate run-escript

Revision 5369 - Directory Listing
Modified Mon Dec 15 04:23:38 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Fixing getsubst for long past directory move.
Also removing obsolete releases.

Revision 5368 - Directory Listing
Modified Mon Dec 15 04:04:51 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

Added commented changes so they don't get lost.

Revision 5367 - Directory Listing
Modified Mon Dec 15 04:02:21 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

Undoing parts of r5363 until tests reflect the change.

Revision 5366 - Directory Listing
Modified Mon Dec 15 03:51:02 2014 UTC (4 years, 2 months ago) by jduplessis
Original Path: trunk

fixed naming conventions + comments

Revision 5365 - Directory Listing
Modified Mon Dec 15 01:46:14 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

mara options.

Revision 5364 - Directory Listing
Modified Mon Dec 15 01:45:43 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

Fixed Voxet origin which refers to cell centre in Voxet lingo.

Revision 5363 - Directory Listing
Modified Mon Dec 15 01:45:09 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

Added 'pressure at 0' option to Isostatic Pressure calculation.

Revision 5362 - Directory Listing
Modified Mon Dec 15 01:36:27 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

making DipoleDipole test more tolerant to cope with gmsh's filthy non-deterministic seeding by output filename

Revision 5361 - Directory Listing
Modified Mon Dec 15 00:53:41 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Partial better fix for natgrid problem

Revision 5360 - Directory Listing
Modified Sun Dec 14 23:57:33 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

fixing sillyness from my previous commit

Revision 5359 - Directory Listing
Modified Sun Dec 14 23:17:37 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

making dcforward tests more verbose when failing

Revision 5358 - Directory Listing
Modified Fri Dec 12 06:25:52 2014 UTC (4 years, 2 months ago) by jduplessis
Original Path: trunk

removed debug

Revision 5357 - Directory Listing
Modified Fri Dec 12 06:09:59 2014 UTC (4 years, 2 months ago) by jduplessis
Original Path: trunk

faster test

Revision 5356 - Directory Listing
Modified Fri Dec 12 04:04:33 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

guineapig intel options files.

Revision 5355 - Directory Listing
Modified Fri Dec 12 03:57:25 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

New options file for openSuse. Add natgridchecking for openSuse

Revision 5354 - Directory Listing
Modified Fri Dec 12 03:36:34 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Install guide fixes

Revision 5353 - Directory Listing
Modified Fri Dec 12 03:22:41 2014 UTC (4 years, 2 months ago) by jduplessis
Original Path: trunk

adding dc_forward example

Revision 5352 - Directory Listing
Modified Fri Dec 12 03:13:14 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Adding new fedora. removing old ones

Revision 5351 - Directory Listing
Modified Fri Dec 12 03:06:55 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

removing some old templates. updating the centos one

Revision 5350 - Directory Listing
Modified Fri Dec 12 03:00:37 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

updating reference meshes to take into account first-tag method

Revision 5349 - Directory Listing
Modified Fri Dec 12 01:32:05 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

more informative skip messages, first tagged element applies for readgmsh instead of last

Revision 5348 - Directory Listing
Modified Fri Dec 12 01:04:31 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

replacing mixed tabs with spaces

Revision 5347 - Directory Listing
Modified Fri Dec 12 01:01:27 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Check if pyproj is available before running example

Revision 5346 - Directory Listing
Modified Thu Dec 11 23:55:13 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

fixing more cases of indexing empty vectors

Revision 5345 - Directory Listing
Modified Thu Dec 11 23:25:08 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

updating reference meshes

Revision 5344 - Directory Listing
Modified Thu Dec 11 23:01:16 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

fixing non-mpi builds

Revision 5343 - Directory Listing
Modified Thu Dec 11 08:21:01 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

some fixes for the new node tagging from gmshreader

Revision 5342 - Directory Listing
Modified Thu Dec 11 03:56:23 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

fixes to readGmsh off-by-one

Revision 5341 - Directory Listing
Modified Thu Dec 11 03:20:36 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

fixing some indexing into empty vectors, related to #291

Revision 5340 - Directory Listing
Modified Thu Dec 11 00:24:58 2014 UTC (4 years, 2 months ago) by jduplessis
Original Path: trunk

updated tags in fly files

Revision 5339 - Directory Listing
Modified Thu Dec 11 00:08:58 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

added an exception for trying to set an escript param that doesn't exist

Revision 5338 - Directory Listing
Modified Wed Dec 10 07:03:24 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

fix for gmsh permissive use of scoped i

Revision 5337 - Directory Listing
Modified Wed Dec 10 05:58:33 2014 UTC (4 years, 2 months ago) by jduplessis
Original Path: trunk

added a nodeid map so that node id's can be used to index the node arrays such as the tag array

Revision 5336 - Directory Listing
Modified Wed Dec 10 05:23:51 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Making params more visible

Revision 5335 - Directory Listing
Modified Wed Dec 10 05:22:27 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

install guide culling

Revision 5334 - Directory Listing
Modified Wed Dec 10 04:10:41 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

more finley test cleanup

Revision 5333 - Directory Listing
Modified Wed Dec 10 02:53:03 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

some more readGmsh cleaning

Revision 5332 - Directory Listing
Modified Wed Dec 10 01:49:15 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

readability cleanup on readGmsh

Revision 5331 - Directory Listing
Modified Wed Dec 10 01:13:34 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Disabling gmshpy until after the release

Revision 5330 - Directory Listing
Modified Wed Dec 10 00:20:05 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Use gmshpy for preference

Revision 5329 - Directory Listing
Modified Tue Dec 9 23:44:48 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Not sure how I missed this one

Revision 5328 - Directory Listing
Modified Tue Dec 9 06:34:08 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

removing unused test file

Revision 5327 - Directory Listing
Modified Tue Dec 9 06:32:11 2014 UTC (4 years, 2 months ago) by jduplessis
Original Path: trunk

fixed continuousFunction mesh tagging

Revision 5326 - Directory Listing
Modified Tue Dec 9 05:04:34 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

reinstating old dudley tests that weren't properly being tested due to constructor problems

Revision 5325 - Directory Listing
Modified Tue Dec 9 04:53:14 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

9000 less tests are skipped, partly removing skips, partly removing duplicate test file

Revision 5324 - Directory Listing
Modified Tue Dec 9 04:43:02 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

fixing python 3 dealing badly with str(generators)

Revision 5323 - Directory Listing
Modified Tue Dec 9 04:01:35 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

fixing another sillyness with import errors

Revision 5322 - Directory Listing
Modified Tue Dec 9 03:53:35 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Added NETCDF_BUILD to escript params. Tests now check this before testing netcdf dependent stuff

Revision 5321 - Directory Listing
Modified Tue Dec 9 03:27:32 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

adding omitted 3D diracdelta interpolation tests

Revision 5320 - Directory Listing
Modified Tue Dec 9 01:39:46 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

new EscriptParam GMSH_SUPPORT and GMSH_MPI for use in python-land, included associated exceptions in DCRes gmsh use and assocaiated skips in relevant tests

Revision 5319 - Directory Listing
Modified Tue Dec 9 00:58:32 2014 UTC (4 years, 2 months ago) by jduplessis
Original Path: trunk

small changes to indentation etc

Revision 5318 - Directory Listing
Modified Tue Dec 9 00:37:06 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

change of speckleys test to match speckleys name

Revision 5317 - Directory Listing
Modified Tue Dec 9 00:36:08 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

speckley and ripley can now interpolate from DiracDeltaFunctions to ContinuousFunction

Revision 5316 - Directory Listing
Modified Mon Dec 8 06:30:49 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

better cleanup of dcres tempfiles

Revision 5315 - Directory Listing
Modified Mon Dec 8 05:08:54 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

resistivity style fixes for consistency, adding skips for non-finley builds

Revision 5314 - Directory Listing
Modified Mon Dec 8 04:28:28 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Trying again to fix this without messing up mpi

Revision 5313 - Directory Listing
Modified Mon Dec 8 04:03:52 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Hide unused mpit thing from non-mpi

Revision 5312 - Directory Listing
Modified Mon Dec 8 00:44:04 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Added 10.10 homebrew template

Revision 5311 - Directory Listing
Modified Mon Dec 8 00:35:45 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Adding 10.10 mp template

Revision 5310 - Directory Listing
Modified Mon Dec 8 00:10:01 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

slurm runner for savanna.

Revision 5309 - Directory Listing
Modified Mon Dec 8 00:08:32 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

catching other case of domainGenerator tests failing

Revision 5308 - Directory Listing
Modified Fri Dec 5 04:58:53 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

more silly importerror fixes in tests

Revision 5307 - Directory Listing
Modified Fri Dec 5 04:30:05 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

fixing inverted boolean for ripley presence

Revision 5306 - Directory Listing
Modified Fri Dec 5 01:49:46 2014 UTC (4 years, 2 months ago) by jduplessis
Original Path: trunk

added skip if gmsh missing

Revision 5305 - Directory Listing
Modified Thu Dec 4 06:48:39 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

This looks like unintended by the last commit.

Revision 5304 - Directory Listing
Modified Thu Dec 4 06:29:13 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

make MPI build work again.

Revision 5303 - Directory Listing
Modified Thu Dec 4 06:17:11 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Changes to keep clang happy

Revision 5301 - Directory Listing
Modified Thu Dec 4 05:58:49 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

A lil' bit more meat in ripley.

Revision 5300 - Directory Listing
Modified Thu Dec 4 05:44:25 2014 UTC (4 years, 2 months ago) by jduplessis
Original Path: trunk

added missing init

Revision 5299 - Directory Listing
Modified Thu Dec 4 04:07:23 2014 UTC (4 years, 2 months ago) by jduplessis
Original Path: trunk

all classes tested, documentation and small fixes to follow

Revision 5298 - Directory Listing
Modified Thu Dec 4 02:54:50 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

Doco updates.

Revision 5297 - Directory Listing
Modified Thu Dec 4 01:58:53 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

More user doco updates.

Revision 5296 - Directory Listing
Modified Wed Dec 3 07:22:17 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

More updates to user doc.

Revision 5295 - Directory Listing
Modified Wed Dec 3 05:35:28 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

fixed undef error and some content.

Revision 5294 - Directory Listing
Modified Wed Dec 3 05:30:18 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

working around oddness when catching ImportErrors after catching a propagated ImportError, cleaning up last of finley examples without domain checks

Revision 5293 - Directory Listing
Modified Wed Dec 3 04:28:17 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

added missing copyright headers in user guide plus fixed minor typo.

Revision 5292 - Directory Listing
Modified Wed Dec 3 04:08:14 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

more corrections to tests

Revision 5291 - Directory Listing
Modified Wed Dec 3 03:55:26 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

version number hack to allow older versions to run

Revision 5290 - Directory Listing
Modified Wed Dec 3 01:15:33 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

fixing some broken imports from earlier commit

Revision 5289 - Directory Listing
Modified Tue Dec 2 23:43:22 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

updating hamster options

Revision 5288 - Directory Listing
Modified Tue Dec 2 23:18:40 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

fixing tests for cases where required domains not built

Revision 5287 - Directory Listing
Modified Tue Dec 2 05:36:36 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Fix for bug#284. Added dummify=False to lambdify calls.

Revision 5286 - Directory Listing
Modified Tue Dec 2 03:45:09 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

removed obsolete (?) tests...

Revision 5285 - Directory Listing
Modified Tue Dec 2 00:52:50 2014 UTC (4 years, 2 months ago) by jfenwick
Original Path: trunk

Fixed array overflow issue#285

Revision 5284 - Directory Listing
Modified Tue Dec 2 00:44:49 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

Lame is now accented in user doc where appropriate

Revision 5283 - Directory Listing
Modified Fri Nov 28 05:38:33 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

updating older templates with v202 options

Revision 5282 - Directory Listing
Modified Fri Nov 28 04:04:10 2014 UTC (4 years, 2 months ago) by jduplessis
Original Path: trunk

dcres inversions won't be added yet

Revision 5281 - Directory Listing
Modified Fri Nov 28 02:43:30 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

updating current dev list, should probably add Ralf for DCres too

Revision 5280 - Directory Listing
Modified Fri Nov 28 02:23:08 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

adding initial 4.0 changelog

Revision 5279 - Directory Listing
Modified Thu Nov 27 00:26:18 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

adding ripley and speckley to user guide, a bit barebones still

Revision 5278 - Directory Listing
Modified Thu Nov 27 00:25:49 2014 UTC (4 years, 2 months ago) by sshaw
Original Path: trunk

sphinxifying older style python doco, including order shifting of module doc

Revision 5277 - Directory Listing
Modified Mon Nov 24 03:29:15 2014 UTC (4 years, 2 months ago) by caltinay
Original Path: trunk

added missing cpus-per-rank option for OpenMPI

Revision 5276 - Directory Listing
Modified Fri Nov 21 04:27:37 2014 UTC (4 years, 3 months ago) by jduplessis
Original Path: trunk

fixed pole-pole gradient

Revision 5275 - Directory Listing
Modified Thu Nov 20 01:27:04 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

Fixed problem introduced earlier.

Revision 5274 - Directory Listing
Modified Wed Nov 19 03:44:48 2014 UTC (4 years, 3 months ago) by sshaw
Original Path: trunk

python3ifying division in downunder, stripping some debug prints

Revision 5273 - Directory Listing
Modified Tue Nov 18 01:08:29 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

fixing some intel warnings.

Revision 5272 - Directory Listing
Modified Tue Nov 18 00:56:54 2014 UTC (4 years, 3 months ago) by sshaw
Original Path: trunk

adding coupler doco, adjusting sphinx to use a math extension to deal with many warnings

Revision 5271 - Directory Listing
Modified Tue Nov 18 00:46:29 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

Re-enabled process binding params for OpenMPI. Not sure if this is a good default though...

Revision 5270 - Directory Listing
Modified Tue Nov 18 00:26:31 2014 UTC (4 years, 3 months ago) by jduplessis
Original Path: trunk

fixed extra brace

Revision 5269 - Directory Listing
Modified Mon Nov 17 23:17:34 2014 UTC (4 years, 3 months ago) by sshaw
Original Path: trunk

removing early return in copuler test

Revision 5268 - Directory Listing
Modified Mon Nov 17 07:10:40 2014 UTC (4 years, 3 months ago) by sshaw
Original Path: trunk

completed speckley->ripley interpolation across multi-axial subdivisions

Revision 5267 - Directory Listing
Modified Mon Nov 17 06:48:27 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

template is not executable...

Revision 5266 - Directory Listing
Modified Mon Nov 17 06:45:01 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

New options 'launcher', 'prelaunch' and 'postlaunch'.
The idea is to avoid system/env-specific hacks to run-escript and provide
a means to configure launchers (i.e. mpirun and friends) at build-time.
Thus bin/run-escript now lives as a template run-escript.in and the actual
launcher is created using the above options when running scons.
Technically not much should have changed as I have tried to set the defaults
to what they were in the original launcher.

Only wheezy_options updated so far until I get feedback...

Revision 5265 - Directory Listing
Modified Mon Nov 17 04:59:25 2014 UTC (4 years, 3 months ago) by jfenwick
Original Path: trunk

Adding missing include which clang noticed.

Revision 5264 - Directory Listing
Modified Mon Nov 17 03:04:10 2014 UTC (4 years, 3 months ago) by sshaw
Original Path: trunk

python3ifying xrange calls

Revision 5263 - Directory Listing
Modified Sun Nov 16 23:35:59 2014 UTC (4 years, 3 months ago) by sshaw
Original Path: trunk

python3ifying prints

Revision 5262 - Directory Listing
Modified Thu Nov 13 08:11:40 2014 UTC (4 years, 3 months ago) by gross
Original Path: trunk

Some fixes to the dcresitivity forward model. simple test added.

Revision 5261 - Directory Listing
Modified Thu Nov 13 04:40:28 2014 UTC (4 years, 3 months ago) by jfenwick
Original Path: trunk

uint ->unsigned int;  using namespace std in speckly Rectangle to allow isnan to work.

Revision 5260 - Directory Listing
Modified Wed Nov 12 05:19:36 2014 UTC (4 years, 3 months ago) by jduplessis
Original Path: trunk

changed to primary potential as an input

Revision 5259 - Directory Listing
Modified Wed Nov 12 01:20:34 2014 UTC (4 years, 3 months ago) by jfenwick
Original Path: trunk

fixed error which I did not know about

Revision 5258 - Directory Listing
Modified Tue Nov 11 04:29:54 2014 UTC (4 years, 3 months ago) by sshaw
Original Path: trunk

replacing a sleep with an MPIbarrier because it's much, much faster in block testing

Revision 5257 - Directory Listing
Modified Tue Nov 11 04:11:28 2014 UTC (4 years, 3 months ago) by sshaw
Original Path: trunk

added a flush and delay to fix race conditions hiding testing summaries from rank zero

Revision 5256 - Directory Listing
Modified Tue Nov 11 03:18:41 2014 UTC (4 years, 3 months ago) by jfenwick
Original Path: trunk

Doesn't work yet but getting some subworld changes in.

Revision 5255 - Directory Listing
Modified Tue Nov 11 01:55:44 2014 UTC (4 years, 3 months ago) by sshaw
Original Path: trunk

adding support for biaxial MPI subdivision for speckly->ripley coupler

Revision 5254 - Directory Listing
Modified Mon Nov 10 09:30:53 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

Fixed indexing of dirac point data while assembling PDE in ripley.

Revision 5253 - Directory Listing
Modified Mon Nov 10 07:07:34 2014 UTC (4 years, 3 months ago) by gross
Original Path: trunk

some work on the DcRes

Revision 5252 - Directory Listing
Modified Mon Nov 10 05:01:31 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

update of other template options files.

Revision 5251 - Directory Listing
Modified Mon Nov 10 04:34:39 2014 UTC (4 years, 3 months ago) by gross
Original Path: trunk

Ricker support velocity outout

Revision 5250 - Directory Listing
Modified Mon Nov 10 04:05:11 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

Updated wheezy template options file and made our rodents import from there.
Had to rename scons/os -> scons/templates to avoid import conflicts.
Removed obsolete option vsl_random and added new options.
Other templates are yet to be updated.

Revision 5249 - Directory Listing
Modified Mon Nov 10 00:47:47 2014 UTC (4 years, 3 months ago) by jduplessis
Original Path: trunk

further name changes

Revision 5248 - Directory Listing
Modified Mon Nov 10 00:37:31 2014 UTC (4 years, 3 months ago) by jduplessis
Original Path: trunk

debug and name changes

Revision 5247 - Directory Listing
Modified Fri Nov 7 02:44:08 2014 UTC (4 years, 3 months ago) by sshaw
Original Path: trunk

fixing non-MPI builds with couplers

Revision 5246 - Directory Listing
Modified Fri Nov 7 01:41:18 2014 UTC (4 years, 3 months ago) by sshaw
Original Path: trunk

adding speckley->ripley MPI Brick coupling for single axis subdivisions

Revision 5245 - Directory Listing
Modified Thu Nov 6 11:14:08 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

CPU optimizations for block size 1 symmetric spmv (DIA) which is now also
faster than non-symmetric on i7.

Revision 5244 - Directory Listing
Modified Thu Nov 6 11:03:58 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

block size 2 optimizations.

Revision 5243 - Directory Listing
Modified Thu Nov 6 10:09:23 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

Significant speed-up for symmetric spmv on CPU. This is now faster than
non-symmetric on i7.

Revision 5242 - Directory Listing
Modified Wed Nov 5 01:34:55 2014 UTC (4 years, 3 months ago) by jduplessis
Original Path: trunk

python 3 print

Revision 5241 - Directory Listing
Modified Tue Nov 4 06:47:42 2014 UTC (4 years, 3 months ago) by jduplessis
Original Path: trunk

non exponential mapping

Revision 5240 - Directory Listing
Modified Tue Nov 4 03:47:26 2014 UTC (4 years, 3 months ago) by sshaw
Original Path: trunk

adding options to record time and cycle number in silo and VTK files

Revision 5239 - Directory Listing
Modified Thu Oct 30 05:36:00 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

More cache-friendly version of CPU-based symmetric-CDS-SpMV for block sizes >2.

Revision 5238 - Directory Listing
Modified Wed Oct 29 05:26:36 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

block size 3 special case on GPU.

Revision 5237 - Directory Listing
Modified Wed Oct 29 04:28:59 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

-Enabled use of texture memory by default (needs config option).
-split symmetric spmv to separate file and added specialized version
for block size 2.

Revision 5236 - Directory Listing
Modified Wed Oct 29 03:19:11 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

well, this was embarrassing...

Revision 5235 - Directory Listing
Modified Wed Oct 29 01:01:44 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

Tweaks to the forward model tests and finally silenced all but rank 0
for unit test output. I don't think this will hide useful info as all
ranks should output the same thing by the TextTestRunner...

Revision 5234 - Directory Listing
Modified Wed Oct 29 00:54:43 2014 UTC (4 years, 3 months ago) by jduplessis
Original Path: trunk

commented out prints

Revision 5233 - Directory Listing
Modified Wed Oct 29 00:49:32 2014 UTC (4 years, 3 months ago) by jduplessis
Original Path: trunk

added changes for polepole models

Revision 5232 - Directory Listing
Modified Wed Oct 29 00:19:06 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

array of mu's should be float even if someone does [1,2].

Revision 5231 - Directory Listing
Modified Tue Oct 28 21:21:15 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

Skipping ripley SystemMatrix tests with >1 rank, some formatting and minor
changes.

Revision 5230 - Directory Listing
Modified Tue Oct 28 07:38:38 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

lowered tolerance so cusp BiCGSTAB solves to required accuracy by this test.

Revision 5229 - Directory Listing
Modified Mon Oct 27 23:39:15 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

build_dir->BUILD_DIR in testrunner

Revision 5228 - Directory Listing
Modified Mon Oct 27 23:31:46 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

updated UMFPACK def in places...

Revision 5227 - Directory Listing
Modified Mon Oct 27 06:09:03 2014 UTC (4 years, 3 months ago) by sshaw
Original Path: trunk

adding forgotten files

Revision 5226 - Directory Listing
Modified Mon Oct 27 05:04:07 2014 UTC (4 years, 3 months ago) by sshaw
Original Path: trunk

extending speckley->ripley interpolation to support MPI

Revision 5225 - Directory Listing
Modified Mon Oct 27 01:33:45 2014 UTC (4 years, 3 months ago) by caltinay
Original Path: trunk

dummy commit to see if submin is happy now.

Revision 5224 - Directory Listing
Modified Mon Oct 27 01:23:31 2014 UTC (4 years, 3 months ago) by jduplessis
Original Path: trunk

fixed issue with point elements

Revision 5223 - Directory Listing
Modified Fri Oct 24 04:34:07 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

Fixed CDS->CDS copy and implemented a kernel for symmetric spmv which is
currently not optimized and thus slow.

Revision 5222 - Directory Listing
Modified Fri Oct 24 04:29:46 2014 UTC (4 years, 4 months ago) by jduplessis
Original Path: trunk

getNumberOfDataPoints is a per rank operation

Revision 5221 - Directory Listing
Modified Thu Oct 23 04:01:49 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

Actually implement transposed SpMV for blocksizes >=3

Revision 5220 - Directory Listing
Modified Thu Oct 23 03:50:37 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

Fixes to CDS SpMV symmetric and tests for blocksizes 1-4 symm/non-symm.

Revision 5219 - Directory Listing
Modified Thu Oct 23 03:47:27 2014 UTC (4 years, 4 months ago) by jduplessis
Original Path: trunk

should now work with mpi

Revision 5218 - Directory Listing
Modified Thu Oct 23 00:37:38 2014 UTC (4 years, 4 months ago) by jduplessis
Original Path: trunk

debug removings

Revision 5217 - Directory Listing
Modified Thu Oct 23 00:18:44 2014 UTC (4 years, 4 months ago) by jduplessis
Original Path: trunk

further debug removings

Revision 5216 - Directory Listing
Modified Thu Oct 23 00:12:22 2014 UTC (4 years, 4 months ago) by jduplessis
Original Path: trunk

further removal of print statements

Revision 5215 - Directory Listing
Modified Thu Oct 23 00:10:19 2014 UTC (4 years, 4 months ago) by jduplessis
Original Path: trunk

fixed mpi version for when mesh does not exists and removed some print statements

Revision 5214 - Directory Listing
Modified Wed Oct 22 23:42:01 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

enable thrust/CUDA on guineapig for testing ripley SystemMatrix.

Revision 5213 - Directory Listing
Modified Wed Oct 22 05:59:37 2014 UTC (4 years, 4 months ago) by jduplessis
Original Path: trunk

nlpde example for user guide

Revision 5212 - Directory Listing
Modified Wed Oct 22 05:06:48 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

Preparing ripley SystemMatrix tests.

Revision 5211 - Directory Listing
Modified Wed Oct 22 04:26:03 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

fixed infinite loop in gmsh reader

Revision 5210 - Directory Listing
Modified Wed Oct 22 03:50:06 2014 UTC (4 years, 4 months ago) by jduplessis
Original Path: trunk

added copyright message

Revision 5209 - Directory Listing
Modified Tue Oct 21 06:50:20 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

Adding memory optimization for symmetric CDS matrices (in ripley).
Only main and upper diagonal blocks are now stored.
SpMV not updated on GPUs yet but we get a speed-up on Xeons.

Revision 5208 - Directory Listing
Modified Tue Oct 21 03:43:14 2014 UTC (4 years, 4 months ago) by jduplessis
Original Path: trunk

fixed may be unitialised error reworked code to add more openMpness

Revision 5207 - Directory Listing
Modified Tue Oct 21 00:51:22 2014 UTC (4 years, 4 months ago) by jduplessis
Original Path: trunk

fixed compiler errors

Revision 5206 - Directory Listing
Modified Mon Oct 20 06:59:57 2014 UTC (4 years, 4 months ago) by jduplessis
Original Path: trunk

working mpi version of readGmsh. tweaks and unit tests to come

Revision 5205 - Directory Listing
Modified Wed Oct 15 22:39:30 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

writeBinaryGrid should check for ReducedSolution as well since a
Projector returns a data object on that function space.

Revision 5204 - Directory Listing
Modified Tue Oct 14 22:33:56 2014 UTC (4 years, 4 months ago) by jduplessis
Original Path: trunk

removed debug print

Revision 5203 - Directory Listing
Modified Tue Oct 14 06:46:34 2014 UTC (4 years, 4 months ago) by jduplessis
Original Path: trunk

removed debug print statement

Revision 5202 - Directory Listing
Modified Mon Oct 13 00:53:00 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

comment debug output (py3 errors)

Revision 5201 - Directory Listing
Modified Fri Oct 10 06:23:03 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

fixing errors in speckley bricks node referencing in multidimensional subdivisions, fixes recent VTK failures

Revision 5200 - Directory Listing
Modified Thu Oct 9 05:18:45 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

removing prints from tests

Revision 5199 - Directory Listing
Modified Thu Oct 9 05:17:02 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

adjusting tests to allow for domain resizing under MPI

Revision 5198 - Directory Listing
Modified Wed Oct 8 08:28:35 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

fixed longstanding lazy test failures due to calling getDataRO() without
resolving Data object first (only in finley).

Revision 5197 - Directory Listing
Modified Wed Oct 8 04:41:15 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

allows absorption zones of zero size in seismic models

Revision 5196 - Directory Listing
Modified Tue Oct 7 02:00:59 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

more type changes/fixes.

Revision 5195 - Directory Listing
Modified Fri Oct 3 02:12:56 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

speckley: more informative functionspace errors for coupled interpolation, removed points from tagsinuse to match ripley

Revision 5194 - Directory Listing
Modified Thu Oct 2 06:36:02 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

Some more long-index work.

Revision 5193 - Directory Listing
Modified Thu Oct 2 06:19:08 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

adding test skip for couplers and multiprocess

Revision 5192 - Directory Listing
Modified Thu Oct 2 04:42:23 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

adding omitted copyright header

Revision 5191 - Directory Listing
Modified Thu Oct 2 04:40:20 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

adding speckley to ripley interpolation (single process only)

Revision 5190 - Directory Listing
Modified Thu Oct 2 01:15:32 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

removing accidentally included and incomplete cross domain work

Revision 5189 - Directory Listing
Modified Thu Oct 2 01:12:57 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

fixing badly behaved dirac points in speckley

Revision 5188 - Directory Listing
Modified Wed Oct 1 21:54:07 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

Fixed logic error.

Revision 5187 - Directory Listing
Modified Wed Oct 1 06:49:24 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

escript, paso, ripley now compiles with index type long.

Revision 5186 - Directory Listing
Modified Wed Oct 1 06:18:02 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

fixing misplaced dirac points in ripley domains with enormous elements

Revision 5184 - Directory Listing
Modified Wed Oct 1 04:19:22 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

New scons option 'domains' to build only specified domains.
Defaults to all. Implements #257

Revision 5183 - Directory Listing
Modified Tue Sep 30 05:55:37 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

More long-index work. Added scons option 'longindices'.
Parts will not compile yet if set to true.

Revision 5182 - Directory Listing
Modified Tue Sep 30 04:03:34 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

more work towards allowing non-int indices.

Revision 5181 - Directory Listing
Modified Tue Sep 30 01:42:49 2014 UTC (4 years, 4 months ago) by gross
Original Path: trunk

for buildbot testing

Revision 5180 - Directory Listing
Modified Thu Sep 25 11:25:29 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

Postpone closing netcdf file to avoid numpy segfault.

Revision 5179 - Directory Listing
Modified Thu Sep 25 07:18:20 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

Work towards allowing non-int index type.

Revision 5178 - Directory Listing
Modified Thu Sep 25 06:31:12 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

updated silo deps on guineapig.

Revision 5177 - Directory Listing
Modified Thu Sep 25 04:37:54 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

more speckley type cleanup (and unused function cleanup)

Revision 5176 - Directory Listing
Modified Thu Sep 25 04:36:28 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

fixes to wave models using wavelet acceleration instead of value

Revision 5175 - Directory Listing
Modified Thu Sep 25 03:58:06 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

some speckley type corrections

Revision 5174 - Directory Listing
Modified Thu Sep 25 01:45:59 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

Report number of matrix entries if verbosity is on.

Revision 5173 - Directory Listing
Modified Thu Sep 25 01:04:26 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

fixing a sillyness in speckley dirac point assignment

Revision 5172 - Directory Listing
Modified Wed Sep 24 06:59:22 2014 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

Implemented writeBinaryGrid for Solution (DegreesOfFreedom). Fixes #280

Revision 5171 - Directory Listing
Modified Wed Sep 24 06:57:33 2014 UTC (4 years, 4 months ago) by sshaw
Original Path: trunk

removing leftover dummy test

Revision 5170 - Directory Listing
Modified Wed Sep 24 00:30:39 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

fixing bug in multi-process speckley with dirac points, some test cleanup

Revision 5169 - Directory Listing
Modified Mon Sep 22 08:46:58 2014 UTC (4 years, 5 months ago) by gross
Original Path: trunk

tIsostaticPressure testing added

Revision 5168 - Directory Listing
Modified Mon Sep 22 05:22:06 2014 UTC (4 years, 5 months ago) by jduplessis
Original Path: trunk

changed version number

Revision 5167 - Directory Listing
Modified Thu Sep 18 04:04:33 2014 UTC (4 years, 5 months ago) by caltinay
Original Path: trunk

updated mole options file.

Revision 5166 - Directory Listing
Modified Wed Sep 17 21:44:41 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

added missed test files

Revision 5165 - Directory Listing
Modified Wed Sep 17 11:40:57 2014 UTC (4 years, 5 months ago) by caltinay
Original Path: trunk

savanna: removed ipo to speed up linking, moved to new intel 15 tool chain,
removed umfpack dependency since we are using MKL.

Revision 5164 - Directory Listing
Modified Wed Sep 17 11:26:09 2014 UTC (4 years, 5 months ago) by caltinay
Original Path: trunk

Slightly better error reporting from CUDA.

Revision 5163 - Directory Listing
Modified Wed Sep 17 08:56:09 2014 UTC (4 years, 5 months ago) by gross
Original Path: trunk

subsidence forward model and testing added

Revision 5162 - Directory Listing
Modified Wed Sep 17 06:38:15 2014 UTC (4 years, 5 months ago) by caltinay
Original Path: trunk

added missing guards

Revision 5161 - Directory Listing
Modified Wed Sep 17 06:37:39 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

fixing odd crashes in speckley saving to silo

Revision 5160 - Directory Listing
Modified Wed Sep 17 05:20:34 2014 UTC (4 years, 5 months ago) by caltinay
Original Path: trunk

Commit 2/2 - .cpp -> .cu

Revision 5159 - Directory Listing
Modified Wed Sep 17 05:19:56 2014 UTC (4 years, 5 months ago) by caltinay
Original Path: trunk

cusp requires thrust which is unlikely to be installed without the CUDA tk.
-> decided to remove cusp-based solvers/matrices for non-CUDA builds.
Commit 1/2 (svn rejects type change in single commit)

Revision 5158 - Directory Listing
Modified Wed Sep 17 04:33:42 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

removed vestigal FunctionOnBoundary and reduced functionspaces from speckley

Revision 5157 - Directory Listing
Modified Wed Sep 17 01:02:58 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

fixing non-MPI builds of speckley

Revision 5156 - Directory Listing
Modified Wed Sep 17 00:40:33 2014 UTC (4 years, 5 months ago) by caltinay
Original Path: trunk

intel 15 doesn't like this.

Revision 5155 - Directory Listing
Modified Tue Sep 16 04:21:15 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

stripping out some leftover commented debug from previous commit

Revision 5154 - Directory Listing
Modified Tue Sep 16 04:19:03 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

updating speckley binary grid reads to interpolate all missing quad points

Revision 5153 - Directory Listing
Modified Tue Sep 16 03:34:31 2014 UTC (4 years, 5 months ago) by caltinay
Original Path: trunk

bump guineapig's options file version.

Revision 5152 - Directory Listing
Modified Tue Sep 16 01:29:30 2014 UTC (4 years, 5 months ago) by jduplessis
Original Path: trunk

add dcresistivity inversion

Revision 5151 - Directory Listing
Modified Mon Sep 15 06:11:46 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

adding simple read/write tests for speckley

Revision 5150 - Directory Listing
Modified Mon Sep 15 06:09:42 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

type corrections to speckley and adding in binarygrid support for brick (element corners only)

Revision 5149 - Directory Listing
Modified Mon Sep 15 01:57:06 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

removed transport from speckley, added read/write binary grids for rectangles

Revision 5148 - Directory Listing
Modified Mon Sep 15 01:25:23 2014 UTC (4 years, 5 months ago) by caltinay
Original Path: trunk

Merging ripley diagonal storage + CUDA support into trunk.
Options file version has been incremented due to new options
'cuda' and 'nvccflags'.

Revision 5145 - Directory Listing
Modified Thu Sep 11 03:28:37 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

fixed corner issue in three-dimensional speckley subdivisions

Revision 5143 - Directory Listing
Modified Wed Sep 10 07:27:59 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

removing some of those omp loop sections until they play well

Revision 5142 - Directory Listing
Modified Wed Sep 10 07:18:34 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

marked loops as omp, wrapped remaining MPI-only function call

Revision 5140 - Directory Listing
Modified Wed Sep 10 05:49:19 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

stripping debug print out of speckley section of weipa

Revision 5139 - Directory Listing
Modified Wed Sep 10 05:42:46 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

speckley brick now supports MPI

Revision 5138 - Directory Listing
Modified Wed Sep 10 04:12:47 2014 UTC (4 years, 5 months ago) by caltinay
Original Path: trunk

Added ABS which was obviously missing in a function that is used to
create balance vector in paso.

Revision 5133 - Directory Listing
Modified Fri Sep 5 00:07:34 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

fixed non-MPI builds with speckley

Revision 5132 - Directory Listing
Modified Thu Sep 4 07:02:24 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

added MPI support and tests to speckley, cleaned out more ghostzone code

Revision 5129 - Directory Listing
Modified Fri Aug 29 05:10:48 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

fixing missed MPI type merge from ripley

Revision 5128 - Directory Listing
Modified Fri Aug 29 00:52:35 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

fixing a bad index calculation

Revision 5127 - Directory Listing
Modified Fri Aug 29 00:30:34 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

more redundant includes removed

Revision 5126 - Directory Listing
Modified Thu Aug 28 23:32:59 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

fixing last remnants of speckley::SystemMatrix

Revision 5125 - Directory Listing
Modified Thu Aug 28 23:16:21 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

removing troublesome future-predicting #include

Revision 5124 - Directory Listing
Modified Thu Aug 28 07:02:55 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

minor comment fix for ripley

Revision 5123 - Directory Listing
Modified Thu Aug 28 07:02:11 2014 UTC (4 years, 5 months ago) by sshaw
Original Path: trunk

Adding speckley (high-order) domain family, doesn't yet support MPI, Reduced functionspaces, or PDEs using A, B and/or C

Revision 5121 - Directory Listing
Modified Wed Aug 20 10:32:40 2014 UTC (4 years, 6 months ago) by caltinay
Original Path: trunk

Made more methods pure virtual in AbstractDomain and moved the generic
implementation into NullDomain.
Made TestDomain derive from NullDomain to inherit the methods.

Revision 5120 - Directory Listing
Modified Wed Aug 20 06:19:20 2014 UTC (4 years, 6 months ago) by caltinay
Original Path: trunk

Some code cleanup and int->dim_t replacements in ripley.

Revision 5119 - Directory Listing
Modified Wed Aug 20 04:10:01 2014 UTC (4 years, 6 months ago) by caltinay
Original Path: trunk

Separated pattern generation from connector generation in ripley Brick
to allow using alternative System Matrices.

Revision 5118 - Directory Listing
Modified Mon Aug 18 11:28:55 2014 UTC (4 years, 6 months ago) by caltinay
Original Path: trunk

Separated generation of paso matrix pattern and coupler/DOF Map
in Rectangle. This is in preparation for introducing non-Paso matrices.
Brick still to do.

Revision 5117 - Directory Listing
Modified Mon Aug 18 05:42:09 2014 UTC (4 years, 6 months ago) by caltinay
Original Path: trunk

Further untangled/simplified paso pattern generation in ripley.

Revision 5116 - Directory Listing
Modified Mon Aug 18 01:56:41 2014 UTC (4 years, 6 months ago) by caltinay
Original Path: trunk

making an example slightly more generic.

Revision 5115 - Directory Listing
Modified Thu Aug 14 05:36:58 2014 UTC (4 years, 6 months ago) by caltinay
Original Path: trunk

Minor tweaks.

Revision 5114 - Directory Listing
Modified Thu Aug 14 05:15:31 2014 UTC (4 years, 6 months ago) by caltinay
Original Path: trunk

Preliminary changes to make ripley ready for other System Matrixes.

Revision 5113 - Directory Listing
Modified Tue Aug 12 23:06:07 2014 UTC (4 years, 6 months ago) by caltinay
Original Path: trunk

new directory for boost install.

Revision 5112 - Directory Listing
Modified Mon Aug 11 04:17:17 2014 UTC (4 years, 6 months ago) by caltinay
Original Path: trunk

Report regularization terms separately when debug output is enabled.

Revision 5111 - Directory Listing
Modified Tue Aug 5 00:19:56 2014 UTC (4 years, 6 months ago) by caltinay
Original Path: trunk

replaced '@expectedFailure' by '@skip' since py3 does not support the former
for test classes.

Revision 5110 - Directory Listing
Modified Fri Aug 1 05:04:59 2014 UTC (4 years, 6 months ago) by jduplessis
Original Path: trunk

replaced atomic with critical

Revision 5109 - Directory Listing
Modified Fri Aug 1 04:39:53 2014 UTC (4 years, 6 months ago) by jduplessis
Original Path: trunk

fix indentation

Revision 5108 - Directory Listing
Modified Fri Aug 1 04:37:45 2014 UTC (4 years, 6 months ago) by jduplessis
Original Path: trunk

removing renamed tests

Revision 5107 - Directory Listing
Modified Thu Jul 24 14:07:14 2014 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

It appears critical for scaling in finley/dudley that IndexList does not
realloc so reimplemented original idea.

Revision 5106 - Directory Listing
Modified Mon Jul 21 11:57:42 2014 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

Avoid some unnecessary reallocation.

Revision 5105 - Directory Listing
Modified Mon Jul 21 10:08:43 2014 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

fix for parmetis-enabled build

Revision 5104 - Directory Listing
Modified Mon Jul 21 07:47:55 2014 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

Fixed a threading performance issue in finley/dudley by preallocating
chunk in vector and using dynamic arrays directly for parallel region.

Revision 5103 - Directory Listing
Modified Thu Jul 17 13:39:02 2014 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

use a vector for index list because we need contiguous storage for efficiency.

Revision 5102 - Directory Listing
Modified Wed Jul 16 00:46:22 2014 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

We were setting --cpus-per-rank without a --bind... option under OpenMPI
but the latter is required according to doco.
This, in combination with setting OMP_PROC_BIND=true, caused all ranks
to run on the same core when running without hostfile (e.g. on guineapig)
so the runtimes exploded.
Added --bind-to-core to fix that issue.

Revision 5101 - Directory Listing
Modified Tue Jul 15 09:50:20 2014 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

Fixed another race with file deletion.

Revision 5100 - Directory Listing
Modified Tue Jul 15 07:36:29 2014 UTC (4 years, 7 months ago) by jduplessis
Original Path: trunk

minor revisions

Revision 5099 - Directory Listing
Modified Mon Jul 14 00:41:14 2014 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

Fix recent mpi test failures by giving ranks>0 some time to check their
output before deleting test files.

Revision 5098 - Directory Listing
Modified Sun Jul 13 14:33:43 2014 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

Finally implemented multipliers for readBinaryGrid under MPI and fixed tests
accordingly.
We can now read data at resolution x into a domain at resolution N*x properly.

Revision 5097 - Directory Listing
Modified Sun Jul 13 01:02:24 2014 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

Fixed undefined behaviour when indexing empty stl containers to pass
pointers (i.e. &vec[0]).

Revision 5096 - Directory Listing
Modified Fri Jul 11 12:32:49 2014 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

More readBinaryGrid tests. There are a few 'expectedFailure's for
>1 rank. This is a shortcoming of the tests, not of the actual
implementation, so they need more work.

Revision 5094 - Directory Listing
Modified Thu Jul 10 02:46:33 2014 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

Back to sh-compatibility

Revision 5093 - Directory Listing
Modified Tue Jul 8 01:54:09 2014 UTC (4 years, 7 months ago) by jfenwick
Original Path: trunk

Document range of random number generator.

