Accessing Software via Modules
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 incompatibilities
- versioning
- dependencies
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 Software compiled against a newer version of the C libraries and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 instance.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 (Fastest Fourier Transform in the West) software library available for it
to work.
Environment Modules
Environment modules are the solution to these problems. 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 implementations the
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 man module.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 Available Modules
To see available software modules, use
module avail:remote$ module avail
---------------- MPI-dependent avx2 modules ----------------- abinit/8.2.2 (chem) ncl/6.4.0 abyss/1.9.0 (bio) ncview/2.1.7 (vis) boost-mpi/1.60.0 (t) plumed/2.3.0 (chem) cdo/1.7.2 (geo) pnetcdf/1.8.1 (io) lammps/20170331 quantumespresso/6.0 (chem) mrbayes/3.2.6 (bio) ray/2.3.1 (bio) [removed most of the output here for clarity] t: Tools for development / Outils de développement vis: Visualisation software / Logiciels de visualisation chem: Chemistry libraries/apps / Logiciels de chimie geo: Geography libraries/apps / Logiciels de géographie phys: Physics libraries/apps / Logiciels de physique Aliases: Aliases exist: foo/1.2.3 (1.2) means that "module load foo/1.2" will load foo/1.2.3 D: Default Module Use "module spider" to find all possible modules. Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
Listing Currently Loaded Modules
You can use the
module list command to see which modules you currently have
loaded in your environment. If you have no modules loaded, you will see a
message telling you soremote$ module list
No Modulefiles Currently Loaded.
Loading and Unloading Software
To load a software module, use
module load. In this example we will use
Python 3.Initially, Python 3 is not loaded. We can test this by using the
which
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.remote$ which python3
python3 not found
We can load the
python3 command with module load:remote$ module load python remote$ which python3
/path/to/python/python3
where
/path/to/python is a directory that depends on the particular cluster setup.So, what just happened?
To understand the output, first we need to understand the nature of the
$PATH
environment variable. $PATH is a special environment variable that controls
where a UNIX system looks for software. Specifically $PATH is a list of
directories (separated by :) that the OS searches through for a command
before giving up and telling us it can't find it. As with all environment
variables we can print it out using echo.remote$ echo $PATH
/path/to/python:/another/path:/some/other/path:/yet/another/path
You'll notice a similarity to the output of the
which command.
In this case, there's only one difference: the different directory at the beginning.
When we ran the module load command, it added a directory to the beginning of our $PATH.
Let's examine what's there:remote$ ls /path/to/python
2to3 idle3.5 pydoc3.5 python3.5m virtualenv 2to3-3.5 pip python python3.5m-config wheel easy_install pip3 python3 python3-config easy_install-3.5 pip3.5 python3.5 pyvenv idle3 pydoc3 python3.5-config pyvenv-3.5
Taking this to its conclusion,
module load will add software to your $PATH.
It "loads" software.
A special note on this - depending on which version of the module program that is installed at your site,
module load will also load required software dependencies.To demonstrate, let’s use
module list. module list shows all loaded software modules.remote$ module list
Currently Loaded Modules: 1) nixpkgs/.16.09 (H,S) 5) intel/2016.4 (t) 2) icc/.2016.4.258 (H) 6) openmpi/2.1.1 (m) 3) gcccore/.5.4.0 (H) 7) StdEnv/2016.4 (S) 4) ifort/.2016.4.258 (H) 8) python/3.5.2 (t) Where: S: Module is Sticky, requires --force to unload or purge m: MPI implementations / Implémentations MPI t: Tools for development / Outils de développement H: Hidden Module
The list of modules available will vary widely by HPC system.
If your system has the
beast module available, then loading beast module (a bioinformatics software package) will do something like this:remote$ module load beast remote$ module list
Currently Loaded Modules: 1) nixpkgs/.16.09 (H,S) 5) intel/2016.4 (t) 9) java/1.8.0_121 (t) 2) icc/.2016.4.258 (H) 6) openmpi/2.1.1 (m) 10) beagle-lib/2.1.2 (bio) 3) gcccore/.5.4.0 (H) 7) StdEnv/2016.4 (S) 11) beast/2.4.0 (chem) 4) ifort/.2016.4.258 (H) 8) python/3.5.2 (t) Where: S: Module is Sticky, requires --force to unload or purge bio: Bioinformatic libraries/apps / Logiciels de bioinformatique m: MPI implementations / Implémentations MPI t: Tools for development / Outils de développement chem: Chemistry libraries/apps / Logiciels de chimie H: Hidden Module
So in this case,
beast also loaded java/1.8.0_121 and beagle-lib/2.1.2 as well.
Let’s try unloading the beast package.remote$ module unload beast remote$ module list
Currently Loaded Modules: 1) nixpkgs/.16.09 (H,S) 5) intel/2016.4 (t) 2) icc/.2016.4.258 (H) 6) openmpi/2.1.1 (m) 3) gcccore/.5.4.0 (H) 7) StdEnv/2016.4 (S) 4) ifort/.2016.4.258 (H) 8) python/3.5.2 (t) Where: S: Module is Sticky, requires --force to unload or purge m: MPI implementations / Implémentations MPI t: Tools for development / Outils de développement H: Hidden Module
So using
module unload “un-loads” a module along with its dependencies.
