NAME
runjob - Run a job in the cluster using NBI::Slurm
VERSION
version 0.15.0
SYNOPSIS
runjob [options] "Command to run"DESCRIPTION
The runjob script allows you to submit a job to the cluster using the NBI::Slurm module.
It provides a command-line interface for setting job parameters, including queue, memory, threads, execution time, and input files.
OPTIONS
- -n, --name STR
-
Specifies the name of the job (optional). If not provided, an automatic name will be generated based on the command being run.
- -q, --queue STR
-
Specifies the queue name for the job. The default value is "qib-short". Note that if you include a "*", it will be replaced by 'short', 'medium', or 'long' depending on the time specified with '--time'.
- -m, --memory INT[SUFFIX]
-
Specifies the amount of memory to use for the job. The default value is 8000 (8GB). You can add a suffix like "900Mb" or "12Gb" (floats are not supported). An integer is interpreted as Mb if > 200, otherwise it is interpreted as Gb.
- -c, --cores, --threads INT
-
Specifies the number of threads (cores) to use for the job. The default value is 1.
- -T, -t, --time STR
-
Specifies the time string for the job. The default value is "2h". The format should be in the form of "
Xd Xh Xm" where X represents the number of days (d), hours (h), and minutes (m) respectively. - --after INT
-
Specifies the job ID to wait for before running the job. This option can be used multiple times to specify multiple jobs to wait for.
- -w, --tmpdir PATH
-
Specifies the temporary (working) directory for the job. The default value is "/tmp".
- -f, --files STR
-
Specifies input files or file patterns for the job. This option can be used multiple times. You can use quoted patterns like "*.fasta" to include multiple files matching the pattern.
- --placeholder STR [default:
#FILE#] -
Specifies a placeholder string to be used in the command for input files. If not provided, the default placeholder is "#FILE#".
- -a, --email-address STR
-
Specifies the email address for job notifications.
- -e, --mail-type STR
-
Specifies the type of email notifications to receive. Options include 'BEGIN', 'END', 'FAIL', 'REQUEUE', 'ALL'.
- -r, --run
-
Runs the job immediately after submitting. If not specified, the script will only print the job script without running it.
- --verbose
-
Enables verbose output, displaying additional information about the job and its options.
- --debug
-
Enables debug mode, providing even more detailed information about the job setup and execution.
- --version
-
Displays the version of the runjob script.
- --gpu
-
Requests GPU resources for the job by adding the SLURM option '--gres=gpu:1'. This allows the job to access GPU hardware on the cluster.
- --option STR
-
Specifies additional SLURM options to be passed directly to the job scheduler. This option can be used multiple times to add multiple custom SLURM directives. For example: '--option="--constraint=gpu"' or '--option="--exclusive"'.
- --help
-
Displays the help message for the script.
CONFIGURATION
The script will look for a configuration file in the user's home directory at ~/.nbislurm.config.
Example configuration:
queue=qib-*,nbi-*
email=my@address
tmpdir=/home/user/slurm
memory=8000
time=3hEXAMPLES
Submitting a job to the default queue with 4Gb memory and running the job:
runjob -m 4Gb -r "ls -l"Submitting a job with a custom name, 2 threads, and running a Python script:
runjob -n "my-job" -c 2 -r "python script.py"Chaining jobs together:
JOB1=$(runjob -r "echo 'Hello, world!'")
runjob --after $JOB1 -r "echo 'Goodbye, world!'"Running a job with multiple input files (use placeholder #FILE#):
runjob -f "*.fasta" -f "data.txt" -r "process_files #FILE#"Using a custom placeholder for input files:
runjob -f "*.fastq" --placeholder "FASTQ" -r "fastqc FASTQ"Submitting a GPU job:
runjob --gpu -r "python gpu_script.py"Adding custom SLURM options:
runjob --option="--constraint=intel" --option="--exclusive" -r "my_program"AUTHOR
Andrea Telatin <proch@cpan.org>
COPYRIGHT AND LICENSE
This software is Copyright (c) 2023-2025 by Andrea Telatin.
This is free software, licensed under:
The MIT (X11) License