Scream Saver Aug 94

THE SGI SCREAM-SAVER

Chemistry Department, Indiana University, August 1994

This newsletter is available at the beginning of each month and covers the chemistry SGI cluster and the software available on it. If you want to subscribe (specify hardcopy or e-mail preference), please send e-mail to Marty Pagel (mpagel@indiana.edu).

Items Covered in this Edition:

C687: Biomolecular Modeling

This graduate-level fall semester course will meet Tuesdays and Thursdays from 7:30 pm to 9:00 pm. Dr. Andy Ellington, the course instructor, has compiled a comprehensive syllabus without being overly ambitious. Lectures will be presented by Andy and a variety of his colleagues, while hands- on experience at SGI workstations will often incorporate the research and ideas of class attendants. A variety of molecular modeling software in the department will be reviewed, although most assignments will focus upon the recently acquired software from Biosym Technologies, including the Viewer, Biopolymer, Discover, Homology, DelPhi, Docking, LUDI, and NMRchitect programs. Notes about modeling software will be available at each Departmental SGI. More than other courses, The time spent learning and performing modeling experiments will directly result in practical understanding and the ability to apply molecular modeling towards the current research of each partiscipant. Furthermore, the skills acquired from this course in biomolecular modeling, one of the fastest growing techniques in chemical research, will certainly be used throughout the career of the professional biochemist. Whether your partiscipation entails attending each session and completing each assignment, or skimming through just one assignment on your own, all professional chemists of the 90's are strongly encouraged to take advantage of this unique opportunity.

Status of the Departmental SGIs

Ken DeHart has recently begun to share the responsibilities of system administration of the departmental SGIs with Marty Pagel. Ken will concentrate upon UNIX system administration tasks, while Marty will shift his attention more towards administration of molecular modeling programs. Both Ken and Marty are available to address troubleshooting of SGI problems, although their other responsibilities may delay their attention to some problems. Your patience is appreciated during busy work periods.

All Departmental and most research SGIs have access to the "server" disks on chemvgx through the network. When network connections are lost, access to chemvgx disks is lost. All workstations have been reconfigured so that the workstation will still function well without the chemvgx disks, although the programs that reside on chemvgx will not be available to the workstation. System administrators of research workstations should contact Marty if particular programs on chemvgx are often used on the research SGI workstation, in which case the program can be placed on the research SGI.

The email program Pine is available on all SGIs by typing pine4 or pine5 (depending upon whether the SGI is running IRIX version 4.x or 5.x). This email program is one of the most user-friendly free email systems for UNIX workstations, and was chosen by UCS for their "EZMAIL" email system. This email program is NOT intended for use as a general email program. Security will not be maintained in Pine on the SGIs, so absolute privacy of email messages is NOT guaranteed. If Pine or the workstation require maintenance due to heavy email use, the sendmail and addressbook features will be removed. Pine is intended to be a user-friendly interface to read email messages that are generated by the system or users ONLY during the use of molecular modeling programs and routine use of the UNIX system. If you like the Pine program, type telnet ezmail and follow the instructions to create a UCS Pine account.

CRON - the UNIX timekeeper

cron is the daemon (UNIX process) which automatically schedules and executes programs and scripts on a periodic basis. System administrators use cron to execute backup routines, disk accounting procedures, and disk clean-up processes late at night, while workstation usage is light. Researchers can use cron to schedule big jobs late at night or on the weekends, so that interactive users won't be slowed during the day. Researchers can also use cron to automate UNIX tasks that are repeated over long time periods.

First, the UNIX program or command should be run manually to verify that it works. Next, a cron configuration file must be made using your favorite editor (jot, vi, emacs, etc.). I like to name my file /usr/people/mpagel/mpagel.crontab. The format of the cron configuration file must be exact. Comments are introduced with a hash mark ("#") in the first column of a line. Each non-comment line in a configuration file contains six fields, each separated by space(s): 

minute   hour   day   month   weekday   command

where minute =  (00 to 59)
      hour =  (00 to 23)
      day = (1 to 31)
      month = (1 to 12)
      weekday = (0 to 6, Sunday = 0)
Each of these fields may contain:
  1. an asterisk ("*") which matches anything
  2. a single integer, which matches exactly
  3. a list of integers separated by commas, which matches any listed value
  4. two integers separated by a dash, matching any value in the indicated range
For instance, the time specification
0,30 9-17 13 * 6
selects all half-hours between 9 am and 5 pm on any Friday the 13th in any month.

command is the /bin/sh command line to be executed. All user accounts on chemistry department SGIs are set up with C-shell accounts. To include a C-shell command, insert /bin/csh before the command.

There can be NO blank lines in this configuration file.

To submit your configuration file, type crontab filename. For instance, when I submit my mpagel.crontab configuration file, I type crontab mpagel.crontab. The commands are executed automatically. Errors are sent to the user via email by the UNIX system.

Future SGI Users Meetings

The SGI Users Meetings has finally found a home and a time. Future meetings will be held on the second Tuesday of each month at 1 pm in room A400.

The topic for September's meeting is "Output from the SGI workstations", which will cover printouts from a variety of programs, making slides, making videos, and sharing data between Internet users.

Topics and speakers are being sought for the October and November meetings. Due to scheduling conflicts with Finals week, no meeting will be held in December.

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Last updated: 01/23/2001