Revision 5092 - Directory Listing
Modified Mon Jul 7 00:47:44 2014 UTC (4 years, 7 months ago) by sshaw
Original Path: trunk

fixing lack of thread binding for intel-based OpenMP, gcc unaffected

Revision 5091 - Directory Listing
Modified Wed Jul 2 05:19:02 2014 UTC (4 years, 7 months ago) by jduplessis
Original Path: trunk

NaN tests for ripley

Revision 5090 - Directory Listing
Modified Wed Jul 2 05:14:11 2014 UTC (4 years, 7 months ago) by jduplessis
Original Path: trunk

tests for replace and has NaN

Revision 5089 - Directory Listing
Modified Tue Jul 1 01:07:16 2014 UTC (4 years, 7 months ago) by jduplessis
Original Path: trunk

fix missing self.__

Revision 5088 - Directory Listing
Modified Tue Jul 1 00:32:22 2014 UTC (4 years, 7 months ago) by jduplessis
Original Path: trunk

option for direct solver with mtInversion

Revision 5082 - Directory Listing
Modified Fri Jun 27 05:36:01 2014 UTC (4 years, 7 months ago) by jfenwick
Original Path: trunk

Thanks to Cihan. Silence annoying warngings

Revision 5081 - Directory Listing
Modified Fri Jun 27 03:48:06 2014 UTC (4 years, 7 months ago) by jduplessis
Original Path: trunk

squirrel options

Revision 5080 - Directory Listing
Modified Wed Jun 25 02:50:56 2014 UTC (4 years, 7 months ago) by sshaw
Original Path: trunk

more StringIO replacements for py3 compatibility

Revision 5079 - Directory Listing
Modified Tue Jun 24 22:50:50 2014 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

bump to py3.4 on piggy.

Revision 5078 - Directory Listing
Modified Tue Jun 24 06:50:21 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

fixing silly leftovers that were missed in previous commits

Revision 5077 - Directory Listing
Modified Tue Jun 24 03:51:19 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

Make readBinaryGrid "public" within the ripley module.

Revision 5076 - Directory Listing
Modified Tue Jun 24 03:41:42 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

more python3 compatibility fixes

Revision 5074 - Directory Listing
Modified Tue Jun 24 00:44:50 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

python3 compatibility fix

Revision 5073 - Directory Listing
Modified Mon Jun 23 22:22:44 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

fixing some py3 warnings.

Revision 5072 - Directory Listing
Modified Mon Jun 23 05:13:30 2014 UTC (4 years, 8 months ago) by jduplessis
Original Path: trunk

paralelize hasNaN and replaceNaN

Revision 5071 - Directory Listing
Modified Mon Jun 23 04:36:14 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

fixing python 3 xrange unfriendliness

Revision 5069 - Directory Listing
Modified Fri Jun 20 06:54:20 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

fixing mismatching identifiers

Revision 5067 - Directory Listing
Modified Fri Jun 20 06:04:58 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

actually fixing python 3 breakage and not the previous commits rewrite of lots of code repetition

Revision 5066 - Directory Listing
Modified Fri Jun 20 06:04:02 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

fixing python 3 breakage

Revision 5061 - Directory Listing
Modified Fri Jun 20 04:10:59 2014 UTC (4 years, 8 months ago) by jfenwick
Original Path: trunk

Added descriptive information to functionspace names

Revision 5060 - Directory Listing
Modified Fri Jun 20 03:29:11 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

more reporting of previously silently skipped/passing tests

Revision 5059 - Directory Listing
Modified Fri Jun 20 03:10:19 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

more test renames, more marking non-test classes, fixed broken test in run_xml

Revision 5058 - Directory Listing
Modified Fri Jun 20 02:03:28 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

more test renames, marking some that look wrongly named as subclass required

Revision 5057 - Directory Listing
Modified Fri Jun 20 01:53:38 2014 UTC (4 years, 8 months ago) by gross
Original Path: trunk

some fixes for MT-TE

Revision 5056 - Directory Listing
Modified Fri Jun 20 01:37:28 2014 UTC (4 years, 8 months ago) by jduplessis
Original Path: trunk

replace nan stuff

Revision 5055 - Directory Listing
Modified Fri Jun 20 01:21:43 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

more test renaming, less silent skipping of tests

Revision 5054 - Directory Listing
Modified Fri Jun 20 00:59:16 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

test name changes so they run again.

Revision 5051 - Directory Listing
Modified Wed Jun 18 05:08:02 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

Added base readBinaryGrid tests and fixed reading doubles with non-native
endianness.

Revision 5050 - Directory Listing
Modified Wed Jun 18 04:17:54 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

more comment cleanup

Revision 5049 - Directory Listing
Modified Wed Jun 18 04:17:26 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

small code documentation cleanup

Revision 5048 - Directory Listing
Modified Fri Jun 13 05:41:15 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

fixed typo in lbfgs-SetOptions.

Revision 5047 - Directory Listing
Modified Fri Jun 13 05:12:03 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

removing dumb 'False and' that was leftover

Revision 5046 - Directory Listing
Modified Fri Jun 13 02:54:29 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

std::isnan -> isnan

Revision 5045 - Directory Listing
Modified Fri Jun 13 02:53:39 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

minor fixes required on cray/py26

Revision 5044 - Directory Listing
Modified Fri Jun 13 01:51:58 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

fixed compiler warnings that appeared due to removing the exceptions.

Revision 5043 - Directory Listing
Modified Thu Jun 12 07:07:27 2014 UTC (4 years, 8 months ago) by jduplessis
Original Path: trunk

skip gmshnamedtags for mpi

Revision 5042 - Directory Listing
Modified Thu Jun 12 06:40:11 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

HTI and VTI are the only cases as ensured by the constructor so don't
throw in parallel region.

Revision 5041 - Directory Listing
Modified Thu Jun 12 05:28:22 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

fixed domainreader test sillyness and moved gmsh detection into testfile from SConscript

Revision 5040 - Directory Listing
Modified Thu Jun 12 05:12:33 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

gravity constant scaling for geodetic coordinates does not appear to be
right so reverting for now.

Revision 5039 - Directory Listing
Modified Thu Jun 12 05:10:38 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

compiler help

Revision 5038 - Directory Listing
Modified Thu Jun 12 04:58:56 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

Missed a few. Should be almost done.

Revision 5037 - Directory Listing
Modified Thu Jun 12 04:39:23 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

more on CAP.

Revision 5034 - Directory Listing
Modified Thu Jun 12 03:14:56 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

More omp compiler helps.

Revision 5033 - Directory Listing
Modified Thu Jun 12 01:04:42 2014 UTC (4 years, 8 months ago) by jduplessis
Original Path: trunk

test file for named tags

Revision 5032 - Directory Listing
Modified Thu Jun 12 01:03:00 2014 UTC (4 years, 8 months ago) by jduplessis
Original Path: trunk

added test for named tags

Revision 5031 - Directory Listing
Modified Thu Jun 12 01:01:21 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

retrieving LinearMappingX from the lost and found bin

Revision 5030 - Directory Listing
Modified Thu Jun 12 00:37:33 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

more missing tests added

Revision 5029 - Directory Listing
Modified Wed Jun 11 23:52:36 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

Continuing the compiler assistance package...

Revision 5028 - Directory Listing
Modified Wed Jun 11 22:49:41 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

this fails without abspath on a system.

Revision 5027 - Directory Listing
Modified Wed Jun 11 07:32:26 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

First commit of a 'compiler assistance package', i.e.
making it easier for compilers to understand OMP loop limits.

Revision 5026 - Directory Listing
Modified Wed Jun 11 06:07:03 2014 UTC (4 years, 8 months ago) by jduplessis
Original Path: trunk

reading physical names should now work properly

Revision 5025 - Directory Listing
Modified Wed Jun 11 05:44:31 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

Fix to gravity model with geodetic coords and another instance of
== badness.

Revision 5024 - Directory Listing
Modified Tue Jun 10 08:46:07 2014 UTC (4 years, 8 months ago) by jfenwick
Original Path: trunk

Fixing more == None

Revision 5023 - Directory Listing
Modified Tue Jun 10 06:37:50 2014 UTC (4 years, 8 months ago) by jfenwick
Original Path: trunk

Replacing ==None and variants with is None in accordance with new warnings.

Revision 5022 - Directory Listing
Modified Tue Jun 10 05:02:47 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

scons runs now remove prior skipped files on a per-file basis

Revision 5021 - Directory Listing
Modified Tue Jun 10 04:44:52 2014 UTC (4 years, 8 months ago) by jfenwick
Original Path: trunk

Making == and != on Data objects throw exceptions to warn people that they probably don't do what they might think they do.
Credit to Jaco and Cihan.

Revision 5020 - Directory Listing
Modified Tue Jun 10 04:07:00 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

remember the good ol' days where no newline at end of files were frowned upon? 
Thanks to crayc++ they're back.

Revision 5019 - Directory Listing
Modified Tue Jun 10 03:57:55 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

scons ends if tests fail again

Revision 5018 - Directory Listing
Modified Tue Jun 10 03:38:29 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

byteswap.h availability does not mean bswapXXX works so check that.
(crayc++ does not support inline assembly)

Revision 5017 - Directory Listing
Modified Tue Jun 10 02:16:18 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

scons now runs tests via a testrunner to collect lists of skipped tests in build/ (examples have their own builder since they aren't unit tests)
fixed hessian regularisation tests falling over by adding a shortcircuit optional arg that returns the pde, not the solution
added missing/omitted tests back into scons tests

Revision 5016 - Directory Listing
Modified Mon Jun 9 09:54:18 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

"The Queen's commit". Happy birthday,

Revision 5015 - Directory Listing
Modified Sun Jun 8 13:09:16 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

Implemented writing of binary grids for FLOAT64 in non-native byte order.
Write tests pass now fully on debian.

This depends on uint64_t which is assumed to be available...

Revision 5014 - Directory Listing
Modified Sun Jun 8 12:05:22 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

built boost 1.55.0 on savanna which fixes the segfaults we have been seeing
for a long time when using shared_from_this() with the intel compiler.

(While Intel couldn't reproduce, I could on epic, magnus, and raijin w/ system
boost+python. Finally found that using 1.53+ modules on raijin did no longer
exhibit the problem.)

Revision 5013 - Directory Listing
Modified Fri Jun 6 07:25:13 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

fix minor typo

Revision 5012 - Directory Listing
Modified Fri Jun 6 07:23:36 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

writeBinaryGrid tests. big endian doubles fail currently.

Revision 5011 - Directory Listing
Modified Fri Jun 6 07:05:50 2014 UTC (4 years, 8 months ago) by jduplessis
Original Path: trunk

updates getInverse for mt

Revision 5010 - Directory Listing
Modified Fri Jun 6 07:00:28 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

fixes #270 (pathological case).

Revision 5009 - Directory Listing
Modified Fri Jun 6 04:36:13 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

deleted strange file which doesn't belong here.

Revision 5008 - Directory Listing
Modified Fri Jun 6 04:31:41 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

some cleanup, renaming and fixing of ripley tests.

Revision 5006 - Directory Listing
Modified Fri Jun 6 03:40:44 2014 UTC (4 years, 8 months ago) by gross
Original Path: trunk

Cross-Gradient testing added. No dramas.

Revision 5005 - Directory Listing
Modified Fri Jun 6 03:11:14 2014 UTC (4 years, 8 months ago) by gross
Original Path: trunk

test for Hessian added. Cross  gradient is still missing.

Revision 5004 - Directory Listing
Modified Fri Jun 6 02:34:27 2014 UTC (4 years, 8 months ago) by gross
Original Path: trunk

two bug fixes in the cross gradient term

Revision 5003 - Directory Listing
Modified Fri Jun 6 00:34:33 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

a more forgiving test class prefix check

Revision 5002 - Directory Listing
Modified Fri Jun 6 00:21:58 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

tweaking test class name to allow unittest to function

Revision 5001 - Directory Listing
Modified Thu Jun 5 23:59:21 2014 UTC (4 years, 8 months ago) by gross
Original Path: trunk

regularization test added.

Revision 5000 - Directory Listing
Modified Thu Jun 5 23:33:16 2014 UTC (4 years, 8 months ago) by jfenwick
Original Path: trunk

Recent release of g++ no longer accepts isnan outside of the std namespace.
Added a general using namespace std _inside_ the function to catch both cases.

Also, 5000th commit

Revision 4999 - Directory Listing
Modified Thu Jun 5 06:39:52 2014 UTC (4 years, 8 months ago) by jfenwick
Original Path: trunk

Fixing weirdness

Revision 4998 - Directory Listing
Modified Thu Jun 5 06:03:08 2014 UTC (4 years, 8 months ago) by jduplessis
Original Path: trunk

implemented hasNaN

Revision 4997 - Directory Listing
Modified Thu Jun 5 05:23:41 2014 UTC (4 years, 8 months ago) by jfenwick
Original Path: trunk

Added missing link

Revision 4996 - Directory Listing
Modified Thu Jun 5 03:56:33 2014 UTC (4 years, 8 months ago) by jfenwick
Original Path: trunk

Changed cookbook back to single spacing from double spacing.
All pdfs now link in the same docguide.tex file which explains what the
various bits of doco are.

Revision 4995 - Directory Listing
Modified Thu Jun 5 03:44:16 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

Doc fixes and ensuring that expensive debug ops will not be processed if debug
mode is disabled.

Revision 4994 - Directory Listing
Modified Thu Jun 5 03:04:57 2014 UTC (4 years, 8 months ago) by jfenwick
Original Path: trunk

Ensure isnan calls the c++ version except on windows compilers

Revision 4993 - Directory Listing
Modified Thu Jun 5 03:04:56 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

fixing the launcher to run on all nodes for savanna

Revision 4992 - Directory Listing
Modified Thu Jun 5 01:38:33 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

Don't obtain/report UTM zone for non-cartesian coordinate systems.

Revision 4991 - Directory Listing
Modified Thu Jun 5 01:01:41 2014 UTC (4 years, 8 months ago) by jduplessis
Original Path: trunk

adding MT data

Revision 4990 - Directory Listing
Modified Wed Jun 4 13:17:15 2014 UTC (4 years, 8 months ago) by jduplessis
Original Path: trunk

added mtMappings

Revision 4989 - Directory Listing
Modified Wed Jun 4 06:22:36 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

marking pdetools.Defect as abstract in doco and preventing it from silently returning lots of zeroes instead of being subclassed

Revision 4986 - Directory Listing
Modified Tue Jun 3 03:09:14 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

adding skips for those tests not previously tested and which will need checking

Revision 4985 - Directory Listing
Modified Mon Jun 2 05:45:58 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

uncommenting decorator that shouldn't have been commented

Revision 4984 - Directory Listing
Modified Mon Jun 2 02:50:34 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

revamping testrunners, now uses automated discovery and allows running specific tests without modifying files (see escriptcore/py_src/testing.py for more info/examples)

Revision 4983 - Directory Listing
Modified Mon Jun 2 02:32:23 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

removing missing/leftover test files from test list

Revision 4982 - Directory Listing
Modified Mon Jun 2 00:41:30 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

removing run_utilOnFinley3.py as it is a duplicate of run_utilOnFinley.py

Revision 4980 - Directory Listing
Modified Sun Jun 1 23:53:11 2014 UTC (4 years, 8 months ago) by gross
Original Path: trunk

more fixes on MT

Revision 4979 - Directory Listing
Modified Sun Jun 1 22:36:16 2014 UTC (4 years, 8 months ago) by gross
Original Path: trunk

some fixes to the MT forward model

Revision 4978 - Directory Listing
Modified Thu May 29 11:55:53 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

Make clear that reversing is not implemented yet for Rectangle.
Implemented reversing in z for Brick.
This needs proper testing...

Revision 4977 - Directory Listing
Modified Thu May 29 08:51:43 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

la la la....

Revision 4976 - Directory Listing
Modified Thu May 29 08:27:53 2014 UTC (4 years, 8 months ago) by gross
Original Path: trunk

gradient for coordinate systems added

Revision 4975 - Directory Listing
Modified Thu May 29 03:44:49 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

Don't cast p0 to a float as it might be a data object.

Revision 4974 - Directory Listing
Modified Wed May 28 08:02:02 2014 UTC (4 years, 8 months ago) by jduplessis
Original Path: trunk

added a data source object for MT2DTE

Revision 4973 - Directory Listing
Modified Wed May 28 06:02:38 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

making verbose-mode logging accurate

Revision 4972 - Directory Listing
Modified Tue May 27 05:33:10 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

small doc grammar changes

Revision 4971 - Directory Listing
Modified Tue May 27 04:52:52 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

debug output clean up.

Revision 4970 - Directory Listing
Modified Tue May 27 03:47:04 2014 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

more bashisms removed (valgrind run) from launcher.

Revision 4969 - Directory Listing
Modified Mon May 26 23:50:52 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

fixing intel's hidden function warning

Revision 4968 - Directory Listing
Modified Mon May 26 04:20:22 2014 UTC (4 years, 8 months ago) by jfenwick
Original Path: trunk

One more time for the dummies

Revision 4967 - Directory Listing
Modified Mon May 26 04:18:19 2014 UTC (4 years, 8 months ago) by sshaw
Original Path: trunk

5.1e-8 is close enough to zero, rounding is breaking this on clang/mac so making it strict <

Revision 4966 - Directory Listing
Modified Mon May 26 02:55:33 2014 UTC (4 years, 8 months ago) by jfenwick
Original Path: trunk

Dealing with non-determinism. We hope.

Revision 4965 - Directory Listing
Modified Fri May 23 22:07:32 2014 UTC (4 years, 9 months ago) by jfenwick
Original Path: trunk

Try to fix this for MPI again

Revision 4964 - Directory Listing
Modified Fri May 23 07:14:25 2014 UTC (4 years, 9 months ago) by gross
Original Path: trunk

MT2D forward pproblem

Revision 4963 - Directory Listing
Modified Fri May 23 05:12:40 2014 UTC (4 years, 9 months ago) by jfenwick
Original Path: trunk

Removed JMPI from ScriptMPI.cpp.
Changed options file to build shared libraries.
Fixed error in unit tests

Revision 4962 - Directory Listing
Modified Fri May 23 02:53:00 2014 UTC (4 years, 9 months ago) by jfenwick
Original Path: trunk

Tests for adding dirac points. There are no tests for what dirac points appear on which ranks.

Revision 4961 - Directory Listing
Modified Thu May 22 03:53:31 2014 UTC (4 years, 9 months ago) by sshaw
Original Path: trunk

another two epydoc leftovers that were missed

Revision 4960 - Directory Listing
Modified Thu May 22 03:35:41 2014 UTC (4 years, 9 months ago) by sshaw
Original Path: trunk

removing vestigal epydoc markup and replacing with sphinx markup

Revision 4959 - Directory Listing
Modified Wed May 21 04:22:14 2014 UTC (4 years, 9 months ago) by gross
Original Path: trunk

added some text on 2D MT TE inversion

Revision 4957 - Directory Listing
Modified Wed May 21 01:31:23 2014 UTC (4 years, 9 months ago) by caltinay
Original Path: trunk

Missed a few unittest wrapper imports.

Revision 4947 - Directory Listing
Modified Mon May 19 03:58:03 2014 UTC (4 years, 9 months ago) by sshaw
Original Path: trunk

adding build fail message for when a boost lib is too old to compile everything anyway (minimum version is currently 1.46)

Revision 4945 - Directory Listing
Modified Thu May 15 09:07:06 2014 UTC (4 years, 9 months ago) by jfenwick
Original Path: trunk

Untested code for adding dirac points to finley domains. Still to do: load(), unit tests

Revision 4943 - Directory Listing
Modified Thu May 15 04:58:35 2014 UTC (4 years, 9 months ago) by sshaw
Original Path: trunk

moving abstract assemblers back into ripley since only ripley uses them (for now)

Revision 4942 - Directory Listing
Modified Thu May 15 03:42:28 2014 UTC (4 years, 9 months ago) by sshaw
Original Path: trunk

each PDE now is responsible for its own assembler, allows multiple types of PDEs to share a domain without interference

Revision 4939 - Directory Listing
Modified Wed May 14 03:56:47 2014 UTC (4 years, 9 months ago) by caltinay
Original Path: trunk

close the file after finishing reading to avoid segfault on centos.

Revision 4938 - Directory Listing
Modified Wed May 14 01:13:23 2014 UTC (4 years, 9 months ago) by jfenwick
Original Path: trunk

Modify unit tests to read their classes from
esys.escriptcore.utestselect

Change the line in that file to switch between unittest and unittest2

Revision 4937 - Directory Listing
Modified Tue May 13 07:07:32 2014 UTC (4 years, 9 months ago) by caltinay
Original Path: trunk

gcc 4.9: error: type qualifiers ignored on function return type [-Werror=ignored-qualifiers]

Revision 4936 - Directory Listing
Modified Tue May 13 07:00:36 2014 UTC (4 years, 9 months ago) by caltinay
Original Path: trunk

Wait a bit after running the mpi-enabled gmsh version to increase probability
of success (yes it's a hack).

Revision 4935 - Directory Listing
Modified Tue May 13 03:49:09 2014 UTC (4 years, 9 months ago) by jfenwick
Original Path: trunk

Fixes for Python3

Revision 4934 - Directory Listing
Modified Tue May 13 00:28:11 2014 UTC (4 years, 9 months ago) by jfenwick
Original Path: trunk

This commit is brought to you by the number 4934 and the tool "meld".
Merge of partially complete split world code from branch.

Revision 4931 - Directory Listing
Modified Mon May 12 02:27:34 2014 UTC (4 years, 9 months ago) by jduplessis
Original Path: trunk

this is a fix for older versions of numpy where passing in an a list of ints causes
 the inver code to break.

Revision 4930 - Directory Listing
Modified Mon May 12 01:56:16 2014 UTC (4 years, 9 months ago) by caltinay
Original Path: trunk

a few constness fixes in abstract and pasowrap SystemMatrix.

Revision 4929 - Directory Listing
Modified Mon May 5 06:20:20 2014 UTC (4 years, 9 months ago) by caltinay
Original Path: trunk

a few non-invasive const fixes in AbstractSystemMatrix.

Revision 4928 - Directory Listing
Modified Mon May 5 03:02:04 2014 UTC (4 years, 9 months ago) by caltinay
Original Path: trunk

fixed a very bad doc string in abstract class.

Revision 4927 - Directory Listing
Modified Fri May 2 02:47:44 2014 UTC (4 years, 9 months ago) by caltinay
Original Path: trunk

Removed the remaining (2) bashism's in run-escript so bash is no longer required.

Revision 4926 - Directory Listing
Modified Thu May 1 05:29:12 2014 UTC (4 years, 9 months ago) by caltinay
Original Path: trunk

trying to make centos happy.

Revision 4920 - Directory Listing
Modified Wed Apr 30 10:17:05 2014 UTC (4 years, 9 months ago) by caltinay
Original Path: trunk

Fixes #253 (unused var in weipa)

Revision 4918 - Directory Listing
Modified Wed Apr 30 06:20:47 2014 UTC (4 years, 9 months ago) by caltinay
Original Path: trunk

instructions for FreeBSD 10.0

Revision 4917 - Directory Listing
Modified Wed Apr 30 05:58:08 2014 UTC (4 years, 9 months ago) by caltinay
Original Path: trunk

export LD_PRELOAD for tests.
added freebsd 10.0 options file.

Revision 4916 - Directory Listing
Modified Wed Apr 30 05:30:36 2014 UTC (4 years, 9 months ago) by sshaw
Original Path: trunk

updating deb changelog

Revision 4915 - Directory Listing
Modified Wed Apr 30 05:29:23 2014 UTC (4 years, 9 months ago) by jfenwick
Original Path: trunk

Fixes for macports

Revision 4914 - Directory Listing
Modified Wed Apr 30 04:58:45 2014 UTC (4 years, 9 months ago) by sshaw
Original Path: trunk

removing spare 'as'

Revision 4913 - Directory Listing
Modified Wed Apr 30 04:57:21 2014 UTC (4 years, 9 months ago) by jfenwick
Original Path: trunk

Reorder homebrew install

Revision 4912 - Directory Listing
Modified Wed Apr 30 04:57:01 2014 UTC (4 years, 9 months ago) by jduplessis
Original Path: trunk

update to comments and fixing of docstring

Revision 4911 - Directory Listing
Modified Wed Apr 30 04:43:23 2014 UTC (4 years, 9 months ago) by jfenwick
Original Path: trunk

fix unused var

Revision 4910 - Directory Listing
Modified Wed Apr 30 02:21:59 2014 UTC (4 years, 9 months ago) by jduplessis
Original Path: trunk

fix docstring error

Revision 4909 - Directory Listing
Modified Wed Apr 30 01:20:22 2014 UTC (4 years, 9 months ago) by caltinay
Original Path: trunk

Fixed Wunused-functions picked up by g++ 4.9

Revision 4908 - Directory Listing
Modified Wed Apr 30 00:24:38 2014 UTC (4 years, 9 months ago) by sshaw
Original Path: trunk

removing runmodel from /bin given it doesn't have x-permissions

Revision 4907 - Directory Listing
Modified Tue Apr 29 12:58:43 2014 UTC (4 years, 9 months ago) by jduplessis
Original Path: trunk

fix docstring indentation isssue for accousticwaveform

Revision 4906 - Directory Listing
Modified Tue Apr 29 05:27:34 2014 UTC (4 years, 9 months ago) by sshaw
Original Path: trunk

restoring lost changes

Revision 4905 - Directory Listing
Modified Tue Apr 29 05:16:13 2014 UTC (4 years, 9 months ago) by sshaw
Original Path: trunk

updated install doc

Revision 4904 - Directory Listing
Modified Tue Apr 29 04:40:30 2014 UTC (4 years, 9 months ago) by jduplessis
Original Path: trunk

removing test print

Revision 4903 - Directory Listing
Modified Tue Apr 29 04:12:59 2014 UTC (4 years, 9 months ago) by jduplessis
Original Path: trunk

updates for centos 6.5 install instructions

Revision 4902 - Directory Listing
Modified Tue Apr 29 04:07:28 2014 UTC (4 years, 9 months ago) by jduplessis
Original Path: trunk

add centos 6.5 scons option file.

Revision 4901 - Directory Listing
Modified Tue Apr 29 03:55:00 2014 UTC (4 years, 9 months ago) by jfenwick
Original Path: trunk

Updated info about macos commandline tools to note existance of xcodebuild command.

Revision 4900 - Directory Listing
Modified Tue Apr 29 01:44:02 2014 UTC (4 years, 9 months ago) by jduplessis
Original Path: trunk

update sympy version check

Revision 4899 - Directory Listing
Modified Tue Apr 29 01:42:23 2014 UTC (4 years, 9 months ago) by jduplessis
Original Path: trunk

sympy version check

Revision 4898 - Directory Listing
Modified Tue Apr 29 01:03:58 2014 UTC (4 years, 9 months ago) by jduplessis
Original Path: trunk

sympy version check

Revision 4897 - Directory Listing
Modified Tue Apr 29 00:43:58 2014 UTC (4 years, 9 months ago) by jduplessis
Original Path: trunk

sympy version check

Revision 4896 - Directory Listing
Modified Tue Apr 29 00:35:22 2014 UTC (4 years, 9 months ago) by jfenwick
Original Path: trunk

Added missing backslash
Corrected spelling mistake

Revision 4895 - Directory Listing
Modified Tue Apr 29 00:21:43 2014 UTC (4 years, 9 months ago) by sshaw
Original Path: trunk

affected tests now skipped if pyproj not installed

Revision 4894 - Directory Listing
Modified Mon Apr 28 04:28:28 2014 UTC (4 years, 9 months ago) by sshaw
Original Path: trunk

adding options for fedora 20, only changes boost_python-mt for now

Revision 4892 - Directory Listing
Modified Mon Apr 28 03:30:29 2014 UTC (4 years, 9 months ago) by caltinay
Original Path: trunk

scaled down grav_netcdf test...

Revision 4891 - Directory Listing
Modified Mon Apr 28 03:20:38 2014 UTC (4 years, 9 months ago) by caltinay
Original Path: trunk

some changes to user guide.

Revision 4890 - Directory Listing
Modified Mon Apr 28 01:24:21 2014 UTC (4 years, 9 months ago) by jduplessis
Original Path: trunk

added suggestion to copy options file from os directory.

Revision 4889 - Directory Listing
Modified Mon Apr 28 01:17:41 2014 UTC (4 years, 9 months ago) by jduplessis
Original Path: trunk

Updated warning message when no options file is provided

Revision 4888 - Directory Listing
Modified Mon Apr 28 00:52:20 2014 UTC (4 years, 9 months ago) by jfenwick
Original Path: trunk

Removing manual pagebreaks

Revision 4887 - Directory Listing
Modified Mon Apr 28 00:34:35 2014 UTC (4 years, 9 months ago) by jduplessis
Original Path: trunk

Minor updates

Revision 4886 - Directory Listing
Modified Sun Apr 27 13:12:23 2014 UTC (4 years, 9 months ago) by jduplessis
Original Path: trunk

rewording and checking

Revision 4885 - Directory Listing
Modified Sun Apr 27 11:48:36 2014 UTC (4 years, 9 months ago) by jduplessis
Original Path: trunk

Small changes

Revision 4884 - Directory Listing
Modified Thu Apr 24 04:47:39 2014 UTC (4 years, 10 months ago) by jduplessis
Original Path: trunk

this file is added so that we can import Symbolic by doing:
    import esys.escript.symbolic as symb instead of 
    import esys.escriptcore.symbolic as symb

the one line containined in the file is on line five for reasons prettiness

Revision 4883 - Directory Listing
Modified Thu Apr 24 00:00:33 2014 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

Updated changes list and sorted dev lists

Revision 4882 - Directory Listing
Modified Wed Apr 23 14:54:26 2014 UTC (4 years, 10 months ago) by jduplessis
Original Path: trunk

fixing small errors

Revision 4881 - Directory Listing
Modified Wed Apr 23 14:20:28 2014 UTC (4 years, 10 months ago) by jduplessis
Original Path: trunk

grammar, spelling and formating changes.

Revision 4880 - Directory Listing
Modified Wed Apr 23 06:10:16 2014 UTC (4 years, 10 months ago) by jduplessis
Original Path: trunk

added sympy to bib and making small grammar, spelling and style changes.

Revision 4879 - Directory Listing
Modified Wed Apr 23 00:50:36 2014 UTC (4 years, 10 months ago) by jduplessis
Original Path: trunk

symbolic part of user guide nearly complete

Revision 4878 - Directory Listing
Modified Wed Apr 23 00:49:10 2014 UTC (4 years, 10 months ago) by jduplessis
Original Path: trunk

adding figures for symbolic part of user guide.

Revision 4877 - Directory Listing
Modified Tue Apr 22 07:24:32 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

new intel cc,mkl & mpi on savanna.

Revision 4876 - Directory Listing
Modified Tue Apr 22 05:43:36 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

fixing package requirements for ubuntu trusty packages

Revision 4875 - Directory Listing
Modified Thu Apr 17 06:14:54 2014 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

Updated changelog

Revision 4874 - Directory Listing
Modified Thu Apr 17 01:13:10 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

fixed ripley dirac test for multiple ranks and added protections against MPI causing problems due to premature exits by some ranks

Revision 4873 - Directory Listing
Modified Wed Apr 16 06:38:51 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

whitespace only changes.

Revision 4872 - Directory Listing
Modified Wed Apr 16 06:08:06 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

adding dirac point interpolation tests for ripley, all ranks will be used in subdividing each axis in turn

Revision 4871 - Directory Listing
Modified Wed Apr 16 05:28:27 2014 UTC (4 years, 10 months ago) by jduplessis
Original Path: trunk

changed symconsts to symconsts to fit the rest of escript

Revision 4870 - Directory Listing
Modified Mon Apr 14 10:50:41 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

Q: ...so what does this papi flag do?
A: darn, you got me.
[now it prints errors with the papi version shipped with debian, hooray]

Revision 4869 - Directory Listing
Modified Mon Apr 14 10:39:22 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

all of paso now lives in its own namespace.

Revision 4868 - Directory Listing
Modified Sat Apr 12 01:50:15 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

don't report an error when there isn't one.....

Revision 4867 - Directory Listing
Modified Fri Apr 11 12:29:49 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

paso: starting to polish

Revision 4866 - Directory Listing
Modified Fri Apr 11 03:28:35 2014 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

Remove reference to epydoc documentation from doxygen (since our debian doc package uses sphinx).

Revision 4865 - Directory Listing
Modified Fri Apr 11 02:38:11 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

bringing doxygen reported version number up to date

Revision 4864 - Directory Listing
Modified Fri Apr 11 02:04:18 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

fixing mkl build.

Revision 4862 - Directory Listing
Modified Thu Apr 10 05:35:56 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

removing leftover debug prints

Revision 4861 - Directory Listing
Modified Thu Apr 10 05:17:47 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

added exception for domain sizes that cause integer overflows

Revision 4860 - Directory Listing
Modified Thu Apr 10 04:08:42 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

wrapping resize exceptions for overly large domains (previous message to user was: 'RuntimeError: vector::_M_fill_insert')

Revision 4859 - Directory Listing
Modified Thu Apr 10 00:23:29 2014 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

Avoid division by zero

Revision 4858 - Directory Listing
Modified Wed Apr 9 23:34:17 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

skipping multirank segywriter tests now that multirank writes throw exceptions

Revision 4857 - Directory Listing
Modified Wed Apr 9 06:54:59 2014 UTC (4 years, 10 months ago) by jduplessis
Original Path: trunk

modified atoms code that when type is set to escript.Symbol, sympy.symbol get added to the type list. This is because escript.symbols are represented by sympy symbols in the _arr list

Revision 4856 - Directory Listing
Modified Wed Apr 9 06:46:55 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

some mopping in paso

Revision 4855 - Directory Listing
Modified Wed Apr 9 06:19:59 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

removing leftover python solveroptions

Revision 4854 - Directory Listing
Modified Wed Apr 9 06:17:09 2014 UTC (4 years, 10 months ago) by gross
Original Path: trunk

FWI is running

Revision 4853 - Directory Listing
Modified Wed Apr 9 05:41:57 2014 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

Added import division and changed a few / to //

Revision 4852 - Directory Listing
Modified Wed Apr 9 03:58:08 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

paso util sweep

Revision 4851 - Directory Listing
Modified Wed Apr 9 03:30:36 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

added exceptions to ripley for more informative deaths to negative element counts

Revision 4850 - Directory Listing
Modified Wed Apr 9 02:26:22 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

adding exception for multi-rank segy write instead of failing to write correctly and reporting success

Revision 4849 - Directory Listing
Modified Wed Apr 9 02:14:58 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

More vacuuming.

Revision 4848 - Directory Listing
Modified Wed Apr 9 00:26:32 2014 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

lots of future print_function

Revision 4847 - Directory Listing
Modified Wed Apr 9 00:11:55 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

fixed awkard integer division in LinearMapping (py3 unaffected)

Revision 4846 - Directory Listing
Modified Tue Apr 8 23:55:38 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

paso::Options.

Revision 4845 - Directory Listing
Modified Tue Apr 8 11:35:27 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

I fink I broke it - now I thixed it.

Revision 4844 - Directory Listing
Modified Tue Apr 8 07:56:52 2014 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

Removing MPIInfo from pythonMPI

Revision 4843 - Directory Listing
Modified Tue Apr 8 05:32:07 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

checkpointing paso::Preconditioner.

Revision 4842 - Directory Listing
Modified Tue Apr 8 04:50:05 2014 UTC (4 years, 10 months ago) by jduplessis
Original Path: trunk

Removing variational problem as it will not be part of the release

Revision 4841 - Directory Listing
Modified Tue Apr 8 03:49:18 2014 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

keeping older compilers happy

Revision 4840 - Directory Listing
Modified Tue Apr 8 03:24:47 2014 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

scons options for trusty

Revision 4839 - Directory Listing
Modified Tue Apr 8 03:14:23 2014 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

Adding initial support for ubuntu trusty

Revision 4838 - Directory Listing
Modified Mon Apr 7 10:16:21 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

Fixing non-mpi build.

Revision 4837 - Directory Listing
Modified Mon Apr 7 05:59:24 2014 UTC (4 years, 10 months ago) by jduplessis
Original Path: trunk

added test for evalf

Revision 4836 - Directory Listing
Modified Mon Apr 7 05:51:55 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

"Some" SystemMatrix clean up.....

Revision 4835 - Directory Listing
Modified Mon Apr 7 04:29:20 2014 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

removing unused MIS

Revision 4833 - Directory Listing
Modified Sun Apr 6 23:30:34 2014 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

Adding missing names.

Revision 4832 - Directory Listing
Modified Fri Apr 4 05:03:45 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

some incredibly long lines are now much, much nicer to read/wrap

Revision 4831 - Directory Listing
Modified Fri Apr 4 02:42:52 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

fixing MKL compile.

Revision 4830 - Directory Listing
Modified Thu Apr 3 04:45:06 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

Removed obsolete file, reverted verbosity of test and a bit more cleanup.

Revision 4829 - Directory Listing
Modified Thu Apr 3 04:02:53 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

checkpointing some SparseMatrix cleanup.

Revision 4828 - Directory Listing
Modified Wed Apr 2 07:01:38 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

more tightly constrained checks on types and lengths of dirac points and tags in ripley python constructors

Revision 4827 - Directory Listing
Modified Wed Apr 2 07:00:15 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

dropping out of domain dirac points for ripley Brick as well

Revision 4826 - Directory Listing
Modified Wed Apr 2 03:54:18 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

changing ripley to drop dirac points outside domain rather than try to map them, matches finley behaviour

Revision 4825 - Directory Listing
Modified Wed Apr 2 03:53:23 2014 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

Addresses issue 241

Revision 4824 - Directory Listing
Modified Tue Apr 1 06:40:19 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

fixed sillyness with serial builds reporting as MPI

Revision 4823 - Directory Listing
Modified Tue Apr 1 05:46:07 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

SolverBuddy documentation changes from old python docstrings to doxygen format

Revision 4822 - Directory Listing
Modified Tue Apr 1 05:05:45 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

now with all required files at no extra cost

Revision 4821 - Directory Listing
Modified Tue Apr 1 04:58:33 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

moved SolverOptions to c++, split into SolverOptions for the options and SolverBuddy as the state as a precursor to per-pde solving... does break some use cases (e.g. pde.getSolverOptions().DIRECT will now fail, new value access is with SolverOptions.DIRECT), examples and documentation updated to match

Revision 4820 - Directory Listing
Modified Tue Apr 1 04:55:49 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

allowing for larger amounts of variable tracking with debug=true (mostly for escriptcpp.cpp)

Revision 4819 - Directory Listing
Modified Tue Apr 1 03:50:23 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

Pattern shared ptrs

Revision 4818 - Directory Listing
Modified Mon Mar 31 00:16:20 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

SystemMatrixPattern shptr

Revision 4817 - Directory Listing
Modified Fri Mar 28 08:04:09 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

Coupler/Connector shared ptrs.

Revision 4816 - Directory Listing
Modified Fri Mar 28 06:16:02 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

paso::SharedComponents now header-only and shared ptr managed.

Revision 4815 - Directory Listing
Modified Fri Mar 28 05:25:56 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

replacing awful config file debugthing

Revision 4814 - Directory Listing
Modified Fri Mar 28 04:31:02 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

paso::Distribution instances are now managed by a boost::shared_ptr, methods
are all inline.

Revision 4811 - Directory Listing
Modified Thu Mar 27 07:00:46 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

moving away from shared pointers in domain components

Revision 4810 - Directory Listing
Modified Thu Mar 27 07:00:30 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

Removed some obsolete checkPtr's. More to come...

Revision 4809 - Directory Listing
Modified Thu Mar 27 05:52:41 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

Removed code duplication and moved IndexList to esysUtils header only.
Renamed AML.cpp which is old,unused code.

Revision 4807 - Directory Listing
Modified Thu Mar 27 04:49:38 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

2 fixes to dirac points which fixes #240.

Revision 4806 - Directory Listing
Modified Thu Mar 27 03:03:13 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

fixed fetch error in type collation for lame assembler

Revision 4805 - Directory Listing
Modified Thu Mar 27 01:31:59 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

changing 2D wave assembler to use shared domain pointer

Revision 4803 - Directory Listing
Modified Wed Mar 26 06:52:28 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

Removed obsolete wrappers for malloc and friends.
Paso_Pattern -> paso::Pattern

Revision 4801 - Directory Listing
Modified Wed Mar 26 03:26:58 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

paso::Coupler and paso::Connector.

Revision 4800 - Directory Listing
Modified Wed Mar 26 01:50:04 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

paso::SystemMatrixPattern

Revision 4799 - Directory Listing
Modified Wed Mar 26 00:37:59 2014 UTC (4 years, 10 months ago) by sshaw
Original Path: trunk

storing the code generators for the relevant chunks of the lame assembler

Revision 4798 - Directory Listing
Modified Tue Mar 25 22:08:30 2014 UTC (4 years, 10 months ago) by caltinay
Original Path: trunk

added missing const.

Revision 4797 - Directory Listing
Modified Mon Mar 24 05:42:42 2014 UTC (4 years, 11 months ago) by caltinay
Original Path: trunk

put SparseMatrix into paso namespace, accompanied by minor code cleanup.

Revision 4795 - Directory Listing
Modified Mon Mar 24 01:50:32 2014 UTC (4 years, 11 months ago) by caltinay
Original Path: trunk

code cleanup of paso::SparseMatrix_MatrixVector and variants.
Mostly a no-op.

