Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

TCP Linda is a parallel execution environment to parallelize Gaussian jobs.  By default, Gaussian jobs are single processor core jobs.  TCP Linda must be used to to parallelize Gaussian.  In order to use TCP Linda you must configure your Gaussian input file to use multiple processors (and possibly multiple nodes).  For multiple node jobs this requires that you know which nodes you will be running on.  However, this information is not known ahead of time.  We have developed a script that will configure your job for you.  Please follow the instructions below.

Info
titleLinda not available on all systems

Linda is only available on DAVinCI.

Info
titleNot all Gaussian calculations can be run in parallel

Please see the Gaussian documentation about the types of calculations that can be done in parallel.

 

Configure SSH Keys

In order for Linda to communicate between nodes you must enable passwordless SSH (SSH keys).  Please see our FAQ for instructions.

Tip
SSH Keys One-Time Setup

You only need to set up SSH keys once.  It will work for all subsequent jobs for the lifetime of your account.

Configure Gaussian

In order to run a Gaussian job on our clusters you must first load the Gaussian module:

Code Block

module load gaussian

Subsequently, you should source the Gaussian command file to set up your environment:

tcsh users:

Code Block

source $g09root/g09/bsd/g09.login

bash users:

Code Block

source $g09root/g09/bsd/g09.profile

...

As stated previously, the node names for your job will not be known ahead of time. So this must be configured dynamically. To build your job submission script such that these jobs can be configured dynamically, use the following command:

Code Block

/opt/apps/scripts/create-gaussian-jobscript inputfile.gjf number_of_nodes

Using our example input file example.gjf and 6 nodes, the command would look like this:

Code Block

/opt/apps/scripts/create-gaussian-jobscript example.gjf 6

This will create a PBS SLURM job script named example.pbsslurm in your current working directory, using example.gjf as the input file and using 6 nodes.  It will build a submission script that will set the Gaussian parameters necessary to run the parallel job.

To submit the job, simply use qsub as follows:

Code Block
sbatch qsub ./example.pbsslurm

Check the contents of the job submission script for the location of your scratch directory (GAUSS_SCRDIR) and the location of your output file.