Loading modules updates a number of environment variables exposing the compiler/application/software we want to use.

Loading modules does not change anything in your /home nor /project storage space - nothing is being installed.

What is being updated are the environment variables within your current session. These are not persistent across other sessions.

You can have two or more sessions opened at the same time, each with different modules loaded - but all still sharing the same file storage system.

Remember, that the order that the system will look within paths is from left to right.

The /apps/u/spack/.

Until gcc/13.2.0 has been loaded, we will not see r/4.4.0 being available.

Can we use R within an environment?

[]$ module purge
[]$ module avail

Do we see R available within the default list of available modules? No.

Can we search for it?

[]$ module spider r

From what is returned by module spider, can you see why it isn’t currently available?

Can we load it?

[]$ module load r/4.4.0

How do we fix this?

The module r/4.4.0 has a dependency on gcc/13.2.0.

Until this module has been loaded, we will not see r/4.4.0 being available.

[]$ module purge
[]$ module load gcc/13.2.0 r/4.4.0

Once r/4.4.0 has been loaded, how many additional dependencies/libraries have also been loaded?

[]$ ml
Currently Loaded Modules:
  1) slurm/latest           (S)  42) libxau/1.0.8
...
 40) libpthread-stubs/0.4        81) r/4.4.0
 41) xproto/7.0.31

A lot! The module system hides the loading of all these additional libraries.

Let’s check R is loaded:

[]$ R --version
R version 4.4.0 (2024-04-24) -- "Puppy Cup"

We know we can only have one compiler loaded at a time.

Can we have more than one language loaded at a time?

First load r/4.4.0, and then python/13.2.0 - what do we notice?

[]$ module purge
[]$ module load gcc/13.2.0 r/4.4.0

[]$ module load python/3.12.0
-------------------------------------------------------------------------------
The following dependent module(s) are not currently loaded: python/3.10.6 (required by: glib/2.78.0, xcb-proto/1.15.2, gobject-introspection/1.76.1)
-------------------------------------------------------------------------------
The following have been reloaded with a version change:
  1) python/3.10.6 => python/3.12.0

[]$  R --version
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
[]$ python --version
Python 3.12.0

Notice: Loading R automatically loaded python/3.10.6. This is actually a dependency that was loaded during the loading of R.

After loading a module, consider calling ml to see what dependencies have also been loaded.

Loading python/3.12.0 replaced this version.

Does replacing python/3.10.6 with python/3.12.0 affect R?

Potentially: We do not know how this is being used and thus can’t say definitively if it does/doesn’t affect the running of R.

We would suggest airing on the side of caution and check everything is running as expected if you notice modules being replaced.

After loading R and Python, what happens if I replace the gcc compiler?

Load the Intel oneApi compiler and see what happens to your environment:

Notice: Loading R automatically loaded python/3.10.6. This is actually a dependency that was loaded during the loading of R.

After loading a module, consider calling ml to see what dependencies have also been loaded.

Loading python/3.12.0 replaced this version.

Remember: You can only have one compiler loaded at a time. Replacing one compiler with another will also remove and modules that have this first compiler as a dependency.

So, with the above, R has been removed and is no longer available, and Python has been removed and reverted back to the System version.

But, what can we see if we list the modules available?

[]$ ml
Currently Loaded Modules30) libxcb/1.14
...
 29) libxau/1.0.8                    58) xtrans/1.4.0
Due to MODULEPATH changes, the following have been reloaded:
  1) slurm/latestberkeley-db/18.1.40     (S)6) libiconv/1.17    8 11) xzpigz/5.4.12.7         1516) berkeleyzlib-dbng/182.1.4
...40
  25) arcclibbsd/10.11.07        (S)   910) libxml2perl/25.1038.30   16) readline/8.2   315) oneapixz/20245.4.1.0

[]$ R --version
-bash: R: 10) ncurses/6.4     17) gdbm/1.23
  4) zlib-ng/2.1.4        11) pigz/2.7        18) perl/5.38.0
  5) zstd/1.5.5           12) tar/1.34command not found

[]$ python --version
Python 3.9.18

[]$ which python
/usr/bin/python