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, July 22 2011

July 22, 2011 5:47 pm EDT

1. Statistics
2. Tip of the Week

STATISTICS

GGATE

Uptime: 34 days
/home directory usage: 34% (7.3 TB available)
/backups directory usage: 78%

Utilization for period from: 06/21/2011 to: 07/21/2011

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

EGATE

Uptime: 137 days
/theoryfs/common directory usage: 41% (395 GB available)
/theoryfs/ccmst directory usage: 95% (46 GB available)

LSF usage for Week 28 (7/11-7/17) (times are in minutes)
GroupJobsTotal CPUAvg CPUAvg WaitAvg Trnr.
Hernandez 154 766735 51% 4979 13553 18716
Sherrill 155 878118 58% 5665 1303 7024
Other 36 529 0% 15 91 107
Total 345 1645381 109% 4769 6645 11521

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

Most productive user of the Week: galen 766735.

TIP OF THE WEEK

By Massimo

Job Arrays with LSF

Last week we discussed how to generate job arrays with Moab/Torque. Job arrays are also possible with LSF (the batch system used by egate and fgate), and are controlled in a similar way.

Job arrays in LSF are generated with the -J option, by adding an index specification to the job name, with the syntax:

-J "job_name[index_list]%job_slot_limit"

Note the use of the double quotes, that are mandatory when specifying a job array. The index_list is composed by three integer numbers with the syntax

start-end:step

Where the step specification is optional (default is one).

The index of the job within and array is stored in the environment variable LSB_JOBINDEX.

A sample job array script for LSF could be the following:

#!/bin/bash
#BSUB -J "job_array[1:10]"
#BSUB -n 8
#BSUB -R "rusage[Memory=1000]"
#BSUB -W 01:00:00:00
#PBS -t 1-10

myprogram < case_${LSB_JOBINDEX}.inp > case_${LSB_JOBINDEX}.out

This generates an array of then parallel jobs using 8 processors, 1000 MB of memory and 1 day of wall time, executing the input files case_1.inp case_2.inp ... case_10.inp.

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.