Pysdlb at 09:57, 16 November 2022

2022-11-16T09:57:26Z

Pysdlb at 16:03, 15 November 2022

2022-11-15T16:03:14Z

Pysdlb: added in left over info from og general modules page

2022-11-08T15:52:51Z

added in left over info from og general modules page

New page

[[FurtherTopics/FurtherTopics #Modules| Back to Further Topics]]
==Additional Module Commands==
=== module show ===

To find out what a module file does, run '''module show modulename'''. This will show you brief information about what the module will do (this information is being updated for existing modules to show more relevant information), along with how the module will update your environment:

<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ module show abyss/1.5.2/gcc-5.2.0
-------------------------------------------------------------------
/trinity/clustervision/CentOS/7/modulefiles/abyss/1.5.2/gcc-5.2.0

module-whatis ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes
prepend-path PATH /trinity/clustervision/CentOS/7/apps/abyss/1.5.2/gcc-5.2.0/bin
prepend-path LD_LIBRARY_PATH /trinity/clustervision/CentOS/7/apps/abyss/1.5.2/gcc-5.2.0/lib
prepend-path C_INCLUDE_PATH /trinity/clustervision/CentOS/7/apps/abyss/1.5.2/gcc-5.2.0/include
prepend-path PKG_CONFIG_PATH /trinity/clustervision/CentOS/7/apps/abyss/1.5.2/gcc-5.2.0/lib/pkgconfig
-------------------------------------------------------------------
</pre>

==== module whatis ====

To find out what modules are available with information about what each application does, run '''module whatis''', for example (selected output):

<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ module whatis
STAR/2016-10-27 : Spliced Transcripts Alignment to a Reference
abyss/1.5.2/gcc-5.2.0: ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes
crop/1.33/gcc-6.3.0 : Crop clustering approach to find common taxonomic units in large datasets
discovardenovo/52488 : DISCOVAR de novo – large genome assembler
expat/gcc/2.2.0 : Expat XML parser
ssw/2016-08-08 : SSW (NASA SolarSoft)
test-modules : Adds modules under development to your module avail list
</pre>

Note: This information is currently being updated for existing modules.

==Module Files==
=== Modulefile actions ===

Typically modulefiles instruct the module command to alter or set shell environment variables such as paths and flags, to provide access to executables or libraries.

<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ module show openmpi/1.10.5/gcc-6.3.0
-------------------------------------------------------------------
/trinity/clustervision/CentOS/7/modulefiles/openmpi/1.10.5/gcc-6.3.0:

module-whatis loads the openmpi/1.10.5/gcc-6.3.0 environment
module load gcc/6.3.0
conflict mpich
conflict openmpi
conflict mvapich2
conflict intel
prepend-path PATH /trinity/clustervision/CentOS/7/apps/openmpi/1.10.5/gcc-6.3.0/bin
prepend-path LD_LIBRARY_PATH /trinity/clustervision/CentOS/7/apps/openmpi/1.10.5/gcc-6.3.0/lib
prepend-path LIBRARY_PATH /trinity/clustervision/CentOS/7/apps/openmpi/1.10.5/gcc-6.3.0/lib
prepend-path INCLUDE /trinity/clustervision/CentOS/7/apps/openmpi/1.10.5/gcc-6.3.0/include
prepend-path C_INCLUDE_PATH /trinity/clustervision/CentOS/7/apps/openmpi/1.10.5/gcc-6.3.0/include
prepend-path MANPATH /trinity/clustervision/CentOS/7/apps/openmpi/1.10.5/gcc-6.3.0/share/man
setenv MPI_HOME /trinity/clustervision/CentOS/7/apps/openmpi/1.10.5/gcc-6.3.0
setenv MPI_RUN /trinity/clustervision/CentOS/7/apps/openmpi/1.10.5/gcc-6.3.0/bin/mpirun
setenv OMPI_HOME /trinity/clustervision/CentOS/7/apps/openmpi/1.10.5/gcc-6.3.0
-------------------------------------------------------------------
</pre>

Other common options set in a module file include the following:

* Paths such as LIBRARY_PATH, CPATH, LD_RUN_PATH
* Compiler flags such as CFLAGS, CPPFLAGS, FCFLAGS and LDFLAGS
* Application-specific paths or options such as MPI_HOME or MPI_RUN
* Manual page location via the MANPATH
* Other modules to load to meet dependencies
* Any conflicting modules that can't be loaded together
* License file locations, for example for Intel Compiler

=== Modulefile naming convention ===

Most modulefiles take the form applicationname/version, for example '''gcc/5.2.0''' for the GNU Compiler Collection version 5.2.0. There are also other versions of GCC, for example '''gcc/5.2.0''', '''gcc/6.3.0'' and '''gcc/7.3.0'''. A similar example is '''matlab/2016a'''

However, due to the specific combinations of some of the tools required to build certain applications which may be relevant to those using the application, a new naming convention is being introduced. These modulefiles will take the form of application/version/ followed by information about the compiler module used to build the application (and possibly the version of MPI), for example:

* '''crop/1.33/gcc-6.3.0'''
* '''openmpi/1.10.5/gcc-5.2.0'''
* '''openmpi/1.10.5/gcc-6.3.0'''
* '''openmpi/1.10.5/intel-2017'''

If a piece of software doesn't have a specific version number, for example when retrieved from ''GitHub'', then the version will often be replaced by the date the application was built, for example '''sparsehash/2016-12-21/gcc-4.9.3'''

===Test modulefiles===

While applications are being installed and tested, they may be put in a test area and not directly available to users. This is to stop people from using modules that may not be correctly configured or are subject to change while testing the installations. To see the modules that are in testing you need to run '''module add test-modules''' before running '''module avail'''

[[Modules #Test Modules| Find out more about test modules]]

==Module Tips and Tricks==
* Loading a module will be active for that session only
* Multiple modules can be loaded in one command, for example '''module add gcc/5.2.0 sparsehash/2016-12-21/gcc-5.2.0'''
* '''module add''' commands should be included in job submission scripts
* The '''module add''' command support tab completion
* You can create private modules in your own home directory
* The '''module add''' commands are recorded to track application usage

[[FurtherTopics/FurtherTopics #Modules| Back to Further Topics]]

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FurtherTopics/Further Modules - Revision history

Pysdlb at 09:57, 16 November 2022

Pysdlb at 16:03, 15 November 2022

Pysdlb: added in left over info from og general modules page