Gaussian Tutorial
Last updated
Last updated
Command
Description
ls
list directories & files in current directory
mkdir newDir
makes a new directory in the current directory
cd ..
back up one directory
cd myDirectory/
open myDirectory
nano file1
opens file1 in nano editor
Ctrl-o , Enter
In nano-saves edits
Ctrl-X
Exits out of nano
The "cd" command is used to move into and out of directories (folders). It's basically equivalent (in Windows Explorer) to clicking on a subfolder of the folder you are in (eg. "cd subfolder/") or hitting the back arrow to move out of a folder into the previous one (eg. "cd ..").
MobaXterm can be freely downloaded here (use the Home Installer Edition): https://mobaxterm.mobatek.net/download.html
Open MobaX.
Log in to Lawrence (refer to the following code).
In MobaX, the file explorer/hierarchy is visible just to the left of the command line interface. Navigate into directories by clicking on them, and out of directories using the "parent directory" button.
Note: entering/exiting a directory in this area doesn't change your current directory in the command line (you'll still be in the same directory as before in the command line). Use the cd command to navigate directories in the command line.
From this section of the MobaX window, you can drag and drop files between Lawrence and your PC as needed.
Once your files are in the proper directories, they can be handled in the same way as the example input files are handled in this tutorial (excluding the steps of copying the example input files into their respective directories).
Open MobaX and log into Lawrence (see section "Getting Started").
Make a directory in your home directory, and navigate into it:
Connect to a node.
Copy the Gaussian test file into your myInteractiveDir directory.
If these commands don't make sense, go to the top section: "Command Line Basics".
To see the Gaussian modules available:
Load one of the Gaussian modules.
Run Gaussian with an input file:
To view the output, open "interactiveOutput.com" with nano or another editor.
To get back out of nano, use the instructions at the bottom of the command line screen, or see "Command Line Basics".
Navigate out of "myInteractiveDir" into your home directory:
Exit the node.
If entering the tutorial at this point, open MobaX and log into Lawrence (see the second half of "Getting Started").
Make a directory in your home directory, and navigate into it:
If these commands don't make sense, go to the top section: "Command Line Basics".
Copy the Gaussian batch job template files into your myBatchDir directory.
Open the file "gaussianBatchTemplate.sh" using nano (or another editor, if you prefer) and note the features described in the image below.
Open the file "test.com" (you will have to exit viewing gaussianBatchTemplate.sh in nano to do this in the same terminal).
In the last line, "test.com" is the input file name and the slurm ID followed by ".out" is the output file name. Also note that the number of CPUs (ntasks) requested matches the %nprocshared (or %nprocs) in the input file.
--ntasks in batch file should equal %nprocshared in input file
Exit nano (Ctrl-x), then run the batch job:
Show the list of jobs running on Lawrence:
Show only your jobs:
When your job is complete, it will not appear on squeue. To see the output of your job when completed, open the ".out" file.
To see how the job went, and look at any errors, open the slurm file.
Note: the number 12345 in slurm-12345.out corresponds to the number of the batch job above.
If entering the tutorial at this point, open MobaX and log into Lawrence (for help, see the section "Getting Started").
Log into a node
Load the Gaussian module:
Launch the Gaussian GUI:
The GUI will open:
