PyLith installation instructions for the recycled cluster (radon) and dell-4300/x22

PyLith (v1.x) makes use of Nemesis, Proj.4, Spatialdata, Pyrex, Pyrexembed, FIAT, numpy and PetSc (development version) which further needs to be compiled with sieve, chaco (for graph partitioning) and boost. Either GNU or the Intel compilers can be used to build PetSc.

Replace $SCRATCH with the absolute path of scratch directory. A good place to get/build all required packages on radon is /tmp (fast).

# module purge all
# module load mpich-gcc (invokes mpich-1.2.7p1 with gcc-4.2.1 compilers)
# mkdir $SCRATCH/Pylith

PetSc
# tar -xzf petsc-dev.tar.gz; cd petsc-dev
# export PETSC_DIR=`pwd`
# ./config/configure.py --with-clanguage=C++ --with-mpi-dir=/opt/mpich-1.2.7p1/32/p4-gcc-4.2.1 --with-blas-lapack-dir=/opt/intel/mkl721 --with-shared=0 --with-debugging=0 --with-sieve=1 --with-chaco=1 --download-chaco=1 --with-boost=1 --download-boost=1 --CXXFLAGS=-DNEW_SECTION
# export PETSC_ARCH=linux-gnu-cxx-opt
# make all

Nemesis
# tar -xzf nemesis-1.0.tar.gz; cd nemesis-1.0
# ./configure --prefix=$SCRATCH/Pylith
# make; make install

Proj.4
# tar -xzf proj-4.6.0.tar.gz; cd proj-4.6.0
# ./configure --prefix=$SCRATCH/Pylith
# make; make install

Pyrexembed
# tar -xzf pyrexembed-1.0.tar.gz; cd pyrexembed-1.0
# python setup.py install --prefix=$SCRATCH/Pylith

Pyrex
# tar -xzf Pyrex-0.9.6.4.tar.gz; cd Pyrex-0.9.6.4
# python setup.py install --prefix=$SCRATCH/Pylith

FIAT
# tar -xzf FIAT-0.3.3.tar.gz; cd FIAT-0.3.3
# python setup.py install --prefix=$SCRATCH/Pylith

Numpy
# tar -xzf numpy-1.0.4.tar.gz; cd numpy-1.0.4
# python setup.py install --prefix=$SCRATCH/Pylith

Spatialdata
# tar -xzf spatialdata.tar.gz; cd spatialdata
# export PATH=$PATH:$SCRATCH/Pylith/bin
# export PYTHONPATH=$PYTHONPATH:$SCRATCH/Pylith/lib/python2.4/site-packages
# export PYTHONPATH=$PYTHONPATH:$SCRATCH/Pylith/lib/python2.4/site-packages/merlin-1.3.egg/merlin
# autoreconf -f -i
{If you get the error "aclocal: couldn't open directory `./m4': No such file or directory" then simply create an empty directory named m4}
# ./configure --prefix=$SCRATCH/Pylith LDFLAGS="-L$SCRATCH/Pylith/lib" CPPFLAGS="-I$SCRATCH/Pylith/include -I/usr/include/python2.4" --enable-pythia
{Do check if the PYTHONPATH variable in Makefile is okay}
#make; make install

NetCDF {optional; used to read Cubit mesh that is stored in Exodus (based on NetCDF) file format}
# tar -xzf netcdf.tar.gz; cd netcdf-3.6.2
# ./configure --disable-examples --disable-f77 --disable-f90 --disable-utilities --prefix=$SCRATCH/pylith
# make; make install

PyLith
# tar -xzf pylith-1.0.2.tgz; cd pylith-1.0.2
{Make sure that PATH, PYTHONPATH, PETSC_DIR and PETSC_ARCH variables are all set}
# ./configure --prefix=$SCRATCH/Pylith --enable-cubit CPPFLAGS="-I$SCRATCH/pylith/include" LDFLAGS="-L$SCRATCH/pylith/lib" CXXFLAGS=-DNEW_SECTION
{If it complains about a missing 'petscconf' then simply create it as a symlink to 'petscvariables' in $PETSC_DIR/$PETSC_ARCH/conf}
# make
# make install

Finally create this file in $HOME/.pyre/pylithapp, add $SCRATCH/Pylith/bin to $PATH and delete PetSc and all other packages.

Test the installation using the strike-slip benchmark problem
# qsub -I -l nodes=2
# pylith strikeslip_cubit.cfg strikeslip_hex8_1000m.cfg timedep.cfg --nodes=2

---
In certain cases, for example when you build PyLith on one machine and use on another, you might have to set/update PYTHONPATH and LD_LIBRARY_PATH variables.