Total: 45min (Teaching:30Min | Discussion:0min | Breaks:0min | Exercises:15Min)
How can we find out which scientific software is installed on the HPC cluster?
How can we access scientific software on the HPC cluster?
Understand how the UNIX system looks for installed software
Understand how to load and use a software package
Search for software with
Load software with
Unload software with
The module system handles software versioning and will prevent package conflicts for you automatically
On a high-performance computing system, it is seldom the case that the software we want to use is available when we log in. It is installed, but we will need to “load” it before it can run.
Before we start using individual software packages, however, we should understand the reasoning behind this approach. The three biggest factors are:
Software incompatibility is a major headache for programmers. Sometimes the presence (or absence) of
a software package will break others that depend on it. Two of the most famous examples are Python 2
and 3 and C compiler versions. Python 3 famously provides a
python command that conflicts with
that provided by Python 2. Software compiled against a newer version of the C libraries and then
used when they are not present will result in a nasty
'GLIBCXX_3.4.20' not found error, for
Software versioning is another common issue. A team might depend on a certain package version for their research project - if the software version was to change (for instance, if a package was updated), it might affect their results. Having access to multiple software versions allow a set of researchers to prevent software versioning issues from affecting their results.
Dependencies are where a particular software package (or even a particular version) depends on having access to another software package (or even a particular version of another software package). For example, the VASP materials science software may depend on having a particular version of the FFTW (the Fastest Fourier Transform in the West) software library available for it to work.
Environment modules are the solution to these problems, and we will return to this after looking at globally installed packages.
Globally installed system packages
In this example we will use Python, which is installed globally on the login node in one particular version.
We can test what the
python command is actually pointing to by another command
which looks for programs the same way that Bash does, so we can use
it to tell us where a particular piece of software is stored.
MY_USER_NAMEd@CLUSTER_NAME ~]$ python --version Python 2.7.5 [MY_USER_NAME@CLUSTER_NAME ~]$ which python /usr/bin/python MY_USER_NAMEd@CLUSTER_NAME ~]$ python3 --version Python 3.6.8 [MY_USER_NAME@CLUSTER_NAME ~]$ which python3 /usr/bin/python3
We can see that
python3 executables are available. The former
points towards a Python 2 version and the latter to a rather old Python 3.6.
What the output of
which tells us is that typing the command
equivalent of running the full command
But how did the shell know that
python should be linked to
To explain this, we first need to understand the nature of the
PATH is a special environment variable that controls where a UNIX system
looks for software. We can inspect its value with the following command (
$ extracts its value, and
echo prints the value):
[MY_USER_NAME@CLUSTER_NAME ~]$ echo $PATH /node/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/cluster/bin:/cluster/home/MY_USER_NAME/.local/bin:/cluster/home/MY_USER_NAME/bin
What we see here is a colon-separated (
:) list of search paths that the shell
is looping through when looking for the
python command. In this case it finds
a match under
/usr/bin, so then it exits the search and replaces
Exercise (10 min)
What happens if there are other matching commands located later in the search
What happens if you have an executable script in your current directory with the same name as a globally installed program?
If there are other matching commands later in the search path, these will be shadowed by first found command. The shell will stop searching for more commands when it has found the command in a directory.
If your current directory is first in the search path it will executed. On the other hand if the directory with the global installed program is first in the search path, it will be executed. To execute a command named python in your current directory, do:
A module is a self-contained description of a software package - it contains the settings required to run a software package and, usually, encodes required dependencies on other software packages.
There are a number of different environment module implementations commonly
used on HPC systems: the two most common are TCL modules and Lmod. Both of
these use similar syntax and the concepts are the same so learning to use one will
allow you to use whichever is installed on the system you are using. In both
module command is used to interact with environment modules. An
additional subcommand is usually added to the command to specify what you want to do. For a list
of subcommands you can use
module -h or
module help. As for all commands, you can
access the full help on the man pages with
On login, you may start out with a default set of modules loaded, or you may start out with an empty environment; this depends on the setup of the system you are using.
