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'''Environment Modules''', or short '''Modules''' are the means by which most of the installed scientific software is provided on the bwHPC clusters.


Software on the bwHPC Clusters is provided as '''Software Environment Modules''', or short '''Modules'''.
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. The bwHPC clusters provide users with the possibility to load and unload complete environments
for compilers, libraries and software packages by a single command.


Modules make it possible to have different versions of a software installed at a the same time.
<!--{| align="right" {{Table|width=40%}} -->
The complete environments for the software package, compilers and libraries and needed by this specific version is then loaded by a single command. This happens usually in the beginning of the jobscript.
{|{{Softwarebox}}
|-
! colspan="2" style="text-align:center" | Modules
<!--
|-
| module load
| category/name
-->
|-
| License
| GPL
|-
| Links
| http://modules.sourceforge.net/
|
|}


= Basic Usage =
<!--
== General Documentation on the Modules Environment Software ==
{| style="width: 100%; border-spacing: 5px;"
| style="text-align:left; color:#000;vertical-align:top;" |__TOC__
|<br><br>[[File:BwUniCluster_modulefiles.png|center|border|400px]]
|-
|}
-->


We will provide an overview of the most important commands in the next sections.


For your reference on what is not covered here, the full documentation written by the software developers is available on the cluster via the commands:
= Description =


<code>module help</code>
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.


<code>man module</code>
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.


Online documentation of the project is available on the [https://lmod.readthedocs.io/en/latest/ Environment Modules Website].
The software stack of bwHPC clusters 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.


== Module categories, versions and defaults ==
A modulefile does not provide configuration of your environment until it is explicitly loaded,
The bwHPC clusters categorize ''Modules'', each software can exist in different versions:
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. For instance
loading the default Intel C and Fortran compiler you must execute:
<pre>
$ module load compiler/intel
</pre>


category/softwarename/version
For instance the Intel compiler X.Y belongs to the category of compilers, therefore the
modulefile ''X.Y'' is placed under the category ''compiler'' and ''intel''.
<br>
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


e.g. if mathematica is installed, it is in the module
= Usage =


math/mathematica
== Documentation ==


Currently all bwHPC software packages are assigned to the following ''Module'' categories:
For help on how to use ''Modules'' software, i.e., the command '''module''',
execute:
<pre>
$ module help
</pre>
or
<pre>
$ man module
</pre>


<code> bio cae chem compiler devel lib math mpi numlib phys system vis </code>
For help on particular version of ''Module'', e.g. Intel compiler version X.Y, execute:
<pre>
$ module help compiler/intel/X.Y
</pre>


<!--
[[:Category:Biology_software|bio]]
[[:Category:Engineering_software|cae]]
[[:Category:Chemistry_software|chem]]
[[:Category:Compiler_software|compiler]]
[[:Category:Debugger_software|devel]]
[[:Category:Mathematics_software|math]]
mpi
[[:Category:Numerical libraries|numlib]]
[[:Category:Physics software|phys]]
[[:Category:System software|system]]
[[:Category:Visualization|vis]]
-->


== Display all available Modules ==
== Display and search available Modules ==
Available ''Modules'' are modulefiles that can be loaded by the user. A ''Module'' must be loaded before it provides changes to your environment. You can display all available ''Modules'' on the system by executing:

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>
<pre>
$ module avail
$ module avail
</pre>
</pre>

The short form the command is:
You can selectively list software in one of those categories using, e.g. for the category "compiler", or just all versions of a certain module:
<pre>
<pre>
$ module av
$ module avail compiler/
$ module avail compiler/gnu
</pre>
</pre>


== module help ==
Available ''Modules'' can be also displayed in different modes, such as
A help message for a specific ''Module'' can be displayed with ''''module help category/softwarename/version''''.
* each ''Module'' per one line
<br>
The help message usually contains additional information about the software and points to the software website and documentation.
<pre>
<pre>
$ module -t avail
$ module help system/example/1.0
----------------- Module Specific Help for "system/example/1.0" ---------------------------
"This module provides a bwhpc-examples job that works on every cluster.

