RE: https://fediscience.org/@snakemake/116295568336688286

This is a big step forward: The SLURM plugin for Snakemake now supports so-called job arrays. These are cluster jobs, with ~ equal resource requirements in terms of memory and compute resources.

The change in itself was big: The purpose of a workflow system is to make use of the vast resources of an HPC cluster. Hence, jobs are submitted to run concurrently. However, for a job array, we have to "wait" for all eligible jobs to be ready. And then we submit.

To preserve concurrent execution of other jobs which are ready to be executed, a thread pool has been introduced. In itself, I do not see job arrays as such a big feature: The LSF system profited much more from arrays than the rather lean SLURM implementation does.

BUT: the new code base will ease further development to pooling many shared memory tasks (applications which support no parallel execution or are confined to one computer by "only" supporting threading). Until then, there is more work to do.

#HPC #SLURM #Snakemake #SnakemakeHackathon2026 #ReproducibleComputing #OpenScience

Beep, Beep - I am your friendly #Snakemake release announcement bot.

There is a new release of the 𝐒𝐧𝐚𝐤𝐞𝐦𝐚𝐤𝐞 𝐄𝐱𝐞𝐜𝐮𝐭𝐨𝐫 𝐏𝐥𝐮𝐠𝐢𝐧 𝐟𝐨𝐫 𝐒𝐋𝐔𝐑𝐌 systems. Its version now is 2.6.0!

Give us some time, and you will automatically find the plugin on #Bioconda and #Pypi.

This plugin is relevant for #HPC users using the #SLURM batch system.
The maintainers are here on Mastodon -
@rupdecat and @johanneskoester.

If you discover any issues, please report them on https://github.com/snakemake/snakemake-executor-plugin-slurm/issues.

See https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v2.6.0 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬

* job arrays: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/174
* Set tmpspace with help of gres="tmpspace:10G" syntax: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/444

𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* logo: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/439

𝐃𝐨𝐜𝐮𝐦𝐞𝐧𝐭𝐚𝐭𝐢𝐨𝐧

* add admin documentation: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/436

A few #slurm tidbits:

Total submitted jobs per user, sorted:
```
squeue | sed 's/ \+/\t/g' | cut -f5 \
| sort | uniq -c | sort -hr
```

Running jobs per user:
```
squeue | grep ' R ' | sed 's/ \+/\t/g' \
| cut -f5 | sort | uniq -c | sort -hr
```

Pending jobs per user:
```
squeue | grep ' PD ' | sed 's/ \+/\t/g' \
| cut -f5 | sort | uniq -c | sort -hr
```

#bash #hpc

Finally, some personal progress: Thanks to @fbartusch a bug of the #SLURM executor plugin for Snakemake was fixed (dealing with nested quoting). A release is upcoming.

And: I generated my first (still faulty) test #nanopub from Snakemake 🥳

#SnakemakeHackathon2026

Beep, Beep - I am your friendly #Snakemake release announcement bot.

There is a new release of the 𝐒𝐧𝐚𝐤𝐞𝐦𝐚𝐤𝐞 𝐄𝐱𝐞𝐜𝐮𝐭𝐨𝐫 𝐏𝐥𝐮𝐠𝐢𝐧 𝐟𝐨𝐫 𝐒𝐋𝐔𝐑𝐌 systems. Its version now is 2.5.3!

Give us some time, and you will automatically find the plugin on #Bioconda and #Pypi.

This plugin is relevant for #HPC users using the #SLURM batch system. If you want to
discuss the release, you will find the maintainers here on Mastodon!
@rupdecat and @johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake-executor-plugin-slurm/issues.

See https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v2.5.3 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* jinja syntax in announce action: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/431

Beep, Beep - I am your friendly #Snakemake release announcement bot.

There is a new release of the {repotitle} systems. Its version now is 2.5.2!

Give us some time, and you will automatically find the plugin on #Bioconda and #Pypi.

This plugin is relevant for #HPC users using the #SLURM batch system. If you want to
discuss the release, you will find the maintainers here on Mastodon!
@rupdecat and @johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake-executor-plugin-slurm/issues.

See https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v2.5.2 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* repo_title -> repotitle because of rendering issues: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/429

Beep, Beep - I am your friendly #Snakemake release announcement bot.

There is a new release of the {repo_title} systems. Its version now is 2.5.1!

Give us some time, and you will automatically find the plugin on #Bioconda and #Pypi.

This plugin is relevant for #HPC users using the #SLURM batch system. If you want to
discuss the release, you will find the maintainers here on Mastodon!
@rupdecat and @johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake-executor-plugin-slurm/issues.

See https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v2.5.1 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* typo: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/427

Beep, Beep - I am your friendly #Snakemake release announcement bot.

There is a new release of the {repo_title} systems. Its version now is 2.5.1!

Give us some time, and you will automatically find the plugin on #Bioconda and #Pypi.

This plugin is relevant for #HPC users using the #SLURM batch system. If you want to
discuss the release, you will find the maintainers here on Mastodon!
@rupdecat and @johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake-executor-plugin-slurm/issues.

See https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v2.5.1 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* typo: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/427

Beep, Beep - I am your friendly #Snakemake release announcement bot.

There is a new release of the {repo_title} systems. Its version now is 2.5.1!

Give us some time, and you will automatically find the plugin on #Bioconda and #Pypi.

This plugin is relevant for #HPC users using the #SLURM batch system. If you want to
discuss the release, you will find the maintainers here on Mastodon!
@rupdecat and @johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake-executor-plugin-slurm/issues.

See https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v2.5.1 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* typo: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/427