Listing currently loaded modules
You can use the
module list command to see which modules you currently have loaded
in your environment. After logging into one of our systems, your environment
should ideally be clean like this:
[MY_USER_NAME@CLUSTER_NAME ~ ]$ module list Currently Loaded Modules: 1) StdEnv (S) Where: S: Module is Sticky, requires --force to unload or purge
You can see that one module is loaded which has special attribute of being
S). That means that it is not usually unloaded, typically because it
is important for the system to function correctly (so
--force removing it is
Finding and listing available modules
One way to look for available software is to search for keywords using
module keyword <KEYWORD>. This will look through the module meta data and return anything that
matches. For example, let’s list bioinformatics programs that can
be loaded using modules with
module keyword bio:
[MY_USER_NAME@CLUSTER_NAME ~]$ module keyword bio --------------------------------------------------------------------------------------------------- The following modules match your search criteria: "bio" --------------------------------------------------------------------------------------------------- ABySS: ABySS/2.0.2-gompi-2019a, ABySS/2.1.5-gompi-2020a Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler AUGUSTUS: AUGUSTUS/3.3.2-intel-2018b-Python-2.7.15, AUGUSTUS/3.3.3-foss-2019b, ... AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences BBMap: BBMap/38.50b-GCC-8.2.0-2.31.1, BBMap/38.79-GCC-8.3.0, BBMap/38.87-iccifort-2020.1.217 BBMap short read aligner, and other bioinformatic tools. bioawk: bioawk/1.0-foss-2018b Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. BioPerl: BioPerl/1.7.2-GCCcore-8.2.0-Perl-5.28.1, BioPerl/1.7.2-GCCcore-8.3.0, ... Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. [removed most of the output here for clarity]
Another option is to search directly on the module name using the
command. If you run this command without any search string it will produce a long
list of all the installed software modules, like this:
[MY_USER_NAME@CLUSTER_NAME ~]$ module avail ---------------------- /cluster/modulefiles/all --------------------------------------------------------------------------- 4ti2/1.6.9-GCC-8.2.0-2.31.1 gmsh/4.5.6-foss-2019b-Python-3.7.4 OpenMPI/3.1.1-gcccuda-2018b ABySS/2.0.2-gompi-2019a gnuplot/5.2.6-GCCcore-8.2.0 OpenMPI/3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30 AdapterRemoval/2.3.1-foss-2018b gnuplot/5.2.8-GCCcore-8.3.0 OpenMPI/3.1.3-GCC-8.2.0-2.31.1 AdapterRemoval/2.3.1-GCC-8.2.0-2.31.1 Go/1.13.1 OpenMPI/3.1.3-gcccuda-2019a ADF/2019.103+StaticMKL gompi/2018b OpenMPI/3.1.4-GCC-8.3.0 AdmixTools/5.1-GCC-7.3.0-2.30 gompi/2019a OpenMPI/3.1.4-gcccuda-2019b ADMIXTURE/1.3.0 gompi/2019b OpenMPI/3.1.4-PGI-19.9-GCC-8.3.0 [removed most of the output here for clarity] ---------------------- /cluster/modulefiles/external ---------------------------------------------------------------------- appusage/1.0 hpcx/2.4 hpcx/2.5 hpcx/2.6 Where: S: Module is Sticky, requires --force to unload or purge L: Module is loaded Aliases: Aliases exist: foo/1.2.3 (1.2) means that "module load foo/1.2" will load foo/1.2.3 Use "module spider" to find all possible modules. Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
You can refine the search by adding a search string to the command, like
module avail <SOFTWARE>. In contrast to the
module keyword search, which will only be
matched to the module name, not to any meta data. For example, we can list all modules
that matched the string ‘python/’ (including the ‘/’):
[MY_USER_NAME@CLUSTER_NAME ~]$ module avail python/ ------------------------------------------------ /cluster/modulefiles/all -------------------------- Biopython/1.72-foss-2018b-Python-2.7.15 netcdf4-python/1.4.1-intel-2018b-Python-3.6.6 Biopython/1.72-foss-2018b-Python-3.6.6 netcdf4-python/1.5.3-foss-2019b-Python-3.7.4 Biopython/1.72-intel-2018b-Python-2.7.15 netcdf4-python/1.5.3-intel-2019b-Python-3.7.4 Biopython/1.73-foss-2019a netcdf4-python/220.127.116.11-foss-2020b Biopython/1.73-intel-2019a netcdf4-python/18.104.22.168-intel-2020b Biopython/1.75-foss-2019b-Python-3.7.4 netcdf4-python/1.5.7-foss-2021b Biopython/1.75-intel-2019b-Python-3.7.4 netcdf4-python/1.5.7-intel-2021a Biopython/1.78-foss-2020a-Python-3.8.2 netcdf4-python/1.5.7-intel-2021b Biopython/1.78-foss-2020b pfft-python/0.1.21-foss-2020a-Python-3.8.2 Biopython/1.78-intel-2020a-Python-3.8.2 Python/2.7.15-foss-2018b Biopython/1.78-intel-2020b Python/2.7.15-fosscuda-2018b Biopython/1.79-foss-2021a Python/2.7.15-GCCcore-8.2.0 Biopython/1.79-foss-2021b Python/2.7.15-intel-2018b Biopython/1.79-intel-2021a Python/2.7.16-GCCcore-8.3.0 Biopython/1.79-intel-2021b Python/2.7.18-GCCcore-9.3.0 bx-python/0.8.2-foss-2018b-Python-2.7.15 Python/2.7.18-GCCcore-10.2.0 bx-python/0.8.4-foss-2019a Python/3.6.6-foss-2018b bx-python/0.8.9-foss-2020a-Python-3.8.2 Python/3.6.6-fosscuda-2018b bx-python/0.8.11-foss-2021a Python/3.6.6-intel-2018b GitPython/3.1.9-GCCcore-9.3.0-Python-3.8.2 Python/3.7.2-GCCcore-8.2.0 IPython/5.8.0-foss-2018b-Python-2.7.15 Python/3.7.4-GCCcore-8.3.0 IPython/7.2.0-foss-2018b-Python-3.6.6 Python/3.8.2-GCCcore-9.3.0 IPython/7.13.0-fosscuda-2020a-Python-3.8.2 Python/3.8.6-GCCcore-10.2.0 IPython/7.15.0-intel-2020a-Python-3.8.2 Python/3.9.5-GCCcore-10.3.0 netcdf4-python/1.4.1-foss-2018b-Python-3.6.6 Python/3.9.6-GCCcore-11.2.0 Use "module spider" to find all possible modules. Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
Loading and unloading software
Any of the software modules that we found in the previous section can be loaded
into our environment using the
module load command. Let’s say we are not happy
with the system version of Python that we get when logging in to the cluster
(see “Globally installed system packages” above). We can then instead load a
module for the Python version that we want:
[MY_USER_NAME@CLUSTER_NAME ~ ]$ module load Python/3.9.6-GCCcore-11.2.0 [MY_USER_NAME@CLUSTER_NAME ~ ]$ which python /cluster/software/Python/3.9.6-GCCcore-11.2.0/bin/python [MY_USER_NAME@CLUSTER_NAME ~ ]$ python --version Python 3.9.6
So, what just happened? Let’s have a look at the
PATH variable again:
[MY_USER_NAME@CLUSTER_NAME ~ ]$ echo $PATH /cluster/software/Python/3.9.6-GCCcore-11.2.0/bin: /cluster/software/OpenSSL/1.1/bin: .... /cluster/bin: /cluster/home/MY_USER_NAME/.local/bin: /cluster/home/MY_USER_NAME/bin
You’ll notice that the output is much longer than it was before we
loaded the Python module, and if you look closely you’ll see that the last
entries of the output are identical to what we had before. This means that by
loading the module, we changed the
PATH by adding entries to the beginning
of the list. This means that the shell will now start looking into the
/cluster/software/Python/3.9.6-GCCcore-11.2.0/bin etc. locations, before
moving on the the “system” paths
Let’s examine what’s there:
[MY_USER_NAME@CLUSTER_NAME ~ ]$ ls -lh /cluster/software/Python/3.9.6-GCCcore-11.2.0/bin .... -rwxrwxr-x 1 vegarde sysapp 264 nov. 4 09:15 py.test lrwxrwxr-x 1 vegarde sysapp 9 nov. 4 08:54 python -> python3.9 lrwxrwxr-x 1 vegarde sysapp 9 nov. 4 08:54 python3 -> python3.9 -rwxrwxr-x 1 vegarde sysapp 13K nov. 4 08:53 python3.9 -rwxrwxr-x 1 vegarde sysapp 3,2K nov. 4 08:54 python3.9-config ....
Taking this to its conclusion,
module load will add software to your
$PATH. It “loads”
software. A special note on this - depending on which version of the
module program that is
installed at your site,
module load will also load required software dependencies.
To demonstrate, let’s use
module list shows all loaded software modules.
[MY_USER_NAME@CLUSTER_NAME ~ ]$ module list Currently Loaded Modules: 1) StdEnv (S) 8) Tcl/8.6.11-GCCcore-11.2.0 (H) 2) GCCcore/11.2.0 9) SQLite/3.36-GCCcore-11.2.0 (H) 3) zlib/1.2.11-GCCcore-11.2.0 (H) 10) XZ/5.2.5-GCCcore-11.2.0 (H) 4) binutils/2.37-GCCcore-11.2.0 (H) 11) GMP/6.2.1-GCCcore-11.2.0 (H) 5) bzip2/1.0.8-GCCcore-11.2.0 (H) 12) libffi/3.4.2-GCCcore-11.2.0 (H) 6) ncurses/6.2-GCCcore-11.2.0 (H) 13) OpenSSL/1.1 (H) 7) libreadline/8.1-GCCcore-11.2.0 (H) 14) Python/3.9.6-GCCcore-11.2.0 Where: S: Module is Sticky, requires --force to unload or purge H: Hidden Module [MY_USER_NAME@CLUSTER_NAME ~ ]$ module purge [MY_USER_NAME@CLUSTER_NAME ~ ]$ module list Currently Loaded Modules: 1) StdEnv (S) Where: S: Module is Sticky, requires --force to unload or purge [MY_USER_NAME@CLUSTER_NAME ~ ]$ module load BLAST+/2.11.0-gompi-2020a [MY_USER_NAME@CLUSTER_NAME ~ ]$ module list Currently Loaded Modules: 1) GCCcore/9.3.0 7) libxml2/2.9.10-GCCcore-9.3.0 13) OpenMPI/4.0.3-GCC-9.3.0 19) libpng/1.6.37-GCCcore-9.3.0 2) zlib/1.2.11-GCCcore-9.3.0 8) libpciaccess/0.16-GCCcore-9.3.0 14) gompi/2020a 20) NASM/2.14.02-GCCcore-9.3.0 3) binutils/2.34-GCCcore-9.3.0 9) hwloc/2.2.0-GCCcore-9.3.0 15) bzip2/1.0.8-GCCcore-9.3.0 21) libjpeg-turbo/2.0.4-GCCcore-9.3.0 4) GCC/9.3.0 10) libevent/2.1.11-GCCcore-9.3.0 16) PCRE/8.44-GCCcore-9.3.0 22) LMDB/0.9.24-GCCcore-9.3.0 5) numactl/2.0.13-GCCcore-9.3.0 11) UCX/1.8.0-GCCcore-9.3.0 17) Boost/1.72.0-gompi-2020a 23) BLAST+/2.11.0-gompi-2020a 6) XZ/5.2.5-GCCcore-9.3.0 12) libfabric/1.11.0-GCCcore-9.3.0 18) GMP/6.2.0-GCCcore-9.3.0 [MY_USER_NAME@CLUSTER_NAME ~ ]$ module unload BLAST+/2.11.0-gompi-2020a [MY_USER_NAME@CLUSTER_NAME ~ ]$ module list Currently Loaded Modules: 1) GCCcore/9.3.0 7) libxml2/2.9.10-GCCcore-9.3.0 13) OpenMPI/4.0.3-GCC-9.3.0 19) libpng/1.6.37-GCCcore-9.3.0 2) zlib/1.2.11-GCCcore-9.3.0 8) libpciaccess/0.16-GCCcore-9.3.0 14) gompi/2020a 20) NASM/2.14.02-GCCcore-9.3.0 3) binutils/2.34-GCCcore-9.3.0 9) hwloc/2.2.0-GCCcore-9.3.0 15) bzip2/1.0.8-GCCcore-9.3.0 21) libjpeg-turbo/2.0.4-GCCcore-9.3.0 4) GCC/9.3.0 10) libevent/2.1.11-GCCcore-9.3.0 16) PCRE/8.44-GCCcore-9.3.0 22) LMDB/0.9.24-GCCcore-9.3.0 5) numactl/2.0.13-GCCcore-9.3.0 11) UCX/1.8.0-GCCcore-9.3.0 17) Boost/1.72.0-gompi-2020a 6) XZ/5.2.5-GCCcore-9.3.0 12) libfabric/1.11.0-GCCcore-9.3.0 18) GMP/6.2.0-GCCcore-9.3.0 So using `module unload` "un-loads" a module not its dependencies. If we wanted to unload everything at once, we could run `module purge` (unloads everything). [MY_USER_NAME@CLUSTER_NAME ~ ]$ module purge The following modules were not unloaded: (Use "module --force purge" to unload all): 1) StdEnv [MY_USER_NAME@CLUSTER_NAME ~ ]$ module list Currently Loaded Modules: 1) StdEnv (S) Where: S: Module is Sticky, requires --force to unload or purge
