[escript] Log of /trunk/ripley

Revision 5254 - Directory Listing
Modified Mon Nov 10 09:30:53 2014 UTC (5 years ago) by caltinay

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

Revision 5237 - Directory Listing
Modified Wed Oct 29 04:28:59 2014 UTC (5 years, 1 month ago) by caltinay

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

Revision 5231 - Directory Listing
Modified Tue Oct 28 21:21:15 2014 UTC (5 years, 1 month ago) by caltinay

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

Revision 5226 - Directory Listing
Modified Mon Oct 27 05:04:07 2014 UTC (5 years, 1 month ago) by sshaw

extending speckley->ripley interpolation to support MPI

Revision 5220 - Directory Listing
Modified Thu Oct 23 03:50:37 2014 UTC (5 years, 1 month ago) by caltinay

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

Revision 5212 - Directory Listing
Modified Wed Oct 22 05:06:48 2014 UTC (5 years, 1 month ago) by caltinay

Preparing ripley SystemMatrix tests.

Revision 5209 - Directory Listing
Modified Tue Oct 21 06:50:20 2014 UTC (5 years, 1 month ago) by caltinay

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

Revision 5205 - Directory Listing
Modified Wed Oct 15 22:39:30 2014 UTC (5 years, 1 month ago) by caltinay

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

Revision 5191 - Directory Listing
Modified Thu Oct 2 04:40:20 2014 UTC (5 years, 2 months ago) by sshaw

adding speckley to ripley interpolation (single process only)

Revision 5187 - Directory Listing
Modified Wed Oct 1 06:49:24 2014 UTC (5 years, 2 months ago) by caltinay

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

Revision 5186 - Directory Listing
Modified Wed Oct 1 06:18:02 2014 UTC (5 years, 2 months ago) by sshaw

fixing misplaced dirac points in ripley domains with enormous elements

Revision 5174 - Directory Listing
Modified Thu Sep 25 01:45:59 2014 UTC (5 years, 2 months ago) by caltinay

Report number of matrix entries if verbosity is on.

Revision 5172 - Directory Listing
Modified Wed Sep 24 06:59:22 2014 UTC (5 years, 2 months ago) by caltinay

Implemented writeBinaryGrid for Solution (DegreesOfFreedom). Fixes #280

Revision 5170 - Directory Listing
Modified Wed Sep 24 00:30:39 2014 UTC (5 years, 2 months ago) by sshaw

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

Revision 5164 - Directory Listing
Modified Wed Sep 17 11:26:09 2014 UTC (5 years, 2 months ago) by caltinay

Slightly better error reporting from CUDA.

Revision 5159 - Directory Listing
Modified Wed Sep 17 05:19:56 2014 UTC (5 years, 2 months ago) by caltinay

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

Revision 5148 - Directory Listing
Modified Mon Sep 15 01:25:23 2014 UTC (5 years, 2 months ago) by caltinay

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

Revision 5121 - Directory Listing
Modified Wed Aug 20 10:32:40 2014 UTC (5 years, 3 months ago) by caltinay

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

Revision 5120 - Directory Listing
Modified Wed Aug 20 06:19:20 2014 UTC (5 years, 3 months ago) by caltinay

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

Revision 5119 - Directory Listing
Modified Wed Aug 20 04:10:01 2014 UTC (5 years, 3 months ago) by caltinay

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

Revision 5118 - Directory Listing
Modified Mon Aug 18 11:28:55 2014 UTC (5 years, 3 months ago) by caltinay

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

Revision 5117 - Directory Listing
Modified Mon Aug 18 05:42:09 2014 UTC (5 years, 3 months ago) by caltinay

Further untangled/simplified paso pattern generation in ripley.

Revision 5114 - Directory Listing
Modified Thu Aug 14 05:15:31 2014 UTC (5 years, 3 months ago) by caltinay

Preliminary changes to make ripley ready for other System Matrixes.

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

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

Revision 5106 - Directory Listing
Modified Mon Jul 21 11:57:42 2014 UTC (5 years, 4 months ago) by caltinay

Avoid some unnecessary reallocation.

