[escript] Log of /release/3.4.2

Revision 4924 - Directory Listing
Modified Wed Apr 30 23:27:04 2014 UTC (3 years, 4 months ago) by sshaw

disabling release use of fast assemblers by default

Revision 4919 - Directory Listing
Modified Wed Apr 30 06:25:55 2014 UTC (3 years, 4 months ago) by jfenwick
Copied from: trunk revision 4918

Because we've got to!

Revision 4918 - Directory Listing
Modified Wed Apr 30 06:20:47 2014 UTC (3 years, 4 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 (3 years, 4 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 (3 years, 4 months ago) by sshaw
Original Path: trunk

updating deb changelog

Revision 4915 - Directory Listing
Modified Wed Apr 30 05:29:23 2014 UTC (3 years, 4 months ago) by jfenwick
Original Path: trunk

Fixes for macports

Revision 4914 - Directory Listing
Modified Wed Apr 30 04:58:45 2014 UTC (3 years, 4 months ago) by sshaw
Original Path: trunk

removing spare 'as'

Revision 4913 - Directory Listing
Modified Wed Apr 30 04:57:21 2014 UTC (3 years, 4 months ago) by jfenwick
Original Path: trunk

Reorder homebrew install

Revision 4912 - Directory Listing
Modified Wed Apr 30 04:57:01 2014 UTC (3 years, 4 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 (3 years, 4 months ago) by jfenwick
Original Path: trunk

fix unused var

Revision 4910 - Directory Listing
Modified Wed Apr 30 02:21:59 2014 UTC (3 years, 4 months ago) by jduplessis
Original Path: trunk

fix docstring error

Revision 4909 - Directory Listing
Modified Wed Apr 30 01:20:22 2014 UTC (3 years, 4 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 (3 years, 4 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 (3 years, 4 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 (3 years, 4 months ago) by sshaw
Original Path: trunk

restoring lost changes

Revision 4905 - Directory Listing
Modified Tue Apr 29 05:16:13 2014 UTC (3 years, 4 months ago) by sshaw
Original Path: trunk

updated install doc

Revision 4904 - Directory Listing
Modified Tue Apr 29 04:40:30 2014 UTC (3 years, 4 months ago) by jduplessis
Original Path: trunk

removing test print

Revision 4903 - Directory Listing
Modified Tue Apr 29 04:12:59 2014 UTC (3 years, 4 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 (3 years, 4 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 (3 years, 4 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 (3 years, 4 months ago) by jduplessis
Original Path: trunk

update sympy version check

Revision 4899 - Directory Listing
Modified Tue Apr 29 01:42:23 2014 UTC (3 years, 4 months ago) by jduplessis
Original Path: trunk

sympy version check

Revision 4898 - Directory Listing
Modified Tue Apr 29 01:03:58 2014 UTC (3 years, 4 months ago) by jduplessis
Original Path: trunk

sympy version check

Revision 4897 - Directory Listing
Modified Tue Apr 29 00:43:58 2014 UTC (3 years, 4 months ago) by jduplessis
Original Path: trunk

sympy version check

Revision 4896 - Directory Listing
Modified Tue Apr 29 00:35:22 2014 UTC (3 years, 4 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 (3 years, 4 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 (3 years, 4 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 (3 years, 4 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 (3 years, 4 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 (3 years, 4 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 (3 years, 4 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 (3 years, 4 months ago) by jfenwick
Original Path: trunk

Removing manual pagebreaks

Revision 4887 - Directory Listing
Modified Mon Apr 28 00:34:35 2014 UTC (3 years, 4 months ago) by jduplessis
Original Path: trunk

Minor updates

Revision 4886 - Directory Listing
Modified Sun Apr 27 13:12:23 2014 UTC (3 years, 4 months ago) by jduplessis
Original Path: trunk

rewording and checking

Revision 4885 - Directory Listing
Modified Sun Apr 27 11:48:36 2014 UTC (3 years, 4 months ago) by jduplessis
Original Path: trunk

Small changes

Revision 4884 - Directory Listing
Modified Thu Apr 24 04:47:39 2014 UTC (3 years, 4 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 (3 years, 4 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 (3 years, 4 months ago) by jduplessis
Original Path: trunk

fixing small errors

Revision 4881 - Directory Listing
Modified Wed Apr 23 14:20:28 2014 UTC (3 years, 4 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 (3 years, 4 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 (3 years, 4 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 (3 years, 4 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 months ago) by jfenwick
Original Path: trunk

Updated changelog

Revision 4874 - Directory Listing
Modified Thu Apr 17 01:13:10 2014 UTC (3 years, 5 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 (3 years, 5 months ago) by caltinay
Original Path: trunk

whitespace only changes.

Revision 4872 - Directory Listing
Modified Wed Apr 16 06:08:06 2014 UTC (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 months ago) by caltinay
Original Path: trunk

paso: starting to polish

Revision 4866 - Directory Listing
Modified Fri Apr 11 03:28:35 2014 UTC (3 years, 5 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 (3 years, 5 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 (3 years, 5 months ago) by caltinay
Original Path: trunk

fixing mkl build.

Revision 4862 - Directory Listing
Modified Thu Apr 10 05:35:56 2014 UTC (3 years, 5 months ago) by sshaw
Original Path: trunk

removing leftover debug prints

Revision 4861 - Directory Listing
Modified Thu Apr 10 05:17:47 2014 UTC (3 years, 5 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 (3 years, 5 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 (3 years, 5 months ago) by jfenwick
Original Path: trunk

Avoid division by zero

Revision 4858 - Directory Listing
Modified Wed Apr 9 23:34:17 2014 UTC (3 years, 5 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 (3 years, 5 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 (3 years, 5 months ago) by caltinay
Original Path: trunk

some mopping in paso

Revision 4855 - Directory Listing
Modified Wed Apr 9 06:19:59 2014 UTC (3 years, 5 months ago) by sshaw
Original Path: trunk

removing leftover python solveroptions

Revision 4853 - Directory Listing
Modified Wed Apr 9 05:41:57 2014 UTC (3 years, 5 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 (3 years, 5 months ago) by caltinay
Original Path: trunk

paso util sweep

Revision 4851 - Directory Listing
Modified Wed Apr 9 03:30:36 2014 UTC (3 years, 5 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 (3 years, 5 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 (3 years, 5 months ago) by caltinay
Original Path: trunk

More vacuuming.

Revision 4848 - Directory Listing
Modified Wed Apr 9 00:26:32 2014 UTC (3 years, 5 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 (3 years, 5 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 (3 years, 5 months ago) by caltinay
Original Path: trunk

paso::Options.

Revision 4845 - Directory Listing
Modified Tue Apr 8 11:35:27 2014 UTC (3 years, 5 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 (3 years, 5 months ago) by jfenwick
Original Path: trunk

Removing MPIInfo from pythonMPI

Revision 4843 - Directory Listing
Modified Tue Apr 8 05:32:07 2014 UTC (3 years, 5 months ago) by caltinay
Original Path: trunk

checkpointing paso::Preconditioner.

Revision 4842 - Directory Listing
Modified Tue Apr 8 04:50:05 2014 UTC (3 years, 5 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 (3 years, 5 months ago) by jfenwick
Original Path: trunk

keeping older compilers happy

Revision 4840 - Directory Listing
Modified Tue Apr 8 03:24:47 2014 UTC (3 years, 5 months ago) by jfenwick
Original Path: trunk

scons options for trusty

Revision 4839 - Directory Listing
Modified Tue Apr 8 03:14:23 2014 UTC (3 years, 5 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 (3 years, 5 months ago) by caltinay
Original Path: trunk

Fixing non-mpi build.

Revision 4837 - Directory Listing
Modified Mon Apr 7 05:59:24 2014 UTC (3 years, 5 months ago) by jduplessis
Original Path: trunk

added test for evalf

Revision 4836 - Directory Listing
Modified Mon Apr 7 05:51:55 2014 UTC (3 years, 5 months ago) by caltinay
Original Path: trunk

"Some" SystemMatrix clean up.....

Revision 4835 - Directory Listing
Modified Mon Apr 7 04:29:20 2014 UTC (3 years, 5 months ago) by jfenwick
Original Path: trunk

removing unused MIS

Revision 4833 - Directory Listing
Modified Sun Apr 6 23:30:34 2014 UTC (3 years, 5 months ago) by jfenwick
Original Path: trunk

Adding missing names.

Revision 4832 - Directory Listing
Modified Fri Apr 4 05:03:45 2014 UTC (3 years, 5 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 (3 years, 5 months ago) by caltinay
Original Path: trunk

fixing MKL compile.

Revision 4830 - Directory Listing
Modified Thu Apr 3 04:45:06 2014 UTC (3 years, 5 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 (3 years, 5 months ago) by caltinay
Original Path: trunk

checkpointing some SparseMatrix cleanup.

Revision 4828 - Directory Listing
Modified Wed Apr 2 07:01:38 2014 UTC (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 months ago) by jfenwick
Original Path: trunk

Addresses issue 241

Revision 4824 - Directory Listing
Modified Tue Apr 1 06:40:19 2014 UTC (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 months ago) by caltinay
Original Path: trunk

Pattern shared ptrs

Revision 4818 - Directory Listing
Modified Mon Mar 31 00:16:20 2014 UTC (3 years, 5 months ago) by caltinay
Original Path: trunk

SystemMatrixPattern shptr

Revision 4817 - Directory Listing
Modified Fri Mar 28 08:04:09 2014 UTC (3 years, 5 months ago) by caltinay
Original Path: trunk

Coupler/Connector shared ptrs.

Revision 4816 - Directory Listing
Modified Fri Mar 28 06:16:02 2014 UTC (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 5 months ago) by caltinay
Original Path: trunk

paso::SystemMatrixPattern

Revision 4799 - Directory Listing
Modified Wed Mar 26 00:37:59 2014 UTC (3 years, 5 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 (3 years, 5 months ago) by caltinay
Original Path: trunk

added missing const.

Revision 4797 - Directory Listing
Modified Mon Mar 24 05:42:42 2014 UTC (3 years, 5 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 (3 years, 5 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 (3 years, 5 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 (3 years, 6 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 (3 years, 6 months ago) by jfenwick
Original Path: trunk

make escriptcore/ visible

Revision 4791 - Directory Listing
Modified Fri Mar 21 03:32:56 2014 UTC (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 months ago) by sshaw
Original Path: trunk

fixed silly naming issue

Revision 4783 - Directory Listing
Modified Thu Mar 20 06:23:23 2014 UTC (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 months ago) by jfenwick
Original Path: trunk

Temporarily adjusting magic numbers

Revision 4778 - Directory Listing
Modified Thu Mar 20 00:41:58 2014 UTC (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 months ago) by sshaw
Original Path: trunk

removing ridiculous remaining return

Revision 4771 - Directory Listing
Modified Wed Mar 19 04:22:37 2014 UTC (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 months ago) by jduplessis
Original Path: trunk

Removed commented for loops

Revision 4767 - Directory Listing
Modified Wed Mar 19 02:48:33 2014 UTC (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 months ago) by gross
Original Path: trunk

mapping test fixed

Revision 4761 - Directory Listing
Modified Tue Mar 18 00:25:55 2014 UTC (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 months ago) by sshaw
Original Path: trunk

completed LameAssemblers

Revision 4749 - Directory Listing
Modified Fri Mar 14 03:05:07 2014 UTC (3 years, 6 months ago) by sshaw
Original Path: trunk

making inversioncostfunctions python3 compatible

Revision 4748 - Directory Listing
Modified Fri Mar 14 00:30:51 2014 UTC (3 years, 6 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 (3 years, 6 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 (3 years, 6 months ago) by gross
Original Path: trunk

mapping for FWI added

Revision 4742 - Directory Listing
Modified Wed Mar 12 07:21:24 2014 UTC (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 months ago) by jfenwick
Original Path: trunk

Fixing print statement

Revision 4714 - Directory Listing
Modified Thu Feb 27 05:04:15 2014 UTC (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 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 (3 years, 6 months ago) by jduplessis
Original Path: trunk

Removed rotation from ydirection test

Revision 4707 - Directory Listing
Modified Fri Feb 21 03:07:09 2014 UTC (3 years, 6 months ago) by jduplessis
Original Path: trunk

Modified domain in tests

Revision 4706 - Directory Listing
Modified Fri Feb 21 02:39:58 2014 UTC (3 years, 6 months ago) by jfenwick
Original Path: trunk

Some additional cleanup I missed

Revision 4705 - Directory Listing
Modified Fri Feb 21 02:36:15 2014 UTC (3 years, 6 months 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 (3 years, 6 months 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 (3 years, 6 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months ago) by gross
Original Path: trunk

data sources support tags now

Revision 4697 - Directory Listing
Modified Wed Feb 19 08:03:56 2014 UTC (3 years, 7 months ago) by gross
Original Path: trunk

data sources support tags now

Revision 4696 - Directory Listing
Modified Wed Feb 19 07:29:50 2014 UTC (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months ago) by gross
Original Path: trunk

acoustic forward problem + testing add

Revision 4687 - Directory Listing
Modified Wed Feb 19 00:03:29 2014 UTC (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months ago) by jduplessis
Original Path: trunk

adding nonlinearpde test for ripley.

Revision 4680 - Directory Listing
Modified Mon Feb 17 04:04:40 2014 UTC (3 years, 7 months ago) by jduplessis
Original Path: trunk

changed name

Revision 4679 - Directory Listing
Modified Mon Feb 17 04:02:56 2014 UTC (3 years, 7 months ago) by jduplessis
Original Path: trunk

Changed name

Revision 4678 - Directory Listing
Modified Mon Feb 17 03:35:08 2014 UTC (3 years, 7 months ago) by jduplessis
Original Path: trunk

adding ripley test for nlpde

Revision 4677 - Directory Listing
Modified Mon Feb 17 02:49:59 2014 UTC (3 years, 7 months ago) by jduplessis
Original Path: trunk

adding nlpde tests

Revision 4676 - Directory Listing
Modified Mon Feb 17 02:41:15 2014 UTC (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months ago) by jfenwick
Original Path: trunk

Ammended install doco for OSX

Revision 4672 - Directory Listing
Modified Thu Feb 13 01:10:29 2014 UTC (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months ago) by jfenwick
Original Path: trunk

I changed some files.
Updated copyright notices, added GeoComp.

Revision 4656 - Directory Listing
Modified Thu Feb 6 05:12:01 2014 UTC (3 years, 7 months ago) by gross
Original Path: trunk

removed unwanted table

Revision 4655 - Directory Listing
Modified Thu Feb 6 04:15:42 2014 UTC (3 years, 7 months ago) by jfenwick
Original Path: trunk

Reverting r4654

Revision 4654 - Directory Listing
Modified Wed Feb 5 06:55:35 2014 UTC (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months ago) by jfenwick
Original Path: trunk

Made index chars unsigned to prevent warnings

Revision 4651 - Directory Listing
Modified Wed Feb 5 05:00:34 2014 UTC (3 years, 7 months ago) by jfenwick
Original Path: trunk

Fixed missing include

Revision 4650 - Directory Listing
Modified Wed Feb 5 04:16:01 2014 UTC (3 years, 7 months 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 4649 - Directory Listing
Modified Wed Feb 5 02:09:21 2014 UTC (3 years, 7 months ago) by caltinay
Original Path: trunk

Forgot something...

Revision 4648 - Directory Listing
Modified Wed Feb 5 02:03:08 2014 UTC (3 years, 7 months ago) by caltinay
Original Path: trunk

Fix segfault reported in #57.

Revision 4647 - Directory Listing
Modified Mon Feb 3 03:29:43 2014 UTC (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months ago) by sshaw
Original Path: trunk

fixed more whitespace issues

Revision 4635 - Directory Listing
Modified Tue Jan 28 03:34:04 2014 UTC (3 years, 7 months 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 (3 years, 7 months ago) by jfenwick
Original Path: trunk

Fixes to keep clang happy

Revision 4633 - Directory Listing
Modified Tue Jan 28 01:04:17 2014 UTC (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months 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 (3 years, 7 months ago) by jduplessis
Original Path: trunk

fixing error in comment

Revision 4626 - Directory Listing
Modified Wed Jan 22 06:07:34 2014 UTC (3 years, 7 months 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 (3 years, 8 months 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 (3 years, 8 months ago) by sshaw
Original Path: trunk

removed some leftover debug prints

Revision 4623 - Directory Listing
Modified Fri Jan 17 05:53:17 2014 UTC (3 years, 8 months 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 (3 years, 8 months 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 (3 years, 8 months ago) by jfenwick
Original Path: trunk

getSampleDataRO is now const

Revision 4620 - Directory Listing
Modified Thu Jan 16 03:17:20 2014 UTC (3 years, 8 months 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 (3 years, 8 months ago) by caltinay
Original Path: trunk

updated gp py3 options.

Revision 4618 - Directory Listing
Modified Wed Jan 15 04:35:19 2014 UTC (3 years, 8 months 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 (3 years, 8 months 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 (3 years, 8 months 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 (3 years, 8 months 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 (3 years, 8 months ago) by caltinay
Original Path: trunk

Corrected a faulty test.

Revision 4613 - Directory Listing
Modified Mon Jan 13 01:09:01 2014 UTC (3 years, 8 months 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 (3 years, 8 months ago) by gross
Original Path: trunk

modifications to sonic seismic

Revision 4611 - Directory Listing
Modified Mon Dec 23 04:03:00 2013 UTC (3 years, 8 months ago) by gross
Original Path: trunk

scaling corrected

Revision 4610 - Directory Listing
Modified Mon Dec 23 00:01:23 2013 UTC (3 years, 8 months ago) by gross
Original Path: trunk

exposed createAbsorbtionLayerFunction

Revision 4609 - Directory Listing
Modified Fri Dec 20 07:56:56 2013 UTC (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 months ago) by jfenwick
Original Path: trunk

Fixed missing \

Revision 4601 - Directory Listing
Modified Tue Dec 17 23:37:08 2013 UTC (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 months ago) by gross
Original Path: trunk

unused variable fixed

Revision 4586 - Directory Listing
Modified Wed Dec 11 06:03:27 2013 UTC (3 years, 9 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 (3 years, 9 months ago) by sshaw
Original Path: trunk

uint -> unsigned int

Revision 4584 - Directory Listing
Modified Wed Dec 11 04:24:15 2013 UTC (3 years, 9 months ago) by sshaw
Original Path: trunk

more buildbot commit testing

Revision 4583 - Directory Listing
Modified Wed Dec 11 02:09:19 2013 UTC (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 months ago) by jfenwick
Original Path: trunk

Some more work on this

Revision 4572 - Directory Listing
Modified Sun Dec 8 00:54:37 2013 UTC (3 years, 9 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 (3 years, 9 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 (3 years, 9 months ago) by gross
Original Path: trunk

strain convention corrected.

Revision 4568 - Directory Listing
Modified Thu Dec 5 23:13:26 2013 UTC (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 months ago) by gross
Original Path: trunk

and another typo fixed.

Revision 4561 - Directory Listing
Modified Wed Dec 4 05:19:32 2013 UTC (3 years, 9 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 (3 years, 9 months ago) by rschaa
Original Path: trunk

Options file for ferret

Revision 4559 - Directory Listing
Modified Wed Dec 4 02:05:34 2013 UTC (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 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 (3 years, 9 months ago) by gross
Original Path: trunk

clarification on receiver array

Revision 4552 - Directory Listing
Modified Mon Dec 2 06:13:47 2013 UTC (3 years, 9 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 (3 years, 9 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 (3 years, 9 months ago) by gross
Original Path: trunk

some modifications

Revision 4549 - Directory Listing
Modified Fri Nov 29 05:24:40 2013 UTC (3 years, 9 months ago) by gross
Original Path: trunk

argument for lumping added.

Revision 4547 - Directory Listing
Modified Thu Nov 28 23:47:27 2013 UTC (3 years, 9 months ago) by jfenwick
Original Path: trunk

Added msec unit

Revision 4546 - Directory Listing
Modified Thu Nov 28 05:30:48 2013 UTC (3 years, 9 months ago) by gross
Original Path: trunk

sonic wave propagation added

Revision 4545 - Directory Listing
Modified Thu Nov 28 05:02:43 2013 UTC (3 years, 9 months ago) by gross
Original Path: trunk

wave simulator base added

Revision 4544 - Directory Listing
Modified Thu Nov 28 04:01:46 2013 UTC (3 years, 9 months ago) by gross
Original Path: trunk

wave simulator base added

Revision 4543 - Directory Listing
Modified Thu Nov 28 03:42:10 2013 UTC (3 years, 9 months ago) by gross
Original Path: trunk

missing retirn statement added

Revision 4542 - Directory Listing
Modified Thu Nov 28 01:33:22 2013 UTC (3 years, 9 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 (3 years, 9 months ago) by gross
Original Path: trunk

Ricker wavelet added

Revision 4540 - Directory Listing
Modified Thu Nov 28 01:06:10 2013 UTC (3 years, 9 months ago) by gross
Original Path: trunk

segy writer added

Revision 4539 - Directory Listing
Modified Thu Nov 28 00:38:10 2013 UTC (3 years, 9 months ago) by gross
Original Path: trunk

segy writer test added.

