monolith

Here you find information about the 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 .modules file:

python/2.3.3
mkl/9.0p18

The Numeric Python module on the system is way too old, so we build our own version with this customize.py file:

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 .bashrc file:

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 customize.py file:

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

where run.sh looks like this:

cd $PBS_O_WORKDIR
mpirun $HOME/gpaw/build/bin.linux-i686-2.3/gpaw-python gpaw-script.py