SingularityContainers - Revision history

Admin at 13:07, 4 September 2025

2025-09-04T13:07:59Z

← Older revision		Revision as of 13:07, 4 September 2025
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	To make ~~SL6/~~SL7/CC8~~/EL9~~ flavours available for everyone while the cluster is using another version, we make use of containers~~. This also works for SL8 and EL9 on the new HTCondor CC7 Cluster, just replace SL7 with the version you want~~.		To make SL7/CC8 flavours available for everyone while the cluster is using another version, we make use of containers.

	<br>		<br>
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	export PATH=$PATH:/group/userscripts/		export PATH=$PATH:/group/userscripts/
	or just call the full path:		or just call the full path:
	/group/userscripts/~~sl6~~		/group/userscripts/sl7

	<br>		<br>
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	sl7 /user/$USER/MYSUPERSCRIPT.sh		sl7 /user/$USER/MYSUPERSCRIPT.sh

	To send it to the cluster, the job.sh file you now will send to ~~qsub~~ should contain:		To send it to the cluster, the job.sh file you now will send to using your .sub file to condor_submit should contain:
	/group/userscripts/sl7 /user/$USER/MYSUPERSCRIPT.sh		/group/userscripts/sl7 /user/$USER/MYSUPERSCRIPT.sh

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	<br>Or you can also create your own container, with for instance specific software versions, it is quite simple.		<br>Or you can also create your own container, with for instance specific software versions, it is quite simple.
	<br>You can use the guide [[SingularityContainerCreation\|here]], or google ''singularity container'' in your favorite search engine :)		<br>You can use the guide [[SingularityContainerCreation\|here]], or google ''singularity container'' in your favorite search engine :)


	~~=== To use EL9 inside a cluster job ===~~

	~~As Centos 7 is soon to be EOL (30/06/2024), we plan on changing the OS of the cluster to an EL9 flavor. Until then, you can use the following to get access to a containter in EL9:~~
	~~singularity exec -B /cvmfs -B /pnfs -B /user -B /scratch /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-el9:latest MYSCRIPT.sh~~

	=== If you need grid commands ===		=== If you need grid commands ===
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	For this reason, CMS also provides some containers. Unfortunately, not all software is inside (python in el9 is lacking atm). But the grid commands do work. For them, run the scrip:		For this reason, CMS also provides some containers. Unfortunately, not all software is inside (python in el9 is lacking atm). But the grid commands do work. For them, run the scrip:
	<pre>		<pre>
			/cvmfs/cms.cern.ch/common/cmssw-el7
			or
	/cvmfs/cms.cern.ch/common/cmssw-el8		/cvmfs/cms.cern.ch/common/cmssw-el8
	or
	~~/cvmfs/cms.cern.ch/common/cmssw-el9~~
	</pre>		</pre>
	Some more info on these containers can be found [http://cms-sw.github.io/singularity.html here]		Some more info on these containers can be found [http://cms-sw.github.io/singularity.html here]

Admin at 14:44, 5 November 2024

2024-11-05T14:44:07Z

← Older revision		Revision as of 14:44, 5 November 2024
Line 51:		Line 51:
	For this reason, CMS also provides some containers. Unfortunately, not all software is inside (python in el9 is lacking atm). But the grid commands do work. For them, run the scrip:		For this reason, CMS also provides some containers. Unfortunately, not all software is inside (python in el9 is lacking atm). But the grid commands do work. For them, run the scrip:
	<pre>		<pre>
	/cvmfs/cms.cern.ch/common/cmssw-~~el9~~		/cvmfs/cms.cern.ch/common/cmssw-el8
	or		or
	/cvmfs/cms.cern.ch/common/cmssw-el9		/cvmfs/cms.cern.ch/common/cmssw-el9
	</pre>		</pre>
	Some more info on these containers can be found [http://cms-sw.github.io/singularity.html here]		Some more info on these containers can be found [http://cms-sw.github.io/singularity.html here]

Admin at 14:43, 5 November 2024

2024-11-05T14:43:50Z

← Older revision		Revision as of 14:43, 5 November 2024
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	/cvmfs/cms.cern.ch/common/cmssw-el9		/cvmfs/cms.cern.ch/common/cmssw-el9
	</pre>		</pre>
			Some more info on these containers can be found [http://cms-sw.github.io/singularity.html here]

Admin at 14:41, 5 November 2024

2024-11-05T14:41:15Z

← Older revision		Revision as of 14:41, 5 November 2024
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	As Centos 7 is soon to be EOL (30/06/2024), we plan on changing the OS of the cluster to an EL9 flavor. Until then, you can use the following to get access to a containter in EL9:		As Centos 7 is soon to be EOL (30/06/2024), we plan on changing the OS of the cluster to an EL9 flavor. Until then, you can use the following to get access to a containter in EL9:
	singularity exec -B /cvmfs -B /pnfs -B /user -B /scratch /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-el9:latest MYSCRIPT.sh		singularity exec -B /cvmfs -B /pnfs -B /user -B /scratch /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-el9:latest MYSCRIPT.sh

