BwUniCluster3.0/Software Modules - Revision history

S Braun: /* EasyBuild modules */

2025-03-25T10:23:27Z

EasyBuild modules

← Older revision		Revision as of 12:23, 25 March 2025
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	allow-modules-tool-mismatch=True		allow-modules-tool-mismatch=True
	</pre>		</pre>
	* add system-wide ~~easybuild~~ module path		* add system-wide EasyBuild module path

	<pre class="example">source /opt/bwhpc/common/etc/easybuild/enable_eb_modules		<pre class="example">source /opt/bwhpc/common/etc/easybuild/enable_eb_modules

S Braun: /* Build individual EasyBuild packages as a user */

2025-03-25T10:20:57Z

Build individual EasyBuild packages as a user

← Older revision		Revision as of 12:20, 25 March 2025
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	module use ~/eb/modules/all		module use ~/eb/modules/all
	</pre>		</pre>
	* find or create ~~easybuild~~ file, you can use any of the ~~easybild~~		* find or create EasyBuild file, you can use any of the EasyBuild

	<pre class="example">ls ~/eb/easybuild-easyconfigs/easybuild/easyconfigs// \| grep eb$		<pre class="example">ls ~/eb/easybuild-easyconfigs/easybuild/easyconfigs// \| grep eb$

S Braun: /* EasyBuild modules */

2025-03-25T10:19:45Z

EasyBuild modules

← Older revision		Revision as of 12:19, 25 March 2025
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	= EasyBuild modules =		= EasyBuild modules =

	With bwUniCluster 3.0 we start an official beta-test to provide toolchains and scientific software built with [https://docs.easybuild.io/ EasyBuild]. EasyBuild is a well established and consistent way to provide scientific software at many HPC sites all over the world. Since the naming of ~~Easybuild~~ modules is consistent users can use modules with the same name at different sites. To make this possible, Easybuild software minimizes the resources used by the local operating system and provides most software independently. This makes scientific results more reproducible.		With bwUniCluster 3.0 we start an official beta-test to provide toolchains and scientific software built with [https://docs.easybuild.io/ EasyBuild]. EasyBuild is a well established and consistent way to provide scientific software at many HPC sites all over the world. Since the naming of EasyBuild modules is consistent users can use modules with the same name at different sites. To make this possible, Easybuild software minimizes the resources used by the local operating system and provides most software independently. This makes scientific results more reproducible.

	<span id="using-easybuild-modules"></span>		<span id="using-easybuild-modules"></span>
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	== EasyBuild conventions ==		== EasyBuild conventions ==

	In theory one could build every software against every library and every compiler. This would lead to an unmaintainable amount of combinations. For this reason the EasyBuild team has decided to provide two so called toolchains a year for the most common compiler suits. Each toolchain defines one version of compiler, MPI library, math libraries and other packages as default for all software ~~build~~ aginst this toolchain. On bwUniCluster 3.0 we start with 3 ~~foss~~, 3 ~~intel~~ and one ~~nvhpc~~ toolchains. For a complete list of EasyBuild toolchains, please see [https://docs.easybuild.io/version-specific/toolchains/ the EasyBuild website]. Currently the 2023a, 2023b, and 2024a toolchains are available, with 2024a being the default one. Some software may not be available for the latest toolchain yet, but may be available for an older toolchain.		In theory one could build every software against every library and every compiler. This would lead to an unmaintainable amount of combinations. For this reason the EasyBuild team has decided to provide two so called toolchains a year for the most common compiler suits. Each toolchain defines one version of compiler, MPI library, math libraries and other packages as default for all software built aginst this toolchain. On bwUniCluster 3.0 we start with 3 FOSS, 3 Intel and one NVHPC toolchains. For a complete list of EasyBuild toolchains, please see [https://docs.easybuild.io/version-specific/toolchains/ the EasyBuild website]. Currently the 2023a, 2023b, and 2024a toolchains are available, with 2024a being the default one. Some software may not be available for the latest toolchain yet, but may be available for an older toolchain.

	EasyBuild currently supports almost 4000 software packages. We can and will only provide a subset, of course. As a start, we provide current versions of popular software packages ~~form~~ bwUniCluster 2.0. Updating and extending EasyBuild packages is a community effort, which should make providing new software easier. We try to provide additional packages if users request the installation. If we can't provide the software you can still use the advantages of EasyBuild by using it to build your private version.		EasyBuild currently supports almost 4000 software packages. We can and will only provide a subset, of course. As a start, we provide current versions of popular software packages from bwUniCluster 2.0. Updating and extending EasyBuild packages is a community effort, which should make providing new software easier. We try to provide additional packages if users request the installation. If we can't provide the software you can still use the advantages of EasyBuild by using it to build your private version.