Revision 5098 - Directory Listing
Modified Sun Jul 13 14:33:43 2014 UTC (5 years, 4 months ago) by caltinay

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

Revision 5097 - Directory Listing
Modified Sun Jul 13 01:02:24 2014 UTC (5 years, 4 months ago) by caltinay

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

Revision 5096 - Directory Listing
Modified Fri Jul 11 12:32:49 2014 UTC (5 years, 4 months ago) by caltinay

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

Revision 5077 - Directory Listing
Modified Tue Jun 24 03:51:19 2014 UTC (5 years, 5 months ago) by caltinay

Make readBinaryGrid "public" within the ripley module.

Revision 5061 - Directory Listing
Modified Fri Jun 20 04:10:59 2014 UTC (5 years, 5 months ago) by jfenwick

Added descriptive information to functionspace names

Revision 5059 - Directory Listing
Modified Fri Jun 20 03:10:19 2014 UTC (5 years, 5 months ago) by sshaw

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

Revision 5058 - Directory Listing
Modified Fri Jun 20 02:03:28 2014 UTC (5 years, 5 months ago) by sshaw

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

Revision 5054 - Directory Listing
Modified Fri Jun 20 00:59:16 2014 UTC (5 years, 5 months ago) by caltinay

test name changes so they run again.

Revision 5051 - Directory Listing
Modified Wed Jun 18 05:08:02 2014 UTC (5 years, 5 months ago) by caltinay

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

Revision 5044 - Directory Listing
Modified Fri Jun 13 01:51:58 2014 UTC (5 years, 5 months ago) by caltinay

fixed compiler warnings that appeared due to removing the exceptions.

Revision 5042 - Directory Listing
Modified Thu Jun 12 06:40:11 2014 UTC (5 years, 5 months ago) by caltinay

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

Revision 5038 - Directory Listing
Modified Thu Jun 12 04:58:56 2014 UTC (5 years, 5 months ago) by caltinay

Missed a few. Should be almost done.

Revision 5027 - Directory Listing
Modified Wed Jun 11 07:32:26 2014 UTC (5 years, 5 months ago) by caltinay

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

Revision 5017 - Directory Listing
Modified Tue Jun 10 02:16:18 2014 UTC (5 years, 6 months ago) by sshaw

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

Revision 5016 - Directory Listing
Modified Mon Jun 9 09:54:18 2014 UTC (5 years, 6 months ago) by caltinay

"The Queen's commit". Happy birthday,

Revision 5015 - Directory Listing
Modified Sun Jun 8 13:09:16 2014 UTC (5 years, 6 months ago) by caltinay

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

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

Revision 5012 - Directory Listing
Modified Fri Jun 6 07:23:36 2014 UTC (5 years, 6 months ago) by caltinay

writeBinaryGrid tests. big endian doubles fail currently.

Revision 5009 - Directory Listing
Modified Fri Jun 6 04:36:13 2014 UTC (5 years, 6 months ago) by caltinay

deleted strange file which doesn't belong here.

Revision 5008 - Directory Listing
Modified Fri Jun 6 04:31:41 2014 UTC (5 years, 6 months ago) by caltinay

some cleanup, renaming and fixing of ripley tests.

Revision 4984 - Directory Listing
Modified Mon Jun 2 02:50:34 2014 UTC (5 years, 6 months ago) by sshaw

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

Revision 4978 - Directory Listing
Modified Thu May 29 11:55:53 2014 UTC (5 years, 6 months ago) by caltinay

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

Revision 4969 - Directory Listing
Modified Mon May 26 23:50:52 2014 UTC (5 years, 6 months ago) by sshaw

fixing intel's hidden function warning

Revision 4957 - Directory Listing
Modified Wed May 21 01:31:23 2014 UTC (5 years, 6 months ago) by caltinay

Missed a few unittest wrapper imports.

