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Christian MeestersDue to maintenance of the cluster I usually work on, only minor updates to the <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SLURM</a> plugin for <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> compatible workflows could be made.However, it now has better GPU support by generic resources. Already on <a href="https://fediscience.org/tags/PyPi" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PyPi</a>, soon on <a href="https://fediscience.org/tags/Bioconda" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioconda</a>, too.

Snakemake Release RobotBeep, Beep - I am your friendly <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Snakemake</a> release announcement bot.There is a new release of the Snakemake executor for <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SLURM</a> on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> systems. Its version is '1.0.0'!See <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v1.0.0" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v1.0.0</a> for details.Give us some time and you will automatically find the plugin on <a href="https://fediscience.org/tags/Bioconda" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioconda</a> and <a href="https://fediscience.org/tags/Pypi" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Pypi</a>.If you want to discuss the release you will find the maintainers here on Mastodon! <a href="https://fediscience.org/@rupdecat" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@rupdecat</a> and <a href="https://fosstodon.org/@johanneskoester" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@johanneskoester</a>If you find any issues, please report them on <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/snakemake/snakemake-executor-plugin-slurm/issues</a><a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Snakemake</a> <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> <a href="https://fediscience.org/tags/ReproducibleComputing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ReproducibleComputing</a> <a href="https://fediscience.org/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ReproducibleResearch</a> <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenScience</a>

Violet``` --job-name call-fastqTask-24-XXX-0 \ --cpus-per-task 1 \ --mem 1024M \ --time 3179733413 \ /share/software/apptainer/1.2.5/bin/apptainer ``` I'm sure slurm will run it someday, I'm sure. if I just keep waiting, it'll run the job that wants a century of walltime. surely. <a class="hashtag" href="https://galaxians.garden/tag/postdoc" rel="nofollow noopener noreferrer" target="_blank">#postdoc</a> pro tip: watch the <a class="hashtag" href="https://galaxians.garden/tag/slurm" rel="nofollow noopener noreferrer" target="_blank">#slurm</a> submissions to be sure the workflow engine is submitting sane things!

WorteksVous cherchez à optimiser vos ressources informatiques pour vos projets de science de la donnée et d'IA ? Découvrez comment <a href="https://mastodon.social/tags/Slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Slurm</a>, un outil Open Source puissant, peut vous aider !<a href="https://mastodon.social/tags/Slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Slurm</a> est un système très évolutif qui permet la gestion de clusters et l'ordonnancement des tâches. Retrouvez sur notre blog comment exploiter au maximum les performances de vos clusters grâce à lui. 🔗 <a href="https://www.worteks.com/blog/comment-utiliser-slurm/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.worteks.com/blog/comment-utiliser-slurm/</a><a href="https://fosstodon.org/@ow2" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@ow2</a> <a href="https://social.openinfra.dev/@OpenInfra" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@OpenInfra</a> <a href="https://mastodon.social/@fsfe" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@fsfe</a><a href="https://mastodon.social/tags/DataScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#DataScience</a> <a href="https://mastodon.social/tags/IA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#IA</a> <a href="https://mastodon.social/tags/AI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#AI</a> <a href="https://mastodon.social/tags/FreeSoftware" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#FreeSoftware</a> <a href="https://mastodon.social/tags/OpenSource" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenSource</a> <a href="https://mastodon.social/tags/LogicielLibre" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#LogicielLibre</a>

Krzysztof Sakrejda<a href="https://bayes.club/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> Cluster based on redhat <a href="https://bayes.club/tags/Linux" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Linux</a> running <a href="https://bayes.club/tags/Nix" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Nix</a> through <a href="https://bayes.club/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#slurm</a>... surely no one will regret that!

