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 Software compiled against a newer version of the C libraries and then used when they are not present will result in a nasty 'GLIBCXX_3.4.20' not found error, for instance.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

yourUsername@eslogin001:~> module list

Currently Loaded Modulefiles:
  1) modules/3.2.10.6
  2) eswrap/1.3.3-1.020200.1280.0
  3) switch/1.0-1.0502.60522.1.61.ari
  4) cce/8.5.8
  5) craype-network-aries
  6) craype/2.5.10
  7) cray-libsci/16.11.1
  8) udreg/2.3.2-1.0502.10518.2.17.ari
  9) ugni/6.0-1.0502.10863.8.29.ari
 10) pmi/5.0.12
 11) dmapp/7.0.1-1.0502.11080.8.76.ari
 12) gni-headers/4.0-1.0502.10859.7.8.ari
 13) xpmem/0.1-2.0502.64982.5.3.ari
 14) dvs/2.5_0.9.0-1.0502.2188.1.116.ari
 15) alps/5.2.4-2.0502.9774.31.11.ari
 16) rca/1.0.0-2.0502.60530.1.62.ari
 17) atp/2.1.0
 18) PrgEnv-cray/5.2.82
 19) pbs/13.0.412.192482
 20) craype-ivybridge
 21) cray-mpich/7.5.5
 22) packages-archer
 23) bolt/0.6
 24) nano/2.2.6
 25) leave_time/1.3.0
 26) quickstart/1.0
 27) ack/2.14
 28) openssl/1.1.0g_build1
 29) curl/7.58.0_build1
 30) git/2.16.2_build1
 31) wget/1.19.4
 32) epcc-tools/9.0

Listing available modules

To see available software modules, use module avail

yourUsername@eslogin001:~> module avail

--------------------- /opt/cray/craype/2.5.10/modulefiles ----------------------
craype-accel-host     craype-hugepages4M    craype-hugepages512M
craype-accel-nvidia20 craype-hugepages8M    craype-intel-knc
craype-accel-nvidia35 craype-hugepages16M   craype-ivybridge
craype-accel-nvidia60 craype-hugepages32M   craype-mic-knl
craype-broadwell      craype-hugepages64M   craype-network-aries
craype-haswell        craype-hugepages128M  craype-network-none
craype-hugepages2M    craype-hugepages256M  craype-sandybridge

---------------------------- /opt/cray/modulefiles -----------------------------
PrgEnv-cray/5.1.29
PrgEnv-cray/5.2.56
PrgEnv-cray/5.2.82(default)
PrgEnv-gnu/5.1.29
PrgEnv-gnu/5.2.56
PrgEnv-gnu/5.2.82(default)
PrgEnv-intel/5.1.29
PrgEnv-intel/5.2.56
PrgEnv-intel/5.2.82(default)
atp/1.7.5
atp/1.8.3
atp/2.1.0(default)
atp/2.1.0_debug
atp/2.1.1
atp/2.1.1_debug
atp/2.1.3
atp/2.1.3_debug
capmc/1.0-1.0702.37257.16.1(default)
ccm/2.2.0-1.0500.43485.5.54
ccm/2.2.0-1.0501.48422.4.56
...

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@eslogin001:~> which python3

which: no python3 in (/home/y07/y07/cse/epcc-archer-tools/bin:/home/y07/y07/cse/wget/wget-1.19.4/build/bin:/home/y07/y07/cse/git/git-2.16.2_build1/install/bin:/home/y07/y07/cse/curl/curl-7.58.0_build1/install/bin:/home/y07/y07/cse/openssl/openssl-1.1.0g_build1/install/bin:/usr/local/packages/cse/ack:/usr/local/packages/cse/quickstart/1.0:/home/y07/y07/cse/leave_time/1.3.0:/home/y07/y07/cse/nano/2.2.6/bin:/usr/local/packages/cse/bolt/0.6/bin:/opt/cray/mpt/7.5.5/gni/bin:/opt/pbs/13.0.412.192482/bin:/opt/cray/rca/1.0.0-2.0502.60530.1.62.ari/bin:/opt/cray/alps/5.2.4-2.0502.9774.31.11.ari/sbin:/opt/cray/dvs/2.5_0.9.0-1.0502.2188.1.116.ari/bin:/opt/cray/xpmem/0.1-2.0502.64982.5.3.ari/bin:/opt/cray/ugni/6.0-1.0502.10863.8.29.ari/bin:/opt/cray/udreg/2.3.2-1.0502.10518.2.17.ari/bin:/opt/cray/craype/2.5.10/bin:/opt/cray/cce/8.5.8/cray-binutils/x86_64-pc-linux-gnu/bin:/opt/cray/cce/8.5.8/craylibs/x86-64/bin:/opt/cray/cce/8.5.8/cftn/bin:/opt/cray/cce/8.5.8/CC/bin:/opt/cray/switch/1.0-1.0502.60522.1.61.ari/bin:/opt/cray/eslogin/eswrap/1.3.3-1.020200.1280.0/bin:/opt/modules/3.2.10.6/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib/mit/bin:/usr/lib/mit/sbin:/sbin:/usr/sbin:.:/usr/lib/qt3/bin:/opt/cray/bin)