Revision 4538 - Directory Listing
Modified Thu Nov 28 00:37:48 2013 UTC (3 years, 9 months ago) by gross
Original Path: trunk

segy writer added

Revision 4537 - Directory Listing
Modified Mon Nov 25 06:44:46 2013 UTC (3 years, 9 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 (3 years, 10 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 (3 years, 10 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 (3 years, 10 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 (3 years, 10 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 (3 years, 10 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 (3 years, 10 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 (3 years, 11 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 (4 years ago) by jfenwick
Original Path: trunk

Single rank rectangle randoms.

Revision 4523 - Directory Listing
Modified Mon Aug 26 23:04:07 2013 UTC (4 years ago) by caltinay
Original Path: trunk

New working raijin options.

Revision 4522 - Directory Listing
Modified Mon Aug 26 22:15:26 2013 UTC (4 years 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 (4 years 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 (4 years, 1 month 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 (4 years, 1 month ago) by caltinay
Original Path: trunk

Initial raijin options file.

Revision 4518 - Directory Listing
Modified Tue Aug 13 01:49:59 2013 UTC (4 years, 1 month 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 (4 years, 1 month 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 (4 years, 1 month 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 (4 years, 1 month ago) by jfenwick
Original Path: trunk

Intel compiler mutter grumble

Revision 4514 - Directory Listing
Modified Mon Aug 5 03:28:44 2013 UTC (4 years, 1 month ago) by jfenwick
Original Path: trunk

Look at the MPI

Revision 4513 - Directory Listing
Modified Mon Aug 5 00:57:34 2013 UTC (4 years, 1 month 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 (4 years, 1 month 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 (4 years, 1 month 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 (4 years, 1 month 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 (4 years, 1 month ago) by jfenwick
Original Path: trunk

Fixed paths for utest.sh

Revision 4508 - Directory Listing
Modified Wed Jul 24 04:23:22 2013 UTC (4 years, 1 month ago) by jfenwick
Original Path: trunk

Moving to escriptcore

Revision 4506 - Directory Listing
Modified Wed Jul 24 01:28:42 2013 UTC (4 years, 1 month 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 (4 years, 1 month ago) by jfenwick
Original Path: trunk

Hopefully addresses mantis721

Revision 4504 - Directory Listing
Modified Mon Jul 22 02:04:34 2013 UTC (4 years, 2 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 (4 years, 2 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 (4 years, 2 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 (4 years, 2 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 (4 years, 2 months ago) by caltinay
Original Path: trunk

updated scons script

Revision 4499 - Directory Listing
Modified Tue Jul 16 05:42:19 2013 UTC (4 years, 2 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 (4 years, 2 months ago) by caltinay
Original Path: trunk

Another special case fix.

Revision 4497 - Directory Listing
Modified Mon Jul 15 23:32:28 2013 UTC (4 years, 2 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 (4 years, 2 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 (4 years, 2 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 (4 years, 2 months ago) by caltinay
Original Path: trunk

Suppressions for savanna runs.

Revision 4493 - Directory Listing
Modified Wed Jul 3 06:32:11 2013 UTC (4 years, 2 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 (4 years, 2 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 (4 years, 2 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 (4 years, 2 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 (4 years, 2 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 (4 years, 2 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 (4 years, 2 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 (4 years, 2 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 (4 years, 2 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 (4 years, 3 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 (4 years, 3 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 (4 years, 3 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 (4 years, 3 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 (4 years, 3 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 (4 years, 3 months ago) by caltinay
Original Path: trunk

Remove superfluous \label

Revision 4462 - Directory Listing
Modified Mon Jun 17 04:12:06 2013 UTC (4 years, 3 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 (4 years, 3 months ago) by caltinay
Original Path: trunk

small py3 fix.

Revision 4455 - Directory Listing
Modified Thu Jun 13 03:13:36 2013 UTC (4 years, 3 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 (4 years, 3 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 (4 years, 3 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 (4 years, 3 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 (4 years, 3 months ago) by jfenwick
Original Path: trunk

Finishing off this end.

Revision 4448 - Directory Listing
Modified Wed Jun 12 23:05:12 2013 UTC (4 years, 3 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 (4 years, 3 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 (4 years, 3 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 (4 years, 3 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 (4 years, 3 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 (4 years, 3 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 (4 years, 3 months ago) by caltinay
Original Path: trunk

cosmetic changes.

Revision 4441 - Directory Listing
Modified Fri Jun 7 02:23:49 2013 UTC (4 years, 3 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 (4 years, 3 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 (4 years, 3 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 (4 years, 3 months ago) by jfenwick
Original Path: trunk

Some changes to packaging

Revision 4437 - Directory Listing
Modified Tue Jun 4 05:37:18 2013 UTC (4 years, 3 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 (4 years, 3 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 (4 years, 3 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 (4 years, 3 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 (4 years, 3 months ago) by caltinay
Original Path: trunk

updated sconscript file

Revision 4431 - Directory Listing
Modified Fri May 31 07:09:03 2013 UTC (4 years, 3 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 (4 years, 3 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 (4 years, 3 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 (4 years, 3 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 (4 years, 3 months ago) by jfenwick
Original Path: trunk

Testing commit

Revision 4425 - Directory Listing
Modified Mon May 27 05:44:28 2013 UTC (4 years, 3 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 (4 years, 3 months ago) by caltinay
Original Path: trunk

SVN server test.

Revision 4422 - Directory Listing
Modified Fri May 24 04:42:29 2013 UTC (4 years, 3 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 (4 years, 4 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 (4 years, 4 months ago) by caltinay
Original Path: trunk

Enabled metis on guineapig.

Revision 4419 - Directory Listing
Modified Mon May 20 05:03:35 2013 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

Fixed a typo.

Revision 4417 - Directory Listing
Modified Mon May 20 02:15:47 2013 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

Retab regularizations.

Revision 4416 - Directory Listing
Modified Fri May 17 02:32:33 2013 UTC (4 years, 4 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 (4 years, 4 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 (4 years, 4 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 (4 years, 4 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 (4 years, 4 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 (4 years, 4 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 (4 years, 4 months ago) by caltinay
Original Path: trunk

Removed references to pyvisi which disappeared a few releases ago...

Revision 4404 - Directory Listing
Modified Sun May 12 23:25:10 2013 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

Retab forwardmodels

Revision 4400 - Directory Listing
Modified Fri May 10 04:05:00 2013 UTC (4 years, 4 months ago) by caltinay
Original Path: trunk

Uaaargh - the minimizer ate my files! Fixed reporting of iteration number in
callback.

Revision 4398 - Directory Listing
Modified Thu May 9 08:42:44 2013 UTC (4 years, 4 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 (4 years, 4 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 (4 years, 4 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 (4 years, 4 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 (4 years, 4 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 (4 years, 4 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 (4 years, 4 months ago) by caltinay
Original Path: trunk

More saveSilo checks.

Revision 4391 - Directory Listing
Modified Mon May 6 02:15:48 2013 UTC (4 years, 4 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 (4 years, 4 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 (4 years, 4 months ago) by caltinay
Original Path: trunk

retab coordinates.py

Revision 4387 - Directory Listing
Modified Thu May 2 00:46:49 2013 UTC (4 years, 4 months ago) by jfenwick
Original Path: trunk

The future is now

Revision 4386 - Directory Listing
Modified Tue Apr 30 02:58:02 2013 UTC (4 years, 4 months ago) by jfenwick
Original Path: trunk

Add missing [0]

Revision 4385 - Directory Listing
Modified Mon Apr 29 06:03:30 2013 UTC (4 years, 4 months ago) by jfenwick
Original Path: trunk

It was bugging me

Revision 4384 - Directory Listing
Modified Sat Apr 27 05:09:37 2013 UTC (4 years, 4 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 (4 years, 4 months ago) by jfenwick
Original Path: trunk

Changes to install doco

Revision 4382 - Directory Listing
Modified Thu Apr 25 04:44:14 2013 UTC (4 years, 4 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 (4 years, 4 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 (4 years, 4 months ago) by jfenwick
Original Path: trunk

Attempt to help windows

Revision 4379 - Directory Listing
Modified Wed Apr 24 20:31:19 2013 UTC (4 years, 4 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 (4 years, 4 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 (4 years, 4 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 (4 years, 5 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 (4 years, 5 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 (4 years, 5 months ago) by gross
Original Path: trunk

some typo fixed.

Revision 4373 - Directory Listing
Modified Mon Apr 22 03:16:24 2013 UTC (4 years, 5 months ago) by gross
Original Path: trunk

more on geodetic coordinates

Revision 4371 - Directory Listing
Modified Fri Apr 19 08:47:57 2013 UTC (4 years, 5 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 (4 years, 5 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 (4 years, 5 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 (4 years, 5 months ago) by jfenwick
Original Path: trunk

put back std::

Revision 4367 - Directory Listing
Modified Wed Apr 17 09:55:25 2013 UTC (4 years, 5 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 (4 years, 5 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 (4 years, 5 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 (4 years, 5 months ago) by caltinay
Original Path: trunk

Decorated some test cases.

Revision 4363 - Directory Listing
Modified Wed Apr 17 01:07:38 2013 UTC (4 years, 5 months ago) by caltinay
Original Path: trunk

retab coordinates.py.

Revision 4362 - Directory Listing
Modified Tue Apr 16 04:37:13 2013 UTC (4 years, 5 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 (4 years, 5 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 (4 years, 5 months ago) by jfenwick
Original Path: trunk

some mismatched memory ops

Revision 4359 - Directory Listing
Modified Fri Apr 12 04:54:20 2013 UTC (4 years, 5 months ago) by gross
Original Path: trunk

more on coordinate systems

Revision 4358 - Directory Listing
Modified Fri Apr 12 04:54:00 2013 UTC (4 years, 5 months ago) by gross
Original Path: trunk

more on coordinate systems

Revision 4357 - Directory Listing
Modified Thu Apr 11 06:07:14 2013 UTC (4 years, 5 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 (4 years, 5 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 (4 years, 5 months ago) by jfenwick
Original Path: trunk

start install guide overhall

Revision 4354 - Directory Listing
Modified Fri Apr 5 03:55:03 2013 UTC (4 years, 5 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 (4 years, 5 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 (4 years, 5 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 (4 years, 5 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 (4 years, 5 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 (4 years, 5 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 (4 years, 5 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 (4 years, 5 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 (4 years, 5 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 months ago) by caltinay
Original Path: trunk

Removed stray print statement.

Revision 4323 - Directory Listing
Modified Tue Mar 19 00:17:36 2013 UTC (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 months ago) by caltinay
Original Path: trunk

Added missing import.

Revision 4307 - Directory Listing
Modified Mon Mar 11 02:46:17 2013 UTC (4 years, 6 months ago) by azadeh
Original Path: trunk

shake29->weasel

Revision 4306 - Directory Listing
Modified Mon Mar 11 02:36:55 2013 UTC (4 years, 6 months ago) by caltinay
Original Path: trunk

python 3 compat.

Revision 4303 - Directory Listing
Modified Mon Mar 11 01:17:39 2013 UTC (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 months ago) by azadeh
Original Path: trunk

changing Magnetic Images

Revision 4297 - Directory Listing
Modified Fri Mar 8 06:14:17 2013 UTC (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 months ago) by caltinay
Original Path: trunk

Assorted spelling fixes.

Revision 4285 - Directory Listing
Modified Thu Mar 7 01:08:43 2013 UTC (4 years, 6 months ago) by caltinay
Original Path: trunk

Corrected some spelling.

Revision 4284 - Directory Listing
Modified Thu Mar 7 00:43:48 2013 UTC (4 years, 6 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 (4 years, 6 months ago) by caltinay
Original Path: trunk

Minor epydoc fixes.

Revision 4282 - Directory Listing
Modified Wed Mar 6 08:33:59 2013 UTC (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 months ago) by caltinay
Original Path: trunk

Some more work.

Revision 4268 - Directory Listing
Modified Mon Mar 4 00:41:08 2013 UTC (4 years, 6 months ago) by gross
Original Path: trunk

some citation fixed.

Revision 4267 - Directory Listing
Modified Fri Mar 1 04:50:54 2013 UTC (4 years, 6 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 (4 years, 6 months ago) by caltinay
Original Path: trunk

Deleted old data files.

Revision 4265 - Directory Listing
Modified Fri Mar 1 00:52:30 2013 UTC (4 years, 6 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 (4 years, 6 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 (4 years, 6 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 (4 years, 6 months ago) by azadeh
Original Path: trunk

adding gravity and magnetic data files which used for inversions

Revision 4256 - Directory Listing
Modified Wed Feb 27 03:25:05 2013 UTC (4 years, 6 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 (4 years, 6 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 (4 years, 6 months ago) by azadeh
Original Path: trunk

added joint result

Revision 4253 - Directory Listing
Modified Wed Feb 27 02:55:32 2013 UTC (4 years, 6 months ago) by azadeh
Original Path: trunk

removed joint result

Revision 4252 - Directory Listing
Modified Wed Feb 27 02:49:06 2013 UTC (4 years, 6 months ago) by azadeh
Original Path: trunk

added magnetic inversion results

Revision 4251 - Directory Listing
Modified Wed Feb 27 02:47:10 2013 UTC (4 years, 6 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 (4 years, 6 months ago) by caltinay
Original Path: trunk

Fix for joint example.

Revision 4249 - Directory Listing
Modified Tue Feb 26 01:01:59 2013 UTC (4 years, 6 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 (4 years, 6 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 (4 years, 6 months ago) by jfenwick
Original Path: trunk

still testing

Revision 4244 - Directory Listing
Modified Mon Feb 25 05:37:50 2013 UTC (4 years, 6 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 (4 years, 6 months ago) by jfenwick
Original Path: trunk

For testing buildbot

Revision 4242 - Directory Listing
Modified Mon Feb 25 03:16:14 2013 UTC (4 years, 6 months ago) by jfenwick
Original Path: trunk

Allow pure virtual classes to be exported to python.
Temporary fix for a ripley interpolation issue

Revision 4241 - Directory Listing
Modified Fri Feb 22 11:35:11 2013 UTC (4 years, 6 months ago) by jfenwick
Original Path: trunk

Added py3 config

Revision 4240 - Directory Listing
Modified Fri Feb 22 01:51:19 2013 UTC (4 years, 6 months 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 (4 years, 6 months 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 (4 years, 6 months 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 (4 years, 6 months 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 (4 years, 6 months 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 (4 years, 6 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months ago) by caltinay
Original Path: trunk

Removed some superfluous files.

Revision 4228 - Directory Listing
Modified Wed Feb 20 03:34:07 2013 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

Tweak & fix for data plotters

Revision 4227 - Directory Listing
Modified Wed Feb 20 03:10:50 2013 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

ER Mapper data source updates.

Revision 4225 - Directory Listing
Modified Wed Feb 20 02:45:09 2013 UTC (4 years, 7 months ago) by azadeh
Original Path: trunk

moving images to figures folder

Revision 4224 - Directory Listing
Modified Wed Feb 20 02:34:18 2013 UTC (4 years, 7 months ago) by azadeh
Original Path: trunk

changing images in cook gravity

Revision 4222 - Directory Listing
Modified Wed Feb 20 01:27:40 2013 UTC (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months ago) by caltinay
Original Path: trunk

Report if pyproj is available.

Revision 4215 - Directory Listing
Modified Tue Feb 19 02:52:40 2013 UTC (4 years, 7 months ago) by azadeh
Original Path: trunk

adding gravity coarse data

Revision 4214 - Directory Listing
Modified Tue Feb 19 02:42:43 2013 UTC (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months ago) by azadeh
Original Path: trunk

adding bar for gravity image

Revision 4206 - Directory Listing
Modified Sun Feb 17 23:32:07 2013 UTC (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months ago) by gross
Original Path: trunk

Clarification of file names.

Revision 4202 - Directory Listing
Modified Thu Feb 14 06:53:41 2013 UTC (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months ago) by azadeh
Original Path: trunk

Fixing some naming clashes

Revision 4192 - Directory Listing
Modified Tue Feb 12 00:28:47 2013 UTC (4 years, 7 months 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 (4 years, 7 months ago) by gross
Original Path: trunk

more on gravity cook book

Revision 4189 - Directory Listing
Modified Mon Feb 11 04:17:00 2013 UTC (4 years, 7 months ago) by gross
Original Path: trunk

some images added

Revision 4188 - Directory Listing
Modified Mon Feb 11 01:51:22 2013 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

Removed unneeded (large) result files.

Revision 4187 - Directory Listing
Modified Mon Feb 11 01:05:10 2013 UTC (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months ago) by gross
Original Path: trunk

modifications to cookbook

Revision 4184 - Directory Listing
Modified Fri Feb 8 04:33:48 2013 UTC (4 years, 7 months ago) by azadeh
Original Path: trunk

new images in cookgravity

Revision 4183 - Directory Listing
Modified Mon Feb 4 02:58:02 2013 UTC (4 years, 7 months ago) by azadeh
Original Path: trunk

joint result image updated

Revision 4182 - Directory Listing
Modified Fri Feb 1 02:29:53 2013 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

Revised Intro/Overview text.

Revision 4178 - Directory Listing
Modified Thu Jan 31 03:18:56 2013 UTC (4 years, 7 months ago) by caltinay
Original Path: trunk

Some more doco.

Revision 4177 - Directory Listing
Modified Thu Jan 31 02:23:02 2013 UTC (4 years, 7 months ago) by azadeh
Original Path: trunk

cook joint and magnetic

Revision 4176 - Directory Listing
Modified Wed Jan 30 05:30:30 2013 UTC (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months ago) by jfenwick
Original Path: trunk

Release title and dep fix

Revision 4167 - Directory Listing
Modified Fri Jan 25 05:21:30 2013 UTC (4 years, 7 months 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 (4 years, 7 months ago) by caltinay
Original Path: trunk

netcdf data source description.

Revision 4162 - Directory Listing
Modified Thu Jan 24 03:53:19 2013 UTC (4 years, 7 months 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 (4 years, 7 months ago) by caltinay
Original Path: trunk

Moved figures to subdir and added more DataSource doco.

Revision 4159 - Directory Listing
Modified Thu Jan 24 00:05:28 2013 UTC (4 years, 7 months ago) by azadeh
Original Path: trunk

dding magnetic images

Revision 4158 - Directory Listing
Modified Wed Jan 23 07:02:21 2013 UTC (4 years, 7 months 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 (4 years, 7 months 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 (4 years, 7 months ago) by azadeh
Original Path: trunk

changes in document

Revision 4155 - Directory Listing
Modified Wed Jan 23 00:05:03 2013 UTC (4 years, 7 months 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 (4 years, 7 months ago) by jfenwick
Original Path: trunk

Round 1 of copyright fixes

Revision 4153 - Directory Listing
Modified Tue Jan 22 01:57:50 2013 UTC (4 years, 7 months 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 (4 years, 7 months ago) by caltinay
Original Path: trunk

Moved figures to subdirectory.

Revision 4151 - Directory Listing
Modified Tue Jan 22 00:23:39 2013 UTC (4 years, 7 months ago) by azadeh
Original Path: trunk

update joint and magnetic cookbook.

Revision 4150 - Directory Listing
Modified Mon Jan 21 04:14:24 2013 UTC (4 years, 8 months 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 (4 years, 8 months ago) by caltinay
Original Path: trunk

Checkpoint - DomainBuilder documented.

Revision 4148 - Directory Listing
Modified Mon Jan 21 01:04:20 2013 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

Updated netcdf gravity inversion example.

Revision 4147 - Directory Listing
Modified Fri Jan 18 03:35:15 2013 UTC (4 years, 8 months 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 (4 years, 8 months 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 (4 years, 8 months 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 (4 years, 8 months 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 (4 years, 8 months 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 (4 years, 8 months ago) by caltinay
Original Path: trunk

Updated example inversion files.