			=== If you need grid commands ===
			The above containers work perfectly on our cluster. However, they have the drawback of not being updated often. Unfortunately, to be able to work in a grid environment, the CA (certificate authority) files need to be kept up-to-date.<br>
			For this reason, CMS also provides some containers. Unfortunately, not all software is inside (python in el9 is lacking atm). But the grid commands do work. For them, run the scrip:
			<pre>
			/cvmfs/cms.cern.ch/common/cmssw-el9
			or
			/cvmfs/cms.cern.ch/common/cmssw-el9
			</pre>

Admin at 08:35, 28 June 2024

2024-06-28T08:35:05Z

← Older revision		Revision as of 08:35, 28 June 2024
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	To make SL6/SL7/CC8 flavours available for everyone while the cluster is using another version, we make use of containers~~. This works for SL7 on the olc PBS cluster that is in SL6~~. This also works for ~~SL6 &~~ SL8 on the new HTCondor CC7 Cluster, just replace SL7 with the version you want.		To make SL6/SL7/CC8/EL9 flavours available for everyone while the cluster is using another version, we make use of containers. This also works for SL8 and EL9 on the new HTCondor CC7 Cluster, just replace SL7 with the version you want.

	<br>		<br>
Line 40:		Line 40:
	<br>Or you can also create your own container, with for instance specific software versions, it is quite simple.		<br>Or you can also create your own container, with for instance specific software versions, it is quite simple.
	<br>You can use the guide [[SingularityContainerCreation\|here]], or google ''singularity container'' in your favorite search engine :)		<br>You can use the guide [[SingularityContainerCreation\|here]], or google ''singularity container'' in your favorite search engine :)


			=== To use EL9 inside a cluster job ===

			As Centos 7 is soon to be EOL (30/06/2024), we plan on changing the OS of the cluster to an EL9 flavor. Until then, you can use the following to get access to a containter in EL9:
			singularity exec -B /cvmfs -B /pnfs -B /user -B /scratch /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-el9:latest MYSCRIPT.sh

Admin at 14:51, 3 June 2022

2022-06-03T14:51:53Z

← Older revision		Revision as of 14:51, 3 June 2022
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	To make SL6/SL7/CC8 flavours available for everyone while the cluster is using another version, we make use of containers. This works for SL7 on the olc PBS cluster that is in SL6. This also works for SL6 & SL8 on the new HTCondor CC7 Cluster, just replace SL7 with the version you want.		To make SL6/SL7/CC8 flavours available for everyone while the cluster is using another version, we make use of containers. This works for SL7 on the olc PBS cluster that is in SL6. This also works for SL6 & SL8 on the new HTCondor CC7 Cluster, just replace SL7 with the version you want.

			<br>
			=== Prerequisites ===
			Helper scripts are in '''/group/userscripts/''', so make sure either it is in your $PATH variable with:
			export PATH=$PATH:/group/userscripts/
			or just call the full path:
			/group/userscripts/sl6

	<br>		<br>

Admin at 10:05, 8 December 2021

2021-12-08T10:05:35Z

← Older revision		Revision as of 10:05, 8 December 2021
Line 1:		Line 1:
	To make SL7 available for everyone while the cluster is ~~still in SL6~~, we make use of containers. This also works for SL6 & SL8 on the new HTCondor CC7 Cluster, just replace SL7 with the version you want.		To make SL6/SL7/CC8 flavours available for everyone while the cluster is using another version, we make use of containers. This works for SL7 on the olc PBS cluster that is in SL6. This also works for SL6 & SL8 on the new HTCondor CC7 Cluster, just replace SL7 with the version you want.

	<br>		<br>

Admin at 10:11, 19 January 2021

2021-01-19T10:11:55Z

← Older revision		Revision as of 10:11, 19 January 2021
Line 1:		Line 1:
	To make SL7 available for everyone while the cluster is still in SL6, we make use of containers.		To make SL7 available for everyone while the cluster is still in SL6, we make use of containers. This also works for SL6 & SL8 on the new HTCondor CC7 Cluster, just replace SL7 with the version you want.

	<br>		<br>

Admin: /* To use SL7 inside a cluster job */

2020-09-02T07:39:40Z

To use SL7 inside a cluster job

← Older revision		Revision as of 07:39, 2 September 2020
Line 14:		Line 14:
	You can simply ask your script to be run inside the sl7 container:		You can simply ask your script to be run inside the sl7 container:
	sl7 /user/$USER/MYSUPERSCRIPT.sh		sl7 /user/$USER/MYSUPERSCRIPT.sh

			To send it to the cluster, the job.sh file you now will send to qsub should contain:
			/group/userscripts/sl7 /user/$USER/MYSUPERSCRIPT.sh

	Please note that you then need, in your script, to go to TMPDIR.		Please note that you then need, in your script, to go to TMPDIR.

OLIVIER DEVROEDE omdevroe@vub.ac.be: /* To use SL7 inside a cluster job */

2019-11-13T14:11:18Z

To use SL7 inside a cluster job

← Older revision		Revision as of 14:11, 13 November 2019
Line 12:		Line 12:
	<br>		<br>
	=== To use SL7 inside a cluster job ===		=== To use SL7 inside a cluster job ===
	You can simply ask your script to be ~~ran~~ inside the sl7 container:		You can simply ask your script to be run inside the sl7 container:
	sl7 /user/$USER/MYSUPERSCRIPT.sh		sl7 /user/$USER/MYSUPERSCRIPT.sh