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EasyBuild

The objective of this tutorial is to show how EasyBuild can be used to ease, automate, and script the build of software on the IT4Innovations clusters. Two use-cases are considered. First, we are going to build a software that is supported by EasyBuild. Then, we will see through a simple example how to add support for a new software in EasyBuild.

The benefit of using EasyBuild for your builds is that it allows automated and reproducible build of software. Once a build has been made, the build script (via the EasyConfig file) or the installed software (via the module file) can be shared with other users.

Short Introduction

EasyBuild is a tool that allows performing automated and reproducible software compilation and installation.

All builds and installations are performed at user level, so you do not need the admin rights. The software is installed in your home directory (by default in $HOME/.local/easybuild/software/) and a module file is generated (by default in $HOME/.local/easybuild/modules/) to use the software.

EasyBuild relies on two main concepts:

  • Toolchains
  • EasyConfig file (our easyconfigs are here)

A detailed documentation is available here.

Toolchains

A toolchain corresponds to a compiler and a set of libraries, which are commonly used to build a software. The two main toolchains frequently used on the IT4Innovations clusters are the foss and intel.

  • foss is based on the GCC compiler and on open-source libraries (OpenMPI, OpenBLAS, etc.).
  • intel is based on the Intel compiler and on Intel libraries (Intel MPI, Intel Math Kernel Library, etc.).

Additional details are available here.

EasyConfig File

The EasyConfig file is a simple text file that describes the build process of a software. For most software that uses standard procedure (like configure, make, and make install), this file is very simple. Many EasyConfig files are already provided with EasyBuild.

By default, EasyConfig files and generated modules are named using the following convention:

software-name-software-version-toolchain-name-toolchain-version(-suffix).eb

Additional details are available here.

EasyBuild on IT4Innovations Clusters

To use EasyBuild on a compute node, load the EasyBuild module:

$ml av easybuild

------------------------------------------ /apps/modules/tools -------------------------------------------
   EasyBuild/4.3.3 (S)    EasyBuild/4.4.2 (S)    EasyBuild/4.5.4 (S)    EasyBuild/4.6.2 (S)
   EasyBuild/4.3.4 (S)    EasyBuild/4.5.0 (S)    EasyBuild/4.5.5 (S)    EasyBuild/4.7.0 (S,D)
   EasyBuild/4.4.0 (S)    EasyBuild/4.5.1 (S)    EasyBuild/4.6.0 (S)
   EasyBuild/4.4.1 (S)    EasyBuild/4.5.3 (S)    EasyBuild/4.6.1 (S)

  Where:
   S:  Module is Sticky, requires --force to unload or purge
   D:  Default Module

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

$ ml EasyBuild

The EasyBuild command is eb. Check the version you have loaded:

$ eb --version
This is EasyBuild 4.7.0 (framework: 4.7.0, easyblocks: 4.7.0) on host login1.karolina.it4i.cz.

To get help on the EasyBuild options, use the -h or -H option flags:

$ eb -h
Usage: eb [options] easyconfig [...]

Builds software based on easyconfig (or parse a directory). Provide one or more easyconfigs or
directories, use -H or --help more information.

Options:
  -h                show short help message and exit
  -H OUTPUT_FORMAT  show full help message and exit

  Debug and logging options (configfile section MAIN):
    -d              Enable debug log mode (default: False)

  Basic options:
    Basic runtime options for EasyBuild. (configfile section basic)
...

Build Software Using Provided EasyConfig File

Search for Available Easyconfig

Searching for available easyconfig files can be done using the --search (long output) and -S (short output) command line options. All easyconfig files available in the robot search path are considered and searching is done case-insensitive.

