Using Modules to Manage Software
The Discovery cluster uses modules to manage the user environment for different third-party software versions. The advantage of the modules approach is that the user is no longer required to explicitly specify paths for different executable versions and to try to keep the PATH, MANPATH related environment variables coordinated. With the modules approach, users simply “load” and “unload” modules to control their environment.
Introduction
Modules provide an easy mechanism for updating a user’s environment especially the PATH, MANPATH, and LD_LIBRARY_PATH environment variables to name a few. When you get a Discovery cluster account, your dot files should be set up correctly to use modules. If you delete or modify these files in such a way as to make modules fail, contact the Discovery consultants for help.
You can modify your environment so that certain modules are loaded whenever you log in.
Use this command to have a module automatically loaded each time you log into the system:
module initadd modulename- where modulename is the name of the module you want loaded.
Module commands
module help – Get a usage list of module options
The listing has been abbreviated to only show those commands discussed on this page.
$ module help Available Commands and Usage: + add|load modulefile [modulefile ...] + rm|unload modulefile [modulefile ...] + switch modulefile1 modulefile2 + display modulefile [modulefile ...] + avail path [path] + list + initadd modulefile [modulefile ...] + help modulefile [modulefile ...] + initrm modulefile [modulefile ...] + initswitch modulefile1 modulefile2
module list – This lists all the modules which are currently loaded into the user’s environment.
$ module list Currently Loaded Modulefiles: 1) modules/3.2.9(default) 7) totalview/8.4(default) 2) matlab/r2013a(default) 8) maple/11.0(default) 3) intel-compilers/13.0(default) 9) mathematica/6.0(default) 4) pgi-compilers/7.1-3(default) 10) idl/7.0(default) 5) mpich/1.2.7p1-intel9.1(default) 11) opendx/4.4.0(default) 6) mpiexec/0.83(default) 12) paraview/3.2.1(default)
module avail – This option lists all the modules which are available to be loaded.
Notice that many of them have version numbers associated with them. Modules make it easy to switch compiler application versions. The default version is identified in the listing.
$module avail ------------------------ /opt/Modules/3.2.9/modulefiles ------------------------ acml/4.1.0-intel(default) mpich/1.2.7p1-pgi7.1.3 dot mpich2/1.0.7rc2-intel9.1(default) idl/7.0(default) mpiexec/0.83(default) intel-compilers/9.1(default) mumps/4.7.3-intel(default) maple/11.0(default) mvapich/0.99-gcc4.1.2 mathematica/6.0(default) mvapich/0.99-intel9.1(default) matlab/r2007b mvapich/0.99-pgi7.1.3 matlab/r2009a(default) mvapich2/0.98-intel9.1(default) mkl/9.0(default) netcdf/3.6.2(default) moduleinfo opendx/4.4.0(default) modules/3.2.6(default) paraview/3.2.1(default) mpich/1.2.7p1-gcc4.1.2 pgi-compilers/7.1-3(default) mpich/1.2.7p1-intel9.1(default) scalapack/1.7.3-intel(default) mpich/1.2.7p1-intel9.1-gcc totalview/8.4(default)
module help modulefile* – To retrieve more information about a module, use this command to display the help information contained within the given module file.
$ module help netcdf ----------- Module Specific Help for 'netcdf/3.6.2' --------------- Sets up the environment to use the netCDf libraries Sets up the netCDF libraries, include files, binaries and man pages. Add $NETCDF_LIB to include the netcdf library when linking your program. Example: ifort -o myprog myproc.f $NETCDF_LIB Add $NETCDF_INCLUDE to include the netcdf include files when compiling. Example: ifort $NETCDF_INCLUDE -c myproc.f
module display modulefile – Use this command to see exactly what a given modulefile will do to your environment, such as what will be added to the PATH, MANPATH, and other environment variables.
$ module display matlab ------------------------------------------------------------------- /opt/Modules/3.2.9/modulefiles/matlab/r2009a: module-whatis loads Matlab version R2009a prepend-path PATH /opt/matlab/Matlab_R2009a/bin -------------------------------------------------------------------
module load modulefile – This adds one or more modulefiles to the user’s current environment. It does so silently unless there is a problem with a modulefile.
If you load the generic name of a module, you will get the default version.
To load a specific version, load the module using its full specification.
module load matlab/r2007b
module unload modulefile – This removes any listed modules from the user’s current environment.
The modules can be removed in any order.
module unload matlab/r2007b
module switch old_modulefile new_modulefile – This command demonstrates the true advantages of modules. Different versions of entire software packages can be replaced with a single module command.
module initadd modulefile – This command modifies your environment so the module is loaded automatically whenever you log in.
module initrm modulefile – This command modifies your environment so the module will not be loaded automatically when you log into the system.
module initswitch modulefile1 modulefile2 – This command modifies your environment so the modulefile2 will be loaded automatically instead of modulefile1.