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 20 2012

January 20, 2012 11:42 am EST

1. Announcements
2. Tip of the Week

ANNOUNCEMENTS

Physical Chemistry Seminar Series

January 27, 2012 4:00 PM – 5:00 PM
MoSE 3201A
Prof. Yasuhiro Tachibana, RMIT University
Semiconductor Quantum Dots for Solar Light Energy Conversion

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

Quantum Espresso

Quantum Espresso is available for parallel jobs on egate, fgate and ggate. Here are sample scripts for job submission. More info can be found at the CCMST wiki.

  • Egate and fgate:
    #! /bin/bash
    #
    # Sample script for parallel Quantum Espresso job
    #
    #PBS -N qe_test
    #PBS -j oe
    #PBS -l nodes=8:ppn=1
    #PBS -l pmem=500mb
    #PBS -V

    #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

    cd ${PBS_O_WORKDIR}

    #define Quantum espresso environment
    ESPRESSO_ROOT=/share/apps/espresso-4.3.2

    #This can be overriden by the "outdir" and "pseudo_dir" input variables
    export ESPRESSO_TMPDIR=/scratch/${USER}/qe/
    export ESPRESSO_PSEUDO=${ESPRESSO_ROOT}/pseudo/

    #make sure the tmp dir exists on each node

    for i in $(cat ${PBS_NODEFILE} | uniq);
    do echo "Creating scratch directoy " ${ESPRESSO_TMPDIR} " on " $i;
    ssh $i mkdir -p ${ESPRESSO_TMPDIR}
    done

    mpirun ${ESPRESSO_ROOT}/bin/pw.x < PP2-pbe_nscf_200.in > PP2-pbe_nscf_200.out
  • Ggate:
    ! /bin/bash
    #
    # Sample script for parallel Quantum Espresso job
    #
    #PBS -N qe_test
    #PBS -j oe
    #PBS -l nodes=8:ppn=1
    #PBS -l pmem=500mb
    #PBS -V

    #set environment for "good" version of openmpi.
    #
    export PATH=/opt/openmpi-1.5.1_intel/bin:${PATH}
    export LD_LIBRARY_PATH=/opt/openmpi-1.5.1_intel/lib:${LD_LIBRARY_PATH}

    cd ${PBS_O_WORKDIR}

    #define Quantum espresso environment
    ESPRESSO_ROOT=/opt/espresso-4.3.1

    #This can be overriden by the "outdir" and "pseudo_dir" input variables
    export ESPRESSO_TMPDIR=/scratch/${USER}/qe/
    export ESPRESSO_PSEUDO=${ESPRESSO_ROOT}/pseudo/

    #make sure the tmp dir exists on each node

    for i in $(cat ${PBS_NODEFILE} | uniq);
    do echo "Creating scratch directoy " ${ESPRESSO_TMPDIR} " on " $i;
    ssh $i mkdir -p ${ESPRESSO_TMPDIR}
    done

    mpirun ${ESPRESSO_ROOT}/bin/pw.x < PP2-pbe_nscf_200.in > PP2-pbe_nscf_200.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.