Revision 4139 - Directory Listing
Modified Tue Jan 15 00:13:28 2013 UTC (4 years, 8 months 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 (4 years, 8 months ago) by gross
Original Path: trunk

some rearrangement of part II

Revision 4137 - Directory Listing
Modified Mon Jan 14 22:59:13 2013 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

Disabled another test.

Revision 4136 - Directory Listing
Modified Mon Jan 14 05:20:34 2013 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

clarifications about cartesian domain

Revision 4135 - Directory Listing
Modified Mon Jan 14 04:54:14 2013 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

Fixed test file.

Revision 4134 - Directory Listing
Modified Sun Jan 13 23:24:35 2013 UTC (4 years, 8 months ago) by caltinay
Original Path: trunk

Removed failing test.

Revision 4133 - Directory Listing
Modified Fri Jan 11 06:41:10 2013 UTC (4 years, 8 months 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 (4 years, 8 months ago) by caltinay
Original Path: trunk

Range of epydoc fixes.

Revision 4131 - Directory Listing
Modified Fri Jan 11 03:54:16 2013 UTC (4 years, 8 months 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 (4 years, 8 months 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 (4 years, 8 months ago) by caltinay
Original Path: trunk

Fixed small typo

Revision 4128 - Directory Listing
Modified Thu Jan 10 02:04:08 2013 UTC (4 years, 8 months 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 (4 years, 8 months ago) by azadeh
Original Path: trunk

add documentation for gravity.

Revision 4126 - Directory Listing
Modified Tue Jan 8 02:37:48 2013 UTC (4 years, 8 months 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 (4 years, 8 months 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 (4 years, 9 months ago) by gross
Original Path: trunk

joint inversion added

Revision 4122 - Directory Listing
Modified Thu Dec 20 05:42:35 2012 UTC (4 years, 9 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 (4 years, 9 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 (4 years, 9 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 (4 years, 9 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 (4 years, 9 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 (4 years, 9 months ago) by gross
Original Path: trunk

some adjustments with names

Revision 4116 - Directory Listing
Modified Fri Dec 14 07:21:14 2012 UTC (4 years, 9 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 (4 years, 9 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 (4 years, 9 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 (4 years, 9 months ago) by caltinay
Original Path: trunk

shake29 options file.

Revision 4112 - Directory Listing
Modified Fri Dec 14 01:51:30 2012 UTC (4 years, 9 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 (4 years, 9 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 (4 years, 9 months ago) by jfenwick
Original Path: trunk

Fixed to use whatever python is leading the path.
Disabled epydoc

Revision 4108 - Directory Listing
Modified Thu Dec 13 06:38:11 2012 UTC (4 years, 9 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 (4 years, 9 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 (4 years, 9 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 (4 years, 9 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 (4 years, 9 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 (4 years, 9 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 (4 years, 9 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 (4 years, 9 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 (4 years, 9 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 (4 years, 9 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 (4 years, 9 months ago) by caltinay
Original Path: trunk

Unbroke my breakage.

Revision 4096 - Directory Listing
Modified Thu Dec 6 04:05:29 2012 UTC (4 years, 9 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 (4 years, 9 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 (4 years, 9 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 (4 years, 9 months ago) by caltinay
Original Path: trunk

Minor change. Test commit.

Revision 4091 - Directory Listing
Modified Mon Nov 26 10:27:29 2012 UTC (4 years, 9 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 (4 years, 9 months ago) by caltinay
Original Path: trunk

Savanna tweaks.

Revision 4089 - Directory Listing
Modified Fri Nov 23 04:41:54 2012 UTC (4 years, 9 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 (4 years, 9 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 (4 years, 9 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 months ago) by jfenwick
Original Path: trunk

Adding some linebreaks

Revision 4083 - Directory Listing
Modified Mon Nov 19 22:19:42 2012 UTC (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 months ago) by jfenwick
Original Path: trunk

Epydoc fixes

Revision 4079 - Directory Listing
Modified Fri Nov 16 07:59:01 2012 UTC (4 years, 10 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 (4 years, 10 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 (4 years, 10 months ago) by caltinay
Original Path: trunk

Minor change.

Revision 4076 - Directory Listing
Modified Thu Nov 15 03:45:24 2012 UTC (4 years, 10 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 (4 years, 10 months ago) by gross
Original Path: trunk

missing latex files

Revision 4074 - Directory Listing
Modified Thu Nov 15 03:30:59 2012 UTC (4 years, 10 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 (4 years, 10 months ago) by jfenwick
Original Path: trunk

Fixing doco build error

Revision 4072 - Directory Listing
Modified Thu Nov 15 01:58:35 2012 UTC (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 months ago) by vboros
Original Path: trunk

Magnetostatics background added

Revision 4066 - Directory Listing
Modified Mon Nov 12 06:18:47 2012 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

renaming wheezyoptions file

Revision 4065 - Directory Listing
Modified Mon Nov 12 04:47:32 2012 UTC (4 years, 10 months ago) by jfenwick
Original Path: trunk

Trying without uml

Revision 4063 - Directory Listing
Modified Fri Nov 9 06:15:00 2012 UTC (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 months ago) by gross
Original Path: trunk

Renaming of filenames

Revision 4054 - Directory Listing
Modified Wed Oct 31 23:27:57 2012 UTC (4 years, 10 months ago) by gross
Original Path: trunk

prilimary checkin

Revision 4053 - Directory Listing
Modified Wed Oct 31 07:27:35 2012 UTC (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 months ago) by caltinay
Original Path: trunk

Fixed typos.

Revision 4048 - Directory Listing
Modified Tue Oct 30 21:54:15 2012 UTC (4 years, 10 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 (4 years, 10 months ago) by gross
Original Path: trunk

More on magnetic inversion

Revision 4046 - Directory Listing
Modified Tue Oct 30 04:43:25 2012 UTC (4 years, 10 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 (4 years, 10 months ago) by caltinay
Original Path: trunk

Imported inversion cookbook.

Revision 4044 - Directory Listing
Modified Tue Oct 30 03:35:17 2012 UTC (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 months ago) by caltinay
Original Path: trunk

Fixed a typo

Revision 4040 - Directory Listing
Modified Sun Oct 28 22:37:45 2012 UTC (4 years, 10 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 (4 years, 10 months ago) by gross
Original Path: trunk

magnetic inversion added

Revision 4038 - Directory Listing
Modified Fri Oct 26 04:47:25 2012 UTC (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 months ago) by gross
Original Path: trunk

some typos fixed.

Revision 4032 - Directory Listing
Modified Wed Oct 24 08:06:15 2012 UTC (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 10 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 months ago) by caltinay
Original Path: trunk

Updated test reference file.

Revision 4010 - Directory Listing
Modified Tue Oct 2 06:57:11 2012 UTC (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 months ago) by caltinay
Original Path: trunk

Removed obsolete files.

Revision 4000 - Directory Listing
Modified Thu Sep 27 01:32:07 2012 UTC (4 years, 11 months ago) by caltinay
Original Path: trunk

s/escript/escore/

Revision 3999 - Directory Listing
Modified Thu Sep 27 01:31:07 2012 UTC (4 years, 11 months ago) by jfenwick
Original Path: trunk

Splitting tests

Revision 3998 - Directory Listing
Modified Thu Sep 27 01:17:28 2012 UTC (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 months ago) by jfenwick
Original Path: trunk

More module fiddles

Revision 3994 - Directory Listing
Modified Wed Sep 26 07:38:38 2012 UTC (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (4 years, 11 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 (5 years 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 (5 years 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 (5 years ago) by caltinay
Original Path: trunk

Use ReducedFunction for data sources.

Revision 3982 - Directory Listing
Modified Fri Sep 21 03:23:22 2012 UTC (5 years 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 (5 years 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 (5 years ago) by caltinay
Original Path: trunk

Now using NullCellValue to initialise data object for ERS reader.

Revision 3978 - Directory Listing
Modified Thu Sep 20 04:36:17 2012 UTC (5 years 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 (5 years ago) by caltinay
Original Path: trunk

Export KMP_MONITOR_STACKSIZE so tests work on savanna.

Revision 3975 - Directory Listing
Modified Thu Sep 20 01:54:06 2012 UTC (5 years 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 (5 years 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 (5 years 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 3969 - Directory Listing
Modified Tue Sep 18 05:34:38 2012 UTC (5 years ago) by jfenwick
Original Path: trunk

Removing reference to nose

Revision 3968 - Directory Listing
Modified Mon Sep 17 06:30:02 2012 UTC (5 years 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 (5 years 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 (5 years 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 (5 years 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 (5 years 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 (5 years 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 (5 years 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 (5 years 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 (5 years 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 (5 years 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 (5 years 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 (5 years 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 (5 years 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 (5 years 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 (5 years 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 (5 years ago) by caltinay
Original Path: trunk

Some test output adjustments.

Revision 3952 - Directory Listing
Modified Sun Sep 2 23:42:25 2012 UTC (5 years 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 (5 years 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 (5 years 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 (5 years ago) by caltinay
Original Path: trunk

Added tests for mappings.

Revision 3948 - Directory Listing
Modified Fri Aug 24 01:01:34 2012 UTC (5 years 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 (5 years 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 (5 years, 1 month 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 (5 years, 1 month ago) by jfenwick
Original Path: trunk

Changing utest behaviour for MPI

Revision 3944 - Directory Listing
Modified Mon Aug 20 02:11:22 2012 UTC (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month 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 (5 years, 1 month ago) by jfenwick
Original Path: trunk

Some more test disabling

Revision 3940 - Directory Listing
Modified Thu Jul 26 05:54:58 2012 UTC (5 years, 1 month 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 months ago) by jfenwick
Original Path: trunk

Fixing spelling

Revision 3928 - Directory Listing
Modified Mon Jul 9 23:23:43 2012 UTC (5 years, 2 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 3923 - Directory Listing
Modified Mon Jul 9 05:12:12 2012 UTC (5 years, 2 months ago) by jfenwick
Original Path: trunk

Fixing build error.

Revision 3922 - Directory Listing
Modified Mon Jul 9 02:19:51 2012 UTC (5 years, 2 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 (5 years, 2 months ago) by jfenwick
Original Path: trunk

Fix build error

Revision 3920 - Directory Listing
Modified Thu Jul 5 03:42:30 2012 UTC (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 2 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 (5 years, 3 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 (5 years, 3 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 (5 years, 3 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 (5 years, 3 months ago) by jfenwick
Original Path: trunk

Copyright changes

Revision 3910 - Directory Listing
Modified Thu Jun 14 00:45:03 2012 UTC (5 years, 3 months ago) by gross
Original Path: trunk

Small bug fixed.

Revision 3909 - Directory Listing
Modified Wed Jun 13 07:03:06 2012 UTC (5 years, 3 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 (5 years, 3 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 (5 years, 3 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 (5 years, 3 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 (5 years, 3 months ago) by gross
Original Path: trunk

length scale changed

Revision 3904 - Directory Listing
Modified Tue Jun 5 08:30:24 2012 UTC (5 years, 3 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 (5 years, 3 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 (5 years, 3 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 (5 years, 4 months ago) by jfenwick
Original Path: trunk

correcting example

Revision 3896 - Directory Listing
Modified Fri May 11 01:31:29 2012 UTC (5 years, 4 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 (5 years, 5 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 (5 years, 5 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 (5 years, 5 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 (5 years, 5 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 (5 years, 5 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 (5 years, 5 months ago) by gross
Original Path: trunk

some minor problems with MPI AMG fixed.

Revision 3883 - Directory Listing
Modified Mon Mar 26 03:24:14 2012 UTC (5 years, 5 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 (5 years, 6 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 (5 years, 6 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 (5 years, 6 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 (5 years, 6 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 (5 years, 6 months ago) by gross
Original Path: trunk

some debug prints removed

Revision 3861 - Directory Listing
Modified Fri Mar 9 02:06:29 2012 UTC (5 years, 6 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 (5 years, 6 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 (5 years, 6 months ago) by jfenwick
Original Path: trunk

Correcting some indent errors

Revision 3851 - Directory Listing
Modified Wed Feb 29 05:23:30 2012 UTC (5 years, 6 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 (5 years, 6 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 (5 years, 6 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 (5 years, 6 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 (5 years, 6 months ago) by caltinay
Original Path: trunk

Added support for OFFSET1 matrices in ripley.

Revision 3837 - Directory Listing
Modified Thu Feb 16 03:58:58 2012 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

Test cleanup.

Revision 3836 - Directory Listing
Modified Thu Feb 16 03:17:18 2012 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

Transport problem support for ripley.

Revision 3835 - Directory Listing
Modified Wed Feb 15 23:19:01 2012 UTC (5 years, 7 months 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 (5 years, 7 months ago) by gross
Original Path: trunk

some declaration problems fixed

Revision 3833 - Directory Listing
Modified Wed Feb 15 06:19:45 2012 UTC (5 years, 7 months 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 (5 years, 7 months ago) by lgao
Original Path: trunk

Add comments for Smoother

Revision 3829 - Directory Listing
Modified Wed Feb 15 03:33:08 2012 UTC (5 years, 7 months ago) by lgao
Original Path: trunk

Fix warnings from another machine.

Revision 3828 - Directory Listing
Modified Wed Feb 15 03:27:58 2012 UTC (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months ago) by gross
Original Path: trunk

LINEAR_CRANK_NICOLSON solver added

Revision 3806 - Directory Listing
Modified Mon Feb 6 02:32:48 2012 UTC (5 years, 7 months ago) by caltinay
Original Path: trunk

ripley::getSize() also returns circumcircle now.

Revision 3805 - Directory Listing
Modified Mon Feb 6 01:42:20 2012 UTC (5 years, 7 months ago) by gross
Original Path: trunk

return circumcircle  now.

Revision 3804 - Directory Listing
Modified Mon Feb 6 00:48:22 2012 UTC (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months ago) by gross
Original Path: trunk

typo in grad calculation fixed.

Revision 3795 - Directory Listing
Modified Thu Feb 2 05:54:34 2012 UTC (5 years, 7 months 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 (5 years, 7 months ago) by gross
Original Path: trunk

uninitialied variable fixed.

Revision 3793 - Directory Listing
Modified Wed Feb 1 07:39:43 2012 UTC (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months 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 (5 years, 7 months ago) by caltinay
Original Path: trunk

Another attempt to fix #649

Revision 3778 - Directory Listing
Modified Fri Jan 20 05:09:52 2012 UTC (5 years, 8 months ago) by gross
Original Path: trunk

better error reporting from UMFPACK

Revision 3775 - Directory Listing
Modified Wed Jan 18 07:26:34 2012 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

Weipa updated

Revision 3774 - Directory Listing
Modified Wed Jan 18 06:29:34 2012 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

dudley, pasowrap, pycad

Revision 3772 - Directory Listing
Modified Wed Jan 18 04:19:33 2012 UTC (5 years, 8 months ago) by jfenwick
Original Path: trunk

Converting finley directories

Revision 3771 - Directory Listing
Modified Wed Jan 18 02:30:48 2012 UTC (5 years, 8 months 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 (5 years, 9 months ago) by gross
Original Path: trunk

inconsistent notation fixed.

Revision 3739 - Directory Listing
Modified Tue Dec 13 00:48:26 2011 UTC (5 years, 9 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 (5 years, 9 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 (5 years, 9 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 (5 years, 9 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 (5 years, 9 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 (5 years, 9 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 (5 years, 9 months ago) by jfenwick
Original Path: trunk

More broken linkage

Revision 3726 - Directory Listing
Modified Thu Dec 8 04:35:52 2011 UTC (5 years, 9 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 (5 years, 9 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 (5 years, 9 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 (5 years, 9 months ago) by gross
Original Path: trunk

integration nodes fixed

Revision 3681 - Directory Listing
Modified Fri Nov 18 04:54:15 2011 UTC (5 years, 10 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 (5 years, 10 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 (5 years, 10 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 (5 years, 10 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 (5 years, 10 months ago) by jfenwick
Original Path: trunk

pasowrap joins the trunk.

Revision 3667 - Directory Listing
Modified Tue Nov 15 23:29:23 2011 UTC (5 years, 10 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 (5 years, 10 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 (5 years, 10 months ago) by gross
Original Path: trunk

ode solver added

Revision 3649 - Directory Listing
Modified Fri Nov 4 04:35:15 2011 UTC (5 years, 10 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 (5 years, 10 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 (5 years, 10 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 (5 years, 10 months ago) by caltinay
Original Path: trunk

Fixed typos.

Revision 3644 - Directory Listing
Modified Thu Oct 27 06:42:56 2011 UTC (5 years, 10 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 (5 years, 10 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 (5 years, 10 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 (5 years, 10 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 (5 years, 10 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 (5 years, 11 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 (5 years, 11 months ago) by caltinay
Original Path: trunk

Fixed minor issues.

Revision 3630 - Directory Listing
Modified Wed Oct 19 03:04:53 2011 UTC (5 years, 11 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 (5 years, 11 months ago) by gross
Original Path: trunk

darcy example added

Revision 3628 - Directory Listing
Modified Wed Oct 19 02:09:36 2011 UTC (5 years, 11 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 (5 years, 11 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 (5 years, 11 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 (5 years, 11 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 (5 years, 11 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 (5 years, 11 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 (5 years, 11 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 (5 years, 11 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 (5 years, 11 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 (5 years, 11 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 (6 years ago) by caltinay
Original Path: trunk

Fixed double/float warning.

Revision 3606 - Directory Listing
Modified Mon Sep 19 16:26:51 2011 UTC (6 years 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 (6 years 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 (6 years 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 (6 years 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 (6 years ago) by caltinay
Original Path: trunk

Fix scons checks on windows

Revision 3601 - Directory Listing
Modified Mon Sep 19 01:21:33 2011 UTC (6 years 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 (6 years 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 (6 years 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 (6 years 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 (6 years 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 (6 years ago) by caltinay
Original Path: trunk

Deleted some obsolete options files.

Revision 3595 - Directory Listing
Modified Thu Sep 15 05:56:47 2011 UTC (6 years 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 (6 years 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 (6 years 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 (6 years 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 (6 years 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 (6 years ago) by jfenwick
Original Path: trunk

Removing Locator.setValue for now

Revision 3583 - Directory Listing
Modified Tue Sep 6 04:27:59 2011 UTC (6 years ago) by caltinay
Original Path: trunk

Updated shake75 options file.

Revision 3582 - Directory Listing
Modified Tue Sep 6 02:02:17 2011 UTC (6 years 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 (6 years 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 (6 years 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 (6 years 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 (6 years 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 (6 years ago) by gross
Original Path: trunk

getFLux fixed and tests added.

Revision 3576 - Directory Listing
Modified Mon Sep 5 06:33:20 2011 UTC (6 years 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 (6 years 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 (6 years 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 (6 years 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 (6 years 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 (6 years 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 (6 years 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 (6 years 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 (6 years ago) by gross
Original Path: trunk

darcy flux documentation updated.

Revision 3565 - Directory Listing
Modified Mon Aug 29 10:28:57 2011 UTC (6 years 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 (6 years 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 (6 years 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 (6 years 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 (6 years ago) by jfenwick
Original Path: trunk

Attempt to fix windows problem

Revision 3560 - Directory Listing
Modified Mon Aug 29 01:10:42 2011 UTC (6 years ago) by gross
Original Path: trunk

lf missing in buildvars print

Revision 3559 - Directory Listing
Modified Fri Aug 26 07:47:27 2011 UTC (6 years 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 (6 years 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 (6 years, 1 month ago) by jfenwick
Original Path: trunk

Fixed icc problem

Revision 3551 - Directory Listing
Modified Fri Aug 19 03:53:41 2011 UTC (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month ago) by jfenwick
Original Path: trunk

Fixing badger options

Revision 3547 - Directory Listing
Modified Tue Aug 2 04:24:09 2011 UTC (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 1 month 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 (6 years, 2 months ago) by gross
Original Path: trunk

and the generator script

Revision 3542 - Directory Listing
Modified Fri Jul 22 06:57:41 2011 UTC (6 years, 2 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 (6 years, 2 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 (6 years, 2 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 (6 years, 3 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 (6 years, 3 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 (6 years, 4 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 (6 years, 4 months ago) by gross
Original Path: trunk

and more typos fixed.

