the goodman group
university of cambridge  

   setting priorities

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has been replaced by the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

Setting Priorities

Long calculations (this means anything that takes more than five minutes of CPU time) must be run at a low priority. If you are using MacroModel or Mopac in the normal way, this will be done for you automatically. If you have written your own program or are using one of the less user-friendly programs that are available, you are responsible for making sure that you are not using too high a proportion of the CPU time.

In addition to reading this page, you should also check on the use of local directories.

Batch Jobs

To submit a batch job, you must use the batch command. For example, to submit a command "LongCalc" to the batch queue, type:
batch << ! 
This will submit the job to the batch queue and give a cryptic message along the lines of:
warning: commands will be executed using /bin/sh 
job 878735933.b at Wed Nov 5 13:18:53 1997
This means that your calculation has batch queue registration number 878735933.b (in this example), and if you make a note of this you will see how it progresses up the queue. In practice, most batch jobs will start within a few minutes. It will automatically set a low priority to the job. When it is complete, it will send you a mail message. Type 'mail' to read the message, then 'd' to delete the message.

In order to find out how long the queues are, type 'rbatch'

In order to find out what jobs you have on the queue, type: at -l

In order to remove your own jobs from the queue, type: at -r 878735933.b (or whatever the appropriate number is)

Some programs, such as MOPAC and Cadpac, which tend to require long calculation times, automatically submit calculations to the batch queue.

The Nice Command

If you have a good reason to run a long calculation without using the batch queue, you must use the nice command. To submit a calculation called "LongCalc" type:

nice +9 LongCalc &
This command is to be used in csh, which is the default shell for the Silicon Graphics Teaching Laboratory.

Checking Priorities

The 'ps' command (process) can be used to give you information about the processes which are running on each workstation. A simplified form is available 'pscheck' This will tell you about your own processes, and show you which columns to check for the priorities and times taken by your calculations.

Whenever you submit a long calculation, use pscheck to make sure that the priority you think that you have used is the priority which is actually being used.

© Goodman Group, 2005-2017; privacy; last updated October 19, 2017

department of chemistry University of Cambridge