Diego "dciangot" Ciangottini<p>Get ready for the interSpace! We are coming to make <a href="https://hachyderm.io/tags/k8s" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>k8s</span></a> extension to <a href="https://hachyderm.io/tags/SLURM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SLURM</span></a>, GPU on-demand VMs and CaaS a <a href="https://hachyderm.io/tags/cncf" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>cncf</span></a> community effort!</p><p><a href="https://l.infn.it/interlink" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">l.infn.it/interlink</span><span class="invisible"></span></a></p><p><a href="https://hachyderm.io/tags/hpc" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>hpc</span></a> <a href="https://hachyderm.io/tags/hybridcloud" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>hybridcloud</span></a> <a href="https://hachyderm.io/tags/gpu" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>gpu</span></a> <a href="https://hachyderm.io/tags/ai" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ai</span></a> <a href="https://hachyderm.io/tags/ml" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ml</span></a> <a href="https://hachyderm.io/tags/interLink" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>interLink</span></a></p>
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#slurm
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statquant<p><a href="https://mastodon.social/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>rstats</span></a> people do anyone know of an example to send jobs to <a href="https://mastodon.social/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>slurm</span></a> using the <a href="https://mastodon.social/tags/mirai" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>mirai</span></a> package?</p>
Violet```<br> --job-name call-fastqTask-24-XXX-0 \<br>--cpus-per-task 1 \<br>--mem 1024M \<br>--time 3179733413 \<br>/share/software/apptainer/1.2.5/bin/apptainer<br>```<br><br>I'm sure slurm will run it someday, I'm sure.<br><br>if I just keep waiting, it'll run the job that wants a century of walltime.<br><br>surely.<br><br><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!
Worteks<p>Vous cherchez à optimiser vos ressources informatiques pour vos projets de science de la donnée et d'IA ?<br>Découvrez comment <a href="https://mastodon.social/tags/Slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Slurm</span></a>, un outil Open Source puissant, peut vous aider !</p><p><a href="https://mastodon.social/tags/Slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Slurm</span></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.<br>🔗 <a href="https://www.worteks.com/blog/comment-utiliser-slurm/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">worteks.com/blog/comment-utili</span><span class="invisible">ser-slurm/</span></a></p><p><span class="h-card" translate="no"><a href="https://fosstodon.org/@ow2" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>ow2</span></a></span> <span class="h-card" translate="no"><a href="https://social.openinfra.dev/@OpenInfra" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>OpenInfra</span></a></span> <span class="h-card" translate="no"><a href="https://mastodon.social/@fsfe" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>fsfe</span></a></span></p><p><a href="https://mastodon.social/tags/DataScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>DataScience</span></a> <a href="https://mastodon.social/tags/IA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>IA</span></a> <a href="https://mastodon.social/tags/AI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>AI</span></a> <a href="https://mastodon.social/tags/FreeSoftware" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>FreeSoftware</span></a> <a href="https://mastodon.social/tags/OpenSource" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenSource</span></a> <a href="https://mastodon.social/tags/LogicielLibre" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>LogicielLibre</span></a></p>
Krzysztof Sakrejda<p><a href="https://bayes.club/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HPC</span></a> Cluster based on redhat <a href="https://bayes.club/tags/Linux" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Linux</span></a> running <a href="https://bayes.club/tags/Nix" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Nix</span></a> through <a href="https://bayes.club/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>slurm</span></a>... surely no one will regret that!</p>
Pierre Lindenbaum<p><a href="https://genomic.social/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>slurm</span></a> + <a href="https://genomic.social/tags/nextflow" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>nextflow</span></a> my colleague cannot run nextflow. In the log I see nextflow.executor.SlurmExecutor - [SLURM] invalid status line: `squeue: error: Invalid user: ?`</p><p>the job is said completed by NF but I can see it running in squeue.</p><p>puzzled</p>
Michael Sumner<p><a href="https://rstats.me/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>rstats</span></a> future_map in <a href="https://rstats.me/tags/furrr" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>furrr</span></a> on <a href="https://rstats.me/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>slurm</span></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 cores</p><p>parallel::parLapply works fine in the small or all 128 cores</p><p>any ideas?</p>
Tyler Smith<p>A little tutorial on speeding up bioinformatic work on a computing cluster by converting your loops to array jobs </p><p><a href="https://ottawa.place/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HPC</span></a> <a href="https://ottawa.place/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a> <a href="https://ottawa.place/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>slurm</span></a></p><p><a href="https://plantarum.ca/2025/01/24/array-jobs/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">plantarum.ca/2025/01/24/array-</span><span class="invisible">jobs/</span></a></p><p>[edit: fixed link]</p>
Christian Meesters<p>Again, 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">#<span>Snakemake</span></a> executor for <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SLURM</span></a> on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HPC</span></a> systems.</p><p>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`. </p><p>See <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v0.12.1" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/releases/tag/v0.12.1</span></a> for details.</p><p><a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenScience</span></a> <a href="https://fediscience.org/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ReproducibleResearch</span></a> <a href="https://fediscience.org/tags/ReproducibleComputing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ReproducibleComputing</span></a></p>