Revision 4794 - Directory Listing
Modified Mon Mar 24 01:01:30 2014 UTC (4 years, 11 months ago) by jduplessis
Original Path: trunk

adding symbolic to user guide, work in progress

Revision 4793 - Directory Listing
Modified Fri Mar 21 06:44:26 2014 UTC (4 years, 11 months ago) by jduplessis
Original Path: trunk

changed 'dict_keys' object to list so that it can be indexed

Revision 4792 - Directory Listing
Modified Fri Mar 21 05:06:11 2014 UTC (4 years, 11 months ago) by jfenwick
Original Path: trunk

make escriptcore/ visible

Revision 4791 - Directory Listing
Modified Fri Mar 21 03:32:56 2014 UTC (4 years, 11 months ago) by jduplessis
Original Path: trunk

changed has_key to in for python 3

Revision 4789 - Directory Listing
Modified Fri Mar 21 00:30:32 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

changing more awkward logic into more obvious (and correct, though i doubt a negative length ever happens) logic

Revision 4788 - Directory Listing
Modified Fri Mar 21 00:11:09 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

fixed a broken numerical comparison

Revision 4787 - Directory Listing
Modified Fri Mar 21 00:08:15 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

changed header guard definition to match header guard check

Revision 4786 - Directory Listing
Modified Thu Mar 20 23:53:44 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

fixed silly naming issue

Revision 4783 - Directory Listing
Modified Thu Mar 20 06:23:23 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

refactored linearPDE tests (removing repetition)

Revision 4782 - Directory Listing
Modified Thu Mar 20 05:16:16 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

cleaned up and simplified run_seismic tests, including specific checking for obspy not being installed

Revision 4781 - Directory Listing
Modified Thu Mar 20 04:57:07 2014 UTC (4 years, 11 months ago) by jduplessis
Original Path: trunk

added test for preservation of data substitutions

Revision 4780 - Directory Listing
Modified Thu Mar 20 03:19:54 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

fixing a race condition in file tests

Revision 4779 - Directory Listing
Modified Thu Mar 20 01:52:49 2014 UTC (4 years, 11 months ago) by jfenwick
Original Path: trunk

Temporarily adjusting magic numbers

Revision 4778 - Directory Listing
Modified Thu Mar 20 00:41:58 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

python3ified tests using deprecated test methods ( #89 and #106 ), added run_seismic into downunder tests (with skips if obspy/segywriters fail to write)

Revision 4777 - Directory Listing
Modified Wed Mar 19 23:52:36 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

replacing xrange with range for python3 compatibility, refs #106

Revision 4776 - Directory Listing
Modified Wed Mar 19 23:31:00 2014 UTC (4 years, 11 months ago) by caltinay
Original Path: trunk

Removed some superfluous checks and typos.

Revision 4775 - Directory Listing
Modified Wed Mar 19 23:12:53 2014 UTC (4 years, 11 months ago) by caltinay
Original Path: trunk

Moved matrix format exception further up the stack which fixes #109.
Also, removed default defines CORE_ID1 and BLOCKTIMER, added the former to
savanna's options.

Revision 4772 - Directory Listing
Modified Wed Mar 19 04:28:53 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

removing ridiculous remaining return

Revision 4771 - Directory Listing
Modified Wed Mar 19 04:22:37 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

fixed multiple ranks trying to unlink tempfiles

Revision 4770 - Directory Listing
Modified Wed Mar 19 03:48:43 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

relevant tests skipped if not built with USE_BOOSTIO

Revision 4769 - Directory Listing
Modified Wed Mar 19 03:43:52 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

added missing ifdefs for library presence

Revision 4768 - Directory Listing
Modified Wed Mar 19 02:51:33 2014 UTC (4 years, 11 months ago) by jduplessis
Original Path: trunk

Removed commented for loops

Revision 4767 - Directory Listing
Modified Wed Mar 19 02:48:33 2014 UTC (4 years, 11 months ago) by jduplessis
Original Path: trunk

Major issues with subs and data objects have been rectified. subs was also not working properly for symbol to symbol substitutions this has been rectified.

Revision 4766 - Directory Listing
Modified Wed Mar 19 00:57:21 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

allowed custom assemblers a value tolerance in tests (for case of 0 to 1 in objects, tolerance of 1e-8)

Revision 4765 - Directory Listing
Modified Wed Mar 19 00:17:16 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

added ripley rectangle reading from compressed files, added unit tests for binaryGrid reads and writes (only single ranks for compressed thus far) (#104)

Revision 4764 - Directory Listing
Modified Tue Mar 18 15:58:21 2014 UTC (4 years, 11 months ago) by gross
Original Path: trunk

mapping test fixed

Revision 4761 - Directory Listing
Modified Tue Mar 18 00:25:55 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

fixed partially overridden class warnings with intel compiler

Revision 4760 - Directory Listing
Modified Mon Mar 17 23:48:37 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

moved functionspace type collation from RipleyDomain into custom assemblers, refs #102

Revision 4759 - Directory Listing
Modified Mon Mar 17 07:52:26 2014 UTC (4 years, 11 months ago) by jfenwick
Original Path: trunk

Throw TypeError on any attempt to use relational ops on Data, FunctionSpace and Domain.  Also fixes a type error in run_mappings.py but the test still fails.

Revision 4758 - Directory Listing
Modified Mon Mar 17 05:00:27 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

fixed classname typo for AcousticVelocityMapping, added exceptions for ordered comparisons with Data objects from python (#107)

Revision 4755 - Directory Listing
Modified Mon Mar 17 02:58:52 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

added conflict test for ripley Brick

Revision 4754 - Directory Listing
Modified Mon Mar 17 02:51:12 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

now with 0% missing files!

Revision 4753 - Directory Listing
Modified Mon Mar 17 02:39:44 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

added exceptions for conflicting assembler types, added tests for lame assemblers

Revision 4751 - Directory Listing
Modified Fri Mar 14 06:49:06 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

completed LameAssemblers

Revision 4749 - Directory Listing
Modified Fri Mar 14 03:05:07 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

making inversioncostfunctions python3 compatible

Revision 4748 - Directory Listing
Modified Fri Mar 14 00:30:51 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

adjusted InversionCostFunction tests to run on arbitrary numbers of ranks

Revision 4744 - Directory Listing
Modified Wed Mar 12 21:30:10 2014 UTC (4 years, 11 months ago) by gross
Original Path: trunk

first version of a FWI

Revision 4743 - Directory Listing
Modified Wed Mar 12 21:09:20 2014 UTC (4 years, 11 months ago) by gross
Original Path: trunk

mapping for FWI added

Revision 4742 - Directory Listing
Modified Wed Mar 12 07:21:24 2014 UTC (4 years, 11 months ago) by jduplessis
Original Path: trunk

updated setitem and getitem to preserve data substitutions

Revision 4741 - Directory Listing
Modified Wed Mar 12 03:31:10 2014 UTC (4 years, 11 months ago) by jfenwick
Original Path: trunk

Fix scoping because my compiler complained. g++4.8 thing?

Revision 4740 - Directory Listing
Modified Wed Mar 12 03:26:13 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

exporting compression support to buildvars

Revision 4739 - Directory Listing
Modified Wed Mar 12 03:25:32 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

fixing test file filename mismatch

Revision 4738 - Directory Listing
Modified Wed Mar 12 01:32:36 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

adding support for reading binary grids from gzip compressed binary files, ripley brick only so far

Revision 4735 - Directory Listing
Modified Mon Mar 10 07:44:58 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

fixing/completing 2D lame assembler

Revision 4733 - Directory Listing
Modified Mon Mar 10 05:57:11 2014 UTC (4 years, 11 months ago) by jduplessis
Original Path: trunk

added a check to only get data substitutions on symbols

Revision 4729 - Directory Listing
Modified Sat Mar 8 00:56:37 2014 UTC (4 years, 11 months ago) by gross
Original Path: trunk

a more general for of the inversioncostfunction has required for waveform inversin

Revision 4727 - Directory Listing
Modified Fri Mar 7 05:28:12 2014 UTC (4 years, 11 months ago) by jduplessis
Original Path: trunk

added an optional evalf input to the evaluator, without this constants such as pi etc wont get evaluated. and renamed constants symconstants

Revision 4726 - Directory Listing
Modified Fri Mar 7 00:23:44 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

Added a success/fail line below config in build process ( redmine #26 )

Revision 4723 - Directory Listing
Modified Wed Mar 5 05:40:25 2014 UTC (4 years, 11 months ago) by jduplessis
Original Path: trunk

fixed presenservation of data objects(data substitutions) when subs is called on a symbol

Revision 4722 - Directory Listing
Modified Wed Mar 5 05:29:25 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

vastly decreased ripley domain setup time under MPI (approximately from O(n*m) to O(n+m), n being shared nodes, m being the rank DOF)

Revision 4721 - Directory Listing
Modified Fri Feb 28 03:51:07 2014 UTC (4 years, 11 months ago) by jfenwick
Original Path: trunk

Fixing strange casts.
Removed old methods.

Revision 4720 - Directory Listing
Modified Fri Feb 28 01:38:09 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

ripley now tested with lame, helmholtz and nolumping linear PDEs

Revision 4719 - Directory Listing
Modified Fri Feb 28 00:27:29 2014 UTC (4 years, 11 months ago) by jfenwick
Original Path: trunk

Modify run_forward test to account for small negative results.

Revision 4718 - Directory Listing
Modified Thu Feb 27 23:43:12 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

Added a missed include guard

Revision 4717 - Directory Listing
Modified Thu Feb 27 12:30:04 2014 UTC (4 years, 11 months ago) by jfenwick
Original Path: trunk

Fix copy error from 3d down to 2d.

Revision 4716 - Directory Listing
Modified Thu Feb 27 11:02:55 2014 UTC (4 years, 11 months ago) by jfenwick
Original Path: trunk

Fixed some bad indenting.
Skip non-linear tests if sympy is not available.

Revision 4715 - Directory Listing
Modified Thu Feb 27 07:57:45 2014 UTC (4 years, 11 months ago) by jfenwick
Original Path: trunk

Fixing print statement

Revision 4714 - Directory Listing
Modified Thu Feb 27 05:04:15 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

made non-linearPDE tests on ripley work with any number of ranks

Revision 4713 - Directory Listing
Modified Thu Feb 27 02:00:15 2014 UTC (4 years, 11 months ago) by jfenwick
Original Path: trunk

Added a temporay fix to get some of the unit tests passing again.
This mechanism will be removed before the release so don't get used to it.

Revision 4712 - Directory Listing
Modified Wed Feb 26 04:08:41 2014 UTC (4 years, 11 months ago) by sshaw
Original Path: trunk

adding skeleton of fast Lame assemblers
adjusted automatic ripley domain subdivision ( should solve issue #94 )
more tab->space conversions

Revision 4711 - Directory Listing
Modified Tue Feb 25 00:04:04 2014 UTC (4 years, 11 months ago) by jfenwick
Original Path: trunk

Another try at this test.

Revision 4710 - Directory Listing
Modified Mon Feb 24 03:41:06 2014 UTC (4 years, 11 months ago) by jfenwick
Original Path: trunk

Fixing not enough elements for small numbers of ranks in test

Revision 4709 - Directory Listing
Modified Mon Feb 24 01:31:00 2014 UTC (4 years, 11 months ago) by jfenwick
Original Path: trunk

Failed to take ripley padding into account when constructing tests.

Revision 4708 - Directory Listing
Modified Fri Feb 21 03:08:05 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

Removed rotation from ydirection test

Revision 4707 - Directory Listing
Modified Fri Feb 21 03:07:09 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

Modified domain in tests

Revision 4706 - Directory Listing
Modified Fri Feb 21 02:39:58 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Some additional cleanup I missed

Revision 4705 - Directory Listing
Modified Fri Feb 21 02:36:15 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Set the randomfill back to generating randoms and updated doco to tell people how to use it.

Revision 4704 - Directory Listing
Modified Fri Feb 21 01:11:30 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

added modification

double *F_p=NULL;
if(!p.F.isEmpty()) {
	p.F.requireWrite();
        F_p=p.F.getSampleDataRW(0);     
}

to all files such they will not operate on an empty F.

Revision 4703 - Directory Listing
Modified Fri Feb 21 00:55:31 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

This version has been tested in some detail. It does not actually do randoms though (since that wrecks the testing).  In will do a commit soon which puts the randomness back

Revision 4702 - Directory Listing
Modified Thu Feb 20 06:36:00 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

updated test_yDirection fixed a couple of small bugs

Revision 4701 - Directory Listing
Modified Thu Feb 20 06:32:12 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

Put in a check to make sure F is not used when empty. This prevents an exception.

Revision 4700 - Directory Listing
Modified Thu Feb 20 03:57:17 2014 UTC (5 years ago) by gross
Original Path: trunk

some more work toward seismic data

Revision 4699 - Directory Listing
Modified Wed Feb 19 09:31:45 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

Added test when adding incorrect Dim And Shape, for tryin to set Unknown Perameter and a test to make sure the definition of y is correct

Revision 4698 - Directory Listing
Modified Wed Feb 19 08:10:12 2014 UTC (5 years ago) by gross
Original Path: trunk

data sources support tags now

Revision 4697 - Directory Listing
Modified Wed Feb 19 08:03:56 2014 UTC (5 years ago) by gross
Original Path: trunk

data sources support tags now

Revision 4696 - Directory Listing
Modified Wed Feb 19 07:29:50 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Correcting python libname for sage.
Fixing bug where the number of values in the shape was not considered for buffer and message size.

Revision 4695 - Directory Listing
Modified Wed Feb 19 06:58:41 2014 UTC (5 years ago) by sshaw
Original Path: trunk

added warning output when saving as silo but not built with silo support (redmine #87 )

Revision 4694 - Directory Listing
Modified Wed Feb 19 06:25:55 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

fixed __getitem__ such that the symbol it return will have the same dimentionality as its parent symbol

Revision 4693 - Directory Listing
Modified Wed Feb 19 06:04:28 2014 UTC (5 years ago) by sshaw
Original Path: trunk

adding HTI support to 3D wave assembler

Revision 4692 - Directory Listing
Modified Wed Feb 19 05:26:55 2014 UTC (5 years ago) by sshaw
Original Path: trunk

fixed duplication for 2D constant data in wave assembler

Revision 4691 - Directory Listing
Modified Wed Feb 19 05:23:17 2014 UTC (5 years ago) by sshaw
Original Path: trunk

added support for HTI waves to the fast wave assembler

Revision 4690 - Directory Listing
Modified Wed Feb 19 05:22:16 2014 UTC (5 years ago) by sshaw
Original Path: trunk

adjusting porcupine config to use MPI by default

Revision 4689 - Directory Listing
Modified Wed Feb 19 05:13:17 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Give the unit test enough room

Revision 4688 - Directory Listing
Modified Wed Feb 19 03:18:58 2014 UTC (5 years ago) by gross
Original Path: trunk

acoustic forward problem + testing add

Revision 4687 - Directory Listing
Modified Wed Feb 19 00:03:29 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Remove randomFill python method from ripley domains.
All random data objects (for all domain types) should be generated 
using esys.escript.RandomData()

The only filtered random we have is gaussian on ripley but
it is triggered by passing the tuple as the last arg of RandomData().

While the interface is a bit more complicated (in that you always need
 to pass in shape and functionspace) it does mean we have a 
common interface for all domains. 

Removed randomFill from DataExpanded.
The reasoning behind this is to force domains to call the util function
themselves and enforce whatever consistancy requirements they have.

Added version of blocktools to deal with 2D case in Ripley.
Use blocktools for the 2D transfers [This was cleaner than modifying the
previous implementation to deal with variable shaped points].

Note that under MPI, ripley can not generate random data (even unfiltered)
if any of its per rank dimensions is <4 elements on any side.

Unit tests for these calls are in but some extra checks still needed.

Revision 4686 - Directory Listing
Modified Tue Feb 18 06:04:13 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

modified nonlinearPDE to be compatible with python 3.

Revision 4685 - Directory Listing
Modified Tue Feb 18 04:19:27 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

Replaced python dictionary iteritems with item for python 3.0 compatibility

Revision 4684 - Directory Listing
Modified Tue Feb 18 01:17:02 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

Removing Finley mesh import which was copied from run_linearPdeOnFinley... as it is not used.

Revision 4683 - Directory Listing
Modified Mon Feb 17 07:03:40 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

adding nonlinearpde test for ripley.

Revision 4678 - Directory Listing
Modified Mon Feb 17 03:35:08 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

adding ripley test for nlpde

Revision 4676 - Directory Listing
Modified Mon Feb 17 02:41:15 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

Unit test for nonlinear pde. 
test that it can generate a solution without error and that the appropriate coefficients are generated when setValue is called.

Revision 4675 - Directory Listing
Modified Mon Feb 17 01:07:12 2014 UTC (5 years ago) by sshaw
Original Path: trunk

expanded tab chars for consistentcy and removed trailing whitespace

Revision 4674 - Directory Listing
Modified Thu Feb 13 23:47:04 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Not using GNU only getopt arguments

Revision 4673 - Directory Listing
Modified Thu Feb 13 08:14:11 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Ammended install doco for OSX

Revision 4672 - Directory Listing
Modified Thu Feb 13 01:10:29 2014 UTC (5 years ago) by sshaw
Original Path: trunk

compacted older style C comparison structure

Revision 4671 - Directory Listing
Modified Thu Feb 13 00:18:10 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Fixed another comparator which wasn't strict

Revision 4670 - Directory Listing
Modified Wed Feb 12 08:24:31 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Correcting comparator function so it acts as < rather than <=

Revision 4669 - Directory Listing
Modified Tue Feb 11 06:10:27 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Replacing .eps figures in user guide with their pdf versions.
If you are creating new figures, then please don't use .eps

Revision 4668 - Directory Listing
Modified Tue Feb 11 03:44:10 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Improvements but still needs more validation

Revision 4667 - Directory Listing
Modified Tue Feb 11 00:47:26 2014 UTC (5 years ago) by sshaw
Original Path: trunk

adjusted launcher to run efficiently/properly on raijin

Revision 4666 - Directory Listing
Modified Mon Feb 10 03:33:51 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

check in util no longer necassary due to wrappings in contants.py

Revision 4665 - Directory Listing
Modified Mon Feb 10 03:29:02 2014 UTC (5 years ago) by caltinay
Original Path: trunk

This should help running on raijin without damaging anything.

Revision 4664 - Directory Listing
Modified Mon Feb 10 01:57:11 2014 UTC (5 years ago) by caltinay
Original Path: trunk

Trying to make the shell on osx happy.

Revision 4663 - Directory Listing
Modified Mon Feb 10 00:48:49 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

Adding wrapper for Symbolic constants such as pi
usage:
	symconsts.pi  ---> gives escript Symbol(sympy.pi)

Revision 4662 - Directory Listing
Modified Sun Feb 9 23:03:45 2014 UTC (5 years ago) by caltinay
Original Path: trunk

Cater for changed interface in sympy 0.7.2.
Also silenced a harmless warning.

Revision 4661 - Directory Listing
Modified Fri Feb 7 03:10:15 2014 UTC (5 years ago) by sshaw
Original Path: trunk

more informative exception for unsupported error message

Revision 4660 - Directory Listing
Modified Fri Feb 7 03:08:49 2014 UTC (5 years ago) by sshaw
Original Path: trunk

fixed dirac point->node mapping issues in ripley when using mpi

Revision 4659 - Directory Listing
Modified Fri Feb 7 00:13:47 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

New solution to cos(sympy.pi). This solution help to keep sympy optional in escript and provides the desired functionality.

Revision 4658 - Directory Listing
Modified Thu Feb 6 13:28:56 2014 UTC (5 years ago) by caltinay
Original Path: trunk

This seems to fix #65 but is a bit scary.
netcdf and gdal (and others?) seem to return bytearrays instead of strings in
py3, which when fed back into a library function caused a segfault.
Not sure if I caught every case and whether this is actually a bug in the lib...

Revision 4657 - Directory Listing
Modified Thu Feb 6 06:12:20 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

I changed some files.
Updated copyright notices, added GeoComp.

Revision 4654 - Directory Listing
Modified Wed Feb 5 06:55:35 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

Modified some of the util function so that they will operate with general sympy objects such as pi.

This is usefull when you want to do 

sin(pi) or cos(pi) for example 

where pi is a sympy object.

Revision 4653 - Directory Listing
Modified Wed Feb 5 05:20:41 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Made index chars unsigned to prevent warnings

Revision 4652 - Directory Listing
Modified Wed Feb 5 05:15:07 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Made index chars unsigned to prevent warnings

Revision 4650 - Directory Listing
Modified Wed Feb 5 04:16:01 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Fixed a spelling error and missing virtual (not sure that one matters).
Added _untested_ 3D gaussian smoothed random data

Revision 4648 - Directory Listing
Modified Wed Feb 5 02:03:08 2014 UTC (5 years ago) by caltinay
Original Path: trunk

Fix segfault reported in #57.

Revision 4647 - Directory Listing
Modified Mon Feb 3 03:29:43 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

Commiting to make sure line 309 doesn't contain print len(u_syms)\n

Revision 4646 - Directory Listing
Modified Mon Feb 3 00:25:58 2014 UTC (5 years ago) by gross
Original Path: trunk

some extensions to synthetic_sonicHTI.py

Revision 4645 - Directory Listing
Modified Mon Feb 3 00:06:24 2014 UTC (5 years ago) by sshaw
Original Path: trunk

further optimisation of wave assemblers, added support for constant data

Revision 4644 - Directory Listing
Modified Mon Feb 3 00:03:52 2014 UTC (5 years ago) by sshaw
Original Path: trunk

fixed indent errors in coalgas, added future print import to seismic_wave, since it was using py3 style prints

Revision 4643 - Directory Listing
Modified Sun Feb 2 23:52:38 2014 UTC (5 years ago) by sshaw
Original Path: trunk

fixed some error message formatting interpreting tuples badly

Revision 4642 - Directory Listing
Modified Fri Jan 31 02:16:45 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Renamed the default options file to make it clear that it was used for g++.
There is now no default mole options file.
This is deliberate. You need to configure your environment based on the compiler you wish to use. (See scripts in /usr/local/env).

If you are doing a lot of building, symlink your chosen file to scons/mole_options.py. DO NOT COMMIT it though.

Revision 4641 - Directory Listing
Modified Fri Jan 31 02:13:47 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

line 966 

	"if not args.has_key(n): args[n]=Data()" was changed to "if not args.has_key(n) and not constants.has_key(n): args[n]=Data()".

also added: 

	args=dict(args.items()+constants.items())

to merge the two dictionaries.

Revision 4640 - Directory Listing
Modified Fri Jan 31 00:56:51 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Ensure that DYLD_LIBRARY_PATH is passed into scons.
Update mole_options to work with g++
(To get this to work, you will need to set up your env vars).

Revision 4639 - Directory Listing
Modified Thu Jan 30 06:43:03 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

They should be equivalent but just in case ! ==  is treated differently to !=

Revision 4638 - Directory Listing
Modified Thu Jan 30 06:25:10 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Fixes necessary to get a clang/macports build working on 10.9

Revision 4636 - Directory Listing
Modified Tue Jan 28 04:24:30 2014 UTC (5 years ago) by sshaw
Original Path: trunk

fixed more whitespace issues

Revision 4635 - Directory Listing
Modified Tue Jan 28 03:34:04 2014 UTC (5 years ago) by sshaw
Original Path: trunk

fixed mixed tabs/spaces for python 3 compatibility

Revision 4634 - Directory Listing
Modified Tue Jan 28 03:33:03 2014 UTC (5 years ago) by jfenwick
Original Path: trunk

Fixes to keep clang happy

Revision 4633 - Directory Listing
Modified Tue Jan 28 01:04:17 2014 UTC (5 years ago) by caltinay
Original Path: trunk

Fixed failure for lazy data when interpolating.

Revision 4630 - Directory Listing
Modified Fri Jan 24 03:32:11 2014 UTC (5 years ago) by sshaw
Original Path: trunk

fixed a leftover from testin gin seismic, changed synthetic_VTI example back to original large 2D problem

Revision 4629 - Directory Listing
Modified Fri Jan 24 03:29:25 2014 UTC (5 years ago) by sshaw
Original Path: trunk

added dirac point interpolation to ripley (and fixed dirac points in Brick)
added fast wave assembler for Brick and minor correction to fast wave assembler for Rectangle

Revision 4628 - Directory Listing
Modified Fri Jan 24 02:09:19 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

Modifying nonlinearPDE.py comments to make the meaning clearer

Revision 4627 - Directory Listing
Modified Fri Jan 24 01:53:33 2014 UTC (5 years ago) by jduplessis
Original Path: trunk

fixing error in comment

Revision 4626 - Directory Listing
Modified Wed Jan 22 06:07:34 2014 UTC (5 years, 1 month ago) by caltinay
Original Path: trunk

Eliminated all const_cast<Data*> hacks in ripley and finley now that
Data.getSampleDataRO returns a const pointer.

Revision 4625 - Directory Listing
Modified Mon Jan 20 03:42:55 2014 UTC (5 years, 1 month ago) by sshaw
Original Path: trunk

amalgamated waveassembler constant construction into the one place

Revision 4624 - Directory Listing
Modified Sun Jan 19 23:03:59 2014 UTC (5 years, 1 month ago) by sshaw
Original Path: trunk

removed some leftover debug prints

Revision 4623 - Directory Listing
Modified Fri Jan 17 05:53:17 2014 UTC (5 years, 1 month ago) by sshaw
Original Path: trunk

added missing files and a spare missing comma, also the ability for finley VTIWaves to not crash

Revision 4622 - Directory Listing
Modified Fri Jan 17 04:55:41 2014 UTC (5 years, 1 month ago) by sshaw
Original Path: trunk

Added dirac support to ripley, added interface for custom assemblers for ripleydomains (also added the custom assembler for 2D VTI waves), changed synthetic_VTI example to use the new, faster custom assembler

Revision 4621 - Directory Listing
Modified Thu Jan 16 10:07:44 2014 UTC (5 years, 1 month ago) by jfenwick
Original Path: trunk

getSampleDataRO is now const

Revision 4620 - Directory Listing
Modified Thu Jan 16 03:17:20 2014 UTC (5 years, 1 month ago) by caltinay
Original Path: trunk

py3 RuntimeError does not have 'message' member.

Revision 4619 - Directory Listing
Modified Thu Jan 16 02:10:26 2014 UTC (5 years, 1 month ago) by caltinay
Original Path: trunk

updated gp py3 options.

Revision 4618 - Directory Listing
Modified Wed Jan 15 04:35:19 2014 UTC (5 years, 1 month ago) by caltinay
Original Path: trunk

Implemented reverse reading of grid data from netcdf files.
Fixes #44.

Revision 4617 - Directory Listing
Modified Wed Jan 15 03:49:19 2014 UTC (5 years, 1 month ago) by caltinay
Original Path: trunk

new name for boost library on guineapig

Revision 4616 - Directory Listing
Modified Tue Jan 14 22:57:47 2014 UTC (5 years, 1 month ago) by caltinay
Original Path: trunk

- Fixed unit test failure by populating missing parts of the struct
- prepared for reversing read order from grids
- worked around a segfault caused by python version in jessie (2.7.6) in
  combination with gdal,pyproj and RTLD_GLOBAL in dlopen flags.

Revision 4615 - Directory Listing
Modified Mon Jan 13 05:05:33 2014 UTC (5 years, 1 month ago) by caltinay
Original Path: trunk

Step 1 for #31: wrap parameters in an object.

Revision 4614 - Directory Listing
Modified Mon Jan 13 02:44:07 2014 UTC (5 years, 1 month ago) by caltinay
Original Path: trunk

Corrected a faulty test.

Revision 4613 - Directory Listing
Modified Mon Jan 13 01:09:01 2014 UTC (5 years, 1 month ago) by caltinay
Original Path: trunk

Addresses #43 - altitude is now scaled according to reference system height
unit.
Also separated out UTM zone determination from the actual projection code
to silence bogus output.

Revision 4612 - Directory Listing
Modified Thu Jan 9 05:30:27 2014 UTC (5 years, 1 month ago) by gross
Original Path: trunk

modifications to sonic seismic

Revision 4611 - Directory Listing
Modified Mon Dec 23 04:03:00 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

scaling corrected

Revision 4610 - Directory Listing
Modified Mon Dec 23 00:01:23 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

exposed createAbsorbtionLayerFunction

Revision 4609 - Directory Listing
Modified Fri Dec 20 07:56:56 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

fix to deal with empty right hand side vector F.

Revision 4608 - Directory Listing
Modified Fri Dec 20 01:53:04 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

tiny grammar fix in user guide

Revision 4607 - Directory Listing
Modified Wed Dec 18 09:46:16 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

include cmath in all cases rather than math.h - the mathinf for intel on windows is still there (in part because we have no way to test if it is still relevant)

Revision 4606 - Directory Listing
Modified Wed Dec 18 08:21:25 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Updating run_models to not call the old DarcyFlow methods

Revision 4605 - Directory Listing
Modified Wed Dec 18 06:05:43 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Mantis issue #675 said

Cihan:
while merging symbolic into trunk I noticed that most dudley tests are
disabled. This happened in revision 3261 where you wrote:

"Disable some unit tests for dudley until I can fix MPI failures"

Is that fixed?

=== I'm renabling most of the test (which pass without difficulty).
But one of them appears to be out of date or something.
More investigation required.

Revision 4604 - Directory Listing
Modified Wed Dec 18 03:29:26 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

fixed tabs/space mix for python3

Revision 4603 - Directory Listing
Modified Wed Dec 18 02:24:32 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Added boost::noncopyable to remaining abstract base classes in the module file.
ie escriptcpp.cpp
Note I have not altered the c++ inheritance (this just just for the boost::python import)

Revision 4602 - Directory Listing
Modified Wed Dec 18 01:15:22 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Fixed missing \

Revision 4601 - Directory Listing
Modified Tue Dec 17 23:37:08 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

downunder: self-demagnetization added as forward model.

Revision 4600 - Directory Listing
Modified Tue Dec 17 04:28:40 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Using section: science in debian/control instead of main.
This new value for section has the virtue of actually existing

Revision 4599 - Directory Listing
Modified Sun Dec 15 23:51:13 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

merged 3.4.1 release changes into trunk

Revision 4598 - Directory Listing
Modified Sun Dec 15 23:39:16 2013 UTC (5 years, 2 months ago) by rschaa
Original Path: trunk

Minor change to figure.
Replaced .pdf with .png

Revision 4597 - Directory Listing
Modified Sun Dec 15 22:36:24 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

unused variable fixed

Revision 4586 - Directory Listing
Modified Wed Dec 11 06:03:27 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

2D guassian smoothing of random data done.
Added more memory non-leaks to the supp file

Revision 4585 - Directory Listing
Modified Wed Dec 11 04:39:54 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

uint -> unsigned int

Revision 4584 - Directory Listing
Modified Wed Dec 11 04:24:15 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

more buildbot commit testing

Revision 4583 - Directory Listing
Modified Wed Dec 11 02:09:19 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

deliberate error to test buildbot

Revision 4582 - Directory Listing
Modified Wed Dec 11 02:08:41 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Added libpython version of suppressions to the aggressive file.
Rectangle now passes correct values around.
Random still to come.

Revision 4581 - Directory Listing
Modified Tue Dec 10 09:32:50 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Some more work on random
Added a more agressive (And smaller) supressions file for python

Revision 4580 - Directory Listing
Modified Tue Dec 10 06:10:44 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

fixed doc building relying on potentially missing python package installs (bug #739)

Revision 4579 - Directory Listing
Modified Tue Dec 10 04:08:20 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

adding porcupine's scons options file

Revision 4578 - Directory Listing
Modified Tue Dec 10 04:07:51 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

fixed gmsh Design deconstructor attempting to access non-existing members or files that were never created
also fixed a loose (non-)integer division for python3

Revision 4577 - Directory Listing
Modified Tue Dec 10 00:50:55 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

Undoing unintended commit of omp wrapper removal

Revision 4576 - Directory Listing
Modified Mon Dec 9 23:35:30 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

python3ified things, replaced mixed whitespace and xrange calls

Revision 4575 - Directory Listing
Modified Mon Dec 9 22:59:31 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Some more work on this

Revision 4574 - Directory Listing
Modified Mon Dec 9 04:29:44 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

some corrections

Revision 4572 - Directory Listing
Modified Sun Dec 8 00:54:37 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Some work on rectangle random MPI

Revision 4571 - Directory Listing
Modified Fri Dec 6 02:47:14 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

replaced a deliberate NULL dereference with abort() to satisfy lion-clang

Revision 4570 - Directory Listing
Modified Fri Dec 6 02:22:37 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

strain convention corrected.

Revision 4568 - Directory Listing
Modified Thu Dec 5 23:13:26 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Package building files for saucy

Revision 4567 - Directory Listing
Modified Thu Dec 5 09:00:23 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Options file for ubuntu 13.10

Revision 4566 - Directory Listing
Modified Thu Dec 5 01:02:47 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

fixed Dudley saveVTK crash on world size > 6 (mantis bug #738)

Revision 4565 - Directory Listing
Modified Wed Dec 4 06:42:30 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

and another typo fixed.

Revision 4561 - Directory Listing
Modified Wed Dec 4 05:19:32 2013 UTC (5 years, 2 months ago) by caltinay
Original Path: trunk

Removed spurious print and some minor changes in inversion example.

Revision 4560 - Directory Listing
Modified Wed Dec 4 03:43:57 2013 UTC (5 years, 2 months ago) by rschaa
Original Path: trunk

Options file for ferret

Revision 4559 - Directory Listing
Modified Wed Dec 4 02:05:34 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

renamed design.Design to design.AbstractDesign as a more explicit/descriptive name, this will break any existing custom implementation until changed to match

updated gmsh.Design docstring to match that of the code

Revision 4558 - Directory Listing
Modified Tue Dec 3 22:37:38 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Moving MeshAdapter constructor call out of smartptr constructor.  I think a throw in there would lead to undefined behaviour

Revision 4557 - Directory Listing
Modified Tue Dec 3 12:53:38 2013 UTC (5 years, 2 months ago) by caltinay
Original Path: trunk

Fixed boost/intel issue in dudley and synced options file with module on
savanna.

Revision 4556 - Directory Listing
Modified Tue Dec 3 05:40:53 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

fixed mixed tabs/spaces and py2 prints breaking the python3 compiler

Revision 4555 - Directory Listing
Modified Tue Dec 3 03:54:20 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

updated doc install instructions to match that required

Revision 4554 - Directory Listing
Modified Tue Dec 3 03:45:56 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

documentation spelling and whitespace corrections, added some Design.setOptions params that were missing from the userguide

Revision 4553 - Directory Listing
Modified Mon Dec 2 07:18:02 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

clarification on receiver array

Revision 4552 - Directory Listing
Modified Mon Dec 2 06:13:47 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

Replaced non-visible (when built) unicode endash with single dash in user guide source

Revision 4551 - Directory Listing
Modified Mon Dec 2 03:32:23 2013 UTC (5 years, 2 months ago) by sshaw
Original Path: trunk

Fixed missing install keyword in instructions

Revision 4550 - Directory Listing
Modified Fri Nov 29 07:44:37 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

some modifications

Revision 4549 - Directory Listing
Modified Fri Nov 29 05:24:40 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

argument for lumping added.

Revision 4547 - Directory Listing
Modified Thu Nov 28 23:47:27 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Added msec unit

Revision 4546 - Directory Listing
Modified Thu Nov 28 05:30:48 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

sonic wave propagation added

Revision 4545 - Directory Listing
Modified Thu Nov 28 05:02:43 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

wave simulator base added

Revision 4544 - Directory Listing
Modified Thu Nov 28 04:01:46 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

wave simulator base added

Revision 4543 - Directory Listing
Modified Thu Nov 28 03:42:10 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

missing retirn statement added

Revision 4542 - Directory Listing
Modified Thu Nov 28 01:33:22 2013 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Moving to new icc and associated modules.

Revision 4541 - Directory Listing
Modified Thu Nov 28 01:17:19 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

Ricker wavelet added

Revision 4540 - Directory Listing
Modified Thu Nov 28 01:06:10 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

segy writer added

Revision 4539 - Directory Listing
Modified Thu Nov 28 00:38:10 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

segy writer test added.

Revision 4538 - Directory Listing
Modified Thu Nov 28 00:37:48 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

segy writer added

Revision 4537 - Directory Listing
Modified Mon Nov 25 06:44:46 2013 UTC (5 years, 2 months ago) by gross
Original Path: trunk

missing references and double labeling fixed.

Revision 4536 - Directory Listing
Modified Thu Nov 21 07:58:32 2013 UTC (5 years, 3 months ago) by jfenwick
Original Path: trunk

Working around intelcc s seeming dislike of boost smart pointers

Revision 4535 - Directory Listing
Modified Wed Nov 20 06:37:53 2013 UTC (5 years, 3 months ago) by gross
Original Path: trunk

strong correlation joint inversion fixed.

Revision 4532 - Directory Listing
Modified Thu Nov 7 04:54:56 2013 UTC (5 years, 3 months ago) by gross
Original Path: trunk

strongly coupled joint inversion added

Revision 4531 - Directory Listing
Modified Mon Nov 4 02:09:05 2013 UTC (5 years, 3 months ago) by jfenwick
Original Path: trunk

Removed strange looking dead code to resolve issue #710

Revision 4530 - Directory Listing
Modified Wed Oct 30 04:34:21 2013 UTC (5 years, 3 months ago) by caltinay
Original Path: trunk

Fix in finley loadMesh which needs to call updateTagList() for all ranks, even
if a rank has no elements.

Revision 4529 - Directory Listing
Modified Fri Oct 25 01:23:27 2013 UTC (5 years, 3 months ago) by caltinay
Original Path: trunk

Ripley can now read grids in non-native byte order. This is in preparation for
Gocad Voxet import.

Revision 4528 - Directory Listing
Modified Sun Sep 29 23:12:19 2013 UTC (5 years, 4 months ago) by caltinay
Original Path: trunk

Added timeStepFormat option to saveESD (mantis 723).

Revision 4526 - Directory Listing
Modified Mon Sep 2 06:34:25 2013 UTC (5 years, 5 months ago) by jfenwick
Original Path: trunk

Single rank rectangle randoms.

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

Steube!!!!!

Revision 4523 - Directory Listing
Modified Mon Aug 26 23:04:07 2013 UTC (5 years, 5 months ago) by caltinay
Original Path: trunk

New working raijin options.

Revision 4522 - Directory Listing
Modified Mon Aug 26 22:15:26 2013 UTC (5 years, 5 months ago) by caltinay
Original Path: trunk

Newer versions of proj require specifying ellipsoid parameter.

Revision 4521 - Directory Listing
Modified Mon Aug 26 11:51:30 2013 UTC (5 years, 5 months ago) by jfenwick
Original Path: trunk

Remove bool_t
Part of random.

Revision 4520 - Directory Listing
Modified Thu Aug 22 06:42:57 2013 UTC (5 years, 6 months ago) by caltinay
Original Path: trunk

Removing spurious usage of C compiler:
-Changed all scons tests to use C++ compiler
-Renamed paso profiling files (unused)
-Updated most options files (removal of options and updated comments)

Revision 4519 - Directory Listing
Modified Mon Aug 19 05:56:22 2013 UTC (5 years, 6 months ago) by caltinay
Original Path: trunk

Initial raijin options file.

Revision 4518 - Directory Listing
Modified Tue Aug 13 01:49:59 2013 UTC (5 years, 6 months ago) by caltinay
Original Path: trunk

The line search step length caching should only be used within esys.downunder
inversions where the inverse Hessian approximation is not very good at the
moment.

Revision 4517 - Directory Listing
Modified Mon Aug 12 05:56:54 2013 UTC (5 years, 6 months ago) by caltinay
Original Path: trunk

Implemented caching (and relaxation) of line search step size alpha.
Experiments show a significant decrease in the number of  iterations required
to converge with this change.

Revision 4516 - Directory Listing
Modified Thu Aug 8 05:41:49 2013 UTC (5 years, 6 months ago) by caltinay
Original Path: trunk

Implemented more CF conventions for the netCDF datasource.
Also added a check to LatLonToUTM to pass through coordinates that are already
projected.
Data gridded by GDAL is now understood.

Revision 4515 - Directory Listing
Modified Mon Aug 5 06:09:01 2013 UTC (5 years, 6 months ago) by jfenwick
Original Path: trunk

Intel compiler mutter grumble

Revision 4514 - Directory Listing
Modified Mon Aug 5 03:28:44 2013 UTC (5 years, 6 months ago) by jfenwick
Original Path: trunk

Look at the MPI

Revision 4513 - Directory Listing
Modified Mon Aug 5 00:57:34 2013 UTC (5 years, 6 months ago) by jfenwick
Original Path: trunk

Dropping VSL random. Random data now uses more general routine.

Revision 4512 - Directory Listing
Modified Mon Jul 29 05:27:16 2013 UTC (5 years, 6 months ago) by caltinay
Original Path: trunk

With current Intel compiler (13.5.192) on savanna any build with OMP and without MPI
will segfault in AbstractDomain->getPtr() for unknown reasons.
Trying a workaround for finley which can be adapted to dudley and ripley if it works.

Revision 4511 - Directory Listing
Modified Thu Jul 25 04:51:02 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

Print a warning on savanna if dev-deps is not loaded when building and add
debug symbols by default.

Revision 4510 - Directory Listing
Modified Thu Jul 25 04:02:07 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

Fixed a path which should fix unit tests.

Revision 4509 - Directory Listing
Modified Wed Jul 24 08:37:29 2013 UTC (5 years, 7 months ago) by jfenwick
Original Path: trunk

Fixed paths for utest.sh

Revision 4508 - Directory Listing
Modified Wed Jul 24 04:23:22 2013 UTC (5 years, 7 months ago) by jfenwick
Original Path: trunk

Moving to escriptcore

Revision 4506 - Directory Listing
Modified Wed Jul 24 01:28:42 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

run-escript -m now takes an optional argument to allow for different valgrind
tools (callgrind & memcheck supported at the moment).

Revision 4505 - Directory Listing
Modified Tue Jul 23 02:09:45 2013 UTC (5 years, 7 months ago) by jfenwick
Original Path: trunk

Hopefully addresses mantis721

Revision 4504 - Directory Listing
Modified Mon Jul 22 02:04:34 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

Fix to verbose parameter reporting in linear pdes

Revision 4503 - Directory Listing
Modified Wed Jul 17 05:27:36 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

Skip new test with >1 rank.

Revision 4502 - Directory Listing
Modified Wed Jul 17 03:12:28 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

Test reading IEEE8ByteReal data from ER Mapper files.

Revision 4501 - Directory Listing
Modified Wed Jul 17 00:02:26 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

This time I fixed the comment instead of the code for this special case.

Revision 4500 - Directory Listing
Modified Tue Jul 16 05:47:11 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

updated scons script

Revision 4499 - Directory Listing
Modified Tue Jul 16 05:42:19 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

finley: mainly const'ness fixes, some formatting.

Revision 4498 - Directory Listing
Modified Tue Jul 16 01:56:37 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

Another special case fix.

