bohr.gbar.dtu.dk

Here you find information about the the system http://www.gbar.dtu.dk/index.php/Hardware.

Follow instructions from http://www.gbar.dtu.dk/index.php/GridEngine to create ~/.grouprc.

Use python2.5 and enable numpy/matplotlib:

alias python="LD_PRELOAD=/opt/csw/lib/libncurses.so /usr/local/gbar/cswbin/python2.5"
export PYTHONPATH=/usr/local/gbar/lib/pythonmodules

To build gpaw add to the gpaw/customize.py:

library_dirs += [‘/opt/csw/lib’]

Download MPIscript.sh and edit it, so it resembles:

#!/bin/sh
# (c) 2000 Sun Microsystems, Inc.
# ---------------------------
# General options
#
#$ -S /bin/sh
#$ -o $JOB_NAME.$JOB_ID.out
#$ -e $JOB_NAME.$JOB_ID.err
# -M User@Domain
# -m es
# ---------------------------
# Execute the job from  the  current  working  directory
#$ -cwd
#
# Parallel environment request
# ---------------------------
# do not change the following line
#$ -l cre
#
#      PE_name  CPU_Numbers_requested
##$ -pe HPC      2
# ------------------------------- Program_name_and_options
LD_LIBRARY_PATH=/opt/csw/lib:${LD_LIBRARY_PATH}
export LD_LIBRARY_PATH
gpawpython=~mdul/gpaw/build/bin.solaris-2.10-sun4u-2.5/gpaw-python
/appl/hgrid/current/bin/mprun -np $NSLOTS $gpawpython gpaw/examples/H.py
# ---------------------------

Submit jobs like this:

qsub -N test -pe HPC 2 MPIscript.sh

Note

All scripts making use of #!/usr/bin/env python must be changed to use #!/usr/bin/env python2.5 instead.