JUSTUS2/Software/Singularity - Revision history

K Siegmund: /* NGC environment modules on JUSTUS 2 */

2025-11-28T16:09:27Z

NGC environment modules on JUSTUS 2

← Older revision		Revision as of 18:09, 28 November 2025
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	'''Note:''' Ready-to-use containers can be pulled from the [https://ngc.nvidia.com/catalog/containers NVIDIA GPU CLOUD (NGC)] catalog.		'''Note:''' Ready-to-use containers can be pulled from the [https://ngc.nvidia.com/catalog/containers NVIDIA GPU CLOUD (NGC)] catalog.

			<!-- veraltet, hat nur das eine alte lammps modul, erstmal unsichtbar
	== NGC environment modules on JUSTUS 2 ==		== NGC environment modules on JUSTUS 2 ==

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	Currently, <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">module load ngc/numlib</span> for numeric libraries and <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">module load ngc/chem</span> for chemistry programs can be selected.		Currently, <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">module load ngc/numlib</span> for numeric libraries and <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">module load ngc/chem</span> for chemistry programs can be selected.
			-->

	== Batch jobs with containers on JUSTUS 2 ==		== Batch jobs with containers on JUSTUS 2 ==

K Siegmund: /* Usage */

2024-04-23T09:49:44Z

Usage

← Older revision		Revision as of 11:49, 23 April 2024
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	== Availability ==		== Availability ==
	Singularity is directly available on all compute nodes (but not on the login nodes). You do not have to load a module.		Singularity is directly available on all compute nodes (but not on the login nodes). You do not have to load a module, but you must use a compute node i.e. via an [[BwForCluster_JUSTUS_2_Slurm_HOWTO#How_to_submit_an_interactive_job.3F\|interactive job]]

	The binary ''singularity'' is main program of the container platform.		The binary ''singularity'' is main program of the container platform.
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	For additional information about how to use Singularity, please consult the [https://sylabs.io/docs/ documentation].		For additional information about how to use Singularity, please consult the [https://sylabs.io/docs/ documentation].

	<font color=red>Important: On JUSTUS 2, Singularity is only available on compute nodes. You must switch to such a node to invoke any ''singularity'' commands.</font>

	== Batch jobs with containers ==		== Batch jobs with containers ==

K Siegmund at 09:47, 23 April 2024

2024-04-23T09:47:37Z

← Older revision		Revision as of 11:47, 23 April 2024
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	\|-		\|-
	! Description !! Content		! Description !! Content
	\|-
	\| module load
	\| system/singularity
	\|-		\|-
	\| License		\| License
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	== Availability ==		== Availability ==
	Singularity is directly available on all compute nodes (but not on the login nodes). You do not have to load a module.		Singularity is directly available on all compute nodes (but not on the login nodes). You do not have to load a module.

	== Program Binaries ==

	The binary ''singularity'' is main program of the container platform.		The binary ''singularity'' is main program of the container platform.
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	# File name for error output		# File name for error output
	#SBATCH --error=singularity_job-%j.err		#SBATCH --error=singularity_job-%j.err

	module load your/singularity/version #(not needed on JUSTUS 2, but could be necessary on other system)

	cd your/workspace		cd your/workspace
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	#SBATCH --gres=gpu:1		#SBATCH --gres=gpu:1
	[…]		[…]

	module load your/singularity/version #(not needed on JUSTUS 2, but could be necessary on other system)

	cd your/workspace		cd your/workspace
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	* [https://en.wikipedia.org/wiki/Singularity_(software) Wikipedia article (english)]		* [https://en.wikipedia.org/wiki/Singularity_(software) Wikipedia article (english)]
	----		----
	[[Category:Software]]

K Siegmund: /* Loading the module */

2024-04-23T09:44:49Z

Loading the module

@@ Line 28: / Line 28: @@
 = Usage =
-== Loading the module ==
+== Availability ==
 == Program Binaries ==

K Siegmund: K Siegmund moved page Singularity to JUSTUS2/Software/Singularity

2023-02-14T09:29:44Z

K Siegmund moved page Singularity to JUSTUS2/Software/Singularity

← Older revision	Revision as of 11:29, 14 February 2023
(No difference)

