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, March 18, 2011

March 18, 2011 11:43 pm EDT

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

ANNOUNCEMENTS

Upcoming Seminars

April 1, 2011 4:00 PM – 5:00 PM
MoSE G011
COPE Seminar Series
Prof. Klaus Mullen, Max Planck Institute for Polymer Research in Mainz

April 11, 2011 11:00 AM – 12:00 PM
MoSE 3201A
Prof. Enrico Clementi, University of Insubria, Italy
With computers from atoms to macromolecular systems

NOTE: Planned Power Outage Postponed

Please note that the power outage for the MS&E building, originally planned for March 26-27 2001 has been postponed until later in the spring semester. Date to be determined.

STATISTICS

FGATE

Uptime: 64 days
/home directory usage: 77% (1.5 TB available)
/backups directory usage: 97%

LSF usage for Week 10 (3/7-3/13) (times are in minutes)
GroupJobsTotal CPUAvg CPUAvg WaitAvg Trnr.
Bredas 21 50599 3% 2409 2840 4389
Hernandez 851 558059 29% 656 220 960
Sherrill 1612 280744 15% 174 460 643
Total 2484 889402 46% 358 398 783

Note: percentages refer to the total CPU time available for the period.

Most productive user of the Week: galen 395303.

EGATE

Uptime: 11 days
/theoryfs/common directory usage: 41% (392GB available)
/theoryfs/ccmst directory usage: 91% (80 GB available)

LSF usage for Week 10 (3/7-3/13) (times are in minutes)
GroupJobsTotal CPUAvg CPUAvg WaitAvg Trnr.
Hernandez 1276 724165 48% 568 606 1818
Sherrill 85 2890 0% 34 178 283
Other 208 23154 2% 111 7 169
Total 1569 750209 50% 478 503 1516

Note: percentages refer to the total CPU time available for the period.

Most productive user of the Week: hagy 387911.

TIP OF THE WEEK

 

By Massimo

Working With Ggate: Sample Job Scripts
  • Single Processor job
    #!/bin/bash
    #
    # sample script for single processor job
    #
    # job name
    #PBS -N sample_job
    # join output and error output
    #PBS -j oe
    # memory request
    #PBS -l pmem=3000mb
    #wall time request (DD:HH:MM:SS)
    #PBS -l walltime=02:30:00
    
    #
    # environment configuration goes here
    #
    
    cd $PBS_O_WORKDIR  # change to the directory the job was submitted from
    
    #
    # commands for running the job go here
    #
    
    
  • Parallel MPICH Job
    #!/bin/bash
    #
    # sample script for parallel job using MPICH
    #
    # job name
    #PBS -N sample_job
    # join output and error output
    #PBS -j oe
    # processor request
    #PBS -l nodes=8:ppn=1
    # memory request
    #PBS -l pmem=3000mb
    #wall time request (DD:HH:MM:SS)
    #PBS -l walltime=02:30:00
    
    #
    # environment configuration goes here
    #
    
    cd $PBS_O_WORKDIR  # change to the directory the job was submitted from
    
    #
    # run job using MPICH over the infiniband interconnect
    # number of processor and host file are taken from the queue
    # environment
    
    mpirun –machine vapi $path_to/app $1 $2
    
    
  • Parallel OPENMPI Job
    #!/bin/bash
    #
    # sample script for parallel job using OPENMPI
    #
    # job name
    #PBS -N sample_job
    # join output and error output
    #PBS -j oe
    # processor request
    #PBS -l nodes=8:ppn=1
    # memory request
    #PBS -l pmem=3000mb
    #wall time request (DD:HH:MM:SS)
    #PBS -l walltime=02:30:00
    
    #
    # environment configuration goes here
    #
    export PATH=/usr/openmpi/bin:${PATH} 
    export LD_LIBRARY_PATH=/usr/lib64/OMPI/gnu:${LD_LIBRARY_PATH}
    
    cd $PBS_O_WORKDIR  # change to the directory the job was submitted from
    
    #
    # run job using MPICH over the infiniband interconnect
    # number of processor and host file are taken from the queue
    # environment.
    
    /usr/openmpi/bin/mpirun $path_to/app $1 $2
    
    

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.