Revision 3523 - Directory Listing
Modified Tue May 24 02:03:37 2011 UTC (6 years, 4 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 (6 years, 4 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 (6 years, 4 months ago) by gross
Original Path: trunk

some fixes for to point interpolation

Revision 3515 - Directory Listing
Modified Thu May 19 08:20:57 2011 UTC (6 years, 4 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 (6 years, 4 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 (6 years, 4 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 (6 years, 4 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 (6 years, 4 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 (6 years, 4 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 (6 years, 4 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 (6 years, 4 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 (6 years, 4 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 (6 years, 4 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 (6 years, 5 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 (6 years, 5 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 (6 years, 5 months ago) by gross
Original Path: trunk

more coal seam gas

Revision 3490 - Directory Listing
Modified Wed Mar 30 02:24:33 2011 UTC (6 years, 5 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 (6 years, 5 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 (6 years, 5 months ago) by gross
Original Path: trunk

some compile fixes

Revision 3486 - Directory Listing
Modified Sun Mar 27 22:27:45 2011 UTC (6 years, 5 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 (6 years, 5 months ago) by gross
Original Path: trunk

some compile fixes

Revision 3484 - Directory Listing
Modified Thu Mar 24 05:42:07 2011 UTC (6 years, 6 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 (6 years, 6 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 (6 years, 6 months ago) by gross
Original Path: trunk

some work on AMG MPI

Revision 3475 - Directory Listing
Modified Thu Mar 17 00:28:08 2011 UTC (6 years, 6 months ago) by caltinay
Original Path: trunk

Removed an obsolete file.

Revision 3470 - Directory Listing
Modified Mon Mar 14 03:50:49 2011 UTC (6 years, 6 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 (6 years, 6 months ago) by jfenwick
Original Path: trunk

Fix docstring in dudley

Revision 3468 - Directory Listing
Modified Tue Feb 22 06:38:57 2011 UTC (6 years, 6 months 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 (6 years, 7 months 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 (6 years, 7 months 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 (6 years, 7 months 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 (6 years, 7 months 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 (6 years, 7 months 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 3462 - Directory Listing
Modified Mon Feb 7 02:01:50 2011 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

Removed debug output.

Revision 3461 - Directory Listing
Modified Sun Feb 6 23:33:37 2011 UTC (6 years, 7 months 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 (6 years, 7 months ago) by jfenwick
Original Path: trunk

Re-enabling MPI on savanna

Revision 3459 - Directory Listing
Modified Wed Feb 2 01:54:45 2011 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

Patch from Terry to fix compilation on Windows with MKL enabled.

Revision 3458 - Directory Listing
Modified Mon Jan 31 07:06:42 2011 UTC (6 years, 7 months ago) by gross
Original Path: trunk

more on AMG under MPI

Revision 3457 - Directory Listing
Modified Thu Jan 27 01:38:17 2011 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

Added missing cookbook figures from Anthony.

Revision 3455 - Directory Listing
Modified Tue Jan 25 04:23:17 2011 UTC (6 years, 7 months ago) by gross
Original Path: trunk

some compilation fixes

Revision 3454 - Directory Listing
Modified Tue Jan 25 04:00:29 2011 UTC (6 years, 7 months ago) by caltinay
Original Path: trunk

Fixed some minor doxygen issues.

Revision 3453 - Directory Listing
Modified Tue Jan 25 03:59:30 2011 UTC (6 years, 7 months 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 (6 years, 7 months 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 (6 years, 7 months ago) by gross
Original Path: trunk

compilation fixes

Revision 3450 - Directory Listing
Modified Fri Jan 21 06:39:56 2011 UTC (6 years, 8 months ago) by gross
Original Path: trunk

more compilation fixing

Revision 3449 - Directory Listing
Modified Fri Jan 21 05:48:15 2011 UTC (6 years, 8 months ago) by gross
Original Path: trunk

compile problem in AMG fixed.

Revision 3448 - Directory Listing
Modified Fri Jan 21 04:38:54 2011 UTC (6 years, 8 months 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 (6 years, 8 months 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 (6 years, 8 months 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 (6 years, 8 months ago) by gross
Original Path: trunk

more work towards MPI AMG

Revision 3444 - Directory Listing
Modified Tue Jan 18 23:17:27 2011 UTC (6 years, 8 months 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 (6 years, 8 months 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 (6 years, 8 months 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 (6 years, 8 months ago) by gross
Original Path: trunk

a second AMG interpolation implemented

Revision 3439 - Directory Listing
Modified Fri Jan 14 00:04:01 2011 UTC (6 years, 8 months 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 (6 years, 8 months ago) by gross
Original Path: trunk

mesh size reduced

Revision 3437 - Directory Listing
Modified Mon Jan 10 05:05:15 2011 UTC (6 years, 8 months 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 (6 years, 8 months 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 (6 years, 8 months ago) by gross
Original Path: trunk

initial value changed

Revision 3434 - Directory Listing
Modified Fri Jan 7 03:35:58 2011 UTC (6 years, 8 months ago) by gross
Original Path: trunk

initial value changed

Revision 3433 - Directory Listing
Modified Fri Jan 7 02:39:05 2011 UTC (6 years, 8 months ago) by gross
Original Path: trunk

initial value changed

Revision 3432 - Directory Listing
Modified Fri Jan 7 01:32:07 2011 UTC (6 years, 8 months 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 (6 years, 8 months ago) by gross
Original Path: trunk

redundant setMinCoarseMatrixSparsity removed.

Revision 3430 - Directory Listing
Modified Thu Jan 6 09:09:19 2011 UTC (6 years, 8 months ago) by gross
Original Path: trunk

import order is critical

Revision 3429 - Directory Listing
Modified Thu Jan 6 07:40:01 2011 UTC (6 years, 8 months ago) by gross
Original Path: trunk

SAMESIGN macro added

Revision 3428 - Directory Listing
Modified Thu Jan 6 01:12:36 2011 UTC (6 years, 8 months 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 (6 years, 8 months ago) by ahallam
Original Path: trunk

Missing script.

Revision 3426 - Directory Listing
Modified Wed Jan 5 02:51:35 2011 UTC (6 years, 8 months ago) by ahallam
Original Path: trunk

Added new example tests.

Revision 3425 - Directory Listing
Modified Wed Jan 5 02:50:38 2011 UTC (6 years, 8 months ago) by ahallam
Original Path: trunk

Added new example tests.

Revision 3424 - Directory Listing
Modified Wed Jan 5 00:24:46 2011 UTC (6 years, 8 months 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 (6 years, 9 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 (6 years, 9 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 (6 years, 9 months ago) by artak
Original Path: trunk

semi-colon is missing

Revision 3417 - Directory Listing
Modified Sun Dec 12 23:40:27 2010 UTC (6 years, 9 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 (6 years, 9 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 (6 years, 9 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 (6 years, 9 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 (6 years, 9 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 (6 years, 9 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 3402 - Directory Listing
Modified Tue Dec 7 07:36:12 2010 UTC (6 years, 9 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 (6 years, 9 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 (6 years, 9 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 (6 years, 9 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 (6 years, 9 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 (6 years, 9 months ago) by gross
Original Path: trunk

wrong pointer handed

Revision 3394 - Directory Listing
Modified Fri Dec 3 06:07:08 2010 UTC (6 years, 9 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 (6 years, 9 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 (6 years, 9 months ago) by ahallam
Original Path: trunk

Updates to cookbook. Includes new section on variable meshing. To be reviewed.

Revision 3390 - Directory Listing
Modified Thu Dec 2 00:34:37 2010 UTC (6 years, 9 months ago) by jfenwick
Original Path: trunk

RandomData added

Revision 3389 - Directory Listing
Modified Wed Dec 1 23:03:35 2010 UTC (6 years, 9 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 (6 years, 9 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 (6 years, 9 months ago) by caltinay
Original Path: trunk

Fixed some annoying typos.

Revision 3386 - Directory Listing
Modified Thu Nov 25 05:05:50 2010 UTC (6 years, 9 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 (6 years, 9 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 (6 years, 9 months ago) by ahallam
Original Path: trunk

Cookbook lumping updates.

Revision 3383 - Directory Listing
Modified Thu Nov 25 02:17:51 2010 UTC (6 years, 9 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 (6 years, 9 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 (6 years, 9 months ago) by ahallam
Original Path: trunk

Proofing of lumping.tex

Revision 3380 - Directory Listing
Modified Wed Nov 24 05:03:25 2010 UTC (6 years, 9 months ago) by gross
Original Path: trunk

update to change list

Revision 3379 - Directory Listing
Modified Wed Nov 24 04:48:49 2010 UTC (6 years, 9 months ago) by gross
Original Path: trunk

some clarification on lumping

Revision 3378 - Directory Listing
Modified Tue Nov 23 05:09:25 2010 UTC (6 years, 9 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 (6 years, 9 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 (6 years, 9 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 (6 years, 9 months ago) by jfenwick
Original Path: trunk

Fix to unit tests

Revision 3374 - Directory Listing
Modified Tue Nov 23 00:30:20 2010 UTC (6 years, 9 months ago) by ahallam
Original Path: trunk

Fixes to example scripts.

Revision 3372 - Directory Listing
Modified Mon Nov 22 23:10:03 2010 UTC (6 years, 9 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 (6 years, 10 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 (6 years, 10 months ago) by ahallam
Original Path: trunk

Rearranged figures for release.

Revision 3369 - Directory Listing
Modified Fri Nov 19 06:26:11 2010 UTC (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 months ago) by caltinay
Original Path: trunk

Fixed compilation without VisIt.

Revision 3364 - Directory Listing
Modified Thu Nov 18 05:51:44 2010 UTC (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 months ago) by caltinay
Original Path: trunk

Minor enhancement.

Revision 3360 - Directory Listing
Modified Thu Nov 18 00:20:21 2010 UTC (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 months ago) by gross
Original Path: trunk

exposure of AMG options

Revision 3351 - Directory Listing
Modified Tue Nov 16 02:39:40 2010 UTC (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 months ago) by caltinay
Original Path: trunk

Renamed MS options file.

Revision 3340 - Directory Listing
Modified Mon Nov 8 01:25:58 2010 UTC (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 months ago) by jfenwick
Original Path: trunk

Fixed bib entry

Revision 3335 - Directory Listing
Modified Wed Nov 3 05:02:57 2010 UTC (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 months ago) by caltinay
Original Path: trunk

Faultsystems2d. not finished yet.

Revision 3328 - Directory Listing
Modified Fri Oct 29 02:21:42 2010 UTC (6 years, 10 months ago) by caltinay
Original Path: trunk

Fixed script filename

Revision 3327 - Directory Listing
Modified Fri Oct 29 02:08:37 2010 UTC (6 years, 10 months ago) by gross
Original Path: trunk

missing omp function added.

Revision 3326 - Directory Listing
Modified Fri Oct 29 00:45:32 2010 UTC (6 years, 10 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 (6 years, 10 months ago) by caltinay
Original Path: trunk

Section 6.1.

Revision 3324 - Directory Listing
Modified Thu Oct 28 23:43:09 2010 UTC (6 years, 10 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 (6 years, 10 months ago) by gross
Original Path: trunk

some openmp fizes.

Revision 3322 - Directory Listing
Modified Thu Oct 28 05:26:37 2010 UTC (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 months ago) by gross
Original Path: trunk

output removed/leaned up

Revision 3313 - Directory Listing
Modified Tue Oct 26 22:00:09 2010 UTC (6 years, 10 months ago) by gross
Original Path: trunk

some print statements removed

Revision 3312 - Directory Listing
Modified Tue Oct 26 07:54:58 2010 UTC (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 months ago) by caltinay
Original Path: trunk

Commented declaremodule and modulesynopsis.

Revision 3305 - Directory Listing
Modified Mon Oct 25 05:04:22 2010 UTC (6 years, 10 months ago) by jfenwick
Original Path: trunk

Fancy shuffling

Revision 3304 - Directory Listing
Modified Mon Oct 25 04:43:48 2010 UTC (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 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 (6 years, 10 months ago) by jfenwick
Original Path: trunk

Some text fixes

Revision 3296 - Directory Listing
Modified Fri Oct 22 02:53:24 2010 UTC (6 years, 11 months ago) by caltinay
Original Path: trunk

hackscore removal.

Revision 3293 - Directory Listing
Modified Thu Oct 21 23:18:32 2010 UTC (6 years, 11 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 (6 years, 11 months ago) by jfenwick
Original Path: trunk

Adding the class file

Revision 3291 - Directory Listing
Modified Thu Oct 21 00:37:42 2010 UTC (6 years, 11 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 (6 years, 11 months ago) by gross
Original Path: trunk

missing factor fixed.

Revision 3288 - Directory Listing
Modified Tue Oct 19 01:08:31 2010 UTC (6 years, 11 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 (6 years, 11 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 (6 years, 11 months ago) by gross
Original Path: trunk

small memory leak fixed.

Revision 3285 - Directory Listing
Modified Tue Oct 19 00:28:00 2010 UTC (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 months ago) by gross
Original Path: trunk

new damage solver

Revision 3275 - Directory Listing
Modified Thu Oct 14 06:15:27 2010 UTC (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 months ago) by gross
Original Path: trunk

header file include added

Revision 3261 - Directory Listing
Modified Mon Oct 11 04:25:42 2010 UTC (6 years, 11 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 (6 years, 11 months ago) by jfenwick
Original Path: trunk

Removing dead files

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

Fixed build error

Revision 3232 - Directory Listing
Modified Fri Oct 1 02:08:38 2010 UTC (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 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 (6 years, 11 months ago) by gross
Original Path: trunk

bug in meanValue fixed.

Revision 3195 - Directory Listing
Modified Wed Sep 22 00:28:04 2010 UTC (7 years ago) by ahallam
Original Path: trunk

Shortened runtime of cookbook examples to aid testing.

Revision 3192 - Directory Listing
Modified Fri Sep 17 04:02:57 2010 UTC (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years ago) by caltinay
Original Path: trunk

Corrected check for python version in launcher, added a function get_buildvar
for convenience.

Revision 3176 - Directory Listing
Modified Sat Sep 11 01:09:54 2010 UTC (7 years ago) by caltinay
Original Path: trunk

Maybe this will finally make the Mac happy.

Revision 3174 - Directory Listing
Modified Fri Sep 10 03:55:18 2010 UTC (7 years ago) by caltinay
Original Path: trunk

Enabled debian's lapack on shake75.

Revision 3167 - Directory Listing
Modified Wed Sep 8 03:24:29 2010 UTC (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years ago) by caltinay
Original Path: trunk

More weipa tests including saveVTK.

Revision 3150 - Directory Listing
Modified Fri Sep 3 05:40:27 2010 UTC (7 years 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 (7 years 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 (7 years 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 (7 years ago) by caltinay
Original Path: trunk

Properly initialise data centering variable.

Revision 3143 - Directory Listing
Modified Fri Sep 3 00:31:55 2010 UTC (7 years 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 3140 - Directory Listing
Modified Thu Sep 2 07:26:43 2010 UTC (7 years ago) by gross
Original Path: trunk

a more robust version of MINRES (really?)

Revision 3135 - Directory Listing
Modified Thu Sep 2 03:28:39 2010 UTC (7 years 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 (7 years 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 (7 years ago) by caltinay
Original Path: trunk

Removed unused variable.

Revision 3131 - Directory Listing
Modified Thu Sep 2 01:40:47 2010 UTC (7 years 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 3128 - Directory Listing
Modified Wed Sep 1 03:54:09 2010 UTC (7 years 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 3120 - Directory Listing
Modified Mon Aug 30 10:48:00 2010 UTC (7 years 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 (7 years 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 (7 years ago) by caltinay
Original Path: trunk

Fixed commit from rev.2867 which broke the ability to specify script parameters.

Revision 3111 - Directory Listing
Modified Thu Aug 26 06:49:42 2010 UTC (7 years ago) by gross
Original Path: trunk

some diagnostics for time step backtracing added

Revision 3109 - Directory Listing
Modified Thu Aug 26 04:33:18 2010 UTC (7 years ago) by caltinay
Original Path: trunk

Added accessor for the simulation cycle and log which directory was used to
restart.

Revision 3107 - Directory Listing
Modified Thu Aug 26 03:41:28 2010 UTC (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years 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 (7 years, 1 month ago) by gross
Original Path: trunk

bug in ILU0 fixed.

Revision 3099 - Directory Listing
Modified Sun Aug 22 04:35:15 2010 UTC (7 years, 1 month 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 (7 years, 1 month ago) by gross
Original Path: trunk

fix to the GaussSeidel

Revision 3097 - Directory Listing
Modified Fri Aug 20 04:59:12 2010 UTC (7 years, 1 month ago) by gross
Original Path: trunk

some modifications to the GaussSeidel

Revision 3096 - Directory Listing
Modified Thu Aug 19 01:40:52 2010 UTC (7 years, 1 month 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 (7 years, 1 month 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 (7 years, 1 month 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 (7 years, 1 month 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 (7 years, 1 month 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 (7 years, 1 month 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 (7 years, 1 month ago) by ahallam
Original Path: trunk

Updates to example scripts - should now be working except for example09b.py which needs more memory.

Revision 3083 - Directory Listing
Modified Tue Aug 3 06:34:35 2010 UTC (7 years, 1 month ago) by caltinay
Original Path: trunk

Updated some svn:ignore props.

Revision 3081 - Directory Listing
Modified Tue Aug 3 05:36:42 2010 UTC (7 years, 1 month ago) by gross
Original Path: trunk

a light restart manager added.

Revision 3078 - Directory Listing
Modified Tue Aug 3 03:12:16 2010 UTC (7 years, 1 month ago) by jfenwick
Original Path: trunk

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

Revision 3076 - Directory Listing
Modified Mon Aug 2 05:21:40 2010 UTC (7 years, 1 month 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 (7 years, 1 month 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 (7 years, 1 month ago) by gross
Original Path: trunk

tolerance for PCG relaxed.

Revision 3073 - Directory Listing
Modified Mon Jul 26 06:10:50 2010 UTC (7 years, 1 month ago) by jfenwick
Original Path: trunk

Rename files to fix build problem

Revision 3069 - Directory Listing
Modified Wed Jul 21 03:24:48 2010 UTC (7 years, 2 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 (7 years, 2 months ago) by ahallam
Original Path: trunk

Missing Figures

Revision 3067 - Directory Listing
Modified Mon Jul 19 00:40:37 2010 UTC (7 years, 2 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 (7 years, 2 months ago) by ahallam
Original Path: trunk

Missing Picture causing errors.

Revision 3065 - Directory Listing
Modified Thu Jul 15 02:59:27 2010 UTC (7 years, 2 months ago) by ahallam
Original Path: trunk

Updates to newer examples.

Revision 3064 - Directory Listing
Modified Thu Jul 15 02:58:23 2010 UTC (7 years, 2 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 (7 years, 2 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 (7 years, 2 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 (7 years, 2 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 (7 years, 2 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 (7 years, 2 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 (7 years, 2 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 (7 years, 2 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 (7 years, 2 months ago) by ahallam
Original Path: trunk

Missing Figures...

Revision 3053 - Directory Listing
Modified Tue Jun 29 01:31:31 2010 UTC (7 years, 2 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 (7 years, 2 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 (7 years, 2 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 (7 years, 2 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 (7 years, 2 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 (7 years, 3 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 (7 years, 3 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 (7 years, 3 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 (7 years, 3 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 (7 years, 3 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 (7 years, 3 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 (7 years, 3 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 (7 years, 3 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 (7 years, 3 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 (7 years, 3 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 (7 years, 3 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 (7 years, 3 months ago) by jfenwick
Original Path: trunk

Adding unit tests for condEval

Revision 3032 - Directory Listing
Modified Mon May 31 02:58:15 2010 UTC (7 years, 3 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 (7 years, 3 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 (7 years, 4 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 (7 years, 4 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 (7 years, 4 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 (7 years, 4 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 (7 years, 4 months ago) by gross
Original Path: trunk

some fix for omp

Revision 3025 - Directory Listing
Modified Thu May 6 01:20:46 2010 UTC (7 years, 4 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 (7 years, 4 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 (7 years, 4 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 (7 years, 4 months ago) by gross
Original Path: trunk

MPI problem fixed.

