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.. _gardar.nhpc.hi.is:
=================
gardar.nhpc.hi.is
=================
Information about the machine http://nhpc.hi.is/content/nhpc-system
Instructions assume **bash**, installation under *${HOME}/global/apps*.
Make sure the following modules are loaded::
$ module list
Currently Loaded Modules:
1) intel/13.1 3) openmpi/1.6.5 5) gold/2.2.0.5
2) mkl/11.0.0 4) python/2.7.5
Setup the root directory::
export APPHOME=${HOME}/global/apps
mkdir -p ${APPHOME}
cd ${APPHOME}
export GPAW_PLATFORM=`python -c "from distutils import util, sysconfig; print(util.get_platform()+'-'+sysconfig.get_python_version())"`
Download software::
svn co -r 3906 https://svn.fysik.dtu.dk/projects/ase/trunk ase.3906
svn co -r 12224 https://svn.fysik.dtu.dk/projects/gpaw/trunk gpaw.12224
wget https://wiki.fysik.dtu.dk/gpaw-files/gpaw-setups-0.9.11271.tar.gz
wget https://wiki.fysik.dtu.dk/gpaw-files/gpaw-setups-0.9.9672.tar.gz
tar zxf gpaw-setups-0.9.11271.tar.gz
tar zxf gpaw-setups-0.9.9672.tar.gz
wget "http://www.tddft.org/programs/octopus/down.php?file=libxc/libxc-2.2.1.tar.gz" -O libxc-2.2.1.tar.gz
tar zxf libxc-2.2.1.tar.gz
and create the modules::
mkdir -p $APPHOME/modulefiles/{ase,gpaw,gpaw-setups,libxc}
cat <<EOF > modulefiles/gpaw/0.11.0.12224
set modulefile [lrange [split [module-info name] {/}] 0 0]
set release [lrange [split [module-info name] {/}] 1 1]
set apphome $APPHOME/gpaw.12224
set appname "gpaw"
prepend-path PATH \$apphome/build/bin.$GPAW_PLATFORM
prepend-path PATH \$apphome/tools
prepend-path PYTHONPATH \$apphome
prepend-path PYTHONPATH \$apphome/build/lib.$GPAW_PLATFORM
EOF
cat <<EOF > modulefiles/ase/3.9.0.3906
set modulefile [lrange [split [module-info name] {/}] 0 0]
set release [lrange [split [module-info name] {/}] 1 1]
set apphome $APPHOME/ase.3906
set appname "ase"
prepend-path PATH \$apphome/tools
prepend-path PYTHONPATH \$apphome
EOF
cat <<EOF > modulefiles/gpaw-setups/0.9.9672
set modulefile [lrange [split [module-info name] {/}] 0 0]
set release [lrange [split [module-info name] {/}] 1 1]
set apphome $APPHOME/gpaw-setups-0.9.9672
set appname "gpaw-setups"
prepend-path GPAW_SETUP_PATH \$apphome
EOF
cat <<EOF > modulefiles/gpaw-setups/0.9.11271
set modulefile [lrange [split [module-info name] {/}] 0 0]
set release [lrange [split [module-info name] {/}] 1 1]
set apphome $APPHOME/gpaw-setups-0.9.11271
set appname "gpaw-setups"
prepend-path GPAW_SETUP_PATH \$apphome
EOF
cat <<EOF > modulefiles/libxc/2.2.1-1
set modulefile [lrange [split [module-info name] {/}] 0 0]
set release [lrange [split [module-info name] {/}] 1 1]
set apphome $APPHOME/libxc-2.2.1-1
set appname "libxc"
prepend-path LD_LIBRARY_PATH \$apphome/lib
prepend-path PATH \$apphome/bin
prepend-path C_INCLUDE_PATH \$apphome/include
prepend-path PKG_CONFIG_PATH \$apphome/lib/pkgconfig
EOF
Build libxc::
cd $APPHOME/libxc-2.2.1
./configure --prefix $APPHOME/libxc-2.2.1-1 --enable-shared
make
make install
and GPAW::
cd $APPHOME
wget https://svn.fysik.dtu.dk/projects/gpaw/trunk/doc/platforms/Linux/customize_gardar.py
cd $APPHOME/gpaw.12224
python setup.py --remove-default-flags --customize=../customize_gardar.py build_ext 2>&1 | tee build_ext.log
The :file:`customize_gardar.py` looks like:
.. literalinclude:: customize_gardar.py
GPAW tests :file:`gpaw-test` can be submitted like this::
qsub -l nodes=1:ppn=8 run.sh
where :file:`run.sh` looks like this::
#!/bin/sh
. /opt/lmod/lmod/init/sh
module use --append ~/global/apps/modulefiles
module load ase/3.9.0.3906
module load gpaw-setups/0.9.11271
module load libxc/2.2.1-1
module load gpaw/0.11.0.12224
export OMP_NUM_THREADS=1
mpiexec `which gpaw-python` `which gpaw-test`
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