Environment Modules: Difference between revisions

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<!--<span style="color:red;font-size:105%;">Important note: bwUniCluster is '''not''' in production mode yet.</span>-->


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.


Full documentation: <code>module help</code> and [https://lmod.readthedocs.io/en/latest/ Environment Modules Website]
The usage of compilers, libraries and software packages requires by default users to set up
manually their session environment. The bwHPC clusters (such as [[bwUniCluster]]) provide users the possibility to load and unload ''complete environments''
for compilers, libraries and software packages by single commands. Because of the
convenient modularity this package is called ''Environment Modules'', or short '''Modules'''.


= Basic Usage =


== Module categories, versions and defaults ==
<!--{| align="right" {{Table|width=40%}} -->
The bwHPC clusters categorize ''Modules'', each software can exist in different versions:
{|{{Softwarebox}}
|-
! colspan="2" style="text-align:center" | Modules
<!--
|-
| module load
| category/name
-->
|-
| License
| GPL
|-
| Links
| http://modules.sourceforge.net/
|
|}


category/softwarename/version
<!--
{| 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]]
|-
|}
-->


e.g. if julia is installed, it is in the module <code>math/julia</code>.


You can load it in the default version just specifying math/julia or a specific version <code> math/julia/1.11.0 </code>
= Description =
Please note, that software may be '''hidden''' from default view using a dot in front of the version; i.e.
the software is still available but not visible in <code>module avail</code> but may still be loaded,
e.g. <code> math/julia/.1.10.0 </code>.


Currently all bwHPC software packages are assigned to one of the following ''Module'' categories:
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> bio cae chem compiler devel lib math mpi numlib phys system vis </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.


== Display and search available Modules ==
The software stack of bwHPC clusters provides a number of modulefiles. You can also
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:
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. For instance
loading the default Intel C and Fortran compiler you must execute:
<pre>
<pre>
$ module load compiler/intel
$ module avail
</pre>
</pre>


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:

= Usage =

== Documentation ==

For help on how to use ''Modules'' software, i.e., the command '''module''',
execute:
<pre>
<pre>
$ module help
$ module avail compiler/
$ module avail compiler/gnu
</pre>
</pre>

or
== module help ==
A help message for a specific ''Module'' can be displayed with ''''module help category/softwarename/version''''.
<br>
The help message usually contains additional information about the software and points to the software website and documentation.
<pre>
<pre>
$ man module
$ module help system/example/1.0
----------------- Module Specific Help for "system/example/1.0" ---------------------------
</pre>
"This module provides a bwhpc-examples job that works on every cluster.


[... rest of the output is omitted in the Wiki for clarity ...]
For help on particular version of ''Module'', e.g. Intel compiler version X.Y, execute:
<pre>
$ module help compiler/intel/X.Y
</pre>
</pre>




== Loading Modules and Check they are loaded ==
== Display all available Modules ==


{|style="background:#deffee; width:100%;"
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
|style="padding:5px; background:#cef2e0; text-align:left"|
section. You can display all available ''Modules'' on the system by executing:
[[Image:Attention.svg|center|25px]]
<pre>
|style="padding:5px; background:#cef2e0; text-align:left"|
$ module avail
Don't use module load in .bashrc → see [[.bashrc Do's and Don'ts]]
</pre>
|}
The short form the command is:
<pre>
$ module av
</pre>


To load a software ''Module'' and display all loaded modules:
Available ''Modules'' can be also displayed in different modes, such as
* each ''Module'' per one line
<pre>
<pre>
$ module -t avail
$ module list
No Modulefiles Currently Loaded.
</pre>
$ module load system/example/1.0
* long
$ module list
<pre>
Currently Loaded Modulefiles:
$ module -l avail
1) system/example/1.0
</pre>
</pre>




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.
== Module categories, versions and defaults ==


== Software job examples ==
The bwHPC clusters (such as [[bwUniCluster]]) traditionally provide a large variety of
bwHPC provides example job scripts for most installed software modules.
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:
{{bwFrameA|
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''.


