ssubmit

Submit sbatch jobs without having to create a submission script

• Motivation
• Install
• Usage

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="0.2.0"  # 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

$ 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> <COMMAND> [-- <REMAINDER>...]

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 (single or double).

REMAINDER is any (optional) sbatch-specific options 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 supported 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.

$ ssubmit -n -m 4g -t 1d dry "rsync -az src/ dest/" -- -c 8
[2022-01-19T08:58:58Z INFO  ssubmit] Dry run requested. Nothing submitted
sbatch -c 8 <script>
=====<script>=====
#!/usr/bin/env bash
#SBATCH --job-name=dry
#SBATCH --mem=4G
#SBATCH --time=24:0:0
#SBATCH --error=%x.err
#SBATCH --output=%x.out
set -euxo pipefail

rsync -az src/ dest/
=====<script>=====

Script settings

The default shebang for the script is #!/usr/bin/env bash. However, if you'd prefer something else, pass this with -S,--shebang.

Additionally, we use set -euxo pipefail by default, which will exit when a command exits with a non-zero exit code (e), error when trying to use an unset variable (u), print all commands that were run to stderr (x), and exit if a command in a pipeline fails (-o pipefail). You can change these setting with -s,--set. You can turn this off by passing -s ''.

Log files

By default, the stderr and stdout of the job are sent to %x.err and %x.out, respectively. %x is a filename pattern for job name. So if the job name is foo, the stderr file will be foo.err. You can see all available patterns in the docs. You don't have to use patterns of course.

Full usage

$ ssubmit --help
ssubmit 0.2.0
Michael Hall <michael@mbh.sh>
Submit sbatch jobs without having to create a submission script

-----------
# EXAMPLES
-----------

Submit a simple rsync command with a 600MB memory limit.

$ ssubmit -m 600m rsync_my_data "rsync -az src/ dest/"

Submit a command that involves piping the output into another command. sbatch options
are passed after a `--`.

$ ssubmit -m 4G align "minimap2 -t 8 ref.fa reads.fq | samtools sort -o sorted.bam" -- -c 8

USAGE:
    ssubmit [OPTIONS] <NAME> <COMMAND> [-- <REMAINDER>...]

ARGS:
    <NAME>
            Name of the job

            See `man sbatch | grep -A 2 'job-name='` for more details.

    <COMMAND>
            Command to be executed by the job

    <REMAINDER>...
            Options to be passed on to sbatch

OPTIONS:
    -e, --error <ERROR>
            File to write job stderr to. (See `man sbatch | grep -A 3 'error='`)

            Run `man sbatch | grep -A 37 '^filename pattern'` to see available patterns.

            [default: %x.err]

    -h, --help
            Print help information

    -m, --mem <size[units]>
            Specify the real memory required per node. e.g., 4.3kb, 7G, 9000, 4.1MB

            Note, floating point numbers will be rounded up. e.g., 10.1G will request 11G. This is
            because sbatch only allows integers. See `man sbatch | grep -A 4 'mem='` for the full
            details.

            [default: 1G]

    -n, --dry-run
            Print the sbatch command and submission script would be executed, but do not execute
            them

    -o, --output <OUTPUT>
            File to write job stdout to. (See `man sbatch | grep -A 3 'output='`)

            Run `man sbatch | grep -A 37 '^filename pattern'` to see available patterns.

            [default: %x.out]

    -s, --set <SET>
            Options for the set command in the shell script

            For example, to exit when the command exits with a non-zero code and to treat unset
            variables as an error during substitution, pass 'eu'. Pass '' or "" to set nothing

            [default: "euxo pipefail"]

    -S, --shebang <SHEBANG>
            The shell shebang for the submission script

            [default: "#!/usr/bin/env bash"]

    -t, --time <TIME>
            Time limit for the job. e.g. 5d, 10h, 45m21s (case insensitive)

            Run `man sbatch | grep -A 7 'time=<'` for more details.

            [default: 1w]

    -V, --version
            Print version information