	<span id="build-individual-easybuild-packages-as-a-user"></span>		<span id="build-individual-easybuild-packages-as-a-user"></span>
	== Build individual EasyBuild packages as a user ==		== Build individual EasyBuild packages as a user ==

	EasyBuild can also be used to compile your own or niche software, based on the available EasyBuild files by creating an independent EasyBuild software and module tree. The bwUnicluster 3.0 EasyBuild tree can be used as a base to build additional software in your ~~home~~ directory.		EasyBuild can also be used to compile your own or niche software, based on the available EasyBuild files by creating an independent EasyBuild software and module tree. The bwUnicluster 3.0 EasyBuild tree can be used as a base to build additional software in your HOME directory.

	We assume the following		We assume the following

	* the sofware will be installed in your ~~home~~ directory in the sub-directory eb		* the sofware will be installed in your HOME directory in the sub-directory <code>eb</code>
	* you have already cloned the git repository from https://github.com/easybuilders/easybuild-easyconfigs to ~/eb/easybuild-easyconfigs		* you have already cloned the git repository from https://github.com/easybuilders/easybuild-easyconfigs to <code>~/eb/easybuild-easyconfigs</code>
	* create an ~~easybuild~~ configuration file in your home at ~/.config/easybuild/config.cfg		* create an EasyBuild configuration file in your home at <code>~/.config/easybuild/config.cfg</code>

	<pre class="example">[basic]		<pre class="example">[basic]

S Braun: /* Using EasyBuild modules */

2025-03-25T10:12:14Z

Using EasyBuild modules

← Older revision		Revision as of 12:12, 25 March 2025
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	== Using EasyBuild modules ==		== Using EasyBuild modules ==

	Users interested in using ~~easyBuild~~ modules need to add the ~~Easybuild~~ module paths to their module environment. This can be done using:		Users interested in using EasyBuild modules need to add the EasyBuild module paths to their module environment. This can be done using:

	<pre class="example">source /opt/bwhpc/common/etc/easybuild/enable_eb_modules		<pre class="example">source /opt/bwhpc/common/etc/easybuild/enable_eb_modules
	</pre>		</pre>
	Now users have acces to a ~~comlete~~ ~~Easybuild~~ module tree, providing compiler toolchains, libraries, and scientific software. The same module commands described above can be used for EasyBuild modules. They can be loaded and unloaded in the same way. Please try not to mix ~~Easybuild~~ modules with the standard modules. There may be unintended consequences. It's always a good idea to [[#purge\|purge]] all modules before loading new ones. If you want to use ~~easybuild~~ modules in your ~~jobscripts~~, please make sure to enable them in your ~~jobscript~~ as well.		Now users have acces to a complete EasyBuild module tree, providing compiler toolchains, libraries, and scientific software. The same module commands described above (Lmod) can be used for EasyBuild modules. They can be loaded and unloaded in the same way. Please try not to mix EasyBuild modules with the standard modules. There may be unintended consequences. It's always a good idea to [[#purge\|purge]] all modules before loading new ones. If you want to use EasyBuild modules in your job scripts, please make sure to enable them in your job script as well.

	To hide the EasyBuild modules again, run:		To hide the EasyBuild modules again, run:
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	<span id="easybuild-conventions"></span>		<span id="easybuild-conventions"></span>

	== EasyBuild conventions ==		== EasyBuild conventions ==

S Braun: /* EasyBuild modules */

2025-03-25T10:09:13Z

EasyBuild modules

← Older revision		Revision as of 12:09, 25 March 2025
Line 360:		Line 360:
	== Using EasyBuild modules ==		== Using EasyBuild modules ==

	Users interested in using easyBuild modules need to add the Easybuild module paths to their module environment. This can be done using		Users interested in using easyBuild modules need to add the Easybuild module paths to their module environment. This can be done using:

	<pre class="example">source /opt/bwhpc/common/etc/easybuild/enable_eb_modules		<pre class="example">source /opt/bwhpc/common/etc/easybuild/enable_eb_modules
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	<pre class="example">source /opt/bwhpc/common/etc/easybuild/disable_eb_modules		<pre class="example">source /opt/bwhpc/common/etc/easybuild/disable_eb_modules
	</pre>		</pre>
	or start again with a clean shell		or start again with a clean shell.

	<span id="easybuild-conventions"></span>		<span id="easybuild-conventions"></span>

P Schuhmacher: /* EasyBuild modules */

2025-02-21T14:27:25Z

EasyBuild modules

← Older revision		Revision as of 16:27, 21 February 2025
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	</pre>		</pre>
	<span id="EasyBuild"></span>		<span id="EasyBuild"></span>
	= ~~<code>~~EasyBuild modules~~</code>~~ =		= EasyBuild modules =

	With bwUniCluster 3.0 we start an official beta-test to provide toolchains and scientific software built with [https://docs.easybuild.io/ EasyBuild]. EasyBuild is a well established and consistent way to provide scientific software at many HPC sites all over the world. Since the naming of Easybuild modules is consistent users can use modules with the same name at different sites. To make this possible, Easybuild software minimizes the resources used by the local operating system and provides most software independently. This makes scientific results more reproducible.		With bwUniCluster 3.0 we start an official beta-test to provide toolchains and scientific software built with [https://docs.easybuild.io/ EasyBuild]. EasyBuild is a well established and consistent way to provide scientific software at many HPC sites all over the world. Since the naming of Easybuild modules is consistent users can use modules with the same name at different sites. To make this possible, Easybuild software minimizes the resources used by the local operating system and provides most software independently. This makes scientific results more reproducible.
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	</pre>		</pre>
	<span id="how_do_modules_work"></span>		<span id="how_do_modules_work"></span>

	= How do Modules work? =		= How do Modules work? =

P Schuhmacher at 14:27, 21 February 2025

2025-02-21T14:27:10Z

← Older revision		Revision as of 16:27, 21 February 2025
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	'''Software (Environment) Modules''', or short '''modules''' are the means by which most of the installed scientific software is provided on ''bwUniCluster 3.0''.		'''Software (Environment) Modules''', or short '''modules''' are the means by which most of the installed scientific software is provided on ''bwUniCluster 3.0''.

	~~The use of different~~ compilers, libraries and software packages requires users to set up a specific session environment suited for the program they want to run. ''bwUniCluster 3.0'' provides users with the possibility to load and unload complete environments for compilers, libraries and software packages using a single command.		Different compilers, libraries and software packages requires users to set up a specific session environment suited for the program they want to run. ''bwUniCluster 3.0'' provides users with the possibility to load and unload complete environments for compilers, libraries and software packages using a single command.

	<span id="basics"></span>		<span id="basics"></span>
	= Basics =		= Basics =

	The Environment ''modules'' package enables dynamic modification of ~~your~~ ~~environment~~. Typically, a modulefile contains instructions that alter or set shell environment variables, such as PATH and MANPATH, to enable access to various installed software.		The Environment ''modules'' package enables dynamic modification of shell environments. Typically, a modulefile contains instructions that alter or set shell environment variables, such as PATH and MANPATH, to enable access to various installed software.

	One of the key features of ~~using~~ Environment ''Modules'' is to ~~allow~~ multiple versions of the same software ~~to be used in your environment~~ in a controlled manner. For example, two different versions of the Intel C compiler can be installed on the system at the same time - the version used is based upon which Intel C compiler modulefile is loaded.		One of the key features of Environment ''Modules'' is the ability to have multiple versions of the same software available in a controlled manner. For example, two different versions of the Intel C compiler can be installed on the system at the same time - the version used is based upon which Intel C compiler modulefile is loaded.

	The software stack of bwUniCluster 3.0 provides a number of modules. Users can also ~~create~~ their own ~~''modules''~~. ''Modules'' may ~~even~~ be shared by users on a system, and users may have their own collection of ''modules'' to supplement or replace the global ''modules''.		The software stack of bwUniCluster 3.0 provides a number of modules. Users can also provide modules for their own software. ''Modules'' may be shared between users on a system, and users may have their own collection of ''modules'' to supplement or replace the global ''modules''.

	To see which modules are currently loaded/enabled one must execute		To see which modules are currently loaded/enabled one must execute
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	= Usage =		= Usage =

	bwUniCluster 3.0 has been set up to use the ''Lmod'' module system. ''Lmod'' is a modern replacement of the older environment modules. The complete ''Lmod'' documentation can be found [[<nowiki/>http://lmod.readthedocs.org/en/latest/][here]].		bwUniCluster 3.0 has been set up to use the ''Lmod'' module system. ''Lmod'' is a modern replacement of the older tcl-based environment modules. The complete ''Lmod'' documentation can be found [[<nowiki/>http://lmod.readthedocs.org/en/latest/][here]].

	<span id="documentation"></span>		<span id="documentation"></span>
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	-h -? -H --help This help message		-h -? -H --help This help message
	...		...
	a lot of ~~output~~		a lot of help
	...		...
	Lmod Web Sites		Lmod Web Sites
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	== Display all available Modules ==		== Display all available Modules ==

	bwUniCluster3.0 comes with a variety of modules pre-installed. Some of these modules may not be available for all users, due to licensing restrictions. You can display all available ''modules'' by running:		bwUniCluster3.0 comes with a variety of modules pre-installed. Some of these modules may not be available for all users of all institutions, due to licensing restrictions. You can display all available ''modules'' by running:

	<pre class="example">$ module avail		<pre class="example">$ module avail
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	== Finding software Modules ==		== Finding software Modules ==

	Currently all bwUniCluster 3.0 software packages are assigned to the following ''Module'' categories ~~(???)~~:		Currently all bwUniCluster 3.0 software packages are assigned to the following ''Module'' categories:

	* bio		* bio
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	</pre>		</pre>
	<span id="EasyBuild"></span>		<span id="EasyBuild"></span>
	= EasyBuild modules =		= <code>EasyBuild modules</code> =

	With bwUniCluster 3.0 we start an official beta-test to provide toolchains and scientific software built with [https://docs.easybuild.io/ EasyBuild]. EasyBuild is a well established and consistent way to provide scientific software at many HPC sites all over the world. Since the naming of Easybuild modules is consistent users can use modules with the same name at different sites. To make this possible, Easybuild software minimizes the resources used by the local operating system and provides most software independently. This makes scientific results more reproducible.		With bwUniCluster 3.0 we start an official beta-test to provide toolchains and scientific software built with [https://docs.easybuild.io/ EasyBuild]. EasyBuild is a well established and consistent way to provide scientific software at many HPC sites all over the world. Since the naming of Easybuild modules is consistent users can use modules with the same name at different sites. To make this possible, Easybuild software minimizes the resources used by the local operating system and provides most software independently. This makes scientific results more reproducible.
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	* the sofware will be installed in your home directory in the sub-directory eb		* the sofware will be installed in your home directory in the sub-directory eb
	* you have already cloned the git repository from https://github.com/easybuilders/easybuild-easyconfigs to ~/eb/easybuild-easyconfigs		* you have already cloned the git repository from https://github.com/easybuilders/easybuild-easyconfigs to ~/eb/easybuild-easyconfigs
	* create an easybuild configuration file		* create an easybuild configuration file in your home at ~/.config/easybuild/config.cfg

	<pre class="example">[basic]		<pre class="example">[basic]
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	</pre>		</pre>
	<span id="how_do_modules_work"></span>		<span id="how_do_modules_work"></span>

	= How do Modules work? =		= How do Modules work? =

P Schuhmacher: /* EasyBuild modules */

2025-02-20T14:34:13Z

EasyBuild modules

← Older revision		Revision as of 16:34, 20 February 2025
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	</pre>		</pre>
	<span id="EasyBuild"></span>		<span id="EasyBuild"></span>
	= ~~<code>~~EasyBuild modules~~</code>~~ =		= EasyBuild modules =

	With bwUniCluster 3.0 we start an official beta-test to provide toolchains and scientific software built with [https://docs.easybuild.io/ EasyBuild]. EasyBuild is a well established and consistent way to provide scientific software at many HPC sites all over the world. Since the naming of Easybuild modules is consistent users can use modules with the same name at different sites. To make this possible, Easybuild software minimizes the resources used by the local operating system and provides most software independently. This makes scientific results more reproducible.		With bwUniCluster 3.0 we start an official beta-test to provide toolchains and scientific software built with [https://docs.easybuild.io/ EasyBuild]. EasyBuild is a well established and consistent way to provide scientific software at many HPC sites all over the world. Since the naming of Easybuild modules is consistent users can use modules with the same name at different sites. To make this possible, Easybuild software minimizes the resources used by the local operating system and provides most software independently. This makes scientific results more reproducible.
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	</pre>		</pre>
	<span id="how_do_modules_work"></span>		<span id="how_do_modules_work"></span>

	= How do Modules work? =		= How do Modules work? =

P Schuhmacher at 14:32, 20 February 2025

2025-02-20T14:32:51Z

Show changes

S Braun: Created page with "

= Introduction = '''Software (Environment) Modules''', or short '''Modules''' are the means by which most of the installed scientific software is provided on bwUniCluster 3.0.
The use of different compilers, libraries and software packages requires users to set up a specific session environment suited for the program they want to run. bwUniCluster 3.0 provides users with the possibility to load and unload complete environments for compiler..."

2025-01-31T15:36:31Z

Created page with "<div id="top"></div> = Introduction = '''Software (Environment) Modules''', or short '''Modules''' are the means by which most of the installed scientific software is provided on bwUniCluster 3.0. The use of different compilers, libraries and software packages requires users to set up a specific session environment suited for the program they want to run. bwUniCluster 3.0 provides users with the possibility to load and unload complete environments for compiler..."

New page

<div id="top"></div>
 
= Introduction =
'''Software (Environment) Modules''', or short '''Modules''' are the means by which most of the installed scientific software is provided on bwUniCluster 3.0.
 
The use of different compilers, libraries and software packages requires users to set up a specific session environment suited for the program they want to run. bwUniCluster 3.0 provides users with the possibility to load and unload complete environments for compilers, libraries and software packages by a single command.
 
 

= Description =
The Environment ''Modules'' package enables dynamic modification of your environment by the
use of so-called ''modulefiles''. A ''modulefile'' contains information to configure the shell
for a program/software . Typically, a modulefile contains instructions that alter or set shell
environment variables, such as PATH and MANPATH, to enable access to various installed
software.
 
One of the key features of using the Environment ''Modules'' software is to allow multiple versions of the same software to be used in your environment in a controlled manner.
For example, two different versions of the Intel C compiler can be installed on the system at the same time - the version used is based upon which Intel C compiler modulefile is loaded.
 
The software stack of bwUniCluster 3.0 provides a number of modulefiles. You can also
create your own modulefiles. ''Modulefiles'' may be shared by many users on a system, and
users may have their own collection of modulefiles to supplement or replace the shared
modulefiles.
 
A modulefile does not provide configuration of your environment until it is explicitly loaded,
i.e., the specific modulefile for a software product or application must be loaded in your environment before the configuration information in the modulefile is effective.
 
If you want to see which modules are loaded you must execute
''''module list''''.
 
<pre>
$ module list
Currently Loaded Modules:
1) compiler/intel/19.1 2) mpi/impi/2019 3) numlib/mkl/2019
</pre>
 

= Usage =
Lmod on bwUniCluster 3.0: A New Environment Module System from http://lmod.readthedocs.org/en/latest/ is installed.
== Documentation ==
Execute ''''module help'''' or ''''man module'''' for help on how to use ''Modules'' software.
<pre>
$ module help
Usage: module [options] sub-command [args ...]

Options:
-h -? -H --help This help message
-s availStyle --style=availStyle Site controlled avail style: system (default: system)
--regression_testing Lmod regression testing
-D Program tracing written to stderr
--debug=dbglvl Program tracing written to stderr (where dbglvl is a number 1,2,3)
--pin_versions=pinVersions When doing a restore use specified version, do not follow defaults
-d --default List default modules only when used with avail
-q --quiet Do not print out warnings
--expert Expert mode
-t --terse Write out in machine readable format for commands: list, avail, spider, savelist
--initial_load loading Lmod for first time in a user shell
--latest Load latest (ignore default)
--ignore_cache Treat the cache file(s) as out-of-date
--novice Turn off expert and quiet flag
--raw Print modulefile in raw output when used with show
-w twidth --width=twidth Use this as max term width
-v --version Print version info and quit
-r --regexp use regular expression match
--gitversion Dump git version in a machine readable way and quit
--dumpversion Dump version in a machine readable way and quit
--check_syntax --checkSyntax Checking module command syntax: do not load
--config Report Lmod Configuration
--config_json Report Lmod Configuration in json format
--mt Report Module Table State
--timer report run times
--force force removal of a sticky module or save an empty collection
--redirect Send the output of list, avail, spider to stdout (not stderr)
--no_redirect Force output of list, avail and spider to stderr
--show_hidden Avail and spider will report hidden modules
--spider_timeout=timeout a timeout for spider
-T --trace

module [options] sub-command [args ...]

Help sub-commands:
------------------
help prints this message
help module [...] print help message from module(s)

Loading/Unloading sub-commands:
-------------------------------
load | add module [...] load module(s)
try-load | try-add module [...] Add module(s), do not complain if not found
del | unload module [...] Remove module(s), do not complain if not found
swap | sw | switch m1 m2 unload m1 and load m2
purge unload all modules
refresh reload aliases from current list of modules.
update reload all currently loaded modules.

Listing / Searching sub-commands:
---------------------------------
list List loaded modules
list s1 s2 ... List loaded modules that match the pattern
avail | av List available modules
avail | av string List available modules that contain "string".
spider List all possible modules
spider module List all possible version of that module file
spider string List all module that contain the "string".
spider name/version Detailed information about that version of the module.
whatis module Print whatis information about module
keyword | key string Search all name and whatis that contain "string".

Searching with Lmod:
--------------------
All searching (spider, list, avail, keyword) support regular expressions:

-r spider '^p' Finds all the modules that start with `p' or `P'
-r spider mpi Finds all modules that have "mpi" in their name.
-r spider 'mpi$ Finds all modules that end with "mpi" in their name.

Handling a collection of modules:
--------------------------------
save | s Save the current list of modules to a user defined "default" collection.
save | s name Save the current list of modules to "name" collection.
reset The same as "restore system"
restore | r Restore modules from the user's "default" or system default.
restore | r name Restore modules from "name" collection.
restore system Restore module state to system defaults.
savelist List of saved collections.
describe | mcc name Describe the contents of a module collection.
disable name Disable (i.e. remove) a collection.

Deprecated commands:
--------------------
getdefault [name] load name collection of modules or user's "default" if no name given.
===> Use "restore" instead <====
setdefault [name] Save current list of modules to name if given, otherwise save as the default list for you the user.
===> Use "save" instead. <====

Miscellaneous sub-commands:
---------------------------
is-loaded modulefile return a true status if module is loaded
is-avail modulefile return a true status if module can be loaded
show modulefile show the commands in the module file.
use [-a] path Prepend or Append path to MODULEPATH.
unuse path remove path from MODULEPATH.
tablelist output list of active modules as a lua table.

Important Environment Variables:
--------------------------------
LMOD_COLORIZE If defined to be "YES" then Lmod prints properties and warning in color.

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Lmod Web Sites

Documentation: http://lmod.readthedocs.org
Github: https://github.com/TACC/Lmod
Sourceforge: https://lmod.sf.net
TACC Homepage: https://www.tacc.utexas.edu/research-development/tacc-projects/lmod

To report a bug please read http://lmod.readthedocs.io/en/latest/075_bug_reporting.html
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Modules based on Lua: Version 8.2 (8.2-1-g9c98036c) 2019-10-30 11:17 -05:00
by Robert McLay mclay@tacc.utexas.edu

</pre>
For help on particular version of ''Module'', e.g. Intel default compiler version, execute
''''module help compiler/intel''''.
<pre>
$ module help compiler/intel
---------------------- Module Specific Help for "compiler/intel/19.1" ----------------------
Intel(R) Compilers 19.1 for Linux*
For details see: https://software.intel.com/en-us/intel-compilers
In case of problems, please contact: Hartmut Häfner <hartmut.haefner@kit.edu>
SCC support end: 2022-12-31
</pre>
 
=== Online Documentation ===
[http://lmod.readthedocs.org Lmod: A New Environment Module System]
 
 

== Display all available Modules ==
Available ''Module'' are modulefiles that can be loaded by the user. A ''Module'' must be loaded before it provides changes to your environment, as described in the introduction to this section. You can display all available ''Modules'' on the system by executing:
<pre>
$ module avail
</pre>
The short form the command is:
<pre>
$ module av
</pre>
Available ''Modules'' can be also displayed in different modes, such as
* each ''Module'' per one line
<pre>
$ module -t avail
</pre>
Some modules may not be available right now, because their requirements are not met. To get a complete list of all possible modules use the [[#Display all possible Modules|module spider command]].
 
 

== Module categories, versions and defaults ==
The bwHPC clusters traditionally provide a large variety of software and software versions. Therefore ''Module'' are divided in category folders containing subfolders of modulefiles again containing modulefile versions, and must be addressed as follows:
category/softwarename/version
For instance all versions of the Intel compiler belong to the category of compilers, thus the corresponding modulefiles are placed under the category ''compiler'' and ''intel''.
 
In case of multiple software versions, one version will be always defined as the '''default'''
version. The ''Module'' of the default can be addressed by simply omitting the version number:
category/softwarename
 

== Finding software Modules ==
Currently all bwUniCluster 3.0 software packages are assigned to the following ''Module'' categories (???):


* bio

* cae

* chem

* compiler

* devel

* lib

* math
* mpi

* numlib

* phys

* system

* toolkit

* vis
You can selectively list software in one of those categories using, e.g. for the category "compiler"
<pre>
$ module avail compiler/
</pre>
Searches are looking for a substring starting at the begin of the name, so this would list all software in categories starting with a "c"
<pre>
$ module avail c
</pre>
while this would find nothing
<pre>
$ module avail hem
</pre>
 

== Loading Modules ==
You can load a ''Module'' software in to your environment to enable easier access to software that
you want to use by executing:
<pre>
$ module load category/softwarename/version
</pre>
or
<pre>
$ module add category/softwarename/version
</pre>
Loading a ''Module'' in this manner affects ONLY your environment for the current session.
 
 
=== Loading conflicts ===
You can not load different versions of the same software at the same time! Loading the Intel compiler in version X while Intel compiler in version Y is loaded leads to an automatic unloading of Intel compiler in version Y.
 
 

=== Showing the changes introduced by a Module ===
Loading a ''Module'' will change the environment of the current shell session. For instance the $PATH variable will be expanded by the software's binary directory. Other ''Module'' variables may even change the behavior of the current shell session or the software program(s) in a more drastic way.
 
