Accessing software via Modules

Last updated on 2024-12-03 | Edit this page

Overview

Questions

  • How do we load and unload software packages?

Objectives

  • Understand how to load and use a software package.

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 Software compiled against a newer version of the C libraries and then used when they are not present will result in a nasty 'GLIBCXX_3.4.20' not found error, for instance.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:

BASH 

userid@ln03:/work/ta180/ta180/userid> module avail

OUTPUT 

----------- /work/y07/shared/archer2-modules/modulefiles-cse-pyvenvs -----------
tensorflow/2.3.1-py38  torch/1.6.0-py38

----------- /work/y07/shared/archer2-modules/modulefiles-cse-pymods ------------
python-netCDF4/1.5.5.1

------------ /work/y07/shared/archer2-modules/modulefiles-cse-utils ------------
bolt/0.7                  ncview/ncview-2.1.7-gcc-10.1.0  vmd/1.9.3-mpi-gcc10
cmake/3.18.4              reframe/3.2                     xios/2.5-gcc10
ed/1.16-gcc10             tcl/8.4.20-gcc10                xthi/1.0
epcc-job-env              tcl/8.5.0-gcc10                 xthi/1.0-gcc10
epcc-reframe/0.1          tcl/8.6.0-gcc10
genmaskcpu/1.0            tcl/8.6.10-gcc10(default)
gnuplot/5.4.1-gcc-10.1.0  tk/8.5.6-gcc10
lzip/1.20-gcc10           tk/8.6.10-gcc10(default)
nco/4.9.6                 visidata/2.1
nco/4.9.6-gcc-10.1.0      vmd/1.9.3-gcc10(default)

------------ /work/y07/shared/archer2-modules/modulefiles-cse-libs -------------
adios/1.13.1     hypre/2.18.0             mumps/5.2.1     superlu-dist/6.1.1
boost/1.72.0     libxml2/2.9.7-gcc-9.3.0  parmetis/4.0.3  superlu/5.2.1
glm/0.9.9.6      matio/1.5.18             petsc/3.13.3    trilinos/12.18.1
gmp/6.1.2-gcc10  metis/5.1.0              scotch/6.0.10
...

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 so

BASH 

userid@ln03:/work/ta180/ta180/userid> module list

OUTPUT 

Currently Loaded Modulefiles:
 1) cpe-cray                          8) perftools-base/20.10.0(default)
 2) cce/10.0.4(default)               9) xpmem/2.2.35-7.0.1.0_1.9__gd50fabf.shasta(default)
 3) craype/2.7.2(default)            10) cray-mpich/8.0.16(default)
 4) craype-x86-rome                  11) cray-libsci/20.10.1.2(default)
 5) libfabric/1.11.0.0.233(default)  12) bolt/0.7
 6) craype-network-ofi               13) /work/y07/shared/archer2-modules/modulefiles-cse/epcc-setup-env
 7) cray-dsmml/0.1.2(default)        14) /usr/local/share/epcc-module/epcc-module-loader

Loading and Unloading Software

To load a software module, use module load. Let’s say we would like to use the NetCDF utility ncdump.

On login, ncdump is not available. 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.

BASH 

 which ncdump

OUTPUT 

which: no ncdump in (/usr/local/maven/bin:/lus/cls01095/work/y07/shared/bolt/0.7/bin:/work/y07/shared/utils/bin:/opt/cray/pe/perftools/20.10.0/bin:/opt/cray/pe/papi/6.0.0.4/bin:/opt/cray/libfabric/1.11.0.0.233/bin:/opt/cray/pe/craype/2.7.2/bin:/opt/cray/pe/cce/10.0.4/cce-clang/x86_64/bin:/opt/cray/pe/cce/10.0.4/binutils/x86_64/x86_64-pc-linux-gnu/bin:/opt/cray/pe/cce/10.0.4/binutils/cross/x86_64-aarch64/aarch64-linux-gnu/../bin:/opt/cray/pe/cce/10.0.4/utils/x86_64/bin:/usr/local/Modules/bin:/usr/local/bin:/usr/bin:/bin:/opt/cray/pe/bin:/usr/lib/mit/bin)

We can find the ncdump command by using module load:

BASH 

 module load cray-hdf5
 module load cray-netcdf
which ncdump

OUTPUT 

/opt/cray/pe/netcdf/4.7.4.2/bin/ncdump

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.

BASH 

 echo $PATH

OUTPUT 

/opt/cray/pe/netcdf/4.7.4.2/bin:/opt/cray/pe/python/3.8.5.0/bin:/lus/cls01095/work/z19/z19/aturner/.local/bin:/lus/cls01095/work/y07/shared/bolt/0.7/bin:/work/y07/shared/utils/bin:/usr/local/maven/bin:/opt/cray/pe/perftools/20.10.0/bin:/opt/cray/pe/papi/6.0.0.4/bin:/opt/cray/libfabric/1.11.0.0.233/bin:/opt/cray/pe/craype/2.7.2/bin:/opt/cray/pe/cce/10.0.4/cce-clang/x86_64/bin:/opt/cray/pe/cce/10.0.4/binutils/x86_64/x86_64-pc-linux-gnu/bin:/opt/cray/pe/cce/10.0.4/binutils/cross/x86_64-aarch64/aarch64-linux-gnu/../bin:/opt/cray/pe/cce/10.0.4/utils/x86_64/bin:/usr/local/Modules/bin:/home/z19/z19/aturner/bin:/usr/local/bin:/usr/bin:/bin:/opt/cray/pe/bin:/usr/lib/mit/bin

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:

BASH 

 ls /opt/cray/pe/netcdf/4.7.4.2/bin

OUTPUT 

nc-config  nccopy  ncdump  ncgen  ncgen3  ncxx4-config  nf-config

In summary, module load will add software to your $PATH. module load may also load additional modules with software dependencies.

To unload a module, use module unload with the relevant module name.

Unload!

Confirm you can unload the cray-netcdf module and check what happens to the PATH environment variable.

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.

BASH 

 module avail cray-netcdf

OUTPUT 

--------------------------- /opt/cray/pe/modulefiles ---------------------------
cray-netcdf-hdf5parallel/4.7.4.0           cray-netcdf/4.7.4.0
cray-netcdf-hdf5parallel/4.7.4.2(default)  cray-netcdf/4.7.4.2(default)

Note that we have two different versions of cray-netcdf (and also two versions of something else cray-netcdf-hdf5parallel which match our search).

Using module swap

Load module cray-netcdf as before. Note that if we do not specifify a particular version, we load a default version. If we wish to change versions, we can use module swap <old-module> <new-module>. Try this to obtain cray-netcdf/4.7.4.0. Check what has happened to the location of the ncdump utility.

Using Software Modules in Scripts

Create a job that is able to run ncdump --version. 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).

BASH 

userid@ln03:/work/ta180/ta180/userid> nano ncdump-module.sh
userid@ln03:/work/ta180/ta180/userid> cat ncdump-module.sh

OUTPUT 

#!/bin/bash
#SBATCH --partition=standard
#SBATCH --qos=short
module load epcc-job-env
module load cray-netcdf
ncdump --version

BASH 

userid@ln03:/work/ta180/ta180/userid>  python-module.sh

Key Points

  • “Load software with module load softwareName.”
  • “Unload software with module purge”
  • “The module system handles software versioning and package conflicts for you automatically.”