module purge is informative. It lets us know that all but a default set of packages
have been unloaded (and how to actually unload these if we truly so desired).
Software versioning & toolchains
So far, we’ve learned how to load and unload software packages. This is very useful. However, we have not yet addressed the issue of software versioning. At some point or other, you will run into issues where only one particular version of some software will be suitable. Perhaps a key bugfix only happened in a certain version, or version X broke compatibility with a file format you use. In either of these example cases, it helps to be very specific about what software is loaded.
Let’s examine the output of
module avail <SOFTWARE> more closely:
[MY_USER_NAME@CLUSTER_NAME ~ ]$ module avail gnuplot ------------------------- /cluster/modulefiles/all -------------------------- gnuplot/5.2.6-GCCcore-8.2.0 gnuplot/5.2.8-GCCcore-9.3.0 gnuplot/5.4.2-GCCcore-10.3.0 gnuplot/5.2.8-GCCcore-8.3.0 gnuplot/5.4.1-GCCcore-10.2.0 gnuplot/5.4.2-GCCcore-11.2.0 Use "module spider" to find all possible modules. Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
You can see that
module avail gnuplot lists six versions of ‘gnuplot’ with
the version number being the first part after the
describes the toolchain with which ‘gnuplot’ was compiled and its version.
So in this case the toolchain
GCCcore in the 11.2.0 version.
Toolchains are standardized bundles used for installing modules. They usually
consist of a compiler, math libraries and MPI implementation. The most common
foss. It is important to know that
modules created with different toolchains are often incompatible. If you try to
load two modules that are based on different toolchains, you will get an error
message from the
module load command. This means that you should always try to
find modules with matching toolchains whenever you need to load more than one
Using software modules in scripts
Here we create a job script that loads a particular version of Python, and prints the version number to the Slurm output file.
[MY_USER_NAME@CLUSTER_NAME ~ ]$ nano python-module.sh [MY_USER_NAME@CLUSTER_NAME ~ ]$ cat python-module.sh #!/bin/bash #SBATCH --nodes=1 #SBATCH --time=00:01:00 #SBATCH --account=<PROJECT_NAME> #SBATCH --mem=1G #SBATCH --job-name=Python_module_test module purge module load Python/3.9.6-GCCcore-11.2.0 python --version [MY_USER_NAME@CLUSTER_NAME ~ ]$ sbatch python-module.sh
For full reproducibility it is always good practice to start your job script by purging any existing modules which you might have loaded when you submit the job script. You can then explicitly load all the dependencies for the current job, which makes it much more robust for future execution.
