| title | teaching | exercises | questions | objectives | keypoints | ||||||
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Accessing software |
30 |
15 |
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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 Software compiled against a newer version of the C libraries and then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 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.
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
{{ site.host_prompt }} module list
{: .bash}
No Modulefiles Currently Loaded.
{: .output}
To see available software modules, use module avail
{{ site.host_prompt }} module avail
{: .bash}
{% include /snippets/14/module_avail.snip %}
{: .output}
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.
{{ site.host_prompt }} which python3
{: .bash}
{% include /snippets/14/which_missing.snip %}
{: .output}
We can load the python3 command with module load:
{% include /snippets/14/load_python.snip %}
{: .bash}
{% include /snippets/14/which_python.snip %}
{: .output}
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.
{{ site.host_prompt }} echo $PATH
{: .bash}
{% include /snippets/14/path.snip %}
{: .output}
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:
{% include /snippets/14/ls_dir.snip %}
{: .bash}
{% include /snippets/14/ls_dir_output.snip %}
{: .output}
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.
{% include /snippets/14/depend_demo.snip %}
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.
{{ site.host_prompt }} module avail
{: .bash}
{% include /snippets/14/module_avail.snip %}
{: .output}
{% include /snippets/14/gcc_example.snip %}
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). {: .challenge}
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? {: .challenge}
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.
{{ site.host_prompt }} git clone https://github.com/lh3/seqtk.git
{: .bash}
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.
{: .output}
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.
{{ site.host_prompt }} cd seqtk
{{ site.host_prompt }} make
{: .bash}
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];
^
{: .output}
It's done! Now all we need to do to use the program is invoke it like any other program.
{{ site.host_prompt }} ./seqtk
{: .bash}
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
{: .output}
We've successfully installed our first piece of software!
{% include links.md %}