$ eb -S git
CFGS1=/apps/easybuild/easyconfigs-it4i
CFGS2=/apps/easybuild/easyconfigs-master/easybuild/easyconfigs
CFGS3=/apps/easybuild/easyconfigs-develop/easybuild/easyconfigs
 * $CFGS1/.gitignore
 * $CFGS1/.gitlab-ci.yml
 * $CFGS1/g/git-lfs/git-lfs-1.1.1.eb
 * $CFGS1/g/git-lfs/git-lfs-2.11.0.eb
 * $CFGS1/g/git-lfs/git-lfs-3.1.2.eb
 * $CFGS1/g/git/git-2.19.1.eb
 * $CFGS1/g/git/git-2.21.0.eb
 * $CFGS1/g/git/git-2.23.0.eb
 * $CFGS1/g/git/git-2.25.1.eb
 * $CFGS1/g/git/git-2.30.1.eb
 * $CFGS1/g/git/git-2.31.1.eb
 * $CFGS1/g/git/git-2.32.0-GCCcore-10.3.0-nodocs-test.eb
 * $CFGS2/b/BCALM/BCALM-2.2.0-fix-nogit.patch
 * $CFGS2/d/dagitty/dagitty-0.2-2-foss-2018b-R-3.5.1.eb
 * $CFGS2/e/EMAN2/EMAN2-2.3_fix_broken_githash_regex_replace.patch
 * $CFGS2/g/GIMIC/GIMIC-2018.04.20_git.patch
 * $CFGS2/g/GitPython/GitPython-2.1.11-foss-2018b-Python-3.6.6.eb
 * $CFGS2/g/GitPython/GitPython-2.1.11-intel-2018b-Python-3.6.6.eb
 * $CFGS2/g/GitPython/GitPython-2.1.15.eb
 * $CFGS2/g/GitPython/GitPython-3.0.3-GCCcore-8.2.0-Python-3.7.2.eb
 * $CFGS2/g/GitPython/GitPython-3.1.0-GCCcore-8.3.0-Python-3.7.4.eb
 * $CFGS2/g/GitPython/GitPython-3.1.9-GCCcore-9.3.0-Python-3.8.2.eb
 * $CFGS2/g/GitPython/GitPython-3.1.14-GCCcore-10.2.0.eb
 * $CFGS2/g/GitPython/GitPython-3.1.18-GCCcore-10.3.0.eb
 * $CFGS2/g/GitPython/GitPython-3.1.24-GCCcore-11.2.0.eb
 * $CFGS2/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb
 * $CFGS2/g/gettext/gettext-0.19.8_fix-git-config.patch
 * $CFGS2/g/git-extras/git-extras-5.1.0-foss-2016a.eb
...

Get an Overview of Planned Installations

You can do a “dry-run” overview by supplying -D/--dry-run (typically combined with --robot, in the form of -Dr):

$ eb git-2.30.1.eb -Dr
== Temporary log file in case of crash /tmp/eb-6vwvor2_/easybuild-vg82aat4.log
Dry run: printing build status of easyconfigs and dependencies
CFGS=/apps/easybuild
 * [x] $CFGS/easyconfigs-master/easybuild/easyconfigs/m/M4/M4-1.4.18.eb (module: M4/1.4.18)
 * [x] $CFGS/easyconfigs-it4i/a/Autoconf/Autoconf-2.69.eb (module: Autoconf/2.69)
 * [ ] $CFGS/easyconfigs-it4i/g/git/git-2.30.1.eb (module: git/2.30.1)
== Temporary log file(s) /tmp/eb-6vwvor2_/easybuild-vg82aat4.log* have been removed.
== Temporary directory /tmp/eb-6vwvor2_ has been removed.

Compile and Install Module

If we try to build git-2.31.1.eb, nothing will happen as it is already installed on the cluster. To enable dependency resolution, use the --robot command line option (or -r for short):

$ eb git-2.31.1.eb -r
== Temporary log file in case of crash /tmp/eb-11d_kpht/easybuild-jmygqpqr.log
== git/2.31.1 is already installed (module found), skipping
== No easyconfigs left to be built.

== Build succeeded for 0 out of 0
== Temporary log file(s) /tmp/eb-11d_kpht/easybuild-jmygqpqr.log* have been removed.
== Temporary directory /tmp/eb-11d_kpht has been removed.

Rebuild git-2.31.1.eb. Use eb --rebuild to rebuild a given easyconfig/module or use eb --force/-f to force the reinstallation of a given easyconfig/module. The behavior of --force is the same as --rebuild and --ignore-osdeps.

$ eb git-2.31.1.eb -r -f
== Temporary log file in case of crash /tmp/eb-wbzf_rxh/easybuild-umq1_01u.log
== resolving dependencies ...
== processing EasyBuild easyconfig /apps/easybuild/easyconfigs-it4i/g/git/git-2.31.1.eb
== building and installing git/2.31.1...
== fetching files...
== creating build dir, resetting environment...
== ... (took 3 secs)
== unpacking...
== ... (took 9 secs)
== patching...
== preparing...
== configuring...
== ... (took 4 secs)
== building...
== ... (took 4 secs)
== testing...
== installing...
== ... (took 2 secs)
== taking care of extensions...
== restore after iterating...
== postprocessing...
== sanity checking...
== cleaning up...
== ... (took 3 secs)
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully (took 30 secs)
== Results of the build can be found in the log file(s)
/home/username/.local/easybuild/software/git/2.31.1/easybuild/easybuild-git-2.31.1-20230315.092001.log

== Build succeeded for 1 out of 1
== Temporary log file(s) /tmp/eb-wbzf_rxh/easybuild-umq1_01u.log* have been removed.
== Temporary directory /tmp/eb-wbzf_rxh has been removed.