Pierre Lindenbaum<a href="https://genomic.social/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#slurm</a> + <a href="https://genomic.social/tags/nextflow" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#nextflow</a> my colleague cannot run nextflow. In the log I see nextflow.executor.SlurmExecutor - [SLURM] invalid status line: `squeue: error: Invalid user: ?`the job is said completed by NF but I can see it running in squeue.puzzled

Snakemake Release RobotBeep, Beep - I am your friendly <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Snakemake</a> release announcement bot.There is a new release of the Snakemake executor for <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SLURM</a> on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> systems. Its version is '0.15.1'!See <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v0.15.1" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v0.15.1</a> for details.Give us some time and you will automatically find the plugin on <a href="https://fediscience.org/tags/Bioconda" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioconda</a> and <a href="https://fediscience.org/tags/Pypi" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Pypi</a>.If you want to discuss the release you will find the maintainers here on Mastodon! <a href="https://fediscience.org/@rupdecat" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@rupdecat</a> and <a href="https://fosstodon.org/@johanneskoester" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@johanneskoester</a>If you find any issues, please report them on <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/snakemake/snakemake-executor-plugin-slurm/issues</a><a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Snakemake</a> <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> <a href="https://fediscience.org/tags/ReproducibleComputing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ReproducibleComputing</a> <a href="https://fediscience.org/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ReproducibleResearch</a> <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenScience</a>

Michael Sumner<a href="https://rstats.me/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a> future_map in <a href="https://rstats.me/tags/furrr" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#furrr</a> on <a href="https://rstats.me/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#slurm</a> has stopped being my friend ... multicore or multisession, both take way longer than normal - tested on small sets with 6 cores, smallish sets with 24, and the real job with 128 coresparallel::parLapply works fine in the small or all 128 coresany ideas?

Christian MeestersWhen reading this call (<a href="https://mast.hpc.social/@sneuwirth/113945330638974358" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://mast.hpc.social/@sneuwirth/113945330638974358</a>) from <a href="https://mast.hpc.social/@sneuwirth" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@sneuwirth</a> I think, I could tell a number of tales from my experience with developing the <a href="https://fediscience.org/tags/Slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Slurm</a> plugin for <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Snakemake</a> (and other software over the years).Particularly, issue reports telling what peculiarities fellow admins thought of (e.g. "we are not allowed to do this" and "we not that". "We have this setting" and "we that".) To develop <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> software is a challenge in its own right. To support workflow software seems to develop into a nice challenge.Could certainly deliver a funny few minutes. 😉 Perhaps I should collect anecdotes and write an article sometime? 🤔

Tyler SmithA little tutorial on speeding up bioinformatic work on a computing cluster by converting your loops to array jobs <a href="https://ottawa.place/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> <a href="https://ottawa.place/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> <a href="https://ottawa.place/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#slurm</a><a href="https://plantarum.ca/2025/01/24/array-jobs/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://plantarum.ca/2025/01/24/array-jobs/</a>[edit: fixed link]

Snakemake Release RobotBeep, Beep - I am your friendly <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Snakemake</a> release announcement bot.There is a new release of the Snakemake executor for <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SLURM</a> on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> systems. Its version is '0.15.0'!See <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v0.15.0" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v0.15.0</a> for details.Give us some time and you will automatically find the plugin on <a href="https://fediscience.org/tags/Bioconda" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioconda</a> and <a href="https://fediscience.org/tags/Pypi" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Pypi</a>.If you want to discuss the release you will find the maintainers here on Mastodon! <a href="https://fediscience.org/@rupdecat" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@rupdecat</a> and <a href="https://fosstodon.org/@johanneskoester" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@johanneskoester</a>If you find any issues, please report them on <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/snakemake/snakemake-executor-plugin-slurm/issues</a><a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Snakemake</a> <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> <a href="https://fediscience.org/tags/ReproducibleComputing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ReproducibleComputing</a> <a href="https://fediscience.org/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ReproducibleResearch</a> <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenScience</a>

Christian MeestersAgain, we have a new patch-level release of the <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Snakemake</a> executor for <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SLURM</a> on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> systems.Turned out, that some clusters do not allow account checking with `sacctmgr` (which was there for historic reasons), hence, we now have a fall-back to `sshare`. See <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v0.12.1" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v0.12.1</a> for details.<a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenScience</a> <a href="https://fediscience.org/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ReproducibleResearch</a> <a href="https://fediscience.org/tags/ReproducibleComputing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ReproducibleComputing</a>

