Computational Resources in Chemistry and Biochemistry
UNIX Primer for the Cluster Gaussian Usage on the Cluster Using the Gaussian newzmat Program
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 DLPOLY.ne 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.
For further information on computing resources in the Department, please contact Copper@chem.udel.edu
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:
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.
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/-]
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:
Visit the Grommet web page for more information on the project.
Machine Name Type [processor(s)/main memory size/local disk storage] grommet SGI Origin 2000 [8x195 MHz R10000/4 GB/63 GB]
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