submit

Generates submission scripts for different clusters architectures based on the gaussian input and output suffixes.

custom

Attention

On the future plans, we are aiming to furhter generalizing the slurm to allow the definition of templates for non-slurm HPCs. If that ends up happening the slurm tool will be renamed as submit, and the custom util will be converter into a specific template for whoever uses it and will not be i included in the pyssianutils distribution.

Checks all .com files in the current directory or the provided folder to generate a submitscript.sh that properly sends them to their queues (Files with a matching .log file are ignored as default). It checks in which queue they should go according to the values of 'nprocshared' and 'mem'. To use the generated script run in the cluster: 'chmod +x submitscript.sh; ./submitscript.sh;' or 'bash submitscript.sh'

usage: pyssianutils submit custom [-h] [--outfile SCRIPTNAME]
                                  [--software {g09,g16}] [--recursive]
                                  [--ascomments] [--suffix SUFFIX SUFFIX]
                                  [--norun]
                                  [folder]

Positional Arguments

folder

Folder where the files are located. If not provided it will use the current working directory.

Named Arguments

--outfile, -o

name of the output file

Default: 'submitscript.sh'

--software

Possible choices: g09, g16

Default: 'g09'

--recursive, -r

If enabled it will recursively search in the subdirectories of the current folder

Default: False

--ascomments

If enabled found .com files with a matching .log are included as comments

Default: False

--suffix

Input and output suffix used for gaussian files

Default: (None, None)

--norun

If enabled the submit command will instead just generate the .com.sub file

Default: False

slurm

Although the slurm subcommand is part of submit, to simplify its input we decided to allow its usage directly from pyssianutils. Thus the documentation of submit slurm is available at the section slurm