THE SGI SCREAM-SAVER
Chemistry Department, Indiana University, Summer 1995
This newsletter is available at the begining of each month and covers the chemistry
SGI cluster and the software available on it. If you want to subscribe, please
contact Marty Pagel (email@example.com) or Kathrine MAnn (MSC, A421)
Items Covered in this Edition:
WHY SHOULD YOU CARE ABOUT ARCHIVING
YOUR FILES? Eventually, all computer disks get full
and files must be removed. Archive your files and
remove them from the SGI workstations before the disk
becomes 100% full, or your SGI will stop working.
Also, the department charges for disk space on
departmental SGI disks. Limit your disk space charges
by archiving. Finally, the department does NOT save
your work. If you have important files, you MUST
archive these files for the future.
A simple program, DAT.floater1 is now available on
all SGIs. This program is started by typing
DAT.floater1 at the prompt in a UNIX window. The
DAT.floater1 program allows you to use the DAT tape drive on
floater1 (room A421) to write files and directories to a
new tape, or append files and directories to a tape.
You can also read files from tape and list the "table of
contents" of the tape. A 'help' option is available which
describes what can and cannot be specified when
reading and writing files and directories. For more
information, type 'man tar' to review the UNIX tar
This program can be run by any user on all SGI
workstations in the Chemistry Department. The
program can archive a single file, the contents of a
directory, or an entire disk. Thus, each user has the
opportunity to write important files to tape and remove
these files from the SGI disk. A 'system backup' option
exists for researach SGI system administrators.
A similar program, DAT.nmrsg1 is also available on
all SGIs to allow users to read and write DAT tapes
using the tape drive on nmrsg1 (root C237).
DAT.splatter, DAT.colossus, and DAT.iumsc3 are
similar programs that are available ONLY on splatter,
colossus, and iumsc3, respectively.
Other programs exist that help you use tape drives.
However, DAT.floater1 has more options, is
customized for our SGI network, and (most
importantly) it is the only program that the department
DAT tapes have a capacity of 2 GBytes, cost $20, and
are available in the Molecular Structure Center (A421).
The floater1 tape drives may be used by SGI users at
any time, except when the drive is reserved for
departmental backups. If you use a tape drive, please
place the "WARNING!!! Drive in use!" sign (which
sits in a box on the shelf above floater1) on top of the
drive to inform other users.
To determine how much disk space is available, type
df -k. To determine how much disk space you are
using, type du -sk $HOME. To determine how much
disk space each of your files and sub-directories
occupies, type du -sk $HOME/*. Type man df and
man du for more information. These commands report
disk space in kilobytes.
Important files can also be compressed, reducing the
size of the file to about 40%. PLEASE COMPRESS
LARGE FILES WHEN ARCHIVING IS NOT
APPROPRIATE. Also, save space on your tape by
compressing your files or directories before archiving.
Type compress filename to compress and rename your
file filename.Z. Type uncompress filename.Z to
uncompress this file. Directories can be compressed,
and wildcard characters (* and ?) can be used.
See the Software List for recent
If you discover that a software program is NOT working
on a Silicon Graphics workstation, please contact Marty Pagel
(5-6492, firstname.lastname@example.org). With over 60 programs
on 31 UNIX workstations, it is impossible to identify problems
with over 1,800 copies of programs unless you and other
users inform your system administrator or Marty.
Our library of programs continually grows; most of these
programs are stored in the /model, /local/bin, and
/usr/local/bin directories. Also, many programs reside
on the departmental server. If you often use a program, and you
would like to run the program from your local SGI (which
is usually faster), contact Marty. If you locate a program that
would help your research and/or the research of the
Chemistry Department, contact Marty about adding it to our SGIs.
Several security improvements were made on all SGI
workstations. One of these security improvements prevents users
from displaying X-window or GL applications running
from a remote SGI on their local SGI monitor. For
you "rlogin chemvgx" from nmrsg1 and try to run
Netscape from chemvgx and display it on nmrsg1, I receive an error
message which attmpts to explain that this is not
possible. To fix this, first type xhost +chemvgx on nmrsg1 before
connecting to chemvgx. This then allows chemvgx
to use nmrsg1 as a display terminal.
New software has been added to the departmental SGIs
and many research lab SGIs. In particular, WebMagic Author is
a "word processing" program which allows you to type
HTML documents for World Wide Web. Also RasMol is
available for visualizing molecular structures.
The Molecular Visualization Facility staff cannot
continue to back up SGI workstations in research labs. The DAT
programs described above (in Archiving your Files
Made Easy) can be used to back up your SGI. You can choose to
make a full backup (all files written to tape) or
an incremental backup (files created withing a specified number of days
are written to tape). Both of these programs
require you to log onto your SGI as root during the backup. If you prefer to
back up your system non-interactively, contact Marty Pagel.