 
All the changes to the current shell session to be invoked by loading the ''Module'' can be reviewed using
 
''''module show category/softwarename/version''''.
 
 
'''Example (Intel compiler)'''
<pre>
$ module show compiler/intel
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/opt/bwhpc/common/modulefiles/Core/compiler/intel/19.1.lua:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
setenv("INTEL_LICENSE_FILE","28518@scclic1.scc.kit.edu")
setenv("AR","/opt/intel/compilers_and_libraries_2020/linux/bin/intel64/xiar")
setenv("CC","/opt/intel/compilers_and_libraries_2020/linux/bin/intel64/icc")
setenv("CXX","/opt/intel/compilers_and_libraries_2020/linux/bin/intel64/icpc")
setenv("F77","/opt/intel/compilers_and_libraries_2020/linux/bin/intel64/ifort")
setenv("FC","/opt/intel/compilers_and_libraries_2020/linux/bin/intel64/ifort")
setenv("CFLAGS","-O2 -xCORE-AVX2")
setenv("CXXFLAGS","-O2 -xCORE-AVX2")
setenv("FFLAGS","-O2 -xCORE-AVX2")
setenv("FCFLAGS","-O2 -xCORE-AVX2")
setenv("INTEL_VERSION","19.1.0.166")
setenv("INTEL_HOME","/opt/intel/compilers_and_libraries_2020/linux")
setenv("INTEL_BIN_DIR","/opt/intel/compilers_and_libraries_2020/linux/bin/intel64")
setenv("INTEL_LIB_DIR","/opt/intel/compilers_and_libraries_2020/linux/lib/intel64")
setenv("INTEL_INC_DIR","/opt/intel/compilers_and_libraries_2020/linux/include")
setenv("INTEL_MAN_DIR","/opt/intel/compilers_and_libraries_2020/linux/man/common")
setenv("INTEL_DOC_DIR","/opt/intel/compilers_and_libraries_2020/linux/documentation/en")
setenv("GDB_VERSION","19.1.0.166")
setenv("GDB_HOME","/opt/intel/debugger_2020/gdb/intel64")
setenv("GDB_BIN_DIR","/opt/intel/debugger_2020/gdb/intel64/bin")
setenv("GDB_LIB_DIR","/opt/intel/debugger_2020/libipt/intel64/lib")
setenv("GDB_INC_DIR","/opt/intel/debugger_2020/gdb/intel64/include")
setenv("GDB_INF_DIR","/opt/intel/documentation_2020/en/debugger/gdb-ia/info")
setenv("GDB_MAN_DIR","/opt/intel/documentation_2020/en/debugger/gdb-ia/man")
setenv("KMP_AFFINITY","noverbose,granularity=core,respect,warnings,compact,1")
prepend_path("PATH","/opt/intel/compilers_and_libraries_2020/linux/bin/intel64")
prepend_path("MANPATH","/opt/intel/compilers_and_libraries_2020/linux/man/common")
prepend_path("LD_LIBRARY_PATH","/opt/intel/compilers_and_libraries_2020/linux/lib/intel64")
whatis("Sets up Intel C/C++ and Fortran compiler version 19.1 (Intel(R) Compilers 19.1 for Linux*) - supported by SCC till 2022-12-31!")
help([[Intel(R) Compilers 19.1 for Linux*
For details see: https://software.intel.com/en-us/intel-compilers
In case of problems, please contact: Hartmut Häfner <hartmut.haefner@kit.edu>
SCC support end: 2022-12-31]])
prepend_path("MODULEPATH","/software/bwhpc/common/modulefiles/Compiler/intel/19.1")
family("compiler")
</pre>
 
 

=== Modules depending on Modules ===
Some program ''Modules'' depend on libraries to be loaded to the user environment. Therefore the
corresponding ''Modules'' of the software must be loaded together with the ''Modules'' of
the libraries.
 
By default such software ''Modules'' try to load required ''Modules'' and corresponding versions automatically.
 
 
 

== Unloading Modules ==
To unload or remove a software ''Module'' execute:
<pre>
$ module unload category/softwarename/version
</pre>
or
<pre>
$ module remove category/softwarename/version
</pre>
 

=== Unloading all loaded modules ===
==== Purge ====
Unloading a ''Module'' that has been loaded by default makes it inactive for the current session only - it will be reloaded the next time you log in.
 
In order to remove all previously loaded software modules from your environment issue the command 'module purge'.
 
Example
<pre>
$ module list
Currently Loaded Modules:
1) compiler/intel/19.1 2) mpi/impi/2019 3) numlib/mkl/2019
$
$ module purge
$ module list
No modules loaded
$
</pre>
Beware!
 
