Running Gaussian 98 Jobs on Darwin

Gaussian 98 jobs must be run as batch jobs under PBS, submitted via the qsub command. (For general information about how to submit PBS batch jobs on darwin, see Submitting Jobs via PBS on Darwin). There are two PBS queues for Gaussian 98 jobs:

g98 Production jobs. The default CPU time limit is 8 hours. There is no maximum CPU time limit.

g98test Test jobs. The maximum CPU time limit is 5 minutes.

The PBS job script file for a Gaussian 98 job should look something like this:

#PBS –q g98 –l cput=24:00:00,ncpus=4

run_g98 test1.com

Specify values for cput (CPU time required) and ncpus (number of CPUs required) that are appropriate for your job. The parameters on the #PBS statement can also be specified on the qsub command, but it is convenient to put them in the job script file so that they aren’t forgotten. The run_g98 command sets up the Gaussian 98 environment, and then invokes the Gaussian 98 command g98 with the specified parameters.

The ncpus resource specification will be very important for job scheduling on darwin, especially after we add another node. Job scheduling is based upon the load level of each node and the number of CPUs that are in use. The PBS scheduler cannot “look inside” of a job to determine how many CPUs it will use, so the scheduler must be told how many CPUs a job will use via the ncpus resource. Please be sure that the value of ncpus is the same as the value of %nproc in the Gaussian 98 .com file. If the value of ncpus is too high, then your job might wait in the queue, even though CPU resources are available. If the value of ncpus is too low, then your job may be cancelled if it actually uses more CPUs than you specified. If ncpus is not specified, PBS will assume that 1 CPU is needed. Note: A single Gaussian 98 job cannot use more than 4 CPUs on darwin.

To submit the job for execution, use the qsub command. Suppose that the job script file as shown above is named test1. Then the job would be submitted for execution via the command:

qsub test1

See the man pages for pbs and qsub for more details about submitting PBS jobs. They can be displayed via the commands:

man pbs

man qsub

Use the qstat –a command to see which jobs are queued/executing on darwin. Currently, only one job at a time is allowed to execute from the g98 queue.

The directory to use for temporary work files on darwin is /scratch (also known as /tmp). The run_g98 command uses that directory by default. If you explicitly specify the pathnames for work files in your .com files, please use /scratch as the directory.

If you run the Gaussian 98 utility newzmat, you will need to set up the Gaussian 98 environment for your interactive session. Place the following two lines in the .login file in your home directory:

setenv g98root /usr/local

source $g98root/g98/bsd/g98.login

For more information about accessing darwin in general, see Darwin Access Notes.