Access Software

You can access pre-installed software or install your own

Modules are a utility which allow users to load and manage applications and their versions. The modules of software packages allow you to dynamically modify your user environment by using “modulefiles.” Each modulefile contains the information needed to configure the shell for an application. After the module software package is initialized, the environment can be modified on a per-module basis using the module command, which interprets modulefiles. Typically, modulefiles instruct the module command to change or set shell environment variables such as PATH, MANPATH, and others. The modulefiles can be shared by many users on a system.

Note: Some modules cannot be used simultaneously, such as an Intel compiler and a GNU compiler. If you attempt to load a module that is incompatible with a currently-loaded module, you will be prompted of the conflict. To avoid the error, you may have to unload or switch modules.

Default Software Stack

LMOD modules are used to provision the software environment for users. The default software stack is built on GNU 8.3.0 and OpenMPI 3.1.3 MPI library.

$user@hpc[~]  module list

Currently Loaded Modules:
  1) autotools   2) prun/1.2   3) gnu8/8.3.0   4) openmpi3/3.1.3   5) ohpc

Switching Software Stacks

However, you may choose to a different software stack built on a different compiler and MPI library combination. It is advisable to stick with one combination of compiler and MPI library for most of your software to avoid conflicts.

You can switch to a software stack based on GNU7 compilers and OpenMPI3 libraries or Intel compilers and OpenMPI3 libraries easily using the module swap option.

GNU7-OpenMPI3 Stack

$user@hpc[~] module swap gnu8 gnu7

The following have been reloaded with a version change:
  1) openmpi3/3.1.3 => openmpi3/3.1.0

$user@hpc[~]  module list

Currently Loaded Modules:
  1) autotools   2) prun/1.2   3) ohpc   4) gnu7/7.3.0   5) openmpi3/3.1.0

Intel-OpenMPI3 Stack

$user@hpc[~]  module swap gnu8 intel

Due to MODULEPATH changes, the following have been reloaded:
  1) openmpi3/3.1.3

$user@hpc[~]  module list

Currently Loaded Modules:
  1) autotools   2) prun/1.2   3) ohpc   4) intel/19.0.3.199   5) openmpi3/3.1.3

You can see a list of all available modules using the module avail command.

$user@host[~]  module avail

-------------------------------------------------------------------- /opt/ohpc/pub/moduledeps/gnu8-openmpi3 --------------------------------------------------------------------
   adios/1.13.1     fftw/3.3.8      mpiP/3.4.1              netcdf/4.6.2          pnetcdf/1.11.0      py3-mpi4py/3.0.0    scorep/4.1            tau/2.28
   boost/1.69.0     hypre/2.15.1    mumps/5.1.2             opencoarrays/2.2.0    ptscotch/6.0.6      py3-scipy/1.2.1     sionlib/1.7.2         trilinos/12.12.1
   dimemas/5.3.4    imb/2018.1      netcdf-cxx/4.3.0        petsc/3.10.3          py2-mpi4py/3.0.0    scalapack/2.0.2     slepc/3.10.2
   extrae/3.5.2     mfem/3.4        netcdf-fortran/4.4.5    phdf5/1.10.4          py2-scipy/1.2.1     scalasca/2.4        superlu_dist/6.1.1

------------------------------------------------------------------------ /opt/ohpc/pub/moduledeps/gnu8 -------------------------------------------------------------------------
   hdf5/1.10.4        likwid/4.3.3    mpich/3.3       ocr/1.0.1         openmpi3/3.1.3 (L)    py2-numpy/1.15.3    superlu/5.2.1
   impi/2019.3.199    metis/5.1.0     mvapich2/2.3    openblas/0.3.5    pdtoolkit/3.25        py3-numpy/1.15.3

-------------------------------------------------------------------------- /opt/ohpc/pub/modulefiles ---------------------------------------------------------------------------
   EasyBuild/3.7.1           clustershell/1.8    gnu7/7.3.0           intel/19.0.3.199        papi/5.6.0        singularity/2.6.0
   autotools          (L)    cmake/3.12.2        gnu8/8.3.0    (L)    llvm5/5.0.1             pmix/2.1.4        valgrind/3.13.0
   charliecloud/0.9.2        cuda/9.2            hwloc/1.11.10        ohpc             (L)    prun/1.2   (L)

  Where:
   L:  Module is loaded

Summary of Module Commands

Command	Description
module list	Lists modules currently located in user's environment
module avail	Lists all available modules on a system in condensed format
module avail -l	Lists all available modules on a system in long format
module display	Shows environment changes that will be made by loading a given module
module load	Loads a module
module unload	Unloads a module
module help	Shows help for a module
module swap	Swaps a currently loaded module for an unloaded module

Modules: Local repository By default the local repository is used as a source of software installations. To list available modules, type module avail. To load a module, use module load module_name. Similarly, unload modules by typing module unload module_name.

Available Modules

To see a list of available modules, type

$user@host[~]  module avail

📝 Note: If you need a module that is not available, please contact us.

You can check for the existence of a module and its versions using module avail <module-name>.

$user@host[~]  module avail cuda

----------------- /software/dev/modulefiles -----------------
cuda/9.2          cuda/10.1(default)       

Working with Modules

When you load a module, your environment is modified to use a specific software package. To load a module:

$user@host[~]  module load chem/vmd

To verify your module has loaded, you can type module list.

To display information about the attributes of the module such as the size of the module, the compiler or the source from which the module was created, etc., use the following command:

$user@host[~]  module display your_module

Removing and Switching Modules

Unloading a module will avoid conflict and/or messages of failure due to different versions or dependencies.

$user@host[~]  module unload cuda/10.1

Switching between different module versions can accomplish the task of having to load, unload and load modules in multiple steps. In the following example, cuda/9.2 is currently loaded. After running the command, cuda/10.1 is unloaded and cuda/9.2 is loaded.

$user@host[~]  module switch cuda/10.1 cuda/9.2

You can unload all the modules on your environment, by executing the module purge command:

$user@host[~] module purge