Using modules on cyclone - Revision history

Ngfih: /* Using modules on cyclone */

2026-03-16T13:29:26Z

Using modules on cyclone

← Older revision		Revision as of 13:29, 16 March 2026
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	== Using modules on ~~cyclone~~==		== Using modules on cyclones==

	~~This page documents how to use Modulefiles on the Abel~~ (~~HPC~~ for ~~UiO~~) and ~~Colossus (HPC for TSD) clusters~~. Same procedure applies on cyclone. For some specific documentation on available modules refer to [[Using cyclone]].		With cyclones follows a collection of EESSI modules - ('''The European Environment for Scientific Software Installation)'''. Access to ESSI is automatic enabled at ssh login, the EESSI modules follow the same std. and documentation as given in Sigma2 documentation:

			https://documentation.sigma2.no/software/eessi.html

			Same procedure applies on cyclone. For some specific documentation on available modules refer to [[Using cyclone]].

	To simplify setting up environments for compilers, MPI-versions and some installed applications, the clusters have the [http://modules.sourceforge.net Environment Modules package] installed. This provides means for dynamic modification of a user's environment via modulefiles.		To simplify setting up environments for compilers, MPI-versions and some installed applications, the clusters have the [http://modules.sourceforge.net Environment Modules package] installed. This provides means for dynamic modification of a user's environment via modulefiles.
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	</code>		</code>

	~~(On Colossus, the module commands can only be used in job scripts.)~~ You can also ask for a specific version of a modulefile:		You can also ask for a specific version of a modulefile:

	<code>		<code>
Line 31:		Line 35:
	The available modulefiles can be listed by module avail. Example output:		The available modulefiles can be listed by module avail. Example output:

	~~<nowiki>~~
	$ module avail		$ module avail
	------------------------ ~~/usr/share/Modules/modulefiles~~ -------------------------		------------------------------------- /vol/vb_apps/modules/all ---------------
	~~dot module~~-~~cvs module~~-~~info modules~~ ~~null use~~.~~own~~		Anaconda3/2021.11 libpng/1.6.37-GCCcore-11.3.0
			Anaconda3/2022.10 libpng/1.6.43-GCCcore-13.3.0
	--------------------------- /~~cluster~~/~~etc/modulefiles --------------------~~--------		Anaconda3/2023.09-0 libtirpc/1.3.5-GCCcore-13.3.0 (D)
	~~454apps/2~~.~~8(default) mcmcphase/~~2.0(~~default~~)		Anaconda3/2024.06-1 libxml2/2.12.7-GCCcore-13.3.0 (D)
	R/2.15.~~1(default) microbiomeutil~~/~~20110519(default)~~		Anaconda3/2025.06-1 (D) Local-netCDF-Fortran-local/4.6.1-gompi-2023b
	R/2.15.1.~~shlib migrate~~/3.3.~~2(default)~~		ANTLR/2.7.7-GCCcore-10.3.0-Java-11 lz4/1.9.4-GCCcore-13.3.0 (D)
	~~abyss~~/1.3.4(~~default~~) ~~mothur~~/1.26.0(~~default~~)		ANTLR/2.7.7-GCCcore-12.3.0-Java-11 M4/1.4.19
	~~adf~~/~~2010~~.~~02b(default) mrbayes/~~3.2.~~1(default)~~		ANTLR/2.7.7-GCCcore-13.3.0 (D) make/4.4.1-GCCcore-12.2.0
	~~adf~~/~~2012~~.~~01b muscle~~/3.8~~.31~~(~~default~~)		Bison/3.7.6-GCCcore-10.3.0 makedepend/1.0.9-GCCcore-13.2.0 (D)
	~~ampliconnoise~~/1.~~25(default) ncl/2~~.1.18(~~default~~)		Bison/3.8.2-GCCcore-13.3.0 Mamba/4.14.0-0
	~~beagle~~/1.0~~(default) newbler~~/2.~~8(default)~~		boto3/1.26.163-GCCcore-12.2.0 Mamba/23.1.0-4
	[...]		boto3/1.28.70-GCCcore-12.3.0 (D) Mamba/23.11.0-0 (D)
	~~</nowiki>~~		CMake/3.24.3-GCCcore-12.2.0 MATLAB/2021b
			CMake/3.29.3-GCCcore-13.3.0 MATLAB/2023a
			CMake/3.31.8 (D) Meson/1.4.0-GCCcore-13.3.0 (D)
			cURL/7.78.0-GCCcore-11.2.0 Miniconda3/4.12.0

			[...]