[... rest of the output is omitted in the Wiki for clarity ...]
</pre>
</pre>

* long

== Loading Modules and Check they are loaded ==
To load a software ''Module'' and display all loaded modules:
<pre>
<pre>
$ module -l avail
$ module list
No Modulefiles Currently Loaded.
$ module load system/example/1.0
$ module list
Currently Loaded Modulefiles:
1) system/example/1.0
</pre>
</pre>


== Display all available and scheduled Modules using a browser GUI ==


Modules make software available only in your current shell. Whenever you login in, you have to load the software again. Please do not auto-load modules in ~/.bashrc, this can lead to problems with system software or other modules you may load later.
A '''GUI-Version of all available and scheduled modules''' is available with our '''CIS''' (Cluster Information System).
<br>
Software Admins are able to '''announce new modules''', versions and complete new software, too.
<br>
Academic users and other interested parties can get a '''summay of all installed modules and module-help informations'''.


== Software job examples ==
[http://cis-hpc.uni-konstanz.de/prod.cis CIS: Cluster Information System]
bwHPC provides example job scripts for most installed software modules.
<br>


For a Software ''Module'' with the sofware called '''SOMESOFTWARE''', you can find the example directory by:
== Module categories, versions and defaults ==
<pre>
$ cd $SOMESOFTWARE_EXA_DIR
</pre>


Copy the whole example folder to your $HOME directory, so you can edit those job examples:
The bwHPC clusters (such as [[bwUniCluster]]) 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 the Intel compiler X.Y belongs to the category of compilers, therefore the
modulefile ''X.Y'' is placed under the category ''compiler'' and ''intel''.


<pre>
In case of multiple software versions, one version will be always defined as the '''default'''
$ cd
version. The ''Module'' of the default can be addressed by simply omitting the version number:
$ mkdir softwarename_examples
category/softwarename
$ echo $SOMESOFTWARE_EXA_DIR
# Please do not proceed if the command above does not provide any text !
# Otherwise you will start to copy all system data (the directory "/").
$ cp -r $SOMESOFTWARE_EXA_DIR/ softwarename_examples/


</pre>
== Finding software Modules ==


If your specific software isn't installed, there is a dummy software example module "system/example" present on all clusters. For this module, the process looks like this:
Currently all bwHPC software packages are assigned to the following ''Module'' categories:
<!-- add wiki category for each of those, possibly just as a link -->
* [[:Category:Biology_software|bio]]
* [[:Category:Engineering_software|cae]]
* [[:Category:Chemistry_software|chem]]
* [[:Category:Compiler_software|compiler]]
* [[:Category:Debugger_software|devel]]
* [[BwHPC_BPG_for_Mathematics|math]]
* mpi
* [[:Category:Numerical libraries|numlib]]
* [[:Category:Physics software|phys]]
* [[:Category:System software|system]]
* [[:Category:Visualization|vis]]


You can selectively list software in one of those categories using, e.g. for the category "compiler"
<pre>
<pre>
# Load the example module
$ module avail compiler/
$ module load system/example/1.0
</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"
# Run example in a temporary directory
<pre>
$ mkdir tmp_example_dir
$ module avail c
$ cp -r $EXAMPLE_EXA_DIR/ softwarename_examples/
</pre>
$ cd tmp_example_dir/bwhpc-examples
while this would find nothing
<pre>
$ module avail hem
</pre>
<br>


# Example jobscript for clusters using the SLURM batch system
== Loading Modules ==
sbatch examples-1.0.slurm
You can load a ''Module'' software in to your environment to enable easier access to software that
# Example jobscript for clusters using PBS
you want to use by executing:
qsub examples-1.0.pbs
<pre>

$ module load category/softwarename/version
# Print the results
cat examples_result.txt
</pre>
</pre>
----
or
<pre>
$ module add category/softwarename/version
</pre>
Loading a ''Module'' in this manner affects ONLY your environment for the current session.