Creating and Removing Users
The following protocol is followed when a new account
is created on a departmental Silicon Graphics. System
administrators of research SGIs are strongly encouraged
to follow the same protocol. Most importantly, the same login
name and UNIX user ID must be used if a research SGI
disk is mounted on another SGI. Questions should be directed
to Marty Pagel, email@example.com.
If the applicant cannot supply his/her UNIX User ID number:
- The applicant must supply his/her:
- Full name
UNIX User ID number
signature acknowledging the he/she agrees to use the
SGI in a responsible, ethical, and unmalicious manner ( see
/local/info/IUCompResp file for "Computer Users'
Responsibilities and Privileges at Indiana University").
Creating the account:
- Log on to a departmental SGI workstation (chemvgx,
floater1, chemlib, or pchem01-06).
- Type /cat/etc/psswd | grep username where username
is the name of the new user. The following is an example of
the text that will appear:
mpagel's UNIX User ID number is 2570.
- If the user doesn't have a departmental SGI account,
use a UNIX User ID number that is NOT currently used in the
/etc/passwd file on your SGI.
- Log in to the SGI as root.
- Create a new account using the toolbox (click on
'System', 'System Manager'. 'Users', 'Open', 'Add', and fill in the
appropriate information. All passwords should have at
least 8 characters, with a least one capitalized character and one
- Keep a written record of the information listed in step #2.
- Inform the new user about his/her login name and password.
Monitoring Disk Space
If you disk is >95% full, you are unnecessarily
stressing the hardware. Using the df and du commands listed above (see
Disk Space), identify users with very large home
directories. Inform them that they must archive and remove files from
the disk. If users do not reduce their disk space
within one week of being informed, contact Marty.
The SGI operating system occupies about 220 MBytes
of disk space. Other software can occupy hundreds more
MBytes. To use disk space more efficiently, many
software programs are located on chemvgx, our departmental server.
Other SGI workstations access the programs on
chemvgx, rather than having their own local copy. If a program is used
often on your SGI workstation, this program can
be placed locally on your SGI, which will make the program run faster.
Contact Marty for details. Several SGI workstations
do not have adequate disk spacefor the operating system or other
software. If your disk is less than 220 MBytes, or
if your disk is full with software, contact Marty.
Maintaining Local Documentation
Please keep a copy of the SGI Users Guide next to
your SGI workstation. Update it regularly with this newsletter and
other information. Direct inquiries by your users
to this Guide before contacting the Molecular Visualization Facility
The Chemistry Department has occasional problems with
chemvgx (the SGI server) and network cables and devices. If
you notice a problem, plase contact Marty. A problem
may disappear: software has been written to fix problems with
the network and other problems once each hour. Coax
ethernet cables extending from your SGI workstation and other
computers shoud be loosely tied out of the way of
feet and hands. They should NOT be tangled with power cords, and
cables should NOT be stressed or bent. PLEASE
check your ethernet cable for these problems. One of our biggest
problems with the building network is CABLE NOISE.
- February 1994
- Special Edition: System Administrators.
- March 1994
- Commands to obtain SGI cluster information
Recent changes made to the chemistry SGI cluster
Availability of chemistry software on the SGIs
Newly intalled internet and other utilities
How to customize your desktop toolchest
How to keep your disk space clean
File compression utilities and how to use them
Where to get help
- April 1994
- Biosym software available on chemvgx
Recent upgrades to the operating system
Where to get a list of frequently-aked-questions
New versions of showcase and explorer on chemvgx
More goodies in the/local directory
Problems with the SGI cluster
Upcoming UID sync-o-thon
Do's and don'ts of powering down a SGI
- May 1994
- New help available on chemvgx
Archiving your files
Using .Xdefaults to set user preferences
Keeping track of the jobs you run
Color printing primer
Synchronization of User ID numbers
- June/July 1994
- Archiving your files made easy
Status of the departmental SGIs
Biosym demos expire 4/8/94
Frequently-asked-questions and newsgroups
- August 1994
- C687: Biomolecular Modeling
Status of the departmental SGIs
CRON - the UNIX Timekeeper
- September 1994
- New departmental SGI charges
Note to Research System Administrators
Status of the deparmental SGIs
- Winter 1995
- About this newsletter
New stuff on the departmental SGIs
Transferring files from SGIs to Macs
Converting Graphics File Formats
The ABSOLUTE FINAL Word on Printing.
- Summer 1995
- Archiving your files made easy
List of available software
Status of the departmental SGIs
Special news for system administrators
Summary of previous newsletters
Look for the Fall 95 Scream Saver later this fall.
Information about the Chemistry Department World
Wide Web (WWW) page, Netscape client and server
notes, and how your lab can join the Internet will be
among the topics covered in this issue.
Back to Scream
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Last updated: 01/23/2001