Revision 4943 - Directory Listing
Modified Thu May 15 04:58:35 2014 UTC (5 years, 6 months ago) by sshaw

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

Revision 4942 - Directory Listing
Modified Thu May 15 03:42:28 2014 UTC (5 years, 6 months ago) by sshaw

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

Revision 4938 - Directory Listing
Modified Wed May 14 01:13:23 2014 UTC (5 years, 6 months ago) by jfenwick

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

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

Revision 4934 - Directory Listing
Modified Tue May 13 00:28:11 2014 UTC (5 years, 6 months ago) by jfenwick

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

Revision 4874 - Directory Listing
Modified Thu Apr 17 01:13:10 2014 UTC (5 years, 7 months ago) by sshaw

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

Revision 4872 - Directory Listing
Modified Wed Apr 16 06:08:06 2014 UTC (5 years, 7 months ago) by sshaw

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

Revision 4861 - Directory Listing
Modified Thu Apr 10 05:17:47 2014 UTC (5 years, 8 months ago) by sshaw

added exception for domain sizes that cause integer overflows

Revision 4860 - Directory Listing
Modified Thu Apr 10 04:08:42 2014 UTC (5 years, 8 months ago) by sshaw

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

Revision 4851 - Directory Listing
Modified Wed Apr 9 03:30:36 2014 UTC (5 years, 8 months ago) by sshaw

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

Revision 4836 - Directory Listing
Modified Mon Apr 7 05:51:55 2014 UTC (5 years, 8 months ago) by caltinay

"Some" SystemMatrix clean up.....

Revision 4828 - Directory Listing
Modified Wed Apr 2 07:01:38 2014 UTC (5 years, 8 months ago) by sshaw

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 (5 years, 8 months ago) by sshaw

dropping out of domain dirac points for ripley Brick as well

Revision 4826 - Directory Listing
Modified Wed Apr 2 03:54:18 2014 UTC (5 years, 8 months ago) by sshaw

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

Revision 4821 - Directory Listing
Modified Tue Apr 1 04:58:33 2014 UTC (5 years, 8 months ago) by sshaw

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 4816 - Directory Listing
Modified Fri Mar 28 06:16:02 2014 UTC (5 years, 8 months ago) by caltinay

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

Revision 4814 - Directory Listing
Modified Fri Mar 28 04:31:02 2014 UTC (5 years, 8 months ago) by caltinay

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 (5 years, 8 months ago) by sshaw

moving away from shared pointers in domain components

Revision 4807 - Directory Listing
Modified Thu Mar 27 04:49:38 2014 UTC (5 years, 8 months ago) by caltinay

2 fixes to dirac points which fixes #240.

Revision 4806 - Directory Listing
Modified Thu Mar 27 03:03:13 2014 UTC (5 years, 8 months ago) by sshaw

fixed fetch error in type collation for lame assembler

Revision 4805 - Directory Listing
Modified Thu Mar 27 01:31:59 2014 UTC (5 years, 8 months ago) by sshaw

changing 2D wave assembler to use shared domain pointer

Revision 4803 - Directory Listing
Modified Wed Mar 26 06:52:28 2014 UTC (5 years, 8 months ago) by caltinay

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

Revision 4801 - Directory Listing
Modified Wed Mar 26 03:26:58 2014 UTC (5 years, 8 months ago) by caltinay

paso::Coupler and paso::Connector.

Revision 4799 - Directory Listing
Modified Wed Mar 26 00:37:59 2014 UTC (5 years, 8 months ago) by sshaw

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

Revision 4780 - Directory Listing
Modified Thu Mar 20 03:19:54 2014 UTC (5 years, 8 months ago) by sshaw

fixing a race condition in file tests

Revision 4779 - Directory Listing
Modified Thu Mar 20 01:52:49 2014 UTC (5 years, 8 months ago) by jfenwick

Temporarily adjusting magic numbers

Revision 4776 - Directory Listing
Modified Wed Mar 19 23:31:00 2014 UTC (5 years, 8 months ago) by caltinay

Removed some superfluous checks and typos.

