Accessing software via Modules
Overview
Teaching: 30 min
Exercises: 15 minQuestions
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 Software compiled against a newer version of the C libraries and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:
userid@uan01:/work/ta028/ta028/userid> module avail
----------- /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
userid@uan01:/work/ta028/ta028/userid> module list
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.
which ncdump
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:
module load cray-netcdf
/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.
echo $PATH
/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:
ls /opt/cray/pe/netcdf/4.7.4.2/bin
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-netcdfmodule and check what happens to thePATHenvironment 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.
module avail cray-netcdf
--------------------------- /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 swapLoad module
cray-netcdfas 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 obtaincray-netcdf/4.7.4.0. Check what has happened to the location of thencdumputility.
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).Solution
userid@uan01:/work/ta028/ta028/userid> nano ncdump-module.sh userid@uan01:/work/ta028/ta028/userid> cat ncdump-module.sh#!/bin/bash #SBATCH --partition=standard #SBATCH --qos=standard #SBATCH --reservation=ta028_180 module load epcc-job-env module load cray-netcdf ncdump --versionuserid@uan01:/work/ta028/ta028/userid> sbatch python-module.sh
Key Points
Load software with
module load softwareName.Unload software with
module purgeThe module system handles software versioning and package conflicts for you automatically.