template

Important

In order to view the available templates, running the slurm util without any subcommand will display the available names.

$ pyssianutils slurm
Available slurm templates:
    example

A single template is packaged by default, under the name of "example". The following arguments are the ones generated for said "example" template.

usage: pyssianutils slurm example [-h] [-l | -r] [-o OUTDIR] [--suffix SUFFIX]
                                  [-ow | --skip]
                                  [--memory MEMORY | --memory-per-cpu]
                                  [--walltime WALLTIME | --use-max-walltime]
                                  [--guess-cores] [--guess-mem]
                                  [--add-memory | --rm-memory]
                                  [--add-nprocs | --rm-nprocs]
                                  [--cores {2,4,8,16,24,32}]
                                  [--partition {example}] [--module {g16}]
                                  [--jobname JOBNAME]
                                  [inputfiles ...]

Positional Arguments

inputfiles

Gaussian input files. If none is provided, it will create a 'dummy_job.slurm' to use as template.

Named Arguments

-l, --listfile

When enabled instead of considering the files provided as the gaussian output files considers the file provided as a list of gaussian output files

Default: False

-r, --folder

Takes the folder and its subfolder hierarchy and creates a new folder with the same subfolder structure. Finds all the .log, attempts to find their companion .com files and creates the new inputs in their equivalent locations in the new folder tree structure.

Default: False

-o, --outdir

Where to create the new files, defaults to the current directory

--suffix

suffix of the generated files

Default: '.slurm'

-ow, --overwrite

When creating the new files if a file with the same name exists overwrites its contents. (The default behaviour is to raise an error to notify the user before overwriting).

Default: False

--skip

Skip the creation of slurm templates that already exist

Default: False

--memory

Memory requested for the calculation. If None is provided it will attempt to guess it from the gaussian input file.

Default: '16GB'

--memory-per-cpu

It will use the max memory per cpu of the partition

Default: False

--walltime

Fixed value of walltime in DD-HH:MM:SS format. If none is provided it will use the default value of '24:00:00'

Default: '24:00:00'

--use-max-walltime

If enabled, use the selected partition's max walltime

Default: False

--guess-cores

attempt to guess the number of cores from the gaussian input file

Default: False

--guess-mem

attempt to guess the memory from the gaussian input file

Default: False

--cores

Possible choices: 2, 4, 8, 16, 24, 32

Number of cores for the calculation

Default: 8

--partition

Possible choices: example

Partition name / Queue that will be used for the calculation

Default: example

--module

Possible choices: g16

alias of the gaussian version and how to load it

Default: g16

--jobname

default name for the job

Default: 'test_job'

inplace modifications

Arguments to modify in-place the provided gaussian input files

--add-memory

Add the "%mem" Link0 option to the provided files

--rm-memory

Remove the "%mem" Link0 option of the provided files

--add-nprocs

Add the "%nprocshared" Link0 option to the provided files

--rm-nprocs

Remove the "%nprocshared" Link0 option of the provided files

Important

The --guess-cores and the --guess-mem flags will show if in the user defaults, the guess_default value in the subsection [submit.slurm] is set to False. If it is set to True, the --fix-cores and --fix-mem will show instead.

Important

The --inplace flag will only show if in the user defaults, the inplace_default value in the subsection of [submit.slurm] is set to False. If it is set to True it will become the default behavior