jobinfo

jobinfo

Get HPC usage metadata for a list of slurm jobids on biowulf

About

This wrapper script works only on BIOWULF! This script usage the “dashboard_cli” utility on biowulf to get HPC usage metadata for a list of slurm jobids. These slurm jobids can be either provided at command line or extracted from a snakemake.log file. Using snakemake.log file option together with –failonly option lists path to the STDERR files for failed jobs. This can be very useful to debug failed Snakemake workflows.

USAGE

$ jobinfo -h

Example

$ jobinfo -j 123456,7891011 $ jobinfo -s /path/to/snakemake.log $ jobinfo -j 123456,7891011 -o /path/to/report.tsv $ jobinfo -s /path/to/snakemake.log –failonly

Functions

Name	Description
check_help	check if usage needs to be printed
exit_w_msg	Gracefully exit with proper message

check_help

jobinfo.check_help(parser)

check if usage needs to be printed

exit_w_msg

jobinfo.exit_w_msg(message)

Gracefully exit with proper message