Submit sbatch jobs without having to create a submission script
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.
tl;dr
curl -sSL install.ssubmit.mbh.sh | sh
# or with wget
wget -nv -O - install.ssubmit.mbh.sh | shYou can pass options to the script like so
$ curl -sSL install.ssubmit.mbh.sh | sh -s -- --help
install.sh [option]
Fetch and install the latest version of ssubmit, if ssubmit is already
installed it will be updated to the latest version.
Options
-V, --verbose
Enable verbose output for the installer
-f, -y, --force, --yes
Skip the confirmation prompt during installation
-p, --platform
Override the platform identified by the installer [default: apple-darwin]
-b, --bin-dir
Override the bin installation directory [default: /usr/local/bin]
-a, --arch
Override the architecture identified by the installer [default: x86_64]
-B, --base-url
Override the base URL used for downloading releases [default: https://github.com/mbhall88/ssubmit/releases]
-h, --help
Display this help message
$ cargo install ssubmit
$ conda install -c conda-forge ssubmit
$ git clone https://github.com/mbhall88/ssubmit.git
$ cd ssubmit
$ cargo build --release
$ target/release/ssubmit -hSubmit 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 8Start an interactive session with 5GB memory for 8 hours
$ ssubmit --interactive -m 5G -t 8h interactiveJobStart an interactive session with custom shell and additional SLURM options
$ ssubmit --interactive -m 16G -t 4h DevSession --shell bash -- --partition=general --qos=normal$ ssubmit -h
Submit sbatch jobs without having to create a submission script
Usage: ssubmit [OPTIONS] <NAME> [COMMAND] [-- <REMAINDER>...]
Arguments:
<NAME> Name of the job
[COMMAND] Command to be executed by the job. For batch jobs, this is required. For interactive jobs (--interactive), this is optional and defaults to starting a shell session
[REMAINDER]... Options to be passed on to sbatch or salloc (for interactive jobs)
Options:
-o, --output <OUTPUT> File to write job stdout to. (See `man sbatch | grep -A 3 'output='`) [default: %x.out]
-e, --error <ERROR> File to write job stderr to. (See `man sbatch | grep -A 3 'error='`) [default: %x.err]
-m, --mem <size[unit]> Specify the real memory required per node. e.g., 4.3kb, 7 Gb, 9000, 4.1MB become 5KB, 7000M, 9000M, and 5M, respectively [env: SSUBMIT_MEMORY=] [default: 1G]
-t, --time <TIME> Time limit for the job. e.g. 5d, 10h, 45m21s (case-insensitive) [env: SSUBMIT_TIME=] [default: 1d]
-S, --shebang <SHEBANG> The shell shebang for the submission script [env: SSUBMIT_SHEBANG=] [default: "#!/usr/bin/env bash"]
-s, --set <SET> Options for the set command in the shell script [env: SSUBMIT_SET=] [default: "euxo pipefail"]
-n, --dry-run Print the sbatch command and submission script that would be executed, but do not execute them
-T, --test-only Return an estimate of when the job would be scheduled to run given the current queue. No job is actually submitted. [sbatch --test-only]
-i, --interactive Request an interactive job session instead of a batch job
--shell <SHELL> Shell to use for interactive sessions [default: auto-detected]
--export <EXPORT> Control which environment variables are exported to the job [default: ALL]
-h, --help Print help (see more with '--help')
-V, --version Print version
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 or salloc).
COMMAND is what you want to be executed by the job. For batch jobs, it must be quoted (single or
double) and is required. For interactive jobs (--interactive), this is optional and defaults to starting an interactive shell session.
REMAINDER is any (optional) sbatch-specific options (for batch jobs) or salloc-specific options (for interactive jobs) you want to pass on. These
must follow a -- after COMMAND (or after NAME if no command is provided for interactive jobs).
You can start interactive job sessions using the --interactive (or -i) flag. This uses salloc instead of sbatch and automatically starts an interactive shell session.
# Start an interactive session with default shell
$ ssubmit --interactive -m 8G -t 4h my_session
# Start an interactive session with a specific shell
$ ssubmit --interactive --shell bash -m 16G -t 8h dev_work
# Start an interactive session with additional SLURM options
$ ssubmit --interactive -m 32G -t 12h gpu_session -- --partition=gpu --gres=gpu:1When using --interactive:
- The command argument is optional and defaults to starting an interactive shell
- If no command is provided,
ssubmitwill automatically detect your current shell and start an interactive session - You can specify a different shell using the
--shelloption - All the same memory and time parsing features work just like with batch jobs
- Additional SLURM options can be passed after
--just like with batch jobs
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. Units are case-insensitive. Memory values over 1M will be rounded up to the nearest whole number.
For example, 1.1M will be rounded up to 2M. If you want to use the default memory limit of your cluster, then just pass
-m 0.
For simplicity's sake, all values over one megabyte are passed to sbatch as megabytes - e.g., 1.1G will be passed as 1100M.
The environment variable SSUBMIT_MEM can be set to a default memory limit. This can be overridden by passing -m.
