Center for Computational Molecular Science and Technology Georgia Institute of Technology Center for Computational Molecular Science and Technology School of Chemistry and Biochemistry

CCMST Weekly News, February 24 2012

February 24, 2012 1:06 pm EST

1. Announcements
2. Tip of the Week

ANNOUNCEMENTS

Cherry Emerson Lecture

March 1, 2012 4:00 PM – 5:00 PM
MoSE G011
Prof. Charles Schmuttenmaer, Yale University
Using Time-Resolved THz Spectroscopy to Study Carrier Dynamics and Solar Energy Conversion in TiO2 Nanotubes and Other Nanostructured Materials.

TIP OF THE WEEK

By Massimo

NWChem 6.1

The latest NWChem release, NWChem 6.1, is now installed on egate, fgate and ggate. The new release offers some new capabilities and improvements, including range-separated density functionals, analytical Hessian for open shell system, DFT-D3 implementation. Please consult the NWChem home page for details about the new release.

Here follow sample scripts for using NWChem 6.1 on the CCMST computers. For details please consult the CCMST wiki page.

  • Egate and Fgate
  • #!/bin/bash
    #PBS -j oe
    #PBS -N PP5
    #PBS -l nodes=4:ppn=2
    #PBS -l pmem=1200mb
    #PBS -l walltime=01:00:00:00
    #PBS -V

    export NWCHEM_TOP=/share/apps/nwchem-6.1
    export NWCHEM_TARGET=LINUX64
    export NWCHEM_BASIS_LIBRARY=${NWCHEM_TOP}/data/libraries/
    export MPIRUN_PATH=/share/apps/openmpi-1.4.4/intel-11/bin/mpirun
    export LD_LIBRARY_PATH=/share/apps/openmpi-1.4.4/intel-11/lib:/opt/intel/Compiler/11.1/075/lib/intel64:/opt/intel/Compiler/11.1/075/mkl/lib/em64t:$LD_LIBRARY_PATH
    export SCRATCH_DIR=/scratch/${USER}

    cd ${PBS_O_WORKDIR}

    ${MPIRUN_PATH} ${NWCHEM_TOP}/bin/nwchem PP5.nw > PP5.out
  • Ggate
  • #!/bin/bash
    #
    # example of parallel job using nwchem 6.1
    #
    #PBS -j oe
    #PBS -N nwchem_example_para
    #PBS -l nodes=2:ppn=8
    #PBS -l pmem=3000mb
    # Job proper starts here
    #
    # Configure NWCHEM environment
    #

    export NWCHEM_TOP=/opt/nwchem-6.1
    export NWCHEM_TARGET=LINUX64
    export NWCHEM_BASIS_LIBRARY=$NWCHEM_TOP/data/libraries/
    export MPIRUN_PATH=/opt/openmpi-1.4.5_intel/bin/mpirun
    export LD_LIBRARY_PATH=/opt/openmpi-1.4.5_intel/lib:/opt/intel/Compiler/11.1/046/lib/intel64:/opt/intel/Compiler/11.1/046/mkl/lib/em64t:${LD_LIBRARY_PATH}
    export SCRATCH_DIR=/scratch/${USER}

    #
    # display number of processors and hosts file.
    #

    NP=`cat ${PBS_NODEFILE} | wc -l`
    echo "number of processes = ${NP}"
    cat ${PBS_NODEFILE}

    #
    # run job
    #

    cd ${PBS_O_WORKDIR}

    ${MPIRUN_PATH} ${NWCHEM_TOP}/bin/nwchem PP10-8-1_1.nw > PP10-8-1_1.out

Do you have usage tips that you want to share with the other CCMST users? Please send them to Massimo (massimo.malagoli@chemistry.gatech.edu) for inclusion in the Tip of the Week section.