Revision 3020 - Directory Listing
Modified Tue May 4 09:10:03 2010 UTC (7 years, 4 months ago) by gross
Original Path: trunk

reactive solver added

Revision 3019 - Directory Listing
Modified Fri Apr 30 06:10:37 2010 UTC (7 years, 4 months ago) by jfenwick
Original Path: trunk

adding Lin options

Revision 3018 - Directory Listing
Modified Thu Apr 29 21:35:24 2010 UTC (7 years, 4 months ago) by gross
Original Path: trunk

some stupid lines removed

Revision 3017 - Directory Listing
Modified Thu Apr 29 03:40:12 2010 UTC (7 years, 4 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 (7 years, 4 months ago) by artak
Original Path: trunk

firstprivate added for OpenMP

Revision 3015 - Directory Listing
Modified Wed Apr 28 05:06:26 2010 UTC (7 years, 4 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 (7 years, 4 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 (7 years, 4 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 (7 years, 4 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 (7 years, 4 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 (7 years, 4 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 (7 years, 5 months ago) by gross
Original Path: trunk

another MPI problem fixed

Revision 3008 - Directory Listing
Modified Thu Apr 22 10:19:20 2010 UTC (7 years, 5 months ago) by gross
Original Path: trunk

MPI problem fixed

Revision 3007 - Directory Listing
Modified Thu Apr 22 09:08:36 2010 UTC (7 years, 5 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 (7 years, 5 months ago) by gross
Original Path: trunk

local_norm_w removed

Revision 3005 - Directory Listing
Modified Thu Apr 22 05:59:31 2010 UTC (7 years, 5 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 (7 years, 5 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 (7 years, 5 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 (7 years, 5 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 (7 years, 5 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 (7 years, 5 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 (7 years, 5 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 (7 years, 6 months ago) by artak
Original Path: trunk

More openMP corrections

Revision 2997 - Directory Listing
Modified Wed Mar 24 01:46:33 2010 UTC (7 years, 6 months ago) by artak
Original Path: trunk

Some openMP corrections

Revision 2996 - Directory Listing
Modified Tue Mar 23 06:24:09 2010 UTC (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 months ago) by gross
Original Path: trunk

isub as private added

Revision 2990 - Directory Listing
Modified Fri Mar 19 05:57:22 2010 UTC (7 years, 6 months ago) by gross
Original Path: trunk

some prints removed.

Revision 2989 - Directory Listing
Modified Thu Mar 18 01:45:55 2010 UTC (7 years, 6 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 (7 years, 6 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 (7 years, 6 months ago) by gross
Original Path: trunk

FCT solver rewritten

Revision 2982 - Directory Listing
Modified Wed Mar 10 04:27:47 2010 UTC (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 months ago) by artak
Original Path: trunk

reached Chapter 4

Revision 2968 - Directory Listing
Modified Wed Mar 3 04:02:30 2010 UTC (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 months ago) by jfenwick
Original Path: trunk

Added MPI aware MIS

Revision 2963 - Directory Listing
Modified Wed Mar 3 01:10:11 2010 UTC (7 years, 6 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 (7 years, 6 months ago) by gross
Original Path: trunk

bar as unit added

Revision 2961 - Directory Listing
Modified Wed Mar 3 00:56:59 2010 UTC (7 years, 6 months ago) by jfenwick
Original Path: trunk

Hacking cookbook

Revision 2960 - Directory Listing
Modified Tue Mar 2 07:54:11 2010 UTC (7 years, 6 months ago) by gross
Original Path: trunk

new DarcyFlux solver

Revision 2959 - Directory Listing
Modified Tue Mar 2 06:27:17 2010 UTC (7 years, 6 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 (7 years, 6 months ago) by artak
Original Path: trunk

more corrections on exmaple 1, up to section 2.1.5

Revision 2956 - Directory Listing
Modified Mon Mar 1 01:31:59 2010 UTC (7 years, 6 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 (7 years, 6 months ago) by jfenwick
Original Path: trunk

Fix hackscore error

Revision 2954 - Directory Listing
Modified Fri Feb 26 06:09:47 2010 UTC (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 months ago) by gross
Original Path: trunk

renaming examples part 1

Revision 2948 - Directory Listing
Modified Thu Feb 25 04:54:30 2010 UTC (7 years, 6 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 (7 years, 6 months 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 (7 years, 6 months 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 (7 years, 6 months 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 (7 years, 6 months 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 (7 years, 7 months 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 (7 years, 7 months ago) by gross
Original Path: trunk

some print statements removed.

Revision 2938 - Directory Listing
Modified Thu Feb 18 00:24:35 2010 UTC (7 years, 7 months 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 (7 years, 7 months ago) by caltinay
Original Path: trunk

Corrected an MPI datatype

Revision 2936 - Directory Listing
Modified Mon Feb 15 03:29:53 2010 UTC (7 years, 7 months ago) by gross
Original Path: trunk

some clarification added.

Revision 2935 - Directory Listing
Modified Mon Feb 15 03:15:59 2010 UTC (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months ago) by gross
Original Path: trunk

more changes on the cookbook

Revision 2930 - Directory Listing
Modified Mon Feb 8 06:25:43 2010 UTC (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months ago) by gross
Original Path: trunk

uninitialised variable error for non-mpi case fixed.

Revision 2914 - Directory Listing
Modified Wed Feb 3 05:38:12 2010 UTC (7 years, 7 months ago) by gross
Original Path: trunk

missing import added.

Revision 2912 - Directory Listing
Modified Wed Feb 3 03:31:24 2010 UTC (7 years, 7 months ago) by gross
Original Path: trunk

some missing functions

Revision 2911 - Directory Listing
Modified Wed Feb 3 03:30:40 2010 UTC (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months ago) by gross
Original Path: trunk

needdirs replaced by mkDir from esys.escript

Revision 2906 - Directory Listing
Modified Tue Feb 2 05:26:03 2010 UTC (7 years, 7 months ago) by gross
Original Path: trunk

some minor :-) fix.

Revision 2905 - Directory Listing
Modified Tue Feb 2 04:26:42 2010 UTC (7 years, 7 months ago) by gross
Original Path: trunk

some missing files.

Revision 2904 - Directory Listing
Modified Tue Feb 2 04:21:52 2010 UTC (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months ago) by caltinay
Original Path: trunk

Added missing declspec to FileSavers.

Revision 2898 - Directory Listing
Modified Mon Feb 1 01:23:46 2010 UTC (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months ago) by gross
Original Path: trunk

more work on cookbook review

Revision 2877 - Directory Listing
Modified Thu Jan 28 00:28:45 2010 UTC (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 7 months ago) by gross
Original Path: trunk

more review on the cookbook.

Revision 2869 - Directory Listing
Modified Mon Jan 25 05:11:28 2010 UTC (7 years, 7 months 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 (7 years, 7 months 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 (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months ago) by gross
Original Path: trunk

projector added to users guide

Revision 2863 - Directory Listing
Modified Thu Jan 21 07:18:37 2010 UTC (7 years, 8 months ago) by gross
Original Path: trunk

fix for mantis 454

Revision 2862 - Directory Listing
Modified Thu Jan 21 04:45:39 2010 UTC (7 years, 8 months ago) by gross
Original Path: trunk

more review in the cookbook

Revision 2861 - Directory Listing
Modified Wed Jan 20 02:47:42 2010 UTC (7 years, 8 months ago) by gross
Original Path: trunk

some modification to the cookbook

Revision 2859 - Directory Listing
Modified Tue Jan 19 05:21:50 2010 UTC (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months ago) by gross
Original Path: trunk

new compressible solver

Revision 2842 - Directory Listing
Modified Thu Jan 14 05:42:02 2010 UTC (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months ago) by caltinay
Original Path: trunk

Enabled Silo on guineapig

Revision 2839 - Directory Listing
Modified Wed Jan 13 23:34:49 2010 UTC (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months ago) by caltinay
Original Path: trunk

Added missing import statement.

Revision 2836 - Directory Listing
Modified Mon Jan 11 01:41:29 2010 UTC (7 years, 8 months ago) by artak
Original Path: trunk

minor adjustments

Revision 2835 - Directory Listing
Modified Mon Jan 11 01:23:52 2010 UTC (7 years, 8 months 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 (7 years, 8 months 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 2831 - Directory Listing
Modified Thu Jan 7 05:08:19 2010 UTC (7 years, 8 months 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 (7 years, 8 months 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 (7 years, 8 months ago) by ahallam
Original Path: trunk

minor updates to cookbook

Revision 2828 - Directory Listing
Modified Tue Dec 22 01:24:40 2009 UTC (7 years, 9 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 (7 years, 9 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 (7 years, 9 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 (7 years, 9 months ago) by jfenwick
Original Path: trunk

More fixes to resolveGroup

Revision 2824 - Directory Listing
Modified Wed Dec 16 01:22:56 2009 UTC (7 years, 9 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 (7 years, 9 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 (7 years, 9 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 (7 years, 9 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 (7 years, 9 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 (7 years, 9 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 (7 years, 9 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 (7 years, 9 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 (7 years, 9 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 (7 years, 9 months ago) by caltinay
Original Path: trunk

Removed minor code duplication.

Revision 2813 - Directory Listing
Modified Tue Dec 8 00:30:13 2009 UTC (7 years, 9 months ago) by caltinay
Original Path: trunk

Added missing include.

Revision 2812 - Directory Listing
Modified Tue Dec 8 00:12:07 2009 UTC (7 years, 9 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 (7 years, 9 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 (7 years, 9 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 (7 years, 9 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 (7 years, 9 months ago) by artak
Original Path: trunk

default coarseneing is Ruge-Stueben.

Revision 2807 - Directory Listing
Modified Mon Dec 7 00:02:55 2009 UTC (7 years, 9 months ago) by artak
Original Path: trunk

Post and pre smoothing parameters are added for AMLI. Little bit reengineering according to Axelson's original AMLI paper.

Revision 2806 - Directory Listing
Modified Fri Dec 4 06:46:13 2009 UTC (7 years, 9 months ago) by caltinay
Original Path: trunk

bin/escript:
 - bail out early if buildvars is not around
 - quote variables to avoid syntax errors
 - some work towards POSIX compliance (s/==/=/ in string comparisons)
 - escript -V was still spitting out 'pre2.0' -> changed to pre4.0
 - fixed minor typos

Revision 2804 - Directory Listing
Modified Fri Dec 4 02:06:51 2009 UTC (7 years, 9 months ago) by artak
Original Path: trunk

Some memory and code optimizations in updateWeights method.

Revision 2803 - Directory Listing
Modified Thu Dec 3 05:35:20 2009 UTC (7 years, 9 months ago) by artak
Original Path: trunk

Parameters are added for post and pre smoothing. Now user can choose number of pre and post smoothing steps in AMG (e.g. setNumPreSweeps(5)).

Revision 2802 - Directory Listing
Modified Thu Dec 3 01:51:55 2009 UTC (7 years, 9 months ago) by artak
Original Path: trunk

Aggressive coarsening is implemented. Removes more elements but adds more iteration steps.

Revision 2801 - Directory Listing
Modified Thu Dec 3 01:45:48 2009 UTC (7 years, 9 months ago) by ahallam
Original Path: trunk

Final updates to first 3 chapters of cookbook before moving on to linear elastic wave equation examples.

Revision 2800 - Directory Listing
Modified Thu Dec 3 01:45:12 2009 UTC (7 years, 9 months ago) by ahallam
Original Path: trunk

Getting rid of unneeded directories

Revision 2799 - Directory Listing
Modified Thu Dec 3 01:35:08 2009 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

resolveGroup function added to python.
Unit tests for resolveGroup, resolve and delay.

Revision 2798 - Directory Listing
Modified Thu Dec 3 01:02:47 2009 UTC (7 years, 9 months ago) by caltinay
Original Path: trunk

Use system NetCDF on guineapig.

Revision 2797 - Directory Listing
Modified Wed Dec 2 23:30:21 2009 UTC (7 years, 9 months ago) by caltinay
Original Path: trunk

Changed NetCDF include path - this should enable netcdf on guineapig.

Revision 2796 - Directory Listing
Modified Wed Dec 2 05:02:43 2009 UTC (7 years, 9 months ago) by caltinay
Original Path: trunk

null-commit to trigger buildbot

Revision 2795 - Directory Listing
Modified Wed Dec 2 02:39:23 2009 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

Removed node limit on lazy expressions.
The parameter LAZY_STR_FMT {0,1,2}  controls how lazy expressions are printed.
0 gives default output
1 gives a tree form.
2 just prints depth

Revision 2794 - Directory Listing
Modified Wed Dec 2 00:43:17 2009 UTC (7 years, 9 months ago) by gross
Original Path: trunk

returning to the older version.

Revision 2793 - Directory Listing
Modified Tue Dec 1 06:10:10 2009 UTC (7 years, 9 months ago) by gross
Original Path: trunk

some new util functions

Revision 2792 - Directory Listing
Modified Tue Dec 1 05:02:18 2009 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

Oops.
matrixInverse now checks MPI to see if any other ranks raised exceptions.

Revision 2791 - Directory Listing
Modified Tue Dec 1 03:36:36 2009 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

Added expression depth to toString for LazyData.

Revision 2790 - Directory Listing
Modified Sun Nov 29 23:57:45 2009 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

Fix scons file for unit tests.

Revision 2789 - Directory Listing
Modified Fri Nov 27 05:40:25 2009 UTC (7 years, 9 months ago) by caltinay
Original Path: trunk

Removed unused variable from OpenMP block.
Fixes compilation error with gcc 4.3.

Revision 2788 - Directory Listing
Modified Fri Nov 27 05:23:14 2009 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

Go back to version 10

Revision 2787 - Directory Listing
Modified Fri Nov 27 05:03:09 2009 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

Worked around icc11 problem in table interpolate.
Best guess is that a stackframe was getting mauled somehow.

Revision 2786 - Directory Listing
Modified Fri Nov 27 01:07:28 2009 UTC (7 years, 9 months ago) by caltinay
Original Path: trunk

Fixed a little typo.

Revision 2785 - Directory Listing
Modified Thu Nov 26 05:17:40 2009 UTC (7 years, 9 months ago) by lgao
Original Path: trunk

Minor fix for unused variables

Revision 2784 - Directory Listing
Modified Thu Nov 26 05:09:14 2009 UTC (7 years, 9 months ago) by artak
Original Path: trunk

More performance tunning. Sparsity check is added. If Coarse level matrix is denser than 1% then stop.

Revision 2783 - Directory Listing
Modified Thu Nov 26 05:07:33 2009 UTC (7 years, 9 months ago) by lgao
Original Path: trunk

process C_TensorBinaryOperation at the level of a whole sample rather than 
each datapoint when an Expanded data is operating with a Constant data. This
could improve the efficiency of the non-lazy version escipt.

Revision 2782 - Directory Listing
Modified Thu Nov 26 04:42:29 2009 UTC (7 years, 9 months ago) by caltinay
Original Path: trunk

Added missing var declaration.

Revision 2781 - Directory Listing
Modified Thu Nov 26 04:12:11 2009 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

Some additional info from Thomas

Revision 2780 - Directory Listing
Modified Thu Nov 26 03:54:24 2009 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

Put the windows instructions back in.
Put more detail in the MPI hints.

Revision 2779 - Directory Listing
Modified Thu Nov 26 03:51:15 2009 UTC (7 years, 9 months ago) by caltinay
Original Path: trunk

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

Revision 2778 - Directory Listing
Modified Thu Nov 26 01:50:30 2009 UTC (7 years, 9 months ago) by caltinay
Original Path: trunk

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

Revision 2777 - Directory Listing
Modified Thu Nov 26 01:06:00 2009 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

Added the LAZY_STACK_PROF #define for Lazy.
If enabled lazy will print the (roughly) maximum stack used by any openmp 
thread over the course of this session.

Revision 2776 - Directory Listing
Modified Wed Nov 25 23:41:16 2009 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

Switching tests which read gmsh to not run under MPI

Revision 2775 - Directory Listing
Modified Wed Nov 25 05:01:43 2009 UTC (7 years, 9 months ago) by ahallam
Original Path: trunk

minor updates to cookbook; new python syntax highlighting

Revision 2774 - Directory Listing
Modified Wed Nov 25 04:24:03 2009 UTC (7 years, 9 months ago) by artak
Original Path: trunk

#ifndef changed to #ifdef in makeNaN

Revision 2773 - Directory Listing
Modified Wed Nov 25 04:02:01 2009 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

Hadn't realised isnan was a macro.
Checking for it rather than FP_NAN

Revision 2772 - Directory Listing
Modified Wed Nov 25 02:02:50 2009 UTC (7 years, 9 months ago) by ahallam
Original Path: trunk

Fixed auto build error for heatrefraction_mesher002.py

Added clear figure line for run_heatrefraction.py process.

Revision 2770 - Directory Listing
Modified Wed Nov 25 01:24:51 2009 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

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

Revision 2769 - Directory Listing
Modified Tue Nov 24 00:36:22 2009 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

Unit tests for NaN handling

Revision 2768 - Directory Listing
Modified Mon Nov 23 23:56:14 2009 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

Dodge problem in NoPDE class

Revision 2767 - Directory Listing
Modified Mon Nov 23 06:00:37 2009 UTC (7 years, 9 months ago) by artak
Original Path: trunk

More openmp calls are added,escpecialy in arg_max method.

Revision 2766 - Directory Listing
Modified Mon Nov 23 05:10:53 2009 UTC (7 years, 9 months ago) by jfenwick
Original Path: trunk

inf, sup and Lsup now correctly handle +-infinity.
They also will return NaN if any part of their input is NaN.

This will break unit tests since it exposes the hidden bug (#447 in mantis)

This code relies on the ability to test for NaNs.
To do this it makes use of macros and functions from C99.
If you do not have a C99 compiler, then you will probably get the old behaviour.
That is, you won't know when you have NaNs.


Also did minor tweak to saveDataCSV doco.

Revision 2765 - Directory Listing
Modified Fri Nov 20 01:49:19 2009 UTC (7 years, 10 months ago) by artak
Original Path: trunk

First steps toward efficiency. Coarsening process is improved. Some profiling tools are added.

Revision 2764 - Directory Listing
Modified Thu Nov 19 23:48:05 2009 UTC (7 years, 10 months ago) by artak
Original Path: trunk

Some openMP calls are removed.

Revision 2763 - Directory Listing
Modified Thu Nov 19 06:28:03 2009 UTC (7 years, 10 months ago) by lgao
Original Path: trunk

Minor fix to my previous commit.

Revision 2762 - Directory Listing
Modified Thu Nov 19 06:24:44 2009 UTC (7 years, 10 months ago) by lgao
Original Path: trunk

fix the compilation problem I introduced for Non-MPI build due
to my last commit for Data::toString().

Revision 2761 - Directory Listing
Modified Thu Nov 19 06:11:07 2009 UTC (7 years, 10 months ago) by artak
Original Path: trunk

AMLI preconditioner (previously called  AMG)

Revision 2760 - Directory Listing
Modified Thu Nov 19 05:22:45 2009 UTC (7 years, 10 months ago) by artak
Original Path: trunk

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

Revision 2759 - Directory Listing
Modified Thu Nov 19 05:19:47 2009 UTC (7 years, 10 months ago) by artak
Original Path: trunk

methods needed for the new AMG preconditioner

Revision 2758 - Directory Listing
Modified Thu Nov 19 04:21:55 2009 UTC (7 years, 10 months ago) by caltinay
Original Path: trunk

Added missing imports. all_tests still fails though due to other problems.

Revision 2757 - Directory Listing
Modified Thu Nov 19 01:04:57 2009 UTC (7 years, 10 months ago) by lgao
Original Path: trunk

Solve the print statement problem for MPI program (matis issue 465).

Revision 2756 - Directory Listing
Modified Thu Nov 19 00:40:02 2009 UTC (7 years, 10 months ago) by gross
Original Path: trunk

missing file added.

Revision 2755 - Directory Listing
Modified Wed Nov 18 23:19:32 2009 UTC (7 years, 10 months ago) by caltinay
Original Path: trunk

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

Revision 2754 - Directory Listing
Modified Wed Nov 18 07:44:26 2009 UTC (7 years, 10 months ago) by gross
Original Path: trunk

tests for macro elements in saveVTK added.

Revision 2753 - Directory Listing
Modified Wed Nov 18 06:06:50 2009 UTC (7 years, 10 months ago) by lgao
Original Path: trunk

fix bugs in minGlobalDataPoint() and maxGlobalDataPoint()

Revision 2752 - Directory Listing
Modified Wed Nov 18 06:01:18 2009 UTC (7 years, 10 months ago) by caltinay
Original Path: trunk

Fixed compilation error in mesh reader when using MPI.

Revision 2751 - Directory Listing
Modified Wed Nov 18 00:30:47 2009 UTC (7 years, 10 months ago) by caltinay
Original Path: trunk

Removed stray forward declaration.

Revision 2750 - Directory Listing
Modified Tue Nov 17 23:39:20 2009 UTC (7 years, 10 months ago) by caltinay
Original Path: trunk

Fixed some compilation errors with OpenMP introduced in last commit.