If we wanted to unload everything at once, we could run module purge (unloads everything).remote$ module purge
The following modules were not unloaded: (Use "module --force purge" to unload all): 1) StdEnv/2016.4 5) ifort/.2016.4.258 2) nixpkgs/.16.09 6) intel/2016.4 3) icc/.2016.4.258 7) imkl/11.3.4.258 4) gcccore/.5.4.0 8) openmpi/2.1.1
Note that
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).Note that this module loading process happens principally through the manipulation of environment variables like $PATH. There is usually little or no data transfer involved.
The module loading process manipulates other special environment variables as well,
including variables that influence where the system looks for software libraries,
and sometimes variables which tell commercial software packages where to find license servers.
The module command also restores these shell environment variables to their previous state when a module is unloaded.
Software Versioning
So far, we've learned how to load and unload software packages.
This is very useful.
However, we have not yet addressed the issue of software versioning.
At some point or other, you will run into issues where only one particular version of some software will be suitable.
Perhaps a key bugfix only happened in a certain version, or version X broke compatibility with a file format you use.
In either of these example cases, it helps to be very specific about what software is loaded.
Let's examine the output of
module avail more closely.remote$ module avail
---------------- MPI-dependent avx2 modules ----------------- abinit/8.2.2 (chem) ncl/6.4.0 abyss/1.9.0 (bio) ncview/2.1.7 (vis) boost-mpi/1.60.0 (t) plumed/2.3.0 (chem) cdo/1.7.2 (geo) pnetcdf/1.8.1 (io) lammps/20170331 quantumespresso/6.0 (chem) mrbayes/3.2.6 (bio) ray/2.3.1 (bio) gcc/4.8.5 gcc/5.4.0 (D) [removed most of the output here for clarity] t: Tools for development / Outils de développement vis: Visualisation software / Logiciels de visualisation chem: Chemistry libraries/apps / Logiciels de chimie geo: Geography libraries/apps / Logiciels de géographie phys: Physics libraries/apps / Logiciels de physique Aliases: Aliases exist: foo/1.2.3 (1.2) means that "module load foo/1.2" will load foo/1.2.3 D: Default Module Use "module spider" to find all possible modules. Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
Let’s take a closer look at the gcc module.
GCC is an extremely widely used C/C++/Fortran compiler.
Tons of software is dependent on the GCC version, and might not compile or run if the wrong version is loaded.
In this case, there are two different versions:
gcc/4.8.5 and gcc/5.4.0.
How do we load each copy, and which copy is the default?In this case,
gcc/5.4.0 has a (D) next to it. This indicates that it is the default
— if we type module load gcc, this is the copy that will be loaded.Filtering Lists
A lot of HPC systems will have so many modules available that looking through the whole of
module avail is just not practical.
You can use module avail gcc to check out the versions of GCC available on yours.
An example output from a different system might be:remote$ module avail gcc
------------------------------------------------- /local/modules/apps -------------------------------------------------- [removed for clarity] ----------------------------------------------- /local/modules/compilers ----------------------------------------------- gcc/6.4.0 gcc/10.2.0 gcc/11.1.0 gcc/12.2.0 gcc/13.2.0 (D) gcc/8.5.0 gcc/10.3.0 gcc/12.1.0 gcc/13.1.0 ------------------------------------------------- /local/modules/libs -------------------------------------------------- [removed for clarity] -------------------------------------------------- /local/modules/mpi -------------------------------------------------- [removed for clarity] Where: D: Default Module
remote$ module load gcc remote$ gcc --version
Lmod is automatically replacing "intel/2016.4" with "gcc/5.4.0". Due to MODULEPATH changes, the following have been reloaded: 1) openmpi/2.1.1 gcc (GCC) 5.4.0 Copyright (C) 2015 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.
Note that three things happened: the default copy of GCC was loaded (version 5.4.0), the
Intel compilers (which conflict with GCC) were unloaded, and software that is dependent
on compiler (OpenMPI) was reloaded. The module system turned what might be a
super-complex operation into a single command.
So how do we load the non-default copy of a software package? In this case, the only
change we need to make is be more specific about the module we are loading. There are
two GCC modules:
gcc/5.4.0 and gcc/4.8.5. To load a non-default module, the only
change we need to make to our module load command is to leave in the version number
after the /.remote$ module load gcc/4.8.5
Inactive Modules: 1) openmpi The following have been reloaded with a version change: 1) gcc/5.4.0 => gcc/4.8.5 gcc (GCC) 4.8.5 Copyright (C) 2015 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.
We now have successfully switched from GCC 5.4.0 to GCC 4.8.5. It is also important to
note that there was no compatible OpenMPI module available for GCC 4.8.5. Because of
this, the module program has “inactivated” the module. All this means for us is that if
we re-load GCC 5.4.0, module will remember OpenMPI used to be loaded and load that
module as well.
remote$ module load gcc/5.4.0
Activating Modules: 1) openmpi/2.1.1 The following have been reloaded with a version change: 1) gcc/4.8.5 => gcc/5.4.0
Using Software Modules in Scripts
Create a job that is able to run
python3 --version. Remember, no software
is loaded by default! Running a job is just like logging on to the system
(you should not assume a module loaded on the login node is loaded on a
compute node).