For a Software ''Module'' with the sofware called '''SOMESOFTWARE''', you can find the example directory by:
In case of multiple software versions, one version will be always defined as the '''default'''
<pre>
version. The ''Module'' of the default can be addressed by simply omitting the version number:
$ cd $SOMESOFTWARE_EXA_DIR
{{bwFrameA|
</pre>
category/softwarename
}}


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


<pre>
Currently all bwHPC software packages are assigned to the following ''Module'' categories:
$ cd
<!-- add wiki category for each of those, possibly just as a link -->
$ mkdir softwarename_examples
* [[:Category:Biology_software|bio]]
$ echo $SOMESOFTWARE_EXA_DIR
* [[:Category:Engineering_software|cae]]
# Please do not proceed if the command above does not provide any text !
* [[:Category:Chemistry_software|chem]]
# Otherwise you will start to copy all system data (the directory "/").
* [[:Category:Compiler_software|compiler]]
$ cp -r $SOMESOFTWARE_EXA_DIR/ softwarename_examples/
* [[:Category:Debugger_software|devel]]
* dot
* lib
* [[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>
$ module avail compiler/
</pre>
</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"
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:

<pre>
<pre>
# Load the example module
$ module avail c
$ module load system/example/1.0
</pre>
while this would find nothing
<pre>
$ module avail hem
</pre>


# Run example in a temporary directory
== Loading Modules ==
$ mkdir tmp_example_dir
You can load a ''Module'' software in to your environment to enable easier access to software that
$ cp -r $EXAMPLE_EXA_DIR/ softwarename_examples/
you want to use by executing:
$ cd tmp_example_dir/bwhpc-examples
<pre>

$ module load category/softwarename/version
# 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
</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.

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>
while it does not load the ''Module''.
<br>
<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>
<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
=== Automatic Loading ===
$EXAMPLE_BIN_DIR
If you frequently use one or more ''Modules'' that are not loaded when you log in to
Upon loading the module, the binaries are added to PATH.
the system, you can set up your environment to automatically load those ''Modules'' for
you. A method for doing this is to modify your shell startup script to include instructions to
load the modulefile automatically.


* Further documentation for using the example can be found in
For example, if you want to automatically load the ''Module'' of Intel's default compiler when you log
https://wiki.bwhpc.de/e/Environment_Modules
in, edit your shell startup script to include the following instructions. This example assumes

that you use bash as your login shell. Edit the <tt>$HOME/.bashrc</tt> file as follows:
* Examples are located at:
{{bwFrameA|
$EXAMPLE_EXA_DIR
<source lang="bash">
]])
## if the ’module’ command is defined, $MODULESHOME will be set

if [ -n "$MODULESHOME" ]; then
</pre>
module load compiler/intel
fi
</source>
}}
From now on, whenever you log in, the default version of the Intel compiler is automatically
loaded in your environment.


=== Modules depending on Modules ===
=== Modules depending on Modules ===
Line 231: Line 182:
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 240: Line 191:
<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:bwHPC|User Environment]]
[[Category:bwUniCluster|Environment Modules]]-->

Latest revision as of 13:42, 12 November 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.

Full documentation: module help and Environment Modules Website

Basic Usage

Module categories, versions and defaults

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

category/softwarename/version

e.g. if julia is installed, it is in the module math/julia.

You can load it in the default version just specifying math/julia or a specific version math/julia/1.11.0 Please note, that software may be hidden from default view using a dot in front of the version; i.e. the software is still available but not visible in module avail but may still be loaded, e.g. math/julia/.1.10.0 .

Currently all bwHPC software packages are assigned to one of 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

Attention.svg

Don't use module load in .bashrc → see .bashrc Do's and Don'ts

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.
Retrieved from "https://wiki.bwhpc.de/wiki/index.php?title=Environment_Modules&oldid=13240"