Exercise (15 min)
This exercise can be performed directly on the login node. Before you start,
run the command
module purge to make sure your environment is clean. Verify
StdEnv is the only loaded module when running
How many programs (not counting versions) are there related to the keyword ‘chemistry’?
Find a module for
Rversion 4.1.2 using
module avail(R is a popular software environment for statistical computing). Load this module and verify that you get a working
Rcommand in your terminal. e.g. using
How many other software packages were loaded alongside the requsted
Bonus: Find a suitable version of
Rubyto load alongside the
Rmodule that you already have. Hint: Here we do not care about which version of
Rubywe are loading, but it needs to be compatible with the modules we have already loaded (
GCCcoreversions needs to be the same).
Depends on cluster, check with
$ module keyword chemistry
which at the time of writing found 5 packages on Saga:
We can search for modules using
module avail, and we can restrict the search by being more specific on version
$ module avail R/4 --------------------------- /cluster/modulefiles/all --------------------------- MUMmer/4.0.0rc1-GCCcore-10.3.0 R/4.2.2-foss-2022b R/4.1.2-foss-2021b RepeatMasker/4.1.4-foss-2022a R/4.2.1-foss-2022a If the avail list is too long consider trying: "module --default avail" or "ml -d av" to just list the default modules. "module overview" or "ml ov" to display the number of modules for each name. Use "module spider" to find all possible modules and extensions. Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
We see there is only one module matching version
4.1.2, so we load this one:
$ module load R/4.1.2-foss-2021b
Finally, we verify that we have the correct version available on the command line:
$ which R /cluster/software/R/4.1.2-foss-2021b/bin/R $ R --version R version 4.1.2 (2021-11-01) -- "Bird Hippie" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see https://www.gnu.org/licenses/.
Check the number of loaded modules with
$ module list ... [removed long output] ... 79) PROJ/8.1.0-GCCcore-11.2.0 80) libgeotiff/1.7.0-GCCcore-11.2.0 (H) 81) pybind11/2.7.1-GCCcore-11.2.0 (H) 82) SciPy-bundle/2021.10-foss-2021b 83) libtirpc/1.3.2-GCCcore-11.2.0 (H) 84) HDF/4.2.15-GCCcore-11.2.0 (H) 85) GDAL/3.3.2-foss-2021b 86) MPFR/4.1.0-GCCcore-11.2.0 (H) 87) libgit2/1.1.1-GCCcore-11.2.0 (H) 88) R/4.1.2-foss-2021b
which in this case outputs 88 different modules. So in addition to the original
StdEnvand the module we actively loaded (
R/4.1.2-foss-2021b), we got many other software packages loaded at the same time.
Bonus: When we look at the output from the
module listcommand above, we see that most of the loaded modules contain the
GCCcore-11.2.0suffix. This means that they were all compiled using the same “core” compiler, and thus should be fully compatible. If we want to load another (seemingly independent) module at the same time, we need to make sure that it is compatible with this core compiler. Searching for
$ module avail ruby --------------------------- /cluster/modulefiles/all --------------------------- Ruby/3.0.1-GCCcore-10.3.0 Ruby/3.0.5-GCCcore-11.3.0 Ruby/3.0.1-GCCcore-11.2.0
were we see that only one has a compatible
GCCcoreversion with our current
R, so this one can be loaded without any problems:
$ module load Ruby/3.0.1-GCCcore-11.2.0 $ ruby --version ruby 3.0.1p64 (2021-04-05 revision 0fb782ee38) [x86_64-linux]
If you try to load any of the other versions of
Ruby, you will get an error message telling you that the site does not allow “automatic swapping of module with the same name”. You can still manually do such swapping of modules, as explained in the same error message, but it is not recommended, as it can lead to weird runtime errors that are hard to debug.