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, January 27 2012

January 27, 2012 12:05 pm EST

1. Announcements
2. Tip of the Week

ANNOUNCEMENTS

MSE Seminar Series

January 30, 2012 4:00 PM – 5:00 PM
Boggs 6A
Prof. Yaroslava Yingling
Materials Science and Engineering, North Carolina State University, Raleigh, NC
Understanding nucleic acid based material properties through molecular modeling

Green Computing Web Site

We are proud to announce that the Green Computing web site is now on-line. The web site can be visited at the address http://www.greencomputing.gatech.edu/ .

The site presents content related to the "Green Computing for Green Energy" NSF-CRIF grant proposal that led to the purchase of the Green Gate computer cluster.

TIP OF THE WEEK

By Massimo

GROMACS

GROMACS is available for parallel jobs on egate, fgate and ggate. Both single and double precision versions of the program suite are available. The double precision version of each executable has the suffix _d. In other words: grompp and mdrun are the single precision versions, while grompp_d and mdrun_d are the double precision versions.

Here are sample scripts for job submission. More info can be found at the CCMST wiki.

  • Egate and Fgate
    #!/bin/bash
    #
    # example of parallel GROMACS job
    #
    #PBS -j oe
    # Job name
    #PBS -N gromacs_job
    # Processors
    #PBS -l nodes=8:ppn=1
    # Memory
    #PBS -l pmem=250mb
    # Wall time
    #PBS -l walltime=00:02:00:00

    #
    # Job proper starts here
    #
    # Configure environment
    #

    #environment for intel libraries
    export PATH=opt/intel/Compiler/11.1/075/bin/intel64:$PATH
    export LD_LIBRARY_PATH=/opt/intel/Compiler/11.1/075/lib/intel64:/opt/intel/Compiler/11.1/075/mkl/lib/em64t:$LD_LIBRARY_PATH

    #environment for openmpi libraries
    export PATH=/share/apps/openmpi-1.4.4/intel-11/bin:$PATH
    export LD_LIBRARY_PATH=/share/apps/openmpi-1.4.4/intel-11/lib:$LD_LIBRARY_PATH
    export MPIRUN_PATH=/share/apps/openmpi-1.4.4/intel-11/bin/mpirun

    #environment for fftw3 libraries
    export LD_LIBRARY_PATH=/share/apps/fftw3/intel-11/lib:$LD_LIBRARY_PATH

    #environment for gromacs
    source /share/apps/gromacs-4.5.5/bin/GMXRC

    #
    # display number of processors and hosts file.
    #

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

    #
    #
    # Run job. Paste your job here. For double precision runs use the suffix _d
    # after the program name (e.g: grompp_d, mdrun_d).
    #
    # Note that mdrun is the only parallel tool in GROMACS, thus all other programs
    # do not need to be started using mpirun

    cd ${PBS_O_WORKDIR}

    grompp -f input.mdp -c confin10.gro -maxwarn 3
    ${MPIRUN_PATH} mdrun -v
  • Ggate
    #!/bin/bash
    #
    # example of parallel GROMACS job
    #
    #PBS -j oe
    # Job name
    #PBS -N gromacs_job
    # Processors
    #PBS -l nodes=8:ppn=1
    # Memory
    #PBS -l pmem=250mb
    # Wall time
    #PBS -l walltime=00:02:00:00

    #
    # Job proper starts here
    #
    # Configure environment
    #

    export MPIRUN_PATH=/opt/openmpi-1.5.1_intel/bin/mpirun
    export LD_LIBRARY_PATH=/opt/openmpi-1.5.1_intel/lib:/opt/intel/Compiler/11.1/046/lib/intel64:/opt/intel/Compiler/11.1/046/mkl/lib/em64t:${LD_LIBRARY_PATH}

    source /opt/gromacs-4.5.4/bin/GMXRC

    #
    # display number of processors and hosts file.
    #

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

    #
    #
    # Run job. Paste your job here. For double precision runs use the suffix _d
    # after the program name (e.g: grompp_d, mdrun_d).
    #
    # Note that mdrun is the only parallel tool in GROMACS, thus all other programs
    # do not need to be started using mpirun

    cd ${PBS_O_WORKDIR}

    grompp -f input.mdp -c confin10.gro -maxwarn 3
    ${MPIRUN_PATH} mdrun -v

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.