We can load the python3 command with module load:

[yourUsername@eslogin001 ~]$ module load anaconda/python3
[yourUsername@eslogin001 ~]$ which python3

/home/y07/y07/cse/anaconda/python3/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@eslogin001:~> echo $PATH

/home/y07/y07/cse/anaconda/python3/bin:/home/y07/y07/cse/epcc-archer-tools/bin:/home/y07/y07/cse/wget/wget-1.19.4/build/bin:/home/y07/y07/cse/git/git-2.16.2_build1/install/bin:/home/y07/y07/cse/curl/curl-7.58.0_build1/install/bin:/home/y07/y07/cse/openssl/openssl-1.1.0g_build1/install/bin:/usr/local/packages/cse/ack:/usr/local/packages/cse/quickstart/1.0:/home/y07/y07/cse/leave_time/1.3.0:/home/y07/y07/cse/nano/2.2.6/bin:/usr/local/packages/cse/bolt/0.6/bin:/opt/cray/mpt/7.5.5/gni/bin:/opt/pbs/13.0.412.192482/bin:/opt/cray/rca/1.0.0-2.0502.60530.1.62.ari/bin:/opt/cray/alps/5.2.4-2.0502.9774.31.11.ari/sbin:/opt/cray/dvs/2.5_0.9.0-1.0502.2188.1.116.ari/bin:/opt/cray/xpmem/0.1-2.0502.64982.5.3.ari/bin:/opt/cray/ugni/6.0-1.0502.10863.8.29.ari/bin:/opt/cray/udreg/2.3.2-1.0502.10518.2.17.ari/bin:/opt/cray/craype/2.5.10/bin:/opt/cray/cce/8.5.8/cray-binutils/x86_64-pc-linux-gnu/bin:/opt/cray/cce/8.5.8/craylibs/x86-64/bin:/opt/cray/cce/8.5.8/cftn/bin:/opt/cray/cce/8.5.8/CC/bin:/opt/cray/switch/1.0-1.0502.60522.1.61.ari/bin:/opt/cray/eslogin/eswrap/1.3.3-1.020200.1280.0/bin:/opt/modules/3.2.10.6/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib/mit/bin:/usr/lib/mit/sbin:/sbin:/usr/sbin:.:/usr/lib/qt3/bin:/opt/cray/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@eslogin001 ~]$ ls /home/y07/y07/cse/anaconda/python3/bin

[output truncated] 

2to3
2to3-3.5
activate
activate-global-python-argcomplete
anaconda
anaconda-navigator
asadmin
assistant
binstar
blaze-server
bokeh
bokeh-server
bundle_image
cfadmin
conda
conda-build
conda-convert
conda-develop
conda-env
conda-index
conda-inspect
condamanager
conda-metapackage
conda-pipbuild
conda-render
conda-server
conda-sign
conda-skeleton

[output truncated]

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 load the abinit module and then use the module list command to show which modules we currently have loaded in our environment. (Abinit is an open source materials science modelling software package.)

yourUsername@eslogin001:~> module load abinit
yourUsername@eslogin001:~> module list

Currently Loaded Modulefiles:
Currently Loaded Modulefiles:
  1) modules/3.2.10.6
  2) eswrap/1.3.3-1.020200.1280.0
 ...
 33) anaconda/python3
 34) abinit/7.10.4

So in this case, loading the abinit module also loaded a variety of other modules. Let’s try unloading the abinit package.

yourUsername@eslogin001:~> module unload abinit
yourUsername@eslogin001:~> module list

Currently Loaded Modulefiles:
  1) modules/3.2.10.6
  2) eswrap/1.3.3-1.020200.1280.0
 ...
 33) anaconda/python3

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).

yourUsername@eslogin001:~> module load abinit
yourUsername@eslogin001:~> module purge

No Modulefiles Currently Loaded.

Note that module purge has removed the anaconda/python3 module as well as abinit and its dependencies.