Revision 2748 - Directory Listing
Modified Tue Nov 17 07:32:59 2009 UTC (7 years, 10 months ago) by gross
Original Path: trunk

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

Revision 2747 - Directory Listing
Modified Tue Nov 17 05:19:59 2009 UTC (7 years, 10 months ago) by lgao
Original Path: trunk

Minor rivision to minGlobalDataPoint()

Revision 2746 - Directory Listing
Modified Tue Nov 17 05:13:51 2009 UTC (7 years, 10 months ago) by lgao
Original Path: trunk

Fix the error in minGlobalDataPoint() and maxGlobalDataPoint() due to 
the fact that the number of samples on one MPI rank could be 0. Therefore,
not every MPI rank has valid min/max data point.

Revision 2745 - Directory Listing
Modified Tue Nov 17 04:23:02 2009 UTC (7 years, 10 months ago) by jfenwick
Original Path: trunk

Added getInfLocator and getSupLocator to pdetools.
This means if you want to use them, you will need to import them.
These methods return a locator to a point with the smallest/largest value.

Added resolve() and delay() to utils.
Now you can do things like:

d=delay(v)
..
..
z=resolve(d+1)

Revision 2744 - Directory Listing
Modified Mon Nov 16 23:45:55 2009 UTC (7 years, 10 months ago) by caltinay
Original Path: trunk

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

Revision 2743 - Directory Listing
Modified Mon Nov 16 05:28:47 2009 UTC (7 years, 10 months ago) by caltinay
Original Path: trunk

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

Revision 2742 - Directory Listing
Modified Thu Nov 12 06:03:37 2009 UTC (7 years, 10 months ago) by jfenwick
Original Path: trunk

Merging changes from the lapack branch.

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

Revision 2738 - Directory Listing
Modified Fri Nov 6 05:33:13 2009 UTC (7 years, 10 months ago) by jfenwick
Original Path: trunk

Taipan and DataVector use size_type (currently long) internally to talk 
about sizes.
[A lot more work needs to be done on this].
Exceptions now give nicer messages and output the problematic numbers.

Some minor doco errors fixed.

escript.util.mkDir
Now checks to see if the pathname already exists as a non-directory.
On suggestion from slanger it now calls makedirs.

Revision 2737 - Directory Listing
Modified Tue Nov 3 00:44:00 2009 UTC (7 years, 10 months ago) by jfenwick
Original Path: trunk

icc will now record compiler options in libraries.
escriptParams now has a pretty printer option for lazy expressions.

Revision 2736 - Directory Listing
Modified Mon Nov 2 04:15:27 2009 UTC (7 years, 10 months ago) by caltinay
Original Path: trunk

Fixed a couple of typos.

Revision 2735 - Directory Listing
Modified Mon Nov 2 02:03:24 2009 UTC (7 years, 10 months ago) by jfenwick
Original Path: trunk

Fixed bug where calling minval() reintroduced laziness after it had been removed.

Revision 2734 - Directory Listing
Modified Fri Oct 30 05:39:48 2009 UTC (7 years, 10 months ago) by jfenwick
Original Path: trunk

Fixed bug in lazy maxval and minval

Revision 2733 - Directory Listing
Modified Mon Oct 26 02:05:11 2009 UTC (7 years, 10 months ago) by caltinay
Original Path: trunk

escriptreader: added debug flag to configure.ac

Revision 2732 - Directory Listing
Modified Mon Oct 26 01:11:31 2009 UTC (7 years, 10 months ago) by jfenwick
Original Path: trunk

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

Revision 2731 - Directory Listing
Modified Thu Oct 22 04:17:21 2009 UTC (7 years, 11 months ago) by trankine
Original Path: trunk

* Added xe.ivec.org options file as reminder for David Schibeci [dschibeci@ccg.murdoch.edu.au]

Revision 2730 - Directory Listing
Modified Thu Oct 22 01:50:27 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

order member variable added to the tests.

Revision 2729 - Directory Listing
Modified Thu Oct 22 01:45:28 2009 UTC (7 years, 11 months ago) by jfenwick
Original Path: trunk

UMFPack and MPI added to guineapig options.
Defaults for omp and mpi removed from SConstruct.

Revision 2727 - Directory Listing
Modified Wed Oct 21 23:56:23 2009 UTC (7 years, 11 months ago) by jfenwick
Original Path: trunk

Added guineapig options

Revision 2726 - Directory Listing
Modified Wed Oct 21 23:50:05 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

New diagonal dominancy based algorithm is added. The coarseneng strategy is changed.

Revision 2725 - Directory Listing
Modified Wed Oct 21 23:44:06 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

AMG unit tests are disabled for 2-nd order elements.

Revision 2723 - Directory Listing
Modified Sun Oct 18 23:44:37 2009 UTC (7 years, 11 months ago) by jfenwick
Original Path: trunk

Use correct types for MPI op parameters

Revision 2722 - Directory Listing
Modified Fri Oct 16 06:45:01 2009 UTC (7 years, 11 months ago) by gross
Original Path: trunk

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

Revision 2721 - Directory Listing
Modified Fri Oct 16 05:40:12 2009 UTC (7 years, 11 months ago) by jfenwick
Original Path: trunk

minval and maxval are now lazy operations (they weren't before).
Whether or not Lsup, sup and inf resolve their arguments before computing answers is controlled by the escriptParam 'RESOLVE_COLLECTIVE'.
Note: integrate() still forces a resolve.

Added some unit tests for operations which weren't tested before.
Added deepcopy implementations for lazy operations which got missed somehow.

Revision 2720 - Directory Listing
Modified Wed Oct 14 23:43:21 2009 UTC (7 years, 11 months ago) by gross
Original Path: trunk

missing modules added

Revision 2719 - Directory Listing
Modified Wed Oct 14 06:38:03 2009 UTC (7 years, 11 months ago) by gross
Original Path: trunk

a new Stokes solver added

Revision 2718 - Directory Listing
Modified Wed Oct 14 04:03:27 2009 UTC (7 years, 11 months ago) by gross
Original Path: trunk

syntax errors fixed.

Revision 2717 - Directory Listing
Modified Wed Oct 14 03:41:20 2009 UTC (7 years, 11 months ago) by gross
Original Path: trunk

implements https://mantis.esscc.uq.edu.au/view.php?id=426

Revision 2716 - Directory Listing
Modified Tue Oct 13 04:58:08 2009 UTC (7 years, 11 months ago) by jfenwick
Original Path: trunk

Small mod - process C_Tensor??Operation on ExpandedData as a whole 
sample rather than a datapoint at a time.
This is just to bring Non-Lazy into line with Lazy.

Revision 2715 - Directory Listing
Modified Sun Oct 11 23:29:56 2009 UTC (7 years, 11 months ago) by lgao
Original Path: trunk

change back to use Intel MPI (avoid the MPT+MKL problem).

Revision 2714 - Directory Listing
Modified Wed Oct 7 23:29:19 2009 UTC (7 years, 11 months ago) by gross
Original Path: trunk

typo in check fixed.

Revision 2713 - Directory Listing
Modified Wed Oct 7 00:35:06 2009 UTC (7 years, 11 months ago) by jfenwick
Original Path: trunk

Fixes for windows.
Copied from Thomas Poulet

Revision 2712 - Directory Listing
Modified Wed Oct 7 00:22:43 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

MKL made default direct solver for AMG

Revision 2711 - Directory Listing
Modified Tue Oct 6 04:43:41 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

Little restructuring for solving memory bug in MKL_free process and making sure LDU factorzation done only once.

Revision 2710 - Directory Listing
Modified Mon Oct 5 23:15:04 2009 UTC (7 years, 11 months ago) by jfenwick
Original Path: trunk

Change to error output requested by Thomas Poulet

Revision 2709 - Directory Listing
Modified Mon Oct 5 06:11:58 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

Paso_MKL1 put back again

Revision 2708 - Directory Listing
Modified Mon Oct 5 05:59:08 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

The n_F==n condition with potentially uninitialized value is fixed.

Revision 2707 - Directory Listing
Modified Fri Oct 2 05:02:59 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

some unnecessary lines are removed

Revision 2706 - Directory Listing
Modified Fri Oct 2 02:15:04 2009 UTC (7 years, 11 months ago) by jfenwick
Original Path: trunk

Perhaps this will stop the cookbook from hating me.

Revision 2705 - Directory Listing
Modified Thu Oct 1 23:21:10 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

Some openMP codes in AMG systems are removed for testing.

Revision 2704 - Directory Listing
Modified Thu Oct 1 05:38:33 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

some clarity in the notations REMOVED changes IN_SET

Revision 2703 - Directory Listing
Modified Thu Oct 1 01:22:36 2009 UTC (7 years, 11 months ago) by jfenwick
Original Path: trunk

Added calls to MPI_Abort to the pythonMPI wrappers.
Now if an uncaught exception is raised on any of the nodes, the whole world should be brought down. I've tested this on a barrier and it works.
One consequence of this is that you should not call sys.exit(2) but we don't recommend using sys.exit anyway.

Revision 2702 - Directory Listing
Modified Wed Sep 30 23:54:17 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

UMFPACK is enabled for savanna

Revision 2701 - Directory Listing
Modified Wed Sep 30 23:21:08 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

MKL test lines are removed

Revision 2700 - Directory Listing
Modified Wed Sep 30 08:28:55 2009 UTC (7 years, 11 months ago) by gross
Original Path: trunk

pycad test fixed.

Revision 2699 - Directory Listing
Modified Wed Sep 30 05:43:20 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

Direct solver switched to UMFPACK, till problem with MKL solved. When all unknows are eliminated then we switch to Jacobi preconditiner.

Revision 2698 - Directory Listing
Modified Wed Sep 30 01:46:31 2009 UTC (7 years, 11 months ago) by jfenwick
Original Path: trunk

Removing extension from some image filenames

Revision 2697 - Directory Listing
Modified Wed Sep 30 01:29:22 2009 UTC (7 years, 11 months ago) by jfenwick
Original Path: trunk

Trying to get cookbook scripts passing.
Split cblib in two to avoid importing pylab in scripts which
don't otheriwse need it.

Revision 2696 - Directory Listing
Modified Wed Sep 30 00:36:05 2009 UTC (7 years, 11 months ago) by lgao
Original Path: trunk

change service0_options.py to use MPT 1.24

Revision 2695 - Directory Listing
Modified Tue Sep 29 06:29:12 2009 UTC (7 years, 11 months ago) by gross
Original Path: trunk

pycad passes on more infromation from gmsh now.

Revision 2694 - Directory Listing
Modified Tue Sep 29 06:00:44 2009 UTC (7 years, 11 months ago) by gross
Original Path: trunk

some hint on how to access gmsh error messages added.

Revision 2693 - Directory Listing
Modified Tue Sep 29 05:47:45 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

sorry python Indentation Error, fixed

Revision 2691 - Directory Listing
Modified Tue Sep 29 05:30:27 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

Projector class had getSolverOptions(), but was returning null, so changed to return correct solver options.

Revision 2690 - Directory Listing
Modified Tue Sep 29 05:23:41 2009 UTC (7 years, 11 months ago) by gross
Original Path: trunk

some description on gmsh reader added.

Revision 2689 - Directory Listing
Modified Tue Sep 29 05:22:51 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

getSolverOptionsDiv was returning Pressure options instead of Div equation options

Revision 2688 - Directory Listing
Modified Tue Sep 29 05:19:43 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

changes to default threshold values

Revision 2687 - Directory Listing
Modified Tue Sep 29 04:23:10 2009 UTC (7 years, 11 months ago) by caltinay
Original Path: trunk

libescriptreader: fixed a path problem when using autotools to build

Revision 2686 - Directory Listing
Modified Tue Sep 29 03:39:36 2009 UTC (7 years, 11 months ago) by artak
Original Path: trunk

 changes the default thresold, bug fixes in RS coupling and extra checks added in Solver

Revision 2685 - Directory Listing
Modified Tue Sep 29 02:22:30 2009 UTC (7 years, 11 months ago) by gross
Original Path: trunk

these files are not needed

Revision 2684 - Directory Listing
Modified Tue Sep 29 02:21:11 2009 UTC (7 years, 11 months ago) by gross
Original Path: trunk

added missing file

Revision 2683 - Directory Listing
Modified Tue Sep 29 02:20:22 2009 UTC (7 years, 11 months ago) by gross
Original Path: trunk

documentation for pycad added.

Revision 2681 - Directory Listing
Modified Thu Sep 24 03:04:04 2009 UTC (7 years, 11 months ago) by ahallam
Original Path: trunk

proof reading and review of cookbook, minor changes only + updated depth profiles to cb from last week

Revision 2680 - Directory Listing
Modified Thu Sep 24 00:40:07 2009 UTC (7 years, 11 months ago) by caltinay
Original Path: trunk

Updated service0 options file to use Silo 4.7 on Savanna

Revision 2679 - Directory Listing
Modified Thu Sep 24 00:36:57 2009 UTC (7 years, 11 months ago) by caltinay
Original Path: trunk

Updated shake75 options file

Revision 2678 - Directory Listing
Modified Wed Sep 23 23:54:16 2009 UTC (7 years, 11 months ago) by jfenwick
Original Path: trunk

Some fixes for compile errors for gcc_testing_version

Revision 2677 - Directory Listing
Modified Tue Sep 22 00:48:00 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

Removed stuff in user guide about needing to make table larger to allow
boundary points.
The table interpolation is now OMP parallel.

Revision 2676 - Directory Listing
Modified Mon Sep 21 08:06:37 2009 UTC (8 years ago) by gross
Original Path: trunk

FaultSystem: MaxValue and MinValue return now a Locator. This makes it possible to extract values of from other data objects at the location of the min/max value

Revision 2675 - Directory Listing
Modified Mon Sep 21 02:32:17 2009 UTC (8 years ago) by gross
Original Path: trunk

getMinValue added to the fault system.

Revision 2674 - Directory Listing
Modified Mon Sep 21 00:37:18 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

Base matplotlib tests on version number.
This will stop the Mac trying to run some tests it can't execute.

Revision 2673 - Directory Listing
Modified Fri Sep 18 05:33:10 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

Some fixes to interpolation

Revision 2672 - Directory Listing
Modified Fri Sep 18 01:46:47 2009 UTC (8 years ago) by ahallam
Original Path: trunk

Heat refraction updates : alex's downhole profiles

Revision 2671 - Directory Listing
Modified Thu Sep 17 06:37:22 2009 UTC (8 years ago) by gross
Original Path: trunk

missing offset added in interpolation table

Revision 2670 - Directory Listing
Modified Thu Sep 17 06:17:57 2009 UTC (8 years ago) by artak
Original Path: trunk

Bug that made MPI tests to fail is fixed.

Revision 2669 - Directory Listing
Modified Thu Sep 17 06:01:30 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

Added a bunch of valgrind supressions. Hopefully this will make it more useful.

Asking for an offset on a DataConstant containing no samples no longer fails under debug builds.
I've disabled the sample and dataPoint bounds checks since they don't make sense on DataConstant.

Revision 2668 - Directory Listing
Modified Thu Sep 17 04:04:09 2009 UTC (8 years ago) by gross
Original Path: trunk

some clarification in the table interpolation

Revision 2667 - Directory Listing
Modified Thu Sep 17 01:49:11 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

Renamed the main cookbook tex file to match our convention.
Replaced doc/cookbook/figures/heatrefraction002contqu.pdf with
a version which is actually pdf. However it needs to be regnerated since
it it sideways.

The examples have had their copyright notices fixed (dates were too early).
sb2.py has been removed since it uses pyvisi.

scons will now build the cookbook as parts of a docs build.
Also in reposnse to :
scons cookbook_pdf

Revision 2666 - Directory Listing
Modified Thu Sep 17 00:10:00 2009 UTC (8 years ago) by artak
Original Path: trunk

OpenMP bug fixed and more openMP code added for cutting blocks.

Revision 2665 - Directory Listing
Modified Wed Sep 16 02:56:02 2009 UTC (8 years ago) by gross
Original Path: trunk

clarification in the fault depth vector

Revision 2664 - Directory Listing
Modified Wed Sep 16 01:06:50 2009 UTC (8 years ago) by artak
Original Path: trunk

Extra check is added for AMG levels. If coursening proccess does not eliminate at least 30% from the fine Matrix then it does not make sense to continue to the next level.

Revision 2663 - Directory Listing
Modified Tue Sep 15 06:04:44 2009 UTC (8 years ago) by gross
Original Path: trunk

finally there is a 3D version for the fault system class

Revision 2662 - Directory Listing
Modified Tue Sep 15 03:05:23 2009 UTC (8 years ago) by artak
Original Path: trunk

Migrating to block_sizes greather than 3 made easy.

Revision 2661 - Directory Listing
Modified Fri Sep 11 00:59:59 2009 UTC (8 years ago) by artak
Original Path: trunk

Finially unit tests for AMG preconditioner for single equations as well as for systems. Minor bug in AMG is also fixed

Revision 2659 - Directory Listing
Modified Thu Sep 10 03:54:50 2009 UTC (8 years ago) by artak
Original Path: trunk

first attempt of AMG on blocks

Revision 2658 - Directory Listing
Modified Thu Sep 10 02:58:44 2009 UTC (8 years ago) by ahallam
Original Path: trunk

Updates to all files scripts to support MPI testing proceedure. Updates to cookbook, new section on functino spaces/domains (needs work). Finalising first 3 chapters for editing.

Revision 2657 - Directory Listing
Modified Thu Sep 10 00:58:19 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

Fixed some spelling errors.
Added text about parallel vis.

Revision 2654 - Directory Listing
Modified Tue Sep 8 07:11:12 2009 UTC (8 years ago) by gross
Original Path: trunk

2D fault systems are now working. 3D still needs work.

Revision 2653 - Directory Listing
Modified Tue Sep 8 04:26:30 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

Fix bug in maxGlobalDataPoint and minGlobalDataPoint.
They now give the correct answers and the datapoint ids returned are globally
correct.

Removed some #defines from before COW
Removed hasNoSamples() - I don't trust myself to use that properly let alone anybody else.

Revision 2652 - Directory Listing
Modified Mon Sep 7 05:04:45 2009 UTC (8 years ago) by artak
Original Path: trunk

Paso_Pattern_coup changed to Paso_Pattern_YS for making clear that it refers to YAIR-SHAPIRA coarsenenig.

Revision 2651 - Directory Listing
Modified Mon Sep 7 03:39:45 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

Fixed latex compile error.
Fixed some overful hboxes

Revision 2650 - Directory Listing
Modified Mon Sep 7 03:38:50 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

Reducing the concentration of stupid.

Revision 2649 - Directory Listing
Modified Mon Sep 7 03:33:55 2009 UTC (8 years ago) by gross
Original Path: trunk

Some small fixes in FaultSystem

Revision 2648 - Directory Listing
Modified Mon Sep 7 00:06:15 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

ecording some changes related to Anthony's cookbook.
These tests still do not run.

test_heatref.py is the current problem.
Current problems include:
undefined symbols
a dependence on X somehow.

I've already addressed the matplotlib X thing somewhere else.
Find and apply.

Revision 2647 - Directory Listing
Modified Fri Sep 4 05:25:25 2009 UTC (8 years ago) by gross
Original Path: trunk

fault system add. There is still an example for the usage missing.

Revision 2646 - Directory Listing
Modified Fri Sep 4 00:13:00 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

Unit tests and user doco for interpolation and saveCSV

Revision 2645 - Directory Listing
Modified Thu Sep 3 02:20:33 2009 UTC (8 years ago) by ahallam
Original Path: trunk

More revisions to cookbook, fixed cblib.py for Scons, new figures.

Revision 2644 - Directory Listing
Modified Wed Sep 2 04:14:03 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

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

Removed some unneeded functions.

Revision 2643 - Directory Listing
Modified Wed Sep 2 00:10:00 2009 UTC (8 years ago) by artak
Original Path: trunk

Saving sparse matrix used before for debuging is removed

Revision 2641 - Directory Listing
Modified Mon Aug 31 07:41:49 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

Fixed some of my stupids related to MPI compile errors.

Revision 2637 - Directory Listing
Modified Fri Aug 28 04:12:24 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

saveDataCSV looks good but does not do MPI yet.
Also not unit tested.

Revision 2636 - Directory Listing
Modified Thu Aug 27 05:26:42 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

Disabling cookbook example checks until we can fix them.

Revision 2635 - Directory Listing
Modified Thu Aug 27 04:54:41 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

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

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

Added pointToStream() in DataTypes to help print points.

