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, September 23 2011

September 23, 2011 7:52 pm EDT

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



*** CCMST Security Breach ***

Today we discovered that there has been unauthorized access to several CCMST clusters, including egate, fgate and ggate. An investigation of the incident in collaboration with Georgia Tech OIT is undergoing, and the clusters have been closed to off-campus access until the matter is investigated.

The investigation, and the following implementation of countermeasures, will cause some disruption on the availability of the CCMST clusters starting from Monday. Depending on the findings, the disruptions of service can go from minor downtime up to extended shutdowns of one or more systems. Users are advised to prepare for the possibility that one or more CCMST machines will not be available for an extended period of time. In particular it is advisable to download off the cluster any recent data, so that data analysis can proceed even if a system is closed to production for some time. Please contact Massimo ( if you have any question. Off campus users should contact Massimo to coordinate access to user data, since direct access to the clusters is turned off at the moment.

Physical Chemistry Seminar Series

September 27, 2011 4:00 PM – 5:00 PM
MoSE 3201A
Prof. Jose Gascon, University of Connecticut
Quantum Chemistry in biologically relevant molecules and molecular events

School Colloquium

September 29, 2011 4:00 PM – 5:00 PM
MoSE G011
Prof. Caren Meyers, Johns Hopkins University
ntracellular delivery of polyphosphonates: The chemistry and biology of bisphosphonamidate prodrugs

AACP Seminar Series

October 3, 2011 7:30 PM – 9:00 PM
MoSE G011
Prof. Steve Buratto, University of California, Santa Barbara
Photophysics of Organic Semiconductors Probed by Single Molecule Fluorescence and High Spatial Resolution Chemical Imaging





Uptime: 97 days
/home directory usage: 43% (6.3 TB available)
/backups directory usage: 93%

Utilization for period from: 08/23/2011 to: 09/22/2011

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


Uptime: 61 days
/home directory usage: 80% (1.2 TB available)
/backups directory usage: 87%

LSF usage for Week 37 (9/12-9/18) (times are in minutes)
GroupJobsTotal CPUAvg CPUAvg WaitAvg Trnr.
Bredas 70 28508 1% 407 4 280
Sherrill 3259 563552 29% 173 348 541
Other 6 12658 1% 2110 0 2150
Total 3335 604719 31% 181 340 539

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

Most productive user of the Week: parker 363558.


Uptime: 2 days
/theoryfs/common directory usage: 44% (373 GB available)
/theoryfs/ccmst directory usage: 96% (40 GB available)

LSF usage for Week 37 (9/12-9/18) (times are in minutes)
GroupJobsTotal CPUAvg CPUAvg WaitAvg Trnr.
Hernandez 92 17260 1% 188 0 189
Sherrill 606 31628 2% 52 40 93
Total 698 48887 3% 70 35 106

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

Most productive user of the Week: kennedy 23313.


By Sean Ryno

NumPy and SciPy on Ggate

The NumPy and SciPy python packages are complementary packages that allow advanced mathematical function in the python environment. NumPy is the base package of the two and amongst other things allows multi-dimensional arrays as well as tools for basic linear algebra, Fourier transforms, and random number generation. The SciPy package builds upon NumPy by allowing higher level functionality such as advanced array creation, numerical integration, and many types of statistical analysis. More information is available at

To use either package on GGate the following must be added to the user's environment variables:

export PYTHONPATH=/usr/lib64/python2.6/site-packages

To run python with these modules python2.6 must be used and can be called simply by issuing the command:


Programs can be run by the following:


Where in the program or interactive environment the following are passed:

import sys
from numpy import *
from scipy import *

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.