Software modules¶

Video

Watch this in our courses: 2021 January

There are hundreds of people using every cluster. They all have different software needs, including conflicting versions required for different projects! How do we handle this without making a mess, or one person breaking the cluster for everyone?

This is actually a very hard, but solved within certain parameters, problem. Software installation and management takes up a huge amount of our time, but we try to make it easy for our users. Still, it can end up taking a lot of your effort as well.

Abstract

We use the standard Lmod module system, which makes more software available by adjusting environment variables like PATH
See the Triton quick reference for a module command cheatsheet.

Local differences

Almost every site uses modules, and most use the same Lmod system we use here. But, the exact module names you can load will be different.

Introduction to modules¶

The answer is the standard “module” system Lmod. It allows us to have unlimited number of different software packages installed, and the user can select what they want. Modules include everything from compilers (+their required development files), libraries, and programs. If you need a program installed, we will put it in the module system.

In a system the size of Triton, it just isn’t possible to install all software by default for every user.

A module lets you adjust what software is available, and makes it easy to switch between different versions.

As an example, let’s inspect the gcc module (abbreviated output shown) with module show gcc:

$ module show gcc
----------------------------------------------------------------------------------------------
   /share/apps/spack/envs/fgci-centos7-generic/lmod/linux-centos7-x86_64/all/gcc/9.2.0.lua:
----------------------------------------------------------------------------------------------
whatis("Name : gcc")
whatis("Version : 9.2.0")
whatis("Short description : The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages.")
whatis("Configure options : --disable-multilib --enable-languages=c,c++,fortran --with-mpfr=/share/apps/spack/envs/fgci-centos7-generic/software/mpfr/3.1.6/m6xmzws --with-gmp=/share/apps/spack/envs/fgci-centos7-generic/software/gmp/6.1.2/mnsg5g2 --enable-lto --with-quad --with-system-zlib --with-mpc=/share/apps/spack/envs/fgci-centos7-generic/software/mpc/1.1.0/uaijipe --with-isl=/share/apps/spack/envs/fgci-centos7-generic/software/isl/0.19/indu5p6")
help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
Fortran, Ada, and Go, as well as libraries for these languages.]])
family("compiler")
prepend_path("PATH","/share/apps/spack/envs/fgci-centos7-generic/software/gcc/9.2.0/dnrscms/bin")
prepend_path("MANPATH","/share/apps/spack/envs/fgci-centos7-generic/software/gcc/9.2.0/dnrscms/share/man")
prepend_path("LIBRARY_PATH","/share/apps/spack/envs/fgci-centos7-generic/software/gcc/9.2.0/dnrscms/lib")
prepend_path("LD_LIBRARY_PATH","/share/apps/spack/envs/fgci-centos7-generic/software/gcc/9.2.0/dnrscms/lib")
prepend_path("LIBRARY_PATH","/share/apps/spack/envs/fgci-centos7-generic/software/gcc/9.2.0/dnrscms/lib64")
prepend_path("LD_LIBRARY_PATH","/share/apps/spack/envs/fgci-centos7-generic/software/gcc/9.2.0/dnrscms/lib64")
prepend_path("CPATH","/share/apps/spack/envs/fgci-centos7-generic/software/gcc/9.2.0/dnrscms/include")
prepend_path("CMAKE_PREFIX_PATH","/share/apps/spack/envs/fgci-centos7-generic/software/gcc/9.2.0/dnrscms/")
setenv("CC","/share/apps/spack/envs/fgci-centos7-generic/software/gcc/9.2.0/dnrscms/bin/gcc")
setenv("CXX","/share/apps/spack/envs/fgci-centos7-generic/software/gcc/9.2.0/dnrscms/bin/g++")
...

The command module show gcc shows some meta-info (name of the module, its version, etc.) When you load this module, it adjusts various environment paths (as you see there), so that when you type gcc it runs the program from /share/apps/spack/envs/fgci-centos7-generic/software/gcc/9.2.0/dnrscms/bin/gcc. This is almost magic: we can have many versions of any software installed, and everyone can pick what they want, with no conflicts.

Loading modules¶

Let’s dive right into an example and load a module.

Local differences

If you are not at Aalto, but in Finland (but not at CSC), then you need to run module load fgci-common first, before any of the other commands will work (and you will need to keep doing this for every other tutorial in this series). You have to do this every time you start a new shell. If you are at CSC or not in Finland, the concepts here also apply to you, but the actual names of the modules loaded may differ.