Revision 4497 - Directory Listing
Modified Mon Jul 15 23:32:28 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

Small fix for non-mpi build.

Revision 4496 - Directory Listing
Modified Mon Jul 15 06:53:44 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

finley (WIP):
-moved all of finley into its namespace
-introduced some shared pointers
-Mesh is now a class
-other bits and pieces...

Revision 4495 - Directory Listing
Modified Fri Jul 5 02:19:47 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

Added support for more input data types in ER Mapper files.
Tests will follow soon.

Revision 4494 - Directory Listing
Modified Thu Jul 4 02:53:47 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

Suppressions for savanna runs.

Revision 4493 - Directory Listing
Modified Wed Jul 3 06:32:11 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

Fixed omp typo - gcc didn't pick it up...

Revision 4492 - Directory Listing
Modified Tue Jul 2 01:44:11 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

Finley changes that were held back while in release mode - moved more stuff
into finley namespace.

Revision 4491 - Directory Listing
Modified Tue Jul 2 01:10:41 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

Reintegrating changes from 3.4 branch (with changes).

Revision 4490 - Directory Listing
Modified Tue Jul 2 00:38:44 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

More python suppressions from savanna.

Revision 4489 - Directory Listing
Modified Fri Jun 28 00:05:31 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

Moved to update 5 of intel libraries/compiler on savanna.

Revision 4483 - Directory Listing
Modified Wed Jun 26 02:36:15 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

Added option to easily run escript with valgrind memcheck.

Revision 4482 - Directory Listing
Modified Tue Jun 25 05:20:01 2013 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

More leak fixes and suppression file additions.

Revision 4481 - Directory Listing
Modified Mon Jun 24 06:22:27 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Hmm. That's a nasty undocumented "feature"...

Revision 4480 - Directory Listing
Modified Mon Jun 24 05:09:52 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

More valgrind suppressions and memory leak fixes identified in various places.

Revision 4479 - Directory Listing
Modified Thu Jun 20 10:54:09 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Missed a subtle fact about the stringstream constructor...

Revision 4478 - Directory Listing
Modified Thu Jun 20 06:34:02 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Moved appendRankToFilename to header within namespace to remove code duplication
and fixed memory leaks this way.

Revision 4477 - Directory Listing
Modified Thu Jun 20 02:41:28 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

escript: use scoped_array instead of scoped_ptr
ripley: netcdf returns a copy of an array so use scoped_array
downunder: s/Sperical/Spherical/
scripts: added a few more suppressions

Revision 4476 - Directory Listing
Modified Thu Jun 20 00:05:53 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Revised valgrind suppressions file with more generic Python & OpenMPI
suppressions.

Revision 4474 - Directory Listing
Modified Wed Jun 19 06:44:47 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Brought over leak fix, gcc 4.8 fix and mismatched new[]/delete fix from release
branch.

Revision 4465 - Directory Listing
Modified Mon Jun 17 06:49:39 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Remove superfluous \label

Revision 4462 - Directory Listing
Modified Mon Jun 17 04:12:06 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Raise exception if background magnetic field has not been set but is required.

Revision 4461 - Directory Listing
Modified Sun Jun 16 23:39:31 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

small py3 fix.

Revision 4455 - Directory Listing
Modified Thu Jun 13 03:13:36 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Removed \LG etc. from inversion document.
Documented new GOCAD Voxet writer. Needs to be mentioned in 'changes' too.

Revision 4454 - Directory Listing
Modified Thu Jun 13 03:12:17 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

More "delete test output files after checking"

Revision 4451 - Directory Listing
Modified Thu Jun 13 01:38:56 2013 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

some pending changes on badger

Revision 4450 - Directory Listing
Modified Thu Jun 13 00:45:59 2013 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

install docs - still waiting on Mac. Removing debug output.

Revision 4449 - Directory Listing
Modified Thu Jun 13 00:24:00 2013 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

Finishing off this end.

Revision 4448 - Directory Listing
Modified Wed Jun 12 23:05:12 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Only one rank should delete file in tests.

Revision 4447 - Directory Listing
Modified Wed Jun 12 13:55:53 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Clean up some generated test files.

Revision 4446 - Directory Listing
Modified Tue Jun 11 04:00:15 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

This should fix the py3 error...

Revision 4445 - Directory Listing
Modified Tue Jun 11 03:35:55 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Apply weight rescaling to input weights before the coordinate scaling.
Also skipping a check when more than 1 rank is used.

Revision 4444 - Directory Listing
Modified Mon Jun 10 07:55:05 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Converted IndexList to a std::list.

Revision 4443 - Directory Listing
Modified Mon Jun 10 04:50:27 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Update test to take into account changed height scale.

Revision 4442 - Directory Listing
Modified Fri Jun 7 07:04:44 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

cosmetic changes.

Revision 4441 - Directory Listing
Modified Fri Jun 7 02:23:49 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

finley now uses Data objects directly instead of going through the C wrapper.

Revision 4440 - Directory Listing
Modified Wed Jun 5 05:22:20 2013 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

options files changes and install changes

Revision 4439 - Directory Listing
Modified Wed Jun 5 02:09:35 2013 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

some work on install doco

Revision 4438 - Directory Listing
Modified Tue Jun 4 09:00:50 2013 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

Some changes to packaging

Revision 4437 - Directory Listing
Modified Tue Jun 4 05:37:18 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

finley:
-Removed obsolete reference files (OpenDX)
-Converted tag map to a std::map
-loosened tests to ignore tag order in file
-added some decorators for test skips

Revision 4435 - Directory Listing
Modified Mon Jun 3 04:27:57 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Fixed a few scaling problems for non-cartesian coordinates in domainbuilder.

Revision 4434 - Directory Listing
Modified Mon Jun 3 00:43:29 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

tab-fixes and an indexing fix.

Revision 4433 - Directory Listing
Modified Fri May 31 12:09:58 2013 UTC (5 years, 8 months ago) by gross
Original Path: trunk

some clarifications on geodetic coordinates. 
order of background magnetic flux density component has been corrected: input is now B_east, B_north, B_vertical.

Revision 4432 - Directory Listing
Modified Fri May 31 07:13:38 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

updated sconscript file

Revision 4431 - Directory Listing
Modified Fri May 31 07:09:03 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

finley ElementFile is now a class...

Revision 4430 - Directory Listing
Modified Fri May 31 00:38:42 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Don't panic - just forgot some brackets... D'oh!

Revision 4429 - Directory Listing
Modified Thu May 30 13:52:01 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

Okay I now know that std::vector<bool> is evil, but WTF happens in this context???
It only crashes with more than one thread and more than one MPI process.

Revision 4428 - Directory Listing
Modified Thu May 30 06:39:10 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

finley's NodeFile is now a class.
Associated changes:
- use of some C++ constructs/functions/types (1st pass)
- removal of obsolete pointer check
- merging of some duplicated code
- ...

Revision 4426 - Directory Listing
Modified Mon May 27 06:14:19 2013 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

Testing commit

Revision 4425 - Directory Listing
Modified Mon May 27 05:44:28 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

svn server test and finley stuff.

Revision 4424 - Directory Listing
Modified Mon May 27 04:48:31 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

SVN server test.

Revision 4423 - Directory Listing
Modified Mon May 27 04:38:59 2013 UTC (5 years, 8 months ago) by caltinay
Original Path: trunk

finley bits.

Revision 4422 - Directory Listing
Modified Fri May 24 04:42:29 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

s/jacobeans/jacobians and other bits and pieces.

Revision 4421 - Directory Listing
Modified Tue May 21 05:16:39 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Finley... there were actually some long-standing errors in the checks.

Revision 4420 - Directory Listing
Modified Mon May 20 07:12:15 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Enabled metis on guineapig.

Revision 4419 - Directory Listing
Modified Mon May 20 05:03:35 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Fixed a typo.

Revision 4417 - Directory Listing
Modified Mon May 20 02:15:47 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Retab regularizations.

Revision 4416 - Directory Listing
Modified Fri May 17 02:32:33 2013 UTC (5 years, 9 months ago) by jfenwick
Original Path: trunk

Renaming a thing and adding some doco.

Revision 4415 - Directory Listing
Modified Fri May 17 00:33:02 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Commented unused var to make compiler happy.

Revision 4414 - Directory Listing
Modified Thu May 16 05:37:32 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Few more bits and pieces in finley.

Revision 4410 - Directory Listing
Modified Tue May 14 11:29:23 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Oops, I saw this coming.

Revision 4408 - Directory Listing
Modified Tue May 14 06:58:43 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Mostly no-op - trying to get some consistency in style while going through a
few files.
Also some minor changes related to C->C++ (e.g. no need to copy vector to pass
to functions etc.)

Revision 4407 - Directory Listing
Modified Tue May 14 05:17:24 2013 UTC (5 years, 9 months ago) by jfenwick
Original Path: trunk

Added output function to arithmetic tuple

Revision 4406 - Directory Listing
Modified Tue May 14 02:54:09 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Removed references to pyvisi which disappeared a few releases ago...

Revision 4405 - Directory Listing
Modified Sun May 12 23:27:33 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Once again..

Revision 4404 - Directory Listing
Modified Sun May 12 23:25:10 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Retab forwardmodels

Revision 4400 - Directory Listing
Modified Fri May 10 04:05:00 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Uaaargh - the minimizer ate my files! Fixed reporting of iteration number in
callback.

Revision 4399 - Directory Listing
Modified Thu May 9 10:46:41 2013 UTC (5 years, 9 months ago) by jfenwick
Original Path: trunk

just fiddling

Revision 4398 - Directory Listing
Modified Thu May 9 08:42:44 2013 UTC (5 years, 9 months ago) by jfenwick
Original Path: trunk

support for supressing doco subpackages. fiddling with one of the imports to try to reduce the number of places where Data appears.  Seriously it looks like we have 8 different Data classes

Revision 4397 - Directory Listing
Modified Thu May 9 06:17:15 2013 UTC (5 years, 9 months ago) by jfenwick
Original Path: trunk

Added some doco to make it a little easier to work out what is going on.
Cleaned up some reST ugliness

Revision 4396 - Directory Listing
Modified Wed May 8 09:27:10 2013 UTC (5 years, 9 months ago) by jfenwick
Original Path: trunk

fix extraction script to pick up more classes. Stop models from importing escript into its namespace

Revision 4395 - Directory Listing
Modified Wed May 8 03:05:05 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Changed trade-off factors for example to avoid unit test failures due to
scaling issues.

Revision 4394 - Directory Listing
Modified Tue May 7 04:56:59 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Fixed rounding with lat/lon coordinates and removed stray print statements.

Revision 4393 - Directory Listing
Modified Mon May 6 03:35:48 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Correct indexing of forward models.

Revision 4392 - Directory Listing
Modified Mon May 6 02:18:33 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

More saveSilo checks.

Revision 4391 - Directory Listing
Modified Mon May 6 02:15:48 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Do not claim success when saving silo without silo support.

Revision 4390 - Directory Listing
Modified Mon May 6 01:59:34 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Fixed advertising of NetCdfData availability.

Revision 4389 - Directory Listing
Modified Mon May 6 01:52:05 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

retab coordinates.py

Revision 4387 - Directory Listing
Modified Thu May 2 00:46:49 2013 UTC (5 years, 9 months ago) by jfenwick
Original Path: trunk

The future is now

Revision 4386 - Directory Listing
Modified Tue Apr 30 02:58:02 2013 UTC (5 years, 9 months ago) by jfenwick
Original Path: trunk

Add missing [0]

Revision 4385 - Directory Listing
Modified Mon Apr 29 06:03:30 2013 UTC (5 years, 9 months ago) by jfenwick
Original Path: trunk

It was bugging me

Revision 4384 - Directory Listing
Modified Sat Apr 27 05:09:37 2013 UTC (5 years, 9 months ago) by jfenwick
Original Path: trunk

Partially complete new install instructions

Revision 4383 - Directory Listing
Modified Fri Apr 26 06:13:12 2013 UTC (5 years, 9 months ago) by jfenwick
Original Path: trunk

Changes to install doco

Revision 4382 - Directory Listing
Modified Thu Apr 25 04:44:14 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Finalised ripley PDE assembly optimisation work.

Stats (combined Rectangle & Brick):
  rev.4369: 7440 constants, 16985 lines, ~17m to compile w/ icc
       NOW: 4038 constants, 13579 lines, ~6.5m to compile w/ icc

Runtime of unit tests a few seconds shorter as well :-)

Revision 4381 - Directory Listing
Modified Thu Apr 25 01:57:54 2013 UTC (5 years, 9 months ago) by caltinay
Original Path: trunk

Prescribe data scale in tests to silence message.

Revision 4380 - Directory Listing
Modified Wed Apr 24 23:59:49 2013 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Attempt to help windows

Revision 4379 - Directory Listing
Modified Wed Apr 24 20:31:19 2013 UTC (5 years, 10 months ago) by gross
Original Path: trunk

more documentation on geodetic coordinates.

Revision 4378 - Directory Listing
Modified Wed Apr 24 06:21:42 2013 UTC (5 years, 10 months ago) by caltinay
Original Path: trunk

ripley work: Almost done - one more round in Brick left....

Revision 4377 - Directory Listing
Modified Tue Apr 23 05:30:02 2013 UTC (5 years, 10 months ago) by caltinay
Original Path: trunk

More work on ripley - Brick is under 10000 lines now.

Revision 4376 - Directory Listing
Modified Mon Apr 22 08:44:45 2013 UTC (5 years, 10 months ago) by gross
Original Path: trunk

domumentation update on coordinate systems - part I

Revision 4375 - Directory Listing
Modified Mon Apr 22 05:35:52 2013 UTC (5 years, 10 months ago) by caltinay
Original Path: trunk

More ripley code cleaning/optimisation.

Revision 4374 - Directory Listing
Modified Mon Apr 22 03:21:48 2013 UTC (5 years, 10 months ago) by gross
Original Path: trunk

some typo fixed.

Revision 4373 - Directory Listing
Modified Mon Apr 22 03:16:24 2013 UTC (5 years, 10 months ago) by gross
Original Path: trunk

more on geodetic coordinates

Revision 4371 - Directory Listing
Modified Fri Apr 19 08:47:57 2013 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

As far as I can tell, passes unit tests on freebsd with non-default compiler==gcc46

Revision 4370 - Directory Listing
Modified Fri Apr 19 06:15:24 2013 UTC (5 years, 10 months ago) by caltinay
Original Path: trunk

WIP: ripley hand-optimisation & further rules to generator
-> drastically reduced number of constants
-> compile time of Brick.cpp less than half of what it was on savanna
-> additional runtime savings
-> to be continued...

Revision 4369 - Directory Listing
Modified Fri Apr 19 02:32:34 2013 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

fix problems revealed on freebsd

Revision 4368 - Directory Listing
Modified Thu Apr 18 02:26:35 2013 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

put back std::

Revision 4367 - Directory Listing
Modified Wed Apr 17 09:55:25 2013 UTC (5 years, 10 months ago) by plaub
Original Path: trunk

Allow access to the individual components of the weighted sum cost function.

Revision 4366 - Directory Listing
Modified Wed Apr 17 04:41:16 2013 UTC (5 years, 10 months ago) by caltinay
Original Path: trunk

Be more careful with namespace & includes.

Revision 4365 - Directory Listing
Modified Wed Apr 17 03:46:22 2013 UTC (5 years, 10 months ago) by caltinay
Original Path: trunk

Skip tests for #ranks > 1 again.

Revision 4364 - Directory Listing
Modified Wed Apr 17 01:56:00 2013 UTC (5 years, 10 months ago) by caltinay
Original Path: trunk

Decorated some test cases.

Revision 4363 - Directory Listing
Modified Wed Apr 17 01:07:38 2013 UTC (5 years, 10 months ago) by caltinay
Original Path: trunk

retab coordinates.py.

Revision 4362 - Directory Listing
Modified Tue Apr 16 04:37:13 2013 UTC (5 years, 10 months ago) by caltinay
Original Path: trunk

Implemented NumpyData downunder source (w/ tests).
Added check of data dimensionality to domainbuilder since data_dim must equal
domain_dim-1 at the moment.

Revision 4361 - Directory Listing
Modified Mon Apr 15 04:43:19 2013 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

beginnings of an option file for macports

Revision 4360 - Directory Listing
Modified Mon Apr 15 02:41:42 2013 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

some mismatched memory ops

Revision 4359 - Directory Listing
Modified Fri Apr 12 04:54:20 2013 UTC (5 years, 10 months ago) by gross
Original Path: trunk

more on coordinate systems

Revision 4358 - Directory Listing
Modified Fri Apr 12 04:54:00 2013 UTC (5 years, 10 months ago) by gross
Original Path: trunk

more on coordinate systems

Revision 4357 - Directory Listing
Modified Thu Apr 11 06:07:14 2013 UTC (5 years, 10 months ago) by caltinay
Original Path: trunk

templated writeBinaryGrid and a bit of cleanup.

Revision 4356 - Directory Listing
Modified Tue Apr 9 00:15:59 2013 UTC (5 years, 10 months ago) by caltinay
Original Path: trunk

Retabbed file for py3 pleasure.

Revision 4355 - Directory Listing
Modified Fri Apr 5 07:25:02 2013 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

start install guide overhall

Revision 4354 - Directory Listing
Modified Fri Apr 5 03:55:03 2013 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

adding option files for distros

Revision 4353 - Directory Listing
Modified Fri Apr 5 00:14:35 2013 UTC (5 years, 10 months ago) by caltinay
Original Path: trunk

For some reason std::isnan<float> is not available on NCI so changed this
to ::isnan. Added options file for NCI vayu.

Revision 4349 - Directory Listing
Modified Wed Apr 3 09:37:54 2013 UTC (5 years, 10 months ago) by gross
Original Path: trunk

first contributions for geodeic coordinates

Revision 4348 - Directory Listing
Modified Tue Apr 2 07:15:43 2013 UTC (5 years, 10 months ago) by caltinay
Original Path: trunk

Reapply some of the spelling fixes that got lost....

Revision 4347 - Directory Listing
Modified Tue Apr 2 04:58:44 2013 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Fixed some const char* conversions

Revision 4346 - Directory Listing
Modified Tue Apr 2 04:46:45 2013 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

Bringing the changes from doubleplusgood branch.
Can't merge directly because svn doesn't transfer changes to renamed files (mutter grumble).

Revision 4344 - Directory Listing
Modified Wed Mar 27 07:58:34 2013 UTC (5 years, 10 months ago) by gross
Original Path: trunk

fix potential at botttom added.

Revision 4342 - Directory Listing
Modified Tue Mar 26 02:31:41 2013 UTC (5 years, 10 months ago) by jfenwick
Original Path: trunk

get rid of the escript link that snuck in somehow.   deal with cases where the root of the install is in a path with spaces in it.

Revision 4341 - Directory Listing
Modified Mon Mar 25 04:01:25 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

GOCAD Voxet writer in weipa.

Revision 4340 - Directory Listing
Modified Fri Mar 22 04:38:36 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

added ripley method that returns grid parameters as python tuple.

Revision 4339 - Directory Listing
Modified Fri Mar 22 02:25:37 2013 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

options file for all standalone builds

Revision 4337 - Directory Listing
Modified Fri Mar 22 00:05:25 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Detect a few more byte swap/endianness headers and silence output from
'detectModule' scons helper

Revision 4334 - Directory Listing
Modified Thu Mar 21 06:00:14 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Preparations for Voxet (GOCAD) binary grid output + code clean up.
Changed node id's order to remove code duplication in weipa.
More work to do...

Revision 4326 - Directory Listing
Modified Wed Mar 20 02:50:46 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Removed stray print statement.

Revision 4323 - Directory Listing
Modified Tue Mar 19 00:17:36 2013 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Bringing across changes from release3.3.1. (Version names are set back to Development).

Revision 4322 - Directory Listing
Modified Mon Mar 18 00:09:02 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Test for calling I/O redirect or not was wrong... fixed.

Revision 4320 - Directory Listing
Modified Fri Mar 15 02:57:15 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Moved file writer helper class to esysUtils and made it header-only. It will
be used by ripley writer methods.

Revision 4311 - Directory Listing
Modified Tue Mar 12 04:26:24 2013 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

gracefully end if pyproj is not installed

Revision 4310 - Directory Listing
Modified Tue Mar 12 03:23:26 2013 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

examples don't FAIL if tool is not installed

Revision 4309 - Directory Listing
Modified Mon Mar 11 05:07:39 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Temporary workaround for sys.exit() causing unclean exit with MPI.

Revision 4308 - Directory Listing
Modified Mon Mar 11 02:47:59 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Added missing import.

Revision 4307 - Directory Listing
Modified Mon Mar 11 02:46:17 2013 UTC (5 years, 11 months ago) by azadeh
Original Path: trunk

shake29->weasel

Revision 4306 - Directory Listing
Modified Mon Mar 11 02:36:55 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

python 3 compat.

Revision 4303 - Directory Listing
Modified Mon Mar 11 01:17:39 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Enabled index in inversion doc. Eliminated some typos.

Revision 4301 - Directory Listing
Modified Mon Mar 11 00:52:31 2013 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Updated copyright on doco that has not existed all the way back to 2003.
Added Azadeh and Vince to credits

Revision 4300 - Directory Listing
Modified Mon Mar 11 00:50:19 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Always invoke external python to check for modules. For some reason scipy
detection did not work properly using the old way.

Revision 4299 - Directory Listing
Modified Mon Mar 11 00:40:09 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Exit with a warning in example files that require unavailable scipy.
bollide->hamster
added warnings to scons for scipy and gdal

Revision 4298 - Directory Listing
Modified Mon Mar 11 00:03:22 2013 UTC (5 years, 11 months ago) by azadeh
Original Path: trunk

changing Magnetic Images

Revision 4297 - Directory Listing
Modified Fri Mar 8 06:14:17 2013 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Removing the sphinx spelling checker since it breaks my build.  Updated the genrst script so that non-package modules still show up in the doco. Still needs a bit of a tweak in the long term

Revision 4295 - Directory Listing
Modified Fri Mar 8 04:42:01 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

de-cluttered sconstruct a bit and fixed a script.

Revision 4294 - Directory Listing
Modified Fri Mar 8 03:37:10 2013 UTC (5 years, 11 months ago) by gross
Original Path: trunk

text for magnetic inversion tutorial added.

Revision 4293 - Directory Listing
Modified Fri Mar 8 00:07:07 2013 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

fixing sneaky bug in grouptest

Revision 4292 - Directory Listing
Modified Thu Mar 7 22:39:32 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Broken? It ain't broken ;-) Sorry Joel.

Revision 4290 - Directory Listing
Modified Thu Mar 7 07:04:29 2013 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Ignore __pycache__ when generating sphinx docs

Revision 4289 - Directory Listing
Modified Thu Mar 7 07:02:59 2013 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

including inversion examples in bundles and tests

Revision 4288 - Directory Listing
Modified Thu Mar 7 06:35:14 2013 UTC (5 years, 11 months ago) by gross
Original Path: trunk

some modifications clarifying the B field orientation

Revision 4287 - Directory Listing
Modified Thu Mar 7 05:26:44 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Removed simpleGeoMagnetic field function from doco and example source.

Revision 4286 - Directory Listing
Modified Thu Mar 7 04:28:11 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Assorted spelling fixes.

Revision 4285 - Directory Listing
Modified Thu Mar 7 01:08:43 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Corrected some spelling.

Revision 4284 - Directory Listing
Modified Thu Mar 7 00:43:48 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Replaced dummy implementations by pure virtual methods.

Revision 4283 - Directory Listing
Modified Thu Mar 7 00:11:36 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Minor epydoc fixes.

Revision 4282 - Directory Listing
Modified Wed Mar 6 08:33:59 2013 UTC (5 years, 11 months ago) by gross
Original Path: trunk

first contribution for the magnetic cookbook.

Revision 4279 - Directory Listing
Modified Wed Mar 6 05:10:44 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Update to API doco and separate section for multiple data sets.

Revision 4278 - Directory Listing
Modified Wed Mar 6 04:45:40 2013 UTC (5 years, 11 months ago) by gross
Original Path: trunk

joint inversion chapter in part I replaced by announcment

Revision 4277 - Directory Listing
Modified Wed Mar 6 01:30:41 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Implemented claimed support for mixing data with different resolutions.

Revision 4274 - Directory Listing
Modified Tue Mar 5 06:10:17 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Small fix to example file.

Revision 4273 - Directory Listing
Modified Tue Mar 5 04:14:44 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

More doco updates and change to the return value of minimizers.

Revision 4272 - Directory Listing
Modified Tue Mar 5 01:06:45 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Finished gravity part in cookbook. Started review of class descriptions.

Revision 4271 - Directory Listing
Modified Mon Mar 4 05:59:59 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Finished data-with-holes section and added a few more notes about optional
arguments further up. Changed example scripts to show usage of special
features.

Revision 4270 - Directory Listing
Modified Mon Mar 4 04:01:28 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Corrected test for modified handling of ER Mapper origin.

Revision 4269 - Directory Listing
Modified Mon Mar 4 00:54:29 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Some more work.

Revision 4268 - Directory Listing
Modified Mon Mar 4 00:41:08 2013 UTC (5 years, 11 months ago) by gross
Original Path: trunk

some citation fixed.

Revision 4267 - Directory Listing
Modified Fri Mar 1 04:50:54 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Updated inversion example scripts, added ER Mapper data, checked results
and corrected some issues. Cookbook does not reflect the changes yet.

Revision 4266 - Directory Listing
Modified Fri Mar 1 01:37:41 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Deleted old data files.

Revision 4265 - Directory Listing
Modified Fri Mar 1 00:52:30 2013 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

because we arent using python 2.5 anymore

Revision 4263 - Directory Listing
Modified Thu Feb 28 05:59:04 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

No more xrange in downunder.

Revision 4262 - Directory Listing
Modified Thu Feb 28 05:49:11 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

removed use of xrange and hack.

Revision 4260 - Directory Listing
Modified Wed Feb 27 04:58:47 2013 UTC (5 years, 11 months ago) by azadeh
Original Path: trunk

adding gravity and magnetic data files which used for inversions

Revision 4259 - Directory Listing
Modified Wed Feb 27 03:52:35 2013 UTC (5 years, 11 months ago) by azadeh
Original Path: trunk

cookmagnetic

Revision 4258 - Directory Listing
Modified Wed Feb 27 03:50:08 2013 UTC (5 years, 11 months ago) by azadeh
Original Path: trunk

cookmagnetic

Revision 4256 - Directory Listing
Modified Wed Feb 27 03:25:05 2013 UTC (5 years, 11 months ago) by azadeh
Original Path: trunk

changing some magnetic result image names

Revision 4255 - Directory Listing
Modified Wed Feb 27 03:06:21 2013 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Hopefully, this will address the interpolation problems.

New canInterpolate() function exposed to python which calls probeInterpolation

AbstractDomain now has an additional virtual.
preferredIntrpolationOnDomain()

This will return 0 if interpolation is impossible, 1 if possible and preferred.
It will return -1 if interpolation is possible and preferred in the 
oposite direction.

A value of -1 does not say that the proposed interpolation is possible or not.
Rather it indicates "please use the other way".
If you really _need_ to test it that way, use probeInterpolationOnDomain

Revision 4254 - Directory Listing
Modified Wed Feb 27 02:59:29 2013 UTC (5 years, 11 months ago) by azadeh
Original Path: trunk

added joint result

Revision 4253 - Directory Listing
Modified Wed Feb 27 02:55:32 2013 UTC (5 years, 11 months ago) by azadeh
Original Path: trunk

removed joint result

Revision 4252 - Directory Listing
Modified Wed Feb 27 02:49:06 2013 UTC (5 years, 11 months ago) by azadeh
Original Path: trunk

added magnetic inversion results

Revision 4251 - Directory Listing
Modified Wed Feb 27 02:47:10 2013 UTC (5 years, 11 months ago) by azadeh
Original Path: trunk

removed old magnetic images
This line, and those below, will be ignored--

D    QLDMagMu10Contour.png
D    QLDMagMu01Slice.png
D    QLDMagMu1Contour.png
D    QLDMagMu100Slice.png
D    QLDMagMu01Contour.png
D    QLDMagMu10Slice.png
D    QLDMagMu100Contour.png
D    QLDMagMu1Slice.png

Revision 4250 - Directory Listing
Modified Wed Feb 27 00:26:12 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

Fix for joint example.

Revision 4249 - Directory Listing
Modified Tue Feb 26 01:01:59 2013 UTC (5 years, 11 months ago) by caltinay
Original Path: trunk

s/shake75/bollide. Made build_full succeed without cppunit.

Revision 4248 - Directory Listing
Modified Mon Feb 25 05:53:55 2013 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

This should not trigger the build

Revision 4246 - Directory Listing
Modified Mon Feb 25 05:49:49 2013 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

still testing

Revision 4244 - Directory Listing
Modified Mon Feb 25 05:37:50 2013 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

More testing and a target in scons for the pdf docs

Revision 4243 - Directory Listing
Modified Mon Feb 25 05:33:01 2013 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

For testing buildbot

Revision 4242 - Directory Listing
Modified Mon Feb 25 03:16:14 2013 UTC (5 years, 11 months ago) by jfenwick
Original Path: trunk

Allow pure virtual classes to be exported to python.
Temporary fix for a ripley interpolation issue

Revision 4240 - Directory Listing
Modified Fri Feb 22 01:51:19 2013 UTC (6 years ago) by jfenwick
Original Path: trunk

options file for a clang buildbot

Revision 4239 - Directory Listing
Modified Fri Feb 22 00:35:01 2013 UTC (6 years ago) by caltinay
Original Path: trunk

initialize utm zone in er mapper reader.

Revision 4238 - Directory Listing
Modified Thu Feb 21 09:58:49 2013 UTC (6 years ago) by jfenwick
Original Path: trunk

fixed some relative imports and uses of xrange

Revision 4237 - Directory Listing
Modified Thu Feb 21 07:27:36 2013 UTC (6 years ago) by jfenwick
Original Path: trunk

Fixed bad tabbing so this revision works with python3 or clang.
(clang at least up to the tests which need pyproj)

Revision 4236 - Directory Listing
Modified Thu Feb 21 05:05:05 2013 UTC (6 years ago) by jfenwick
Original Path: trunk

Noted that saveDX and saveVTK have been removed.

Revision 4233 - Directory Listing
Modified Thu Feb 21 02:00:09 2013 UTC (6 years ago) by caltinay
Original Path: trunk

updated content file (wishlist). Added byte swapping to plotter.

Revision 4232 - Directory Listing
Modified Wed Feb 20 08:31:31 2013 UTC (6 years ago) by jfenwick
Original Path: trunk

Fixed the WrappedArray class so it doesn't generate warnings

Revision 4231 - Directory Listing
Modified Wed Feb 20 07:41:52 2013 UTC (6 years ago) by jfenwick
Original Path: trunk

Updating doco for pyproj and a few other minor inconsistancies.  The inversion doco still needs to mention them.

Revision 4230 - Directory Listing
Modified Wed Feb 20 03:57:37 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Removed some superfluous files.

Revision 4228 - Directory Listing
Modified Wed Feb 20 03:34:07 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Tweak & fix for data plotters

Revision 4227 - Directory Listing
Modified Wed Feb 20 03:10:50 2013 UTC (6 years ago) by caltinay
Original Path: trunk

ER Mapper data source updates.

Revision 4225 - Directory Listing
Modified Wed Feb 20 02:45:09 2013 UTC (6 years ago) by azadeh
Original Path: trunk

moving images to figures folder

Revision 4224 - Directory Listing
Modified Wed Feb 20 02:34:18 2013 UTC (6 years ago) by azadeh
Original Path: trunk

changing images in cook gravity

Revision 4222 - Directory Listing
Modified Wed Feb 20 01:27:40 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Disabled docs about NonlinearPDE and removed inversion from user's guide.

Revision 4221 - Directory Listing
Modified Wed Feb 20 01:24:29 2013 UTC (6 years ago) by caltinay
Original Path: trunk

The numpy 1.7 macro does not help since the new style API/macros are not
present in 1.6. So when compiling with numpy 1.7 werror needs to be set to
False.

Revision 4220 - Directory Listing
Modified Wed Feb 20 01:17:30 2013 UTC (6 years ago) by azadeh
Original Path: trunk

adding gravity images with color bar in a folder

Revision 4219 - Directory Listing
Modified Wed Feb 20 00:26:19 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Not sure why, but this fixes all failures in the linearPDE tests with ripley.

Revision 4218 - Directory Listing
Modified Tue Feb 19 06:11:35 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Added gravity data in ER Mapper format and inversion script for it.

Revision 4217 - Directory Listing
Modified Tue Feb 19 06:09:51 2013 UTC (6 years ago) by caltinay
Original Path: trunk

numpy 1.7 introduced a warning for deprecation of certain APIs. We have to
acknowledge that to get rid of the warning...

Revision 4216 - Directory Listing
Modified Tue Feb 19 05:15:38 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Report if pyproj is available.

Revision 4215 - Directory Listing
Modified Tue Feb 19 02:52:40 2013 UTC (6 years ago) by azadeh
Original Path: trunk

adding gravity coarse data

Revision 4214 - Directory Listing
Modified Tue Feb 19 02:42:43 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Added capstartfalse/true to escript cookbook figures with no caption so
the build succeeds with the hypcap package enabled.

Revision 4213 - Directory Listing
Modified Tue Feb 19 01:16:29 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Some cleanup and more consistent logging.

Revision 4212 - Directory Listing
Modified Tue Feb 19 00:11:28 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Even friendlier message when pyproj is not installed but required.

Revision 4211 - Directory Listing
Modified Mon Feb 18 23:54:46 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Implemented interpolation from Reduced[Face]Elements to [Face]Elements and
changed regularization to compute gradient on Function instead of
ReducedFunction. Results differ slightly so this should help with the accuracy.

Revision 4210 - Directory Listing
Modified Mon Feb 18 23:47:09 2013 UTC (6 years ago) by jfenwick
Original Path: trunk

Added suggests for new libraries used by downunder.

Revision 4209 - Directory Listing
Modified Mon Feb 18 06:00:56 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Fixed joint example file, added ER Mapper plot script, updated content file.

Revision 4208 - Directory Listing
Modified Mon Feb 18 05:02:28 2013 UTC (6 years ago) by jfenwick
Original Path: trunk

rename so the poor case-sensitive mac can checkout

Revision 4207 - Directory Listing
Modified Mon Feb 18 03:17:11 2013 UTC (6 years ago) by azadeh
Original Path: trunk

adding bar for gravity image

Revision 4206 - Directory Listing
Modified Sun Feb 17 23:32:07 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Import minimizers by default so the exception classes are exposed.

Revision 4205 - Directory Listing
Modified Fri Feb 15 06:02:07 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Work on inversion cookbook. Also tweak to hyperref and a few more references.

Revision 4204 - Directory Listing
Modified Thu Feb 14 08:06:26 2013 UTC (6 years ago) by gross
Original Path: trunk

more on gravity and cleaning up file names

Revision 4203 - Directory Listing
Modified Thu Feb 14 07:05:58 2013 UTC (6 years ago) by gross
Original Path: trunk

Clarification of file names.

Revision 4202 - Directory Listing
Modified Thu Feb 14 06:53:41 2013 UTC (6 years ago) by gross
Original Path: trunk

Some adjustments to the sturture and naming

Revision 4201 - Directory Listing
Modified Thu Feb 14 06:40:01 2013 UTC (6 years ago) by caltinay
Original Path: trunk

DomainBuilder now ensures all data is in same UTM zone (with test).

Revision 4200 - Directory Listing
Modified Thu Feb 14 04:35:38 2013 UTC (6 years ago) by azadeh
Original Path: trunk

adding content folder to show input files

Revision 4199 - Directory Listing
Modified Wed Feb 13 08:39:05 2013 UTC (6 years ago) by gross
Original Path: trunk

more in the inversion cook-book

Revision 4198 - Directory Listing
Modified Wed Feb 13 06:49:10 2013 UTC (6 years ago) by gross
Original Path: trunk

name adjustments and remove unused files

Revision 4197 - Directory Listing
Modified Wed Feb 13 05:53:19 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Changes to netCDF data source:
-removed assumptions
-added parameters to override data/error variable names, scale factor and null
value.

Revision 4196 - Directory Listing
Modified Wed Feb 13 00:58:37 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Small fix so ERS files with DOS newline are parsed correctly.

Revision 4195 - Directory Listing
Modified Tue Feb 12 04:08:19 2013 UTC (6 years ago) by jfenwick
Original Path: trunk

Fixing case mismatch that was preventing bibtex from building

Revision 4194 - Directory Listing
Modified Tue Feb 12 03:04:17 2013 UTC (6 years ago) by azadeh
Original Path: trunk

Fixing some naming clashes

Revision 4192 - Directory Listing
Modified Tue Feb 12 00:28:47 2013 UTC (6 years ago) by gross
Original Path: trunk

problem with nc reader for dudley and finley fixed: the reader builds now the taginuse lists.

Revision 4191 - Directory Listing
Modified Mon Feb 11 08:22:47 2013 UTC (6 years ago) by gross
Original Path: trunk

more on gravity cook book

Revision 4188 - Directory Listing
Modified Mon Feb 11 01:51:22 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Removed unneeded (large) result files.

Revision 4187 - Directory Listing
Modified Mon Feb 11 01:05:10 2013 UTC (6 years ago) by azadeh
Original Path: trunk

adding gravity magnetic and joint inversion files in netcdf format

Revision 4186 - Directory Listing
Modified Mon Feb 11 00:47:34 2013 UTC (6 years ago) by azadeh
Original Path: trunk

adding gravity plots with different Mu

Revision 4185 - Directory Listing
Modified Fri Feb 8 09:06:21 2013 UTC (6 years ago) by gross
Original Path: trunk

modifications to cookbook

Revision 4184 - Directory Listing
Modified Fri Feb 8 04:33:48 2013 UTC (6 years ago) by azadeh
Original Path: trunk

new images in cookgravity

Revision 4183 - Directory Listing
Modified Mon Feb 4 02:58:02 2013 UTC (6 years ago) by azadeh
Original Path: trunk

joint result image updated

Revision 4182 - Directory Listing
Modified Fri Feb 1 02:29:53 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Revised Intro/Overview text.

Revision 4177 - Directory Listing
Modified Thu Jan 31 02:23:02 2013 UTC (6 years ago) by azadeh
Original Path: trunk

cook joint and magnetic

Revision 4176 - Directory Listing
Modified Wed Jan 30 05:30:30 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Removed tests that are known not to work.

Revision 4175 - Directory Listing
Modified Wed Jan 30 05:01:50 2013 UTC (6 years ago) by caltinay
Original Path: trunk

joint netcdf example and some minor fixes to other example/test case.

Revision 4174 - Directory Listing
Modified Wed Jan 30 03:21:27 2013 UTC (6 years ago) by caltinay
Original Path: trunk

ripley's readBinaryGrid and readNcGrid now filter out NaN leaving the relevant
destination data points untouched.

Revision 4173 - Directory Listing
Modified Wed Jan 30 03:05:01 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Do not use -ffast-math by default (see mantis 691).

Revision 4172 - Directory Listing
Modified Wed Jan 30 01:24:03 2013 UTC (6 years ago) by azadeh
Original Path: trunk

cookjoint
--This line, and those below, will be ignored

M    CookJoint.tex

Revision 4168 - Directory Listing
Modified Fri Jan 25 07:31:47 2013 UTC (6 years ago) by jfenwick
Original Path: trunk

Release title and dep fix

Revision 4167 - Directory Listing
Modified Fri Jan 25 05:21:30 2013 UTC (6 years ago) by jfenwick
Original Path: trunk

fixes for doco for earlier releases

Revision 4164 - Directory Listing
Modified Thu Jan 24 05:34:13 2013 UTC (6 years ago) by caltinay
Original Path: trunk

netcdf data source description.

Revision 4162 - Directory Listing
Modified Thu Jan 24 03:53:19 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Added missing example file to display netcdf data.

Revision 4160 - Directory Listing
Modified Thu Jan 24 00:13:32 2013 UTC (6 years ago) by caltinay
Original Path: trunk

Moved figures to subdir and added more DataSource doco.

Revision 4158 - Directory Listing
Modified Wed Jan 23 07:02:21 2013 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

Write output even when max iterations reached.

Revision 4157 - Directory Listing
Modified Wed Jan 23 03:52:07 2013 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

added magnetic netcdf example (no data yet).

Revision 4156 - Directory Listing
Modified Wed Jan 23 03:45:14 2013 UTC (6 years, 1 month ago) by azadeh
Original Path: trunk

changes in document

Revision 4155 - Directory Listing
Modified Wed Jan 23 00:05:03 2013 UTC (6 years, 1 month ago) by jfenwick
Original Path: trunk

Removed some incorrect ACcESS copyright attributions [2010 or later] since ACcESS did not exist at that point. Also added 2013 to a couple of files which I missed.

Revision 4154 - Directory Listing
Modified Tue Jan 22 09:30:23 2013 UTC (6 years, 1 month ago) by jfenwick
Original Path: trunk

Round 1 of copyright fixes

Revision 4153 - Directory Listing
Modified Tue Jan 22 01:57:50 2013 UTC (6 years, 1 month ago) by gross
Original Path: trunk

no driver example added. Doe not work yet.

Revision 4152 - Directory Listing
Modified Tue Jan 22 00:29:03 2013 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

Moved figures to subdirectory.

Revision 4151 - Directory Listing
Modified Tue Jan 22 00:23:39 2013 UTC (6 years, 1 month ago) by azadeh
Original Path: trunk

update joint and magnetic cookbook.

Revision 4150 - Directory Listing
Modified Mon Jan 21 04:14:24 2013 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

Raise an exception if some methods are called after domain creation.

Revision 4149 - Directory Listing
Modified Mon Jan 21 02:03:31 2013 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

Checkpoint - DomainBuilder documented.

Revision 4148 - Directory Listing
Modified Mon Jan 21 01:04:20 2013 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

Updated netcdf gravity inversion example.

Revision 4147 - Directory Listing
Modified Fri Jan 18 03:35:15 2013 UTC (6 years, 1 month ago) by gross
Original Path: trunk

added some words in the overview and clean-up of bib.

Revision 4146 - Directory Listing
Modified Fri Jan 18 01:36:49 2013 UTC (6 years, 1 month ago) by gross
Original Path: trunk

some remarks on the class dependency added.

