Submit sbatch jobs without the need to create a script

Related tags

Miscellaneous wrapper cluster sbatch slurm
Overview

ssubmit

Rust CI codecov Crates.io

Submit sbatch jobs without having to create a submission script

Motivation

This project is motivated by the fact that I want to just be able to submit commands as jobs and I don't want to fluff around with making a submission script.

ssubmit wraps that whole process and lets you live your best lyf #blessed.

Install

Precompiled binary

Run this little scriptlet or download for you system from the releases page.

VERSION="0.1.1"  # ssubmit version you want
OS=$(uname -s)                                                                                                       
if [ "$OS" = "Linux" ]; then                                                                                         
    triple="x86_64-unknown-linux-musl"                                                                              
elif [ "$OS" = "Darwin" ]; then                                                                                        
    triple="x86_64-apple-darwin"                                                         
else                                                      
    echo "ERROR: $OS not a recognised operating system"
fi              
if [ -n "$triple" ]; then   
    URL="https://github.com/mbhall88/ssubmit/releases/download/${VERSION}/ssubmit-${VERSION}-${triple}.tar.gz"
    wget "$URL" -O - | tar -xzf -
    ./ssubmit --help             
fi

Cargo

$ cargo install ssubmit

Build from source

$ git clone https://github.com/mbhall88/ssubmit.git
$ cd ssubmit
$ cargo build --release
$ target/release/ssubmit -h

Usage

Submit an rsync job named "foo" and request 350MB of memory and a one week time limit

$ ssubmit -m 350m -t 1w foo "rsync -az src/ dest/"

Submit a job that needs 8 CPUs

out.paf" -- -c 8"> 
$ ssubmit -m 16g -t 1d align "minimap2 -t 8 ref.fa query.fq > out.paf" -- -c 8

The basic anatomy of a ssubmit call is

ssubmit [OPTIONS] 
    
     [-- 
    
     ...]

NAME is the name of the job (the --job-name parameter in sbatch).

COMMAND is what you want to be executed by the job. It must be quoted (siungle or double).

REMAINDER is any (optional) sbatch-specific parameters you want to pass on. These must follow a -- after COMMAND.

Memory

Memory (-m,--mem) is intended to be a little more user-friendly than the sbatch --mem option. For example, you can pass -m 0.5g and ssubmit will interpret and convert this as 500M. However, -m 1.7G will be rounded up to 2G. One place where this option differs from sbatch is that if you don't give units, it will be interpreted as bytes - i.e., -m 1000 will be converted to 1K. Units are case insensitive.

Time

As with memory, time (-t,--time) is intended to be simple. If you want a time limit of three days, then just pass -t 3d. Want two and a half hours? Then -t 2h30m works. If you want to just use the default limit of your cluster, then just pass -t 0. You can also just pass the time format sbatch uses and this will be seamlessly passed on. For a full list of support time units, check out the duration-str repo.

Dry run

You can see what ssubmit would do without actually submitting a job using dry run (-n,--dry-run). This will print the sbatch command and also the submission script that would have been provided.

=====
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Owner
Michael Hall
Bioinformatics PhD Student at EMBL-EBI and University of Cambridge in @iqbal-lab-org Interested in Microbial Genomics.
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