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Merging changes from new doco branch. All docstrings are now in reStructured text. A few email addresses have been fixes as well.
Updating copyright notices
I may get into trouble for this. boost-python 1.34 does have a docstring_options class, but does not have a 3 argument constructor for it. So the test has been modified to #if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1) If you wish to make things more delicate, one can define a 2 argument construction of docopt just for 1.34 (with an #elif). Probably not worth the effort frankly. Hope that this has not broken anything for anyone else. The SVN logs suggest this is a little fragile..... Also, please be aware that much of our chemistry interface code, that we wish to use with escript, makes extensive use of boost python. Having two different boost versions mucking with the python interpreter sounds like a really bad idea, I'm sure you'll agree. The problem is that it is not a simple task for us to build new versions of boost-python on all our platforms. Consequently, it would be nice to be informed when you guys intend to upgrade a support library of this nature so that we can plan and allocate resources to keep up. Cheers.
docstring_options was added in boost 1.34 - macro'd it out if you are compiling earlier than that.
Fixing some warnings from epydoc. Disabled c++ signatures in python docstrings. Removed references to Bruce in epydoc and the users guide.
convection.py checkpointing uses mkdir/rmdir, and under MPI there was a race condition. mkdir needs to be run on only one CPU and then a barrier to prevent working processors from using the directory before it exists. Added methods domain.MPIBarrier and domain.onMasterProcessor() to implement this technique. A more general solution might be possible in the future.
Closing the moreshared branch
first version of testing for transport solver.
Copyright updated in all files
The new MPI parallel ReadMesh is now the default after having passed all tests both with and without MPI. If you have been using ReadMesh you should notice no difference. If you were using ReadMeshMPI then change to ReadMesh.
Fixed serialization of I/O for MPI...code didn't compile without MPI
Serialized parallel I/O when writing mesh or data to NetCDF file on multiple MPI processors. Added domain method getMPIComm() to complement getMPISize() and getMPIRank().
Added new test suite run_inputOutput.py to systematically test I/O. Can determine if two domains are same with Fourier analysis. Added new method getNumDataPointsGlobal to return number of DPs of a distributed mesh. Reading of tags in ReadMeshMPI failed occasionally, should be more robust now.
some more work on the transport solver.
new upwinding algorithm (still fails)
And get the *(&(*&(* name right
Restore the trunk that existed before the windows changes were committed to the (now moved to branches) old trunk.
Make a temp copy of the trunk before checking in the windows changes
some tests got deactivated. they are back now.
explicit upwinding scheme added.
finley interface to paso's transport solver added.
first steps towards a flux controlled transport solver.
Partial implementation of ReadMeshMPI. Will eventually replace ReadMesh but for now has a different name.
Created LoadMesh to read a mesh from a distributed NetCDF file. Can read nodes but not elements yet.
First cut implementation of mesh.dump() using NetCDF. TagMap not saved yet. The code for Points probably works but has not been tested.
Modified scons target release_src to include lib/ and include/ since their presence is required for a build. Modified mydomain.print_mesh_info(True) to include more useful info about a distributed domain. Added mypde.getOperator().print_matrix_info(True) to tell about a distributed matrix.
Implemented domain.print_mesh_info() so we can see the distribution of elements & nodes. Implemented -DBOUNDS_CHECK to catch an error with periodicN=True.
The MPI branch is hereby closed. All future work should be in trunk. Previously in revision 1295 I merged the latest changes to trunk into trunk-mpi-branch. In this revision I copied all files from trunk-mpi-branch over the corresponding trunk files. I did not use 'svn merge', it was a copy.
a frame for an improved lumping procedure added.
Small bug in ReadMeh call fixed. Test for typ of verbose argument in pdetools.SaddlePointSolver added.
reduced integration schemes are implemented now for grad, integrate, etc. Tests still to be added.
first steps toward reduced element integration order. The escript bit is done but the finley part still needs work.
clear name tagging is supported now.
gmsh file reader for finley
Problem in Mesh_findMatchingFaces.c fixed: default tolerance in python interface was set too tight.
Can now compile and run with MPI on shake71
In case of an error in paso a seg fault occured. this was caused by inproper deallocation of memory in this case. this problem is fixed now.
+ NEW BUILD SYSTEM
This commit contains the new build system with cross-platform support.
Most things work are before though you can have more control.
ENVIRONMENT settings have changed:
+ You no longer require LD_LIBRARY_PATH or PYTHONPATH to point to the
esysroot for building and testing performed via scons
+ ACcESS altix users: It is recommended you change your modules to load
the latest intel compiler and other libraries required by boost to match
the setup in svn (you can override). The correct modules are as follows
module load intel_cc.9.0.026
export
MODULEPATH=${MODULEPATH}:/data/raid2/toolspp4/modulefiles/gcc-3.3.6
module load boost/1.33.0/python-2.4.1
module load python/2.4.1
module load numarray/1.3.3
restructure escript source tree move src/Data/* -> src remove inc modify #includes and cpppath settings accordingly
rationalise all #includes
reorganise finley src tree to remove inc dir and src/finley directory
reorganised esysUtils to remove inc directory
adjust include file names to allow for new finley source tree structure
copy finleyC and CPPAdapter to finley and finley/CPPAdapter to facilitate scons builds
move all directories from trunk/esys2 into trunk and remove esys2
Merge of development branch dev-02 back to main trunk on 2005-10-25
Merge of development branch dev-02 back to main trunk on 2005-09-01
Merge of development branch back to main trunk on 2005-07-08
Merge of development branch back to main trunk on 2005-05-06
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