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 25 2011

March 25, 2011 3:04 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 Distinguished Lecture Series
Prof. Klaus Mullen, Max Planck Institute for Polymer Research in Mainz

April 4, 2011 7:30 PM – 9:00 PM
AACP Seminar Series
MoSE G011
Prof. James Kindt, Emory University
Atomistic simulation of mixed-lipid bilayers: Mixed methods for mixed membranes

April 6, 2011 4:00 PM – 5:00 PM
MoSE G011
Peter B. Sherry Lecture
Prof. Zhenan Bao, Stanford University
Materials Design and Processes for Large-Area Flexible Electronics

April 7, 2011 11:30 AM – 12:30 PM
MoSE 1201A
Undergraduate Seminar
Prof. Zhenan Bao, Stanford University
Organic Transistor Based Sensors for Flexible Artificial Electronic Skin

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: 70 days
/home directory usage: 75% (1.5 TB available)
/backups directory usage: 100%

LSF usage for Week 11 (3/14-3/20) (times are in minutes)
GroupJobsTotal CPUAvg CPUAvg WaitAvg Trnr.
Bredas 41 22401 1% 546 218 1393
Hernandez 643 346030 18% 538 524 1089
Sherrill 2486 221320 11% 89 261 355
Other 6 47948 2% 7991 0 8414
Total 3176 637698 33% 201 314 533

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

Most productive user of the Week: loriab 221320.

EGATE

Uptime: 18 days
/theoryfs/common directory usage: 41% (392GB available)
/theoryfs/ccmst directory usage: 93% (66 GB available)

LSF usage for Week 11 (3/14-3/20) (times are in minutes)
GroupJobsTotal CPUAvg CPUAvg WaitAvg Trnr.
Hernandez 947 918392 61% 970 619 1629
Sherrill 427 72194 5% 169 386 557
Other 207 159269 11% 769 16 796
Total 1581 1149855 76% 727 477 1230

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

Most productive user of the Week: galen 500917.

TIP OF THE WEEK

 

By Massimo

Working With Ggate: Interactive Jobs

The recommended way of running interactive jobs on ggate is by requesting and interactive jobs to the scheduler. Interactive jobs can be submitted by specifying the -I option to the submission command:

bsub -I

or, using Moab syntax:

msub -I

Interactive jobs are queued and scheduled as any other jobs, but at the moment of execution, an interactive shell is connected to the terminal from which the submission command was issued. NOTE: the ggate scheduler is configured to do scheduling iteration every 2-3 minutes, thus when requesting an interactive jobs it is likely that you will have to wait at least a couple of minutes before obtaining a shell prompt. Then you might have to wait longer in case there are not enough resources for the job.

Resources for interactive jobs are specified in the same way as for the other jobs, except that usually resource requests are specified directly on the command line using the -l switch:

bsub -I -l pmem=500mb,walltime=01:00:00

The above command requests an interactive job using 500 MB of memory for a total length of 1 hour. Note that interactive jobs are subject to the same rule as other jobs: if the jobs exceeds the memory or wall time request, it will be terminated by the scheduler.

Interactive jobs can be parallel: just add the processor request to the submitting command, for example

bsub -I -l nodes=4:ppn=1

In this case, once the interactive shell is started, the environment variable PBS_NODEFILE will point to the node file showing which are the other processors assigned to the job.

 

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.