Linux Software

Using Modules to Manage Access to Software

On mimi, users should not have to modify their path directly.  Instead, the module utility is used to set environment variables for software and libraries, including a lot of software that is loaded by default.  Simply ``load'' and ``unload'' modules to control your environment.

Modules environment management package provides support for dynamic modification of the user environment via modulefiles. Each modulefile contains all the information needed to configure the shell for a particular application. Typically, a modulefile modifies environment variables like PATH, MANPATH, LD_LIBRARY_PATH and XXXX_HOME (where XXX is the name of a software/library in capital letter) to give access to an application or library.

What is loaded now?

[mimi ~]$  module list

Currently Loaded Modulefiles:
  1) geosciences   2) use.own

What is available?

To see which modulefiles are available on your system, enter this command:

[mimi ~]$  module avail [string]

The module avail command produces an alphabetical listing of every modulefile in your module use path and has no option for "grepping." Therefore, it is usually more useful to use the command with an string argument:

[mimi ~]$  module avail python

---------------------------------------------------- /opt/software/easybuild/modules/all ----------------------------------------------------
   flatbuffers-python/2.0-GCCcore-11.2.0    Python/2.7.18-GCCcore-11.2.0-bare    Python/3.9.6-GCCcore-11.2.0                                
   netcdf4-python/1.5.7-foss-2021b          Python/2.7.18-GCCcore-11.3.0-bare    Python/3.10.4-GCCcore-11.3.0-bare                          
   pkgconfig/1.5.5-GCCcore-11.2.0-python    Python/3.9.5-GCCcore-10.3.0-bare     Python/3.10.4-GCCcore-11.3.0                               
   protobuf-python/3.17.3-GCCcore-10.3.0    Python/3.9.5-GCCcore-10.3.0          Python/3.10.8-GCCcore-12.2.0-bare                          
   protobuf-python/3.17.3-GCCcore-11.2.0    Python/3.9.6-GCCcore-11.2.0-bare     Python/3.10.8-GCCcore-12.2.0                               

Loading and Unloading Modules

If a modulefile is not already loaded, use the module load command to load:

[mimi ~]$  module load netCDF/4.9.0-gompi-2022b

If you want to remove a software/library from your user environment you may unload it:

mimi ~]$  module unload netcdf/4.2.0_intel

You need to unload the same version you previously loaded.

Module Swapping

Alternatively, you can use the module swap command to unload one module and load the comparable module:

[mimi ~]$  module load netCDF/4.9.0-gompi-2022b

[mimi ~]$  module list

Currently Loaded Modules:
  1) GCCcore/12.2.0                  8) libpciaccess/0.17-GCCcore-12.2.0  15) UCC/1.1.0-GCCcore-12.2.0    22) lz4/1.9.4-GCCcore-12.2.0
  2) zlib/1.2.12-GCCcore-12.2.0      9) hwloc/2.8.0-GCCcore-12.2.0        16) OpenMPI/4.1.4-GCC-12.2.0    23) zstd/1.5.2-GCCcore-12.2.0
  3) binutils/2.39-GCCcore-12.2.0   10) OpenSSL/1.1                       17) gompi/2022b                 24) bzip2/1.0.8-GCCcore-12.2.0
  4) GCC/12.2.0                     11) libevent/2.1.12-GCCcore-12.2.0    18) Szip/2.1.1-GCCcore-12.2.0   25) netCDF/4.9.0-gompi-2022b
  5) numactl/2.0.16-GCCcore-12.2.0  12) UCX/1.13.1-GCCcore-12.2.0         19) HDF5/1.14.0-gompi-2022b
  6) XZ/5.2.7-GCCcore-12.2.0        13) libfabric/1.16.1-GCCcore-12.2.0   20) cURL/7.86.0-GCCcore-12.2.0
  7) libxml2/2.10.3-GCCcore-12.2.0  14) PMIx/4.2.2-GCCcore-12.2.0         21) gzip/1.12-GCCcore-12.2.0

[mimi ~]$  module swap netCDF/4.8.1-gompi-2021b

The following have been reloaded with a version change:
  1) GCC/12.2.0 => GCC/11.2.0                                        11) gompi/2022b => gompi/2021b
  2) GCCcore/12.2.0 => GCCcore/11.2.0                                12) hwloc/2.8.0-GCCcore-12.2.0 => hwloc/2.5.0-GCCcore-11.2.0
  3) HDF5/1.14.0-gompi-2022b => HDF5/1.12.1-gompi-2021b              13) libevent/2.1.12-GCCcore-12.2.0 => libevent/2.1.12-GCCcore-11.2.0
  4) OpenMPI/4.1.4-GCC-12.2.0 => OpenMPI/4.1.1-GCC-11.2.0            14) libfabric/1.16.1-GCCcore-12.2.0 => libfabric/1.13.2-GCCcore-11.2.0
  5) PMIx/4.2.2-GCCcore-12.2.0 => PMIx/4.1.0-GCCcore-11.2.0          15) libpciaccess/0.17-GCCcore-12.2.0 => libpciaccess/0.16-GCCcore-11.2.0
  6) Szip/2.1.1-GCCcore-12.2.0 => Szip/2.1.1-GCCcore-11.2.0          16) libxml2/2.10.3-GCCcore-12.2.0 => libxml2/2.9.10-GCCcore-11.2.0
  7) UCX/1.13.1-GCCcore-12.2.0 => UCX/1.11.2-GCCcore-11.2.0          17) netCDF/4.9.0-gompi-2022b => netCDF/4.8.1-gompi-2021b
  8) XZ/5.2.7-GCCcore-12.2.0 => XZ/5.2.5-GCCcore-11.2.0              18) numactl/2.0.16-GCCcore-12.2.0 => numactl/2.0.14-GCCcore-11.2.0
  9) binutils/2.39-GCCcore-12.2.0 => binutils/2.37-GCCcore-11.2.0    19) zlib/1.2.12-GCCcore-12.2.0 => zlib/1.2.11-GCCcore-11.2.0
 10) cURL/7.86.0-GCCcore-12.2.0 => cURL/7.78.0-GCCcore-11.2.0

Loading modules automatically

By default, one module is loaded at login (geosciences). However, you may want to customize your environment and load modules that you use often at login. It is recommended that you do this by creating a ~/.modulerc file. This file must contain the special modulefile token "#%Module1.0" on the first line followed by one or more module commands:

#%Module1.0

set version 1.0
module load netCDF/4.9.0-gompi-2022b

This will cause this version of netCDF to be automatically loaded when you log in.

Adding your our modulefile

Create a directory called privatemodules in your home directory. Then type the command:

module load use.own

and any personal module files in this directory will become available for you to list, load or unload. As previously explained, you can add it to ~/.modulerc to load it automatically at login.

Our modulefiles are in /opt/software/custom/modules and they can be copied to use as templates.