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

Revision 2634 - Directory Listing
Modified Thu Aug 27 04:03:32 2009 UTC (8 years ago) by ahallam
Original Path: trunk

Updates to cookbook. Updates to scripts. Updates to figures. Working examples added to SCons. Data folder structure included minus data. More folder rejigging.

Revision 2632 - Directory Listing
Modified Wed Aug 26 22:18:19 2009 UTC (8 years ago) by ahallam
Original Path: trunk

Regigger of cookbook directory structure. Examlples->examples/cookbook TEXT->doc/cookbook Figures-> doc/cookbook/figures

Revision 2629 - Directory Listing
Modified Tue Aug 25 06:39:26 2009 UTC (8 years ago) by trankine
Original Path: trunk

Changes to work on Windows with boost 1.39.0. Using command separator &. Note: there are still 2 CheckFunc that fail (but can be bypassed as the rest of the build works).

Revision 2628 - Directory Listing
Modified Tue Aug 25 03:50:00 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

Fixed linkage on getTestDomainFunctionSpace.

added Data.interpolateTable to perform 2D interpolation.
It needs better unit tests though.

Revision 2626 - Directory Listing
Modified Mon Aug 24 00:48:31 2009 UTC (8 years ago) by jfenwick
Original Path: trunk

Making arg0 and arg params in C_GeneralTensorProduct non-optional.
[The using the default args caused an exception.]

Revision 2625 - Directory Listing
Modified Fri Aug 21 06:30:25 2009 UTC (8 years, 1 month ago) by jfenwick
Original Path: trunk

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

Revision 2620 - Directory Listing
Modified Thu Aug 20 06:24:00 2009 UTC (8 years, 1 month ago) by gross
Original Path: trunk

some small additions to pycad to make life a bit easier.

Revision 2608 - Directory Listing
Modified Tue Aug 18 01:25:18 2009 UTC (8 years, 1 month ago) by jfenwick
Original Path: trunk

Updating Lutz' email

Revision 2607 - Directory Listing
Modified Tue Aug 18 01:02:56 2009 UTC (8 years, 1 month ago) by jfenwick
Original Path: trunk

Added getMPIWorldSum function to the esys.escript module.
This function takes an integer from each member of the MPIWorld.
This will hopefully address mantis issue 359

Added unit tests for most of the c++ free functions in the module.

Revision 2606 - Directory Listing
Modified Thu Aug 13 04:32:23 2009 UTC (8 years, 1 month ago) by ahallam
Original Path: trunk

Updates to first chapter in cookbook -> approaching completion.
New figures added for model descriptions.
Scripts updated to use pylab/matplotlib and movie making scripts added for *.avi creation.
Still to finalise in chapter 1
- twodheatdiff model of intrusion
	-contouring

- heat refraction scripts and begin cookbook sections
	- pycad discussion
	- steady state pde discussion
	- quiver plot discussion

Revision 2605 - Directory Listing
Modified Wed Aug 12 22:30:47 2009 UTC (8 years, 1 month ago) by gross
Original Path: trunk

some changes to the cook book

Revision 2604 - Directory Listing
Modified Wed Aug 12 01:21:46 2009 UTC (8 years, 1 month ago) by jfenwick
Original Path: trunk

The prefix option for building escript now works correctly.
This fixes mantis issue #362.

Revision 2603 - Directory Listing
Modified Wed Aug 12 00:44:35 2009 UTC (8 years, 1 month ago) by jfenwick
Original Path: trunk

Compute nodes will now read the correct options file and use the correct compiler.
I have added env_export to the service0 options file.
Use this if there are variables from the calling environment which need to be passed through scons. (In this case the INTEL_LICENSE_FILE variable).

There are still some issues with icpc linking.

Revision 2602 - Directory Listing
Modified Tue Aug 11 00:38:42 2009 UTC (8 years, 1 month ago) by jfenwick
Original Path: trunk

Merging changes made for release3.0 back to trunk.

Revision 2600 - Directory Listing
Modified Fri Aug 7 04:47:49 2009 UTC (8 years, 1 month ago) by jfenwick
Original Path: trunk

Using the 'agg' backend in matplotlib to avoid reference to the X Display.

Revision 2599 - Directory Listing
Modified Fri Aug 7 00:16:02 2009 UTC (8 years, 1 month ago) by caltinay
Original Path: trunk

saveESD: added option to save mesh at each timestep if required.

Revision 2598 - Directory Listing
Modified Thu Aug 6 03:47:56 2009 UTC (8 years, 1 month ago) by gross
Original Path: trunk

small fix in ReversedCurve clas

Revision 2597 - Directory Listing
Modified Thu Aug 6 03:30:09 2009 UTC (8 years, 1 month ago) by ahallam
Original Path: trunk

Updates to: cookbook documentation; heat refraction problems; mencoder investigation for *.png animation

Revision 2596 - Directory Listing
Modified Thu Aug 6 03:09:03 2009 UTC (8 years, 1 month ago) by lgao
Original Path: trunk

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

Revision 2595 - Directory Listing
Modified Thu Aug 6 00:49:09 2009 UTC (8 years, 1 month ago) by gross
Original Path: trunk

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

Revision 2594 - Directory Listing
Modified Thu Aug 6 00:47:48 2009 UTC (8 years, 1 month ago) by gross
Original Path: trunk

change to the default value for toListOfTuples

Revision 2592 - Directory Listing
Modified Thu Aug 6 00:43:19 2009 UTC (8 years, 1 month ago) by gross
Original Path: trunk

additional tests for the Locator

Revision 2588 - Directory Listing
Modified Wed Aug 5 22:42:36 2009 UTC (8 years, 1 month ago) by ahallam
Original Path: trunk

Heat diffraction initial committal 2 weeks work.

Revision 2581 - Directory Listing
Modified Wed Aug 5 01:11:33 2009 UTC (8 years, 1 month ago) by jfenwick
Original Path: trunk

Fixed unit test for missing matplotlib case.

Revision 2580 - Directory Listing
Modified Tue Aug 4 08:24:12 2009 UTC (8 years, 1 month ago) by gross
Original Path: trunk

another example for the usage of matplot lib added to users guide.

Revision 2578 - Directory Listing
Modified Tue Aug 4 04:05:36 2009 UTC (8 years, 1 month ago) by jfenwick
Original Path: trunk

Fixed problem with unit tests

Revision 2575 - Directory Listing
Modified Mon Aug 3 23:38:33 2009 UTC (8 years, 1 month ago) by jfenwick
Original Path: trunk

Fixed some grammar note about Lenny not working.

Revision 2574 - Directory Listing
Modified Mon Aug 3 09:09:20 2009 UTC (8 years, 1 month ago) by gross
Original Path: trunk

matplotlib description added to usersguide

Revision 2573 - Directory Listing
Modified Mon Aug 3 04:30:09 2009 UTC (8 years, 1 month ago) by gross
Original Path: trunk

some more fixes on solver options.

Revision 2568 - Directory Listing
Modified Fri Jul 31 05:37:41 2009 UTC (8 years, 1 month ago) by jfenwick
Original Path: trunk

Updated install guide to include the correct version of python.
Updated Mac build instructions not to use numarray or frameworks.
Removed (commented out) references to MacPorts in the Mac instructions.
- These need to be updated and Artak isn't here.

Removed (commented out) references to windows in the install guide.
CSIRO won't have a windows release ready yet.

Revision 2567 - Directory Listing
Modified Fri Jul 31 01:17:37 2009 UTC (8 years, 1 month ago) by jfenwick
Original Path: trunk

Added example options file for Mac

Revision 2566 - Directory Listing
Modified Wed Jul 29 01:39:16 2009 UTC (8 years, 1 month ago) by artak
Original Path: trunk

AMG on systems not supported yet exeption is added

Revision 2565 - Directory Listing
Modified Tue Jul 28 05:50:15 2009 UTC (8 years, 1 month ago) by artak
Original Path: trunk

stopping criteria is slightly changed.

Revision 2564 - Directory Listing
Modified Tue Jul 28 04:46:38 2009 UTC (8 years, 1 month ago) by gross
Original Path: trunk

reduced PDE solutions added to topography

Revision 2563 - Directory Listing
Modified Tue Jul 28 03:50:45 2009 UTC (8 years, 1 month ago) by gross
Original Path: trunk

reengineered version of the mountain class so it becomes easier to use for the convection code

Revision 2562 - Directory Listing
Modified Tue Jul 28 01:25:12 2009 UTC (8 years, 1 month ago) by artak
Original Path: trunk

inplace bugs are fixed

Revision 2561 - Directory Listing
Modified Mon Jul 27 07:38:45 2009 UTC (8 years, 1 month ago) by gross
Original Path: trunk

small bug in the calculation of the errors fixed.

Revision 2560 - Directory Listing
Modified Mon Jul 27 07:38:00 2009 UTC (8 years, 1 month ago) by gross
Original Path: trunk

a test for unique PropertySet name added.

Revision 2559 - Directory Listing
Modified Mon Jul 27 05:19:21 2009 UTC (8 years, 1 month ago) by artak
Original Path: trunk

typo: MaxIter changed IterMax

Revision 2558 - Directory Listing
Modified Mon Jul 27 05:03:32 2009 UTC (8 years, 1 month ago) by gross
Original Path: trunk

a table added showing the available solver options for finley paso.

Revision 2557 - Directory Listing
Modified Mon Jul 27 04:46:37 2009 UTC (8 years, 1 month ago) by artak
Original Path: trunk

minor comments changed

Revision 2556 - Directory Listing
Modified Mon Jul 27 02:05:20 2009 UTC (8 years, 1 month ago) by artak
Original Path: trunk

memory leack fixed

Revision 2555 - Directory Listing
Modified Mon Jul 27 01:50:16 2009 UTC (8 years, 1 month ago) by artak
Original Path: trunk

Pattern_free for Aggregiation coarsening is added.

Revision 2554 - Directory Listing
Modified Fri Jul 24 05:38:54 2009 UTC (8 years, 1 month ago) by gross
Original Path: trunk

bug with MKL call fixed.

Revision 2553 - Directory Listing
Modified Fri Jul 24 01:30:14 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Added another citation.

Revision 2551 - Directory Listing
Modified Thu Jul 23 09:19:15 2009 UTC (8 years, 2 months ago) by gross
Original Path: trunk

a problem with the sparse matrix unrolling fixed.

Revision 2550 - Directory Listing
Modified Tue Jul 21 03:36:13 2009 UTC (8 years, 2 months ago) by gross
Original Path: trunk

AMG throws an error now if block size not 1

Revision 2549 - Directory Listing
Modified Mon Jul 20 06:43:47 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Remainder of copyright date fixes

Revision 2548 - Directory Listing
Modified Mon Jul 20 06:20:06 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Updating copyright notices

Revision 2547 - Directory Listing
Modified Mon Jul 20 05:50:46 2009 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

More work on the install guide.

Revision 2546 - Directory Listing
Modified Mon Jul 20 05:35:08 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Updated builddeb script to include the architecture in the package filename.
(the architecture is also written into the control file).
Modified dependencies to not include VTK.
Added python-matplotlib as a "Recomends" dependency.

This means we can build 64bit debs now.

Revision 2545 - Directory Listing
Modified Mon Jul 20 04:54:57 2009 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

Install guide: fixed a minor typo

Revision 2544 - Directory Listing
Modified Mon Jul 20 04:50:38 2009 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

Enable building doxygen docs for the escriptreader library.

Revision 2543 - Directory Listing
Modified Mon Jul 20 04:38:21 2009 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

Install guide: fixed latex compilation due to incompatible hyperref package.

Revision 2542 - Directory Listing
Modified Mon Jul 20 04:18:27 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Importing esys.pyvisi now generates a warning.

Revision 2541 - Directory Listing
Modified Mon Jul 20 00:25:55 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Added matplotlib to the stand-alone path.
Removed VTK

Revision 2540 - Directory Listing
Modified Mon Jul 20 00:09:55 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Deprecating pyvisi in the user guide.

Revision 2539 - Directory Listing
Modified Sat Jul 18 02:47:34 2009 UTC (8 years, 2 months ago) by artak
Original Path: trunk

the line added in RS for symetricity brings factorization failure in heatedblock example

Revision 2538 - Directory Listing
Modified Fri Jul 17 06:24:15 2009 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

Install guide: Reworked introduction and enabled hyperref package

Revision 2537 - Directory Listing
Modified Fri Jul 17 05:50:35 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Operation_make_pyvisi_go_away: Stage 1 of PI

Removing pyvisi example files.

Revision 2536 - Directory Listing
Modified Thu Jul 16 23:53:07 2009 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

installguide: Fixed typos, minor semantics, repetitions and whitespace issues.

Revision 2535 - Directory Listing
Modified Thu Jul 16 23:39:58 2009 UTC (8 years, 2 months ago) by gross
Original Path: trunk

LinearPDE is now updating stiffness matrix and right hand side even only geometry is modified. fix for 333

Revision 2534 - Directory Listing
Modified Thu Jul 16 06:49:19 2009 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

Changed examples, tests and tutorials to save VTK files as .vtu instead .xml.
Visit doesn't know what to do with xml's and vtu is the proper extension
anyway.

Revision 2533 - Directory Listing
Modified Wed Jul 15 05:57:01 2009 UTC (8 years, 2 months ago) by gross
Original Path: trunk

finley delivers now a status identifier of the mesh.

Revision 2532 - Directory Listing
Modified Fri Jul 10 01:13:44 2009 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

libescriptreader: fixed a typo in configure script and added missing lib
to Makefile.

Revision 2531 - Directory Listing
Modified Thu Jul 9 23:56:57 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Setting always build on the api_epydoc target as a quick work around

Revision 2530 - Directory Listing
Modified Thu Jul 9 06:08:44 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Some changes relating to install from source.

Revision 2529 - Directory Listing
Modified Thu Jul 9 06:06:35 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Some changes to the install guide.
More work to do.

Revision 2528 - Directory Listing
Modified Wed Jul 8 23:27:49 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Added stand-alone example options file for install instructions.

Revision 2526 - Directory Listing
Modified Wed Jul 8 05:52:06 2009 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

util: Updated saveESD to allow saving of time series. Combined with an update
of the visit plugin this fixes issue 325.

Revision 2525 - Directory Listing
Modified Wed Jul 8 03:41:15 2009 UTC (8 years, 2 months ago) by caltinay
Original Path: trunk

libescriptreader: Added 'timestep increment' option to allow time series files
to be named like file.0, file.10, file.20 etc.

Revision 2524 - Directory Listing
Modified Wed Jul 8 00:39:26 2009 UTC (8 years, 2 months ago) by artak
Original Path: trunk

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

Revision 2523 - Directory Listing
Modified Wed Jul 8 00:07:36 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Fixed bug in MPI form of mkDir

Revision 2522 - Directory Listing
Modified Tue Jul 7 06:17:47 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Split test_util_spatial_functions.py into three python files (it had three classes in it).
This reduces memory required to compile down to about 600Mb each as opposed to >1Gb.

This should not affect the tests performed.

Revision 2521 - Directory Listing
Modified Tue Jul 7 00:08:58 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

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

Revision 2520 - Directory Listing
Modified Mon Jul 6 03:13:11 2009 UTC (8 years, 2 months ago) by artak
Original Path: trunk

AMG now takes as an input Paso_options for selecting coarsenening algorithm and treshold variable.

Revision 2519 - Directory Listing
Modified Mon Jul 6 00:43:08 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Correcting some doxygen errors

Revision 2518 - Directory Listing
Modified Fri Jul 3 07:43:11 2009 UTC (8 years, 2 months ago) by gross
Original Path: trunk

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

Revision 2517 - Directory Listing
Modified Fri Jul 3 05:27:45 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Fixed bug in Locator

Revision 2516 - Directory Listing
Modified Fri Jul 3 02:51:05 2009 UTC (8 years, 2 months ago) by gross
Original Path: trunk

files are not needed anymore.

Revision 2515 - Directory Listing
Modified Fri Jul 3 00:59:05 2009 UTC (8 years, 2 months ago) by gross
Original Path: trunk

missing files for documentation

Revision 2514 - Directory Listing
Modified Fri Jul 3 00:57:45 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Fixed compile warning on Mac

Revision 2513 - Directory Listing
Modified Thu Jul 2 08:42:11 2009 UTC (8 years, 2 months ago) by gross
Original Path: trunk

some fixes in wave.py example

Revision 2512 - Directory Listing
Modified Thu Jul 2 05:34:14 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Made the warnings against linking gomp a bit more detailed.
Commented out gomp from the linux sample.

Revision 2509 - Directory Listing
Modified Thu Jul 2 04:51:51 2009 UTC (8 years, 2 months ago) by artak
Original Path: trunk

Now one can choose coarsening method from python for AMG. Some commented lines are removed.

Revision 2508 - Directory Listing
Modified Thu Jul 2 04:33:25 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Ensured that example files are copied with build_py_tests rather than py_tests.
This means that:
build_full
will set up all the files ready for utest.sh

Revision 2507 - Directory Listing
Modified Thu Jul 2 03:14:35 2009 UTC (8 years, 2 months ago) by artak
Original Path: trunk

some profiling tools added

Revision 2506 - Directory Listing
Modified Thu Jul 2 01:23:30 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Fix to allow binary unit tests to run.
Note: I have only fixed the non-windows systems and I don't know if they
have the same problem.

Diagnosis of the utest problems continues.

Revision 2505 - Directory Listing
Modified Thu Jul 2 00:46:53 2009 UTC (8 years, 2 months ago) by lgao
Original Path: trunk

adding config file for Lin's machine

Revision 2504 - Directory Listing
Modified Wed Jul 1 07:27:17 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

First stage of fix to utest.sh

Revision 2503 - Directory Listing
Modified Wed Jul 1 05:05:08 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Fixing doc build so examples tar and zip are built properly.
Fixed image filenames in user guide.

Please do not put extensions on image files.

Revision 2502 - Directory Listing
Modified Tue Jun 30 05:49:22 2009 UTC (8 years, 2 months ago) by gross
Original Path: trunk

tests for examples added. utest is not working yet.

Revision 2501 - Directory Listing
Modified Tue Jun 30 04:43:01 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Caching now works.
Number of levels and nodes permitted in a lazy expression has increased to 70 and 15000.

Revision 2500 - Directory Listing
Modified Tue Jun 30 00:42:38 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Experimental per node cache for lazy evaluation is now available via the 
LAZY_NODE_STORAGE #define 
It's a bit slower and larger for small problems but a bit faster and 
smaller for large (drucker prager) problems.

Revision 2498 - Directory Listing
Modified Mon Jun 29 04:25:23 2009 UTC (8 years, 2 months ago) by gross
Original Path: trunk

new function MaskFromTag

Revision 2497 - Directory Listing
Modified Mon Jun 29 00:04:45 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Calling resolve now replaces resolved expression with an identity node.

Revision 2496 - Directory Listing
Modified Fri Jun 26 06:09:47 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Added lazy version of swapaxes operation.

Revision 2495 - Directory Listing
Modified Fri Jun 26 03:39:21 2009 UTC (8 years, 2 months ago) by ahallam
Original Path: trunk

Many revisions to Head Diff Documentation, One grammar correction to user guide.

Revision 2494 - Directory Listing
Modified Thu Jun 25 05:00:57 2009 UTC (8 years, 2 months ago) by ahallam
Original Path: trunk

Many updates to onedheatdiff in example and documentation. Still in need of some TLC however.

Revision 2493 - Directory Listing
Modified Thu Jun 25 02:58:52 2009 UTC (8 years, 2 months ago) by jfenwick
Original Path: trunk

Taipan now prints an error message if new[] throws.
Note, the exception is rethrown after the message is printed.

Revision 2492 - Directory Listing
Modified Wed Jun 24 01:28:57 2009 UTC (8 years, 2 months ago) by gross
Original Path: trunk

MPI_DOUBLE changed to MPI_INT as lowProc is int

Revision 2491 - Directory Listing
Modified Wed Jun 24 00:03:08 2009 UTC (8 years, 2 months ago) by gross
Original Path: trunk

some modifications to the OPENMPI launcher.

Revision 2490 - Directory Listing
Modified Tue Jun 23 06:02:26 2009 UTC (8 years, 3 months ago) by artak
Original Path: trunk

adjusting to new Paso_Options.

Revision 2489 - Directory Listing
Modified Tue Jun 23 06:00:25 2009 UTC (8 years, 3 months ago) by artak
Original Path: trunk

void *solver; is added to Paso_SpaseMatrix struct. Paso_MKL will need this.

