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has been replaced by the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 << !
LongCalc
!
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.
|
