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

What is happening to our environment when we’re loading modules?

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

[]$ module load gcc/13.2.0 python/xz/53.4.1-uainak7/bin:/apps/u/spack/gcc/13.2.0/libiconv/1.17-3dj22ny/bin:12.0
[]$ echo $PATH
/apps/u/spack/gcc/13.2.0/gdbmpython/1.23-idyayjv/bin:/apps/u/spack/gcc/13.2.0/readline/8.2-j6zrtuz3.12.0-ovfqpv2/bin:
/apps/u/spack/gcc/13.2.0/ncurses/6.4-y257enz/bin:/apps/u/spack/gcc/13.2.0/expat/2.5.0-3aw2urqutil-linux-uuid/2.38.1-x54sns7/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

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

The /apps/u/spack/gcc/13.2.0/python/3.12.0-ovfqpv2/bin path is before the /usr/bin/ so it is picking up python/3.12.0 before the system’s version.

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?

Notice from the module spider r/4.4.0 that this module has a dependency on gcc/13.2.0.

Until gcc/13.2.0 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?

[]$ ml
Currently Loaded Modules:
  1) slurm/latest           (S)  42) libxau/1.0.8

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

...
 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"

Question: 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 you 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 affect modules that have the first compiler as a dependency.

So, with the above, R has been made inactive and is no longer available, and Python has also been made inactive and reverts back to the System version.

[]$ ml
Currently Loaded Modules:
  1) slurm/latest    (S)   8) xz/5.4.1        15) berkeley-db/18.1.40
...
  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 active to use - and thus R can not be called.

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

• Only one compiler/version can be loaded into your environment at a time.

• Can only load languages/applications built with the same compiler. 

• But, even this can introduce dependency issues.

Try answers the following questions:

• What modules are available that relate to netcdf?

• What modules become available after loading nvhpc-sdk/24.3?

• How would you identify modules that have no dependencies?