Revision 2488 - Directory Listing
Modified Tue Jun 23 05:56:33 2009 UTC (8 years, 3 months ago) by artak
Original Path: trunk

Paso_MKL1 supports Paso_SparseMatrix type with offset1

Revision 2487 - Directory Listing
Modified Tue Jun 23 04:26:07 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

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

Revision 2486 - Directory Listing
Modified Tue Jun 23 03:38:54 2009 UTC (8 years, 3 months ago) by gross
Original Path: trunk

a bit more info are printed for the DarcyFlux now.

Revision 2485 - Directory Listing
Modified Mon Jun 22 07:27:31 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Added unit test file.

Revision 2484 - Directory Listing
Modified Mon Jun 22 04:22:19 2009 UTC (8 years, 3 months ago) by gross
Original Path: trunk

numarray removed from docu; Locator revised.

Revision 2483 - Directory Listing
Modified Mon Jun 22 03:33:43 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

And Joel closes the barn door.

Revision 2482 - Directory Listing
Modified Fri Jun 19 05:56:20 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Added run_data_access.py to unit tests - tests things like toListOfTuples.
Corrected some doco comments.
Added TestDomain class to escript.
This should allow more testing without resorting to finley.

Revision 2481 - Directory Listing
Modified Fri Jun 19 04:29:06 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Corrected a comment and fixed more bugs in the bulk copyFromArrayToOffset method.

Revision 2479 - Directory Listing
Modified Thu Jun 18 06:50:37 2009 UTC (8 years, 3 months ago) by gross
Original Path: trunk

paso returns now some diagnostics. SCSL has been removed.

Revision 2478 - Directory Listing
Modified Thu Jun 18 06:20:57 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Fixed bug when creating scalar expanded data.
Fixed some comments and moved a variable into anonymous namespace

Revision 2477 - Directory Listing
Modified Wed Jun 17 06:22:15 2009 UTC (8 years, 3 months ago) by gross
Original Path: trunk

modification to the cookbook

Revision 2476 - Directory Listing
Modified Wed Jun 17 04:42:13 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Added maxGlobalDataPoint.
Not currently unit tested.

Revision 2475 - Directory Listing
Modified Wed Jun 17 01:48:46 2009 UTC (8 years, 3 months ago) by artak
Original Path: trunk

AMG now takes into account new SolverOptions class, namely one can select coarsening algorithms from python. Not all options are included into AMG, this will be implemented later on.

Revision 2474 - Directory Listing
Modified Tue Jun 16 06:32:15 2009 UTC (8 years, 3 months ago) by gross
Original Path: trunk

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

Revision 2473 - Directory Listing
Modified Mon Jun 15 02:21:07 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Change logging functions so I don't get confused about what they do.
Added parameter to name the log file if called directly.

Revision 2472 - Directory Listing
Modified Thu Jun 11 23:33:47 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Added new params to control auto resolving for lazy data

Revision 2471 - Directory Listing
Modified Thu Jun 11 23:33:06 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Fixed extract of ndarray from xml to properly return booleans.
Modified some strings which had numarray:: in them

Revision 2470 - Directory Listing
Modified Thu Jun 11 08:32:32 2009 UTC (8 years, 3 months ago) by gross
Original Path: trunk

SolverOption class added. It is not linked with anything.

Revision 2469 - Directory Listing
Modified Thu Jun 11 04:52:14 2009 UTC (8 years, 3 months ago) by ahallam
Original Path: trunk

Week 11: Close to finishing wave equation, looking at adding friction to wave equation.

Revision 2468 - Directory Listing
Modified Thu Jun 11 02:55:51 2009 UTC (8 years, 3 months ago) by gross
Original Path: trunk

some more work toward numpy

Revision 2467 - Directory Listing
Modified Tue Jun 9 23:12:04 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Fixed a missing file.

Revision 2466 - Directory Listing
Modified Tue Jun 9 05:02:56 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Fixed build from source instructions for linux to include offscreen rendering by default!

Revision 2465 - Directory Listing
Modified Tue Jun 9 05:01:36 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Changed the default behaviour of Data::toListOfTuples() so that scalars are returned in tuples.
This is to match the behaviour of getTupleForDataPoint.

Revision 2464 - Directory Listing
Modified Tue Jun 9 04:14:07 2009 UTC (8 years, 3 months ago) by artak
Original Path: trunk

updated to use openmpi

Revision 2463 - Directory Listing
Modified Tue Jun 9 03:51:23 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Added an svn-ignore, added changes and references section to user guide.

Revision 2462 - Directory Listing
Modified Fri Jun 5 06:04:01 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Modified wrapper script to correctly point at numpy in standalone builds.
Updated build from source doco for linux to take numpy into account.
Also removed backticks in favour of $()  - it should be the same but latex won't eat them

Revision 2461 - Directory Listing
Modified Fri Jun 5 05:06:31 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Trying to presize a list to reduce runtime of toListOfTuples

Revision 2460 - Directory Listing
Modified Fri Jun 5 05:04:45 2009 UTC (8 years, 3 months ago) by ahallam
Original Path: trunk

Week 10:
Continued work on wave equation and tutorial write up.

Revision 2459 - Directory Listing
Modified Thu Jun 4 06:17:54 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Removed some commented out code.
Added toListOfTuples to the DataObject.

Revision 2458 - Directory Listing
Modified Wed Jun 3 06:18:21 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Various numarray erasures

Revision 2456 - Directory Listing
Modified Wed Jun 3 03:54:25 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Switching savanna scons to use python-2.6.2 and boost-1.39

Revision 2455 - Directory Listing
Modified Wed Jun 3 03:29:07 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

Merging changes from numpy branch.

Revision 2450 - Directory Listing
Modified Tue Jun 2 01:22:11 2009 UTC (8 years, 3 months ago) by artak
Original Path: trunk

First version of 'greedy' algorithm for Ruge Stuben and Aggregiation.

Revision 2448 - Directory Listing
Modified Fri May 29 04:47:48 2009 UTC (8 years, 3 months ago) by ahallam
Original Path: trunk

Week 9: implemented cosine taper for wave function, need to work on direct method without lumping, wave propagation velocity is still not correct

Revision 2446 - Directory Listing
Modified Fri May 29 04:24:01 2009 UTC (8 years, 3 months ago) by gross
Original Path: trunk

same adjustment of nameing

Revision 2445 - Directory Listing
Modified Fri May 29 03:23:25 2009 UTC (8 years, 3 months ago) by gross
Original Path: trunk

some improvement on convection which ios now working again

Revision 2443 - Directory Listing
Modified Fri May 29 01:44:22 2009 UTC (8 years, 3 months ago) by ahallam
Original Path: trunk

Fixing some things

Revision 2442 - Directory Listing
Modified Fri May 29 00:39:44 2009 UTC (8 years, 3 months ago) by artak
Original Path: trunk

Some bugs are fixed.

Revision 2440 - Directory Listing
Modified Wed May 27 08:45:55 2009 UTC (8 years, 3 months ago) by gross
Original Path: trunk

convection works now again.

Revision 2439 - Directory Listing
Modified Tue May 26 04:34:21 2009 UTC (8 years, 3 months ago) by artak
Original Path: trunk

AMG now works with blocksize 3. Logical block sizes replaced with real block size before starting AMG. But this happens only when we use AMG as a preconditioner.

Revision 2438 - Directory Listing
Modified Tue May 26 02:26:52 2009 UTC (8 years, 3 months ago) by gross
Original Path: trunk

new version of power law (blame Hans)

Revision 2436 - Directory Listing
Modified Mon May 25 05:05:00 2009 UTC (8 years, 3 months ago) by jfenwick
Original Path: trunk

A fix for escript not compiling on boost 1.39.

Revision 2434 - Directory Listing
Modified Thu May 21 07:59:53 2009 UTC (8 years, 4 months ago) by ahallam
Original Path: trunk

Week 8: Still working on seismic wave propagation. Need to come up with a smooth source function next week. All TEXT files up to date.

Revision 2433 - Directory Listing
Modified Wed May 20 08:43:43 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

some documentation on power law added

Revision 2432 - Directory Listing
Modified Wed May 20 06:06:20 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

power law and incompressible flow is running now

Revision 2431 - Directory Listing
Modified Wed May 20 03:39:57 2009 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Added at the request of Dian.

Revision 2430 - Directory Listing
Modified Wed May 20 03:20:57 2009 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Use Variables class instead of Options in scons versions which support 
it.

Revision 2429 - Directory Listing
Modified Tue May 19 10:04:54 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

pycad allows noe to set the number of elements per line and the generation of quadrilateral elements over serfaces.

Revision 2428 - Directory Listing
Modified Tue May 19 04:04:11 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

problem for python2.4 fixed: IOError has no attribute message.

Revision 2427 - Directory Listing
Modified Fri May 15 04:29:01 2009 UTC (8 years, 4 months ago) by ahallam
Original Path: trunk

Week 7: Work done on wave problem.

Revision 2426 - Directory Listing
Modified Fri May 15 04:28:31 2009 UTC (8 years, 4 months ago) by ahallam
Original Path: trunk

Week 7: Work done on wave problem.

Revision 2425 - Directory Listing
Modified Thu May 14 09:06:35 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

bug in getListOfTags fixed and some tested added

Revision 2424 - Directory Listing
Modified Thu May 14 05:15:47 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

small bug fixed.

Revision 2423 - Directory Listing
Modified Thu May 14 05:02:20 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

* handling LD_LIBRARY_PATH for Windows (that only uses PATH)
* passing PATH env var in mpi call for Windows

Revision 2422 - Directory Listing
Modified Thu May 14 03:17:28 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

bug in testing saveVTK fixed

Revision 2421 - Directory Listing
Modified Thu May 14 02:29:06 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

vtk writer supports now meta data and meta data schema

Revision 2420 - Directory Listing
Modified Thu May 14 02:28:58 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

vtk writer supports now meta data and meta data schema

Revision 2419 - Directory Listing
Modified Thu May 14 01:56:18 2009 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Use os.path.join instead of os.sep in tests
If you can read this message it means svn commit mails are working again.
... Or you are looking at the logs

Revision 2418 - Directory Listing
Modified Wed May 13 08:36:04 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

redirect stdout to NULL instead of /dev/null for Windows

Revision 2417 - Directory Listing
Modified Wed May 13 08:18:47 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

some remarks on load and dump added to the users guide.

Revision 2416 - Directory Listing
Modified Wed May 13 06:03:59 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

* fix Windows MPI case: export system variables
* define ESCRIPT_NUM_PROC and ESCRIPT_NUM_NODES
* cleanup using os.path.join()

Revision 2415 - Directory Listing
Modified Wed May 13 02:48:39 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

FileWriter added: this class takes care of writing data which are global in MPI to a file. It is recommended to use this class rather then the build in open as it takes care of the case of many processors.

Revision 2414 - Directory Listing
Modified Tue May 12 03:33:49 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

added flags (commented out) to compile MPI version on Windows (Visual Studio 2003) using MPICH2

Revision 2413 - Directory Listing
Modified Tue May 12 01:26:20 2009 UTC (8 years, 4 months ago) by artak
Original Path: trunk

There was a bug in computing logical_block_size. It was always returning 0.

Revision 2412 - Directory Listing
Modified Fri May 8 04:27:17 2009 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Clean up cookbook-
Cleaned up the svn:ignore
removed some latex intermediate files

Revision 2411 - Directory Listing
Modified Fri May 8 03:13:15 2009 UTC (8 years, 4 months ago) by ahallam
Original Path: trunk

Week 6 I think?? Started work on 2d wave solution, want to change from verlet according to lutz. Have semi finished heat diffusion but is ready for review and further modification in the future. Added new sections to first chapter, may or may not be needed but added as a reminder anyway.

Revision 2409 - Directory Listing
Modified Tue May 5 06:22:11 2009 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

bin/escript is now under version control.
The wrapper template is no longer used.
Extraneous output doc removed from scons during build.

note: finleypython is no longer built (it was deprecated anyway).

Revision 2405 - Directory Listing
Modified Wed Apr 29 23:57:38 2009 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Another attempt at building the doco.
--transform is not supported by savanna's tar

Revision 2404 - Directory Listing
Modified Wed Apr 29 06:53:36 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

documentation for units added.

Revision 2403 - Directory Listing
Modified Wed Apr 29 06:08:18 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

units support Celsius, Farenheit and kelvin now

Revision 2402 - Directory Listing
Modified Wed Apr 29 06:02:21 2009 UTC (8 years, 4 months ago) by jfenwick
Original Path: trunk

Fixing the build of example tar and zip files so they don't have full 
paths.

Revision 2401 - Directory Listing
Modified Wed Apr 29 04:23:07 2009 UTC (8 years, 4 months ago) by ahallam
Original Path: trunk

End Week 5:
Renamed *.tex files to more logical, changed to chapter format as HEAT_DIFFUSION.tex
Editted and Reviewed text portion and some python scripts for heat diffusion.
Looking to push for finalisation on heat diffusion in the next couple of week to begin next modelling problem/Chapter.

Revision 2399 - Directory Listing
Modified Tue Apr 28 12:04:34 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

some improvements on units

Revision 2398 - Directory Listing
Modified Tue Apr 28 04:41:53 2009 UTC (8 years, 4 months ago) by gross
Original Path: trunk

first version of units in escript

Revision 2397 - Directory Listing
Modified Fri Apr 24 04:24:28 2009 UTC (8 years, 4 months ago) by ahallam
Original Path: trunk

End Week 4, Finalised 1D examples, need work on text but script ok.
Begining of 2D example builds on 1D. Script semi-finalised, text to complete.

Revision 2394 - Directory Listing
Modified Fri Apr 17 01:32:30 2009 UTC (8 years, 5 months ago) by caltinay
Original Path: trunk

Updated shake75 options file.

Revision 2393 - Directory Listing
Modified Thu Apr 16 04:24:07 2009 UTC (8 years, 5 months ago) by ahallam
Original Path: trunk

End Day Commit
Working on onedheatdiff_var001

Revision 2392 - Directory Listing
Modified Thu Apr 16 01:53:23 2009 UTC (8 years, 5 months ago) by ahallam
Original Path: trunk

Initial Commital of CookBook to SVN
Has 2.5 Weeks work and semi completed first heat diffusion tutorial

Revision 2391 - Directory Listing
Modified Thu Apr 16 01:08:57 2009 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Minor tweak to title page.
Better handling of alternative names in SConstruct.

Revision 2390 - Directory Listing
Modified Wed Apr 15 06:46:42 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

some minor fixes.

Revision 2389 - Directory Listing
Modified Wed Apr 15 06:46:01 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

some minor fixes.

Revision 2388 - Directory Listing
Modified Wed Apr 15 06:21:25 2009 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

scons files executed on compute nodes will use the config file for the service node (when we get the other issues 
sorted).

Revision 2387 - Directory Listing
Modified Wed Apr 15 05:05:27 2009 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Changed the figure eps->pdf to use a builder to make hypothetical windows doc building easier.

Revision 2386 - Directory Listing
Modified Wed Apr 15 03:54:25 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

some minor fixes

Revision 2385 - Directory Listing
Modified Wed Apr 15 03:52:38 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

two fixes dealing with zero samples under MPI

Revision 2384 - Directory Listing
Modified Wed Apr 15 00:17:20 2009 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Added getDataRW to DataC

Revision 2383 - Directory Listing
Modified Tue Apr 14 03:53:56 2009 UTC (8 years, 5 months ago) by artak
Original Path: trunk

-h parameter added for help

Revision 2382 - Directory Listing
Modified Tue Apr 14 03:48:22 2009 UTC (8 years, 5 months ago) by artak
Original Path: trunk

Testing environment now mor flexible. Added a lot of options.

Revision 2381 - Directory Listing
Modified Tue Apr 14 03:46:59 2009 UTC (8 years, 5 months ago) by artak
Original Path: trunk

Ruge Stuben and Aggregiation is added for testing performance of AMG solver.

Revision 2378 - Directory Listing
Modified Thu Apr 9 01:09:08 2009 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Added warning when openmp params are specified by escript was build without openmp.
escript now reports the number of threads requested.

Revision 2377 - Directory Listing
Modified Wed Apr 8 07:57:55 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

a namespace  problem in pycad fixed.

Revision 2376 - Directory Listing
Modified Tue Apr 7 06:21:31 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

output form others than the master process can now be switched off (stderr is still redirected to master)

Revision 2374 - Directory Listing
Modified Tue Apr 7 00:26:49 2009 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Modified utest to use the wrapper script.

Revision 2373 - Directory Listing
Modified Mon Apr 6 23:49:31 2009 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Minor spelling and man page tweaks.

Revision 2372 - Directory Listing
Modified Mon Apr 6 23:36:15 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

changes to the urls

Revision 2371 - Directory Listing
Modified Mon Apr 6 11:48:32 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

missing  citations and references added

Revision 2370 - Directory Listing
Modified Mon Apr 6 06:41:49 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

some modifications to docu for MPI

Revision 2369 - Directory Listing
Modified Mon Apr 6 05:32:12 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

some fixed for mpich2

Revision 2368 - Directory Listing
Modified Mon Apr 6 05:05:35 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

some fixes for MKL and Mpisize>1

Revision 2367 - Directory Listing
Modified Mon Apr 6 04:51:49 2009 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Added version number to deb files.
Fixed tests to check for ppmtompeg before running

Revision 2366 - Directory Listing
Modified Mon Apr 6 03:10:55 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

starter for MPICH and MPICH2 add

Revision 2365 - Directory Listing
Modified Mon Apr 6 01:25:25 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

all tests passed under scons on 4 mpi processes with  openmpi on shake34

Revision 2364 - Directory Listing
Modified Fri Apr 3 08:06:30 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

MPI intel works now for the escript wrapper.

Revision 2363 - Directory Listing
Modified Fri Apr 3 03:56:19 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

scons should now be able to run tests under MPI and OpenMP

Revision 2362 - Directory Listing
Modified Fri Apr 3 02:41:14 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

escript wrapper does not use Compiled.with.*

Revision 2361 - Directory Listing
Modified Fri Apr 3 00:37:25 2009 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Hopefully fixing the bad figures.
It turns out latex2html can not handle the optional angle= param in 
\includegraphics

Revision 2360 - Directory Listing
Modified Thu Apr 2 04:12:12 2009 UTC (8 years, 5 months ago) by artak
Original Path: trunk

AMG now checks how many elemens left. if n_F<500, then it does not coursen further.

Revision 2359 - Directory Listing
Modified Thu Apr 2 03:50:33 2009 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Moved man page for easier testing.
Modified the wrapper script to take into account debian packaging.
This setting is recorded in the escript wrapper automatically by the package building script.

Revision 2358 - Directory Listing
Modified Wed Apr 1 22:25:24 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

mpi is not really ready yet.

Revision 2357 - Directory Listing
Modified Wed Apr 1 06:01:56 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

fixes to run escript command with SGI MPT

Revision 2356 - Directory Listing
Modified Wed Apr 1 04:46:22 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

more on escript command.

Revision 2354 - Directory Listing
Modified Wed Apr 1 04:01:58 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

some modifications to the Darcy flux solver to make it faster and more robust.

Revision 2353 - Directory Listing
Modified Wed Apr 1 01:49:47 2009 UTC (8 years, 5 months ago) by artak
Original Path: trunk

AMG levels parameter moved to options file. Now one can set how many levels AMG will go in SetDefauls. Default value is 3.

Revision 2352 - Directory Listing
Modified Wed Apr 1 01:15:15 2009 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Updated doco to reflect changed env variables

Revision 2351 - Directory Listing
Modified Tue Mar 31 08:26:41 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

some fixes in the transport solver

Revision 2350 - Directory Listing
Modified Tue Mar 31 08:26:05 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

more escript wrapper stuff

Revision 2349 - Directory Listing
Modified Mon Mar 30 08:14:23 2009 UTC (8 years, 5 months ago) by gross
Original Path: trunk

first version of escript command: no MPI support yet.

Revision 2347 - Directory Listing
Modified Mon Mar 30 06:07:47 2009 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Added windows notes to install guide.

Revision 2346 - Directory Listing
Modified Mon Mar 30 05:05:44 2009 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Added instructions to test installations.

Revision 2345 - Directory Listing
Modified Mon Mar 30 04:44:06 2009 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Added proper man page (with formatting and everything).
Updated package description.

Revision 2344 - Directory Listing
Modified Mon Mar 30 02:13:58 2009 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Change __url__ to launchpad site

Revision 2343 - Directory Listing
Modified Mon Mar 30 01:34:45 2009 UTC (8 years, 5 months ago) by jfenwick
Original Path: trunk

Added -b option to wrapper script. For the running of non-python 
binaries.