Revision 4775 - Directory Listing
Modified Wed Mar 19 23:12:53 2014 UTC (5 years, 8 months ago) by caltinay

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 (5 years, 8 months ago) by sshaw

removing ridiculous remaining return

Revision 4771 - Directory Listing
Modified Wed Mar 19 04:22:37 2014 UTC (5 years, 8 months ago) by sshaw

fixed multiple ranks trying to unlink tempfiles

Revision 4770 - Directory Listing
Modified Wed Mar 19 03:48:43 2014 UTC (5 years, 8 months ago) by sshaw

relevant tests skipped if not built with USE_BOOSTIO

Revision 4769 - Directory Listing
Modified Wed Mar 19 03:43:52 2014 UTC (5 years, 8 months ago) by sshaw

added missing ifdefs for library presence

Revision 4766 - Directory Listing
Modified Wed Mar 19 00:57:21 2014 UTC (5 years, 8 months ago) by sshaw

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 (5 years, 8 months ago) by sshaw

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

Revision 4761 - Directory Listing
Modified Tue Mar 18 00:25:55 2014 UTC (5 years, 8 months ago) by sshaw

fixed partially overridden class warnings with intel compiler

Revision 4760 - Directory Listing
Modified Mon Mar 17 23:48:37 2014 UTC (5 years, 8 months ago) by sshaw

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

Revision 4755 - Directory Listing
Modified Mon Mar 17 02:58:52 2014 UTC (5 years, 8 months ago) by sshaw

added conflict test for ripley Brick

Revision 4753 - Directory Listing
Modified Mon Mar 17 02:39:44 2014 UTC (5 years, 8 months ago) by sshaw

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

Revision 4738 - Directory Listing
Modified Wed Mar 12 01:32:36 2014 UTC (5 years, 8 months ago) by sshaw

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 (5 years, 9 months ago) by sshaw

fixing/completing 2D lame assembler

Revision 4722 - Directory Listing
Modified Wed Mar 5 05:29:25 2014 UTC (5 years, 9 months ago) by sshaw

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 (5 years, 9 months ago) by jfenwick

Fixing strange casts.
Removed old methods.

Revision 4720 - Directory Listing
Modified Fri Feb 28 01:38:09 2014 UTC (5 years, 9 months ago) by sshaw

ripley now tested with lame, helmholtz and nolumping linear PDEs

Revision 4717 - Directory Listing
Modified Thu Feb 27 12:30:04 2014 UTC (5 years, 9 months ago) by jfenwick

Fix copy error from 3d down to 2d.

Revision 4716 - Directory Listing
Modified Thu Feb 27 11:02:55 2014 UTC (5 years, 9 months ago) by jfenwick

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

Revision 4714 - Directory Listing
Modified Thu Feb 27 05:04:15 2014 UTC (5 years, 9 months ago) by sshaw

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

Revision 4712 - Directory Listing
Modified Wed Feb 26 04:08:41 2014 UTC (5 years, 9 months ago) by sshaw

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

Revision 4710 - Directory Listing
Modified Mon Feb 24 03:41:06 2014 UTC (5 years, 9 months ago) by jfenwick

Fixing not enough elements for small numbers of ranks in test

Revision 4709 - Directory Listing
Modified Mon Feb 24 01:31:00 2014 UTC (5 years, 9 months ago) by jfenwick

Failed to take ripley padding into account when constructing tests.

Revision 4705 - Directory Listing
Modified Fri Feb 21 02:36:15 2014 UTC (5 years, 9 months ago) by jfenwick

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

Revision 4703 - Directory Listing
Modified Fri Feb 21 00:55:31 2014 UTC (5 years, 9 months ago) by jfenwick

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 4696 - Directory Listing
Modified Wed Feb 19 07:29:50 2014 UTC (5 years, 9 months ago) by jfenwick

Correcting python libname for sage.
Fixing bug where the number of values in the shape was not considered for buffer and message size.

Revision 4693 - Directory Listing
Modified Wed Feb 19 06:04:28 2014 UTC (5 years, 9 months ago) by sshaw

adding HTI support to 3D wave assembler

Revision 4692 - Directory Listing
Modified Wed Feb 19 05:26:55 2014 UTC (5 years, 9 months ago) by sshaw

fixed duplication for 2D constant data in wave assembler

Revision 4691 - Directory Listing
Modified Wed Feb 19 05:23:17 2014 UTC (5 years, 9 months ago) by sshaw

added support for HTI waves to the fast wave assembler

Revision 4687 - Directory Listing
Modified Wed Feb 19 00:03:29 2014 UTC (5 years, 9 months ago) by jfenwick

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 4684 - Directory Listing
Modified Tue Feb 18 01:17:02 2014 UTC (5 years, 9 months ago) by jduplessis

Removing Finley mesh import which was copied from run_linearPdeOnFinley... as it is not used.