= Additional Usage Recommendations =


=== Loading conflicts ===
=== Loading conflicts ===
By default you can not load different versions of same software ''Module'' in same session. Loading for example Intel compiler version X while Intel compiler version Y is loaded results in error message as follows:
By default you can not load different versions of same software ''Module'' in same session. Loading for example Intel compiler version X while Intel compiler version Y is loaded results in error message as follows:
{{bwFrameA|
<source lang="bash">
<source lang="bash">
ERROR:150: Module 'compiler/intel/X' conflicts with the currently loaded module(s) 'compiler/intel/Y'
Module 'compiler/intel/X' conflicts with the currently loaded module(s) 'compiler/intel/Y'
</source>
</source>
}}
The solution is [[#Unloading Modules|unloading]] or switching ''Modules''.
The solution is [[#Unloading Modules|unloading]] or switching ''Modules''.



=== Showing the changes introduced by a Module ===
=== 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.
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.
<br>

Loaded ''Modules'' may also invoke an additional set of environment variables, which e.g. point to directories or destinations of documentation and examples. Their nomenclature is systematic:
Loaded ''Modules'' may also invoke an additional set of environment variables, which e.g. point to directories or destinations of documentation and examples. Their nomenclature is systematic:
{|{{Table|width=50%}}
{| width=600px class="wikitable"
|-
|-
! Variable
! Variable
! Pointing to
! Pointing to
|-
|-
| $FOO_HOME
| $SWN_HOME
| Root directory of the software package
| Root directory of the software package
|-
|-
| $FOO_DOC_DIR
| $SWN_DOC_DIR
| Documentation
| Documentation
|-
|-
| $FOO_EXA_DIR
| $SWN_EXA_DIR
| Examples
| Examples
|-
|-
| $FOO_BPR_URL
| $SWN_BPR_URL
| URL of software's Wiki article
| URL of software's Wiki article
|-
|-
| and many many more...
| &nbsp;
|}
|}
with FOO being the placeholder of the software ''Module'' name.
with SWN being the place holder of the software ''Module'' name.
<br>
All the changes to the current shell session to be invoked by loading the ''Module'' can be reviewed using ''''module show category/softwarename/version''''.
<br>
<pre>
$ module show system/example/1.0
---------------------------------------------------------------------------------------------------
/opt/bwhpc/common/modulefiles/Core/system/example/1.0.lua:
---------------------------------------------------------------------------------------------------
whatis("A generic module containing a working bwhpc-examples job.")
setenv("EXAMPLE_VERSION","1.0")
setenv("EXAMPLE_HOME","/opt/bwhpc/common/system/example/1.0")
setenv("EXAMPLE_BIN_DIR","/opt/bwhpc/common/system/example/1.0/bin")
setenv("EXAMPLE_EXA_DIR","/opt/bwhpc/common/system/example/1.0/bwhpc-examples")
prepend_path("PATH","/opt/bwhpc/common/system/example/1.0/bin")
help([["This module provides a bwhpc-examples job that works on every cluster.
The module is used as example in the bwHPC-Wiki and therefore should be installed on every cluster,
such that users can try the commands out.

* The executable of this module can be found in the folder
$EXAMPLE_BIN_DIR
Upon loading the module, the binaries are added to PATH.

* Further documentation for using the example can be found in
https://wiki.bwhpc.de/e/Environment_Modules

* Examples are located at:
$EXAMPLE_EXA_DIR
]])


All the changes to the current shell session to be invoked by loading the ''Module'' can be reviewed using
<pre>
$ module show category/softwarename/0.0.0
</pre>
</pre>
while it does not load the ''Module''.
<br>
<!-- 2014-05-08, RB: Depreciated, if really necessary then only for login, i.e. to be placed in .profile
=== Automatic Loading ===
-->


=== Modules depending on Modules ===
=== Modules depending on Modules ===
Line 213: Line 200:
corresponding ''Modules'' of the software must be loaded together with the ''Modules'' of
corresponding ''Modules'' of the software must be loaded together with the ''Modules'' of
the libraries.
the libraries.
<br>

By default such software ''Modules'' try to load required ''Modules'' and corresponding versions automatically. However, automatic loading might fail if a different version of that required ''Module''
By default such software ''Modules'' try to load required ''Modules'' and corresponding versions automatically. However, automatic loading might fail if a different version of that required ''Module''
is already loaded (cf. [[#Loading conflicts|Loading conflicts]]).
is already loaded (cf. [[#Loading conflicts|Loading conflicts]]).
<br>



== Unloading Modules ==
== Unloading Modules ==
Line 222: Line 209:
<pre>
<pre>
$ module unload category/softwarename/version
$ module unload category/softwarename/version
</pre>
or
<pre>
$ module remove category/softwarename/version
</pre>
</pre>


=== Unloading all loaded modules ===
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'.

