Gaussian is an electronic structure modeling program that Yale has licensed for its HPC clusters. The latest version is Gaussian 09, and only that version is currently installed on Yale’s clusters.
When running Gaussian, it is recommended that users request exclusive access to allocated nodes (e.g., by requesting 8 cpus per node) and that they specify the largest possible memory allocation for the number of nodes requested. In addition, in most cases, the scratch storage location (set by the environment variable GAUSS_SCRDIR) should be on the local parallel file system of the cluster, rather than in the user’s home directory.
Before running Gaussian 09, you must set up a number of environment variables. This is accomplished most easily by loading the Gaussian 09 module file using:
$ module load Applications/Gaussian
To run Gaussian 09 in parallel, you may find it simplest to use the script par_g09 instead of executing Gaussian 09 directly. par_g09 takes 1 optional argument and is used as shown here:
$ par_g09 [num_proc_shared] < g09_input > g09_output
When included in a PBS script, par_g09 will set the following Gaussian 09 input variables:
%LindaWorkers: List of nodes that will act as parallel workers during parallel portions of the Gaussian computations. The list is created automatically based on the nodes allocated to the particular job. Workers communicate using the Network Linda system provided with the Gaussian software.
%NProcShared: Number of shared-memory processes per Linda worker.
It is highly recommended that users run 1 Linda worker per node with %NProcShared=8 on the Omega cluster. (This is the default behavior of par_g09.) However, users may easily override the value of %NProcShared by supplying the optional num_proc_shared argument to par_g09. (Of course, both variables may be overridden by including them in the Gaussian input file.)
On the Grace cluster, there are up to 20 processors and 128 GB of memory per node, so it may often work well to use just a single node with many shared-memory processors, in which case you can simply modify the Gaussian input file and skip the use of the par_g09 script. If you do wish to use multiple nodes on the Grace cluster, please pay careful attention to the Slurm parameters you use, particular to the setting of
--mem-per-cpu to ensure that each of the nodes you request has sufficient resources available.
In connection with Gaussian, we have also installed GaussView 5, Gaussian Inc.'s advanced and powerful graphical interface for Gaussian. With GaussView, you can import or build the molecular structures that interest you; set up, launch, monitor and control Gaussian calculations; and retrieve and view the results, all without ever leaving the application. GaussView 5 includes many new features designed to make working with large systems of chemical interest convenient and straightforward. It also provides full support for all of the new modeling methods and features in Gaussian 09.
In order to use GaussView, you must run an X Server on your desktop or laptop, and you must enable X forwarding when logging into the cluster. For Windows machines, we recommend the XWin32 X server, available from the ITS software site. For Macs, we recommend the XQuartz X server available at no cost from www.xquartz.org. Loading the module file for Gaussian automatically sets up your environment for GaussView, as well. In most cases, you simply type the command "gv". GaussView 5 may not be compatible with certain versions of the X servers you may run on your desktop or laptop. If you encounter problems, these can often be overcome by starting GaussView with the command "gv -mesagl" or "gv -soft".
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