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. One thing to note is that passing a single digit, without a unit, will be interpreted by
slurm as minutes. However, not providing a unit in the example of 5m3 will be interpreted as 5 minutes and 3 seconds.
The environment variable SSUBMIT_TIME can be set to a default time limit. This can be overridden by passing -t.
By default, ssubmit exports all environment variables to the job using --export=ALL. This ensures that your job has access to the same environment as your current shell session.
You can control which environment variables are exported using the --export option:
# Export all environment variables (default behavior)
$ ssubmit -m 2g analysis "python script.py"
# Export no environment variables
$ ssubmit --export NONE -m 2g analysis "python script.py"
# Export specific environment variables only
$ ssubmit --export "PATH,HOME,USER,PYTHONPATH" -m 2g analysis "python script.py"This option is passed directly to sbatch as --export=<value>, so it supports all the same values as the sbatch --export option. Common values include:
ALL- Export all environment variables (default)NONE- Export no environment variables- Comma-separated list (e.g.,
PATH,HOME) - Export only the specified variables
Note that if you specify --export in the remainder arguments (after --), it will override the default --export=ALL behavior.
You can see what ssubmit would do without actually submitting a job using dry run
(-n,--dry-run). This will print the sbatch command (for batch jobs) or salloc command (for interactive jobs) that would have been executed.
For batch jobs, it also shows the submission script:
$ 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 --export=ALL -c 8 <script>
=====<script>=====
#!/usr/bin/env bash
#SBATCH --job-name=dry
#SBATCH --mem=4000M
#SBATCH --time=24:0:0
#SBATCH --error=%x.err
#SBATCH --output=%x.out
set -euxo pipefail
rsync -az src/ dest/
=====<script>=====For interactive jobs, it shows the salloc command:
$ ssubmit --interactive -n -m 8G -t 4h my_session
[2022-01-19T08:58:58Z INFO ssubmit] Dry run requested. Nothing submitted
salloc --job-name my_session --mem 8000M --time 4:0:0 srun --pty zsh -lThe default shebang for the script is #!/usr/bin/env bash. However, if you'd prefer
something else, pass this with -S,--shebang or set the environment variable SSUBMIT_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 or the environment variable SSUBMIT_SET. You can turn this off
by passing -s ''.
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.
$ ssubmit --help
ssubmit 1.0.0
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
Start an interactive session with 5GB memory for 8 hours.
$ ssubmit --interactive -m 5G -t 8h interactiveJob
Start an interactive session with custom shell and additional SLURM options.
$ ssubmit --interactive -m 16G -t 4h DevSession --shell bash -- --partition=general --qos=normal
Submit a job with no environment variable export.
$ ssubmit --export NONE -m 2G analysis "python script.py"
Usage: ssubmit [OPTIONS] <NAME> [COMMAND] [-- <REMAINDER>...]
Arguments:
<NAME>
Name of the job
See `man sbatch | grep -A 2 'job-name='` for more details.
[COMMAND]
Command to be executed by the job
For batch jobs, this is required. For interactive jobs (--interactive),
this is optional and defaults to starting a shell session.
[REMAINDER]...
Options to be passed on to sbatch or salloc (for interactive jobs)
Options:
-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]
-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]
-m, --mem <size[unit]>
Specify the real memory required per node. e.g., 4.3kb, 7 Gb, 9000, 4.1MB become 5KB, 7000M, 9000M, and 5M, respectively.
If no unit is specified, megabytes will be used, as per the sbatch default. The value will be rounded up to the nearest megabyte. If the value is less than 1M, it will be rounded up to the nearest kilobyte. See `man sbatch | grep -A 4 'mem='` for the full details.
[env: SSUBMIT_MEMORY=]
[default: 1G]
-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. If a single digit is passed, it will be passed straight to sbatch (i.e. minutes). However, 5m5 will be considered 5 minutes and 5 seconds.
[env: SSUBMIT_TIME=]
[default: 1d]
-S, --shebang <SHEBANG>
The shell shebang for the submission script
[env: SSUBMIT_SHEBANG=]
[default: "#!/usr/bin/env bash"]
-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
[env: SSUBMIT_SET=]
[default: "euxo pipefail"]
-n, --dry-run
Print the sbatch command and submission script that would be executed, but do not execute them
-T, --test-only
Return an estimate of when the job would be scheduled to run given the current queue. No job is actually submitted. [sbatch --test-only]
-i, --interactive
Request an interactive job session instead of a batch job
This will use `salloc` instead of `sbatch` and automatically start an interactive shell.
The command argument becomes optional and defaults to the user's shell.
--shell <SHELL>
Shell to use for interactive sessions
Only used when --interactive is specified. Defaults to the user's login shell.
[default: auto-detected]
--export <EXPORT>
Control which environment variables are exported to the job
Passed directly to sbatch as --export=<value>. Use 'NONE' to export no variables, 'ALL' to export all variables, or specify specific variables like 'PATH,HOME'.
[default: ALL]
-h, --help
Print help (see a summary with '-h')
-V, --version
Print version