Let’s assume you’ve written a Python script that is only compatible with Python version 3.7.0 or higher. You open a shell to find out where and what version our Python is. The which program looks up the current detected version of a program - very useful when testing modules.:

$ which python3
/usr/bin/python3
$ python3 -V
Python 3.6.8

But you need a newer version of Python. To this end, you can load the anaconda module using the module load anaconda command, that has a more up to date Python with lots of libraries already included:

$ module load anaconda
$ which python
/share/apps/anaconda-ci/fgci-centos7-generic/software/anaconda/2020-03-tf2/521551bc/bin/python
$ python -V
Python 3.6.10 :: Anaconda, Inc.

As you see, you now have a newer version of Python, in a different directory.

You can see a list of the all the loaded modules in our working shell using the module list command:

$ module list
Currently Loaded Modules:
  1) anaconda/2020-03-tf2

Note

The module load and module list commands can be abbreviated as ml

Let’s use the module purge command to unload all the loaded modules (anaconda in this case):

$ module purge

Or explicitly unload the anaconda module by using the module unload anaconda command:

$ module unload anaconda

You can load any number of modules in your open shell, your scripts, etc. You could load modules in your ~/.bash_profile, but then it will always automatically load it - perhaps even if you don’t expect it. Watch out for this if you get un-explainable bugs - it may be best to explicitly load what you need.

Type-along: Where is Matlab?¶

Let’s say you want to use Matlab. You log in and try in the shell:

$ matlab
-bash: matlab: command not found

So first search for it using the module spider command:

$ module spider matlab

----------------------------------------------------------------------------
  matlab:
----------------------------------------------------------------------------
     Versions:
        matlab/r2012a
        matlab/r2014a
        matlab/r2015b
        matlab/r2016a
        matlab/r2016b
        matlab/r2017b
        matlab/r2018a
        matlab/r2018b
        matlab/r2019a
        matlab/r2019b

We see there are a lot of versions available.

Load the latest version of Matlab as:

$ module load matlab

It never hurts to double check the version and in fact is recommended. So let’s do just that:

$ module list
Currently Loaded Modules:
  1) matlab/r2019b

Type-along: Where is R?¶

If you don’t specify the version - just as the above Matlab example - the default version of the module is usually loaded, which is usually the latest version. The default version, however,is not always latest version. To see an example, let’s see what versions of R are available:

$ module spider r

----------------------------------------------------------------------------
  r:
----------------------------------------------------------------------------
     Versions:
        r/3.4.3-python-2.7.14
        r/3.4.3-python2
        r/3.4.3-python3
        r/3.5.0-python-2.7.14
        r/3.5.0-python2
        r/3.5.3-python-2.7.14
        r/3.6.1-python3

Let’s try loading the default version:

$ module load r

You can list all the dependencies the R module requires and loads:

$ module list
Currently Loaded Modules:
  1) pcre/8.42        12) libpthread-stubs/0.4  23) libxml2/2.9.9        34) jdk/8u181-b13          45) libice/1.0.9
  2) ncurses/6.1      13) xproto/7.0.31         24) font-util/1.3.2      35) fontconfig/2.12.3      46) libx11/1.6.7
  3) zlib/1.2.11      14) libxau/1.0.8          25) libxft/2.3.2         36) pixman/0.34.0          47) libsm/1.2.2
  4) readline/7.0     15) libxcb/1.13           26) tk/8.6.8             37) cairo/1.14.12-python2  48) libxt/1.1.5
  5) sqlite/3.23.1    16) libxext/1.3.3         27) python/2.7.15        38) libjpeg-turbo/1.5.90   49) harfbuzz/1.4.6-python2
  6) openssl/1.0.2k   17) libxscrnsaver/1.2.2   28) tar/1.31             39) libtiff/4.0.9          50) gobject-introspection/1.49.2-python2
  7) tcl/8.6.8        18) libpng/1.6.34         29) gettext/0.19.8.1     40) bzip2/1.0.6            51) pango/1.41.0-python2
  8) kbproto/1.0.7    19) renderproto/0.11.1    30) gdbm/1.18.1          41) freetype/2.7.1         52) openblas/0.3.2
  9) xextproto/7.3.0  20) libxrender/0.9.10     31) perl/5.26.2          42) libssh2/1.8.0          53) r/3.4.3-python2
 10) libbsd/0.9.1     21) libiconv/1.15         32) libffi/3.2.1         43) curl/7.60.0
 11) libxdmcp/1.1.2   22) xz/5.2.4              33) glib/2.56.1-python2  44) icu4c/60.1

The last loaded module clearly shows that the version of the R loaded is r/3.4.3-python2. To load the latest version of R, use the fullName of the module:

$ module load r/3.6.1-python3

Module versions¶

What’s the difference between module load r and module load r/3.6.1-python3?

