Gaussian16

Supports parallel execution on one node.

Version System A System B System C
Gaussian16 Revision C.01 (default) + + +
Gaussian16 Revision B.01 + + +
Gaussian16 Revision A.03 + + +

Supports parallel execution on multiple nodes.

Version System A System B System C
Gaussian16 Revision C.01 LINDA + +
Gaussian16 Revision B.01 LINDA + +
Gaussian16 Revision A.03 LINDA + +

Version System A System B System C
Revision 6.1.1 (default) + +
Revision 6.0.16 + +

Key: AU = Available for academic users only, ― = Not available for use.

You must register for use of Gaussian via the User Portal.

Modules software package dynamically adjusts the environment settings for using applications, by using the module command. It also makes changing the environment settings easy when switching between different versions of applications.
For details, see Modules.

Version Module File Note
Gaussian16 Revision C.01 gaussian16/c01 Gaussview 6.1.1 is available
Gaussian16 Revision B.01 gaussian16/b01 Gaussview 6.0.16 is available
Gaussian16 Revision A.03 gaussian16/a03 Gaussview 6.0.16 is available

The module file is the same as one w/o LINDA.

Version Module File Note
Gaussian16 Revision C.01 LINDA gaussian16/c01 Gaussview 6.1.1 is available
Gaussian16 Revision B.01 LINDA gaussian16/b01 Gaussview 6.0.16 is available
Gaussian16 Revision A.03 LINDA gaussian16/a03 Gaussview 6.0.16 is available

You can see the list of module files available by using the module avail command.

Gaussian is an electronic structure modeling program. It allows users to investigate and estimate characteristics of molecules and reactions in various conditions from the basic formula of quantum mechanics. Gaussian can be used for investigating characteristics which are impossible or difficult to make observations by the experimentation.

On every updates, Gaussian is reinforced by functional expansion of the ONIOM method and the solvation model, addition of new functions, and many other new features. It is also consolidated in its parallel computation capability. For more details, see the information at Official Gaussian Website.

  • Single point energy calculation

    • Energy calculation of molecular systems, Molecular Orbital Method Calculation, and prediction of multiple moments and atomic charges
  • Structure optimization

    • Potential energy, optimization and convergence criteria, minimization, and transition structure search
  • Calculation of vibration frequency

    • Calculation of vibration frequency, interpretation of normal vibration, and characterization of stationary point
  • ONIOM functions

    • Modeling process on a high accuracy layer
    • Customization and efficient ONIOM calculation of molecular mechanics
    • ONIOM calculation of electric and electromagnetic properties

  • Chemistry
  • Chemical engineering
  • Biochemistry
  • Physics, etc.

Set up the environment by using the module command.(The module file you want is loaded.)

$ module load gaussian16

  • Format

    tssrun g16  input_file
  • Example (4 threads on one node)

    $ tssrun -A t=4:c=4 g16  water.com

Parallel execution is available via -A option. Note that the progress is not shown on the terminal as the progress and results are written in .log file. For details of tssrun , see Interactive Processing.

An Example of jobscript is shown below.

  • System A

    #!/bin/bash
    #QSUB -q gr19999a
    #QSUB -ug gr19999
    #QSUB -A p=1:t=4:c=4:m=90G
    
    aprun -n $QSUB_PROCS -d $QSUB_THREADS -N $QSUB_PPN g16  test0000.com
  • System B

    #!/bin/bash
    #QSUB -q gr19999b
    #QSUB -ug gr19999
    #QSUB -A p=1:t=4:c=4:m=120G
    
    g16  test0000.com    

The subg command is used for submitting batch jobs specifying a queue name, an input file, and other parameters. The qsub command options and parallel execution on multiple nodes are available via the subg command.

  • Gaussian16
    subg16 queue_name input_file  [-scrdir dir] [qsub_command_option ...]

$ subg16  eb water.com

$ subg16  gr19999b water.com -A p=1:t=4:c=4:m=30G

This feature is supported only on the system B/C.

Execute the module command to make a environment settings.

$ module load gaussian16/a03

Include "%LindaWorkers=LINDA" at the beginning of the input file to specify inter-node parallelization. The number of nodes should be specified by "-A p" option for subg command (mentioned later). Also, use the %NProcShared to specify the number of processors, when executing a shared memory parallel execution per node together.

e.g.)

%LindaWorkers=LINDA
%NprocShared=16

When executing Gaussian with Linda, use the subg command to submit a job.

subg16 queue_name input_file  [-scrdir dir] [qsub_command_option ...]

input file

%LindaWorkers=LINDA
%NprocShared=16

submission command (note: the values of t and c must be same as %NprocShared)

$ subg16  gr19999b water.com -A p=2:t=16:c=16:m=120G

Burst Buffer (IME) is the name of a high-speed temporary storage system which is different from the normal file system, and enables high-speed reading and writing of files. Gaussian generates RWF files, scratch files, and so on during job execution, and reads and writes files regularly and frequently. Therefore it is expected to improve the computing speed and reduce the load on the file system by using the burst buffer.

Application Request is required to use the burst buffer. System A does not support the job execution using this method.

subg16 queue_name input_file  [-scrdir dir] [-bb capacity={IMESize}] [qsub_command_option ...]

$ subg16 gr19999b water.com -A p=1:t=4:c=4:m=30G -bb capacity=200G

When you specify to use the burst buffer(-bb option), please execute the job after placing the file on the large volume disk (/LARGE0).

When the job which uses the burst buffer is executed, "{input file name}.SCRDIR" directory is newly created under the current directory. Although RWF files and scratch files generated during the job execution are output to the directory, the file size will be "0 byte" until the job is finished since reading and writing is performed on the IME during the job execution. When the calculation process of Gaussian is finished, the data synchronization from IME to LARGE will be started automatically. Therefore, please wait to access and read/write files to "{input file name}.SCRDIR" directory until the job is finished.

When an input file with the same name is executed by multiple jobs at the same time, you may get unintended calculation results or the calculation process may be terminated in the middle. When you run multiple jobs at the same time, please be careful not to share the input file with the same name.

Please see the below.

How can I restart a job that was interrupted?

$ xrun gview

GaussView is a GUI application, so you need to log in to the supercomputer system using the Exceed onDemand. For how to install and how to use, see Logging In With Exceed onDemand.

GaussView sometimes works normally by using -soft option on startup.

$ xrun gview -soft

No documents

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