Revision 4683 - Directory Listing
Modified Mon Feb 17 07:03:40 2014 UTC (5 years, 9 months ago) by jduplessis

adding nonlinearpde test for ripley.

Revision 4675 - Directory Listing
Modified Mon Feb 17 01:07:12 2014 UTC (5 years, 9 months ago) by sshaw

expanded tab chars for consistentcy and removed trailing whitespace

Revision 4668 - Directory Listing
Modified Tue Feb 11 03:44:10 2014 UTC (5 years, 9 months ago) by jfenwick

Improvements but still needs more validation

Revision 4661 - Directory Listing
Modified Fri Feb 7 03:10:15 2014 UTC (5 years, 10 months ago) by sshaw

more informative exception for unsupported error message

Revision 4660 - Directory Listing
Modified Fri Feb 7 03:08:49 2014 UTC (5 years, 10 months ago) by sshaw

fixed dirac point->node mapping issues in ripley when using mpi

Revision 4657 - Directory Listing
Modified Thu Feb 6 06:12:20 2014 UTC (5 years, 10 months ago) by jfenwick

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

Revision 4653 - Directory Listing
Modified Wed Feb 5 05:20:41 2014 UTC (5 years, 10 months ago) by jfenwick

Made index chars unsigned to prevent warnings

Revision 4652 - Directory Listing
Modified Wed Feb 5 05:15:07 2014 UTC (5 years, 10 months ago) by jfenwick

Made index chars unsigned to prevent warnings

Revision 4650 - Directory Listing
Modified Wed Feb 5 04:16:01 2014 UTC (5 years, 10 months ago) by jfenwick

Fixed a spelling error and missing virtual (not sure that one matters).
Added _untested_ 3D gaussian smoothed random data

Revision 4645 - Directory Listing
Modified Mon Feb 3 00:06:24 2014 UTC (5 years, 10 months ago) by sshaw

further optimisation of wave assemblers, added support for constant data

Revision 4638 - Directory Listing
Modified Thu Jan 30 06:25:10 2014 UTC (5 years, 10 months ago) by jfenwick

Fixes necessary to get a clang/macports build working on 10.9

Revision 4633 - Directory Listing
Modified Tue Jan 28 01:04:17 2014 UTC (5 years, 10 months ago) by caltinay

Fixed failure for lazy data when interpolating.

Revision 4629 - Directory Listing
Modified Fri Jan 24 03:29:25 2014 UTC (5 years, 10 months ago) by sshaw

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 4626 - Directory Listing
Modified Wed Jan 22 06:07:34 2014 UTC (5 years, 10 months ago) by caltinay

Eliminated all const_cast<Data*> hacks in ripley and finley now that
Data.getSampleDataRO returns a const pointer.

Revision 4623 - Directory Listing
Modified Fri Jan 17 05:53:17 2014 UTC (5 years, 10 months ago) by sshaw

added missing files and a spare missing comma, also the ability for finley VTIWaves to not crash

Revision 4622 - Directory Listing
Modified Fri Jan 17 04:55:41 2014 UTC (5 years, 10 months ago) by sshaw

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 4618 - Directory Listing
Modified Wed Jan 15 04:35:19 2014 UTC (5 years, 10 months ago) by caltinay

Implemented reverse reading of grid data from netcdf files.
Fixes #44.

Revision 4616 - Directory Listing
Modified Tue Jan 14 22:57:47 2014 UTC (5 years, 10 months ago) by caltinay

- Fixed unit test failure by populating missing parts of the struct
- prepared for reversing read order from grids
- worked around a segfault caused by python version in jessie (2.7.6) in
  combination with gdal,pyproj and RTLD_GLOBAL in dlopen flags.

Revision 4615 - Directory Listing
Modified Mon Jan 13 05:05:33 2014 UTC (5 years, 10 months ago) by caltinay

Step 1 for #31: wrap parameters in an object.

