Sisältö
 
Tehdyt toimenpiteet

Gaussian

Quantum chemistry ( ab initio HF, DFT )

Description

Gaussian uses electronic structure theory in computing many properties of molecules and reactions, including the following:
  • Molecular energies and structures (transition states, reactions)
  • Molecular orbitals
  • Atomic charges and electrostatic potential
  • Vibrational frequencies and NMR properties
Calculations can be carried out on systems in the gas phase or in solution, and in their ground state or in an excited state.


Version


Available Gaussian 09 version:

  • Revision C.01 is available on Vuori, Hippu1-2, Hippu3-4 (Release notes)
  • Revision A.01 is available on Murska, Hippu and Vuori and through SOMA2 modeling environment (GUI through web browser)

Gaussian 03 (Revision E.01) is still available on Murska and on Hippu. If you are interested to run even older versions of Gaussian, please contact our chemistry specialists for details.


See the results of Gaussian 03 performance tests on Murska!


Usage


To be able to use Gaussian at CSC your user-id has to be added to Gaussian users group. Send a request to CSC's user manager, usermgr@csc.fi.

Prepare the input file jobname.com

The input file specifies the following:


For optimal performance of Gaussian jobs on CSC's servers it is beneficial to make some efficiency considerations.

Some hints on how to estimate memory and disk requirements can be found here.

Especially the  %mem and MaxDisk parameters are important..


Submit the Gaussian job:

  • On Vuori:

    • The  Gaussian 09 version is selected by the command:

    module load gaussian/G09RevC.01     (gaussian/G09RevA.01)

    Vuori is available for serial and parallel Gaussian runs. IMPORTANT: All files needed by a job must be copied to $WRKDIR. Submitting jobs is similar to Murska, but give the time request including seconds (asks for 12 hours):

    subg09 12:00:00 test

  • In Vuori it is suggested to use either one core or all 12 cores of a node (specify this with the %NProcShared=12 in the com-file). For more hints give subg09 without arguments in Vuori. Jobs that are very disk I/O intensive clearly benefit from using the local disks for runtime scratch data. This can be done by using a  command like:

  • subg09_tmp 12:00:00 test 200000
  • The last parameter reserves 200000MB ~ 200GB of local disk. At present, the maximum allowed is 800GB

      • On Hippu:

        Hippu is available especially for short serial Gaussian runs. Please run long and parallel jobs in Vuori IMPORTANT: All files needed by a job must be copied to $FCWRKDIR.
        Submit an interactive gaussian run: 
        module load gaussian/G09RevC.01

        Previous command will set up Gaussian environment. To set up a Gaussian environment for Gaussian 03 job, use: module load gaussian.

        • To launch a job with an input file test.com:

        nohup g09 test &

        To launch a Gaussian 03 job, use: nohup g03 test &. Shared memory parallel execution is requested by including the command %NProcShared=N in the input file. Also a parallel job is submitted with the above command in Hippu.

      • On Murska:

        Murska is available for serial and parallel Gaussian runs. IMPORTANT: All files needed by a job must be copied to $WRKDIR
        • A Gaussian (serial or parallel) job is submitted with: 
          subg09 cpu_time jobname    (subg03)
          Example: A job called test.com which requires 12 hours (hh:mm): 
          subg09 12:00 test
        • The number of processors (for a parallel job) and requested memory are given in .com file.
        • The maximum number of processors on Murska is 4.
        • The maximum memory on Murska is  32 GB.
        • The maximum cpu_time is 48 h for jobs in parallel queue and 7 days for jobs in serial queue.
        • Long run queue for very long parallel jobs (up to 21 days) is also available. NOTE: batch jobs in longrun queue can be interrupted due to service break.  
        • Give jobname without extension (e.g. test instead of test.com)
        • Alternatively on Murska, Molden can be used to generate input file and submit a job to batch queue. Results can be visualized as well.


      Additional info and manuals

      Further information

      Please contact CSC's Helpdesk, helpdesk (ät) csc.fi, for more information.

      Field of science:
      Chemistry
      Available:
      • hippu
      • murska
      • vuori
      License:
      G