the goodman group
university of cambridge  

   upgrade 1997

The Silicon Graphics Teaching Laboratory
has been replaced by the
Chemi cal Information Laboratory
and this information is for historical interest only

Upgrade 1997

Some of the Silicon Graphics Teaching Laboratory workstations were upgraded early in 1997. This began the move towards IRIX 6. Most users should only have noticed an increase in speed and quality of graphics. The major programs used on the workstations, in particular, MacroModel, Cerius2, Sybyl, Cadpac, Netscape, and Mopac should not be adversely affected.

Since the laboratory now has a mixture of different processors and systems, there are some programs which do not work on all of the machines. So far as possible, these are detailed below.

Ftp Security Problem

2-9-97: A problem with ftp security has been temporarily remedied by disabling incoming ftp file transfers on the new workstations. A better solution has been used on the older workstations. The service will be restored as soon as possible.

The following programs no longer work on the older workstations (acal, bcal, ccal, dcal, ecal)

  • Nothing

The following programs have been upgraded

  • lp: Use lp and lpstat instead of lpr and lpq
    The new workstations do not run the BSD print spooler. Text files may be printed to the department line printer using the 'lp' command, instead of the old 'lpr' command. This line printer is the default printer, so be careful not to send images or postscript files to it. The printer queue is now examined with the 'lpstat' command, which replaces the 'lpq' command on the machines.
  • Babel
  • boltz
  • gnuplot
  • Eadfrith
  • Mopac: Mopac has been recompiled. Mopac7 is now the default. Use the command 'rmopac' to run mopac.
  • Various conversion routines:
    mm2cad, mm2cos, mm2mop, mm2mopM, mult2mop, c2mm, mop2mm, csd2mmod, etc.
  • rbatch
  • rload
  • rrf
  • Scian Scian has been upgraded. Demos are in the directory /usr/local/scian/demos. Scian will display PDB files, and a wide range of other data
  • xv
You should notice no differences with the upgraded versions. If you discover any problems, please notify Jonathan Goodman.

The following programs will be upgraded as soon as possible

  • xmgr

The following programs cannot be upgraded and will stop working

No IRIX 6 version of Xmol is currently available. Use Rasmol, Eadfrith, or MacroModel instead.

This archiving utility may disappear

The zip editor has moved. It can still be used on the older workstations if you type zip_ed instead of zip. It will never work on the newer workstations. Use jot, vi or emacs instead. A new command called zip may be introduced to compress files.

Other programs are being checked....

If you write your own programs:

ELF replaces COFF
IRIX 4 only ran COFF executable files. IRIX 5 runs both COFF and ELF. IRIX 6 runs only ELF. This means that any program which was compiled under IRIX 4 will not run under IRIX 6. The programs provided in /usr/local and /use/bigdisk are being converted to ELF, and it is hoped that all of them will continue to be available. If you are running any old programs yourself, recompilation will be necessary.

OpenGL replaces GL
GL, which stands for Graphics Language, will be replaced by OpenGL, which is very different. All graphics programs will require substantial alterations before they can be recompiled under IRIX 6. Program written in GL can be compiled under IRIX 5, and then run under IRIX 6, although this may occasionally cause problems. For a transitional period, fcal and gcal will continue to run IRIX 5.

If these changes are likely to cause problems for you, please notify Jonathan Goodman as soon as possible.

© Goodman Group, 2005-2017; privacy; last updated November 16, 2017

department of chemistry University of Cambridge