Accessing software

Overview

Teaching: 30 min
Exercises: 15 min

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 often the case that no software is loaded by default. If we want to use a software package, we will need to “load” it ourselves.

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 Software compiled against a newer version of the C libraries and then used when they are not present will result in a nasty 'GLIBCXX_3.4.20' not found error, for instance.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 Fourer 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 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, the null module is a special module that is automatically loaded as a placeholder if automatic loading is performed.

[yourUsername@cl1 ~]$ module list

Currently Loaded Modulefiles:
  1) null

Listing available modules

To see available software modules, use module avail

[yourUsername@cl1 ~]$ module avail

------------------------- /apps/local/modules/biology --------------------------
rosetta/2020.11

----------------------- /apps/local/modules/environment ------------------------
openifs/40r1

------------------------ /apps/local/modules/materials -------------------------
ansys/18.2

------------------------- /apps/local/modules/physics --------------------------
comsol/1068666/5.5      star-ccm-plus/2019.1.1
comsol/all_licences/5.5 star-ccm-plus/2019.3

 [removed most of the output her for clarity]

There is also the possibility of loading inherited modules from old systems such as Raven and HPC Wales but this is not recommended and was only used to aide migration to Hawk. Loading either raven and hpcw modules will change the available modules.

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.

[yourUsername@cl1 ~]$ which python3

/usr/bin/which: no python3 in (/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/c.username/bin)

We can load the python3 command with module load:

[yourUsername@cl1 ~]$ module load python
[yourUsername@cl1 ~]$ which python3

/apps/languages/python/3.7.0/el7/AVX512/intel-2018/bin/python3

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.

[yourUsername@cl1 ~]$ echo $PATH

/apps/languages/python/3.7.0/el7/AVX512/intel-2018/bin:/apps/compilers/intel/2018.2/compilers_and_libraries_2018/linux/bin/intel64:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/c.username/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:

[yourUsername@cl1 ~]$ ls /apps/languages/python/3.7.0/el7/AVX512/intel-2018/bin

2to3              f2py       nosetests-3.4  python3
2to3-3.7          idle3      pip            python3.7
chardetect        idle3.7    pip3           python3.7-config
cygdb             iptest     pip3.7         python3.7m
cython            iptest3    pydoc3         python3.7m-config
cythonize         ipython    pydoc3.7       python3-config
doesitcache       ipython3   pygmentize     pyvenv
easy_install      natsort    pytest         pyvenv-3.7
easy_install-3.7  nosetests  py.test        wheel

Taking this to it’s 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.

[yourUsername@cl1 ~]$ module list

Currently Loaded Modulefiles:
  1) system/auto             3) python/3.7.0
  2) compiler/intel/2018/2

Hawk:

[yourUsername@cl1 ~]$ module load plink
[yourUsername@cl1 ~]$ module list

Currently Loaded Modulefiles:
  1) system/auto             4) mkl/2018/3
  2) compiler/intel/2018/2   5) plink/2.0
  3) python/3.7.0

Sunbird:

[yourUsername@sl2(Sunbird) ~]$ module load febio
[yourUsername@sl2(Sunbird) ~]$ module list

Currently Loaded Modulefiles:
  1) system/auto             4) mkl/2018/3
  2) compiler/intel/2018/2   5) febio/4.0
  3) python/3.7.0

So in this case, loading the plink module (a bioinformatics software package) or febio module (medical application software package), also loaded mkl/2018/3 as well. Let’s try unloading the plink or febio package.

Hawk:

[yourUsername@cl1 ~]$ module unload plink
[yourUsername@cl1 ~]$ module list

Sunbird:

[yourUsername@sl2(Sunbird) ~]$ module unload febio
[yourUsername@sl2(Sunbird) ~]$ module list

Currently Loaded Modulefiles:
  1) system/auto             3) mkl/2018/3
  2) compiler/intel/2018/3   4) python/3.7.0

So using module unload “un-loads” a module but NOT its dependencies. If we wanted to unload everything at once, we could run module purge (unloads everything).

[yourUsername@cl1 ~]$ module purge
[yourUsername@cl1 ~]$ module list

No Modulefiles Currently Loaded.

Note is has unloaded everything, including the original null package that was used as a placeholder for initialisation.

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.

[yourUsername@cl1 ~]$ module avail

------------------------- /apps/local/modules/biology --------------------------
rosetta/2020.11

----------------------- /apps/local/modules/environment ------------------------
openifs/40r1

------------------------ /apps/local/modules/materials -------------------------
ansys/18.2

------------------------- /apps/local/modules/physics --------------------------
comsol/1068666/5.5      star-ccm-plus/2019.1.1
comsol/all_licences/5.5 star-ccm-plus/2019.3

 [removed most of the output her for clarity]

Let’s take a closer look at the compiler/gnu 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 versions from: compiler/gnu/4/8.5 to compiler/gcc/9/2.0. How do we load each copy and which copy is the default?