<br>
In order to remove all previously loaded software modules from your environment issue the following command:
<pre>
<pre>
$ module list
Currently Loaded Modulefiles:
1) devel/gdb/7.7
2) compiler/intel/14.0
3) mpi/openmpi/1.8-intel-14.0(default)
$
$ module purge
$ module purge
</pre>


== Display your loaded Modules ==
All ''Modules'' that are currently loaded for you can be displayed by the
command:
<pre>
$ module list
$ module list
No Modulefiles Currently Loaded.
$
</pre>
</pre>
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.


== Other Module commands ==

=== module whatis ===
= Software job examples =
A short description for a specific ''Module'' can be displayed with ''''module whatis category/softwarename/version''''

The ''Modules'' installed on bwHPC systems provide job examples to help you get started using the software or submitting jobs with this software. Examples can be found via a convenient
variable $FOO_EXA_DIR (for a ''Module'' called '''foo'''). It is advisable to copy the whole example folder to your $HOME directory, so you can edit those job examples.

For copying the entire job examples folder of software '''foo''' to your working directory, execute:
<pre>
<pre>
$ module load catogory/softwarename
$ module whatis system/example/1.0
system/example/1.0 : A generic module containing a working bwhpc-examples job.
$ cp -R $FOO_EXA_DIR .
</pre>
</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 a result like this:
<pre>
$ type module
module is a function
module ()
{
eval `/usr/bin/modulecmd bash $*`
}
</pre>

In this function, modulecmd 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).




----
[[Category:System software]][[Category:bwUniCluster|Environment Modules]][[Category:ForHLR Phase I|Environment Modules]]
<!--[[Category:bwHPC|User Environment]]
[[Category:bwUniCluster|Environment Modules]]-->

Latest revision as of 14:57, 8 October 2024

Software on the bwHPC Clusters is provided as Software Environment Modules, or short Modules.

Modules make it possible to have different versions of a software installed at a the same time. The complete environments for the software package, compilers and libraries and needed by this specific version is then loaded by a single command. This happens usually in the beginning of the jobscript.

Basic Usage

General Documentation on the Modules Environment Software

We will provide an overview of the most important commands in the next sections.

For your reference on what is not covered here, the full documentation written by the software developers is available on the cluster via the commands:

module help

man module

Online documentation of the project is available on the Environment Modules Website.

Module categories, versions and defaults

The bwHPC clusters categorize Modules, each software can exist in different versions:

category/softwarename/version

For instance the Intel compiler X.Y belongs to the category of compilers, therefore the modulefile X.Y is 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

e.g. if mathematica is installed, it is in the module

math/mathematica

Currently all bwHPC software packages are assigned to the following Module categories:

bio cae chem compiler devel lib math mpi numlib phys system vis


Display and search available Modules

Available Modules are modulefiles that can be loaded by the user. A Module must be loaded before it provides changes to your environment. You can display all available Modules on the system by executing:

$ module avail

You can selectively list software in one of those categories using, e.g. for the category "compiler", or just all versions of a certain module:

$ module avail compiler/
$ module avail compiler/gnu

module help

A help message for a specific Module can be displayed with 'module help category/softwarename/version'.
The help message usually contains additional information about the software and points to the software website and documentation.

$ module help system/example/1.0 
----------------- Module Specific Help for "system/example/1.0" ---------------------------
"This module provides a bwhpc-examples job that works on every cluster.

[... rest of the output is omitted in the Wiki for clarity ...]


Loading Modules and Check they are loaded

To load a software Module and display all loaded modules:

$ module list
No Modulefiles Currently Loaded.
$ module load system/example/1.0
$ module list
Currently Loaded Modulefiles:
  1) system/example/1.0


Modules make software available only in your current shell. Whenever you login in, you have to load the software again. Please do not auto-load modules in ~/.bashrc, this can lead to problems with system software or other modules you may load later.

