Gaussian

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Gaussian

Gaussian

Submitting Jobs

Please first read the Software: Slurm page to get a core understanding on how Slurm works.

Selecting the Correct Gaussian Module

We currently have three Gaussian related module versions:

  1. gaussian/16.AVX.b01 : This module is compiled for AVX compatible nodes - which can be used across nodes on moran and teton.
  2. gaussian/16.AVX2.b01 : This module is compiled for AVX2 compatible nodes - which can only be used on nodes on teton.
  3. gaussian/103 : This module provides access to the Gaussian 09 Chemistry software.

(Read Advanced Vector Extensions for an introduction to the difference between AVX and AVX2.)

With respect to the module versions, if you are going to use/load the AVX2 related module then you must explicitly request to use the teton partition by adding the following line to your script: #SBATCH --partition=teton

Basic Slurm Script Examples

A basic script for Gaussian 16 with the AVX module will take the form:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=120G
#SBATCH --time=1-00:00:00
#SBATCH --account=your_account_name

## Specify the stdout file
#SBATCH --output=runjob-%j.out
## Specify the stderr file
#SBATCH --error=runjob-%j.err

module load gaussian/16.AVX.b01

srun g16 $1 $2

A basic script for Gaussian 16 with the AVX2 module will take the form:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=120G
#SBATCH --time=1-00:00:00
#SBATCH --account=your_account_name
#SBATCH --partition=teton

## Specify the stdout file
#SBATCH --output=runjob-%j.out
## Specify the stderr file
#SBATCH --error=runjob-%j.err

module load gaussian/16.AVX2.b01

srun g16 $1 $2

Modify the various parameters according to your needs.
Also, make sure these match up with the input parameters you're using that get passed into the gaussian application:

%nprocshared==16
%mem=60GB

Memory Considerations

Note:

  • The amount of memory your require is a bit of a dark-art and will depend on your input files and number of cores requested, so this does take an element of experimenting and analysis.
  • The freqmem utility takes parameters for a frequency calculation and determines the amount of memory required to complete all steps in one pass for maximum efficiency. Use this to approximate memory requirements.
  • According to the Gaussian 16 Rev. C.01 Release Notes under the Parallel Perf. tab: The memory allocation section recommends setting %mem to half the total memory you allocate for your job. Or, in other words, once you've approximated you memory needs for gaussian, then within the batch script request twice as much.



Potential Issues

Error: illegal instruction, illegal opcode - Check module and selected partition

If you get an error of the form below:

Error: illegal instruction, illegal opcode
   rax 00000000000007c1, rbx 00000000000007c9, rcx 00007ffd70e117d0
   rdx 000000000396ddc0, rsp 00007ffd70e116a0, rbp 00007ffd70e116a0
   rsi 00000000038e6100, rdi 0000000000000000, r8  00000000038cbf70
   r9  00000000038cbf70, r10 00007ffd70e117d0, r11 000000000396ddc0
   r12 00007ffd70e1d980, r13 00000000038c4e88, r14 00007ffd70e117d0
   r15 000000000396ddc0
  /lib64/libpthread.so.0(+0xf5e0) [0x2abf903875e0]
  /apps/u/opt/gaussian16-b.01/AVX2/g16/l1.exe() [0x49095f]
  /apps/u/opt/gaussian16-b.01/AVX2/g16/l1.exe() [0x490b48]
  /apps/u/opt/gaussian16-b.01/AVX2/g16/l1.exe() [0x40ef9d]
  /apps/u/opt/gaussian16-b.01/AVX2/g16/l1.exe() [0x40b6d4]
  /apps/u/opt/gaussian16-b.01/AVX2/g16/l1.exe() [0x40b137]
  /apps/u/opt/gaussian16-b.01/AVX2/g16/l1.exe() [0x40b084]
  /lib64/libc.so.6(__libc_start_main+0xf5) [0x2abf908b7c05]
  /apps/u/opt/gaussian16-b.01/AVX2/g16/l1.exe() [0x4057f9]

Then you have likely loaded the AVX2 module but have not explicitly requested to use the teton partition.
Add #SBATCH --partition=teton to your slurm related script.


GaussView

"GaussView 6 is the latest iteration of a graphical interface used with Gaussian. It aids in the creation of Gaussian input files, enables the user to run Gaussian calculations from a graphical interface without the need for using a command line instruction, and helps in the interpretation of Gaussian output (e.g., you can use it to plot properties, animate vibrations, visualize computed spectra, etc.)."

Using Gaussian View from Teton requires the following steps:

  1. Access FastX: Use Research:FastX to start up a GUI from a browser, into Teton.
  2. Open XFCE Session: Once logged in (requiring Two Factor authentication) launch an XFCE session in single mode.
  3. Open Console: Once the session is started, open a console.
  4. (Optional) Confirm which module you require: module spider gaussian
  5. Load the Gaussian module: From the command line load the appropriate version of the Gaussian module you wish to use i.e. AVX or AVX2: e.g. module load gaussian/16.AVX2.b01
  6. Start GaussView: From the command line: gv
  7. Log Out: Once finished, remember to close GaussView and log out. Click your username in the top right corner of the browser window, and 'Log Out’.
GaussView.png

Using FastX off-campus: FastX can be used off campus, but you must have WyoSecure setup and be logged into the VPN before trying to access the FastX site. If your are not logged into the VPN you will experience an "fastx.arcc.uwyo.edu's server IP address could not be found" error message. For articles on setting up Pulse see:

The original FastX page also talks about connecting via WyoSecure (UW's VPN) using Pulse, and the the FastX desktop client.

Note: Pulse is supported via UW IT (not ARCC directly) so please direct issues with regards to setting up Pulse and general WyoSecure access to the IT helpdesk who will be able to assist you.

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