the goodman group
university of cambridge  

   using a local directory

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has been replaced by the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

Using a local directory

The Silicon Graphics Teaching Laboratory is set up so that each user's home directory is automatically mounted on whichever workstation is being used. This means that whichever workstation you choose to log on to, your files are all available for you to use, but they are usually being transferred over the network from another machine. This is convenient, and the details can be ignored for short calculations.

If, however, you are doing a calculation which requires a lot of disk access (i.e. any program which takes more than a few seconds to run, including MOPAC and CADPAC calculations, and MacroModel Monte-Carlo searches or Molecular Dynamics simulations), you should make sure that you are using disk space on the same machine for which you are using the CPU. This prevents the job slowing down (and slowing everyone else's calculations) by congesting the network.

The simplest way to do this is to use the /var/tmp directory. Each workstation has a /var/tmp to which you have write access. Before submitting a long calculation:

  • Make yourself a subdirectory in /var/tmp
    You do this by typing:
    • cd /var/tmp
    • mkdir USERID
      (Type your own userid instead of USERID. This should discourage anyone else from using this directory)
    • cd USERID
  • Change directory into your own subdirectory on /var/tmp
  • Now submit your calculation. If you are running a MOPAC or CADPAC calculation, copy the .dat file into the /var/tmp subdirectory, and then use the rcadpac or rmopac command. If you are running MacroModel, make sure you are in this directory before you start MacroModel running.
Following this procedure will make your calculations run much faster. However, note:
  • Each workstation has a different /var/tmp directory. To retrieve your calculation, you will need to log on to whichever workstation you used to start the calculation, or use ftp or telnet to retrieve the files.
  • Whenever the disks get full, the /var/tmp directories may be cleared. As soon as the calculation is finished, copy the data back to your home directory, and delete it from /var/tmp

© Goodman Group, 2005-2017; privacy; last updated October 18, 2017

department of chemistry University of Cambridge