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on ess: link against python 2.4.3 now.
Can now compile with openmp on cyclone. Had to fix a bug in scons in intelc.py to allow use of Intel compilers.
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.
Minor repairs to scons files
Repaired all targets for: scons docs It runs all these targets: release_examples guide_pdf api_epydoc api_doxygen
The OMP_NUM_THREADS environment variable is now imported into the scons evironment.
Finished renaming of boost_lib to boost_libs and boost_lib_path to boost_libs_path.
Changes to link against NetCDF/3.6.1 module installation with linkage and compilation consistent with other libraries currently dynamically linked. Unaligned access error appears linked to escript implementation and NetCDF/3.6.1 module tests for 64bit file access pass. This module differs from the previous module as assertions are disabled and compiler optimisation is invoked _without_ symbol table/lookup.
fixes to get netcdf going on the altix
escript data objects can now be saved to netCDF files, see http://www.unidata.ucar.edu/software/netcdf/. Currently only constant data are implemented with expanded and tagged data to follow. There are two new functions to dump a data object s=Data(...) s.dump(<filename>) and to recover it s=load(<filename>, domain) Notice that the function space of s is recovered but domain is still need. dump and load will replace archive and extract. The installation needs now the netCDF installed.
reverse orientation added but does not work for 2D yet.
some performance problems wit openmp fixed.
first steps toward UMFPACK
changes to escript/py_src/pdetools.py and /escript/src/Data.h/.cpp to make the Locator work in MPI. escript::Data::mindp now returns a 3 tuple, with the MPI rank of the process on which the minimum value occurs included. escript::Data::convertToNumArrayFromDPNo also takes the ProcNo to perform the MPI reduction. This had to be implemented in both the MPI and non-MPI versions to allow the necesary changes to the Python code in pdetools.py. In the non-MPI version ProcNo is set to 0. This works for the explicit scripts tested thus far, however if it causes problems in your scripts contact Ben or Lutz, or revert the three files (pdetools.py, Data.h and Data.cpp) to the previous version.
Large number of changes to Finley for meshing in MPI. - optimisation and neatening up of rectcanglular mesh generation code - first and second order 1D, 2D and 3D rectangular meshes are now available in finley and escript using MPI. - reduced meshes now generated in MPI, and interpolation to and from reduced data types now supported.
basic code for persistence of jacobeans added. routines are not called yet
- removed the need to uncomment #define PASO_MPI when building MPI version, now passed as an argument to the compiler.
- added directory pythonMPI to the source tree. this directory contains
the c++ wrapper that is used to run python scripts in parallel for the
MPI version of escript/finley
- updated the SConstruct and ./scons/ess_options.py for conditional MPI
compilation. To compile the MPI version on ESS uncomment the #define
PASO_MPI in ./paso/src/Paso.h and add the command line option
useMPI=yes when running scons.
- fixed a compile time error in the MPI build in
finley/src/CPPAdapter/MeshAdapterFactory.cpp
Changes relating to the MPI version of escript The standard OpenMP version of escript is unchanged - updated data types (Finley_Mesh, Finley_NodeFile, etc) to store meshes over multiple MPI processes. - added CommBuffer code in Paso for communication of Data associated with distributed meshes - updates in Finley and Escript to support distributed data and operations on distributed data (such as interpolation). - construction of RHS in MPI, so that simple explicit schemes (such as /docs/examples/wave.py without IO and the Locator) can run in MPI. - updated mesh generation for first order line, rectangle and brick meshes and second order line meshes in MPI. - small changes to trunk/SConstruct and trunk/scons/ess_options.py to build the MPI version, these changes are turned off by default.
ess_options.py is updated and synchronised with the esys/env module. In turn, this module is used to build and setup the user environments of esys/current and esys/current-debug.
Removed -ansi_alias compiler option to icpc. It was causing the compiler to optimize away the default constructor DataAbstract::DataAbstract and breaking the tests.
+ 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
More copyright.
papi switched off on altix
eigenvalues: compiles and passes tests on altix now
define epydoc PYTHONPATH setting
define locations of doxygen/epydoc executables
minor comment and formatting changes
The sparse solver can be called by paso now. the building has been change to reduce some code redundancy: now all scons SCscripts are importing scons/esys_options.py which imports platform specific settings.
fixed typo in options string
fixed specification of solver libs
pass in solver libraries to link with via options files now
pass in platform specific libraries via options files now
fix compiler options to enable compilation on gcc platforms
added some comments and reasonable default values
fix quoting of library names
add names of python and boost libraries to config file
import compile options into bruce unit test builds from options file now
pass in correct options to archiver for static libraries
implement switching of debug compiler options based on command line flag 'debug'
pass in cc/cxx settings from config file
first pass at importing compile options from an external file'
added directory and first draft file to hold options settings for different configurations (debug/nodebug, host, etc)
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