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, April 8, 2011

April 8, 2011 10:52 pm EDT

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

ANNOUNCEMENTS

Upcoming Seminars

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

April 14, 2011 4:00 PM – 5:00 PM
MoSE G011
School Colloquia
Prof. Ben McCall, University of Illinois at Urbana-Champaign
Astrochemistry: From H3+ to C60

STATISTICS

FGATE

Uptime: 85 days
/home directory usage: 76% (1.5 TB available)
/backups directory usage: 100%

LSF usage for Week 13 (3/28-4/3) (times are in minutes)
GroupJobsTotal CPUAvg CPUAvg WaitAvg Trnr.
Bredas 89 127540 7% 1433 469 1622
Hernandez 916 819655 42% 895 778 1721
Sherrill 624 140048 7% 224 568 797
Other 25 71866 4% 2875 0 1253
Total 1654 1159109 60% 701 670 1360

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

Most productive user of the Week: galen 580664.

EGATE

Uptime: 32 days
/theoryfs/common directory usage: 44% (372GB available)
/theoryfs/ccmst directory usage: 94% (56 GB available)

LSF usage for Week 13 (3/28-4/3) (times are in minutes)
GroupJobsTotal CPUAvg CPUAvg WaitAvg Trnr.
Hernandez 12803 1133595 75% 89 280 397
Sherrill 7 72573 5% 10368 85 10684
Other 86 24774 2% 288 0 152
Total 12896 1230944 81% 95 278 401

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

Most productive user of the Week: galen 629868.

TIP OF THE WEEK

By Massimo

Working on Ggate: bpsh

Here is an in depth look at bpsh the Scyld Clusterware command line utility used to interact with compute nodes:

  • Usage: bpsh [options] nodenumber command [command-args]. Where nodenumber is either an explicit node name (i.e.: n2), or the node number (compute nodes start at 0, and -1 is the head node), or a list of nodes (i.e.: 0,1,...). Note that the head node (-1) cannot be the first of the list.
  • The option -a executes the command on all the compute nodes currently on-line.
  • The option -p prepends the node number to the output of the command.
  • -s list sequentially the output from each node.
  • -d prints a divider line between the sequential output from each node.

Examples:

  • bpsh 5 ls /scratch/malagoli shows the contents of the scratch directory of node 5.
  • bpsh -ad ls /scratch/malagoli shows the contents of all the local scratch directories, with separated output from each node.
  • bpsh n12 rm -rf /scratch/malagoli/badjob deletes the scratch files of a bad job on node n12.

Note that bpsh takes a single command as input. To execute multiple commands at the same time, or to use wild cards (i.e. *) in the command arguments, use the command bprsh instead:

  • bprsh -a rm -rf /scratch/malagoli/* clears all the scratch directories on all the compute nodes.

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.