F Wagner: /* NGC environment modules on JUSTUS 2 */

2022-05-14T13:00:05Z

NGC environment modules on JUSTUS 2

← Older revision		Revision as of 15:00, 14 May 2022
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	$ mpirun -n 2 lmp -in in.lj.txt -var x 8 -var y 8 -var z 8 -k on g 2 -sf kk -pk kokkos cuda/aware on neigh full \		$ mpirun -n 2 lmp -in in.lj.txt -var x 8 -var y 8 -var z 8 -k on g 2 -sf kk -pk kokkos cuda/aware on neigh full \
	comm device binsize 2.8		comm device binsize 2.8
	$ module unload 29Oct2020		$ module unload 29Oct2020-lammps
	$ module unload ngc/chem		$ module unload ngc/chem
	</pre>		</pre>

F Wagner: /* Examples */

2022-05-14T12:59:40Z

Examples

← Older revision		Revision as of 14:59, 14 May 2022
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	$ module load ngc/chem		$ module load ngc/chem
	$ module avail		$ module avail
	$ module load 29Oct2020		$ module load 29Oct2020-lammps
	$ wget https://lammps.sandia.gov/inputs/in.lj.txt		$ wget https://lammps.sandia.gov/inputs/in.lj.txt
	$ export SINGULARITY_BINDPATH=$(pwd)		$ export SINGULARITY_BINDPATH=$(pwd)

F Wagner: /* NGC environment modules on JUSTUS 2 */

2022-05-13T09:49:04Z

NGC environment modules on JUSTUS 2

← Older revision		Revision as of 11:49, 13 May 2022
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	Currently, <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">module load ngc/.numlib</span> for numeric libraries and <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">module load ngc/.chem</span> for chemistry programs can be selected.		Currently, <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">module load ngc/numlib</span> for numeric libraries and <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">module load ngc/chem</span> for chemistry programs can be selected.

	== Batch jobs with containers on JUSTUS 2 ==		== Batch jobs with containers on JUSTUS 2 ==

F Wagner: /* NGC environment modules on JUSTUS 2 */

2022-05-13T09:48:31Z

NGC environment modules on JUSTUS 2

← Older revision		Revision as of 11:48, 13 May 2022
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	2) PyTorch container		2) PyTorch container
	<pre>		<pre>
	$ module load ngc/.numlib		$ module load ngc/numlib
	$ module load 20.12-torch-py3		$ module load 20.12-torch-py3
	$ python3		$ python3
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	>>> quit()		>>> quit()
	$ module unload 20.12-torch-py3		$ module unload 20.12-torch-py3
	$ module unload ngc/.numlib		$ module unload ngc/numlib
	</pre>		</pre>
	'''Note:''' Use the container in the same manner as an interactive shell.		'''Note:''' Use the container in the same manner as an interactive shell.
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	3) LAMMPS container		3) LAMMPS container
	<pre>		<pre>
	$ module load ngc/.chem		$ module load ngc/chem
	$ module avail		$ module avail
	$ module load 29Oct2020		$ module load 29Oct2020
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	comm device binsize 2.8		comm device binsize 2.8
	$ module unload 29Oct2020		$ module unload 29Oct2020
	$ module unload ngc/.chem		$ module unload ngc/chem
	</pre>		</pre>
	'''Note:''' Use <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">SINGULARITY_BINDPATH=<PATH></span> to mount the directory with the input file.		'''Note:''' Use <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">SINGULARITY_BINDPATH=<PATH></span> to mount the directory with the input file.

F Wagner: /* Batch jobs with containers on JUSTUS 2 */

2022-05-12T09:37:00Z

Batch jobs with containers on JUSTUS 2

← Older revision		Revision as of 11:37, 12 May 2022
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	Run a GROMACS container with Singularity as a batch job:		Run a GROMACS container with Singularity as a batch job:
	<pre>		<pre>
	$ salloc ~~--nodes=1~~ --ntasks=1 # obtain compute node		$ salloc --ntasks=1 # obtain compute node
	$ WORKSPACE=`ws_allocate gromacs 3` # allocate workspace		$ WORKSPACE=`ws_allocate gromacs 3` # allocate workspace
	$ cd $WORKSPACE # change to workspace		$ cd $WORKSPACE # change to workspace