G03 on Redwood at MCSR
See also Gaussian 03 on Sweetgum and Mimosa and PBS at MCSR.
Gaussian 03 is installed on redwood. This installation of Gaussian (as opposed to the one on mimosa) uses shared memory (rather than message passing via LINDA) to achieve parallelization. However, not all calculation types may achieve good speed-ups. Care should be taken not to request more CPUs than your Gaussian job can use efficiently.
In particular, CCSD problems are not sufficiently parallelizable to approach linear speed-up, and should not be run on redwood.
For most computations that ARE parallelizable, running on 2 processors has the best speedup and performance. For MP2 jobs, you might want to use 6 processors. These job naturally separate into a series of 6 batches of integral computations. Remember, the more processors you use, the more overhead you get. You should never run a serial G03 job on redwood (use mimosa instead) Also, interactive processes are limited to 30 minutes, and will be automatically killed if they exceed this interactive limit (i-limit)..
When considering requests for queue access and when administering the queues themselves, MCSR staff will give priority to those users
whose jobs can make the most use of the parallel computing capacity of redwood.
Smaller and more serial jobs will fare better
on sweetum or mimosa.
Steps for running a Gaussian 03 job on redwood:
For help or to report difficulties running Gaussian 03 on redwood, please e-mail
and tell us the location of your input file, the syntax you used to submit the job, and the error/problem you are seeing.
- If you don't have a redwood account, apply for one via the MCSR Online Account Manager.
- Ensure that you have a file called .cshrc in your $HOME directory on redwood, and that it contains at least these lines:
setenv g03root /usr/local/appl
setenv GAUSS_SCRDIR /tmp/$USER
If you get an error message like this:
Input/Output Error 177: Creat Failure
then you might need to make sure you have created your own named directory under /tmp, like this:
mkdir -p /tmp/$USER
- If you plan to run on more than one processor, make sure that your Gaussian input file contains a line such as this one (which specifies that this job will use 2 processors):
- Use the g03sub utility to submit your G03 job. The syntax is:
g03sub [-t time][-n nprocs] jobs
So, to submit a 2-processor job for an input file named myfile.com requiring 100 hours, you would include these two directives in your input file:
and submit the job like this:
g03sub -t 100:00:00 -n 2 myfile.com
This script will create a PBS script for you and then submit it to PBS.