Revision 4143 - Directory Listing
Modified Thu Jan 17 08:48:47 2013 UTC (6 years, 1 month ago) by gross
Original Path: trunk

documentation of minimizer update plus clarification of notations on the code

Revision 4142 - Directory Listing
Modified Tue Jan 15 09:06:06 2013 UTC (6 years, 1 month ago) by gross
Original Path: trunk

documentation of inversion cost function added

Revision 4141 - Directory Listing
Modified Tue Jan 15 04:11:12 2013 UTC (6 years, 1 month ago) by jfenwick
Original Path: trunk

Fixed to scripts to allow doco to build in pbuilder.
Looking for libraries in the place they were built is a good I've found.

Revision 4140 - Directory Listing
Modified Tue Jan 15 02:34:41 2013 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

Updated example inversion files.

Revision 4139 - Directory Listing
Modified Tue Jan 15 00:13:28 2013 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

Added L-BFGS reference and some minor changes.

Revision 4138 - Directory Listing
Modified Mon Jan 14 23:57:00 2013 UTC (6 years, 1 month ago) by gross
Original Path: trunk

some rearrangement of part II

Revision 4137 - Directory Listing
Modified Mon Jan 14 22:59:13 2013 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

Disabled another test.

Revision 4136 - Directory Listing
Modified Mon Jan 14 05:20:34 2013 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

clarifications about cartesian domain

Revision 4135 - Directory Listing
Modified Mon Jan 14 04:54:14 2013 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

Fixed test file.

Revision 4134 - Directory Listing
Modified Sun Jan 13 23:24:35 2013 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

Removed failing test.

Revision 4133 - Directory Listing
Modified Fri Jan 11 06:41:10 2013 UTC (6 years, 1 month ago) by gross
Original Path: trunk

some documentation on Inversion Cost function added.

Revision 4132 - Directory Listing
Modified Fri Jan 11 05:46:49 2013 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

Range of epydoc fixes.

Revision 4131 - Directory Listing
Modified Fri Jan 11 03:54:16 2013 UTC (6 years, 1 month ago) by gross
Original Path: trunk

documentaion of inversion driver API added.

Revision 4130 - Directory Listing
Modified Thu Jan 10 03:38:17 2013 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

Do not end document after chapter :-)

Revision 4129 - Directory Listing
Modified Thu Jan 10 03:30:45 2013 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

Fixed small typo

Revision 4128 - Directory Listing
Modified Thu Jan 10 02:04:08 2013 UTC (6 years, 1 month ago) by caltinay
Original Path: trunk

Use fixed low number of iterations for the callback test.

Revision 4127 - Directory Listing
Modified Thu Jan 10 00:46:56 2013 UTC (6 years, 1 month ago) by azadeh
Original Path: trunk

add documentation for gravity.

Revision 4126 - Directory Listing
Modified Tue Jan 8 02:37:48 2013 UTC (6 years, 1 month ago) by gross
Original Path: trunk

some work on the level set class. no testing yet.

Revision 4125 - Directory Listing
Modified Wed Jan 2 06:15:00 2013 UTC (6 years, 1 month ago) by gross
Original Path: trunk

some fixes in the inversion set-up

Revision 4124 - Directory Listing
Modified Fri Dec 21 01:35:43 2012 UTC (6 years, 2 months ago) by gross
Original Path: trunk

joint inversion added

Revision 4122 - Directory Listing
Modified Thu Dec 20 05:42:35 2012 UTC (6 years, 2 months ago) by gross
Original Path: trunk

More work towards joint inversion. There is now one class for inversion cost function which can handle all relevant cases 
for a single model inversion, cross gradient case and functional dependence of physical parameters.

Revision 4121 - Directory Listing
Modified Wed Dec 19 00:24:50 2012 UTC (6 years, 2 months ago) by gross
Original Path: trunk

changes to the boundary conditions.

Revision 4120 - Directory Listing
Modified Tue Dec 18 04:49:37 2012 UTC (6 years, 2 months ago) by gross
Original Path: trunk

some improvements to the robutness of the minimizer:
  a break down in the orthogonalization is hnadles via a restart.
  a restart can now be set manually
  the iteration throughs now an exception in case of failure.

It is also possible to set the density anomaly to zero for regions below a certain depth.

Revision 4119 - Directory Listing
Modified Mon Dec 17 04:53:15 2012 UTC (6 years, 2 months ago) by gross
Original Path: trunk

some adjustments to the documentation

Revision 4118 - Directory Listing
Modified Mon Dec 17 00:50:47 2012 UTC (6 years, 2 months ago) by jfenwick
Original Path: trunk

Some tweaks for auto building - need more though

Revision 4117 - Directory Listing
Modified Fri Dec 14 07:29:35 2012 UTC (6 years, 2 months ago) by gross
Original Path: trunk

some adjustments with names

Revision 4116 - Directory Listing
Modified Fri Dec 14 07:21:14 2012 UTC (6 years, 2 months ago) by gross
Original Path: trunk

tests for oscillatory data added.

Revision 4115 - Directory Listing
Modified Fri Dec 14 04:48:48 2012 UTC (6 years, 2 months ago) by gross
Original Path: trunk

terminolgy for magnetic flux density clarified. clean up on synthetic data

Revision 4114 - Directory Listing
Modified Fri Dec 14 04:24:46 2012 UTC (6 years, 2 months ago) by caltinay
Original Path: trunk

Time to remove deprecated saveVTK/DX methods from Data and Domain.

Revision 4113 - Directory Listing
Modified Fri Dec 14 01:54:53 2012 UTC (6 years, 2 months ago) by caltinay
Original Path: trunk

shake29 options file.

Revision 4112 - Directory Listing
Modified Fri Dec 14 01:51:30 2012 UTC (6 years, 2 months ago) by caltinay
Original Path: trunk

Added simple gravity inversion example to be included in cookbook.

Revision 4111 - Directory Listing
Modified Fri Dec 14 01:46:13 2012 UTC (6 years, 2 months ago) by jfenwick
Original Path: trunk

Fixed the genrst script to be executable

Revision 4110 - Directory Listing
Modified Fri Dec 14 01:21:33 2012 UTC (6 years, 2 months ago) by jfenwick
Original Path: trunk

Fixed to use whatever python is leading the path.
Disabled epydoc

Revision 4109 - Directory Listing
Modified Fri Dec 14 01:08:52 2012 UTC (6 years, 2 months ago) by caltinay
Original Path: trunk

Fixed tests.

Revision 4108 - Directory Listing
Modified Thu Dec 13 06:38:11 2012 UTC (6 years, 2 months ago) by caltinay
Original Path: trunk

Changed methods to add padding areas.

Revision 4107 - Directory Listing
Modified Thu Dec 13 05:54:03 2012 UTC (6 years, 2 months ago) by jfenwick
Original Path: trunk

Now building doc using sphinx. Doc builds will fail until I get stuff installed on savanna

Revision 4106 - Directory Listing
Modified Thu Dec 13 05:08:44 2012 UTC (6 years, 2 months ago) by gross
Original Path: trunk

some clarification on how to handle back ground magnetic field plus renaming of SyntheticData

Revision 4105 - Directory Listing
Modified Thu Dec 13 04:11:59 2012 UTC (6 years, 2 months ago) by caltinay
Original Path: trunk

Updated test to reflect interface changes.

Revision 4104 - Directory Listing
Modified Thu Dec 13 03:30:23 2012 UTC (6 years, 2 months ago) by jfenwick
Original Path: trunk

Ensuring we are using new-style classes
This may not be strictly necessary since our code does not depend on the difference.

Revision 4103 - Directory Listing
Modified Wed Dec 12 07:03:02 2012 UTC (6 years, 2 months ago) by jfenwick
Original Path: trunk

Got rid of some unwanted sidebar elts. Correctly detect standalone functions exposed by boost

Revision 4102 - Directory Listing
Modified Wed Dec 12 06:17:03 2012 UTC (6 years, 2 months ago) by gross
Original Path: trunk

more improvements on rescaling of weights. We now try to balance the gradients rather than the values.

Revision 4101 - Directory Listing
Modified Wed Dec 12 04:22:58 2012 UTC (6 years, 2 months ago) by jfenwick
Original Path: trunk

First attempt at a sphinx generated API docs
In the project root:

mkdir doctest
python doc/sphinx_api/genrst.py
cd doctest
make html

should do

Revision 4100 - Directory Listing
Modified Tue Dec 11 06:55:20 2012 UTC (6 years, 2 months ago) by gross
Original Path: trunk

minimizer uses now a relative change to solution to terminate iteration. Gravity still has problems

Revision 4099 - Directory Listing
Modified Tue Dec 11 04:04:47 2012 UTC (6 years, 2 months ago) by gross
Original Path: trunk

Clarification of terminology and scaling.
Joint inversion is not working yet.

Revision 4098 - Directory Listing
Modified Fri Dec 7 03:45:20 2012 UTC (6 years, 2 months ago) by caltinay
Original Path: trunk

Unbroke my breakage.

Revision 4097 - Directory Listing
Modified Fri Dec 7 01:18:35 2012 UTC (6 years, 2 months ago) by caltinay
Original Path: trunk

Minor edits.

Revision 4096 - Directory Listing
Modified Thu Dec 6 04:05:29 2012 UTC (6 years, 2 months ago) by jfenwick
Original Path: trunk

temporary doc fixes and moving tsunami out of the way

Revision 4095 - Directory Listing
Modified Wed Dec 5 05:32:22 2012 UTC (6 years, 2 months ago) by caltinay
Original Path: trunk

A bit of doco cleanup.

Revision 4093 - Directory Listing
Modified Fri Nov 30 04:52:01 2012 UTC (6 years, 2 months ago) by gross
Original Path: trunk

There is now a coherent implementation of gravity and magnetic forward model including an update of the user's guide.

Revision 4092 - Directory Listing
Modified Thu Nov 29 10:42:39 2012 UTC (6 years, 2 months ago) by caltinay
Original Path: trunk

Minor change. Test commit.

Revision 4091 - Directory Listing
Modified Mon Nov 26 10:27:29 2012 UTC (6 years, 2 months ago) by gross
Original Path: trunk

Some terminology introduced and magnetic inversion corrected.

Revision 4090 - Directory Listing
Modified Mon Nov 26 03:51:04 2012 UTC (6 years, 2 months ago) by caltinay
Original Path: trunk

Savanna tweaks.

Revision 4089 - Directory Listing
Modified Fri Nov 23 04:41:54 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Switch to new toolchain on Savanna.

Revision 4088 - Directory Listing
Modified Thu Nov 22 23:31:37 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Use kronecker, not numpy's identity in wave (why do these issues come up now?)

Revision 4087 - Directory Listing
Modified Thu Nov 22 22:28:01 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Moved matplotlib imports in test scripts before escript since there is an
import chain which pulls it so the use() function has no effect.

Revision 4086 - Directory Listing
Modified Wed Nov 21 02:48:12 2012 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Doco for 1D interpolation [resolves #631]

Revision 4085 - Directory Listing
Modified Tue Nov 20 07:04:11 2012 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

nonuniformInterolate and Slope added.
Doco later

Revision 4084 - Directory Listing
Modified Tue Nov 20 06:22:07 2012 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Adding some linebreaks

Revision 4083 - Directory Listing
Modified Mon Nov 19 22:19:42 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

removed manually set weights from scripts.

Revision 4082 - Directory Listing
Modified Mon Nov 19 06:16:06 2012 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Minor changes to install doco

Revision 4081 - Directory Listing
Modified Mon Nov 19 02:35:18 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Updated unit test to test LinearMapping instead of old ScalingMapping

Revision 4080 - Directory Listing
Modified Mon Nov 19 01:45:38 2012 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Epydoc fixes

Revision 4079 - Directory Listing
Modified Fri Nov 16 07:59:01 2012 UTC (6 years, 3 months ago) by gross
Original Path: trunk

some modifications to scaling in downunder. still not perfect.

Revision 4078 - Directory Listing
Modified Fri Nov 16 07:50:49 2012 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Unit tests for binary install with no scons and no source tree.
Script for installing and testing a .deb within a chroot.

Revision 4077 - Directory Listing
Modified Fri Nov 16 04:31:02 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Minor change.

Revision 4076 - Directory Listing
Modified Thu Nov 15 03:45:24 2012 UTC (6 years, 3 months ago) by gross
Original Path: trunk

    def getDirectionalDerivative(self, m, d, grad_m):

Revision 4075 - Directory Listing
Modified Thu Nov 15 03:31:37 2012 UTC (6 years, 3 months ago) by gross
Original Path: trunk

missing latex files

Revision 4074 - Directory Listing
Modified Thu Nov 15 03:30:59 2012 UTC (6 years, 3 months ago) by gross
Original Path: trunk

this will break the downundermodule: major revision of the classes.

Revision 4073 - Directory Listing
Modified Thu Nov 15 03:28:33 2012 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Fixing doco build error

Revision 4072 - Directory Listing
Modified Thu Nov 15 01:58:35 2012 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Fix to prevent escript from segfaulting on quantal

Revision 4070 - Directory Listing
Modified Tue Nov 13 07:55:22 2012 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

File for quantal. Now to work out why on earth quantal manages to make epydoc segfault

Revision 4069 - Directory Listing
Modified Tue Nov 13 07:47:16 2012 UTC (6 years, 3 months ago) by gross
Original Path: trunk

ArithmeticTuple supports empty data object as components now.

Revision 4068 - Directory Listing
Modified Tue Nov 13 04:42:08 2012 UTC (6 years, 3 months ago) by vboros
Original Path: trunk

Small corrections to the magnetic forward model

Revision 4067 - Directory Listing
Modified Mon Nov 12 07:35:14 2012 UTC (6 years, 3 months ago) by vboros
Original Path: trunk

Magnetostatics background added

Revision 4066 - Directory Listing
Modified Mon Nov 12 06:18:47 2012 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

renaming wheezyoptions file

Revision 4065 - Directory Listing
Modified Mon Nov 12 04:47:32 2012 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Trying without uml

Revision 4063 - Directory Listing
Modified Fri Nov 9 06:15:00 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Fixed a typo in method description.

Revision 4062 - Directory Listing
Modified Fri Nov 9 04:53:08 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Start of module reference section in inversion guide.

Revision 4061 - Directory Listing
Modified Fri Nov 9 04:05:28 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Updated data source test cases.

Revision 4060 - Directory Listing
Modified Fri Nov 9 03:50:19 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

-Overhaul of inversion data sources. Domain is now generated and managed by separate class.
-Removed UBCDataSource which was only used for testing.
-Updated example scripts.

Revision 4059 - Directory Listing
Modified Fri Nov 9 03:20:23 2012 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Start of substitution for rules

Revision 4058 - Directory Listing
Modified Fri Nov 2 06:47:06 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

-Ripley now checks for input fs when calling gradient
-interactive mode works again when filename is supplied (typo)
-forward model PDE sets symmetry on now

Revision 4057 - Directory Listing
Modified Fri Nov 2 04:15:09 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

toc/hyperref fixes for inversion pdf.

Revision 4056 - Directory Listing
Modified Thu Nov 1 07:20:38 2012 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Allow doxygen to build in another target
Debian build stuff begins

Revision 4055 - Directory Listing
Modified Thu Nov 1 00:22:01 2012 UTC (6 years, 3 months ago) by gross
Original Path: trunk

Renaming of filenames

Revision 4054 - Directory Listing
Modified Wed Oct 31 23:27:57 2012 UTC (6 years, 3 months ago) by gross
Original Path: trunk

prilimary checkin

Revision 4053 - Directory Listing
Modified Wed Oct 31 07:27:35 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Do not fix potential on sides of domain by default.

Revision 4052 - Directory Listing
Modified Wed Oct 31 05:50:35 2012 UTC (6 years, 3 months ago) by gross
Original Path: trunk

missing references added (mantis id=683)

Revision 4051 - Directory Listing
Modified Wed Oct 31 03:40:47 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Split inversion cookbook into two parts...

Revision 4050 - Directory Listing
Modified Wed Oct 31 01:01:24 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Changed initial Hessian in magnetic test and removed some debug output.

Revision 4049 - Directory Listing
Modified Wed Oct 31 00:50:50 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Fixed typos.

Revision 4048 - Directory Listing
Modified Tue Oct 30 21:54:15 2012 UTC (6 years, 3 months ago) by gross
Original Path: trunk

fixed modification in the DataSource creator

Revision 4047 - Directory Listing
Modified Tue Oct 30 09:10:07 2012 UTC (6 years, 3 months ago) by gross
Original Path: trunk

More on magnetic inversion

Revision 4046 - Directory Listing
Modified Tue Oct 30 04:43:25 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Deprecated saveDX and made sure DeprecationWarnings are shown (py2.7 disabled
those). Also a fix to $BUILD_DIR being non-absolute.

Revision 4045 - Directory Listing
Modified Tue Oct 30 03:57:22 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Imported inversion cookbook.

Revision 4044 - Directory Listing
Modified Tue Oct 30 03:35:17 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Some doco fixes for downunder.

Revision 4043 - Directory Listing
Modified Tue Oct 30 03:34:43 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Compile fixes for install guide.

Revision 4042 - Directory Listing
Modified Mon Oct 29 05:55:58 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

New SaveSilo tests (only run if Silo module available and MPI size=1).
Tests are somewhat limited due to missing functionality in Silo module (devs
contacted about that).

Revision 4041 - Directory Listing
Modified Sun Oct 28 23:42:35 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Fixed a typo

Revision 4040 - Directory Listing
Modified Sun Oct 28 22:37:45 2012 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Some py3 changes that didn't get committed for some reason

Revision 4039 - Directory Listing
Modified Fri Oct 26 07:34:06 2012 UTC (6 years, 3 months ago) by gross
Original Path: trunk

magnetic inversion added

Revision 4038 - Directory Listing
Modified Fri Oct 26 04:47:25 2012 UTC (6 years, 3 months ago) by jfenwick
Original Path: trunk

Minor fix to control file

Revision 4037 - Directory Listing
Modified Fri Oct 26 03:04:30 2012 UTC (6 years, 3 months ago) by gross
Original Path: trunk

some modifictaions to make implementation for magnetic inversion easier

Revision 4036 - Directory Listing
Modified Thu Oct 25 06:21:03 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Added saveVTK tests for ripley domains.

Revision 4035 - Directory Listing
Modified Thu Oct 25 03:10:14 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Tweaked scons files so tests work even when specifying non-absolute build_dir.

Revision 4034 - Directory Listing
Modified Thu Oct 25 02:54:01 2012 UTC (6 years, 3 months ago) by caltinay
Original Path: trunk

Fixes to inversion. Using resetRightHandSideCoefficients() now.

Revision 4033 - Directory Listing
Modified Wed Oct 24 08:14:41 2012 UTC (6 years, 4 months ago) by gross
Original Path: trunk

some typos fixed.

Revision 4032 - Directory Listing
Modified Wed Oct 24 08:06:15 2012 UTC (6 years, 4 months ago) by gross
Original Path: trunk

Gravity inversion is disconnect from DataSource objects now in order to allow for more  flexibility
when it comes to the definition of of Mapping and Regulariztion. GravityInversion does not hold a reference to the datasource object anymore.

use   inv=GravityInversion()
      inv.setUp(datasource) 

rather than inv.setDataSource(datasource); inv.setUp()

Revision 4031 - Directory Listing
Modified Wed Oct 24 03:36:37 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Added option -x to run xterm to run-escript and replaced a few bashims.

Revision 4030 - Directory Listing
Modified Wed Oct 24 00:57:36 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Silenced the no-visit-in-path warning and fixed not-in-path run-escript in
utest.sh.

Revision 4029 - Directory Listing
Modified Wed Oct 24 00:29:15 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Reapplied changes from rev. 3853 which got lost in a merge...

Revision 4028 - Directory Listing
Modified Tue Oct 23 05:16:38 2012 UTC (6 years, 4 months ago) by gross
Original Path: trunk

changes in pycad to address feature request 0000661

Revision 4027 - Directory Listing
Modified Tue Oct 23 04:56:33 2012 UTC (6 years, 4 months ago) by gross
Original Path: trunk

setting a constant value to the initial solution of the Transport problem 
had a problem. initial data object needs to be expanded before copied to the 
paso transport object.

Revision 4025 - Directory Listing
Modified Mon Oct 22 08:18:47 2012 UTC (6 years, 4 months ago) by gross
Original Path: trunk

 linearPDE.resetRightHandSideCoefficients has been implemented and tested.

Revision 4024 - Directory Listing
Modified Mon Oct 22 06:11:29 2012 UTC (6 years, 4 months ago) by gross
Original Path: trunk

tag testing for finley and dudley files added.

Revision 4023 - Directory Listing
Modified Tue Oct 16 04:17:48 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Another fix to the PDE assembly logic in ripley.

Revision 4022 - Directory Listing
Modified Mon Oct 15 23:52:24 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Fixed checks in ripley::addPDEToRHS().

Revision 4021 - Directory Listing
Modified Mon Oct 15 02:31:00 2012 UTC (6 years, 4 months ago) by jfenwick
Original Path: trunk

Doco fixes.
Unit test fix for sys.version_info type change

Revision 4020 - Directory Listing
Modified Thu Oct 11 22:27:33 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Removed print() that slipped in in last commit.

Revision 4019 - Directory Listing
Modified Thu Oct 11 08:12:55 2012 UTC (6 years, 4 months ago) by jfenwick
Original Path: trunk

More tabbing errors,
range/xrange
...

Revision 4018 - Directory Listing
Modified Thu Oct 11 04:43:39 2012 UTC (6 years, 4 months ago) by jfenwick
Original Path: trunk

Used "new" raise syntax in a few places
Fixed some tabbing
Fixed some funnies involving changes to xrange/range
added a quick and nasty __hash__ function to Symbol
   def __hash__(self):
        return id(self)
This does mean that __hash__ and == do not match exactly.   Not sure if that matters for our purposes

Revision 4017 - Directory Listing
Modified Thu Oct 11 03:13:28 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Modified a test so roundoff errors don't cause failures.

Revision 4016 - Directory Listing
Modified Tue Oct 9 03:50:27 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Skip data source tests under MPI for now as there is no straightforward way
of comparing the data (saveVTK appears to be the best option).

Revision 4015 - Directory Listing
Modified Mon Oct 8 01:19:04 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Updated savanna options file to use latest compiler, mkl

Revision 4014 - Directory Listing
Modified Thu Oct 4 03:28:35 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Changed data source to use ripley's netCDF reader,
added tests and changed ERMapper test to have different x and y sizes.

Revision 4013 - Directory Listing
Modified Thu Oct 4 03:13:27 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Implemented netCDF grid reader analogous to binary grid reader in ripley.

Revision 4012 - Directory Listing
Modified Wed Oct 3 02:25:10 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Initialize X_reduced in forward model to avoid issues later on.

Revision 4011 - Directory Listing
Modified Wed Oct 3 00:47:55 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Updated test reference file.

Revision 4010 - Directory Listing
Modified Tue Oct 2 06:57:11 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Fixed a potential div by zero in ripley's automatic domain subdivider....

Revision 4009 - Directory Listing
Modified Tue Oct 2 05:53:37 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

don't try to flip y-coord in reader. some more fixes and doco.

Revision 4008 - Directory Listing
Modified Tue Oct 2 04:33:27 2012 UTC (6 years, 4 months ago) by gross
Original Path: trunk

point coordinates are now written in %.14e rather then %f. This fixes accuracy problems when it comes to geometrically small domains.

Revision 4007 - Directory Listing
Modified Tue Oct 2 02:12:01 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Doco updates.
Data source paddings now take x,y not xy,z as Z padding can be done by setting
vertical extents.

Revision 4006 - Directory Listing
Modified Fri Sep 28 06:16:46 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Update vm options to use pip-installed numpy.

Revision 4005 - Directory Listing
Modified Fri Sep 28 06:09:03 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

test fixes, doco updates, annoyance removals.

Revision 4004 - Directory Listing
Modified Fri Sep 28 04:45:25 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

don't use escript.escript.Data...

Revision 4003 - Directory Listing
Modified Fri Sep 28 00:20:01 2012 UTC (6 years, 4 months ago) by jfenwick
Original Path: trunk

Load balancing on unit tests

Revision 4002 - Directory Listing
Modified Fri Sep 28 00:16:56 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Fixed a memory leak (freeing paso coupler) in ripley.

Revision 4001 - Directory Listing
Modified Thu Sep 27 01:35:52 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Removed obsolete files.

Revision 4000 - Directory Listing
Modified Thu Sep 27 01:32:07 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

s/escript/escore/

Revision 3999 - Directory Listing
Modified Thu Sep 27 01:31:07 2012 UTC (6 years, 4 months ago) by jfenwick
Original Path: trunk

Splitting tests

Revision 3998 - Directory Listing
Modified Thu Sep 27 01:17:28 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Finley now throws in ownSample() for reduced function with mpisize>1.

Revision 3997 - Directory Listing
Modified Thu Sep 27 01:09:12 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Add note to documentation that saveDataCSV will not work in all cases.

Revision 3996 - Directory Listing
Modified Thu Sep 27 00:54:10 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Don't test saveCSV for cases it does not work with.

Revision 3995 - Directory Listing
Modified Wed Sep 26 12:43:17 2012 UTC (6 years, 4 months ago) by jfenwick
Original Path: trunk

More module fiddles

Revision 3994 - Directory Listing
Modified Wed Sep 26 07:38:38 2012 UTC (6 years, 4 months ago) by jfenwick
Original Path: trunk

Install doco still needs work.
Removing some of the weird:
     esys.finley.finley
type modules

Revision 3993 - Directory Listing
Modified Wed Sep 26 07:00:55 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Addressing mantis 651. Test for finley will fail under MPI since there is
sth wrong with the way ReducedContinuousFunction samples are interrogated.

Revision 3992 - Directory Listing
Modified Wed Sep 26 02:50:48 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Data.cpp: Removed some namespace ambiguities which fixes doxygen warnings, some
cleanup and reindent.
*: doxygen fixes.

Revision 3991 - Directory Listing
Modified Tue Sep 25 23:52:22 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

Updated doxygen cfg file and made a few first changes to doco.

Revision 3990 - Directory Listing
Modified Tue Sep 25 05:03:20 2012 UTC (6 years, 4 months ago) by caltinay
Original Path: trunk

First set of assorted epydoc fixes/additions.

Revision 3989 - Directory Listing
Modified Tue Sep 25 02:21:54 2012 UTC (6 years, 4 months ago) by jfenwick
Original Path: trunk

More copyright fixes.
pyvisi traces removed.
Some install doco

Revision 3988 - Directory Listing
Modified Mon Sep 24 01:08:19 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Scale coordinates if pyproj is not available

Revision 3987 - Directory Listing
Modified Sun Sep 23 23:24:37 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Fix to test which fails when ripley adjusts number of elements (domain decomp.)

Revision 3986 - Directory Listing
Modified Sun Sep 23 23:01:10 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Added explicit cast to make osx happy.

Revision 3985 - Directory Listing
Modified Fri Sep 21 06:44:17 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Unit test for ER Mapper reader.

Revision 3984 - Directory Listing
Modified Fri Sep 21 06:41:54 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

invert Y coordinate in ripley's 3d data reader. This needs to be configurable
and added to 2d as well...

Revision 3983 - Directory Listing
Modified Fri Sep 21 06:41:03 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Use ReducedFunction for data sources.

Revision 3982 - Directory Listing
Modified Fri Sep 21 03:23:22 2012 UTC (6 years, 5 months ago) by jfenwick
Original Path: trunk

More edits + removing pyvisi from trunk

Revision 3981 - Directory Listing
Modified Fri Sep 21 02:47:54 2012 UTC (6 years, 5 months ago) by jfenwick
Original Path: trunk

First pass of updating copyright notices

Revision 3980 - Directory Listing
Modified Fri Sep 21 01:55:39 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Now using NullCellValue to initialise data object for ERS reader.

Revision 3979 - Directory Listing
Modified Thu Sep 20 06:18:49 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Fixed tests under MPI.

Revision 3978 - Directory Listing
Modified Thu Sep 20 04:36:17 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Make sympy optional as it was intended initially. Trying to instantiate anything
from symbolic will raise an exception if sympy is not available.

Revision 3977 - Directory Listing
Modified Thu Sep 20 04:27:10 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Export KMP_MONITOR_STACKSIZE so tests work on savanna.

Revision 3976 - Directory Listing
Modified Thu Sep 20 03:26:47 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

fixed python-2.7'ism.

Revision 3975 - Directory Listing
Modified Thu Sep 20 01:54:06 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Merged symbolic branch into trunk. Curious what daniel and spartacus have to
say...

Revision 3972 - Directory Listing
Modified Wed Sep 19 03:08:39 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Can now constrain sides of domain.

Revision 3971 - Directory Listing
Modified Wed Sep 19 02:55:35 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Implemented binary grid reader in ripley which is now used in ER Mapper source.
Interface/details likely to change but need to get this running now.

Revision 3970 - Directory Listing
Modified Wed Sep 19 02:28:27 2012 UTC (6 years, 5 months ago) by jfenwick
Original Path: trunk

More install doc fixes

Revision 3969 - Directory Listing
Modified Tue Sep 18 05:34:38 2012 UTC (6 years, 5 months ago) by jfenwick
Original Path: trunk

Removing reference to nose

Revision 3968 - Directory Listing
Modified Mon Sep 17 06:30:02 2012 UTC (6 years, 5 months ago) by jfenwick
Original Path: trunk

Starting updates to the install guide

Revision 3967 - Directory Listing
Modified Mon Sep 17 04:02:58 2012 UTC (6 years, 5 months ago) by jfenwick
Original Path: trunk

Changes to SConstruct to allow building with clang

Revision 3966 - Directory Listing
Modified Mon Sep 17 00:45:39 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Changed unit scale for ER Mapper files. Fixed an issue with UBC source.

Revision 3965 - Directory Listing
Modified Fri Sep 14 01:23:17 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Data sources have to end up in the Function fs or we get into trouble when
interpolating. Now using setValueOfDataPoint() which doesn't seem to slow
things down too much.

Revision 3964 - Directory Listing
Modified Thu Sep 13 03:49:55 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Hopefully this will fix the interpolation in data sources.

Revision 3963 - Directory Listing
Modified Thu Sep 13 01:39:00 2012 UTC (6 years, 5 months ago) by jfenwick
Original Path: trunk

Fix to keep the warning-free-build happy

Revision 3962 - Directory Listing
Modified Tue Sep 11 09:12:07 2012 UTC (6 years, 5 months ago) by jfenwick
Original Path: trunk

Fix in brick for ambiguous typing.

Python work around for unit tests.
Passing cpp tests as well.

omp is disabled due to a weird linking error.

Revision 3961 - Directory Listing
Modified Tue Sep 11 07:21:41 2012 UTC (6 years, 5 months ago) by jfenwick
Original Path: trunk

Options file for mole.
Work around for python compile errors

Revision 3960 - Directory Listing
Modified Mon Sep 10 01:39:40 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Added accessors to fwd model, regularization and cost function plus access
to gravity survey data.

Revision 3959 - Directory Listing
Modified Fri Sep 7 04:48:07 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

support for geodetic coordinates in ER Mapper files. Correction to UTM
conversion (now assumes southern hemisphere).

Revision 3958 - Directory Listing
Modified Fri Sep 7 02:56:42 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Fixes to netcdf data source and new ERS (ER Mapper) datasource.

Revision 3957 - Directory Listing
Modified Wed Sep 5 23:49:23 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Do not require pyproj module-wide. Print a warning if it is not available but
needed instead of raising an exception.

Revision 3956 - Directory Listing
Modified Wed Sep 5 04:57:43 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Fixes to netcdf reader for inversions.

Revision 3955 - Directory Listing
Modified Tue Sep 4 01:44:41 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Added CentOS 6 vm options file.

Revision 3954 - Directory Listing
Modified Tue Sep 4 01:43:58 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Fixed an issue with incompatible nose.

Revision 3953 - Directory Listing
Modified Mon Sep 3 00:57:12 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Some test output adjustments.

Revision 3952 - Directory Listing
Modified Sun Sep 2 23:42:25 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Made a test slightly more relaxed since roundoff errors caused it to fail on
one system.

Revision 3951 - Directory Listing
Modified Tue Aug 28 23:58:08 2012 UTC (6 years, 5 months ago) by caltinay
Original Path: trunk

Fixed tests with python versions <2.7.

Revision 3950 - Directory Listing
Modified Fri Aug 24 06:10:02 2012 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

More tests and corrections in the alternative minimizers.

Revision 3949 - Directory Listing
Modified Fri Aug 24 02:37:47 2012 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

Added tests for mappings.

Revision 3948 - Directory Listing
Modified Fri Aug 24 01:01:34 2012 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

Some interface changes to make the inversion more flexible.

Revision 3947 - Directory Listing
Modified Wed Aug 22 23:19:10 2012 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

Compiling and installing downunder module now. Adjusted import statements
accordingly. Added a gravity test run.

Revision 3946 - Directory Listing
Modified Wed Aug 22 02:08:12 2012 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

Initial import of inversion code from devteam area, rev. 51.
Nothing is scons built/installed/tested yet.

Revision 3945 - Directory Listing
Modified Tue Aug 21 04:11:13 2012 UTC (6 years, 6 months ago) by jfenwick
Original Path: trunk

Changing utest behaviour for MPI

Revision 3944 - Directory Listing
Modified Mon Aug 20 02:11:22 2012 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

Fixed ordering of Hex's in weipa's ripley writer.
Fixed an issue with auto domain subdivisions in ripley Brick.

Revision 3943 - Directory Listing
Modified Thu Aug 9 04:43:24 2012 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

Added heuristics for number of domain subdivisions to ripley so ripley domains
can now be created without specifying the values manually (but a warning will
be printed).

Revision 3942 - Directory Listing
Modified Fri Jul 27 01:04:48 2012 UTC (6 years, 6 months ago) by jfenwick
Original Path: trunk

Porting changes back from 3.3 release branch

Revision 3941 - Directory Listing
Modified Fri Jul 27 00:38:10 2012 UTC (6 years, 6 months ago) by jfenwick
Original Path: trunk

Some more test disabling

Revision 3940 - Directory Listing
Modified Thu Jul 26 05:54:58 2012 UTC (6 years, 6 months ago) by jfenwick
Original Path: trunk

Disabling tests which do not allow MPI
Previously we allowed these if there was only one rank

Revision 3939 - Directory Listing
Modified Mon Jul 23 01:50:46 2012 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

Added return value checks for freopen in mpi redirect code. Ubuntu has a
warn_unused_result attribute set for the function.
Re-indented the file while at it.

Revision 3934 - Directory Listing
Modified Fri Jul 13 09:01:16 2012 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Added unit test for tagreader

Revision 3931 - Directory Listing
Modified Tue Jul 10 00:39:09 2012 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Fixing spelling

Revision 3928 - Directory Listing
Modified Mon Jul 9 23:23:43 2012 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Do not allow attempts to setValue using a Locator which does not match the funcionSpace of the Data

Revision 3927 - Directory Listing
Modified Mon Jul 9 11:11:47 2012 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Avoid warning

Revision 3923 - Directory Listing
Modified Mon Jul 9 05:12:12 2012 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Fixing build error.

Revision 3922 - Directory Listing
Modified Mon Jul 9 02:19:51 2012 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Adds setvalue to locator
Addresses mantis #531

Revision 3921 - Directory Listing
Modified Thu Jul 5 05:02:49 2012 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Fix build error

Revision 3920 - Directory Listing
Modified Thu Jul 5 03:42:30 2012 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Copied over tagname reading stuff from finley

Revision 3919 - Directory Listing
Modified Thu Jul 5 03:12:02 2012 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Don't know what caused this to show as an error.
Compiler update perhaps?

Revision 3918 - Directory Listing
Modified Thu Jul 5 02:44:07 2012 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Added unit test which uses the TestDomain to check reduction.
TestDomains can no longer be created directly from python 
(fixes problem I had earlier)

TestDomain can now create testdomains with aribtrarily sized 
coordinate vectors.

Revision 3917 - Directory Listing
Modified Thu Jul 5 00:17:50 2012 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Fixing a bug in lazy reduction operations.
Will add extra test to prevent regression once I can find out why the test is crashing

Revision 3916 - Directory Listing
Modified Wed Jul 4 06:16:52 2012 UTC (6 years, 7 months ago) by jfenwick
Original Path: trunk

Deal correctly with scalars passed into inplace update operators.
Fixes mantis 669

Revision 3915 - Directory Listing
Modified Mon Jun 25 02:17:58 2012 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

Added declspecs for all ripley classes.

Revision 3914 - Directory Listing
Modified Wed Jun 20 04:51:47 2012 UTC (6 years, 8 months ago) by jfenwick
Original Path: trunk

Only allow setX from ContinuousFunctions.
This addresses mantis 644.

Revision 3913 - Directory Listing
Modified Tue Jun 19 06:21:58 2012 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

Fixed misuse of getSampleDataRO with lazy data in ripley.

Revision 3912 - Directory Listing
Modified Fri Jun 15 05:02:42 2012 UTC (6 years, 8 months ago) by jfenwick
Original Path: trunk

GetMeshFromFile wrapper to load .fly or .msh depending on the extension.
Note that this only works on one of the two formats named .msh

Addresses mantis issue 641.

Revision 3911 - Directory Listing
Modified Thu Jun 14 01:01:03 2012 UTC (6 years, 8 months ago) by jfenwick
Original Path: trunk

Copyright changes

Revision 3910 - Directory Listing
Modified Thu Jun 14 00:45:03 2012 UTC (6 years, 8 months ago) by gross
Original Path: trunk

Small bug fixed.

Revision 3909 - Directory Listing
Modified Wed Jun 13 07:03:06 2012 UTC (6 years, 8 months ago) by gross
Original Path: trunk

darcy solver removes hydrostatic pressure from problem now

Revision 3908 - Directory Listing
Modified Wed Jun 13 05:43:45 2012 UTC (6 years, 8 months ago) by caltinay
Original Path: trunk

Fixed an error in ripley computing shared node id's.
pythonMPIredirect now redirects again.

Revision 3907 - Directory Listing
Modified Fri Jun 8 01:20:09 2012 UTC (6 years, 8 months ago) by jfenwick
Original Path: trunk

Only switch on useElementsOnFace  by default where we actually support it

Revision 3906 - Directory Listing
Modified Thu Jun 7 11:00:50 2012 UTC (6 years, 8 months ago) by jfenwick
Original Path: trunk

Disable AMG on MPI builds

Revision 3905 - Directory Listing
Modified Tue Jun 5 08:33:41 2012 UTC (6 years, 8 months ago) by gross
Original Path: trunk

length scale changed

Revision 3904 - Directory Listing
Modified Tue Jun 5 08:30:24 2012 UTC (6 years, 8 months ago) by gross
Original Path: trunk

incorrect macro element argument removed

Revision 3903 - Directory Listing
Modified Tue Jun 5 08:26:20 2012 UTC (6 years, 8 months ago) by gross
Original Path: trunk

offset removed: not clear why this was there

Revision 3901 - Directory Listing
Modified Wed May 23 08:09:45 2012 UTC (6 years, 9 months ago) by jfenwick
Original Path: trunk

Rectangle and Brick use rich face element by default. 
This is to address issue #653

Updated unit tests to explicitly not use them where they didn't
specify previoulsy

Revision 3897 - Directory Listing
Modified Wed May 16 03:17:26 2012 UTC (6 years, 9 months ago) by jfenwick
Original Path: trunk

correcting example

Revision 3896 - Directory Listing
Modified Fri May 11 01:31:29 2012 UTC (6 years, 9 months ago) by caltinay
Original Path: trunk

Re-enable numpy header detection with python 2.

Revision 3895 - Directory Listing
Modified Mon Apr 16 00:09:42 2012 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Adding some files which went missing in the merge

Revision 3894 - Directory Listing
Modified Wed Apr 11 03:13:15 2012 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Still need to add notes to the install guide about Python3.

Revision 3893 - Directory Listing
Modified Wed Apr 11 01:40:10 2012 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Pycad now generates scripts with floating points at 6 decimal places.
Tests have been ammended to match this.

Revision 3892 - Directory Listing
Modified Tue Apr 10 08:57:23 2012 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Merged changes across from the attempt2 branch.
This version builds and passes python2 tests.
It also passes most python3 tests.

Revision 3887 - Directory Listing
Modified Thu Apr 5 03:14:59 2012 UTC (6 years, 10 months ago) by gross
Original Path: trunk

low level system in AMG is created one only now.

Revision 3886 - Directory Listing
Modified Thu Apr 5 00:50:30 2012 UTC (6 years, 10 months ago) by gross
Original Path: trunk

some minor problems with MPI AMG fixed.

Revision 3885 - Directory Listing
Modified Wed Apr 4 22:12:26 2012 UTC (6 years, 10 months ago) by gross
Original Path: trunk

some fix in AMG

Revision 3884 - Directory Listing
Modified Wed Apr 4 04:55:43 2012 UTC (6 years, 10 months ago) by gross
Original Path: trunk

some fix in AMG

Revision 3883 - Directory Listing
Modified Mon Mar 26 03:24:14 2012 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

Modified dlopenflags in escript's init module so newer MKL libraries can
successfully load support libraries.

Revision 3882 - Directory Listing
Modified Thu Mar 22 02:15:57 2012 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

Added another constraint for the numpy optimized array access: endianness.
The scipy netcdf reader gave me big endian data which resulted in garbage.
Can use the astype() method in python to convert.

Revision 3867 - Directory Listing
Modified Thu Mar 15 05:45:54 2012 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

weipa treats shapes (1,) and (1,1) as scalars. Fixes bogus output in VTK writer.

Revision 3866 - Directory Listing
Modified Wed Mar 14 02:06:13 2012 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

Use system silo on guineapig now.

Revision 3865 - Directory Listing
Modified Mon Mar 12 23:49:05 2012 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

Re-enabled threaded MKL on epic.

Revision 3863 - Directory Listing
Modified Mon Mar 12 00:15:40 2012 UTC (6 years, 11 months ago) by gross
Original Path: trunk

some debug prints removed

Revision 3861 - Directory Listing
Modified Fri Mar 9 02:06:29 2012 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

Added options file that disables openMP and replaces the MKL library for savanna.

Revision 3853 - Directory Listing
Modified Thu Mar 1 07:25:03 2012 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

Fixed hybrid mode when using OpenMPI by adding --cpus-per-rank argument to
mpirun in the launcher. Updated epic options file accordingly.

