Environment Modules
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
The documentation written by the software developers is available on the cluster via the commands:
module help
man modules
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
Currently all bwHPC software packages are assigned to the following Module categories:
bio cae chem compiler devel 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 compiler/gnu/9.2 ----------- Module Specific Help for 'compiler/gnu/9.2' ----------- This module provides the GNU compiler collection version 9.2.0 via commands [... 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 compiler/gnu/9.2 $ module list Currently Loaded Modulefiles: 1) compiler/gnu/9.2
Module make software available only in your current shell. Whenever you login in, you have to load the software again. Please don not auto-load modules in .bashrc on login, this can lead to problems with other modules you may load later.
Software job examples
bwHPC provides example job scripts for most installed software modules.
It uses a variable named $SWN_EXA_DIR for a Module called SWN. To copy the whole example folder to your $HOME directory, so you can edit those job examples.
To copy the entire job examples folder of software swn to your working directory, execute:
$ module load catogory/softwarename $ cp -R $SWN_EXA_DIR ./software-examples
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 compiler/gnu/9.2 ------------------------------------------------------------------- /opt/bwhpc/common/modulefiles/compiler/gnu/9.2: setenv GNU_VERSION 9.2.0 setenv GNU_HOME /opt/bwhpc/common/compiler/gnu/9.2.0 setenv GNU_BIN_DIR /opt/bwhpc/common/compiler/gnu/9.2.0/bin setenv GNU_MAN_DIR /opt/bwhpc/common/compiler/gnu/9.2.0/man setenv GNU_LIB_DIR /opt/bwhpc/common/compiler/gnu/9.2.0/lib64 setenv GNU_LIB_DIR2 /opt/bwhpc/common/compiler/gnu/9.2.0/lib prepend-path PATH /opt/bwhpc/common/compiler/gnu/9.2.0/bin prepend-path MANPATH /opt/bwhpc/common/compiler/gnu/9.2.0/man prepend-path LD_LIBRARY_PATH /opt/bwhpc/common/compiler/gnu/9.2.0/lib64:/opt/bwhpc/common/compiler/gnu/9.2.0/lib setenv CC gcc setenv CXX g++ setenv F77 gfortran setenv FC gfortran setenv F90 gfortran module-whatis GNU compiler suite version 9.2.0 (gcc, g++, gfortran, gccgo) conflict compiler/gnu -------------------------------------------------------------------
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
or
$ module remove 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 compiler/gnu/9.2 compiler/gnu/9.2 : GNU compiler suite version 9.2.0 (gcc, g++, gfortran, gccgo)