Tyler Smith<p>A very niche post on using <a href="https://ottawa.place/tags/emacs" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>emacs</span></a> and <a href="https://ottawa.place/tags/orgmode" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>orgmode</span></a> to manage <a href="https://ottawa.place/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>slurm</span></a> job submission scripts:</p><p><a href="https://plantarum.ca/2025/01/10/slurm-yasnippet/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">plantarum.ca/2025/01/10/slurm-</span><span class="invisible">yasnippet/</span></a></p><p><a href="https://ottawa.place/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a></p>
Christian Meesters<p>We have a new release for the <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SLURM</span></a> support plugin of <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Snakemake</span></a> !</p><p>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!).</p><p>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"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/releases/tag/v0.12.0</span></a></p><p>It took a while to get to this release (stress, family, and sickness took a toll). Hopefully, future release will not take that long to be realized — the feature request list is considerable. 😉 </p><p><a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HPC</span></a> <a href="https://fediscience.org/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ReproducibleResearch</span></a> <a href="https://fediscience.org/tags/ReproducibleComputing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ReproducibleComputing</span></a> <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenScience</span></a></p>
Tyler Smith<p>Using <a href="https://ottawa.place/tags/emacs" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>emacs</span></a> to handle the boilerplate for <a href="https://ottawa.place/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>slurm</span></a> submission scripts. </p><p>Blogpost in progress, spent the last few minutes of my week playing with gifs:</p><p><a href="https://ottawa.place/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a> <a href="https://ottawa.place/tags/hpc" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>hpc</span></a></p>
TOV<p>On 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.</p><p><a href="https://fosstodon.org/tags/Linux" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Linux</span></a> <a href="https://fosstodon.org/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>slurm</span></a> <a href="https://fosstodon.org/tags/network" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>network</span></a> <a href="https://fosstodon.org/tags/monitor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>monitor</span></a></p>
Christian Meesters<p>Does anyone have a working <a href="https://fediscience.org/tags/GitHub" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>GitHub</span></a> action to create a fake <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SLURM</span></a> cluster within a CI action?</p><p>(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"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/actions/runs/12235923998/job/34193736191?pr=159</span></a>)</p><p><a href="https://fediscience.org/tags/askfedi" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>askfedi</span></a> <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HPC</span></a></p>
Bruno<p>Slurm 24.11 is out!<br><a href="https://www.schedmd.com/slurm-version-24-11-0-is-now-available/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">schedmd.com/slurm-version-24-1</span><span class="invisible">1-0-is-now-available/</span></a></p><p><a href="https://mast.hpc.social/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>slurm</span></a> <a href="https://mast.hpc.social/tags/hpc" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>hpc</span></a></p>
Quinn<p>Welp…lines. So many lines. <a href="https://mast.hpc.social/tags/SC24" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SC24</span></a> <a href="https://mast.hpc.social/tags/Slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Slurm</span></a></p><p>Someone get the Slurm crew on solving this queue!!</p>
Aalto Scientific Computing<p>How busy is the <a href="https://fosstodon.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HPC</span></a> cluster? Maybe the real question is "how long do I have to wait?". Our new blog post goes into some of these questions we get asked sometimes, and the high-level picture probably applies other places too.<br><a href="https://aaltoscicomp.github.io/blog/2024/how-busy-is-the-cluster/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">aaltoscicomp.github.io/blog/20</span><span class="invisible">24/how-busy-is-the-cluster/</span></a> <br><a href="https://fosstodon.org/tags/SciComp" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SciComp</span></a> <a href="https://fosstodon.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HPC</span></a> <a href="https://fosstodon.org/tags/ComputationalScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ComputationalScience</span></a> <a href="https://fosstodon.org/tags/Slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Slurm</span></a></p>
Michael Sumner<p>and so, do I have any other <a href="https://rstats.me/tags/Pawsey" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Pawsey</span></a> or <a href="https://rstats.me/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>slurm</span></a> users in <a href="https://rstats.me/tags/RStats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>RStats</span></a> who've been through the wringer with <a href="https://rstats.me/tags/targets" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>targets</span></a>?? so far the crew.cluster issues tab, and the minimal tests is my friend</p><p>3/2</p>
Jean-Mi aux Miches Moches<p>Depends on core utils, and colout: <a href="https://github.com/nojhan/colout" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="">github.com/nojhan/colout</span><span class="invisible"></span></a><br /><a href="https://mamot.fr/tags/shell" class="mention hashtag" rel="tag">#<span>shell</span></a> <a href="https://mamot.fr/tags/bash" class="mention hashtag" rel="tag">#<span>bash</span></a> <a href="https://mamot.fr/tags/slurm" class="mention hashtag" rel="tag">#<span>slurm</span></a> <a href="https://mamot.fr/tags/HPC" class="mention hashtag" rel="tag">#<span>HPC</span></a></p>
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