In this case, compiler/gcc/9/2.0 is the latest version. This indicates that it is the default - if we type module load compiler/gnu, this is the copy that will be loaded.

[yourUsername@cl1 ~]$ module load compiler/gnu
[yourUsername@cl1 ~]$ gcc --version

gcc (GCC) 9.2.0
Copyright (C) 2019 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.

This module system just loaded the GCC compilers into the environment, you can mix multiple compilers (if Intel C++ requires a recent GCC compiler for C++ compatability) it can be done. Some other module systems have more login available to automatically unload modules if conflicts are detected but not currently used on Hawk.

Now lets switch to a new compiler. Either using:

[yourUsername@cl1 ~]$ module unload compiler
[yourUsername@cl1 ~]$ module load compiler/gnu/4/8.5
[yourUsername@cl1 ~]$ module list
[yourUsername@cl1 ~]$ gcc --version

Alternatively using the module switch command.

[yourUsername@cl1 ~]$ module switch compiler/gnu/4/8.5

Currently Loaded Modulefiles:
  1) system/auto          2) compiler/gnu/4/8.5

gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-36)
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 9.2.0 to GCC 4.8.5.

Some modules have (default) at the end of the module listing in avail. For example for python

[yourUsername@cl1 ~]$ module avail python

--------------------------- /apps/modules/languages ----------------------------
python/3.5.9             python/3.7.7-intel2020u1 python-numpy/1.14.5
python/3.6.3-intel2018u3 python-h5py/2.8.0        python-pyside/1.2.4
python/3.6.9-intel2019u5 python-matplotlib/2.2.2  python-scipy/1.1.0
python/3.7.0(default)    python-mayavi/4.6.0      python-vtk/8.1.0

In this case python/3.7.0 is the default package.

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). Running module purge as first command in the job is recommended.

Loading a module by default

Adding a set of module load commands to all of your scripts and having to manually load modules every time you log on can be tiresome. Fortunately, there is a way of specifying a set of “default modules” that always get loaded, regardless of whether or not you’re logged on or running a job. Every user has two hidden files in their home directory: .bashrc and .bash_profile (you can see these files with ls -la ~). These scripts are run every time you log on or run a job. To aide with changes to the system, a .myenv file is sourced by .bashrc. Adding a module load command to .myenv means that that module will always be loaded. Modify either your .myenv scripts to load a commonly used module like Python. Does your python3 --version job from before still need module load to run?

Installing software of our own

Most HPC clusters have a pretty large set of preinstalled software. Nonetheless, it’s unlikely that all of the software we’ll need will be available. Sooner or later, we’ll need to install some software of our own.

Though software installation differs from package to package, the general process is the same: download the software, read the installation instructions (important!), install dependencies, compile, then start using our software.

As an example we will install the bioinformatics toolkit seqtk. We’ll first need to obtain the source code from GitHub using git.

[yourUsername@cl1 ~]$ git clone https://github.com/lh3/seqtk.git

Cloning into 'seqtk'...
remote: Counting objects: 316, done.
remote: Total 316 (delta 0), reused 0 (delta 0), pack-reused 316
Receiving objects: 100% (316/316), 141.52 KiB | 0 bytes/s, done.
Resolving deltas: 100% (181/181), done.

Now, using the instructions in the README.md file, all we need to do to complete the install is to cd into the seqtk folder and run the command make.

[yourUsername@cl1 ~]$ cd seqtk
[yourUsername@cl1 ~]$ make

gcc -g -Wall -O2 -Wno-unused-function seqtk.c -o seqtk -lz -lm
seqtk.c: In function ‘stk_comp’:
seqtk.c:399:16: warning: variable ‘lc’ set but not used [-Wunused-but-set-variable]
    int la, lb, lc, na, nb, nc, cnt[11];
                ^

It’s done! Now all we need to do to use the program is invoke it like any other program.

[yourUsername@cl1 ~]$ ./seqtk

Usage:   seqtk <command> <arguments>
Version: 1.2-r101-dirty

Command: seq       common transformation of FASTA/Q
         comp      get the nucleotide composition of FASTA/Q
         sample    subsample sequences
         subseq    extract subsequences from FASTA/Q
         fqchk     fastq QC (base/quality summary)
         mergepe   interleave two PE FASTA/Q files
         trimfq    trim FASTQ using the Phred algorithm

         hety      regional heterozygosity
         gc        identify high- or low-GC regions
         mutfa     point mutate FASTA at specified positions
         mergefa   merge two FASTA/Q files
         famask    apply a X-coded FASTA to a source FASTA
         dropse    drop unpaired from interleaved PE FASTA/Q
         rename    rename sequence names
         randbase  choose a random base from hets
         cutN      cut sequence at long N
         listhet   extract the position of each het

We’ve successfully installed our first piece of software!

Key Points

Discover available software with module avail

Load software with module load softwareName

Unload software with module purge

The module system handles software versioning and package conflicts for you automatically.

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Accessing software

Overview