http://giwiki.gi.ucsc.edu/index.php?action=history&feed=atom&title=Cluster_EtiquetteCluster Etiquette - Revision history2026-05-08T10:00:58ZRevision history for this page on the wikiMediaWiki 1.40.0http://giwiki.gi.ucsc.edu/index.php?title=Cluster_Etiquette&diff=514&oldid=prevWeiler at 17:28, 2 August 20242024-08-02T17:28:23Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>3: Don't use too much storage. Use http://logserv.gi.ucsc.edu/cgi-bin/private-groups.cgi to look at how your storage use is divided among your directories, and clean up large chunks of data that you do not need.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>3<ins style="font-weight: bold; text-decoration: none;">: Please do not pin cluster resources with interactive jobs and let them sit idle. Sometimes folks will open an interactive cluster job with a week long runtime and just let it sit in order to "hold" a spot in the queue for when they might eventually want to run something. This is a waste of resources, and it also forces other who have work ready to go to wait in the queue while nodes sit idle. If you use an interactive job via '''srun''' or '''salloc''', please start it immediately upon launch and close it immediately upon the job's completion.</ins></div></td></tr>
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<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">4</ins>: Don't use too much storage. Use http://logserv.gi.ucsc.edu/cgi-bin/private-groups.cgi to look at how your storage use is divided among your directories, and clean up large chunks of data that you do not need.</div></td></tr>
</table>Weilerhttp://giwiki.gi.ucsc.edu/index.php?title=Cluster_Etiquette&diff=483&oldid=prevWeiler at 03:25, 3 May 20242024-05-03T03:25:13Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:25, 2 May 2024</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>1: Always test your job by running one first. Just one. Note how much RAM, how many CPU cores and how much time it takes to run. Then, when you submit 50 or 100 of those, you can specify limits in your Slurm batch file on how long the job should run, how much RAM it should use and how much time it takes. In that case, slurm can stop jobs that inadvertently go too long or use too many resources.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>1: Always test your job by running one first. Just one. Note how much RAM, how many CPU cores and how much time it takes to run. Then, when you submit 50 or 100 of those, you can specify limits in your Slurm batch file on how long the job should run, how much RAM it should use and how much time it takes. In that case, slurm can stop jobs that inadvertently go too long or use too many resources.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>2: Don't run too many jobs at once if they use a lot of disk I/O. If every job reads in a 100GB file, and you launch 20 of them at the same time, you could bring down the <del style="font-weight: bold; text-decoration: none;">file server serving </del>/private/groups. Run only maybe 5 at once in that case, or introduce a random delay at the start of your jobs. You can limit your concurrent jobs by specifying something like this in your job batch file:</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>2: Don't run too many jobs at once if they use a lot of disk I/O. If every job reads in a 100GB file, and you launch 20 of them at the same time, you could bring down the /private/groups <ins style="font-weight: bold; text-decoration: none;">filesystem</ins>. Run only maybe 5 at once in that case, or introduce a random delay at the start of your jobs. You can limit your concurrent jobs by specifying something like this in your job batch file:</div></td></tr>
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</table>Weilerhttp://giwiki.gi.ucsc.edu/index.php?title=Cluster_Etiquette&diff=482&oldid=prevWeiler at 03:24, 3 May 20242024-05-03T03:24:15Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:24, 2 May 2024</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>When running jobs on the cluster, you must be very aware of how those jobs will affect other users.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>When running jobs on the cluster, you must be very aware of how those jobs will affect other users.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>1: Always test your job by running one first. Just one. Note how much RAM, how many CPU cores and how much time it takes to run. Then, when you submit 50 or 100 of those, you can specify limits in your Slurm batch file on how long the job should run, how much RAM it should use and how much time it takes. In that case, slurm can stop <del style="font-weight: bold; text-decoration: none;">jibs </del>that <del style="font-weight: bold; text-decoration: none;">inadvertantly </del>go too long or use too many resources.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>1: Always test your job by running one first. Just one. Note how much RAM, how many CPU cores and how much time it takes to run. Then, when you submit 50 or 100 of those, you can specify limits in your Slurm batch file on how long the job should run, how much RAM it should use and how much time it takes. In that case, slurm can stop <ins style="font-weight: bold; text-decoration: none;">jobs </ins>that <ins style="font-weight: bold; text-decoration: none;">inadvertently </ins>go too long or use too many resources.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>2: Don't run too many jobs at once if they use a lot of disk I/O. If every job reads in a 100GB file, and you launch 20 of them at the same time, you could bring down the file server serving /private/groups. Run only maybe 5 at once in that case, or introduce a random delay at the start of your jobs. You can limit your concurrent jobs by specifying something like this in your job batch file:</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>2: Don't run too many jobs at once if they use a lot of disk I/O. If every job reads in a 100GB file, and you launch 20 of them at the same time, you could bring down the file server serving /private/groups. Run only maybe 5 at once in that case, or introduce a random delay at the start of your jobs. You can limit your concurrent jobs by specifying something like this in your job batch file:</div></td></tr>