Revision 4599 - Directory Listing
Modified Sun Dec 15 23:51:13 2013 UTC (5 years, 11 months ago) by sshaw

merged 3.4.1 release changes into trunk

Revision 4586 - Directory Listing
Modified Wed Dec 11 06:03:27 2013 UTC (5 years, 11 months ago) by jfenwick

2D guassian smoothing of random data done.
Added more memory non-leaks to the supp file

Revision 4583 - Directory Listing
Modified Wed Dec 11 02:09:19 2013 UTC (5 years, 11 months ago) by jfenwick

deliberate error to test buildbot

Revision 4582 - Directory Listing
Modified Wed Dec 11 02:08:41 2013 UTC (5 years, 11 months ago) by jfenwick

Added libpython version of suppressions to the aggressive file.
Rectangle now passes correct values around.
Random still to come.

Revision 4581 - Directory Listing
Modified Tue Dec 10 09:32:50 2013 UTC (5 years, 11 months ago) by jfenwick

Some more work on random
Added a more agressive (And smaller) supressions file for python

Revision 4576 - Directory Listing
Modified Mon Dec 9 23:35:30 2013 UTC (5 years, 11 months ago) by sshaw

python3ified things, replaced mixed whitespace and xrange calls

Revision 4529 - Directory Listing
Modified Fri Oct 25 01:23:27 2013 UTC (6 years, 1 month ago) by caltinay

Ripley can now read grids in non-native byte order. This is in preparation for
Gocad Voxet import.

Revision 4495 - Directory Listing
Modified Fri Jul 5 02:19:47 2013 UTC (6 years, 5 months ago) by caltinay

Added support for more input data types in ER Mapper files.
Tests will follow soon.

Revision 4482 - Directory Listing
Modified Tue Jun 25 05:20:01 2013 UTC (6 years, 5 months ago) by caltinay

More leak fixes and suppression file additions.

Revision 4477 - Directory Listing
Modified Thu Jun 20 02:41:28 2013 UTC (6 years, 5 months ago) by caltinay

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 4398 - Directory Listing
Modified Thu May 9 08:42:44 2013 UTC (6 years, 7 months ago) by jfenwick

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 4382 - Directory Listing
Modified Thu Apr 25 04:44:14 2013 UTC (6 years, 7 months ago) by caltinay

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 4378 - Directory Listing
Modified Wed Apr 24 06:21:42 2013 UTC (6 years, 7 months ago) by caltinay

ripley work: Almost done - one more round in Brick left....

Revision 4377 - Directory Listing
Modified Tue Apr 23 05:30:02 2013 UTC (6 years, 7 months ago) by caltinay

More work on ripley - Brick is under 10000 lines now.

Revision 4375 - Directory Listing
Modified Mon Apr 22 05:35:52 2013 UTC (6 years, 7 months ago) by caltinay

More ripley code cleaning/optimisation.

Revision 4370 - Directory Listing
Modified Fri Apr 19 06:15:24 2013 UTC (6 years, 7 months ago) by caltinay

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 (6 years, 7 months ago) by jfenwick

fix problems revealed on freebsd

Revision 4366 - Directory Listing
Modified Wed Apr 17 04:41:16 2013 UTC (6 years, 7 months ago) by caltinay

Be more careful with namespace & includes.

Revision 4357 - Directory Listing
Modified Thu Apr 11 06:07:14 2013 UTC (6 years, 7 months ago) by caltinay

templated writeBinaryGrid and a bit of cleanup.

Revision 4353 - Directory Listing
Modified Fri Apr 5 00:14:35 2013 UTC (6 years, 8 months ago) by caltinay

For some reason std::isnan<float> is not available on NCI so changed this
to ::isnan. Added options file for NCI vayu.

Revision 4346 - Directory Listing
Modified Tue Apr 2 04:46:45 2013 UTC (6 years, 8 months ago) by jfenwick

Bringing the changes from doubleplusgood branch.
Can't merge directly because svn doesn't transfer changes to renamed files (mutter grumble).