'module purge' is working without any further inquiry.
 
 

== Display your loaded Modules ==
All ''Modules'' that are currently loaded for you can be displayed by the
command ''''module list''''. [[#Purge|See example above]].
 
Note: You only have to load further ''Modules'', if you want to use additional software
packages or to change the version of an already loaded software.
 
 

== Display all possible Modules ==
Modulefiles can be searched by the user. You can dipslay all possible modules by executing:
<pre>
$ module spider

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
The following is a list of the modules and extensions currently available:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
cae/abaqus: cae/abaqus/2018, cae/abaqus/2019

cae/adina: cae/adina/9.1.2

cae/ansys: cae/ansys/19.2, cae/ansys/2019R3, cae/ansys/2020R1

cae/comsol: cae/comsol/5.4, cae/comsol/5.5

cae/cst: cae/cst/2018

cae/lsdyna: cae/lsdyna/901

cae/openfoam: cae/openfoam/v1912, cae/openfoam/2.4.x, cae/openfoam/6, cae/openfoam/7

cae/paraview: cae/paraview/5.8

cae/starccm+: cae/starccm+/14.02.010, cae/starccm+/2019.2.1

cae/starcd: cae/starcd/4.28

compiler/clang: compiler/clang/9.0

compiler/gnu: compiler/gnu/9.2

compiler/intel: compiler/intel/18.0, compiler/intel/19.0, compiler/intel/19.1

compiler/pgi: compiler/pgi/2019

devel/cmake: devel/cmake/3.16

devel/cuda: devel/cuda/9.2, devel/cuda/10.0, devel/cuda/10.2

devel/gdb: devel/gdb/9.1

devel/python: devel/python/3.7.4_gnu_9.2, devel/python/3.8.1_gnu_9.2, devel/python/3.8.1_intel_19.1

math/R: math/R/3.6.3

math/julia: math/julia/1.3.1

mpi/impi: mpi/impi/2018, mpi/impi/2019, mpi/impi/2020

mpi/openmpi: mpi/openmpi/4.0

numlib/mkl: numlib/mkl/2018, numlib/mkl/2019, numlib/mkl/2020

numlib/python_numpy: numlib/python_numpy/1.17.2_python_3.7.4_gnu_9.2

numlib/python_scipy: numlib/python_scipy/1.3.1_numpy_1.17.2_python_3.7.4_gnu_9.2

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

To learn more about a package execute:

$ module spider Foo

where "Foo" is the name of a module.

To find detailed information about a particular package you
must specify the version if there is more than one version:

$ module spider Foo/11.1

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
</pre>
''''module spider name/version'''' : If you search the full name and version of the module, the search gives detailed information about that module version.
<pre>
$ module spider devel/cmake

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
devel/cmake: devel/cmake/3.16
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

This module can be loaded directly: module load devel/cmake/3.16

Help:
Home page: https://www.cmake.org
Online Documentation: https://www.cmake.org/HTML/Documentation.html
Local Documentation: /opt/bwhpc/common/devel/cmake/3.16.4/docFAQ: https://gitlab.kitware.com/cmake/community/wikis/FAQ

In case of problems, please contact 'bwunicluster-hotline (at) lists.kit.edu'
or submit a trouble ticket at http://www.support.bwhpc-c5.de.

</pre>
Moreover, you can see the dependencies of the module with using the same command. For example, if the following is executed, you can see which modules need to be loaded before loading the module mpi/impi/2019
<pre>
$ module spider mpi/impi/2019

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
mpi/impi: mpi/impi/2019
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

You will need to load all module(s) on any one of the lines below before the "mpi/impi/2019" module is available to load.

compiler/clang/9.0
compiler/gnu/9.2
compiler/intel/18.0
compiler/intel/19.0
compiler/intel/19.1

Help:
Intel(R) MPI Library

</pre>
 

= How do Modules work? =
The default shell on the bwHPC clusters is bash, so explanations and examples will be shown for bash. In general, programs cannot modify the environment of the shell they are being run from, so how can the module command do exactly that?
 
The module command is not a program, but a bash-function.
You can view its content using:
<pre>
$ type module
</pre>
and you will get the following result:
<pre>
$ type module
module is a function
module ()
{
eval $($LMOD_CMD bash "$@");
[ $? = 0 ] && eval $(${LMOD_SETTARG_CMD:-:} -s sh)
}
</pre>
In this function, lmod is called. Its output to stdout is then executed inside your current shell using the bash-internal ''eval'' command. As a consequence, all output that you see from the module is transmitted via stderr (output handle 2) or in some cases even stdin (output handle 0).
 
 
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