newcell.crc.nd.edu

Here you find information about the the system http://crcmedia.hpcc.nd.edu/wiki/index.php/Available_Hardware.

The installation of user’s packages on newcell described below uses modules, and assumes csh shell:

  • packages are installed under ~/CAMd:

    mkdir ~/CAMd
    cd ~/CAMd
    
  • module files are located under ~/CAMd/modulefiles

  • download the customize_newcell.py file:

    wget https://svn.fysik.dtu.dk/projects/gpaw/trunk/doc/platforms/Linux/customize_newcell.py
    
    scalapack = False
    
    extra_compile_args = ['-O3', '-std=c99', '-fpic']
    
    compiler = '/afs/crc.nd.edu/x86_64_linux/openmpi/1.3.2/gnu/bin/mpicc'
    
    libraries = ['mkl_def', 'mkl_lapack', 'mkl_core', 'mkl_sequential', 'mkl_gf_lp64', 'iomp5']
    
    mkl_lib_path = '/opt/crc/scilib/mkl/10.1.0.015/lib/em64t/'
    ompi_lib_path = '/afs/crc.nd.edu/x86_64_linux/openmpi/1.3.2/gnu/lib/'
    
    library_dirs = [mkl_lib_path, ompi_lib_path]
    
    extra_link_args =['-Wl,-rpath='+mkl_lib_path+',-rpath='+ompi_lib_path]
    
    define_macros += [('GPAW_NO_UNDERSCORE_CBLACS', '1')]
    define_macros += [('GPAW_NO_UNDERSCORE_CSCALAPACK', '1')]
    
  • install packages, deploy modules and test with install_newcell.csh, buy running csh install_newcell.csh:

    setenv APPS "/afs/crc.nd.edu/user/j/jbray2/CAMd"
    setenv MODULEFILES "${APPS}/modulefiles"
    
    set nose_version=0.11.3
    wget http://python-nose.googlecode.com/files/nose-${nose_version}.tar.gz
    tar zxf nose-${nose_version}.tar.gz
    cd nose-${nose_version}
    python setup.py install --root=${APPS}/nose-${nose_version}-1
    cd ..
    
    set numpy_version=1.4.1
    wget http://downloads.sourceforge.net/numpy/numpy-${numpy_version}.tar.gz
    tar zxf numpy-${numpy_version}.tar.gz
    cd  numpy-${numpy_version}
    python setup.py install --root=${APPS}/numpy-${numpy_version}-1
    cd ..
    
    set ase_version=3.4.1.1765
    wget https://wiki.fysik.dtu.dk/ase-files/python-ase-${ase_version}.tar.gz
    tar zxf python-ase-${ase_version}.tar.gz
    
    set gpaw_version=0.7.2.6974
    wget https://wiki.fysik.dtu.dk/gpaw-files/gpaw-${gpaw_version}.tar.gz
    tar zxf gpaw-${gpaw_version}.tar.gz
    
    set gpaw_setups_version=0.6.6300
    wget http://wiki.fysik.dtu.dk/gpaw-files/gpaw-setups-${gpaw_setups_version}.tar.gz
    tar zxf gpaw-setups-${gpaw_setups_version}.tar.gz
    
    mkdir -p ${MODULEFILES}/nose
    cat <<EOF > ${MODULEFILES}/nose/${nose_version}-1
    #%Module1.0
    set apps_path ${APPS}
    prepend-path    PATH                \$apps_path/nose-${nose_version}-1/usr/bin
    prepend-path    PYTHONPATH          \$apps_path/nose-${nose_version}-1/usr/lib/python2.4/site-packages/
    unset apps_path
    EOF
    
    mkdir -p ${MODULEFILES}/numpy
    cat <<EOF > ${MODULEFILES}/numpy/${numpy_version}-1
    #%Module1.0
    set apps_path ${APPS}
    prereq nose # nose
    prepend-path    PATH                \$apps_path/numpy-${numpy_version}-1/usr/bin
    prepend-path    PYTHONPATH          \$apps_path/numpy-${numpy_version}-1/usr/lib64/python2.4/site-packages/
    unset apps_path
    EOF
    
    mkdir -p ${MODULEFILES}/campos-ase3
    cat <<EOF > ${MODULEFILES}/campos-ase3/${ase_version}-1
    #%Module1.0
    set apps_path ${APPS}
    prereq nose
    prereq numpy
    prepend-path    PATH                \$apps_path/python-ase-${ase_version}/tools
    prepend-path    PYTHONPATH          \$apps_path/python-ase-${ase_version}/
    unset apps_path
    EOF
    
    mkdir -p ${MODULEFILES}/campos-gpaw-setups
    cat <<EOF > ${MODULEFILES}/campos-gpaw-setups/${gpaw_setups_version}-1
    #%Module1.0
    set apps_path ${APPS}
    prepend-path    GPAW_SETUP_PATH     \$apps_path/gpaw-setups-${gpaw_setups_version}
    unset apps_path
    EOF
    
    mkdir -p ${MODULEFILES}/campos-gpaw
    cat <<EOF > ${MODULEFILES}/campos-gpaw/${gpaw_version}-1
    #%Module1.0
    set apps_path ${APPS}
    prereq ompi/1.3.2-gnu
    prereq numpy
    prereq campos-ase3
    prereq campos-gpaw-setups
    prepend-path    PATH                \$apps_path/gpaw-${gpaw_version}/tools
    prepend-path    PATH                \$apps_path/gpaw-${gpaw_version}/build/bin.linux-x86_64-2.4
    prepend-path    PYTHONPATH          \$apps_path/gpaw-${gpaw_version}/
    prepend-path    PYTHONPATH          \$apps_path/gpaw-${gpaw_version}/build/lib.linux-x86_64-2.4
    setenv OMP_NUM_THREADS 1
    unset apps_path
    EOF
    
    module avail
    
    module use --append ${MODULEFILES}
    module load nose
    module load numpy
    module load campos-ase3
    # test numpy
    python -c "import numpy; numpy.test()"
    # test ase
    mkdir -p tmp
    cd tmp
    testase.py --no-display
    cd ..
    # build gpaw
    cd gpaw-${gpaw_version}
    module load ompi/1.3.2-gnu
    python setup.py build_ext --customize=../customize_newcell.py --remove-default-flags
    cd ..
    module load campos-gpaw-setups
    module load campos-gpaw
    

    Note that every time you wish to install a new version of a package, and deploy new module file, better keep the old module file.

  • submit the test job:

    qsub submit.csh
    

    using the following submit.csh:

    #!/bin/csh
    
    #$ -q short
    #$ -pe ompi-8 8
    #$ -l arch=lx24-amd64
    ##$ -M jbray2@nd.edu
    ##$ -m abe
    
    module load ompi/1.3.2-gnu
    
    module use --append /afs/crc.nd.edu/user/j/jbray2/CAMd/modulefiles
    module load nose
    module load numpy
    module load campos-ase3
    module load campos-gpaw-setups
    module load campos-gpaw
    
    setenv P4_GLOBMEMSIZE 268435456
    setenv P4_SOCKBUFSIZE 262144
    
    echo job was accepted on:
    date
    
    mpirun -np $NSLOTS `which gpaw-python` `which gpaw-test`
    
    echo Job has completed.
    date
    
    exit 0