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 22 2011

April 22, 2011 7:34 pm EDT

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


Upcoming Seminars

April 28, 2011 4:00 PM – 5:00 PM
MoSE G011
School Colloquia
Prof. Larry Que, University of Minnesota
Hydrocarbon oxidations by bio-inspired nonheme iron catalysts

Ggate Upgrade April 26-28, 2011

Ggate will undergo maintenance from Tuesday April 26 through Thursday April 28 for an hardware and software upgrade. The upgrade will add 16 new compute nodes, each one with 16 cores 64GB of memory and 4.5 TB of scratch disk space. These are hybrid CPU-GPU nodes: 14 of the nodes have two Nvidia Tesla cards, while two nodes carry the new Fermi cards (one card per node). During the upgrade we will also reconfigure the Icebreaker storage server.

The details of the upgrade are the following:

  1. Sometimes on Monday (April 25th) evening the job queues will be closed, so that no new jobs will be started (one will still be able to submit jobs, but they will sit in queue).
  2. On Tuesday (April 26th), probably in the afternoon, ggate will be shut down. Any job still running at that time will be killed.
  3. The machine should resume production on Thursday (April 28).
  4. Please note: The configuration of the icebreaker scratch storage server will be changed, and the current /data partition will be eliminated, please copy any important data out of this partition prior to the upgrade, or the data will be lost. The user home directories are not affected by the upgrade, only the /data partition will be eliminated.

Please contact Massimo ( if you have any question.



Uptime: 126 days
/home directory usage: 14% (9.5 TB available)
/backups directory usage: 48%

Utilization for period from 03/22/2011 to: 04/21/2011

Note: Full statistics for ggate are available online at: (the link works only for the Gatech Chemistry network)


Uptime: 99 days
/home directory usage: 80% (1.2 TB available)
/backups directory usage: 100%

LSF usage for Week 15 (4/11-4/17) (times are in minutes)
GroupJobsTotal CPUAvg CPUAvg WaitAvg Trnr.
Bredas 19 92773 5% 4883 1045 4440
Hernandez 170 862380 45% 5073 5444 10643
Sherrill 292 424025 22% 1452 1724 3332
Other 15 13560 1% 904 40 738
Total 496 1392737 72% 2808 2922 5802

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

Most productive user of the Week: galen 828243.


Uptime: 46 days
/theoryfs/common directory usage: 82% (124 GB available)
/theoryfs/ccmst directory usage: 95% (50 GB available)

LSF usage for Week 15 (4/11-4/17) (times are in minutes)
GroupJobsTotal CPUAvg CPUAvg WaitAvg Trnr.
Hernandez 239903 1021129 68% 4 633 637
Other 226 10155 1% 45 2 48
Total 240129 1031284 68% 4 632 637

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

Most productive user of the Week: galen 789724.


By Massimo

Working on Ggate: copying data to/from compute nodes

There are several ways to get data from the master node to compute nodes;

  1. NFS. The easiest way to transfer data to the compute nodes is via NFS. All files in your /home directory are shared by default to all compute nodes via NFS. Opening an NFS-shared file on a compute node will, in fact, open the file on the master node; no actual copying takes place.
  2. Copying data via bpcp. To copy a file, rather than changing the original across the network, you can use the bpcp command. This works much like the standard Unix file-copying command cp, in that you pass it a file to copy as one argument and the destination as the next argument. Like the Unix scp, the file paths may be qualified by a computer host name. With bpcp, you can indicate the node number for the source file, destination file, or both. To do this, prepend the node number with a colon before the file name, to specify that the file is on that node or should be copied to that node. For example, to copy the file /tmp/foo to the same location on node 1, you would use the following command:
    bpcp /tmp/foo 1:/tmp/foo

Do you have usage tips that you want to share with the other CCMST users? Please send them to Massimo ( for inclusion in the Tip of the Week section.