Revision 4340 - Directory Listing
Modified Fri Mar 22 04:38:36 2013 UTC (6 years, 8 months ago) by caltinay

added ripley method that returns grid parameters as python tuple.

Revision 4337 - Directory Listing
Modified Fri Mar 22 00:05:25 2013 UTC (6 years, 8 months ago) by caltinay

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 (6 years, 8 months ago) by caltinay

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 4284 - Directory Listing
Modified Thu Mar 7 00:43:48 2013 UTC (6 years, 9 months ago) by caltinay

Replaced dummy implementations by pure virtual methods.

Revision 4277 - Directory Listing
Modified Wed Mar 6 01:30:41 2013 UTC (6 years, 9 months ago) by caltinay

Implemented claimed support for mixing data with different resolutions.

Revision 4255 - Directory Listing
Modified Wed Feb 27 03:06:21 2013 UTC (6 years, 9 months ago) by jfenwick

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 4242 - Directory Listing
Modified Mon Feb 25 03:16:14 2013 UTC (6 years, 9 months ago) by jfenwick

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

Revision 4211 - Directory Listing
Modified Mon Feb 18 23:54:46 2013 UTC (6 years, 9 months ago) by caltinay

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 4176 - Directory Listing
Modified Wed Jan 30 05:30:30 2013 UTC (6 years, 10 months ago) by caltinay

Removed tests that are known not to work.

Revision 4174 - Directory Listing
Modified Wed Jan 30 03:21:27 2013 UTC (6 years, 10 months ago) by caltinay

ripley's readBinaryGrid and readNcGrid now filter out NaN leaving the relevant
destination data points untouched.

Revision 4078 - Directory Listing
Modified Fri Nov 16 07:50:49 2012 UTC (7 years ago) by jfenwick

Unit tests for binary install with no scons and no source tree.
Script for installing and testing a .deb within a chroot.

Revision 4058 - Directory Listing
Modified Fri Nov 2 06:47:06 2012 UTC (7 years, 1 month ago) by caltinay

-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 4035 - Directory Listing
Modified Thu Oct 25 03:10:14 2012 UTC (7 years, 1 month ago) by caltinay

Tweaked scons files so tests work even when specifying non-absolute build_dir.

Revision 4023 - Directory Listing
Modified Tue Oct 16 04:17:48 2012 UTC (7 years, 1 month ago) by caltinay

Another fix to the PDE assembly logic in ripley.

Revision 4022 - Directory Listing
Modified Mon Oct 15 23:52:24 2012 UTC (7 years, 1 month ago) by caltinay

Fixed checks in ripley::addPDEToRHS().

Revision 4013 - Directory Listing
Modified Thu Oct 4 03:13:27 2012 UTC (7 years, 2 months ago) by caltinay

Implemented netCDF grid reader analogous to binary grid reader in ripley.

Revision 4010 - Directory Listing
Modified Tue Oct 2 06:57:11 2012 UTC (7 years, 2 months ago) by caltinay

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 (7 years, 2 months ago) by caltinay

don't try to flip y-coord in reader. some more fixes and doco.

Revision 4007 - Directory Listing
Modified Tue Oct 2 02:12:01 2012 UTC (7 years, 2 months ago) by caltinay

Doco updates.
Data source paddings now take x,y not xy,z as Z padding can be done by setting
vertical extents.

Revision 4002 - Directory Listing
Modified Fri Sep 28 00:16:56 2012 UTC (7 years, 2 months ago) by caltinay

Fixed a memory leak (freeing paso coupler) in ripley.

Revision 3996 - Directory Listing
Modified Thu Sep 27 00:54:10 2012 UTC (7 years, 2 months ago) by caltinay

Don't test saveCSV for cases it does not work with.

Revision 3994 - Directory Listing
Modified Wed Sep 26 07:38:38 2012 UTC (7 years, 2 months ago) by jfenwick

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 (7 years, 2 months ago) by caltinay

Addressing mantis 651. Test for finley will fail under MPI since there is
sth wrong with the way ReducedContinuousFunction samples are interrogated.

Revision 3991 - Directory Listing
Modified Tue Sep 25 23:52:22 2012 UTC (7 years, 2 months ago) by caltinay

Updated doxygen cfg file and made a few first changes to doco.