Tyler SmithA very niche post on using <a href="https://ottawa.place/tags/emacs" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#emacs</a> and <a href="https://ottawa.place/tags/orgmode" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#orgmode</a> to manage <a href="https://ottawa.place/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#slurm</a> job submission scripts:<a href="https://plantarum.ca/2025/01/10/slurm-yasnippet/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://plantarum.ca/2025/01/10/slurm-yasnippet/</a><a href="https://ottawa.place/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a>

Christian MeestersWe have a new release for the <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SLURM</a> support plugin of <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Snakemake</a> !It's a minor feature release which enables custom log directories and auto-deletion of successful job logs (such that not zillions of zero-meaning files accumulate!).Check it out at: <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v0.12.0" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v0.12.0</a>It took a while to get to this release (stress, family, and sickness took a toll). Hopefully, a future release will not take that long to be realized — the feature request list is considerable. 😉 <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> <a href="https://fediscience.org/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ReproducibleResearch</a> <a href="https://fediscience.org/tags/ReproducibleComputing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ReproducibleComputing</a> <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenScience</a>

Tyler SmithUsing <a href="https://ottawa.place/tags/emacs" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#emacs</a> to handle the boilerplate for <a href="https://ottawa.place/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#slurm</a> submission scripts. Blogpost in progress, spent the last few minutes of my week playing with gifs:<a href="https://ottawa.place/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> <a href="https://ottawa.place/tags/hpc" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#hpc</a>

TOVOn Linux, Slurm is also a command-line network monitoring tool in real time. This tool lets you monitor traffic on your network and display the statistics with an ASCII graph. Three different types of graphs are available on this tool.<a href="https://fosstodon.org/tags/Linux" class="mention hashtag" rel="tag">#Linux</a> <a href="https://fosstodon.org/tags/slurm" class="mention hashtag" rel="tag">#slurm</a> <a href="https://fosstodon.org/tags/network" class="mention hashtag" rel="tag">#network</a> <a href="https://fosstodon.org/tags/monitor" class="mention hashtag" rel="tag">#monitor</a>

Christian MeestersDoes anyone have a working <a href="https://fediscience.org/tags/GitHub" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GitHub</a> action to create a fake <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SLURM</a> cluster within a CI action?(ours keeps failing, e.g. <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/actions/runs/12235923998/job/34193736191?pr=159" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/snakemake/snakemake-executor-plugin-slurm/actions/runs/12235923998/job/34193736191?pr=159</a>)<a href="https://fediscience.org/tags/askfedi" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#askfedi</a> <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a>

BrunoSlurm 24.11 is out! <a href="https://www.schedmd.com/slurm-version-24-11-0-is-now-available/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.schedmd.com/slurm-version-24-11-0-is-now-available/</a><a href="https://mast.hpc.social/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#slurm</a> <a href="https://mast.hpc.social/tags/hpc" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#hpc</a>

QuinnWelp…lines. So many lines. <a href="https://mast.hpc.social/tags/SC24" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SC24</a> <a href="https://mast.hpc.social/tags/Slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Slurm</a>Someone get the Slurm crew on solving this queue!!

:rss: DevelopersIOまるクラ勉強会で「AWS ParallelClusterとTrainiumを使って大規模言語モデルをトレーニングする入門」というタイトルで登壇しました <a href="https://dev.classmethod.jp/articles/marukura-parallel-cluster-de-trainium-and-neuron/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://dev.classmethod.jp/articles/marukura-parallel-cluster-de-trainium-and-neuron/</a><a href="https://rss-mstdn.studiofreesia.com/tags/dev_classmethod" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#dev_classmethod</a> <a href="https://rss-mstdn.studiofreesia.com/tags/%E3%81%BE%E3%82%8B%E3%82%AF%E3%83%A9%E5%8B%89%E5%BC%B7%E4%BC%9A" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#まるクラ勉強会</a> <a href="https://rss-mstdn.studiofreesia.com/tags/%E6%A9%9F%E6%A2%B0%E5%AD%A6%E7%BF%92" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#機械学習</a> <a href="https://rss-mstdn.studiofreesia.com/tags/%E7%94%9F%E6%88%90AI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#生成AI</a> <a href="https://rss-mstdn.studiofreesia.com/tags/AWS_ParallelCluster_3" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#AWS_ParallelCluster_3</a> <a href="https://rss-mstdn.studiofreesia.com/tags/Slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Slurm</a>

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