Let’s set up an environment to enable us to run Python scripts:

Can we combine the two module load commands into a single line?

What is the difference, what happens, when we try the following two methods:

[]$ module purge
[]$ module load python/3.12.0 gcc/13.2.0
vs
[]$ module purge
[]$ module load gcc/13.2.0 python/3.12.0

Order matters!

Dependencies must be loaded first, from left to right.

Now lets load a version of Python and see what happens:

[]$ module load gcc/13.2.0 python/3.12.0
[]$ echo $PATH
/apps/u/spack/gcc/13.2.0/python/3.12.0-ovfqpv2/bin:/apps/u/spack/gcc/13.2.0/util-linux-uuid/2.38.1-x54sns7/bin:
/apps/u/spack/gcc/13.2.0/sqlite/3.43.2-vkxcwyj/bin:/apps/u/spack/gcc/13.2.0/openssl/3.1.3-shbr5xo/bin:
/apps/u/spack/gcc/13.2.0/gettext/0.22.3-54ib6sn/bin:/apps/u/spack/gcc/13.2.0/tar/1.34-drux4fh/bin:
/apps/u/spack/gcc/13.2.0/pigz/2.7-6mr4kci/bin:/apps/u/spack/gcc/13.2.0/libxml2/2.10.3-5toq4pi/bin:
/apps/u/spack/gcc/13.2.0/xz/5.4.1-uainak7/bin:/apps/u/spack/gcc/13.2.0/libiconv/1.17-3dj22ny/bin:
/apps/u/spack/gcc/13.2.0/gdbm/1.23-idyayjv/bin:/apps/u/spack/gcc/13.2.0/readline/8.2-j6zrtuz/bin:
/apps/u/spack/gcc/13.2.0/ncurses/6.4-y257enz/bin:/apps/u/spack/gcc/13.2.0/expat/2.5.0-3aw2urq/bin:
/apps/u/spack/gcc/13.2.0/bzip2/1.0.8-7q5awx3/bin:/apps/u/spack/gcc/11.4.1/gcc/13.2.0-sxnvmb2/bin:
/apps/u/spack/gcc/13.2.0/zstd/1.5.5-ibvf7gj/bin:/apps/s/arcc/1.0/bin:
/apps/s/slurm/latest/bin:/home/<username>/.local/bin:/home/<username>/bin:/usr/share/Modules/bin:
/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin

[]$ which python
/apps/u/spack/gcc/13.2.0/python/3.12.0-ovfqpv2/bin/python

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

Can we use R within an environment?

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

Can we search for it?

[]$ module spider r
# What do we see and why?

# Does this work? 

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 it

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.

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

[]$ 
# How many dependencies have automatically been loaded?
[]$ ml

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?

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:

[]$ module load oneapi/2024.1.0
Lmod is automatically replacing "gcc/13.2.0" with "oneapi/2024.1.0".
Inactive Modules:
  1) cairo/1.16.0                    30) libxcb/1.14
...
 29) libxau/1.0.8                    58) xtrans/1.4.0
Due to MODULEPATH changes, the following have been reloaded:
  1) berkeley-db/18.1.40     6) libiconv/1.17     11) pigz/2.7         16) zlib-ng/2.1.4
...
  5) libbsd/0.11.7          10) perl/5.38.0       15) xz/5.4.1

[]$ R --version
-bash: R: command not found

[]$ python --version
Python 3.9.18
[]$ which python
/usr/bin/python

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 Modules:
  1) slurm/latest    (S)   8) xz/5.4.1        15) berkeley-db/18.1.40
  2) arcc/1.0        (S)   9) libxml2/2.10.3  16) readline/8.2
  3) oneapi/2024.1.0      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/1.34        19) libmd/1.0.4
  6) bzip2/1.0.8          13) gettext/0.22.3  20) libbsd/0.11.7
  7) libiconv/1.17        14) pkgconf/1.9.5

  Where:
   S:  Module is Sticky, requires --force to unload or purge

Inactive Modules:
...
  13) python/3.10.6            42) libtirpc/1.3.3
...
  29) pixman/0.42.2            58) r/4.4.0

Yes, both R and Python are listed.

But these are listed as Inactive Modules, so are no longer available to use.

We would suggest, as a good practice, always perform a module purge before changing compilers and generate a clean environment.

[]$ module purge
[]$ module load oneapi/2024.1.0
[]$ ml
Currently Loaded Modules:
  1) slurm/latest (S)   2) arcc/1.0 (S)   3) oneapi/2024.1.0