neolith.nsc.liu.se

Here you find information about the system https://www.nsc.liu.se/systems/neolith.

The installation of user’s packages on neolith described below uses cmod modules:

packages are installed under ~/apps:
```
mkdir ~/apps
```
module files are located under ~/modulefiles:
```
mkdir ~/modulefiles
```

build nose:

cd ~/apps
wget https://python-nose.googlecode.com/files/nose-0.10.1.tar.gz
tar zxf nose-0.10.1.tar.gz
cd nose-0.10.1
python setup.py install --root=~/apps/nose-0.10.1-1

build numpy:

cd ~/apps
wget https://downloads.sourceforge.net/numpy/numpy-1.3.0.tar.gz
tar zxf numpy-1.3.0.tar.gz
cd  numpy-1.3.0
python setup.py install --root=~/apps/numpy-1.3.0-1

build ase:

cd ~/apps
svn co https://svn.fysik.dtu.dk/projects/ase/trunk ase
cd ase
python setup.py sdist; cp dist/python-ase-*.tar.gz ..
cd ..
tar zxf python-ase-3.2.0.962.tar.gz

build gpaw-setups:

cd ~/apps
wget --no-check-certificate "https://wiki.fysik.dtu.dk/gpaw-files/gpaw-setups-0.5.3574.tar.gz"
tar zxf gpaw-setups-0.5.3574.tar.gz

deploy modules:

export MODULEFILES="/home/x_andke/modulefiles"
export APPS="/home/x_andke/apps"

mkdir ${MODULEFILES}/numpy
cat <<EOF > ${MODULEFILES}/numpy/1.3.0-1.el5.gfortran.python2.4.default.blas.lapack
\$(/etc/cmod/modulegroups numpy numpy/1.3.0-1.el5.gfortran.python2.4.default.blas.lapack)
#prereq python-nose # nose
prepend-path    PATH            ${APPS}/numpy-1.3.0-1/usr/bin
prepend-path    PYTHONPATH      ${APPS}/numpy-1.3.0-1/usr/lib64/python2.4/site-packages
EOF
ln -s ${MODULEFILES}/numpy/1.3.0-1.el5.gfortran.python2.4.default.blas.lapack ${MODULEFILES}/numpy/default

mkdir ${MODULEFILES}/nose
cat <<EOF > ${MODULEFILES}/nose/0.10.1-1.el5.gfortran.python2.4
\$(/etc/cmod/modulegroups nose nose/0.10.1-1.el5.gfortran.python2.4)
prepend-path    PATH            ${APPS}/nose-0.10.1-1/usr/bin
prepend-path    PYTHONPATH      ${APPS}/nose-0.10.1-1/usr/lib/python2.4/site-packages
EOF
ln -s ${MODULEFILES}/nose/0.10.1-1.el5.gfortran.python2.4 ${MODULEFILES}/nose/default

mkdir ${MODULEFILES}/campos-ase3
cat <<EOF > ${MODULEFILES}/campos-ase3/3.2.0.962-1.el5.python2.4
\$(/etc/cmod/modulegroups campos-ase3 campos-ase3/3.2.0.962-1.el5.python2.4)
#prereq numpy # numpy
prepend-path    PATH            ${APPS}/python-ase-3.2.0.962/tools
prepend-path    PYTHONPATH      ${APPS}/python-ase-3.2.0.962
EOF
ln -s ${MODULEFILES}/campos-ase3/3.2.0.962-1.el5.python2.4 ${MODULEFILES}/campos-ase3/default

mkdir ${MODULEFILES}/campos-gpaw-setups
cat <<EOF > ${MODULEFILES}/campos-gpaw-setups/0.5.3574-1.el5
\$(/etc/cmod/modulegroups campos-gpaw-setups campos-gpaw-setups/0.5.3574-1.el5)
prepend-path    GPAW_SETUP_PATH      ${APPS}/gpaw-setups-0.5.3574
EOF
ln -s ${MODULEFILES}/campos-gpaw-setups/0.5.3574-1.el5 ${MODULEFILES}/campos-gpaw-setups/default

mkdir ${MODULEFILES}/campos-gpaw
cat <<EOF > ${MODULEFILES}/campos-gpaw/0.6.3934-1.el5.gfortran.python2.4.openmpi.mkl.10.0.4.023.mkl_lapack
\$(/etc/cmod/modulegroups campos-gpaw campos-gpaw/0.6.3934-1.el5.gfortran.python2.5.openmpi.mkl.10.0.4.023.mkl_lapack)
#prereq numpy # numpy
#prereq campos-ase3 # ase
#prereq campos-gpaw-setups # gpaw-setups
prepend-path    PATH            ${APPS}/gpaw-0.6.3934/tools
prepend-path    PATH            ${APPS}/gpaw-0.6.3934/build/bin.linux-x86_64-2.4
prepend-path    PYTHONPATH      ${APPS}/gpaw-0.6.3934
EOF
ln -s ${MODULEFILES}/campos-gpaw/0.6.3934-1.el5.gfortran.python2.4.openmpi.mkl.10.0.4.023.mkl_lapack ${MODULEFILES}/campos-gpaw/default

Note that every time you wish to install a new version of a package, you (svn up is necessary), create new tarball, and deploy new module file, keeping the old module file.

test numpy installation:

module use ${MODULEFILES}
module load nose
module load numpy
python -c "import numpy; numpy.test()"

use customize_neolith.py:

# 19 Nov 2009: problems with scalapack
#scalapack = True

extra_compile_args = ['-fast', '-std=c99', '-fPIC']

compiler = 'icc'

libraries = ['mkl_core', 'mkl_sequential', 'mkl_gf_lp64', 'iomp5']
#libraries = ['mkl_core', 'mkl_intel_thread', 'mkl_gf_lp64', 'mkl_blacs_intelmpi_lp64', 'mkl_scalapack_lp64', 'iomp5']

mkl_lib_path = '/software/intel/mkl/10.2.1.017/lib/em64t/'

library_dirs = [mkl_lib_path]

extra_link_args =['-Wl,-rpath='+mkl_lib_path]

define_macros += [('GPAW_NO_UNDERSCORE_CBLACS', '1')]
define_macros += [('GPAW_NO_UNDERSCORE_CSCALAPACK', '1')]

to build gpaw:

cd ~/apps
svn co https://svn.fysik.dtu.dk/projects/gpaw/trunk gpaw
cd gpaw
python setup.py sdist; cp dist/gpaw-*.tar.gz ..
cd ..
tar zxf gpaw-0.6.3934.tar.gz
cd gpaw-0.6.3934
wget https://svn.fysik.dtu.dk/projects/gpaw/trunk/doc/platforms/Linux/customize_neolith.py -O customize.py
module load openmpi/1.2.7-i101017
python setup.py build_ext --remove-default-flags

test gpaw installation by loading the modules:

module load campos-ase3
module load campos-gpaw-setups
module load campos-gpaw
export OMP_NUM_THREADS=1

and run the tests.

logout, and login again.

submit a test job:

cp ~/apps/gpaw-0.6.3934/test/CH4.py ~/
cd
sbatch -N 1 --tasks-per-node 4 submit.sh

using the following submit.sh:

#!/bin/bash
#SBATCH -N 1
#SBATCH -t 00:10:00

export OMP_NUM_THREADS=1
. /etc/cmod/path.sh
module use /home/x_andke/modulefiles
module load openmpi/1.2.7-i101017
module load nose
module load numpy
module load campos-ase3
module load campos-gpaw-setups
module load campos-gpaw

mpprun --force-mpi="openmpi/1.2.7-i101017" `which gpaw-python` ./CH4.py