Here you find information about the system http://www.nsc.liu.se/systems/retiredsystems/monolith/.
The Monolith machine is a cluster of 2.4Ghz Xeon processors with 2GB of memory. The ScaMPI implementation of MPI has a problem, but we can use MPICH.
Add these two line to the
The Numeric Python module on the system is way too old, so we build
our own version with this
use_system_lapack = 1 mkl = '/usr/local/intel/ict/l_ict_p_3.0.023/cmkl/9.0' lapack_library_dirs = [mkl + '/lib/32'] lapack_libraries = ['mkl', 'mkl_lapack', 'g2c'] use_dotblas = 1 dotblas_include_dirs = [mkl + '/include'] dotblas_cblas_header = '<mkl_cblas.h>'
Set these environment variables in the
export PYTHONPATH=$HOME/campos-ase-2.3.4:$HOME/gpaw:$HOME/lib/python/Numeric export GPAW_SETUP_PATH=$HOME/setups export LD_LIBRARY_PATH=$MKL_ROOT
and build GPAW (
python setup.py build_ext) with this
extra_compile_args += ['-w1'] mpicompiler = 'icc -Nmpich' custom_interpreter = True compiler = 'icc'
Jobs can be submitted like this:
qsub -l nodes=2:ppn=2 -A <account> -l walltime=2:00:00 \ -m abe run.sh
run.sh looks like this:
cd $PBS_O_WORKDIR mpirun $HOME/gpaw/build/bin.linux-i686-2.3/gpaw-python gpaw-script.py