Revision 3852 - Directory Listing
Modified Thu Mar 1 05:34:52 2012 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

Correcting some indent errors

Revision 3851 - Directory Listing
Modified Wed Feb 29 05:23:30 2012 UTC (6 years, 11 months ago) by jfenwick
Original Path: trunk

Start of cross-compile build for py3

Revision 3850 - Directory Listing
Modified Tue Feb 28 06:04:42 2012 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

Support for CSC in ripley.

Revision 3843 - Directory Listing
Modified Mon Feb 27 05:50:58 2012 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

Updated epic options, disabled OpenMP until problems solved.

Revision 3842 - Directory Listing
Modified Mon Feb 27 04:19:16 2012 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

Updated savanna libraries and compiler version.

Revision 3841 - Directory Listing
Modified Mon Feb 27 04:18:53 2012 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

Added support for OFFSET1 matrices in ripley.

Revision 3836 - Directory Listing
Modified Thu Feb 16 03:17:18 2012 UTC (7 years ago) by caltinay
Original Path: trunk

Transport problem support for ripley.

Revision 3835 - Directory Listing
Modified Wed Feb 15 23:19:01 2012 UTC (7 years ago) by gross
Original Path: trunk

and another attempt to fix MPI compilation

Revision 3834 - Directory Listing
Modified Wed Feb 15 07:09:09 2012 UTC (7 years ago) by gross
Original Path: trunk

some declaration problems fixed

Revision 3833 - Directory Listing
Modified Wed Feb 15 06:19:45 2012 UTC (7 years ago) by lgao
Original Path: trunk

Fix the merging problem for this file.

Revision 3830 - Directory Listing
Modified Wed Feb 15 04:27:47 2012 UTC (7 years ago) by lgao
Original Path: trunk

Add comments for Smoother

Revision 3829 - Directory Listing
Modified Wed Feb 15 03:33:08 2012 UTC (7 years ago) by lgao
Original Path: trunk

Fix warnings from another machine.

Revision 3828 - Directory Listing
Modified Wed Feb 15 03:27:58 2012 UTC (7 years ago) by lgao
Original Path: trunk

Fix all warnings reported on guineapig.

Revision 3827 - Directory Listing
Modified Tue Feb 14 11:42:08 2012 UTC (7 years ago) by lgao
Original Path: trunk

 Merge branch "amg_from_3530" back into trunk.

Revision 3825 - Directory Listing
Modified Tue Feb 14 06:11:58 2012 UTC (7 years ago) by gross
Original Path: trunk

don't call MPI withing parallel regions

Revision 3823 - Directory Listing
Modified Mon Feb 13 08:09:32 2012 UTC (7 years ago) by gross
Original Path: trunk

some fixes for openmp/mpi compilation and linearNC can now handel constraints.

Revision 3822 - Directory Listing
Modified Mon Feb 13 06:22:06 2012 UTC (7 years ago) by gross
Original Path: trunk

Transport solver supports now constraints (except the linear CN)

Revision 3816 - Directory Listing
Modified Thu Feb 9 05:46:36 2012 UTC (7 years ago) by caltinay
Original Path: trunk

WrappedArray now honours the 'strides' field in the numpy array interface
and supports more data types. Fixes test failures on savanna which for some
reason did not surface on other machines.

Revision 3814 - Directory Listing
Modified Thu Feb 9 00:11:08 2012 UTC (7 years ago) by caltinay
Original Path: trunk

Changes to savanna options file to use intel 12 and numpy 1.6.1.

Revision 3808 - Directory Listing
Modified Mon Feb 6 06:17:47 2012 UTC (7 years ago) by gross
Original Path: trunk

some modifications to the test examples

Revision 3807 - Directory Listing
Modified Mon Feb 6 06:14:25 2012 UTC (7 years ago) by gross
Original Path: trunk

LINEAR_CRANK_NICOLSON solver added

Revision 3806 - Directory Listing
Modified Mon Feb 6 02:32:48 2012 UTC (7 years ago) by caltinay
Original Path: trunk

ripley::getSize() also returns circumcircle now.

Revision 3804 - Directory Listing
Modified Mon Feb 6 00:48:22 2012 UTC (7 years ago) by caltinay
Original Path: trunk

Fixed utest.sh generator so tests can be run if the installation prefix is
not `pwd`

Revision 3803 - Directory Listing
Modified Fri Feb 3 06:16:30 2012 UTC (7 years ago) by caltinay
Original Path: trunk

Fixes to ripley unit test setup

Revision 3802 - Directory Listing
Modified Fri Feb 3 06:05:57 2012 UTC (7 years ago) by caltinay
Original Path: trunk

Quick fix for potential invalid memory access in paso.

Revision 3801 - Directory Listing
Modified Fri Feb 3 05:21:02 2012 UTC (7 years ago) by caltinay
Original Path: trunk

Fixed OpenMP bug in paso local AMG.

Revision 3800 - Directory Listing
Modified Fri Feb 3 01:18:06 2012 UTC (7 years ago) by caltinay
Original Path: trunk

Fixed integration with constant data on ripley.

Revision 3799 - Directory Listing
Modified Thu Feb 2 10:41:28 2012 UTC (7 years ago) by gross
Original Path: trunk

test for gradient of constant data added

Revision 3798 - Directory Listing
Modified Thu Feb 2 09:47:27 2012 UTC (7 years ago) by gross
Original Path: trunk

test for interpolation of constant data added

Revision 3797 - Directory Listing
Modified Thu Feb 2 09:28:59 2012 UTC (7 years ago) by gross
Original Path: trunk

test for integration of constant data added.

Revision 3796 - Directory Listing
Modified Thu Feb 2 06:26:15 2012 UTC (7 years ago) by gross
Original Path: trunk

typo in grad calculation fixed.

Revision 3795 - Directory Listing
Modified Thu Feb 2 05:54:34 2012 UTC (7 years ago) by caltinay
Original Path: trunk

Had to remove 'nowait' directive from PDE boundary conditions since all
4 (2D) / 8 (3D) values are updated the way it is implemented. This caused
race conditions when updating RHS.

Revision 3794 - Directory Listing
Modified Wed Feb 1 23:02:26 2012 UTC (7 years ago) by gross
Original Path: trunk

uninitialied variable fixed.

Revision 3793 - Directory Listing
Modified Wed Feb 1 07:39:43 2012 UTC (7 years ago) by gross
Original Path: trunk

new implementation of FCT solver with some modifications to the python interface

Revision 3792 - Directory Listing
Modified Wed Feb 1 06:16:25 2012 UTC (7 years ago) by caltinay
Original Path: trunk

Merged ripley rectangular domain into trunk.

Revision 3788 - Directory Listing
Modified Mon Jan 30 04:41:33 2012 UTC (7 years ago) by caltinay
Original Path: trunk

Fixed showEscriptParams() which hasn't worked for 2 years or so.

Revision 3787 - Directory Listing
Modified Fri Jan 27 01:43:47 2012 UTC (7 years ago) by caltinay
Original Path: trunk

Changed test cases from y.interpolateTable(...x...) to x.interpolateTable(...y...)

Revision 3786 - Directory Listing
Modified Wed Jan 25 04:46:39 2012 UTC (7 years ago) by jfenwick
Original Path: trunk

Made 2D interpolation call consistant with 1D and 3D.
Doco updates later

Revision 3784 - Directory Listing
Modified Wed Jan 25 01:31:42 2012 UTC (7 years ago) by caltinay
Original Path: trunk

Implemented optimized copy from numpy in WrappedArray (#652).

Revision 3782 - Directory Listing
Modified Tue Jan 24 01:30:38 2012 UTC (7 years, 1 month ago) by caltinay
Original Path: trunk

Another attempt to fix #649

Revision 3778 - Directory Listing
Modified Fri Jan 20 05:09:52 2012 UTC (7 years, 1 month ago) by gross
Original Path: trunk

better error reporting from UMFPACK

Revision 3775 - Directory Listing
Modified Wed Jan 18 07:26:34 2012 UTC (7 years, 1 month ago) by jfenwick
Original Path: trunk

Weipa updated

Revision 3774 - Directory Listing
Modified Wed Jan 18 06:29:34 2012 UTC (7 years, 1 month ago) by jfenwick
Original Path: trunk

dudley, pasowrap, pycad

Revision 3772 - Directory Listing
Modified Wed Jan 18 04:19:33 2012 UTC (7 years, 1 month ago) by jfenwick
Original Path: trunk

Converting finley directories

Revision 3771 - Directory Listing
Modified Wed Jan 18 02:30:48 2012 UTC (7 years, 1 month ago) by jfenwick
Original Path: trunk

First stage of 2.6/3 conversion

Revision 3747 - Directory Listing
Modified Thu Dec 15 02:13:14 2011 UTC (7 years, 2 months ago) by gross
Original Path: trunk

inconsistent notation fixed.

Revision 3739 - Directory Listing
Modified Tue Dec 13 00:48:26 2011 UTC (7 years, 2 months ago) by caltinay
Original Path: trunk

Ok, the python wrappers do use esysUtils for the exception translator.
Anything else?

Revision 3738 - Directory Listing
Modified Tue Dec 13 00:37:55 2011 UTC (7 years, 2 months ago) by caltinay
Original Path: trunk

Windoze: Fixed warning and linker error
Don't look for non-existing pasowrap tests.

Revision 3737 - Directory Listing
Modified Tue Dec 13 00:04:39 2011 UTC (7 years, 2 months ago) by caltinay
Original Path: trunk

Reordered and removed superfluous libraries from link lines. Hope W32 likes
that.

Revision 3736 - Directory Listing
Modified Mon Dec 12 01:26:51 2011 UTC (7 years, 2 months ago) by jfenwick
Original Path: trunk

Fixed apparent multiple instances of Esys

Revision 3734 - Directory Listing
Modified Fri Dec 9 04:48:08 2011 UTC (7 years, 2 months ago) by caltinay
Original Path: trunk

pycad kept creating temporary files. This should hopefully fix it.

Revision 3729 - Directory Listing
Modified Thu Dec 8 06:46:49 2011 UTC (7 years, 2 months ago) by jfenwick
Original Path: trunk

Fixed mistake in Finley_Assemble_PDE and the dudley equivalent.

Cihan - you might want to look to see if Ripley is affected

Revision 3727 - Directory Listing
Modified Thu Dec 8 04:55:56 2011 UTC (7 years, 2 months ago) by jfenwick
Original Path: trunk

More broken linkage

Revision 3726 - Directory Listing
Modified Thu Dec 8 04:35:52 2011 UTC (7 years, 2 months ago) by jfenwick
Original Path: trunk

Fixing some broken linkage on windows

Revision 3723 - Directory Listing
Modified Wed Dec 7 05:59:04 2011 UTC (7 years, 2 months ago) by caltinay
Original Path: trunk

Don't eat exceptions when using MPI with one rank.

Revision 3720 - Directory Listing
Modified Wed Dec 7 04:32:21 2011 UTC (7 years, 2 months ago) by caltinay
Original Path: trunk

Fixed off-by-one error in FunctionSpace

Revision 3689 - Directory Listing
Modified Wed Nov 23 01:39:45 2011 UTC (7 years, 3 months ago) by gross
Original Path: trunk

integration nodes fixed

Revision 3681 - Directory Listing
Modified Fri Nov 18 04:54:15 2011 UTC (7 years, 3 months ago) by caltinay
Original Path: trunk

Moved implementation of getTransportTypeId() and getSystemMatrixTypeId() into
pasowrap.

Revision 3678 - Directory Listing
Modified Thu Nov 17 06:32:05 2011 UTC (7 years, 3 months ago) by jfenwick
Original Path: trunk

Reversing other changes which made it in somehow

Revision 3677 - Directory Listing
Modified Thu Nov 17 04:01:12 2011 UTC (7 years, 3 months ago) by caltinay
Original Path: trunk

Fixed order of libraries which makes static esysUtils work again.

Revision 3676 - Directory Listing
Modified Thu Nov 17 03:52:25 2011 UTC (7 years, 3 months ago) by jfenwick
Original Path: trunk

Removed some debug text
Corrected some dudley where they should not have been.
Set savanna to build shared for now

Revision 3675 - Directory Listing
Modified Thu Nov 17 00:53:38 2011 UTC (7 years, 3 months ago) by jfenwick
Original Path: trunk

pasowrap joins the trunk.

Revision 3667 - Directory Listing
Modified Tue Nov 15 23:29:23 2011 UTC (7 years, 3 months ago) by gross
Original Path: trunk

better consistence of script and notation

Revision 3666 - Directory Listing
Modified Tue Nov 15 23:10:20 2011 UTC (7 years, 3 months ago) by gross
Original Path: trunk

fix for https://mantis.esscc.uq.edu.au/view.php?id=647

Revision 3650 - Directory Listing
Modified Fri Nov 4 07:02:55 2011 UTC (7 years, 3 months ago) by gross
Original Path: trunk

ode solver added

Revision 3649 - Directory Listing
Modified Fri Nov 4 04:35:15 2011 UTC (7 years, 3 months ago) by gross
Original Path: trunk

gmsh reader understand name tags now.

Revision 3647 - Directory Listing
Modified Tue Nov 1 23:33:18 2011 UTC (7 years, 3 months ago) by lgao
Original Path: trunk

With this option file, unit tests finished successfully with the following order to load module: 

module load mpi/gcc/openmpi/1.4.3
module load python/2.6.7
module load boost/1.46.1-python-2.6
module load netcdf/4.0.1
module load scons/2.0.1-python-2.6
module load intel-compilers/11.1.075
module load intel-mkl/10.3.5.220
module load python-numpy/1.3.0-python-2.6
module load cppunit/1.12.1
module load python-matplotlib/0.98.5.3-python-2.6
module load hdf5/1.8.6
module load silo/4.7.2
module load hypre/2.0.0

HYPRE is loaded but not used yet since the installed hypre module on epic comes with static library only.

Revision 3646 - Directory Listing
Modified Fri Oct 28 05:20:38 2011 UTC (7 years, 3 months ago) by lgao
Original Path: trunk

working option file on epic

Revision 3645 - Directory Listing
Modified Fri Oct 28 00:11:30 2011 UTC (7 years, 3 months ago) by caltinay
Original Path: trunk

Fixed typos.

Revision 3644 - Directory Listing
Modified Thu Oct 27 06:42:56 2011 UTC (7 years, 3 months ago) by gross
Original Path: trunk

hint to add surface items in pycad

Revision 3643 - Directory Listing
Modified Thu Oct 27 06:23:16 2011 UTC (7 years, 3 months ago) by caltinay
Original Path: trunk

Updated savanna options file. We're now using silo 4.8, netcdf 4.1.1 and boost 1.42 on savanna.

Revision 3642 - Directory Listing
Modified Thu Oct 27 03:41:51 2011 UTC (7 years, 3 months ago) by caltinay
Original Path: trunk

Assorted spelling/comment fixes in paso.

Revision 3641 - Directory Listing
Modified Thu Oct 27 02:16:12 2011 UTC (7 years, 3 months ago) by gross
Original Path: trunk

more work on the assemblage

Revision 3639 - Directory Listing
Modified Tue Oct 25 02:13:26 2011 UTC (7 years, 4 months ago) by caltinay
Original Path: trunk

Assorted spelling fixes in finley C.

Revision 3637 - Directory Listing
Modified Fri Oct 21 04:29:33 2011 UTC (7 years, 4 months ago) by caltinay
Original Path: trunk

Fixed memory leaks in loadMesh() for dudley and finley.

Revision 3635 - Directory Listing
Modified Fri Oct 21 00:26:01 2011 UTC (7 years, 4 months ago) by caltinay
Original Path: trunk

Fixed minor issues.

Revision 3630 - Directory Listing
Modified Wed Oct 19 03:04:53 2011 UTC (7 years, 4 months ago) by gross
Original Path: trunk

minor fix to dary flux

Revision 3629 - Directory Listing
Modified Wed Oct 19 03:04:27 2011 UTC (7 years, 4 months ago) by gross
Original Path: trunk

darcy example added

Revision 3628 - Directory Listing
Modified Wed Oct 19 02:09:36 2011 UTC (7 years, 4 months ago) by caltinay
Original Path: trunk

Prepend our libraries instead of appending. This should fix HYPRE link
issue on epic.

Revision 3627 - Directory Listing
Modified Fri Oct 14 13:54:49 2011 UTC (7 years, 4 months ago) by caltinay
Original Path: trunk

Reverted some changes that slipped in and caused the Silo writer to not behave.

Revision 3626 - Directory Listing
Modified Fri Oct 14 02:34:55 2011 UTC (7 years, 4 months ago) by gross
Original Path: trunk

Silo and cppunit added for epic (there is still a problem with hypre)

Revision 3625 - Directory Listing
Modified Thu Oct 13 01:54:27 2011 UTC (7 years, 4 months ago) by gross
Original Path: trunk

missing argument in gmsh reader documentation added

Revision 3624 - Directory Listing
Modified Wed Oct 12 07:58:25 2011 UTC (7 years, 4 months ago) by gross
Original Path: trunk

changes for epic.ivec.org

Revision 3623 - Directory Listing
Modified Tue Oct 11 03:59:40 2011 UTC (7 years, 4 months ago) by caltinay
Original Path: trunk

Added option to enable/disable saving of mesh data in weipa.
Now defaults to false since it's mainly for debugging.
Fixes #640.

Revision 3622 - Directory Listing
Modified Thu Oct 6 08:06:41 2011 UTC (7 years, 4 months ago) by trankine
Original Path: trunk

Epic.ivec.org scons build template

Revision 3619 - Directory Listing
Modified Wed Oct 5 03:53:34 2011 UTC (7 years, 4 months ago) by gross
Original Path: trunk

some rescaling of permeability in the darcy solver added

Revision 3618 - Directory Listing
Modified Fri Sep 30 04:07:09 2011 UTC (7 years, 4 months ago) by jfenwick
Original Path: trunk

Allowed 'no' as an mpi type.
Allowed SVN_VERSION to be specified from the command line.
TO BE USED ONLY FOR RELEASE PURPOSES where you do not have a .svn checkout

Revision 3616 - Directory Listing
Modified Fri Sep 30 00:56:37 2011 UTC (7 years, 4 months ago) by jfenwick
Original Path: trunk

Center a table that I noticed and use upquote package to stop LaTeX from
mucking about with ' in python code.

Fixes #632

Revision 3607 - Directory Listing
Modified Mon Sep 19 22:08:24 2011 UTC (7 years, 5 months ago) by caltinay
Original Path: trunk

Fixed double/float warning.

Revision 3606 - Directory Listing
Modified Mon Sep 19 16:26:51 2011 UTC (7 years, 5 months ago) by trankine
Original Path: trunk

Trial nosetests runner tests for better integration

Revision 3605 - Directory Listing
Modified Mon Sep 19 07:47:23 2011 UTC (7 years, 5 months ago) by trankine
Original Path: trunk

cppunit actually does do the install step in the msvc project files and does put the build products where scons can find them.

Revision 3604 - Directory Listing
Modified Mon Sep 19 04:47:53 2011 UTC (7 years, 5 months ago) by caltinay
Original Path: trunk

Changed detection of pdflatex since some versions of scons require .ltx or
.latex file extensions when pdflatex is not available.
Also added cleanup of utest.sh and buildvars file.

Revision 3603 - Directory Listing
Modified Mon Sep 19 03:42:53 2011 UTC (7 years, 5 months ago) by caltinay
Original Path: trunk

Fixed some unused var errors in non-mpi build.

Revision 3602 - Directory Listing
Modified Mon Sep 19 02:38:11 2011 UTC (7 years, 5 months ago) by caltinay
Original Path: trunk

Fix scons checks on windows

Revision 3601 - Directory Listing
Modified Mon Sep 19 01:21:33 2011 UTC (7 years, 5 months ago) by trankine
Original Path: trunk

Updating cgisrv3 options for external cppunit - because I cant see brackets.

Revision 3600 - Directory Listing
Modified Mon Sep 19 00:58:15 2011 UTC (7 years, 5 months ago) by trankine
Original Path: trunk

Updating cgisrv3 options for external cppunit

Revision 3599 - Directory Listing
Modified Fri Sep 16 01:34:46 2011 UTC (7 years, 5 months ago) by caltinay
Original Path: trunk

Updated install guide to mention external CppUnit dependency for unit tests.

Revision 3598 - Directory Listing
Modified Fri Sep 16 01:01:17 2011 UTC (7 years, 5 months ago) by caltinay
Original Path: trunk

New config option build_shared (which replaces share_paso & share_esysUtils).
Also enabled building escriptreader library on Windows which should now
work in both shared and static mode.

Revision 3597 - Directory Listing
Modified Thu Sep 15 06:03:17 2011 UTC (7 years, 5 months ago) by caltinay
Original Path: trunk

Switching to external cppunit:
-removed tools/CppUnitTest
-updated scons script and files
-updated tests to changed API
-updated readme

Bumped scons options file version to 201. Additions:
-cppunit*
-boomeramg*
-vsl_random

Revision 3596 - Directory Listing
Modified Thu Sep 15 05:58:15 2011 UTC (7 years, 5 months ago) by caltinay
Original Path: trunk

Deleted some obsolete options files.

Revision 3595 - Directory Listing
Modified Thu Sep 15 05:56:47 2011 UTC (7 years, 5 months ago) by caltinay
Original Path: trunk

Skip some more gmsh-dependend tests if gmsh is not available.

Revision 3594 - Directory Listing
Modified Thu Sep 15 00:45:04 2011 UTC (7 years, 5 months ago) by caltinay
Original Path: trunk

Added missing declspecs in paso. Thanks Terry.

Revision 3589 - Directory Listing
Modified Mon Sep 12 03:25:25 2011 UTC (7 years, 5 months ago) by gross
Original Path: trunk

This fixes the bug 616. Problem was that the Coupler used the pattern of original rather than unrolled pattern.

Revision 3586 - Directory Listing
Modified Fri Sep 9 04:02:29 2011 UTC (7 years, 5 months ago) by caltinay
Original Path: trunk

run_domainreaders now passes some parameters to the constructors so
kwargs is tested to be working. Addresses #578.

Revision 3585 - Directory Listing
Modified Wed Sep 7 06:16:08 2011 UTC (7 years, 5 months ago) by caltinay
Original Path: trunk

Fix for #582: Determine if gmsh was compiled with MPI support and use
MPI_Comm_spawn to invoke it if necessary.

Revision 3584 - Directory Listing
Modified Tue Sep 6 11:08:34 2011 UTC (7 years, 5 months ago) by jfenwick
Original Path: trunk

Removing Locator.setValue for now

Revision 3583 - Directory Listing
Modified Tue Sep 6 04:27:59 2011 UTC (7 years, 5 months ago) by caltinay
Original Path: trunk

Updated shake75 options file.

Revision 3582 - Directory Listing
Modified Tue Sep 6 02:02:17 2011 UTC (7 years, 5 months ago) by gross
Original Path: trunk

some clarification of the documentation on the Stokes solver.

Revision 3581 - Directory Listing
Modified Tue Sep 6 00:52:58 2011 UTC (7 years, 5 months ago) by gross
Original Path: trunk

Used python 2.7 syntax. Sorry!

Revision 3580 - Directory Listing
Modified Tue Sep 6 00:31:35 2011 UTC (7 years, 5 months ago) by gross
Original Path: trunk

error handeling for python compilation improved.

Revision 3579 - Directory Listing
Modified Mon Sep 5 23:25:01 2011 UTC (7 years, 5 months ago) by jfenwick
Original Path: trunk

Stopping unit test from failing until I can get it working

Revision 3578 - Directory Listing
Modified Mon Sep 5 23:18:45 2011 UTC (7 years, 5 months ago) by gross
Original Path: trunk

Missing dependence added (?) and typo in test files fixed.

Revision 3577 - Directory Listing
Modified Mon Sep 5 08:22:52 2011 UTC (7 years, 5 months ago) by gross
Original Path: trunk

getFLux fixed and tests added.

Revision 3576 - Directory Listing
Modified Mon Sep 5 06:33:20 2011 UTC (7 years, 5 months ago) by caltinay
Original Path: trunk

Fixed two more instances of macro-dependent unused vars.

Revision 3575 - Directory Listing
Modified Fri Sep 2 08:31:08 2011 UTC (7 years, 5 months ago) by jfenwick
Original Path: trunk

Fixing bug I introduced with the last commit

Revision 3574 - Directory Listing
Modified Fri Sep 2 07:19:31 2011 UTC (7 years, 5 months ago) by jfenwick
Original Path: trunk

Added setValue to locator.
Some unit tests added but they aren't being triggered for some reason

Revision 3573 - Directory Listing
Modified Fri Sep 2 05:51:02 2011 UTC (7 years, 5 months ago) by jfenwick
Original Path: trunk

Added more comprehensible doco about 3D interpolation.
Also fixed a bug but this may break code which previously used 3D interpolation.

This fixes mantis #581

Revision 3572 - Directory Listing
Modified Thu Sep 1 07:54:42 2011 UTC (7 years, 5 months ago) by jfenwick
Original Path: trunk

Comment out a non-existant function from the Finley interface and (hopefully)
fix mantis bug #623

Revision 3571 - Directory Listing
Modified Thu Sep 1 03:53:23 2011 UTC (7 years, 5 months ago) by gross
Original Path: trunk

LinearSolver option RILU has been removed from the documentation it is not supported yet.

Revision 3570 - Directory Listing
Modified Thu Sep 1 03:11:26 2011 UTC (7 years, 5 months ago) by jfenwick
Original Path: trunk

Fixed some bib entries, changed visit script in guide to use " instead of '.
Reworded a sentence.

Revision 3569 - Directory Listing
Modified Thu Sep 1 02:42:36 2011 UTC (7 years, 5 months ago) by gross
Original Path: trunk

Darcy flow solver and docu reviewed. Coupled solvers have been removed.

Revision 3568 - Directory Listing
Modified Tue Aug 30 08:23:24 2011 UTC (7 years, 5 months ago) by gross
Original Path: trunk

darcy flux documentation updated.

Revision 3567 - Directory Listing
Modified Tue Aug 30 07:55:02 2011 UTC (7 years, 5 months ago) by gross
Original Path: trunk

FIXME and TODO fixed.

Revision 3566 - Directory Listing
Modified Tue Aug 30 07:37:55 2011 UTC (7 years, 5 months ago) by gross
Original Path: trunk

small fix to units

Revision 3565 - Directory Listing
Modified Mon Aug 29 10:28:57 2011 UTC (7 years, 5 months ago) by jfenwick
Original Path: trunk

surely it will accept this one

Revision 3564 - Directory Listing
Modified Mon Aug 29 09:09:30 2011 UTC (7 years, 5 months ago) by jfenwick
Original Path: trunk

In case windows is case sensitive

Revision 3563 - Directory Listing
Modified Mon Aug 29 04:26:46 2011 UTC (7 years, 5 months ago) by jfenwick
Original Path: trunk

Another try to fix the windows issue

Revision 3562 - Directory Listing
Modified Mon Aug 29 03:31:13 2011 UTC (7 years, 5 months ago) by jfenwick
Original Path: trunk

Removed DLL export from non-exported methods

Revision 3561 - Directory Listing
Modified Mon Aug 29 02:51:05 2011 UTC (7 years, 5 months ago) by jfenwick
Original Path: trunk

Attempt to fix windows problem

Revision 3560 - Directory Listing
Modified Mon Aug 29 01:10:42 2011 UTC (7 years, 5 months ago) by gross
Original Path: trunk

lf missing in buildvars print

Revision 3559 - Directory Listing
Modified Fri Aug 26 07:47:27 2011 UTC (7 years, 5 months ago) by jfenwick
Original Path: trunk

Silence some warnings unused var warnings under gcc.

Revision 3558 - Directory Listing
Modified Fri Aug 26 06:09:02 2011 UTC (7 years, 5 months ago) by jfenwick
Original Path: trunk

Merged changes from dirac.
Now the only way to add diracPoints is to use the constructor

Revision 3552 - Directory Listing
Modified Mon Aug 22 00:05:17 2011 UTC (7 years, 6 months ago) by jfenwick
Original Path: trunk

Fixed icc problem

Revision 3551 - Directory Listing
Modified Fri Aug 19 03:53:41 2011 UTC (7 years, 6 months ago) by jfenwick
Original Path: trunk

Changing unit test calls to use non deprecated forms (python2.7)
fixes bug #568

Revision 3550 - Directory Listing
Modified Fri Aug 19 01:51:35 2011 UTC (7 years, 6 months ago) by jfenwick
Original Path: trunk

Switching from rand() to boost::random for non-VSL randoms

Revision 3549 - Directory Listing
Modified Tue Aug 9 06:40:06 2011 UTC (7 years, 6 months ago) by jfenwick
Original Path: trunk

Fix for issue #617
A couple of extra tests to make sure it doesn't happen again

Revision 3548 - Directory Listing
Modified Tue Aug 9 04:00:27 2011 UTC (7 years, 6 months ago) by jfenwick
Original Path: trunk

Fixing badger options

Revision 3547 - Directory Listing
Modified Tue Aug 2 04:24:09 2011 UTC (7 years, 6 months ago) by lgao
Original Path: trunk

Set "lapack" to "mkl" before the mantis bug 0000616 is solved.

Revision 3546 - Directory Listing
Modified Thu Jul 28 01:32:20 2011 UTC (7 years, 6 months ago) by jfenwick
Original Path: trunk

Replaced 'and' with && since windows doesn't seem to understand it

Revision 3545 - Directory Listing
Modified Wed Jul 27 06:29:09 2011 UTC (7 years, 6 months ago) by lgao
Original Path: trunk

Turn off VSL for random data before the MKL library link line problem has been solved.

Revision 3544 - Directory Listing
Modified Wed Jul 27 06:19:10 2011 UTC (7 years, 6 months ago) by jfenwick
Original Path: trunk

Temporary fix to get windows to compile

Revision 3543 - Directory Listing
Modified Fri Jul 22 06:58:03 2011 UTC (7 years, 7 months ago) by gross
Original Path: trunk

and the generator script

Revision 3542 - Directory Listing
Modified Fri Jul 22 06:57:41 2011 UTC (7 years, 7 months ago) by gross
Original Path: trunk

first attempts toward a multi grid solver

Revision 3541 - Directory Listing
Modified Fri Jul 22 03:21:06 2011 UTC (7 years, 7 months ago) by trankine
Original Path: trunk

migration to system maintained dependancies (not per build). will allow multi builders

Revision 3538 - Directory Listing
Modified Mon Jul 4 00:13:02 2011 UTC (7 years, 7 months ago) by jfenwick
Original Path: trunk

Added paper with current dev team to the references section.

Revision 3529 - Directory Listing
Modified Thu May 26 00:36:10 2011 UTC (7 years, 9 months ago) by caltinay
Original Path: trunk

Re-enable VisIt and Silo on savanna and use gcc-4.6 on shake75.

Revision 3527 - Directory Listing
Modified Tue May 24 06:59:20 2011 UTC (7 years, 9 months ago) by gross
Original Path: trunk

modifications to the coal seam gas

Revision 3526 - Directory Listing
Modified Tue May 24 05:01:46 2011 UTC (7 years, 9 months ago) by gross
Original Path: trunk

coal code uses nodal wells now

Revision 3525 - Directory Listing
Modified Tue May 24 04:04:58 2011 UTC (7 years, 9 months ago) by gross
Original Path: trunk

and more typos fixed.

Revision 3523 - Directory Listing
Modified Tue May 24 02:03:37 2011 UTC (7 years, 9 months ago) by caltinay
Original Path: trunk

Fixed declaration order (register const) for gcc-4.6

Revision 3522 - Directory Listing
Modified Tue May 24 00:57:58 2011 UTC (7 years, 9 months ago) by gross
Original Path: trunk

(almost) full support for Point elements

Revision 3520 - Directory Listing
Modified Mon May 23 06:24:30 2011 UTC (7 years, 9 months ago) by gross
Original Path: trunk

some fixes for to point interpolation

Revision 3519 - Directory Listing
Modified Mon May 23 05:55:47 2011 UTC (7 years, 9 months ago) by gross
Original Path: trunk

compiler fixes

Revision 3515 - Directory Listing
Modified Thu May 19 08:20:57 2011 UTC (7 years, 9 months ago) by gross
Original Path: trunk

some first work for DiracFunctions

Revision 3514 - Directory Listing
Modified Thu May 19 04:48:34 2011 UTC (7 years, 9 months ago) by caltinay
Original Path: trunk

Fixed __truediv__ and added __rtruediv__ for new python division operator.

Revision 3513 - Directory Listing
Modified Thu May 19 04:45:19 2011 UTC (7 years, 9 months ago) by lgao
Original Path: trunk

When "werror" is set to True, scons build will complains about compilation failure of some boost "multi-array" test case. This causes recently unit-tests failures. So I set "werror" back to False before someone who has the knowledge fixes the problem.

Revision 3511 - Directory Listing
Modified Tue May 17 23:56:13 2011 UTC (7 years, 9 months ago) by lgao
Original Path: trunk

Fixed the scons build problem in case MPI is not in use (this 
is the reason why unit tests failed to execute properly for the
past several days).

Revision 3510 - Directory Listing
Modified Fri May 13 06:09:49 2011 UTC (7 years, 9 months ago) by gross
Original Path: trunk

some fixes for the compilation without BOOMERAMG

Revision 3508 - Directory Listing
Modified Fri May 13 04:15:29 2011 UTC (7 years, 9 months ago) by lgao
Original Path: trunk

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

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

Revision 3506 - Directory Listing
Modified Wed May 11 01:59:45 2011 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

Use VSL if MKLRANDOM is defined.
Use different seeds for different ranks/threads.
Use different seeds for successive calls with no seed given.

Revision 3505 - Directory Listing
Modified Fri Apr 29 07:09:45 2011 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

arithmetic operations now return NotImplemented if they don't know what to do.
Fixes mantis issue #54

Revision 3504 - Directory Listing
Modified Thu Apr 28 12:55:05 2011 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

Move arithmetic ops into explicitly named methods

Revision 3502 - Directory Listing
Modified Thu Apr 28 05:06:24 2011 UTC (7 years, 9 months ago) by gross
Original Path: trunk

Darcy flow solver is now supporting 4 solvers

Revision 3500 - Directory Listing
Modified Mon Apr 11 03:09:06 2011 UTC (7 years, 10 months ago) by gross
Original Path: trunk

GMRES solver for new DarcyFlux solver added

Revision 3498 - Directory Listing
Modified Thu Apr 7 01:12:59 2011 UTC (7 years, 10 months ago) by lgao
Original Path: trunk

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

Revision 3494 - Directory Listing
Modified Tue Apr 5 04:12:08 2011 UTC (7 years, 10 months ago) by gross
Original Path: trunk

more coal seam gas

Revision 3490 - Directory Listing
Modified Wed Mar 30 02:24:33 2011 UTC (7 years, 10 months ago) by caltinay
Original Path: trunk

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

Revision 3489 - Directory Listing
Modified Wed Mar 30 00:46:04 2011 UTC (7 years, 10 months ago) by caltinay
Original Path: trunk

Fixed a few warnings emitted by gcc-4.6.

Revision 3487 - Directory Listing
Modified Mon Mar 28 03:44:22 2011 UTC (7 years, 10 months ago) by gross
Original Path: trunk

some compile fixes

Revision 3486 - Directory Listing
Modified Sun Mar 27 22:27:45 2011 UTC (7 years, 10 months ago) by gross
Original Path: trunk

bug in eigenvector calculation fixed (see mantis=594)

Revision 3485 - Directory Listing
Modified Thu Mar 24 22:44:40 2011 UTC (7 years, 11 months ago) by gross
Original Path: trunk

some compile fixes

Revision 3484 - Directory Listing
Modified Thu Mar 24 05:42:07 2011 UTC (7 years, 11 months ago) by gross
Original Path: trunk

some work on coal gas

Revision 3483 - Directory Listing
Modified Wed Mar 23 04:18:35 2011 UTC (7 years, 11 months ago) by gross
Original Path: trunk

Ops: AMG MPI chould not be called yet.

Revision 3482 - Directory Listing
Modified Wed Mar 23 04:06:52 2011 UTC (7 years, 11 months ago) by gross
Original Path: trunk

some work on AMG MPI

Revision 3478 - Directory Listing
Modified Wed Mar 23 04:02:39 2011 UTC (7 years, 11 months ago) by gross
Original Path: trunk

coal gas stuff

Revision 3475 - Directory Listing
Modified Thu Mar 17 00:28:08 2011 UTC (7 years, 11 months ago) by caltinay
Original Path: trunk

Removed an obsolete file.

Revision 3470 - Directory Listing
Modified Mon Mar 14 03:50:49 2011 UTC (7 years, 11 months ago) by caltinay
Original Path: trunk

Fix for mantis issue 591 (added __truediv__ methods to Data class).

Revision 3469 - Directory Listing
Modified Tue Feb 22 06:39:16 2011 UTC (8 years ago) by jfenwick
Original Path: trunk

Fix docstring in dudley

Revision 3468 - Directory Listing
Modified Tue Feb 22 06:38:57 2011 UTC (8 years ago) by jfenwick
Original Path: trunk

Made constructors more efficient.
Only has a very minor affect on performance

Revision 3467 - Directory Listing
Modified Tue Feb 8 09:31:46 2011 UTC (8 years ago) by caltinay
Original Path: trunk

Fixed unit test after last change.

Revision 3466 - Directory Listing
Modified Tue Feb 8 05:16:21 2011 UTC (8 years ago) by caltinay
Original Path: trunk

Added TEMP and friends to the list of env vars exported by scons.
Modified pycad's gmsh command line since the mesh filename may also contain
spaces.

Revision 3465 - Directory Listing
Modified Tue Feb 8 00:11:15 2011 UTC (8 years ago) by caltinay
Original Path: trunk

Use the subprocess module within pycad's Triangle.

Revision 3464 - Directory Listing
Modified Mon Feb 7 05:17:11 2011 UTC (8 years ago) by caltinay
Original Path: trunk

Use the subprocess module with argument list to run gmsh from pycad to avoid
having to deal with spaces in path names.

Revision 3463 - Directory Listing
Modified Mon Feb 7 02:09:57 2011 UTC (8 years ago) by caltinay
Original Path: trunk

Check for gmsh in main SConstruct file and skip tests that depend on it when
the executable is not found.

Revision 3461 - Directory Listing
Modified Sun Feb 6 23:33:37 2011 UTC (8 years ago) by caltinay
Original Path: trunk

Re-enabled silo on savanna as well.

Revision 3460 - Directory Listing
Modified Sun Feb 6 23:24:22 2011 UTC (8 years ago) by jfenwick
Original Path: trunk

Re-enabling MPI on savanna

Revision 3459 - Directory Listing
Modified Wed Feb 2 01:54:45 2011 UTC (8 years ago) by caltinay
Original Path: trunk

Patch from Terry to fix compilation on Windows with MKL enabled.

Revision 3457 - Directory Listing
Modified Thu Jan 27 01:38:17 2011 UTC (8 years ago) by caltinay
Original Path: trunk

Added missing cookbook figures from Anthony.

Revision 3454 - Directory Listing
Modified Tue Jan 25 04:00:29 2011 UTC (8 years ago) by caltinay
Original Path: trunk

Fixed some minor doxygen issues.

Revision 3453 - Directory Listing
Modified Tue Jan 25 03:59:30 2011 UTC (8 years ago) by caltinay
Original Path: trunk

Disabled C99 extensions on guineapig again.

Revision 3452 - Directory Listing
Modified Tue Jan 25 01:53:57 2011 UTC (8 years ago) by caltinay
Original Path: trunk

Fixed building cookbook, including toc (scons scans for keywords in the tex
files but not in .cls as it seems).
Also fixed a few epydoc warnings and typos.

Revision 3451 - Directory Listing
Modified Sun Jan 23 23:11:01 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

compilation fixes

Revision 3450 - Directory Listing
Modified Fri Jan 21 06:39:56 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

more compilation fixing

Revision 3449 - Directory Listing
Modified Fri Jan 21 05:48:15 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

compile problem in AMG fixed.

Revision 3448 - Directory Listing
Modified Fri Jan 21 04:38:54 2011 UTC (8 years, 1 month ago) by ahallam
Original Path: trunk

Quick final changes to cookbook to accomodate example10c problem. 'So long and thanks for all the fish.'

Revision 3447 - Directory Listing
Modified Fri Jan 21 04:33:42 2011 UTC (8 years, 1 month ago) by ahallam
Original Path: trunk

example10c removed from testing as it is not in the cookbook.

Revision 3446 - Directory Listing
Modified Thu Jan 20 06:47:07 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

and more work toward AMG MPI

Revision 3445 - Directory Listing
Modified Wed Jan 19 06:02:15 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

more work towards MPI AMG

Revision 3444 - Directory Listing
Modified Tue Jan 18 23:17:27 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

run_domainreaders.py can only be run for MPI ranks = 1 as gmsh does not support MPI yet

Revision 3443 - Directory Listing
Modified Tue Jan 18 05:38:48 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

test for AMG fixed. New test set guarantees SPD stiffness matrix. Previously this was not guaranteed and could lead to singular coarse level matrices (which cause MKL based runs to fail)

Revision 3441 - Directory Listing
Modified Fri Jan 14 01:09:09 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

clarifiaction of function names as a first step towards a MPI version of AMG

Revision 3440 - Directory Listing
Modified Fri Jan 14 00:04:53 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

a second AMG interpolation implemented

Revision 3439 - Directory Listing
Modified Fri Jan 14 00:04:01 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

some modifications to fix the cook examples runs for testing

Revision 3438 - Directory Listing
Modified Thu Jan 13 23:24:50 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

mesh size reduced

Revision 3437 - Directory Listing
Modified Mon Jan 10 05:05:15 2011 UTC (8 years, 1 month ago) by plaub
Original Path: trunk

Fixed test for new default arguments

Revision 3436 - Directory Listing
Modified Mon Jan 10 02:06:07 2011 UTC (8 years, 1 month ago) by plaub
Original Path: trunk

Added/modified AMG tests:

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

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

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

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

Revision 3435 - Directory Listing
Modified Fri Jan 7 03:40:39 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

initial value changed

Revision 3434 - Directory Listing
Modified Fri Jan 7 03:35:58 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

initial value changed

Revision 3433 - Directory Listing
Modified Fri Jan 7 02:39:05 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

initial value changed

Revision 3432 - Directory Listing
Modified Fri Jan 7 01:32:07 2011 UTC (8 years, 1 month ago) by jfenwick
Original Path: trunk

Made import statements a bit more specific to clean up the epydoc

Revision 3431 - Directory Listing
Modified Fri Jan 7 01:19:21 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

redundant setMinCoarseMatrixSparsity removed.