If we try to build git-2.30.1.eb:

$ eb git-2.30.1.eb -r
== Temporary log file in case of crash /tmp/eb-s3t9lwk_/easybuild-cvx5kpna.log
== resolving dependencies ...
== processing EasyBuild easyconfig /apps/easybuild/easyconfigs-it4i/g/git/git-2.30.1.eb
== building and installing git/2.30.1...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== ... (took 10 secs)
== patching...
== preparing...
== configuring...
== ... (took 4 secs)
== building...
== ... (took 4 secs)
== testing...
== installing...
== ... (took 3 secs)
== taking care of extensions...
== restore after iterating...
== postprocessing...
== sanity checking...
== cleaning up...
== ... (took 3 secs)
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully (took 29 secs)
== Results of the build can be found in the log file(s)
/home/username/.local/easybuild/software/git/2.30.1/easybuild/easybuild-git-2.30.1-20230315.092117.log

== Build succeeded for 1 out of 1
== Temporary log file(s) /tmp/eb-s3t9lwk_/easybuild-cvx5kpna.log* have been removed.
== Temporary directory /tmp/eb-s3t9lwk_ has been removed.

If we try to build git-2.30.1, but we used easyconfig git-2.25.1.eb, change the version command --try-software-version=2.30.1:

$ eb git-2.25.1.eb -r --try-software-version=2.30.1
== Temporary log file in case of crash /tmp/eb-lw9itci8/easybuild-qzb7j64j.log
== resolving dependencies ...
== processing EasyBuild easyconfig /tmp/eb-lw9itci8/tweaked_easyconfigs/git-2.30.1.eb
== building and installing git/2.30.1...
== fetching files...
== ... (took 4 secs)
== creating build dir, resetting environment...
== unpacking...
== ... (took 9 secs)
== patching...
== preparing...
== configuring...
== ... (took 4 secs)
== building...
== ... (took 4 secs)
== testing...
== installing...
== ... (took 4 secs)
== taking care of extensions...
== restore after iterating...
== postprocessing...
== sanity checking...
== cleaning up...
== ... (took 3 secs)
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully (took 33 secs)
== Results of the build can be found in the log file(s)
/home/username/.local/easybuild/software/git/2.30.1/easybuild/easybuild-git-2.30.1-20230315.092313.log

== Build succeeded for 1 out of 1
== Temporary log file(s) /tmp/eb-lw9itci8/easybuild-qzb7j64j.log* have been removed.
== Temporary directory /tmp/eb-lw9itci8 has been removed.

MODULEPATH

To see the newly installed modules, you need to add the path where they were installed to the MODULEPATH. On the cluster, you have to use the module use command:

$ module use $HOME/.local/easybuild/modules/all/

or modify your .bash_profile:

$ cat ~/.bash_profile
# .bash_profile

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi

# User specific environment and startup programs

module use $HOME/.local/easybuild/modules/all/

PATH=$PATH:$HOME/bin

export PATH

Build Software Using Your Own EasyConfig File

For this example, we create an EasyConfig file to build Git 2.38.1 with the foss toolchain. Open your favorite editor and create a file named git-2.18.1-foss-2022b.eb with the following content:

$ vim git-2.38.1-foss-2022b.eb

easyblock = 'ConfigureMake'

name = 'git'
version = '2.38.1'

homepage = 'https://git-scm.com/'
description = """Git is a free and open source distributed version control system designed
to handle everything from small to very large projects with speed and efficiency."""

toolchain = {'name': 'foss', 'version': '2022b'}

source_urls = ['https://github.com/git/git/archive']
sources = ['v%(version)s.tar.gz']

builddependencies = [
    ('binutils', '2.39'),
    ('Autotools', '20220317'),
]

dependencies = [
    ('cURL', '7.86.0'),
    ('expat', '2.4.9'),
    ('gettext', '0.21.1'),
    ('Perl', '5.36.0'),
]

preconfigopts = 'make configure && '

# Work around git build system bug.  If LIBS contains -lpthread, then configure
# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS.
configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'"

postinstallcmds = ['cd contrib/subtree; make install']

sanity_check_paths = {
    'files': ['bin/git'],
    'dirs': ['libexec/git-core', 'share'],
}

moduleclass = 'tools'

This is a simple EasyConfig. Most of the fields are self-descriptive. No build method is explicitly defined, so it uses by default the standard configure/make/make install approach.

