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 9 2011

December 9, 2011 1:55 pm EST

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

ANNOUNCEMENTS

Fgate Reinstalled

Fgate has been reinstalled and reconfigured and it is now back into production, although in limited capacity, as few nodes are still down with hardware ad software problems. Logins to fgate 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 fgate for info on the new configuration.

STATISTICS

GGATE

Uptime: 27 days
/home directory usage: 61% (4.7 TB available)
/backups directory usage: 100%

Utilization for period from: 11/08/2011 to: 12/08/2011

TIP OF THE WEEK

By Massimo

Environment Setting for Batch Execution on Egate and Fgate

We have seen how the environment variables for compilers and MPI libraries can be set interactively using the module command.

The module command is not available inside the batch execution environment, thus to run jobs that need a particular environment (compiler and/or MPI libraries) one can do two things:

  • 1. Load the chosen environment before submitting the job, then export the current environment to the job shell using the following PBS directive inside the job script:
#PBS -V
  • 2. Explicitly set the environment inside the job script. The following tables show the module commands and explicit environment settings for each combination of software:
Compiler Module Command Environment Settings
GNU (default) none none
Intel 11 module load intel/intel-11
 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
Intel 12 module load intel/intel-12
 export PATH=/opt/intel/composerxe-2011.2.137/bin/intel64:$PATH
export LD_LIBRARY_PATH=/opt/intel/composerxe-2011.2.137/compiler/lib/intel64:\
/opt/intel/composerxe-2011.2.137/mkl/lib/intel64:$LD_LIBRARY_PATH
MPI Module Command Environment Settings Batch Execution Command
MPICH2 GNU
export PATH=/share/apps/mpich2-1.4.1p1/gnu/bin:\
$PATH
export LD_LIBRARY_PATH=\
/share/apps/mpich2-1.4.1p1/gnu/lib:\
$LD_LIBRARY_PATH
mpiexec -rmk pbs myprog.exe
intel-11
export PATH=/share/apps/mpich2-1.4.1p1/intel-11/bin:\
$PATH
export LD_LIBRARY_PATH=\
/share/apps/mpich2-1.4.1p1/intel-11/lib:\
$LD_LIBRARY_PATH
mpiexec -rmk pbs myprog.exe
intel-12
export PATH=/share/apps/mpich2-1.4.1p1/intel-12/bin:\
$PATH
export LD_LIBRARY_PATH=\
/share/apps/mpich2-1.4.1p1/intel-12/lib:\
$LD_LIBRARY_PATH
mpiexec -rmk pbs myprog.exe
OPENMPI GNU
export PATH=/share/apps/openmpi-1.4.4/gnu/bin:\
$PATH
export LD_LIBRARY_PATH=\
/share/apps/openmpi-1.4.4/gnu/lib:\
$LD_LIBRARY_PATH
mpirun myprog.exe
intel-11
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
mpirun myprog.exe
intel-12
export PATH=/share/apps/openmpi-1.4.4/intel-12/bin:\
$PATH
export LD_LIBRARY_PATH=\
/share/apps/openmpi-1.4.4/intel-12/lib:\
$LD_LIBRARY_PATH
mpirun myprog.exe

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.