Revision 3430 - Directory Listing
Modified Thu Jan 6 09:09:19 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

import order is critical

Revision 3429 - Directory Listing
Modified Thu Jan 6 07:40:01 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

SAMESIGN macro added

Revision 3428 - Directory Listing
Modified Thu Jan 6 01:12:36 2011 UTC (8 years, 1 month ago) by jfenwick
Original Path: trunk

Fixed errors (and space/tabs) in geometry.py
Added unit tests

Revision 3427 - Directory Listing
Modified Thu Jan 6 00:11:45 2011 UTC (8 years, 1 month ago) by ahallam
Original Path: trunk

Missing script.

Revision 3426 - Directory Listing
Modified Wed Jan 5 02:51:35 2011 UTC (8 years, 1 month ago) by ahallam
Original Path: trunk

Added new example tests.

Revision 3425 - Directory Listing
Modified Wed Jan 5 02:50:38 2011 UTC (8 years, 1 month ago) by ahallam
Original Path: trunk

Added new example tests.

Revision 3424 - Directory Listing
Modified Wed Jan 5 00:24:46 2011 UTC (8 years, 1 month ago) by gross
Original Path: trunk

memory leak in UMFPACK interface fixed

Revision 3423 - Directory Listing
Modified Thu Dec 16 04:24:13 2010 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Fix a typo in geometry.py

Revision 3422 - Directory Listing
Modified Mon Dec 13 23:27:47 2010 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

Updated shake75 options file to use visit 2.2

Revision 3421 - Directory Listing
Modified Mon Dec 13 23:15:01 2010 UTC (8 years, 2 months ago) by artak
Original Path: trunk

semi-colon is missing

Revision 3417 - Directory Listing
Modified Sun Dec 12 23:40:27 2010 UTC (8 years, 2 months ago) by artak
Original Path: trunk

Treat warnings as errors is disabled.

Revision 3412 - Directory Listing
Modified Fri Dec 10 02:03:49 2010 UTC (8 years, 2 months ago) by gross
Original Path: trunk

some fixes for MKL lapack

Revision 3410 - Directory Listing
Modified Thu Dec 9 07:02:52 2010 UTC (8 years, 2 months ago) by ahallam
Original Path: trunk

Minor changes to cookbook, gravity example.

Revision 3409 - Directory Listing
Modified Thu Dec 9 07:01:23 2010 UTC (8 years, 2 months ago) by ahallam
Original Path: trunk

minor changes to examples before holiday.

Revision 3406 - Directory Listing
Modified Wed Dec 8 01:09:37 2010 UTC (8 years, 2 months ago) by ahallam
Original Path: trunk

Updates to cookbook documentation for release.

Revision 3405 - Directory Listing
Modified Wed Dec 8 01:09:06 2010 UTC (8 years, 2 months ago) by ahallam
Original Path: trunk

Changes to example09 for memory footprint. One change too help wording in layer_cake function. example09b removed from testing. Not for impending release.

Revision 3403 - Directory Listing
Modified Tue Dec 7 08:13:51 2010 UTC (8 years, 2 months ago) by gross
Original Path: trunk

some small fixes

Revision 3402 - Directory Listing
Modified Tue Dec 7 07:36:12 2010 UTC (8 years, 2 months ago) by gross
Original Path: trunk

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

additional diagnostics for AMG

Revision 3400 - Directory Listing
Modified Mon Dec 6 02:23:07 2010 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

Moved vtkCellType.h to weipa where it belongs now.

Revision 3399 - Directory Listing
Modified Mon Dec 6 02:02:16 2010 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

Updated VTK files to reflect changes to the writer.

Revision 3398 - Directory Listing
Modified Mon Dec 6 00:02:33 2010 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

Fixed the quad mask in a very specific case and changed saveVTK to write a
specific value for unused nodes instead of the first one which breaks unit
tests depending on the number of ranks used.
Still need to rebaseline some VTK files so the tests pass.

Revision 3397 - Directory Listing
Modified Sun Dec 5 22:46:25 2010 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

Fixed an issue in saveVTK/Silo.

Revision 3396 - Directory Listing
Modified Fri Dec 3 08:24:16 2010 UTC (8 years, 2 months ago) by gross
Original Path: trunk

wrong pointer handed

Revision 3395 - Directory Listing
Modified Fri Dec 3 06:30:35 2010 UTC (8 years, 2 months ago) by gross
Original Path: trunk

small correction

Revision 3394 - Directory Listing
Modified Fri Dec 3 06:07:08 2010 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Nasty hack to dodge a linking issue for serial builds on savanna

Revision 3393 - Directory Listing
Modified Fri Dec 3 04:14:56 2010 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

shake24 (darwin) needs -L/usr/lib to pull correct gcc library.
The python library path was also not entirely correct - fixed.

Revision 3392 - Directory Listing
Modified Thu Dec 2 03:26:29 2010 UTC (8 years, 2 months ago) by ahallam
Original Path: trunk

Updates to cookbook. Includes new section on variable meshing. To be reviewed.

Revision 3391 - Directory Listing
Modified Thu Dec 2 02:25:53 2010 UTC (8 years, 2 months ago) by gross
Original Path: trunk

seg fault fixed.

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

RandomData added

Revision 3389 - Directory Listing
Modified Wed Dec 1 23:03:35 2010 UTC (8 years, 2 months ago) by ahallam
Original Path: trunk

Some changes to the cookbook examples. Starting Inversion experimentation.

Revision 3388 - Directory Listing
Modified Mon Nov 29 06:07:07 2010 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

Added quotes around some variables to fix running scripts located in a
directory whose name contains spaces.

Revision 3387 - Directory Listing
Modified Thu Nov 25 07:09:23 2010 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

Fixed some annoying typos.

Revision 3386 - Directory Listing
Modified Thu Nov 25 05:05:50 2010 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

scons choked on the newlines within the parameter list. Fixed.

Revision 3385 - Directory Listing
Modified Thu Nov 25 04:41:33 2010 UTC (8 years, 2 months ago) by ahallam
Original Path: trunk

Updates to cookbook, something is wrong with the sconstruct though

Revision 3384 - Directory Listing
Modified Thu Nov 25 03:28:01 2010 UTC (8 years, 2 months ago) by ahallam
Original Path: trunk

Cookbook lumping updates.

Revision 3383 - Directory Listing
Modified Thu Nov 25 02:17:51 2010 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

Fixed some typos and added missing symlinks.

Revision 3382 - Directory Listing
Modified Thu Nov 25 00:43:18 2010 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

I've added better credits for dev team.
There is a new page just before the contents page with current dev team 
and a more detailed list in the user guide appendix.

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

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

Revision 3381 - Directory Listing
Modified Wed Nov 24 23:37:55 2010 UTC (8 years, 2 months ago) by ahallam
Original Path: trunk

Proofing of lumping.tex

Revision 3380 - Directory Listing
Modified Wed Nov 24 05:03:25 2010 UTC (8 years, 3 months ago) by gross
Original Path: trunk

update to change list

Revision 3379 - Directory Listing
Modified Wed Nov 24 04:48:49 2010 UTC (8 years, 3 months ago) by gross
Original Path: trunk

some clarification on lumping

Revision 3378 - Directory Listing
Modified Tue Nov 23 05:09:25 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Pass dictionary of data objects to EscriptDataset as kwargs in DataManager.

Revision 3377 - Directory Listing
Modified Tue Nov 23 02:01:20 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Removed empty esys, include and lib directories since the install prefix is
variable now. Don't shoot me for this if this hurts.

Revision 3376 - Directory Listing
Modified Tue Nov 23 01:56:20 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Invoke run-escript instead of escript in runTest.

Revision 3375 - Directory Listing
Modified Tue Nov 23 00:37:23 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Fix to unit tests

Revision 3374 - Directory Listing
Modified Tue Nov 23 00:30:20 2010 UTC (8 years, 3 months ago) by ahallam
Original Path: trunk

Fixes to example scripts.

Revision 3373 - Directory Listing
Modified Tue Nov 23 00:29:07 2010 UTC (8 years, 3 months ago) by ahallam
Original Path: trunk

New figures.

Revision 3372 - Directory Listing
Modified Mon Nov 22 23:10:03 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Added missing import to fix unit test

Revision 3371 - Directory Listing
Modified Mon Nov 22 06:13:47 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Sort data objects by name before passing them to the EscriptDataset object.
This addresses #537.

Revision 3370 - Directory Listing
Modified Sun Nov 21 23:22:25 2010 UTC (8 years, 3 months ago) by ahallam
Original Path: trunk

Rearranged figures for release.

Revision 3369 - Directory Listing
Modified Fri Nov 19 06:26:11 2010 UTC (8 years, 3 months ago) by gross
Original Path: trunk

matrix balance introduced in paso

Revision 3368 - Directory Listing
Modified Fri Nov 19 05:59:46 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

3d interpolateTable support.
New more generic interface for table interpolation.
tests and doco updated

Revision 3367 - Directory Listing
Modified Fri Nov 19 02:07:25 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

added quick intro to visualization with VisIt and fixed a file reference.

Revision 3366 - Directory Listing
Modified Thu Nov 18 23:41:42 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

esys.weipa Python interface documentation.

Revision 3365 - Directory Listing
Modified Thu Nov 18 10:49:40 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Fixed compilation without VisIt.

Revision 3364 - Directory Listing
Modified Thu Nov 18 05:51:44 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Expose visitInitialize and visitPublishData through the python interface.

Revision 3363 - Directory Listing
Modified Thu Nov 18 05:49:45 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Catch some corner cases in weipa's VisIt controller to make it more foolproof
and allow reinitialization.

Revision 3362 - Directory Listing
Modified Thu Nov 18 04:59:44 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Made the VisIt interface less verbose in non-debug mode and removed unused
includes.

Revision 3361 - Directory Listing
Modified Thu Nov 18 01:56:36 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Minor enhancement.

Revision 3360 - Directory Listing
Modified Thu Nov 18 00:20:21 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Fix some epydoc errors
Fixed issue 564
removed minimize.py since it hasn't worked in who knows how long

Revision 3359 - Directory Listing
Modified Wed Nov 17 23:32:36 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Fixing problem with ./utest.sh including full build path

Revision 3358 - Directory Listing
Modified Wed Nov 17 08:02:32 2010 UTC (8 years, 3 months ago) by gross
Original Path: trunk

a more flexiblae version of safeDiv

Revision 3357 - Directory Listing
Modified Wed Nov 17 06:21:37 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Fixed a crash when loading data from netCDF files.

Revision 3356 - Directory Listing
Modified Wed Nov 17 05:27:47 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Finley type Finley_Tri3Face_Contact is no longer untested within weipa.

Revision 3355 - Directory Listing
Modified Tue Nov 16 06:35:06 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

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

Revision 3354 - Directory Listing
Modified Tue Nov 16 04:48:09 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Fix problem with superclass init

Revision 3353 - Directory Listing
Modified Tue Nov 16 04:32:40 2010 UTC (8 years, 3 months ago) by gross
Original Path: trunk

some clarification on AMG in the documentation

Revision 3352 - Directory Listing
Modified Tue Nov 16 03:58:09 2010 UTC (8 years, 3 months ago) by gross
Original Path: trunk

exposure of AMG options

Revision 3351 - Directory Listing
Modified Tue Nov 16 02:39:40 2010 UTC (8 years, 3 months ago) by gross
Original Path: trunk

modified approach for AMG coarsning using a panel

Revision 3350 - Directory Listing
Modified Mon Nov 15 05:14:43 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Fixed MSVC90 file as per Gordon's report.

Revision 3349 - Directory Listing
Modified Mon Nov 15 05:09:56 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

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

Revision 3348 - Directory Listing
Modified Fri Nov 12 05:55:50 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Added weipa import statements to the relevant parts in user guide and cookbook.
Documented the deprecation of esys.escript.saveVTK in the changes chapter.

Revision 3347 - Directory Listing
Modified Fri Nov 12 04:58:27 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

-Do not compare mesh variables (like owner, color etc) in the saveVTK tests
since they depend on the number of ranks.
-Fixed a problem where ranks without data samples can't know whether a
reduced mesh is to be used or not.

Revision 3346 - Directory Listing
Modified Fri Nov 12 01:19:02 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Replaced usage of esys.escript.util.saveVTK by weipa.saveVTK in all python
scripts.

Revision 3345 - Directory Listing
Modified Thu Nov 11 23:51:45 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Moved dudley saveVTK tests to weipa and removed unneeded files.

Revision 3344 - Directory Listing
Modified Thu Nov 11 23:26:52 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

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

Revision 3343 - Directory Listing
Modified Wed Nov 10 02:01:29 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Rename users guide to user.pdf from guide.pdf to match the conventions 
we follow with the other files.

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

Revision 3342 - Directory Listing
Modified Tue Nov 9 03:41:58 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Fixed interpolation for Line3Macro elements in weipa.

Revision 3341 - Directory Listing
Modified Mon Nov 8 21:34:01 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Renamed MS options file.

Revision 3340 - Directory Listing
Modified Mon Nov 8 01:25:58 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Relax python version check.
Only checks X.Y not X.Y.Z
Fixes mantis #556

Revision 3339 - Directory Listing
Modified Fri Nov 5 05:30:31 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Fixed more package clashing problems.
Package install.pdf not install.tex
Changed title on most documents to esys-Escript except for the cookbook coz I like ti that way.

Revision 3338 - Directory Listing
Modified Fri Nov 5 03:50:51 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Remove old name for man page to prevent clash with erlang.
Changed default library to link for boost to boost_python-mt

Revision 3337 - Directory Listing
Modified Fri Nov 5 03:20:19 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Work around weird scons behaviour

Revision 3336 - Directory Listing
Modified Fri Nov 5 00:28:44 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Fixed bib entry

Revision 3335 - Directory Listing
Modified Wed Nov 3 05:02:57 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Fix the launcher so that it can give an environment even if buildvars is not present.
Environment now includes scons for standalone builds.
Fixes and cleanup for the install documentation.
scons TEMPLATES updated to define the optionfile version by default.

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

Revision 3334 - Directory Listing
Modified Wed Nov 3 00:46:56 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Added 3.2 to changes page

Revision 3333 - Directory Listing
Modified Mon Nov 1 06:08:05 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Updated lapack paths on guineapig.

Revision 3332 - Directory Listing
Modified Mon Nov 1 05:26:55 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Copy run-escript over for a prefix install.
Fixes mantis issue: 551

Revision 3331 - Directory Listing
Modified Mon Nov 1 05:21:18 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Appendix done. Fixed some overfull hboxes.

Revision 3330 - Directory Listing
Modified Mon Nov 1 04:29:09 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Finished user's guide chapters up to Appendix.

Revision 3329 - Directory Listing
Modified Fri Oct 29 05:55:55 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Faultsystems2d. not finished yet.

Revision 3328 - Directory Listing
Modified Fri Oct 29 02:21:42 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Fixed script filename

Revision 3327 - Directory Listing
Modified Fri Oct 29 02:08:37 2010 UTC (8 years, 3 months ago) by gross
Original Path: trunk

missing omp function added.

Revision 3326 - Directory Listing
Modified Fri Oct 29 00:45:32 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

6.2 Darcy Flux. Note that I commented the gravity flow subsection since it's
not written.

Revision 3325 - Directory Listing
Modified Fri Oct 29 00:30:51 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Section 6.1.

Revision 3324 - Directory Listing
Modified Thu Oct 28 23:43:09 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Finished pycad chapter 5, regenerated eps files

Revision 3323 - Directory Listing
Modified Thu Oct 28 09:53:46 2010 UTC (8 years, 3 months ago) by gross
Original Path: trunk

some openmp fizes.

Revision 3322 - Directory Listing
Modified Thu Oct 28 05:26:37 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Adapt install guide to new style.
Simplify package building scripts to autodetect necessary info and build control file automatically.

Revision 3321 - Directory Listing
Modified Thu Oct 28 05:02:41 2010 UTC (8 years, 3 months ago) by gross
Original Path: trunk

a problem with surface orientation fixed.

Revision 3320 - Directory Listing
Modified Thu Oct 28 03:29:51 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

This fixes the scons warning about not finding the Intel top dir on Savanna.

Revision 3319 - Directory Listing
Modified Thu Oct 28 03:14:27 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

export PATH to scons when creating environment so tools in non-default
locations such as latex on savanna are found.

Revision 3318 - Directory Listing
Modified Thu Oct 28 01:05:36 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

This should fix building paso without OpenMP.

Revision 3317 - Directory Listing
Modified Thu Oct 28 00:50:41 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

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

Revision 3316 - Directory Listing
Modified Wed Oct 27 01:43:21 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Finished Chapter 4, added missing bibliography entries for Trilinos and SuperLU

Revision 3315 - Directory Listing
Modified Wed Oct 27 01:20:27 2010 UTC (8 years, 3 months ago) by gross
Original Path: trunk

bug in sparse matrixmatrix fixed.

Revision 3314 - Directory Listing
Modified Tue Oct 26 22:22:20 2010 UTC (8 years, 3 months ago) by gross
Original Path: trunk

output removed/leaned up

Revision 3313 - Directory Listing
Modified Tue Oct 26 22:00:09 2010 UTC (8 years, 3 months ago) by gross
Original Path: trunk

some print statements removed

Revision 3312 - Directory Listing
Modified Tue Oct 26 07:54:58 2010 UTC (8 years, 3 months ago) by gross
Original Path: trunk

last step for a clean up version of the AMG

Revision 3311 - Directory Listing
Modified Tue Oct 26 05:43:25 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Added raggedbottom to last page before appendix.
Condensed the latex picture figures a bit

Revision 3310 - Directory Listing
Modified Tue Oct 26 03:58:17 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Fixed some pdf bookmarks and added the index package

Revision 3309 - Directory Listing
Modified Tue Oct 26 03:56:26 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Updated escript section with added DataManager reference.

Revision 3308 - Directory Listing
Modified Tue Oct 26 03:24:54 2010 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Moved listing and class up a level.
Removed hackscore from cookbook.
Made cookbook use the new stuff - removed old stuff

Revision 3307 - Directory Listing
Modified Tue Oct 26 01:19:19 2010 UTC (8 years, 3 months ago) by caltinay
Original Path: trunk

Put index back in and added link to index and biblio to the TOC.

Revision 3306 - Directory Listing
Modified Mon Oct 25 05:09:13 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Commented declaremodule and modulesynopsis.

Revision 3305 - Directory Listing
Modified Mon Oct 25 05:04:22 2010 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Fancy shuffling

Revision 3304 - Directory Listing
Modified Mon Oct 25 04:43:48 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Disabled building html user's guide - it doesn't read the class file properly
and the PDF now supports links.

Revision 3303 - Directory Listing
Modified Mon Oct 25 04:33:31 2010 UTC (8 years, 4 months ago) by gross
Original Path: trunk

more clean up work on the AMG

Revision 3302 - Directory Listing
Modified Mon Oct 25 01:50:07 2010 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Fixed appendix so hyperref generates links properly

Revision 3301 - Directory Listing
Modified Mon Oct 25 01:27:54 2010 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Modified layout of descriptions.
Fixed some overfull hboxes

Revision 3300 - Directory Listing
Modified Mon Oct 25 00:22:14 2010 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Some text fixes

Revision 3296 - Directory Listing
Modified Fri Oct 22 02:53:24 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

hackscore removal.

Revision 3293 - Directory Listing
Modified Thu Oct 21 23:18:32 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

user's guide builds again with new class file. The cleanup can commence...

Revision 3292 - Directory Listing
Modified Thu Oct 21 05:02:49 2010 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Adding the class file

Revision 3291 - Directory Listing
Modified Thu Oct 21 00:37:42 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Work on user's guide up to section 3.2 (exclusive), including some text on
new DataManager class.
Also reworked a couple of images.
This should be the last commit of the guide before changes to the latex class.

Revision 3289 - Directory Listing
Modified Wed Oct 20 07:07:11 2010 UTC (8 years, 4 months ago) by gross
Original Path: trunk

missing factor fixed.

Revision 3288 - Directory Listing
Modified Tue Oct 19 01:08:31 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Corrections to user guide sections 1.5 and 1.6.
Converted backgrounds of the very complex stokes flow eps files by raster
images leaving the vectors untouched so the change is barely visible but
makes loading the PDF page some orders of magnitude faster.

Revision 3287 - Directory Listing
Modified Tue Oct 19 00:42:22 2010 UTC (8 years, 4 months ago) by gross
Original Path: trunk

complaint from valgrind about an uninitialized value fixed (no impact on result)

Revision 3286 - Directory Listing
Modified Tue Oct 19 00:36:27 2010 UTC (8 years, 4 months ago) by gross
Original Path: trunk

small memory leak fixed.

Revision 3285 - Directory Listing
Modified Tue Oct 19 00:28:00 2010 UTC (8 years, 4 months ago) by gross
Original Path: trunk

bug in initialization step fixed.

Revision 3284 - Directory Listing
Modified Mon Oct 18 23:48:04 2010 UTC (8 years, 4 months ago) by gross
Original Path: trunk

old AMLI code collected in a single file. It does not compile and should be merged with RecILU

Revision 3283 - Directory Listing
Modified Mon Oct 18 22:39:28 2010 UTC (8 years, 4 months ago) by gross
Original Path: trunk

AMG reengineered, BUG is Smoother fixed.

Revision 3282 - Directory Listing
Modified Fri Oct 15 06:59:32 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Don't build guide_pdf when only guide_html was requested.

Revision 3281 - Directory Listing
Modified Fri Oct 15 06:52:34 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

latex2html doesn't like './' in graphicspath, so removed it.

Revision 3280 - Directory Listing
Modified Fri Oct 15 05:11:11 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Corrections to 1.4 of the user's guide.

Revision 3279 - Directory Listing
Modified Fri Oct 15 04:02:06 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Some corrections to 1.3 of user's guide and defined graphicspath globally.

Revision 3278 - Directory Listing
Modified Fri Oct 15 02:00:45 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Updated section 1.2 of user's guide.

Revision 3277 - Directory Listing
Modified Fri Oct 15 01:06:24 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

This should keep scons happy on systems without pdflatex issuing a warning
to the user. Also updated all other doc sconscript files to use a global
release_dir prefix so we can easily move the files somewhere else if req'd.

Revision 3276 - Directory Listing
Modified Thu Oct 14 21:38:05 2010 UTC (8 years, 4 months ago) by gross
Original Path: trunk

new damage solver

Revision 3275 - Directory Listing
Modified Thu Oct 14 06:15:27 2010 UTC (8 years, 4 months ago) by gross
Original Path: trunk

As it turns out the tangential operator implementation is not a good idea.
This a check in to save the last version of this approach before starting using a different method.

Revision 3274 - Directory Listing
Modified Thu Oct 14 06:14:30 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Some initial corrections to the user's guide.

Revision 3273 - Directory Listing
Modified Thu Oct 14 05:44:08 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Fixed guide_html dependencies so the pages are really rebuilt when source
files change.

Revision 3272 - Directory Listing
Modified Thu Oct 14 04:02:06 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Similar to last commit but for cookbook. Can't test since cookbook doesn't
build at the moment.

Revision 3271 - Directory Listing
Modified Thu Oct 14 02:16:00 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

-use existing scons pdflatex target for user's guide
-create temporary files in build directory rather than source directory
-make latex less verbose if verbosity option is off
This fixes #291 for user's guide.

Revision 3270 - Directory Listing
Modified Thu Oct 14 00:30:11 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

added -dEPSCrop option to ps2pdf so graphics are cropped as expected.

Revision 3269 - Directory Listing
Modified Wed Oct 13 03:21:50 2010 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

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

Revision 3268 - Directory Listing
Modified Wed Oct 13 02:16:23 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Do not ignore unknown options since the warnings are not easily visible,
bail out instead.

Revision 3267 - Directory Listing
Modified Wed Oct 13 02:12:06 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Renamed restarts.py to datamanager.py, added a method to explicitly set the
domain without adding data. Calling export() without domain/data will now
output a warning. Some additional cleanup.

Revision 3266 - Directory Listing
Modified Wed Oct 13 00:32:46 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Disable MPI on shake24 due to conflicting installations in default locations.

Revision 3265 - Directory Listing
Modified Tue Oct 12 04:42:03 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Updated relevant sections in install guide to reflect scons option changes.
Standalone section needs to be updated before the release.

Revision 3264 - Directory Listing
Modified Tue Oct 12 04:40:06 2010 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Minor changes to avoid optimiser bug in intel-10

Revision 3263 - Directory Listing
Modified Tue Oct 12 01:16:21 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Updated convection script to use escript DataManager.

Revision 3262 - Directory Listing
Modified Mon Oct 11 07:19:40 2010 UTC (8 years, 4 months ago) by gross
Original Path: trunk

header file include added

Revision 3261 - Directory Listing
Modified Mon Oct 11 04:25:42 2010 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Disable some unit tests for dudley until I can fix MPI failures

Revision 3260 - Directory Listing
Modified Mon Oct 11 03:41:35 2010 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Removing dead files

Revision 3259 - Directory Listing
Modified Mon Oct 11 01:48:14 2010 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Merging dudley and scons updates from branches

Revision 3250 - Directory Listing
Modified Thu Oct 7 01:49:18 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Fixed a declaration/definition mismatch.

Revision 3245 - Directory Listing
Modified Tue Oct 5 23:17:56 2010 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Removing out of date scripts

Revision 3233 - Directory Listing
Modified Mon Oct 4 00:54:26 2010 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Fixed build error

Revision 3232 - Directory Listing
Modified Fri Oct 1 02:08:38 2010 UTC (8 years, 4 months ago) by ahallam
Original Path: trunk

Updates to cookbook, new chapter DC Resis and IP. Using new packages hyperref, natbib

Revision 3222 - Directory Listing
Modified Wed Sep 29 03:55:44 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

This should make windoze happy.

Revision 3209 - Directory Listing
Modified Mon Sep 27 01:54:46 2010 UTC (8 years, 4 months ago) by caltinay
Original Path: trunk

Added missing libraries to escriptconvert.

Revision 3208 - Directory Listing
Modified Sun Sep 26 23:31:17 2010 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

List tests as not working with MPI

Revision 3201 - Directory Listing
Modified Thu Sep 23 06:54:18 2010 UTC (8 years, 5 months ago) by gross
Original Path: trunk

bug in meanValue fixed.

Revision 3195 - Directory Listing
Modified Wed Sep 22 00:28:04 2010 UTC (8 years, 5 months ago) by ahallam
Original Path: trunk

Shortened runtime of cookbook examples to aid testing.

Revision 3193 - Directory Listing
Modified Tue Sep 21 06:56:44 2010 UTC (8 years, 5 months ago) by gross
Original Path: trunk

more clean up in AMG

Revision 3192 - Directory Listing
Modified Fri Sep 17 04:02:57 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

- weipa's saveVTK will now save multiple files if the data objects to write are
  not on the same mesh.
- the save* methods now also add the appropriate file extension if not already
  supplied

Revision 3191 - Directory Listing
Modified Fri Sep 17 00:44:20 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Use consistent naming for domain, mesh and 'chunks'

Revision 3190 - Directory Listing
Modified Thu Sep 16 23:29:09 2010 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Disable some cookbook examples until we can get issues sorted out

Revision 3188 - Directory Listing
Modified Thu Sep 16 04:36:38 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Fixed deletion of old restart directories with a checkpoint freq>1.

Revision 3186 - Directory Listing
Modified Thu Sep 16 01:23:53 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Added checkpoint frequency setting to DataManager so that visualisation files
can be created independent of restart files. Also removed the overhead of
creating an EscriptDataset instance for the restart-only case.

Revision 3185 - Directory Listing
Modified Thu Sep 16 00:30:09 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Weipa now supports initialization from DataConstant instances.

Revision 3183 - Directory Listing
Modified Tue Sep 14 23:09:59 2010 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Adding timing information to unit tests.

Revision 3182 - Directory Listing
Modified Tue Sep 14 06:05:55 2010 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Temporarily removing example8c from unit testing.
It seems to lock the test - or it runs for rediculous timeframes.

Revision 3181 - Directory Listing
Modified Tue Sep 14 05:01:00 2010 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

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

Revision 3180 - Directory Listing
Modified Tue Sep 14 03:39:55 2010 UTC (8 years, 5 months ago) by gross
Original Path: trunk

some fixes for the case that no direc solver is available.

Revision 3178 - Directory Listing
Modified Tue Sep 14 00:31:59 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Corrected check for python version in launcher, added a function get_buildvar
for convenience.

Revision 3177 - Directory Listing
Modified Mon Sep 13 10:30:24 2010 UTC (8 years, 5 months ago) by gross
Original Path: trunk

running vresion

Revision 3176 - Directory Listing
Modified Sat Sep 11 01:09:54 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Maybe this will finally make the Mac happy.

Revision 3175 - Directory Listing
Modified Fri Sep 10 09:03:38 2010 UTC (8 years, 5 months ago) by gross
Original Path: trunk

intial checkin

Revision 3174 - Directory Listing
Modified Fri Sep 10 03:55:18 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Enabled debian's lapack on shake75.

Revision 3168 - Directory Listing
Modified Wed Sep 8 23:01:25 2010 UTC (8 years, 5 months ago) by ahallam
Original Path: trunk

Missing *.png

Revision 3167 - Directory Listing
Modified Wed Sep 8 03:24:29 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Only run pyvisi tests if VTK was enabled at configuration time.

Revision 3166 - Directory Listing
Modified Tue Sep 7 23:47:06 2010 UTC (8 years, 5 months ago) by ahallam
Original Path: trunk

Fix doc build error. I will add the figure when I come in tomorrow and turn Darra on.

Revision 3165 - Directory Listing
Modified Tue Sep 7 09:15:16 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Next attempt at fixing mac test failure.

Revision 3164 - Directory Listing
Modified Tue Sep 7 09:10:09 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Do not use VTK on guineapig - pyvisi is deprecated anyway.

Revision 3162 - Directory Listing
Modified Tue Sep 7 05:29:32 2010 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Changes to match packages in the debian repo.
Also got rid of lib/pyversion

Revision 3160 - Directory Listing
Modified Mon Sep 6 09:17:28 2010 UTC (8 years, 5 months ago) by gross
Original Path: trunk

bug fixed in RILU and test modified.

Revision 3159 - Directory Listing
Modified Mon Sep 6 06:59:31 2010 UTC (8 years, 5 months ago) by gross
Original Path: trunk

AMG is using now a simpler interface to the Smoothers.

Revision 3158 - Directory Listing
Modified Mon Sep 6 06:09:11 2010 UTC (8 years, 5 months ago) by gross
Original Path: trunk

GS and Jacobi are now used through the same interface.

Revision 3154 - Directory Listing
Modified Sun Sep 5 22:49:51 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Possible fix for mac linker error.

Revision 3153 - Directory Listing
Modified Sun Sep 5 01:31:49 2010 UTC (8 years, 5 months ago) by ahallam
Original Path: trunk

Updates to cookbook. Fixes to SWP and new Gravitational Potential

Revision 3151 - Directory Listing
Modified Fri Sep 3 05:46:12 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

More weipa tests including saveVTK.

Revision 3150 - Directory Listing
Modified Fri Sep 3 05:40:27 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Removed executable prop from non-executables.

Revision 3148 - Directory Listing
Modified Fri Sep 3 02:09:47 2010 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Another attempt to patch the X issue

Revision 3147 - Directory Listing
Modified Fri Sep 3 02:03:05 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Don't clear domain on error. Moved adding Metadata-tags to the C++ level.

Revision 3146 - Directory Listing
Modified Fri Sep 3 01:29:21 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Properly initialise data centering variable.

Revision 3143 - Directory Listing
Modified Fri Sep 3 00:31:55 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

-Moved finley specifics into weipa subclasses
-EscriptDataset is now the only weipa class exported in Windows
-Some weipa code cleanup

Revision 3142 - Directory Listing
Modified Thu Sep 2 23:58:47 2010 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Trying to fix X problem

Revision 3140 - Directory Listing
Modified Thu Sep 2 07:26:43 2010 UTC (8 years, 5 months ago) by gross
Original Path: trunk

a more robust version of MINRES (really?)

Revision 3139 - Directory Listing
Modified Thu Sep 2 06:37:43 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Fixed a typo.

Revision 3135 - Directory Listing
Modified Thu Sep 2 03:28:39 2010 UTC (8 years, 5 months ago) by ahallam
Original Path: trunk

Updates to cookbook scripts. Gravitation Examples.

Revision 3133 - Directory Listing
Modified Thu Sep 2 02:04:29 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Added methods to set mesh labels and units to DataManager.

Revision 3132 - Directory Listing
Modified Thu Sep 2 01:48:31 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Removed unused variable.

Revision 3131 - Directory Listing
Modified Thu Sep 2 01:40:47 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

DataManager now uses Python magic to figure out how to load the domain without
hardcoding anything finley-specific.

Revision 3129 - Directory Listing
Modified Wed Sep 1 07:58:23 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Fixed unit test.

Revision 3128 - Directory Listing
Modified Wed Sep 1 03:54:09 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

-Added mesh axis label/unit and variable unit support to weipa's Silo writer
-Created EscriptDataset python wrapper
-Some code cleanup and a ghost zone fix for the VisIt interface

Revision 3125 - Directory Listing
Modified Tue Aug 31 05:37:30 2010 UTC (8 years, 5 months ago) by gross
Original Path: trunk

more code cleaning

Revision 3120 - Directory Listing
Modified Mon Aug 30 10:48:00 2010 UTC (8 years, 5 months ago) by gross
Original Path: trunk

first iteration on Paso code clean up

Revision 3116 - Directory Listing
Modified Mon Aug 30 00:54:52 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Prepared weipa to use Silo's HDF5 driver & compression which performs better
than the default PDB. Code is disabled though because NetCDF 4 is currently
interfering (Unidata has been contacted). Added a note about this.

Revision 3113 - Directory Listing
Modified Fri Aug 27 04:04:56 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Fixed commit from rev.2867 which broke the ability to specify script parameters.

Revision 3112 - Directory Listing
Modified Thu Aug 26 07:10:36 2010 UTC (8 years, 5 months ago) by gross
Original Path: trunk

missing include added.

Revision 3111 - Directory Listing
Modified Thu Aug 26 06:49:42 2010 UTC (8 years, 5 months ago) by gross
Original Path: trunk

some diagnostics for time step backtracing added

Revision 3110 - Directory Listing
Modified Thu Aug 26 05:42:18 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Fixed a typo.

Revision 3109 - Directory Listing
Modified Thu Aug 26 04:33:18 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Added accessor for the simulation cycle and log which directory was used to
restart.

Revision 3108 - Directory Listing
Modified Thu Aug 26 03:43:05 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

More weipa tests.

Revision 3107 - Directory Listing
Modified Thu Aug 26 03:41:28 2010 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Removed ugly #defines in favour of a class.

Revision 3106 - Directory Listing
Modified Wed Aug 25 08:15:38 2010 UTC (8 years, 6 months ago) by caltinay
Original Path: trunk

Fixed export when 'work_dir' is set to sth other than the current dir.

Revision 3105 - Directory Listing
Modified Wed Aug 25 04:37:52 2010 UTC (8 years, 6 months ago) by gross
Original Path: trunk

bug fixed in the Gauss Seidel

Revision 3104 - Directory Listing
Modified Wed Aug 25 00:53:25 2010 UTC (8 years, 6 months ago) by caltinay
Original Path: trunk

Set up initial test suite files for weipa and some basic preliminary tests.

Revision 3102 - Directory Listing
Modified Tue Aug 24 06:14:21 2010 UTC (8 years, 6 months ago) by caltinay
Original Path: trunk

Inject the DataManager class to the escript namespace.

Revision 3101 - Directory Listing
Modified Tue Aug 24 06:08:12 2010 UTC (8 years, 6 months ago) by caltinay
Original Path: trunk

weipa's saveVTK now stores metadata schema & string as expected.

Revision 3100 - Directory Listing
Modified Mon Aug 23 09:31:09 2010 UTC (8 years, 6 months ago) by gross
Original Path: trunk

bug in ILU0 fixed.

Revision 3099 - Directory Listing
Modified Sun Aug 22 04:35:15 2010 UTC (8 years, 6 months ago) by ahallam
Original Path: trunk

Gravitational Potential Example- Needs some tuning.

Revision 3098 - Directory Listing
Modified Fri Aug 20 08:08:27 2010 UTC (8 years, 6 months ago) by gross
Original Path: trunk

fix to the GaussSeidel

Revision 3097 - Directory Listing
Modified Fri Aug 20 04:59:12 2010 UTC (8 years, 6 months ago) by gross
Original Path: trunk

some modifications to the GaussSeidel

Revision 3096 - Directory Listing
Modified Thu Aug 19 01:40:52 2010 UTC (8 years, 6 months ago) by caltinay
Original Path: trunk

-New VisIt simulation control interface in weipa (uses VisIt's simv2)
-Rewrote restarts.py to be a more generic data manager for restarts and exports
-Removed weipa python file since the functionality is now handled by restarts.py

Revision 3095 - Directory Listing
Modified Tue Aug 17 03:42:31 2010 UTC (8 years, 6 months ago) by caltinay
Original Path: trunk

Fixed building libescriptreader for the VisIt plugin.

Revision 3094 - Directory Listing
Modified Fri Aug 13 08:38:06 2010 UTC (8 years, 6 months ago) by gross
Original Path: trunk

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

Revision 3093 - Directory Listing
Modified Fri Aug 13 08:07:45 2010 UTC (8 years, 6 months ago) by gross
Original Path: trunk

problem with no MPI compilation fixed

Revision 3092 - Directory Listing
Modified Fri Aug 13 07:55:03 2010 UTC (8 years, 6 months ago) by caltinay
Original Path: trunk

Added getDataFlat() which will be used by the VisIt simulation interface

Revision 3091 - Directory Listing
Modified Fri Aug 13 07:47:57 2010 UTC (8 years, 6 months ago) by caltinay
Original Path: trunk

-fixed cleanup on error when invoking escriptconvert in parallel
-fixed saving VTK files on one rank if data was loaded in chunks
-cleaned up EscriptDataset and split a couple of methods

Revision 3089 - Directory Listing
Modified Mon Aug 9 07:20:58 2010 UTC (8 years, 6 months ago) by ahallam
Original Path: trunk

Updates to example scripts - should now be working except for example09b.py which needs more memory.

Revision 3084 - Directory Listing
Modified Wed Aug 4 03:26:50 2010 UTC (8 years, 6 months ago) by gross
Original Path: trunk

small bug fixed.

Revision 3083 - Directory Listing
Modified Tue Aug 3 06:34:35 2010 UTC (8 years, 6 months ago) by caltinay
Original Path: trunk

Updated some svn:ignore props.

Revision 3081 - Directory Listing
Modified Tue Aug 3 05:36:42 2010 UTC (8 years, 6 months ago) by gross
Original Path: trunk

a light restart manager added.

Revision 3078 - Directory Listing
Modified Tue Aug 3 03:12:16 2010 UTC (8 years, 6 months ago) by jfenwick
Original Path: trunk

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

Revision 3077 - Directory Listing
Modified Mon Aug 2 23:01:14 2010 UTC (8 years, 6 months ago) by jfenwick
Original Path: trunk

Fix my error

Revision 3076 - Directory Listing
Modified Mon Aug 2 05:21:40 2010 UTC (8 years, 6 months ago) by jfenwick
Original Path: trunk

Removing hardcoded savanna from the SConstruct file.

Revision 3075 - Directory Listing
Modified Wed Jul 28 02:51:20 2010 UTC (8 years, 6 months ago) by ahallam
Original Path: trunk

Updates to cookbook example. Lumping turned off for order 2 models until bug resolves.

Revision 3074 - Directory Listing
Modified Tue Jul 27 01:47:45 2010 UTC (8 years, 6 months ago) by gross
Original Path: trunk

tolerance for PCG relaxed.

Revision 3073 - Directory Listing
Modified Mon Jul 26 06:10:50 2010 UTC (8 years, 7 months ago) by jfenwick
Original Path: trunk

Rename files to fix build problem

Revision 3071 - Directory Listing
Modified Wed Jul 21 05:37:30 2010 UTC (8 years, 7 months ago) by gross
Original Path: trunk

new darcy flux

Revision 3069 - Directory Listing
Modified Wed Jul 21 03:24:48 2010 UTC (8 years, 7 months ago) by ahallam
Original Path: trunk

Updates to layer cake and cookbook as well as examples.

Revision 3068 - Directory Listing
Modified Mon Jul 19 00:43:31 2010 UTC (8 years, 7 months ago) by ahallam
Original Path: trunk

Missing Figures

Revision 3067 - Directory Listing
Modified Mon Jul 19 00:40:37 2010 UTC (8 years, 7 months ago) by ahallam
Original Path: trunk

Cookbook Updates - Chapter 9 - New figures.

Revision 3066 - Directory Listing
Modified Sun Jul 18 23:32:07 2010 UTC (8 years, 7 months ago) by ahallam
Original Path: trunk

Missing Picture causing errors.

Revision 3065 - Directory Listing
Modified Thu Jul 15 02:59:27 2010 UTC (8 years, 7 months ago) by ahallam
Original Path: trunk

Updates to newer examples.

Revision 3064 - Directory Listing
Modified Thu Jul 15 02:58:23 2010 UTC (8 years, 7 months ago) by ahallam
Original Path: trunk

Updates to cookbook with fixed images and new chaper for 3d seismic model. New chapter is now added.

Revision 3063 - Directory Listing
Modified Thu Jul 15 02:57:46 2010 UTC (8 years, 7 months ago) by ahallam
Original Path: trunk

Updates to cookbook with fixed images and new chaper for 3d seismic model.

Revision 3062 - Directory Listing
Modified Wed Jul 14 00:18:30 2010 UTC (8 years, 7 months ago) by ahallam
Original Path: trunk

Joels suggested changes for naming conventions. The function is now located in esys.pycad.extras as layer_cake.