</table>Weilerhttp://giwiki.gi.ucsc.edu/index.php?title=Cluster_Etiquette&diff=471&oldid=prevAnovak: Link to the storage visualization2024-03-06T17:24:37Z<p>Link to the storage visualization</p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 10:24, 6 March 2024</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> some_command $input</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> some_command $input</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">3: Don't use too much storage. Use http://logserv.gi.ucsc.edu/cgi-bin/private-groups.cgi to look at how your storage use is divided among your directories, and clean up large chunks of data that you do not need.</ins></div></td></tr>
</table>Anovakhttp://giwiki.gi.ucsc.edu/index.php?title=Cluster_Etiquette&diff=431&oldid=prevWeiler at 21:54, 25 October 20232023-10-25T21:54:52Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 14:54, 25 October 2023</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>1: Always test your job by running one first. Just one. Note how much RAM, how many CPU cores and how much time it takes to run. Then, when you submit 50 or 100 of those, you can specify limits in your Slurm batch file on how long the job should run, how much RAM it should use and how much time it takes. In that case, slurm can stop jibs that inadvertantly go too long or use too many resources.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>1: Always test your job by running one first. Just one. Note how much RAM, how many CPU cores and how much time it takes to run. Then, when you submit 50 or 100 of those, you can specify limits in your Slurm batch file on how long the job should run, how much RAM it should use and how much time it takes. In that case, slurm can stop jibs that inadvertantly go too long or use too many resources.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>2: Don't run too many jobs at once if they use a lot of disk I/O. If every job reads in a 100GB file, and you launch 20 of them, you could bring down the file server serving /private/groups. Run only maybe 5 at once in that case. You can limit your concurrent jobs by specifying something like this in your job batch file:</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>2: Don't run too many jobs at once if they use a lot of disk I/O. If every job reads in a 100GB file, and you launch 20 of them <ins style="font-weight: bold; text-decoration: none;">at the same time</ins>, you could bring down the file server serving /private/groups. Run only maybe 5 at once in that case<ins style="font-weight: bold; text-decoration: none;">, or introduce a random delay at the start of your jobs</ins>. You can limit your concurrent jobs by specifying something like this in your job batch file:</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> #SBATCH --array=[1-279]%10</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> #SBATCH --array=[1-279]%10</div></td></tr>
</table>Weilerhttp://giwiki.gi.ucsc.edu/index.php?title=Cluster_Etiquette&diff=430&oldid=prevWeiler at 21:32, 25 October 20232023-10-25T21:32:39Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 14:32, 25 October 2023</td>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Begin!</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">When running jobs on the cluster, you must be very aware of how those jobs will affect other users.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">1: Always test your job by running one first. Just one. Note how much RAM, how many CPU cores and how much time it takes to run. Then, when you submit 50 or 100 of those, you can specify limits in your Slurm batch file on how long the job should run, how much RAM it should use and how much time it takes. In that case, slurm can stop jibs that inadvertantly go too long or use too many resources.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">2: Don't run too many jobs at once if they use a lot of disk I/O. If every job reads in a 100GB file, and you launch 20 of them, you could bring down the file server serving /private/groups. Run only maybe 5 at once in that case. You can limit your concurrent jobs by specifying something like this in your job batch file:</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> #SBATCH --array=[1-279]%10</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> inputList=$1</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> input=$(sed -n "$SLURM_ARRAY_TASK_ID"p $inputList)</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> some_command $input</ins></div></td></tr>
</table>Weilerhttp://giwiki.gi.ucsc.edu/index.php?title=Cluster_Etiquette&diff=428&oldid=prevWeiler: Created page with "Begin!"2023-10-23T23:42:12Z<p>Created page with "Begin!"</p>
<p><b>New page</b></p><div>Begin!</div>Weiler