• Compilers and eco systems: GNU family, Intel’s oneAPI, Nvidia’s hpc-sdk

• Languages: C/C+, Fortran, Go, Java, Julia, Perl, Python, R, Ruby, Rust

• Scientific libraries and toolkits: Built with a specific compiler: GNU by default

• Standalone applications and utilities: Installed using:

  • Conda environments.

  • Containers: running Singularity (not Docker).

    • We can create a Singularity image from a Docker image.

  • Linux based Binaries/Executables

Check the MedicineBow Software Page.

Use module list to view the modules you are currently loaded in your session:

Use module avail to see what modules are currently available that you can be loaded your current session:

# What's available within my 'current' environment.
# With respect to what modules I 'currently' have loaded.
[]$ module avail
...

Some software has to be built with respect to a compiler.

By default we build using the GNU family of compilers for C/C++ and Fortran.

Some commands have shortcuts. Using ml is the a shortcut to module list.

[]$ module load purge
[]$ module load gcc/1314.2.0
[]$ ml
Currently Loaded Modules:
  1) slurm/latest (S)   3) gmp/6.2.1  (S)   5) mpc/1.3.1_x86_64
      72) zstdarcc/1.5.50    2) arcc/1.0     (S)   46) mpfrzlib-ng/4.2.01.4_x86_64
  63) zlib-nggmp/6.2.1.4_x86_64        7) zstd/1.5.5_x86_64__programs_True
  84) gccmpfr/134.2.0

_x86_64       8) gcc/14.2.0

There are libraries that need to be loaded for gcc to work.

They are loaded automatically so you don’t have to.

Question What changed?

We can now wee see all the modules available that have been compiled with gcc/1314.2.0

These are only available after the gcc/14.2.0 module has been loaded.

Let’s see what happens to our environment if we load a different compiler.

[]# module load nvhpc-sdk/24.3
Lmod is automatically replacing "gcc/14.2.0" with "nvhpc-sdk/24.3".

Again, what happened?

[]$ ml
Currently Loaded Modules:
  1) slurm/latest (S)   2) arcc/1.0 (S)   3) nvhpc-sdk/24.3

[]$ module avail
# Modules relating to 

Only modules relating to nvhpc-sdk/24.3

are

now

available.

Use the module purge command to reset your environment to the initial defaults.

Again, what has changed?

We are back to having the two modules slurm/latest and arcc/1.0 loaded (by default) and the initial set of available modules.

The more modules you have loaded, the more dependencies you will have loaded and the more likely you are to forget what you have loaded…

As mentioned earlier, do not use the --force option to unload the slurm and arcc modules.

[]$ module spider openmpi
----------------------------------------------------------------------------
  openmpi: openmpi/4.1.6
----------------------------------------------------------------------------
     OtherVersions:
possible modules matches:      openmpi/4.1.6
  nvhpc-openmpi3      You will need to load all module(s) on any one of the lines below before the "openmpi/4.1.6" module is available to load.

      arcc/1.0  gcc/13.2.0
...

If you module spider a specific version it will list the dependencies that are required to first be loaded before it can be used:

[]$ module spider openmpi/5.0.5
----------------------------------------------------------------------------
  openmpi: openmpi/5.0.5
----------------------------------------------------------------------------
    You will need to load all module(s) on any one of the lines below before the "openmpi/5.0.5" module is available to load.
      arcc/1.0  gcc/14.2.0
    Help:
      An open source Message Passing Interface implementation. ...

Try loading before loading gcc/14.2.0:

[]$ module purge
[]$ module load openmpi/5.0.5
Lmod has detected the following error: These module(s) or extension(s) exist
but cannot be loaded as requested: "openmpi/5.0.5"
   Try: "module spider openmpi/5.0.5" to see how to load the module(s).

Load the required dependencies, then re-try:

[]$ module load gcc/14.2.0
[]$ module load openmpi/5.0.5
[]$

Let’s check everything has been loaded successfully:

[]$ which mpicc
/apps/u/opt/gcc/14.2.0/openmpi/5.0.5/bin/mpicc

[]$ mpicc --version
gcc (Spack GCC) 14.2.0
Copyright (C) 2024 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

After loading openmpi/5.0.5 what do we notice about what is now loaded and available?

[]$ ml
[]$ module avail

Notice we have opened up an additional set of modules:

---- /apps/s/lmod/mf/spack/linux-rhel9-x86_64/openmpi/5.0.5-jk3nxsx/gcc/14.2.0 ----
   adios2/2.9.2-ompi                        netcdf-cxx4/4.3.1-ompi
...
   ior/3.3.0-ompi                           wannier90/3.1.0-ompi
   netcdf-c/4.9.2-ompi
...

Due to dependencies, there can be a hierarchy of core modules that need to be loaded to make other libraries and software available.

For example, some libraries, such as fftw, need to be built with gcc/14.2.0 and use the openmpi/5.0.5 library.

Typically their version number will be prefixed with -ompi.

Try: []$ module spider fftw

What do we notice about the required dependencies for the following versions of Python?

[]$ module spider python/3.10.6
[]$ module spider python/3.12.0
[]$ module spider python2

The two python/3.x versions have both been installed using both the gcc/13.2.0 and gcc/14.2.0 compilers.

You need to choose which gcc compiler version first before we can use them.

[]$ module spider python/3.10.6
[]$ module spider python/3.12.0
...
    You will need to load all module(s) on any one of the lines below before the "python/3.12.0" module is available to load.
      arcc/1.0  gcc/13.2.0
      arcc/1.0  gcc/14.2.0
...      

The python/2 module has no dependencies, can can be loaded straight away:

[]$ module spider python2
----------------------------------------------------------------------------
  python2: python2/2.7.18
----------------------------------------------------------------------------
    You will need to load all module(s) on any one of the lines below before the "python2/2.7.18" module is available to load.
      arcc/1.0

The module command has lots more sub-commands:

[]$ module
Modules based on Lua: Version 8.7  2022-04-16 13:49 -05:00
    by Robert McLay mclay@tacc.utexas.edu

module [options] sub-command [args ...]

Help sub-commands:
---------------------------------------
  python2: python2/2.7.18
--
  help                              prints this message
  help                module [...]  print help message from module(s)

Loading/Unloading sub-commands:
--------------------------------------------------------------------------
    You will need to load all module(s) on any one of the lines below before the "python2/2.7.18" module is available to load.
      arcc/1.0--
  load | add          module [...]  load module(s)
 ...