neolith.nsc.liu.se

Here you find information about the the system http://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 http://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 http://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 "http://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