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, December 2 2011

December 2, 2011 3:55 pm EST

1. Announcements
2. Statistics
3. Tip of the Week

ANNOUNCEMENTS

Egate Reinstalled

Egate has been reinstalled and reconfigured and it is now back into production. Logins to egate are now managed through the campus directory, thus the cluster is now accessible using the Georgia Tech ID. Jobs are now managed by a PBS/Torque batch queue with the Moab scheduler. Please refer to the new wiki page for egate for info on the new configuration.

Fgate Being Reinstalled

Fgate is currently down and undergoing reinstall. The procedure should be completed over the weekend, and fgate should be back on line early next week. Login for the new fgate will be through Georgia Tech ID.

STATISTICS

GGATE

Uptime: 20 days
/home directory usage: 58% (4.7 TB available)
/backups directory usage: 94%

Utilization for period from: 11/01/2011 to: 12/01/2011

Note: Full statistics for ggate are available online at: http://ggate.chemistry.gatech.edu:8080 (the link works only for the Gatech Chemistry network)

TIP OF THE WEEK

By Massimo

New Batch Jobs on Egate

Jobs on egate are run on the PBS-Torque batch environment. This is similar to the LSF environment of old egate, with just some slight modifications.

here are the most useful commands (see the man pages for details):

qsub
submit a job to the queue. Typical usage is with a job script file, e.g: qsub myjob.pbs.
qstat
display the status of your jobs
showq
displays all jobs in queue: running, idle and blocked
qdel jobid
remove a job (running or queued) from the queue. Here jobid is the numerical job id of the job, as displayed by the qstat command.
Single Processor Job
#!/bin/bash
#job name
#PBS -N test
# Join output and error channell
#PBS -j oe
# define e-mail address
#PBS -M user@host
# send e-mail when jobs ends or aborts:
#PBS -m ae
# wall time request (GG:HH:MM:SS)
#PBS -l walltime=00:01:00:00
# memory request (Mbytes)
#PBS -l pmem=1000mb
# export current environment to job
#PBS -V

#Job proper starts here

#Additional environment setting, if necessary
export PATH=/some/dir/:$PATH

#run job

# PBS_O_WORKDIR is the directory where the qsub command was executed
cd $PBS_O_WORKDIR

Parallel job
#!/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-6.0
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

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.