Let us build Git with this EasyConfig file:

$ eb git-2.38.1-foss-2022b.eb -r
== Temporary log file in case of crash /tmp/eb-2aiq9qr8/easybuild-eb4zenze.log
== resolving dependencies ...
== processing EasyBuild easyconfig /home/username/git-2.38.1-foss-2022b.eb
== building and installing git/2.38.1-foss-2022b...
== fetching files...
== ... (took 3 secs)
== creating build dir, resetting environment...
== unpacking...
== ... (took 11 secs)
== patching...
== preparing...
== ... (took 2 secs)
== configuring...
== ... (took 7 secs)
== building...
== ... (took 7 secs)
== testing...
== installing...
== ... (took 2 secs)
== taking care of extensions...
== restore after iterating...
== postprocessing...
== sanity checking...
== ... (took 1 secs)
== cleaning up...
== ... (took 4 secs)
== creating module...
== ... (took 1 secs)
== permissions...
== packaging...
== COMPLETED: Installation ended successfully (took 41 secs)
== Results of the build can be found in the log file(s)
/home/username/.local/easybuild/software/git/2.38.1-foss-2022b/easybuild/easybuild-git-2.38.1-20230315.0957
22.log

== Build succeeded for 1 out of 1
== Temporary log file(s) /tmp/eb-2aiq9qr8/easybuild-eb4zenze.log* have been removed.
== Temporary directory /tmp/eb-2aiq9qr8 has been removed.

We can now check that our version of Git is available via the modules:

$ ml av git

------------------------------- /home/username/.local/easybuild/modules/all -------------------------------
   git/2.38.1-foss-2022b

------------------------------------------ /apps/modules/devel -------------------------------------------
   libgit2/1.1.0-GCCcore-10.3.0

------------------------------------------ /apps/modules/tools -------------------------------------------
   git-lfs/3.1.2                            git/2.32.0-GCCcore-10.3.0-nodocs
   git/2.28.0-GCCcore-10.2.0-nodocs         git/2.33.1-GCCcore-11.2.0-nodocs
   git/2.31.1                               git/2.36.0-GCCcore-11.3.0-nodocs
   git/2.32.0-GCCcore-10.3.0-nodocs-test    git/2.38.1-GCCcore-12.2.0-nodocs (D)

  Where:
   D:  Default Module

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

Advanced EasyBuild Configuration

By creating the ~/.config/easybuild/config.cfg file, you can easily specify the desired location of your software, CUDA compute capabilities, and other options that you would usually have to specify within your easyconfig or from the command line. To get an overview of all available options, use eb --confighelp command.

You can use our template to set all of the usual EasyBuild variables:

[MAIN]

[basic]
locks-dir=EASYBUILD_ROOT/.locks/
robot=/apps/easybuild/easyconfigs-it4i:/apps/easybuild/easyconfigs-master/easybuild/easyconfigs:/apps/easybuild/easyconfigs-develop/easybuild/easyconfigs
robot-paths=/apps/easybuild/easyconfigs-it4i:/apps/easybuild/easyconfigs-master/easybuild/easyconfigs:/apps/easybuild/easyconfigs-develop/easybuild/easyconfigs

[config]
buildpath=/dev/shm/USER/build
installpath=EASYBUILD_ROOT
installpath-modules=EASYBUILD_ROOT/modules
installpath-software=EASYBUILD_ROOT/all
moduleclasses=python
repository=FileRepository
repositorypath=EASYBUILD_ROOT/file-repository
sourcepath=EASYBUILD_ROOT/sources

[easyconfig]
local-var-naming-check=error

[override]
# 8.0 for Karolina, 7.0 for Barbora
cuda-compute-capabilities=CUDA_CC
detect-loaded-modules=purge
enforce-checksums=True
silence-deprecation-warnings=True
trace=True

Note

Do not forget to add the path to your modules to MODULEPATH using the module use command in your ~/.bashrc to be able to lookup and use your installed modules.

Template requires you to fill in the EASYBUILD_ROOT, CUDA_CC, and USER variables. EASYBUILD_ROOT is the top level directory which will hold all of your EasyBuild related data. CUDA_CC defines the CUDA compute capabilities of graphics cards, and USER should preferably be set to your username.

If you plan on writing more than one or two of your own easyconfigs, it might be useful to setup a custom easyconfig repository. Simply prepend it's path to the robot and robot-paths variables.

A detailed documentation regarding EasyBuild configuration is available here.