University of Delaware | Department of Chemistry and Biochemistry | Chemistry Computing Cluster

Computational Resources in Chemistry and Biochemistry
  UNIX Primer for the Cluster
Gaussian Usage on the Cluster
Using the Gaussian newzmat Program

Computing News
Counting High-Demand Jobs on the SGI's
As a general rule, users are asked to police themselves and limit the number of high-demand jobs running on machines in the Chemistry Cluster at any one time. As more jobs requiring massive amounts of CPU time (hence, high-demand) are added to a machine, the less time each of the jobs will get. So in essence, by running too many simultaneous high-demand jobs at once, you simply lengthen the amount of time all of the jobs will take! A rule of thumb which works well is to limit each SGI in the cluster to 2 high-demand jobs per processor. For alfred, eugene, groucho, chico, harpo, zeppo, irene and alice, this means only 2 such jobs should be running at any one time.

To help users figure out how many high-demand jobs are running on a machine, I'm pleased to introduce the highDemandJobs command. Type this command, and you'll get a list of each job which is considered high-demand:
    alfred 1% highDemandJobs
    High-Demand Jobs on alfred
    Username        PID Command   State     Time
    mlassman     112057 l502.exe  WL  1-06:03:00 
      wenbin     116676 WL    17:32:42 
    alfred 2%

Random Password Generator Installed
A new utility called 'RndPasswd' has been added to the cluster. The program will generate a random password; it does not change your password, it merely makes a suggestion for a new password. You can then use the 'yppasswd' program to actually change your cluster password. For instance:
    alfred 1% RndPasswd
    Enter the length of the password [ 6 <= length <= 12 ]:  6
    New password `U@mlLt1`.
    alfred 2%

New Gaussian Setup Command
All Gaussian users on the cluster should note (as described on the login screen for all SGI's on the cluster) that Gaussian should now be set up using the 'setGauss' command. Using that command alone, with no arguments on the command line, will automatically set up the default version of Gaussian (in other words, the newest version). If you need a specific version other than the current newest version, simply add the version number to the command line. For instance, to configure Gaussian 98 version A6, you would type
    alfred 1% setGauss a6
    alfred 2%
If the version you enter is unavailable on the SGI which you are logged in to, the default version will be configured. Currently, the deprecated Gaussian setup commands 'setg98' and 'setg98.a9' remain available to you. They are, in turn, actually just aliases to 'setGauss a6' and 'setGauss a9', respectively. You may also use the command 'setGauss info' to get a list of the versions available on the SGI you're logged in to.
Department Facilities
Basic Hardware Resources
The Department of Chemistry and Biochemistry maintains a cluster of Silicon Graphics workstations used for computational research and coursework. The Chemistry Computer Cluster, as it is known, consists of:
Machine Name Type [processor(s)/main memory size/local disk storage]
bigdog SGI Origin 2000 [6x195 MHz R10000/512 MB/22 GB]
alfred SGI Indigo2 [195 MHz R10000/256 MB/20 GB]
eugene SGI Indigo2 [195 MHz R10000/256 MB/20 GB]
zeppo SGI O2 [300 MHz R12000/256 MB/-]
harpo SGI Octane [195 MHz R10000/512 MB/-]
groucho SGI O2 [300 MHz R12000/256 MB/-]
chico SGI Octane [195 MHz R10000/512 MB/-]
alice SGI Octane [195 MHz R12000/512 MB/-]
irene SGI Octane [195 MHz R12000/512 MB/-]
If you are a faculty, staff, or student in the Department then you may request an account on the cluster. Please visit the New Account Request Form web page.

Special Hardware Resources: Grommet
The Chemistry Department is also home to the Large-Scale Computational Facility for the Chemical Sciences and Engineering (a.k.a. Grommet), a project funded by the NSF's MRI program. The research groups involved in this grant come from the departments of Chemistry and Biochemistry, Physics, Chemical Engineering, and Mechanical Engineering. The centerpiece of the facility is a Silicon Graphics Origin 2000:
Machine Name Type [processor(s)/main memory size/local disk storage]
grommet SGI Origin 2000 [8x195 MHz R10000/4 GB/63 GB]
Visit the Grommet web page for more information on the project.

Special Hardware Resources: University Computing Facilities
For larger computing problems, researchers in the Department can also use the University's Large-Scale Computing Facility, providing access to an eight-processor Cray J90 as well as a twelve-processor Silicon Graphics Power Challenge system.

Available Software Titles
Availability of the titles listed here may be unlimited (any SGI on the cluster) or on a limited basis (per SGI licensing):
Software Title Version(s) Availability
Gaussian Suite (g03/gv) 03.b04 all machines
Gaussian Suite (g98/gv) 98.a11 all machines
Gamess March 2000 Release all machines
Spartan 5.1.3 alfred, eugene
Acdelrys Insight II LifeSciences 2000.1, MaterialScience 4.0.0 all machines
Mathematica 4.0 all machines
Molden 3.4 all machines
CAChe 3.5 single machine, LDL-209
For further information on computing resources in the Department, please contact

page last updated 10/31/2003 | contact the chemistry web-master | page design by J. T. Frey