Revision 3061 - Directory Listing
Modified Tue Jul 13 23:34:10 2010 UTC (8 years, 7 months ago) by ahallam
Original Path: trunk

function LayerCake fixed is now under esys.pycad.layer_cake

Revision 3060 - Directory Listing
Modified Tue Jul 13 00:55:09 2010 UTC (8 years, 7 months ago) by ahallam
Original Path: trunk

Adding layer cake builder to pycad

Revision 3059 - Directory Listing
Modified Tue Jul 6 03:31:48 2010 UTC (8 years, 7 months ago) by jfenwick
Original Path: trunk

Fix error message in launcher. Allow non-data objects to be passed to condEval

Revision 3056 - Directory Listing
Modified Mon Jul 5 00:07:16 2010 UTC (8 years, 7 months ago) by jfenwick
Original Path: trunk

Have the escript launcher check the PBS_NODEFILE variable for hosts.

Revision 3055 - Directory Listing
Modified Sun Jul 4 21:52:36 2010 UTC (8 years, 7 months ago) by ahallam
Original Path: trunk

3d wave equation and ABC

Revision 3054 - Directory Listing
Modified Wed Jun 30 02:22:25 2010 UTC (8 years, 7 months ago) by ahallam
Original Path: trunk

Missing Figures...

Revision 3053 - Directory Listing
Modified Tue Jun 29 01:31:31 2010 UTC (8 years, 7 months ago) by jfenwick
Original Path: trunk

Fixes to deal with new savanna configuration.
Blocking out missing images.

Revision 3052 - Directory Listing
Modified Tue Jun 29 00:57:45 2010 UTC (8 years, 7 months ago) by lgao
Original Path: trunk

Revert the commit of this options file made by my last commit for Gauss-Seidel.

Revision 3051 - Directory Listing
Modified Tue Jun 29 00:45:49 2010 UTC (8 years, 7 months ago) by lgao
Original Path: trunk

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

Revision 3050 - Directory Listing
Modified Sun Jun 27 22:54:12 2010 UTC (8 years, 7 months ago) by jfenwick
Original Path: trunk

Visual studio 2008 (v9.0) with Microsoft MPI libraries.
Courtesy of Gordon German.

Revision 3047 - Directory Listing
Modified Thu Jun 24 00:33:05 2010 UTC (8 years, 8 months ago) by jfenwick
Original Path: trunk

Adding user name to tmpfiles.
Changing name of cluster options file to savanna from service0

Revision 3046 - Directory Listing
Modified Tue Jun 22 08:01:55 2010 UTC (8 years, 8 months ago) by gross
Original Path: trunk

some examples for a simple subduction model

Revision 3045 - Directory Listing
Modified Fri Jun 18 06:38:18 2010 UTC (8 years, 8 months ago) by lgao
Original Path: trunk

Enable MKL and Lapack (the unit test problem has been fixed after Artak's commit).

Revision 3043 - Directory Listing
Modified Fri Jun 18 04:45:14 2010 UTC (8 years, 8 months ago) by artak
Original Path: trunk

Problem with latest MKL should be fixed now. The problem was solving unrolled block matrix with MKL.

Revision 3042 - Directory Listing
Modified Fri Jun 18 04:01:43 2010 UTC (8 years, 8 months ago) by lgao
Original Path: trunk

Disable Lapack to disable MKL.

Revision 3041 - Directory Listing
Modified Fri Jun 18 04:01:40 2010 UTC (8 years, 8 months ago) by artak
Original Path: trunk

Should be faster with openmp. Some ROW-COL conversion.

Revision 3040 - Directory Listing
Modified Fri Jun 18 03:05:17 2010 UTC (8 years, 8 months ago) by lgao
Original Path: trunk

Using lastest MKL library and set "usemkl=no" before the
problem with MKL in unit tests is solved ("maximum number 
of iteration step reached" for test_***_AMG_System).

Revision 3039 - Directory Listing
Modified Tue Jun 15 07:21:56 2010 UTC (8 years, 8 months ago) by caltinay
Original Path: trunk

Fix the NetCDF 4.1 issue (hopefully) - MPICH and IntelMPI have the required
definition.

Revision 3038 - Directory Listing
Modified Tue Jun 15 07:08:46 2010 UTC (8 years, 8 months ago) by lgao
Original Path: trunk

Update the path to Intel-mpi 4.0.0.027

Revision 3037 - Directory Listing
Modified Mon Jun 14 00:59:30 2010 UTC (8 years, 8 months ago) by caltinay
Original Path: trunk

Renamed escriptexport to weipa. Fixes #475.

Revision 3036 - Directory Listing
Modified Mon Jun 14 00:13:18 2010 UTC (8 years, 8 months ago) by caltinay
Original Path: trunk

Fixed compilation with MPI and NetCDF 4.1. Removed obsolete options file.

Revision 3035 - Directory Listing
Modified Thu Jun 10 01:48:41 2010 UTC (8 years, 8 months ago) by jfenwick
Original Path: trunk

Lazy node support for conditional evaluation.
It should be a complete operation now.

Revision 3034 - Directory Listing
Modified Wed Jun 9 03:24:23 2010 UTC (8 years, 8 months ago) by jfenwick
Original Path: trunk

Adding unit tests for condEval

Revision 3033 - Directory Listing
Modified Wed Jun 2 10:17:00 2010 UTC (8 years, 8 months ago) by gross
Original Path: trunk

fix for overflow

Revision 3032 - Directory Listing
Modified Mon May 31 02:58:15 2010 UTC (8 years, 8 months ago) by jfenwick
Original Path: trunk

Add work around for windows not liking chained X::Y::Z.
TestDomain now supports tags and getX.
This is to allow testing for some features without invoking finley

Revision 3031 - Directory Listing
Modified Thu May 27 04:04:33 2010 UTC (8 years, 8 months ago) by jfenwick
Original Path: trunk

Adding condEval function to Data.
Unit tests and a different name to follow.

Revision 3030 - Directory Listing
Modified Fri May 21 05:25:20 2010 UTC (8 years, 9 months ago) by lgao
Original Path: trunk

Update savanna_options file to use the correct silo module.

Revision 3029 - Directory Listing
Modified Fri May 21 02:01:37 2010 UTC (8 years, 9 months ago) by ahallam
Original Path: trunk

small updates and work on seismic code

Revision 3028 - Directory Listing
Modified Thu May 13 03:41:27 2010 UTC (8 years, 9 months ago) by gross
Original Path: trunk

a new test problem (doesn't use unit testing)

Revision 3027 - Directory Listing
Modified Wed May 12 05:26:09 2010 UTC (8 years, 9 months ago) by gross
Original Path: trunk

some little fixes in an old script

Revision 3026 - Directory Listing
Modified Mon May 10 06:23:49 2010 UTC (8 years, 9 months ago) by gross
Original Path: trunk

some fix for omp

Revision 3025 - Directory Listing
Modified Thu May 6 01:20:46 2010 UTC (8 years, 9 months ago) by ahallam
Original Path: trunk

Updates to wave equation examples. Pressure wave examples should be completed now. Working on seismic wave examples. Cookbook chapter for pressure wave examples also added.

Revision 3024 - Directory Listing
Modified Wed May 5 01:12:32 2010 UTC (8 years, 9 months ago) by jfenwick
Original Path: trunk

Some savanna fixes but not complete

Revision 3023 - Directory Listing
Modified Wed May 5 01:00:16 2010 UTC (8 years, 9 months ago) by lgao
Original Path: trunk

Option file update for machine "sunzi".

Revision 3021 - Directory Listing
Modified Tue May 4 10:14:12 2010 UTC (8 years, 9 months ago) by gross
Original Path: trunk

MPI problem fixed.

Revision 3020 - Directory Listing
Modified Tue May 4 09:10:03 2010 UTC (8 years, 9 months ago) by gross
Original Path: trunk

reactive solver added

Revision 3019 - Directory Listing
Modified Fri Apr 30 06:10:37 2010 UTC (8 years, 9 months ago) by jfenwick
Original Path: trunk

adding Lin options

Revision 3018 - Directory Listing
Modified Thu Apr 29 21:35:24 2010 UTC (8 years, 9 months ago) by gross
Original Path: trunk

some stupid lines removed

Revision 3017 - Directory Listing
Modified Thu Apr 29 03:40:12 2010 UTC (8 years, 9 months ago) by artak
Original Path: trunk

Some AMLI for systems fixes

Revision 3016 - Directory Listing
Modified Wed Apr 28 05:28:44 2010 UTC (8 years, 9 months ago) by artak
Original Path: trunk

firstprivate added for OpenMP

Revision 3015 - Directory Listing
Modified Wed Apr 28 05:06:26 2010 UTC (8 years, 9 months ago) by artak
Original Path: trunk

OpenMP commented out for now

Revision 3014 - Directory Listing
Modified Wed Apr 28 04:05:21 2010 UTC (8 years, 9 months ago) by gross
Original Path: trunk

a more stable handling of divergence in the CN or BE

Revision 3013 - Directory Listing
Modified Wed Apr 28 03:47:51 2010 UTC (8 years, 9 months ago) by artak
Original Path: trunk

Block separation part commented out for AMG preconditioner

Revision 3012 - Directory Listing
Modified Wed Apr 28 03:39:22 2010 UTC (8 years, 9 months ago) by lgao
Original Path: trunk

Fix the MPI compilation bug.

Revision 3011 - Directory Listing
Modified Wed Apr 28 02:21:23 2010 UTC (8 years, 9 months ago) by artak
Original Path: trunk

New method added for unrolling System matrix. Direct solver now uses unrolled copy of the AMG matrix.

Revision 3010 - Directory Listing
Modified Tue Apr 27 05:10:46 2010 UTC (8 years, 9 months ago) by artak
Original Path: trunk

Preparation for AMG on Systems without cut using frobenius norm

Revision 3009 - Directory Listing
Modified Thu Apr 22 11:17:42 2010 UTC (8 years, 10 months ago) by gross
Original Path: trunk

another MPI problem fixed

Revision 3008 - Directory Listing
Modified Thu Apr 22 10:19:20 2010 UTC (8 years, 10 months ago) by gross
Original Path: trunk

MPI problem fixed

Revision 3007 - Directory Listing
Modified Thu Apr 22 09:08:36 2010 UTC (8 years, 10 months ago) by gross
Original Path: trunk

typo for MPI cse fixed

Revision 3006 - Directory Listing
Modified Thu Apr 22 08:31:28 2010 UTC (8 years, 10 months ago) by gross
Original Path: trunk

local_norm_w removed

Revision 3005 - Directory Listing
Modified Thu Apr 22 05:59:31 2010 UTC (8 years, 10 months ago) by gross
Original Path: trunk

early call of setPreconditioner in FCT solver removed.

Revision 3004 - Directory Listing
Modified Wed Apr 14 05:27:30 2010 UTC (8 years, 10 months ago) by ahallam
Original Path: trunk

Sampling theorem, stability requirements, Laplacian discussion, Pressure wave PDE

Revision 3003 - Directory Listing
Modified Wed Apr 7 02:29:57 2010 UTC (8 years, 10 months ago) by ahallam
Original Path: trunk

Pressure wave working, accelleration example, new entries to cookbook for example 7.

Revision 3002 - Directory Listing
Modified Wed Apr 7 02:25:45 2010 UTC (8 years, 10 months ago) by gross
Original Path: trunk

gmsh now supports the Mesh.SubdivisionAlgorithm and Mesh.Algorithm3D option.
The Mesh.Algorithm, Mesh.Smoothing, Mesh.Optimization options are now set in the
.geo file rather than in the command line.

Revision 3001 - Directory Listing
Modified Wed Mar 31 04:29:10 2010 UTC (8 years, 10 months ago) by ahallam
Original Path: trunk

Pressue wave problem, looking at sampling theorem, and Crank-Nicolson

Revision 3000 - Directory Listing
Modified Tue Mar 30 03:10:13 2010 UTC (8 years, 10 months ago) by lgao
Original Path: trunk

Gauss_Seidel preconditioner is now SPD.

Revision 2999 - Directory Listing
Modified Fri Mar 26 00:00:39 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

NE set to 10 elemennt, because 6 is too small for mpi=8 job.

Revision 2998 - Directory Listing
Modified Wed Mar 24 04:00:20 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

More openMP corrections

Revision 2997 - Directory Listing
Modified Wed Mar 24 01:46:33 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

Some openMP corrections

Revision 2996 - Directory Listing
Modified Tue Mar 23 06:24:09 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

Tests are added for GAUSS_SEIDEL

Revision 2995 - Directory Listing
Modified Tue Mar 23 06:14:26 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

AMG levels maximum set 5

Revision 2994 - Directory Listing
Modified Tue Mar 23 06:13:14 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

AMG levels maximum set 5

Revision 2993 - Directory Listing
Modified Tue Mar 23 04:29:30 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

Some optimization on GAUSS_SEIDEL sweeps.

Revision 2992 - Directory Listing
Modified Tue Mar 23 04:16:28 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

Sweeps bug is fixed and some more comments added about how sweeps computed

Revision 2991 - Directory Listing
Modified Mon Mar 22 05:42:48 2010 UTC (8 years, 11 months ago) by gross
Original Path: trunk

isub as private added

Revision 2990 - Directory Listing
Modified Fri Mar 19 05:57:22 2010 UTC (8 years, 11 months ago) by gross
Original Path: trunk

some prints removed.

Revision 2989 - Directory Listing
Modified Thu Mar 18 01:45:55 2010 UTC (8 years, 11 months ago) by gross
Original Path: trunk

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

Revision 2988 - Directory Listing
Modified Tue Mar 16 06:14:30 2010 UTC (8 years, 11 months ago) by gross
Original Path: trunk

C-level lumping switched on

Revision 2987 - Directory Listing
Modified Tue Mar 16 01:32:43 2010 UTC (8 years, 11 months ago) by gross
Original Path: trunk

FCT solver rewritten

Revision 2982 - Directory Listing
Modified Wed Mar 10 04:27:47 2010 UTC (8 years, 11 months ago) by caltinay
Original Path: trunk

Some minor corrections to the cookbook (mainly word repetitions and typos).

Revision 2980 - Directory Listing
Modified Tue Mar 9 03:50:58 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

minor change to fix latest bug

Revision 2979 - Directory Listing
Modified Tue Mar 9 02:54:32 2010 UTC (8 years, 11 months ago) by ahallam
Original Path: trunk

cookbook review final final 3.1 - artak and tony corrections

Revision 2977 - Directory Listing
Modified Tue Mar 9 00:33:28 2010 UTC (8 years, 11 months ago) by ahallam
Original Path: trunk

cookbook review final 3.1

Revision 2976 - Directory Listing
Modified Mon Mar 8 01:18:33 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

Lame equation is corrected. Options for using smoother in AMG is added. A book on AMG is cited for standard coarsening.

Revision 2975 - Directory Listing
Modified Thu Mar 4 05:44:12 2010 UTC (8 years, 11 months ago) by ahallam
Original Path: trunk

Cookbook modifications Review -> Not quite finished yet.
New figure.

Revision 2974 - Directory Listing
Modified Thu Mar 4 03:09:35 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

forgot to skip example06.py as well

Revision 2973 - Directory Listing
Modified Thu Mar 4 03:07:22 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

example05c.py is not tested if matplotlib library version is too old, where quiver() does not support angle parameter.

Revision 2972 - Directory Listing
Modified Thu Mar 4 01:33:38 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

DONE. Einstain Summation Convention (ESC, what an irony, reminds me ESC button) is removed from cookbook as it is not used anywhere in the cookbook.

Revision 2971 - Directory Listing
Modified Wed Mar 3 23:19:00 2010 UTC (8 years, 11 months ago) by jfenwick
Original Path: trunk

I hate voodoo.
Putting pdfinfo directive in two places in the cookbook header so that
both versions of evince get the right title.

Revision 2970 - Directory Listing
Modified Wed Mar 3 05:23:50 2010 UTC (8 years, 11 months ago) by jfenwick
Original Path: trunk

Fix out of date comment

Revision 2969 - Directory Listing
Modified Wed Mar 3 04:27:00 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

reached Chapter 4

Revision 2968 - Directory Listing
Modified Wed Mar 3 04:02:30 2010 UTC (8 years, 11 months ago) by caltinay
Original Path: trunk

Updated service0 & shake75 options to use cxx_extra

Revision 2967 - Directory Listing
Modified Wed Mar 3 03:50:46 2010 UTC (8 years, 11 months ago) by caltinay
Original Path: trunk

scons now understands cc_extra and cxx_extra. The former applies only to the
C compiler, the latter to the C++ compiler which fixes #510.

Revision 2966 - Directory Listing
Modified Wed Mar 3 03:19:39 2010 UTC (8 years, 11 months ago) by jfenwick
Original Path: trunk

Fixing non-ansi compliant code

Revision 2965 - Directory Listing
Modified Wed Mar 3 01:53:41 2010 UTC (8 years, 11 months ago) by jfenwick
Original Path: trunk

Added MPI aware MIS

Revision 2964 - Directory Listing
Modified Wed Mar 3 01:21:09 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

up to Chapter 3

Revision 2963 - Directory Listing
Modified Wed Mar 3 01:10:11 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

up to section 2.1.9

Revision 2962 - Directory Listing
Modified Wed Mar 3 01:03:56 2010 UTC (8 years, 11 months ago) by gross
Original Path: trunk

bar as unit added

Revision 2961 - Directory Listing
Modified Wed Mar 3 00:56:59 2010 UTC (8 years, 11 months ago) by jfenwick
Original Path: trunk

Hacking cookbook

Revision 2960 - Directory Listing
Modified Tue Mar 2 07:54:11 2010 UTC (8 years, 11 months ago) by gross
Original Path: trunk

new DarcyFlux solver

Revision 2959 - Directory Listing
Modified Tue Mar 2 06:27:17 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

more corrections on exmaple 1, up to section 2.1.5

Revision 2958 - Directory Listing
Modified Tue Mar 2 06:00:39 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

more corrections on exmaple 1, up to section 2.1.5

Revision 2957 - Directory Listing
Modified Tue Mar 2 01:28:19 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

more corrections

Revision 2956 - Directory Listing
Modified Mon Mar 1 01:31:59 2010 UTC (8 years, 11 months ago) by artak
Original Path: trunk

First corrections: NEEDS MORE AND MORE...

Revision 2955 - Directory Listing
Modified Mon Mar 1 00:54:37 2010 UTC (8 years, 11 months ago) by jfenwick
Original Path: trunk

Fix hackscore error

Revision 2954 - Directory Listing
Modified Fri Feb 26 06:09:47 2010 UTC (8 years, 11 months ago) by gross
Original Path: trunk

bug introduced by a smart programmer to the Locator has been fixed?

Revision 2953 - Directory Listing
Modified Thu Feb 25 10:00:23 2010 UTC (8 years, 11 months ago) by gross
Original Path: trunk

final touch to the naming in the cookbook

Revision 2952 - Directory Listing
Modified Thu Feb 25 09:52:10 2010 UTC (8 years, 11 months ago) by gross
Original Path: trunk

even more renaming in the cookbook

Revision 2951 - Directory Listing
Modified Thu Feb 25 07:43:40 2010 UTC (8 years, 11 months ago) by gross
Original Path: trunk

more renaming in the cookbook

Revision 2950 - Directory Listing
Modified Thu Feb 25 07:33:16 2010 UTC (8 years, 11 months ago) by gross
Original Path: trunk

more renames in the cookbook.

Revision 2949 - Directory Listing
Modified Thu Feb 25 05:23:11 2010 UTC (8 years, 11 months ago) by gross
Original Path: trunk

renaming examples part 1

Revision 2948 - Directory Listing
Modified Thu Feb 25 04:54:30 2010 UTC (8 years, 11 months ago) by gross
Original Path: trunk

a new almost completed version of the cookbook

Revision 2944 - Directory Listing
Modified Tue Feb 23 23:51:20 2010 UTC (9 years ago) by jfenwick
Original Path: trunk

Fix latex markup in pdf title.
It turns out \pdfinfo must come after \maketitle if you don't want the
latex version of the title.

This behaviour does not happen in evince 2.22.2 (standard in lenny) but does
happen in more recent versions.

Revision 2943 - Directory Listing
Modified Tue Feb 23 01:49:27 2010 UTC (9 years ago) by artak
Original Path: trunk

VTK as a required package is removed from cookbook

Revision 2942 - Directory Listing
Modified Mon Feb 22 05:43:44 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Fixed a small typo in the cookbook abstract.

Revision 2941 - Directory Listing
Modified Mon Feb 22 05:17:43 2010 UTC (9 years ago) by caltinay
Original Path: trunk

saveESD now doesn't store the absolute path to the files in the ESD file so
the whole dataset can be moved easily.

Revision 2940 - Directory Listing
Modified Fri Feb 19 00:38:45 2010 UTC (9 years ago) by caltinay
Original Path: trunk

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

Revision 2939 - Directory Listing
Modified Thu Feb 18 04:16:59 2010 UTC (9 years ago) by gross
Original Path: trunk

some print statements removed.

Revision 2938 - Directory Listing
Modified Thu Feb 18 00:24:35 2010 UTC (9 years ago) by caltinay
Original Path: trunk

saveESD: Add a warning about the experimental status of ESD.
Save the ESD file within the data directory.

Revision 2937 - Directory Listing
Modified Tue Feb 16 00:01:52 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Corrected an MPI datatype

Revision 2936 - Directory Listing
Modified Mon Feb 15 03:29:53 2010 UTC (9 years ago) by gross
Original Path: trunk

some clarification added.

Revision 2935 - Directory Listing
Modified Mon Feb 15 03:15:59 2010 UTC (9 years ago) by gross
Original Path: trunk

pycad support 3D transfinite meshing now.

Revision 2934 - Directory Listing
Modified Fri Feb 12 05:09:06 2010 UTC (9 years ago) by gross
Original Path: trunk

gmsh reader supports second order recs and hex now

Revision 2933 - Directory Listing
Modified Tue Feb 9 03:27:37 2010 UTC (9 years ago) by gross
Original Path: trunk

test for positivity of initial solution in transport solver has been switched on again

Revision 2931 - Directory Listing
Modified Mon Feb 8 06:45:41 2010 UTC (9 years ago) by gross
Original Path: trunk

more changes on the cookbook

Revision 2930 - Directory Listing
Modified Mon Feb 8 06:25:43 2010 UTC (9 years ago) by caltinay
Original Path: trunk

escriptconvert can now convert both to Silo and VTK and is thus built by
default

Revision 2929 - Directory Listing
Modified Mon Feb 8 05:13:27 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Implemented mantis issue 464 in dataexporter: better resolution for Tri6 and
Tet10 elements via point-in-triangle and point-in-tetrahedron tests.

Revision 2926 - Directory Listing
Modified Thu Feb 4 23:13:53 2010 UTC (9 years ago) by jfenwick
Original Path: trunk

Attempting to fix a problem with windows linking in the ironically named INKNOWWHATIMDOING section

Revision 2925 - Directory Listing
Modified Thu Feb 4 23:12:34 2010 UTC (9 years ago) by jfenwick
Original Path: trunk

Update savanna to build c99 style

Revision 2924 - Directory Listing
Modified Thu Feb 4 05:30:53 2010 UTC (9 years ago) by trankine
Original Path: trunk

* windows specific "we cant work out autolink" workaround
http://old.nabble.com/boost-1.41-and-autolink-%28maybe-the-wrong-list%29-td27040284.html

Revision 2923 - Directory Listing
Modified Thu Feb 4 04:05:36 2010 UTC (9 years ago) by jfenwick
Original Path: trunk

Bringing non-release specific things from stage3.1 r2922 back to trunk

Revision 2919 - Directory Listing
Modified Thu Feb 4 00:53:58 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Took over Macro element handling from finley.saveVTK.

Revision 2918 - Directory Listing
Modified Thu Feb 4 00:53:37 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Quick fix for Windows scons problem due to the same files being compiled twice
in the same directory. Visit plugin is not for Windows anyway so disabled it
there.

Revision 2917 - Directory Listing
Modified Wed Feb 3 06:19:50 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Fix for the fix ;-) The dataexporter is used in a context where HAVE_MPI is set
but mpi not initialised -> have to check for mpiSize.

Revision 2915 - Directory Listing
Modified Wed Feb 3 05:55:16 2010 UTC (9 years ago) by gross
Original Path: trunk

uninitialised variable error for non-mpi case fixed.

Revision 2911 - Directory Listing
Modified Wed Feb 3 03:30:40 2010 UTC (9 years ago) by jfenwick
Original Path: trunk

Changed name of launcher and rotated figure correctly.

Revision 2910 - Directory Listing
Modified Wed Feb 3 03:22:31 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Added a libescriptreader.a target which does not depend on escript or finley
at runtime. This will be used for the VisIt plugin so is not built by default.

Revision 2907 - Directory Listing
Modified Wed Feb 3 01:39:15 2010 UTC (9 years ago) by gross
Original Path: trunk

needdirs replaced by mkDir from esys.escript

Revision 2904 - Directory Listing
Modified Tue Feb 2 04:21:52 2010 UTC (9 years ago) by gross
Original Path: trunk

more revision on cookbook: example 1 and 2 have been swapped.

Revision 2903 - Directory Listing
Modified Tue Feb 2 00:20:52 2010 UTC (9 years ago) by lgao
Original Path: trunk

Switch to MKL 10.2.2.025 on service0.

Revision 2902 - Directory Listing
Modified Mon Feb 1 23:53:16 2010 UTC (9 years ago) by lgao
Original Path: trunk

Switch to Parmetis 3.1.1 on service0.

Revision 2900 - Directory Listing
Modified Mon Feb 1 06:05:38 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Switch to Silo 4.7.2 on service0 (bug fix release).

Revision 2899 - Directory Listing
Modified Mon Feb 1 01:55:53 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Added missing declspec to FileSavers.

Revision 2898 - Directory Listing
Modified Mon Feb 1 01:23:46 2010 UTC (9 years ago) by caltinay
Original Path: trunk

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

Revision 2897 - Directory Listing
Modified Mon Feb 1 01:22:50 2010 UTC (9 years ago) by lgao
Original Path: trunk

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

Revision 2896 - Directory Listing
Modified Sun Jan 31 22:17:22 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Added missing extern C for finley include.

Revision 2895 - Directory Listing
Modified Fri Jan 29 04:58:16 2010 UTC (9 years ago) by caltinay
Original Path: trunk

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

Revision 2893 - Directory Listing
Modified Fri Jan 29 03:41:33 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Link to esysUtils to be able to use escript exceptions.

Revision 2891 - Directory Listing
Modified Fri Jan 29 00:26:07 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Fix for ambiguous call to sqrt...

Revision 2890 - Directory Listing
Modified Fri Jan 29 00:22:39 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Oh, apparently a 'defect in the standard' and VC++ didn't like it. Hopefully,
this should fix it.

Revision 2888 - Directory Listing
Modified Fri Jan 29 00:07:00 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Looks like netcdf.hh doesn't exist on Windows so changed to netcdfcpp.h.

Revision 2887 - Directory Listing
Modified Thu Jan 28 05:49:09 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Fixed a compile issue with MPI.

Revision 2886 - Directory Listing
Modified Thu Jan 28 05:39:23 2010 UTC (9 years ago) by caltinay
Original Path: trunk

New version of saveVTK within dataexporter. Not pythonised yet since it needs
more testing and release 3.1 will not ship dataexporter.

Revision 2884 - Directory Listing
Modified Thu Jan 28 05:00:59 2010 UTC (9 years ago) by jfenwick
Original Path: trunk

Updated various nan checks to consider the windows _isnan

The default compiler flags have changed as well.
+ intel will now take -std=c99 instead of -ansi
+ gcc has -ansi removed which means it defaults to gnu99

We could have set gcc to -std=c99 as well but that gives a 
warning on g++ which gets converted into an error by our
pedantic warning.

Rationale:
We need something more than ansi to get proper nan handling.
- We currently don't have any code which does not comply with ansi
  but the nan checks don't work.

Impact:
If we want our code to still be able to compile on older compilers
(at reduced functionality) we need to be careful not to introduce other
c99-isms.
If we don't care, then it's time for some celebratory // comments.

Revision 2883 - Directory Listing
Modified Thu Jan 28 02:28:27 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Switch to gcc 4.4 on guineapig

Revision 2882 - Directory Listing
Modified Thu Jan 28 02:27:49 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Scons now allows to specify which C & C++ compiler to use via cc and cxx
variables. Fixes mantis # 485.

Revision 2881 - Directory Listing
Modified Thu Jan 28 02:03:15 2010 UTC (9 years ago) by jfenwick
Original Path: trunk

Don't panic.
Updating copyright stamps

Revision 2880 - Directory Listing
Modified Thu Jan 28 01:21:30 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Better resolution for Hex27 & Rec9 data in dataexporter (mantis #486).
Saved Silo data resolution is now equal to finley.SaveVTK generated data in
all cases.

Revision 2879 - Directory Listing
Modified Thu Jan 28 01:00:26 2010 UTC (9 years ago) by jfenwick
Original Path: trunk

Move definition of build_platform on t.poulet suggestion.
Redefine the IS_NAN macro to replace versions commented as
'This does not work'
If you are not compiling with a c99 compliant compiler you will not 
recognise nulls but this seems to be the best we can do right now 
without checking for explicit bit patterns.

Revision 2878 - Directory Listing
Modified Thu Jan 28 00:59:30 2010 UTC (9 years ago) by gross
Original Path: trunk

more work on cookbook review

Revision 2877 - Directory Listing
Modified Thu Jan 28 00:28:45 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Fixes to Silo writer: Multivars for tensors are now correct even with empty
ranks.

Revision 2875 - Directory Listing
Modified Wed Jan 27 04:09:24 2010 UTC (9 years ago) by jfenwick
Original Path: trunk

Updated version string to something which won't keep changing

Revision 2873 - Directory Listing
Modified Wed Jan 27 01:09:33 2010 UTC (9 years ago) by caltinay
Original Path: trunk

Fix for mantis #480 when parmetis is off.

Revision 2872 - Directory Listing
Modified Wed Jan 27 00:59:58 2010 UTC (9 years ago) by artak
Original Path: trunk

/home/ changed to /Users/ for mac

Revision 2870 - Directory Listing
Modified Mon Jan 25 08:34:15 2010 UTC (9 years ago) by gross
Original Path: trunk

more review on the cookbook.

Revision 2869 - Directory Listing
Modified Mon Jan 25 05:11:28 2010 UTC (9 years ago) by gross
Original Path: trunk

back to the old version. The last checkin was a mistake.

Revision 2868 - Directory Listing
Modified Mon Jan 25 04:44:45 2010 UTC (9 years ago) by artak
Original Path: trunk

Some fixes for 3.1 release. Notes about Snow Leopard is added and installing from ports removed.

Revision 2867 - Directory Listing
Modified Fri Jan 22 06:28:02 2010 UTC (9 years, 1 month ago) by gross
Original Path: trunk

now option -i is used if no script is given

Revision 2866 - Directory Listing
Modified Fri Jan 22 05:38:56 2010 UTC (9 years, 1 month ago) by gross
Original Path: trunk

small fix for the case n=1 under mpi

Revision 2865 - Directory Listing
Modified Fri Jan 22 03:19:32 2010 UTC (9 years, 1 month ago) by gross
Original Path: trunk

launcher for MPI supports now -i option (see mantis 361)

Revision 2864 - Directory Listing
Modified Fri Jan 22 03:09:55 2010 UTC (9 years, 1 month ago) by gross
Original Path: trunk

projector added to users guide

Revision 2863 - Directory Listing
Modified Thu Jan 21 07:18:37 2010 UTC (9 years, 1 month ago) by gross
Original Path: trunk

fix for mantis 454

Revision 2862 - Directory Listing
Modified Thu Jan 21 04:45:39 2010 UTC (9 years, 1 month ago) by gross
Original Path: trunk

more review in the cookbook

Revision 2861 - Directory Listing
Modified Wed Jan 20 02:47:42 2010 UTC (9 years, 1 month ago) by gross
Original Path: trunk

some modification to the cookbook

Revision 2860 - Directory Listing
Modified Tue Jan 19 05:25:39 2010 UTC (9 years, 1 month ago) by gross
Original Path: trunk

prints removed.

Revision 2859 - Directory Listing
Modified Tue Jan 19 05:21:50 2010 UTC (9 years, 1 month ago) by gross
Original Path: trunk

a work around for gcc 4.4 added.

Revision 2858 - Directory Listing
Modified Tue Jan 19 01:07:52 2010 UTC (9 years, 1 month ago) by gross
Original Path: trunk

small fixes with the reduced solution for the transport problem

Revision 2857 - Directory Listing
Modified Mon Jan 18 07:44:42 2010 UTC (9 years, 1 month ago) by gross
Original Path: trunk

test for ApproximationOrder added and Transport type problem now choose reduced when necessary only.

Revision 2856 - Directory Listing
Modified Mon Jan 18 04:14:37 2010 UTC (9 years, 1 month ago) by gross
Original Path: trunk

FunctionSpaces provide now some information about their approximation order.

Revision 2854 - Directory Listing
Modified Mon Jan 18 01:54:04 2010 UTC (9 years, 1 month ago) by caltinay
Original Path: trunk

Fixed a compile error and removed unneeded member.

Revision 2853 - Directory Listing
Modified Mon Jan 18 01:46:05 2010 UTC (9 years, 1 month ago) by caltinay
Original Path: trunk

Do not attempt to read node file data if #nodes=0.

Revision 2852 - Directory Listing
Modified Mon Jan 18 00:22:23 2010 UTC (9 years, 1 month ago) by jfenwick
Original Path: trunk

Fix MPI issue in toString.
Fixes unit tet failure in myfistrscript.py

Revision 2850 - Directory Listing
Modified Fri Jan 15 07:14:25 2010 UTC (9 years, 1 month ago) by gross
Original Path: trunk

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

Revision 2848 - Directory Listing
Modified Fri Jan 15 03:44:44 2010 UTC (9 years, 1 month ago) by caltinay
Original Path: trunk

Removed unneeded member and initialised some others in the constructor.

Revision 2847 - Directory Listing
Modified Fri Jan 15 03:35:05 2010 UTC (9 years, 1 month ago) by caltinay
Original Path: trunk

Improved error handling when using MPI and fixed Silo output when not all
ranks contribute to a data variable.

Revision 2846 - Directory Listing
Modified Fri Jan 15 03:16:08 2010 UTC (9 years, 1 month ago) by caltinay
Original Path: trunk

removeGhostNodes is broken and unnecessary anyway so removed.

Revision 2845 - Directory Listing
Modified Fri Jan 15 03:10:42 2010 UTC (9 years, 1 month ago) by caltinay
Original Path: trunk

escriptconvert passes MPI communicator to EscriptDataset now so files are
read/written in parallel.

Revision 2844 - Directory Listing
Modified Fri Jan 15 00:23:39 2010 UTC (9 years, 1 month ago) by jfenwick
Original Path: trunk

Fixed some options to deal with silo errors.

Revision 2843 - Directory Listing
Modified Thu Jan 14 05:51:28 2010 UTC (9 years, 1 month ago) by gross
Original Path: trunk

new compressible solver

Revision 2842 - Directory Listing
Modified Thu Jan 14 05:42:02 2010 UTC (9 years, 1 month ago) by caltinay
Original Path: trunk

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

Revision 2841 - Directory Listing
Modified Thu Jan 14 01:02:56 2010 UTC (9 years, 1 month ago) by jfenwick
Original Path: trunk

Unit tests for 2838 and adding setTags variant which takes a string instead of a tag num.

Revision 2840 - Directory Listing
Modified Thu Jan 14 01:00:15 2010 UTC (9 years, 1 month ago) by caltinay
Original Path: trunk

Enabled Silo on guineapig

Revision 2839 - Directory Listing
Modified Wed Jan 13 23:34:49 2010 UTC (9 years, 1 month ago) by artak
Original Path: trunk

minor compiliation problem under MKL is fixed.

Revision 2838 - Directory Listing
Modified Wed Jan 13 06:01:03 2010 UTC (9 years, 1 month ago) by jfenwick
Original Path: trunk

Vector, Tensor, Tensor3, Tensor4 can now take a (nested) sequence for 
their initial value.

Revision 2837 - Directory Listing
Modified Wed Jan 13 01:28:23 2010 UTC (9 years, 1 month ago) by caltinay
Original Path: trunk

Added missing import statement.

Revision 2836 - Directory Listing
Modified Mon Jan 11 01:41:29 2010 UTC (9 years, 1 month ago) by artak
Original Path: trunk

minor adjustments

Revision 2835 - Directory Listing
Modified Mon Jan 11 01:23:52 2010 UTC (9 years, 1 month ago) by artak
Original Path: trunk

Default smoother set to Gauss-Seidel. This one more robust than jacobi, but jacobi is faster.

Revision 2834 - Directory Listing
Modified Thu Jan 7 06:06:56 2010 UTC (9 years, 1 month ago) by caltinay
Original Path: trunk

Reduced elements are now handled separate from the main elements within the
data exporter. This simplifies usage considerably.

Revision 2833 - Directory Listing
Modified Thu Jan 7 05:44:46 2010 UTC (9 years, 1 month ago) by artak
Original Path: trunk

minor openmp fix

Revision 2831 - Directory Listing
Modified Thu Jan 7 05:08:19 2010 UTC (9 years, 1 month ago) by artak
Original Path: trunk

Splitting can be read from file. This is useful for testing.

Revision 2830 - Directory Listing
Modified Thu Jan 7 04:49:55 2010 UTC (9 years, 1 month ago) by caltinay
Original Path: trunk

saveSilo now passes MPI communicator to data exporter.

Revision 2829 - Directory Listing
Modified Wed Jan 6 02:51:31 2010 UTC (9 years, 1 month ago) by ahallam
Original Path: trunk

minor updates to cookbook

Revision 2828 - Directory Listing
Modified Tue Dec 22 01:24:40 2009 UTC (9 years, 2 months ago) by artak
Original Path: trunk

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

Revision 2827 - Directory Listing
Modified Fri Dec 18 03:41:09 2009 UTC (9 years, 2 months ago) by jfenwick
Original Path: trunk

There is now a mechanism to pass a C function into escript and invoke it on each datapoint with:

applyBinaryCFunction

Warning in order to use this function your escript must be compiled with 
scons ...  iknowwhatimdoing=yes

---------------------
Because this code relies on casts that the C standard does not allow some code has been moved into Dodgy{.h .cpp}

Scons files have been modified to treat these files specially [Warnings are not errors for these files.]

Revision 2826 - Directory Listing
Modified Fri Dec 18 01:33:35 2009 UTC (9 years, 2 months ago) by artak
Original Path: trunk

MINRES anf TFQMR add initioal guess. Tolerance for both solvers changed. However tolerance computaion needs to be more involved than it is now to avoid unnecessary very small tolerances.

Revision 2825 - Directory Listing
Modified Thu Dec 17 00:10:06 2009 UTC (9 years, 2 months ago) by jfenwick
Original Path: trunk

More fixes to resolveGroup

Revision 2824 - Directory Listing
Modified Wed Dec 16 01:22:56 2009 UTC (9 years, 2 months ago) by jfenwick
Original Path: trunk

ResolveGroup fixed so it actually resolves groups.
Children, when you iterate backwards remember its i>=0 not i>0

Revision 2822 - Directory Listing
Modified Mon Dec 14 03:10:16 2009 UTC (9 years, 2 months ago) by caltinay
Original Path: trunk

dataexporter: Ensure that NetCDF files created using N ranks are only loaded
when mpi size equals N or 1.

Revision 2821 - Directory Listing
Modified Fri Dec 11 07:00:35 2009 UTC (9 years, 2 months ago) by caltinay
Original Path: trunk

EscriptDataset takes an optional communicator now.

Revision 2820 - Directory Listing
Modified Thu Dec 10 05:03:11 2009 UTC (9 years, 2 months ago) by artak
Original Path: trunk

Paso Testing tools now can select coarseing.The builld_PasoTests target is also added to scons.

Revision 2819 - Directory Listing
Modified Thu Dec 10 04:12:35 2009 UTC (9 years, 2 months ago) by caltinay
Original Path: trunk

Added include to make badger happy. Hope everyone's happy now.

Revision 2818 - Directory Listing
Modified Thu Dec 10 04:10:16 2009 UTC (9 years, 2 months ago) by caltinay
Original Path: trunk

dataexporter links against escript now to make the Mac happy.

Revision 2817 - Directory Listing
Modified Thu Dec 10 02:12:33 2009 UTC (9 years, 2 months ago) by artak
Original Path: trunk

test is added for selecting standard coarsening.

Revision 2816 - Directory Listing
Modified Thu Dec 10 02:09:43 2009 UTC (9 years, 2 months ago) by artak
Original Path: trunk

Standard coarsening is added to options list.

Revision 2815 - Directory Listing
Modified Tue Dec 8 08:15:19 2009 UTC (9 years, 2 months ago) by gross
Original Path: trunk

this fixes a problem of element distribution attribute for lines

Revision 2814 - Directory Listing
Modified Tue Dec 8 01:50:29 2009 UTC (9 years, 2 months ago) by caltinay
Original Path: trunk

Removed minor code duplication.

Revision 2813 - Directory Listing
Modified Tue Dec 8 00:30:13 2009 UTC (9 years, 2 months ago) by caltinay
Original Path: trunk

Added missing include.

Revision 2812 - Directory Listing
Modified Tue Dec 8 00:12:07 2009 UTC (9 years, 2 months ago) by caltinay
Original Path: trunk

Implemented saveSilo within a new dataexporter module. If Silo is not available
at compile time the function throws. Ultimately, saveVTK will be moved here as
well.

Revision 2811 - Directory Listing
Modified Mon Dec 7 05:57:16 2009 UTC (9 years, 2 months ago) by caltinay
Original Path: trunk

Fixed compilation when silo is not used.

Revision 2810 - Directory Listing
Modified Mon Dec 7 04:13:49 2009 UTC (9 years, 2 months ago) by caltinay
Original Path: trunk

Reincarnation of the escriptreader as a more flexible escriptexport library:
 - can be initialised with instances of escript::Data and Finley_Mesh
 - is now MPI aware at the EscriptDataset level including Silo writer
 - now uses boost shared pointers
The lib is currently only used by the escriptconvert tool but this is going to
change...

Revision 2809 - Directory Listing
Modified Mon Dec 7 03:39:37 2009 UTC (9 years, 2 months ago) by jfenwick
Original Path: trunk

TestDomain now divides the total number of samples between ranks rather 
than putting all samples on all ranks.

Revision 2808 - Directory Listing
Modified Mon Dec 7 00:26:45 2009 UTC (9 years, 2 months ago) by artak
Original Path: trunk

default coarseneing is Ruge-Stueben.