THE SGI SCREAM-SAVER

Chemistry Department, Indiana University, October 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, contact Marty Pagel (mpagel@indiana.edu, 5-6492, C237C) or Kathrine Mann (A421).

Items Covered in this Edition:

How to obtain information about the SGI cluster

The news command has been added to make this easy. Use it to see the current status of the Chemistry SGI cluster. It works on all SGIs on which we have superuser privileges (chemvgx, floater1, chemlib, nmrsg1, iumsc1-4, pchem01-06, acniris, dwilliams, grieco, inorganic3, jwz1, mdholl2, montgomery, roush, and widlanski).

To view older news, type more /local/info/news.old. To view even older news, see the news files in /local/info.

Big changes on the SGI cluster

As part of the SGI cluster reorganization, a distribution directory (/local) is now available on all Chemistry SGI workstations. Here is a description of the contents of this distribution directory:
/local/bin
The directory containing the executables of the public utilities described in (4) below
/local/motd
The clusterwide message-of-the-day file (users see this when they open up a new UNIX window
/local/info
The information directory, including news
/local/examples
The directory which WILL SOON contain examples of good start-up files, such as .cshrc, .login, etc.
The old /local directory is now called /model and contains all of the chemistry modelling software. The old /struct directory remains unchanged. In addition, we have installed the files necessary to make all public software work on all machines.

Chemistry software available on the SGIs

After reorganization, the following software is available on all SGIs: The following software is available on some SGIs: For most software you need only type the name of the software on your machine to start it.

Other nifty utilities now available

We have installed the following utilities on all SGIs: Type the name of the software to start it (for example, type xrn to start the news reader). man pages for all exept mosaic are available on all SGIs.

How to customize your toolchest

We discuss below simple things that you can do to customize your desktop toolchest. Toolchest controls the menus that appear in the upper left corner of your screen (type man toolchest to learn more about toolchest). The file that controls the toolchest is in your home directory and is called .chestrc

Most users will find that they don't have a .chestrc in their home directory. The default chestrc, /usr/lib/X11/system.chestrc, is then used. In order to customize the toolchest when you don't have your own .chestrc, type cp /usr/lib/X11/system.chestrc ~/.chestrc, and then modify your .chestrc using your favorite editor.

Listed below is a small piece of /usr/lib/X11/system.chestrc on chemvgx (we have deleted many lines for brevity). Assume that your SGI is called your_sgi. Let's add a menu item called "Machines" to the toolchest, so that choosing "Machines" with the mouse lists a submenu with remote machine names. Selecting a remote machine name from the submenu will then open a window that will be displayed on your_sgi. 

################################
#                              #
# Default chest RESOURCE       #
# DESCRIPTION FILE             #
#                              #
# after we have copied it to   #
# home directory as ~/.chestrc #
#                              #
################################
#
# Menu pane descriptions
#
# Top Level menu Description
#
Menu Toolchest
{
 "System"       f.menu System
  no-label      f.separator
 "Windows"      f.meu Windows
    .
    .
    .
# We add the following line:
 "Machines"     f.menu Machines
}

# We add this entire menu:
Menu Machines
{
 "chemvgx"  f.checkexec "rsh chemvgx
            xterm -display your_sgi:0"
 "nmrsg1"   f.checkexec "rsh nmrsg1
            xterm -display your_sgi:0"
    .
    .
    .
}
f.checkexecc checs to see whether the program you want to run (rsh in this case) is available on your_sgi. All of the f. entries are the actual actions you want the computer to take when you choose the entries. no-label tells the computer to put nothing in the menu box. Instead, f.separator puts a separator in the menu to delineate different items.

Thus, you can add or delete whatever menus you like. The next time you log in, you will see your customized menu in the upper left of the screen.

How to reduce your disk space

Disk space is always in short supply. When a disk gets full, nobody can work on the computer until files are removed or reduced in size. There are three steps that you can do to reduce the amount of data stored in your directory.

First, delete unnecessary files on a regular basis. In particular, files named core contain information about a process that has crashed. These core files are usually very big and should be removed (unless you want to investigate why the process crashed). Type find $HOME -name core -print to search for these core files.

Second, important research can be archived on tape or optical disk and deleted from the SGI disk. Backup tapes and optical disks and procedures for data archival are available from system administrators. While copies of files are stored via system backup procedures, system backups rarely retain more than the most recent month of files. Do not rely upon backups to archive your data.

third, important files used in current research can be compressed, reducing the size of the file by about 40%. Please compress large data sets of data that need to be accessible, but are seldom accessed. Type compress filename to compress your file into a file named filename.Z. Type uncompress filename.Zto uncompress this file. Type man compress for more information.

Another file compression tool which does somewhat better compression is the GNU zip. gzip filename will compress your file and rename it to filename.gz. To uncompress, use gunzip filename.gz

Where to get help

Help is available on the SGIs in two forms. Type insight to read the on-line IRIX manual on the Indys. Later this semester, we expect to receive new software which will provice this on-line insight manual on all SGIs. Type man commandname to read the UNIX manual page about a specific UNIX command. Type man -kkeyword for help on a particular subject. man pages tailored to commands specific to Chemistry Department SGIs are also available.

Printed documentation can provice a foundation toward solving your problems. A binder of local documentation is provided at each departmental SGI, which includes notes about UNIX, molecular modeling procedures, examples of printouts, and other SGI applications. Research SGIs should have similar local documentation. Software manuals and texts owned by the department are also available.

Colleagues can be a good source of information, especially when learning about new software. Each SGI in a research lab is administered by an experienced user, who should be contacted when problems arise. The departmental SGIs are administered by Marty Pagel (mpagel@indiana.edu, 5-6492), and he is available to respond to your questions and suggestions.

Upcoming events in March

Molecular Modeling club meets every other Wednesday at 7:30 pm in A500. Topics range across a variety of modeling and visualization applications, and presentations and discussions are informal. We are searching for volunteers to speak at the April 27 meeting. Speakers include:
Wed, March 2: Jim Nolan, "Modeling the structure of RNA"
Wed, March 16: Nancy Brichford and Marty Pagel, "Electrostatics and Dock3.0"
Wed, March 30: Anurag Shankar, "Visualization and video animation on the SGI"
Thr, April 13 (NOON): Kevin Gilbert, "PCMODEL"

The next SGI users group meeting will meet April 7, noon to 1pm, in A400.

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Last updated: 01/23/2001