Overview
Gaussian is a computer program used by chemists, chemical engineers, biochemists, physicists, and other scientists. It utilizes fundamental laws of quantum mechanics to predict energies, molecular structures, spectroscopic data (NMR, IR, UV, etc) and much more advanced calculations. GaussView is a graphical interface used with Gaussian.
Gaussian 16 is the latest in the Gaussian series of programs. It provides state-of-the-art capabilities for electronic structure modeling. Gaussian 16 is licensed for a wide variety of computer systems. All versions of Gaussian 16 contain every scientific/modeling feature, and none imposes any artificial limitations on calculations other than your computing resources and patience.
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
Use the module name gaussian
to discover versions available and to load the application.
Selecting the Correct Gaussian Module
Version | Cluster | |
---|---|---|
gaussian/16.AVX2.b01 | beartooth, teton | This module is compiled for AVX2 compatible nodes - which can only be used on the |
gaussian/16.AVX.b01 | teton | This module is compiled for AVX compatible nodes - which can be used across all nodes on Teton. |
gaussian/103 | teton | This module provides access to the Gaussian 09 Chemistry software. |
Read Advanced Vector Extensions for an introduction to the difference between AVX and AVX2.
Multicore
Gaussian can be run across multiple cores and nodes. 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, for example:
%nprocshared==16 %mem=60GB
These parameters are typically defined within the .gjf
files.
Remember to use the following form of the command srun g16 ...
Memory Considerations
The amount of memory you 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 your 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.)."
GaussView can be run from an Interactive Desktop from our SouthPass service. Once your have started an Interactive Desktop session, open a terminal, load your gaussian module and then type gv
from the command-line.