Software Modules Lmod - Revision history

J Kucera at 12:38, 10 October 2024

2024-10-10T12:38:13Z

← Older revision		Revision as of 14:38, 10 October 2024
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	=== Why we use module system? Modules load scientific software ===		=== Why we use module system? Modules load scientific software ===
	The module system on JUSTUS 2 is managed by '''Lmod''' (https://lmod.readthedocs.io/en/latest/).		The module system on JUSTUS 2 is managed by '''[https://lmod.readthedocs.io/en/latest/ Lmod]''' (https://lmod.readthedocs.io/en/latest/).
	The module system incorporates majority of the computational software available - this includes among others compilers, mpi libraries, numerical libraries, computational		The module system incorporates majority of the computational software available - this includes among others compilers, mpi libraries, numerical libraries, computational
	chemistry packages, python specific libraries etc.. <br><br>'''The programs managed by the module system are by default not utilizable. It has to be "loaded" to become executable.'''		chemistry packages, python specific libraries etc.. <br><br>'''The programs managed by the module system are by default not utilizable. It has to be "loaded" to become executable.'''

K Siegmund at 08:07, 23 April 2024

2024-04-23T08:07:17Z

← Older revision		Revision as of 10:07, 23 April 2024
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	<br>		<br>
	----		----
	[[Category:bwForCluster_JUSTUS_2\|JUSTUS 2]]
	[[#top\|Back to top]]		[[#top\|Back to top]]

K Siegmund: /* Module dependencies (why there is no mpi module?) */

2023-06-20T08:47:50Z

Module dependencies (why there is no mpi module?)

← Older revision		Revision as of 10:47, 20 June 2023
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	Thus, an user who wants to load a specific mpi must chose (load) a particular compiler prior the mpi module load. Note, that the mpi modules also remains		Thus, an user who wants to load a specific mpi must chose (load) a particular compiler prior the mpi module load. Note, that the mpi modules also remains
	"invisible" for "module av <mpi_name>" command until a certain compiler is not loaded. This due to the module hierarchy of Lmod. More details about the hierarchy		"invisible" for "module av <mpi_name>" command until a certain compiler is not loaded. This due to the module hierarchy of Lmod. More details about the hierarchy
	is below in ~~https://wiki.bwhpc.de/e/~~Software_Modules_Lmod#Semi_hierarchical_layout_of_modules_on_JUSTUS_2.		is below in [[Software_Modules_Lmod#Semi_hierarchical_layout_of_modules_on_JUSTUS_2]]

K Siegmund: /* Use 'module help' command */

2023-06-20T08:47:18Z

Use 'module help' command

← Older revision		Revision as of 10:47, 20 June 2023
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	=== Use 'module help' command ===		=== Use 'module help' command ===
	see [[~~//wiki.bwhpc.de/e/~~Software_Modules_Lmod#Providing_a_specific_help_for_a_particular_module]]		see [[Software_Modules_Lmod#Providing_a_specific_help_for_a_particular_module]]

	=== Check content of $<SOFTWARE_NAME>_EXA_DIR folder ===		=== Check content of $<SOFTWARE_NAME>_EXA_DIR folder ===

J Kucera: /* Scientific Software management through the module system Lmod */

2021-12-11T12:07:16Z

Scientific Software management through the module system Lmod

← Older revision		Revision as of 14:07, 11 December 2021
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	</pre>		</pre>
	<pre>		<pre>
	1. ~~load~~ the module with gaussian software package of version 16, revision C.01		1. loads the module with gaussian software package of version 16, revision C.01
	2. ~~print~~ out the list of currently load modules		2. prints out the list of currently load modules
	3. ~~provide~~ the user help for the particular gaussian module		3. provides the user help for the particular gaussian module
	4. ~~copy~~ the template batch script which was specifically designed for submission of g16 jobs into SLURM workload manager on JUSTUS 2.		4. copies the template batch script which was specifically designed for submission of g16 jobs into SLURM workload manager on JUSTUS 2.
	</pre>		</pre>

J Kucera: /* Scientific Software management through the module system Lmod */

2021-12-11T12:06:36Z

Scientific Software management through the module system Lmod

← Older revision		Revision as of 14:06, 11 December 2021
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	= Scientific Software management through the module system Lmod =		= Scientific Software management through the module system Lmod =
	The following sections covers the basic module commands needed to find and load the ~~application~~ installed on the JUSTUS 2.<br>		The following sections covers the basic module commands needed to find and load the scientific applications installed on the JUSTUS 2.<br>

	JUSTUS 2 uses Linux operating system. The standard Linux packages are installed on the front end nodes (login and visualisation nodes).		JUSTUS 2 uses Linux operating system. The standard Linux packages are installed on the front end nodes (login and visualisation nodes).

J Kucera: /* Load only those modules that are needed for the current application */

2021-12-10T16:39:10Z

Load only those modules that are needed for the current application

← Older revision		Revision as of 18:39, 10 December 2021
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	Only load modules that are needed for the current script or workflow you are running, to reduce the chance of unexpected behavior caused by module conflicts.		Only load modules that are needed for the current script or workflow you are running, to reduce the chance of unexpected behavior caused by module conflicts.

	Typical error sometimes seen on the cluster is this:		'''Typical error''' sometimes seen on the cluster by loading of vasp module is this:
	<pre>		<pre>
	ml compiler/intel/19.1.2		ml compiler/intel/19.1.2
Line 339:		Line 339:
	ml chem/vasp/5.4.4.3.16052018		ml chem/vasp/5.4.4.3.16052018
	</pre>		</pre>
	for loading of vasp module.<br>

	The ~~right~~ way is indeed only:		'''The correct way''' is indeed only:
	<pre>		<pre>
	ml chem/vasp/5.4.4.3.16052018		ml chem/vasp/5.4.4.3.16052018

J Kucera: /* Load only those modules that are needed for the current application */

2021-12-10T16:37:30Z

Load only those modules that are needed for the current application

@@ Line 332: / Line 332: @@
 === Load only those modules that are needed for the current application ===
 Only load modules that are needed for the current script or workflow you are running, to reduce the chance of unexpected behavior caused by module conflicts.
 === Do not use module commands in .bashrc, .bash_profile etc. scripts ===

J Kucera: /* Why we use module system? Modules load scientific software */

2021-12-10T16:26:19Z

Why we use module system? Modules load scientific software

← Older revision		Revision as of 18:26, 10 December 2021
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	module load <module_name>		module load <module_name>
	</pre>		</pre>
	The activation is realized by dynamical modification of the user's shell environment. This simply includes adding new paths to bin directories with the specific software into the PATH environmental variable. Typically, Lmod modifies PATH and LD_LIBRARY_PATH as well as it sets new variables as, for example <SOFTWARE_NAME>_EXA_DIR containing path to directory with the examples for a specific software.		The activation is realized by '''dynamical modification of the user's shell environment'''. This simply includes '''adding new paths''' to bin directories with the specific software '''into the PATH environmental variable'''. Typically, Lmod modifies '''PATH''' and '''LD_LIBRARY_PATH''' as well as it '''sets new variables''' as, for example '''<SOFTWARE_NAME>_EXA_DIR''' containing path to directory with the examples for a specific software.
	<br><br>		<br><br>
	Example: compare the content of $PATH environmental variable before and after the load of the gaussian module:		Example: compare the content of $PATH environmental variable before and after the load of the gaussian module:

J Kucera: /* Why we use module system? Modules load scientific software */

2021-12-10T16:24:45Z

Why we use module system? Modules load scientific software

← Older revision		Revision as of 18:24, 10 December 2021
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	<br>		<br>

	Among the main functionalities of Lmod belongs '''module load''' to make variety of the software packages pre-installed on the cluster accessible. This is feasible by only a single command:		Among the main functionalities of Lmod belongs '''module load''' to make variety of the software packages pre-installed on the cluster accessible. '''This is feasible by only a single command''':
	<br>		<br>
	<pre>		<pre>