	You can also specify a name:		You can also specify a name:

	~~<nowiki>~~
	$ module avail ~~blast~~		$ module avail Anaconda
	--------------------------- /~~cluster~~/~~etc~~/~~modulefiles ---~~-------------------------		------------------------------------- /vol/vb_apps/modules/all -------------------------
	~~blast~~/2.2.~~26(default) blast+~~/2.~~2.26~~(~~default~~)		Anaconda3/2021.11 Anaconda3/2023.09-0 Anaconda3/2025.06-1 (D)
	</~~nowiki>~~		Anaconda3/2022.10 Anaconda3/2024.06-1

	You will get a list of current loaded modulefiles by		You will get a list of current loaded modulefiles by

	~~<nowiki>~~
	$ module list		$module list
	Currently Loaded ~~Modulefiles~~:		Currently Loaded Modules:
	1) ~~intel~~/~~2011~~.10 2) R/~~2.15~~.1		1) EESSI/2023.06 2) Anaconda3/2024.06-1
	~~</nowiki>~~

	A help text exists for most of the modulefiles; to view it, type		help text exists for most of the modulefiles; to view it, type

	<code>		<code>
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	'''Personalize default modulefiles'''		'''Personalize default modulefiles'''

	You may add loading of modulefiles to your .bash_profile file to make sure your favorite modulefile is always loaded when logging in. For instance, to always have ~~the intel modulefile~~ load on login, add:		You may add loading of modulefiles to your .bash_profile file to make sure your favorite modulefile is always loaded when logging in. For instance, to always have Anaconda load on login, add:

	<code>		<code>
	module load ~~intel~~		module load Anaconda3/2024.06-1
	</code>		</code>

	to the .bash_profile file.		to the .bash_profile file.

Csp001 at 13:50, 29 September 2018

2018-09-29T13:50:45Z

← Older revision		Revision as of 13:50, 29 September 2018
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	== Using modules on cyclone==		== Using modules on cyclone==

	This page documents how to use Modulefiles on the Abel (HPC for UiO) and Colossus (HPC for TSD) clusters. Same procedure applies on cyclone.		This page documents how to use Modulefiles on the Abel (HPC for UiO) and Colossus (HPC for TSD) clusters. Same procedure applies on cyclone. For some specific documentation on available modules refer to [[Using cyclone]].

	To simplify setting up environments for compilers, MPI-versions and some installed applications, the clusters have the [http://modules.sourceforge.net Environment Modules package] installed. This provides means for dynamic modification of a user's environment via modulefiles.		To simplify setting up environments for compilers, MPI-versions and some installed applications, the clusters have the [http://modules.sourceforge.net Environment Modules package] installed. This provides means for dynamic modification of a user's environment via modulefiles.

Ngfih at 09:49, 19 September 2018

2018-09-19T09:49:31Z

← Older revision		Revision as of 09:49, 19 September 2018
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	For further documentation, please refer to the [http://modules.sourceforge.net Environment Modules homepage]		For further documentation, please refer to the [http://modules.sourceforge.net Environment Modules homepage]

	Personalize default modulefiles		'''Personalize default modulefiles'''

	You may add loading of modulefiles to your .bash_profile file to make sure your favorite modulefile is always loaded when logging in. For instance, to always have the intel modulefile load on login, add:		You may add loading of modulefiles to your .bash_profile file to make sure your favorite modulefile is always loaded when logging in. For instance, to always have the intel modulefile load on login, add:

Hso039 at 08:48, 18 September 2018

2018-09-18T08:48:03Z

← Older revision		Revision as of 08:48, 18 September 2018
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	Personalize default modulefiles		Personalize default modulefiles

	You may add loading of modulefiles to your .~~bash_login~~ file to make sure your favorite modulefile is always loaded when logging in. For instance, to always have the intel modulefile load on login, add:		You may add loading of modulefiles to your .bash_profile file to make sure your favorite modulefile is always loaded when logging in. For instance, to always have the intel modulefile load on login, add:

	<code>		<code>
Line 86:		Line 86:
	</code>		</code>

	to the .~~bash_login~~ file.		to the .bash_profile file.

Hso039 at 08:32, 18 September 2018

2018-09-18T08:32:33Z

← Older revision		Revision as of 08:32, 18 September 2018
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	The available modulefiles can be listed by module avail. Example output:		The available modulefiles can be listed by module avail. Example output:

	<nowiki>		<nowiki>
	$ module avail		$ module avail
	------------------------ /usr/share/Modules/modulefiles -------------------------		------------------------ /usr/share/Modules/modulefiles -------------------------
Line 50:		Line 50:
	You can also specify a name:		You can also specify a name:

	<nowiki>		<nowiki>
	$ module avail blast		$ module avail blast
	--------------------------- /cluster/etc/modulefiles ----------------------------		--------------------------- /cluster/etc/modulefiles ----------------------------
Line 58:		Line 58:
	You will get a list of current loaded modulefiles by		You will get a list of current loaded modulefiles by

	<nowiki>		<nowiki>
	$ module list		$ module list
	Currently Loaded Modulefiles:		Currently Loaded Modulefiles:

Hso039 at 08:31, 18 September 2018

2018-09-18T08:31:19Z

← Older revision		Revision as of 08:31, 18 September 2018
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	<code>		<code>
	module load modulefile		module load modulefile

	module unload modulefile		module unload modulefile
	</code>		</code>
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	The available modulefiles can be listed by module avail. Example output:		The available modulefiles can be listed by module avail. Example output:

	<~~code~~>		<nowiki>
	$ module avail		$ module avail
	------------------------ /usr/share/Modules/modulefiles -------------------------		------------------------ /usr/share/Modules/modulefiles -------------------------
Line 45:		Line 46:
	beagle/1.0(default) newbler/2.8(default)		beagle/1.0(default) newbler/2.8(default)
	[...]		[...]
	</~~code~~>		</nowiki>

	You can also specify a name:		You can also specify a name:

	<~~code~~>		<nowiki>
	$ module avail blast		$ module avail blast
	--------------------------- /cluster/etc/modulefiles ----------------------------		--------------------------- /cluster/etc/modulefiles ----------------------------
	blast/2.2.26(default) blast+/2.2.26(default)		blast/2.2.26(default) blast+/2.2.26(default)
	</~~code~~>		</nowiki>

	You will get a list of current loaded modulefiles by		You will get a list of current loaded modulefiles by

	<~~code~~>		<nowiki>
	$ module list		$ module list
	Currently Loaded Modulefiles:		Currently Loaded Modulefiles:
	1) intel/2011.10 2) R/2.15.1		1) intel/2011.10 2) R/2.15.1
	</~~code~~>		</nowiki>

	A help text exists for most of the modulefiles; to view it, type		A help text exists for most of the modulefiles; to view it, type

Hso039: Created page with "== Using modules on cyclone== This page documents how to use Modulefiles on the Abel (HPC for UiO) and Colossus (HPC for TSD) clusters. Same procedure applies on cyclone. To..."

2018-09-18T08:30:19Z

Created page with "== Using modules on cyclone== This page documents how to use Modulefiles on the Abel (HPC for UiO) and Colossus (HPC for TSD) clusters. Same procedure applies on cyclone. To..."

New page

== Using modules on cyclone==

This page documents how to use Modulefiles on the Abel (HPC for UiO) and Colossus (HPC for TSD) clusters. Same procedure applies on cyclone.

To simplify setting up environments for compilers, MPI-versions and some installed applications, the clusters have the [http://modules.sourceforge.net Environment Modules package] installed. This provides means for dynamic modification of a user's environment via modulefiles.

Each modulefile contains the information needed to configure the shell for an environment. Typically, a modulefile modifies environment variables like PATH, MANPATH, LD_LIBRARY_PATH, CPATH and PKG_CONFIG_PATH to give access to an application or library.

Modulefiles can be used from most shells, as well as Perl and Python. Modulefiles can be loaded/unloaded on the command line or within your scripts by typing:

<code>
module load modulefile
module unload modulefile
</code>

(On Colossus, the module commands can only be used in job scripts.) You can also ask for a specific version of a modulefile:

<code>
module load modulefile/version
</code>

For the purpose of reproducability, we encourage users to load specific versions of modulefiles. Also, we recommend using

<code>
module purge
</code>

prior to any module load commands in job scripts, to prevent inheriting environment variables set by module commands in the shell used when submitting the job.

The available modulefiles can be listed by module avail. Example output:

<code>
$ module avail
------------------------ /usr/share/Modules/modulefiles -------------------------
dot module-cvs module-info modules null use.own

--------------------------- /cluster/etc/modulefiles ----------------------------
454apps/2.8(default) mcmcphase/2.0(default)
R/2.15.1(default) microbiomeutil/20110519(default)
R/2.15.1.shlib migrate/3.3.2(default)
abyss/1.3.4(default) mothur/1.26.0(default)
adf/2010.02b(default) mrbayes/3.2.1(default)
adf/2012.01b muscle/3.8.31(default)
ampliconnoise/1.25(default) ncl/2.1.18(default)
beagle/1.0(default) newbler/2.8(default)
[...]
</code>

You can also specify a name:

<code>
$ module avail blast
--------------------------- /cluster/etc/modulefiles ----------------------------
blast/2.2.26(default) blast+/2.2.26(default)
</code>

You will get a list of current loaded modulefiles by

<code>
$ module list
Currently Loaded Modulefiles:
1) intel/2011.10 2) R/2.15.1
</code>

A help text exists for most of the modulefiles; to view it, type

<code>
module help modulefile
</code>

To view exactly what a modulefile is doing to your environment, type

<code>
module show modulefile
</code>

For further documentation, please refer to the [http://modules.sourceforge.net Environment Modules homepage]

Personalize default modulefiles

You may add loading of modulefiles to your .bash_login file to make sure your favorite modulefile is always loaded when logging in. For instance, to always have the intel modulefile load on login, add:

<code>
module load intel
</code>

to the .bash_login file.