Software job examples

bwHPC provides example job scripts for most installed software modules.

For a Software Module with the sofware called SOMESOFTWARE, you can find the example directory by:

$ cd  $SOMESOFTWARE_EXA_DIR

Copy the whole example folder to your $HOME directory, so you can edit those job examples:

$ cd
$ mkdir softwarename_examples
$ echo $SOMESOFTWARE_EXA_DIR
# Please do not proceed if the command above does not provide any text !
# Otherwise you will start to copy all system data (the directory "/").
$ cp -r $SOMESOFTWARE_EXA_DIR/ softwarename_examples/

If your specific software isn't installed, there is a dummy software example module "system/example" present on all clusters. For this module, the process looks like this:

# Load the example module
$ module load system/example/1.0

# Run example in a temporary directory
$ mkdir tmp_example_dir
$ cp -r $EXAMPLE_EXA_DIR/ softwarename_examples/
$ cd tmp_example_dir/bwhpc-examples

# Example jobscript for clusters using the SLURM batch system
sbatch examples-1.0.slurm
# Example jobscript for clusters using PBS
qsub examples-1.0.pbs

# Print the results
cat examples_result.txt

Additional Usage Recommendations

Loading conflicts

By default you can not load different versions of same software Module in same session. Loading for example Intel compiler version X while Intel compiler version Y is loaded results in error message as follows:

Module 'compiler/intel/X' conflicts with the currently loaded module(s) 'compiler/intel/Y'

The solution is unloading or switching Modules.

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.
Loaded Modules may also invoke an additional set of environment variables, which e.g. point to directories or destinations of documentation and examples. Their nomenclature is systematic:

Variable Pointing to
$SWN_HOME Root directory of the software package
$SWN_DOC_DIR Documentation
$SWN_EXA_DIR Examples
$SWN_BPR_URL URL of software's Wiki article
and many many more...  

with SWN being the place holder of the software Module name.
All the changes to the current shell session to be invoked by loading the Module can be reviewed using 'module show category/softwarename/version'.

$ module show system/example/1.0
---------------------------------------------------------------------------------------------------
   /opt/bwhpc/common/modulefiles/Core/system/example/1.0.lua:
---------------------------------------------------------------------------------------------------
whatis("A generic module containing a working bwhpc-examples job.")
setenv("EXAMPLE_VERSION","1.0")
setenv("EXAMPLE_HOME","/opt/bwhpc/common/system/example/1.0")
setenv("EXAMPLE_BIN_DIR","/opt/bwhpc/common/system/example/1.0/bin")
setenv("EXAMPLE_EXA_DIR","/opt/bwhpc/common/system/example/1.0/bwhpc-examples")
prepend_path("PATH","/opt/bwhpc/common/system/example/1.0/bin")
help([["This module provides a bwhpc-examples job that works on every cluster.
The module is used as example in the bwHPC-Wiki and therefore should be installed on every cluster,
such that users can try the commands out.

* The executable of this module can be found in the folder
  $EXAMPLE_BIN_DIR
  Upon loading the module, the binaries are added to PATH.

* Further documentation for using the example can be found in
  https://wiki.bwhpc.de/e/Environment_Modules

* Examples are located at:
  $EXAMPLE_EXA_DIR
]])

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. However, automatic loading might fail if a different version of that required Module is already loaded (cf. Loading conflicts).

Unloading Modules

To unload or to remove a software Module execute:

$ module unload category/softwarename/version

Unloading all loaded modules

In order to remove all previously loaded software modules from your environment issue the command 'module purge'.

$ module list
Currently Loaded Modulefiles:
  1) devel/gdb/7.7
  2) compiler/intel/14.0
  3) mpi/openmpi/1.8-intel-14.0(default)
$
$ module purge
$ module list
No Modulefiles Currently Loaded.
$ 

Other Module commands

module whatis

A short description for a specific Module can be displayed with 'module whatis category/softwarename/version'

$ module whatis system/example/1.0 
system/example/1.0  : A generic module containing a working bwhpc-examples job.