HPC Gaussian FAQ
Supercomputer documentation is always a work in progress! Please email questions, corrections, or suggestions to the HPC support team at firstname.lastname@example.org as usual. Thanks!
For help getting started with Gaussian, see the Gaussian README page.
Frequently Asked Questions
- 1. How do I submit a Gaussian job?
- 2. How do I combine multiple Gaussian jobs within a single input file?
- 3. Can I use a checkpoint file created on a different computer or operating system?
- 4. How do I convert a binary checkpoint file into a format that I can actually read?
- 5. How do access Gaussian utilities such as formchk??
- 6. How do I change the number of processors used from the default of 8?
Create a Gaussian input file, then use the batchg09 command to build the job script and submit it to the batch scheduler:
where infile.com is the name of your Gaussian input file. You may omit the .com extension from the batchg09 command. Any sbatch options may be added except for the -q option.
Gaussian jobs will be routed to a queue running on a DLX Hi-Mem node. batchg09 defaults with 8 cores or one socket.
Yes, combine multiple Gaussian calculations by using the Link 1 command. Separate the input for each successive job from that of the preceding job with the Link 1 separator.
Frequency Calculation on XYZ at STP
. . .
%Chk = frequency
#B3LYP/6-31-G(d,p) Geom=Checkpoint Guess=Read Freq=(ReadFC,ReadIsotopes)
Frequency Calculation on XYZ at Elevated Temperature
A blank line must be included between the last line of the first job and the --Link 1-- separator. Failure to include a blank line will result in a segmentation violation error when the job is run.
If the checkpoint file from the first job is to be used in a subsequent job, then the names specified with the %Chk command in the Link 0 section of each job must be identical. Otherwise, the second job will not be able to find the checkpoint file from the first job, which will cause the second job to fail.
Yes, but you must convert the file from binary to text on the source machine before you transfer it to the DLX. The Gaussian utility chkmove will convert a binary format checkpoint file to and from text format. Although the file is text, it is basically unreadable, but the text format allows the checkpoint file to be transfered between different computers and operating systems. The chkmove utility will only work on checkpoint files from completed calculations. If the file is from a failed job or some intermediate calculation, such as an unconverged optimization or numerical frequency, then chkmove cannot convert the checkpoint file.
To transfer a checkpoint file named mycheckfile.chk from machine ABC to the DLX cluster:
- Login to machine ABC and convert mycheckfile.chk from binary to a text format with this command:chkmove f mycheckfile.chk mycheckfile.xfr
where f indicates conversion from binary to text and .xfr is the extension for text checkpoint files.
- Transfer mycheckfile.xfr from the machine ABC to the DLX by any means convenient.
- Convert mycheckfile.xfr from text back to binary with this command:chkmove u mycheckfile.xfr mycheckfile.chk
where u indicates conversion from text to binary.
The Gaussian utilities are located in a release-dependent directory. Before running chkmove, use this command:
to make sure the appropriate paths and environment variables are set. This is not done automatically, to allow the use of earlier releases of Gaussian (for which the setup is somewhat different). Do this once per login session or add it to your startup file (such as .bashrc).
The Gaussian utility formchk will convert data in a binary checkpoint file to a formatted text format that is readable. To reformat the binary checkpoint file mycheckfile.chk into a format that is readable, issue this command:
where .fchk is the extension for formatted checkpoint files on UNIX systems.
-3 Produce a version 3 formatted checkpoint file, including all features supported in Gaussian 09 (e.g., user-defined MM types, redundant coordinate definitions, values, forces, and the Hessian).
-2 Produce a version 2 formatted checkpoint file. This was the version used with Gaussian 03.
-c Causes the molecular mechanics atom types to appear in the formatted checkpoint file as strings rather than integers.
By default formchk produces a formatted checkpoint file that is backwardly compatible with all previous versions of Gaussian.
The Gaussian utilities are located in a release-dependent directory. Before running formchk, use this commad:
to make sure the appropriate paths and environment variables are set. This is not done automatically, to allow the use of earlier releases of Gaussian where the setup is somewhat different. Do this once per login session or add it to your startup file (such as .bashrc).
There are two steps. First, use %nproc=nn in your Gaussian input (.com) file to specify the number of processors. Then use the -n nn option when submitting the job with batchg09. Use the same number (nn) in both places. If the -n option is omitted, batchg09 will read your command file to get the number of processors to use. If you specify both %nproc and -n, but the numbers do not match, the job will not be submitted.