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, 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 two biggest factors are software incompatibilities and versioning.
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Software compiled against a newer version of the C libraries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.
Environment modules are the solution to these problems. A module is a self-contained software package - it contains all of the files required to run a software packace and loads required dependencies.
To see available software modules, use module avail
[remote]$ module avail
----------------------------- MPI-dependent avx2 modules -------------------------------
abinit/8.2.2 (chem) lammps/20170331 plumed/2.3.0 (chem)
abyss/1.9.0 (bio) mrbayes/3.2.6 (bio) pnetcdf/1.8.1 (io)
boost-mpi/1.60.0 (t) ncl/6.4.0 quantumespresso/6.0 (chem)
cdo/1.7.2 (geo) ncview/2.1.7 (vis) 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".
To load a software module, use module load.
In this example we will use Python 3.
Intially, 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
/usr/bin/which: no python3 in (/opt/software/slurm/16.05.9/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/openmpi/2.1.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/ifort/2016.4.258/compilers_and_libraries_2016.4.258/linux/bin/intel64:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/icc/2016.4.258/compilers_and_libraries_2016.4.258/linux/bin/intel64:/opt/software/bin:/opt/puppetlabs/puppet/bin:/opt/software/slurm/current/bin:/opt/software/slurm/bin:/cvmfs/soft.computecanada.ca/easybuild/bin:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/bin:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/sbin:/cvmfs/soft.computecanada.ca/custom/bin:/opt/software/slurm/current/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/yourUsername/.local/bin:/home/yourUsername/bin)
We can load the python3 command with module load:
[remote]$ module load python
[remote[$ which python3
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/python-3.5.2/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 ennvironment 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
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/python-3.5.2/bin:/opt/software/slurm/16.05.9/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/openmpi/2.1.1/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/ifort/2016.4.258/compilers_and_libraries_2016.4.258/linux/bin/intel64:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/icc/2016.4.258/compilers_and_libraries_2016.4.258/linux/bin/intel64:/opt/software/bin:/opt/puppetlabs/puppet/bin:/opt/software/slurm/current/bin:/opt/software/slurm/bin:/cvmfs/soft.computecanada.ca/easybuild/bin:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/bin:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/sbin:/cvmfs/soft.computecanada.ca/custom/bin:/opt/software/slurm/current/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/yourUsername/.local/bin:/home/yourUsername/bin
You’ll notice a similarity to the output of the which command.
In this case, there’s only one difference:
the /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/python-3.5.2/bin directory at the beginning.
When we ran module load python/3.5.2,
it added this directory to the beginning of our $PATH.
Let’s examine what’s there:
[remote]$ ls /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/python-3.5.2/bin
2to3 idle3 pip3.5 python3 python3.5m-config virtualenv
2to3-3.5 idle3.5 pydoc3 python3.5 python3-config wheel
easy_install pip pydoc3.5 python3.5-config pyvenv
easy_install-3.5 pip3 python python3.5m pyvenv-3.5
Taking this to it’s conclusion, module load will add software to your $PATH.
It “loads” software.
A special note on this -
depending on which version of the module program that is installed at your site,
module load will also load required software dependencies.
To demonstrate, let’s use module list.
module list shows all loaded software modules.
[remote]$ module list
Currently Loaded Modules:
1) nixpkgs/.16.09 (H,S) 3) gcccore/.5.4.0 (H) 5) intel/2016.4 (t) 7) StdEnv/2016.4 (S)
2) icc/.2016.4.258 (H) 4) ifort/.2016.4.258 (H) 6) openmpi/2.1.1 (m) 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
[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, loading the beast module (a bioinformatics software package),
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) 3) gcccore/.5.4.0 (H) 5) intel/2016.4 (t) 7) StdEnv/2016.4 (S)
2) icc/.2016.4.258 (H) 4) ifort/.2016.4.258 (H) 6) openmpi/2.1.1 (m) 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 it’s 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 3) icc/.2016.4.258 5) ifort/.2016.4.258 7) imkl/11.3.4.258
2) nixpkgs/.16.09 4) gcccore/.5.4.0 6) intel/2016.4 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).
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
----------------------------------------------------------- Core Modules -----------------------------------------------------------
StdEnv/2016.4 (S,L) imkl/11.3.4.258 (L,math,D:11) mcr/R2014b (t) python/3.5.2 (t,D:3:3.5)
bioperl/1.7.1 (bio) imkl/2017.1.132 (math,2017) mcr/R2015a (t) qt/4.8.7 (t)
eclipse/4.6.0 (t) impute2/2.3.2 (bio) mcr/R2015b (t) qt/5.6.1 (t,D)
eigen/3.3.2 (math) intel/2016.4 (L,t,D:16:2016) mcr/R2016a (t) signalp/4.1f (bio)
fastqc/0.11.5 (bio) intel/2017.1 (t,17:2017) mcr/R2016b (t,D) spark/2.1.0 (t)
g2clib/1.6.0 jasper/1.900.1 (vis) minimac2/2014.9.15 (bio) spark/2.1.1 (t,D)
g2lib/1.4.0 java/1.8.0_121 (L,t) perl/5.22.2 (t) tbb/2017.2.132 (t)
gatk/3.7 (bio) mach/1.0.18 (bio) pgi/17.3 (t) tmhmm/2.0c (bio)
gcc/4.8.5 (t) mcr/R2013a (t) picard/2.1.1 (bio) trimmomatic/0.36 (bio)
gcc/5.4.0 (t,D) mcr/R2014a (t) python/2.7.13 (t,2:2.7)
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.
[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
[remote]$ gcc --version
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 worker node).
Loading a module by default
Adding a set of
module loadcommands 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:
.bashrcand.bash_profile(you can see these files withls -la ~). These scripts are run every time you log on or run a job. Adding amodule loadcommand to one of these shell scripts means that that module will always be loaded. Modify either your.bashrcor.bash_profilescripts to load a commonly used module like Python. Does yourpython3 --versionjob from before still needmodule loadto run?
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.
[remote]$ 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.
[remote]$ cd seqtk
[remote]$ 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.
[remote]$ ./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 softwareNameUnload software with
module purgeThe module system handles software versioning and package conflicts for you automatically.
You can edit your
.bashrcfile to automatically load a software package.