The first loading r loads the version that Lmod assumes to be the latest one. This is necessarily not the latest one. The second loading r/3.6.1-python3 loads that exact version, which is supposed to not change. If you’re not interested about the specific version, you can load it without the version (but then when stuff randomly stops working, you’re going to have to figure out what happened). Once you are past that (possibly from day one!), it’s usually a good idea to load specific version, so that your environment will stay the same until you are done.

This is most important for compiled software, but applies to everything.

What’s going on under the hood here?¶

In Linux systems, different environment variables like $PATH and $LD_LIBRARY_PATH help figure out how to run programs. Modules just cleverly manipulate these so that you can find the software you need, even if there are multiple versions available. You can see these variables with the echo command, e.g. echo $PATH.

When you load a module in a shell, the module command changes the current shell’s environment variables, and the environment variables are passed on to all the child processes.

You can explore more with module show NAME.

Making a module collection¶

There is a basic dependency/conflict system to handle module dependency. Each time you load a module, it resolves all the dependencies. This can result in long loading times or be annoying to do each time you log in to the system. However, there is a solution: module save COLLECTION_NAME and module restore COLLECTION_NAME

Let’s see how to do this in an example.

Let’s say that for compiling / running your program you need:

a compiler

CMake

MPI libraries

FFTW libraries

BLAS libraries

You could run this each time you want to compile/run your code:

$ module load gcc/9.2.0 cmake/3.15.3 openmpi/3.1.4 fftw/3.3.8-openmpi openblas/0.3.7
$ module list           # 15 modules

Let’s say this environment works for you. Now you can save it with module save MY-ENV-NAME. Then module purge to unload everything. Now, do module restore MY-ENV-NAME:

$ module save my-env
$ module purge
$ module restore my-env
$ module list           # same 15 modules

Generally, it is a good idea to save your modules as a collection to have your desired modules all set up each time you want to re-compile/re-build.

So the subsequent times that you want to compile/build, you simply module restore my-env and this way you can be sure you have the same previous environment.

Note

You may occasionally need to rebuild your collections in case we re-organize things (it will prompt you to rebuild your collection and you simply save it again).

Full reference¶

Command	Description
`module load` NAME	load module
`module avail`	list all modules
`module spider` NAME	search modules
`module list`	list currently loaded modules
`module show` NAME	details on a module
`module help` NAME	details on a module
`module unload` NAME	unload a module
`module save` ALIAS	save module collection to this alias (saved in `~/.lmod.d/`)
`module savelist`	list all saved collections
`module describe` ALIAS	details on a collection
`module restore` ALIAS	load saved module collection (faster than loading individually)
`module purge`	unload all loaded modules (faster than unloading individually)

Final notes¶

If you have loaded modules when you build/install software, remember to load the same modules when you run the software (also in Slurm jobs). You’ll learn about running jobs later, but the module load should usually be put into the job script.

The modules used to compile and run a program become part of its environment and must always be loaded.

We use the Lmod system and Lmod works by changing environment variables. Thus, they must be sourced by a shell and are only transferred to child processes. Anything that clears the environment clears the loaded modules too. Module loading is done by special functions (not scripts) that are shell-specific and set environment variables.

Triton modules are also available on Aalto Linux: use module load triton-modules to make them available.

Some modules are provided by Aalto Science-IT, some by CSC. You could even make your own user modules.

Exercises¶

Before each exercise, run module purge to clear all modules.

Then, if you are in the FCCI (Finnish universities) but not at Aalto, run module load fgci-common before the exercises to make the Aalto modules available.

Modules-1: Basics

module avail and check what you see. Find a software that has many different versions available. Load the oldest version.

Modules-2: Modules and PATH

PATH is an environment variable that shows from where programs are run. See it’s current value using echo $PATH.

type is a command line tool (a shell builtin, so your shell may not support it, but bash and zsh do) which tells you the full path of what will be run for a given command name - basically it looks up the command in PATH

Run echo $PATH and type python.
module load anaconda
Re-run echo $PATH and type python. How does it change?

Modules-3: Complex module and PATH

Check the value of $PATH. Then, load the module py-gpaw. List what it loaded. Check the value of PATH again. Why is there so much stuff? Can you find a module command that explains it?

(advanced) Modules-4: Modules and PATH

Same as number 2, but use env | sort > filename to store environment variables, then swap to py-gpaw/1.3.0-openmpi-scalapack-python3. Do the same, and compare the two outputs using diff.

Modules-5: Modules and dependencies

Load a module with many dependencies, such as r-ggplot2 and save it as a collection. Compare the time needed to load the module and the collection. (Does time not work? Change your shell to bash, see the previous tutorial)

(advanced) Modules-6: Module contents

Load openfoam-org/7-openmpi-metis. Use which to find where executable blockMesh is coming from and then use ldd to find out what libraries it uses.

What’s next?¶

The next tutorial covers data storage.