Revision 3984 - Directory Listing
Modified Fri Sep 21 06:41:54 2012 UTC (7 years, 2 months ago) by caltinay

invert Y coordinate in ripley's 3d data reader. This needs to be configurable
and added to 2d as well...

Revision 3982 - Directory Listing
Modified Fri Sep 21 03:23:22 2012 UTC (7 years, 2 months ago) by jfenwick

More edits + removing pyvisi from trunk

Revision 3981 - Directory Listing
Modified Fri Sep 21 02:47:54 2012 UTC (7 years, 2 months ago) by jfenwick

First pass of updating copyright notices

Revision 3978 - Directory Listing
Modified Thu Sep 20 04:36:17 2012 UTC (7 years, 2 months ago) by caltinay

Make sympy optional as it was intended initially. Trying to instantiate anything
from symbolic will raise an exception if sympy is not available.

Revision 3975 - Directory Listing
Modified Thu Sep 20 01:54:06 2012 UTC (7 years, 2 months ago) by caltinay

Merged symbolic branch into trunk. Curious what daniel and spartacus have to
say...

Revision 3971 - Directory Listing
Modified Wed Sep 19 02:55:35 2012 UTC (7 years, 2 months ago) by caltinay

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 3963 - Directory Listing
Modified Thu Sep 13 01:39:00 2012 UTC (7 years, 2 months ago) by jfenwick

Fix to keep the warning-free-build happy

Revision 3962 - Directory Listing
Modified Tue Sep 11 09:12:07 2012 UTC (7 years, 2 months ago) by jfenwick

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 3944 - Directory Listing
Modified Mon Aug 20 02:11:22 2012 UTC (7 years, 3 months ago) by caltinay

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 (7 years, 4 months ago) by caltinay

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 3915 - Directory Listing
Modified Mon Jun 25 02:17:58 2012 UTC (7 years, 5 months ago) by caltinay

Added declspecs for all ripley classes.

Revision 3913 - Directory Listing
Modified Tue Jun 19 06:21:58 2012 UTC (7 years, 5 months ago) by caltinay

Fixed misuse of getSampleDataRO with lazy data in ripley.

Revision 3908 - Directory Listing
Modified Wed Jun 13 05:43:45 2012 UTC (7 years, 5 months ago) by caltinay

Fixed an error in ripley computing shared node id's.
pythonMPIredirect now redirects again.

Revision 3892 - Directory Listing
Modified Tue Apr 10 08:57:23 2012 UTC (7 years, 8 months ago) by jfenwick

Merged changes across from the attempt2 branch.
This version builds and passes python2 tests.
It also passes most python3 tests.

Revision 3841 - Directory Listing
Modified Mon Feb 27 04:18:53 2012 UTC (7 years, 9 months ago) by caltinay

Added support for OFFSET1 matrices in ripley.

Revision 3836 - Directory Listing
Modified Thu Feb 16 03:17:18 2012 UTC (7 years, 9 months ago) by caltinay

Transport problem support for ripley.

Revision 3806 - Directory Listing
Modified Mon Feb 6 02:32:48 2012 UTC (7 years, 10 months ago) by caltinay

ripley::getSize() also returns circumcircle now.

Revision 3800 - Directory Listing
Modified Fri Feb 3 01:18:06 2012 UTC (7 years, 10 months ago) by caltinay

Fixed integration with constant data on ripley.

Revision 3795 - Directory Listing
Modified Thu Feb 2 05:54:34 2012 UTC (7 years, 10 months ago) by caltinay

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 3793 - Directory Listing
Modified Wed Feb 1 07:39:43 2012 UTC (7 years, 10 months ago) by gross

new implementation of FCT solver with some modifications to the python interface

Revision 3792 - Directory Listing
Modified Wed Feb 1 06:16:25 2012 UTC (7 years, 10 months ago) by caltinay

Merged ripley rectangular domain into trunk.

Revision 3542 - Directory Listing
Modified Fri Jul 22 06:57:41 2011 UTC (8 years, 4 months ago) by gross

first attempts toward a multi grid solver

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