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@eslogin001:~> module avail

--------------------- /opt/cray/craype/2.5.10/modulefiles ----------------------
craype-accel-host     craype-hugepages4M    craype-hugepages512M
craype-accel-nvidia20 craype-hugepages8M    craype-intel-knc
craype-accel-nvidia35 craype-hugepages16M   craype-ivybridge
craype-accel-nvidia60 craype-hugepages32M   craype-mic-knl
craype-broadwell      craype-hugepages64M   craype-network-aries
craype-haswell        craype-hugepages128M  craype-network-none
craype-hugepages2M    craype-hugepages256M  craype-sandybridge

---------------------------- /opt/cray/modulefiles -----------------------------
PrgEnv-cray/5.1.29
PrgEnv-cray/5.2.56
PrgEnv-cray/5.2.82(default)
PrgEnv-gnu/5.1.29
PrgEnv-gnu/5.2.56
PrgEnv-gnu/5.2.82(default)
PrgEnv-intel/5.1.29
PrgEnv-intel/5.2.56
PrgEnv-intel/5.2.82(default)
atp/1.7.5
atp/1.8.3
atp/2.1.0(default)
atp/2.1.0_debug
atp/2.1.1
atp/2.1.1_debug
atp/2.1.3
atp/2.1.3_debug
capmc/1.0-1.0702.37257.16.1(default)
ccm/2.2.0-1.0500.43485.5.54
ccm/2.2.0-1.0501.48422.4.56
...

Let’s take a closer look at the gcc module. GCC is an extremely widely used C/C++/Fortran compiler. Lots of software is dependent on the GCC version, and might not compile or run if the wrong version is loaded. There are many different versions and subversions: gcc/4.8.1, gcc/6.3.0, gcc/7.3.0, … How do we know what is available and which copy is the default?

You can look at the availabilty of different versions:

yourUsername@eslogin001:~> module avail gcc

------------------------------- /opt/modulefiles -------------------------------
gcc/4.8.1          gcc/5.1.0          gcc/6.3.0(default)
gcc/4.9.2          gcc/5.3.0          gcc/7.2.0
gcc/4.9.3          gcc/6.1.0          gcc/7.3.0

In this case, gcc/6.3.0 has a (default) next to it. This indicates that it is the default - if we type module load gcc, this is the copy that will be loaded.

yourUsername@eslogin001:~> module load gcc
yourUsername@eslogin001:~> gcc --version

gcc (GCC) 6.3.0 20161221 (Cray Inc.)
Copyright (C) 2016 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.

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. To load a non-default module, we need to make add the version number after the / in our module load command

yourUsername@eslogin001:~> module load gcc/7.3.0

gcc/7.3.0(3):ERROR:150: Module 'gcc/7.3.0' conflicts with the currently loaded module(s) 'gcc/6.3.0'
gcc/7.3.0(3):ERROR:102: Tcl command execution failed: conflict gcc

What happened? The module command is telling us that we cannot have two gcc modules loaded at the same time as this could cause confusion about which version you are using. We need to remove the default version before we load the new version.

yourUsername@eslogin001:~> module unload gcc
yourUsername@eslogin001:~> module load gcc/7.3.0
yourUsername@eslogin001:~> gcc --version

gcc (GCC) 7.3.0 20180125 (Cray Inc.)
Copyright (C) 2017 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 6.3.0 to GCC 7.3.0.

As switching between different versions of the same module is often used you can use module swap rather than unloading one version before loading another. The equivalent of the steps above would be:

yourUsername@eslogin001:~> module purge
yourUsername@eslogin001:~> module load gcc
yourUsername@eslogin001:~> gcc --version
yourUsername@eslogin001:~> module swap gcc gcc/7.3.0
yourUsername@eslogin001:~> gcc --version

gcc (GCC) 6.3.0 20161221 (Cray Inc.)
Copyright (C) 2016 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.

gcc (GCC) 7.3.0 20180125 (Cray Inc.)
Copyright (C) 2017 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 achieves the same result as unload followed by load but in a single step.

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).

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. Adding a module load command to one of these shell scripts means that that module will always be loaded. Modify either your .bashrc or .bash_profile 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@eslogin001:~> module switch openssl openssl/1.1.1c_build1
yourUsername@eslogin001:~> 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@eslogin001:~> cd seqtk
yourUsername@eslogin001:~> 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@eslogin001:~> ./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

Load software with module load softwareName

Unload software with module purge

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

You can edit your .bashrc file to automatically load a software package.

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Introduction to High-Performance Computing

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Accessing software

Overview