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Commit 9762f239 authored by David Hrbáč's avatar David Hrbáč
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Merge branch 'eb' into 'master' 

add eb tutorial

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See merge request !120
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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 software that is supported by EasyBuild. In a second time, 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 reproducable 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.
!!! Warning ""
You need to have Lmod activated to have the modules produced in Lua language.
## Short Introduction
EasyBuild is a tool that allows to perform automated and reproducible compilation and installation of software.
All builds and installations are performed at user level, so you don't 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
Detailed documentations is available [here](http://easybuild.readthedocs.io).
## 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 on [here](https://github.com/hpcugent/easybuild/wiki/Compiler-toolchains).
## EasyConfig File
An 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 on [here](https://github.com/hpcugent/easybuild-easyconfigs).
## EasyBuild on IT4Innovations Clusters
To use EasyBuild on a compute node, load the EasyBuild module:
```console
$ ml av EasyBuild
-------------------------- /apps/modules/modulefiles/tools ---------------------
EasyBuild/2.8.1 EasyBuild/3.0.0 EasyBuild/3.0.2 EasyBuild/3.1.0 (S,D)
Where:
S: Module is Sticky, requires --force to unload or purge
D: Default Module
$ ml EasyBuild
```
The EasyBuild command is eb. Check the version you have loaded:
```console
$ eb --version
This is EasyBuild 3.1.0 (framework: 3.1.0, easyblocks: 3.1.0) on host login2
```
To get help on the EasyBuild options, use the -h or -H option flags:
```console
$ 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 (def 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.
```console
$ eb -S git
CFGS1=/apps/easybuild/easyconfigs/easybuild/easyconfigs
* $CFGS1/g/git-lfs/git-lfs-1.1.1.eb
* $CFGS1/g/git/git-1.7.12-goalf-1.1.0-no-OFED.eb
* $CFGS1/g/git/git-1.7.12-goolf-1.4.10.eb
* $CFGS1/g/git/git-1.7.12-ictce-4.0.6.eb
* $CFGS1/g/git/git-1.7.12-ictce-5.3.0.eb
* $CFGS1/g/git/git-1.8.2-cgmpolf-1.1.6.eb
* $CFGS1/g/git/git-1.8.2-cgmvolf-1.1.12rc1.eb
* $CFGS1/g/git/git-1.8.2-cgmvolf-1.2.7.eb
* $CFGS1/g/git/git-1.8.2-cgoolf-1.1.7.eb
* $CFGS1/g/git/git-1.8.2-gmvolf-1.7.12.eb
* $CFGS1/g/git/git-1.8.2-gmvolf-1.7.12rc1.eb
* $CFGS1/g/git/git-1.8.2-goolf-1.4.10.eb
* $CFGS1/g/git/git-1.8.3.1-goolf-1.4.10.eb
* $CFGS1/g/git/git-1.8.5.6-GCC-4.9.2.eb
* $CFGS1/g/git/git-2.10.2.eb
* $CFGS1/g/git/git-2.11.0-GNU-4.9.3-2.25.eb
* $CFGS1/g/git/git-2.11.0.eb
* $CFGS1/g/git/git-2.2.2-GCC-4.9.2.eb
* $CFGS1/g/git/git-2.4.1-GCC-4.9.2.eb
* $CFGS1/g/git/git-2.7.3-GNU-4.9.3-2.25.eb
* $CFGS1/g/git/git-2.7.3-foss-2015g.eb
* $CFGS1/g/git/git-2.8.0-GNU-4.9.3-2.25.eb
* $CFGS1/g/git/git-2.8.0-foss-2016a.eb
* $CFGS1/g/git/git-2.8.0-intel-2017.00.eb
* $CFGS1/g/git/git-2.8.0.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**):
```console
$ eb git-2.8.0.eb -Dr
eb git-2.8.0.eb -Dr
== temporary log file in case of crash /tmp/eb-JcU1eA/easybuild-emly2F.log
Dry run: printing build status of easyconfigs and dependencies
CFGS=/apps/easybuild/easyconfigs/easybuild/easyconfigs
* [x] $CFGS/c/cURL/cURL-7.37.1.eb (module: cURL/7.37.1)
* [x] $CFGS/e/expat/expat-2.1.0.eb (module: expat/2.1.0)
* [x] $CFGS/g/gettext/gettext-0.19.2.eb (module: gettext/0.19.2)
* [x] $CFGS/p/Perl/Perl-5.20.2-bare.eb (module: Perl/5.20.2-bare)
* [x] $CFGS/m/M4/M4-1.4.17.eb (module: M4/1.4.17)
* [x] $CFGS/a/Autoconf/Autoconf-2.69.eb (module: Autoconf/2.69)
* [ ] $CFGS/g/git/git-2.8.0.eb (module: git/2.8.0)
== Temporary log file(s) /tmp/eb-JcU1eA/easybuild-emly2F.log* have been removed.
== Temporary directory /tmp/eb-JcU1eA has been removed.
```
### Compile and Install Module
If we try to build *git-2.8.0.eb*, nothing will be done as it is already installed on the cluster. To enable dependency resolution, use the **--robot** command line option (or **-r** for short):
```console
$ eb git-2.8.0.eb -r
== temporary log file in case of crash /tmp/eb-PXe3Zo/easybuild-hEckF4.log
== git/2.8.0 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-PXe3Zo/easybuild-hEckF4.log* have been removed.
== Temporary directory /tmp/eb-PXe3Zo has been removed.
```
Rebuild *git-2.8.0.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**.
```console
$ eb git-2.8.0.eb -r -f
== temporary log file in case of crash /tmp/eb-JS_Fb5/easybuild-OwJZKn.log
== resolving dependencies ...
== processing EasyBuild easyconfig /apps/easybuild/easyconfigs/easybuild/easyconfigs/g/git/git-2.8.0.eb
== building and installing git/2.8.0...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully
== Results of the build can be found in the log file(s) /apps/all/git/2.8.0/easybuild/easybuild-git-2.8.0-20170221.110059.log
== Build succeeded for 1 out of 1
== Temporary log file(s) /tmp/eb-JS_Fb5/easybuild-OwJZKn.log\* have been removed.
== Temporary directory /tmp/eb-JS_Fb5 has been removed.
```
If we try to build *git-2.11.0.eb*:
```console
== temporary log file in case of crash /tmp/eb-JS_Fb5/easybuild-OwXCKn.log
== resolving dependencies ...
== processing EasyBuild easyconfig /apps/easybuild/easyconfigs/easybuild/easyconfigs/g/git/git-2.11.0.eb
== building and installing git/2.11.0...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully
== Results of the build can be found in the log file(s) /apps/all/git/2.11.0/easybuild/easybuild-git-2.11.0-20170221.110059.log
== Build succeeded for 1 out of 1
== Temporary log file(s) /tmp/eb-JS_Fb5/easybuild-OwXCKn.log\* have been removed.
== Temporary directory /tmp/eb-JS_Fb5 has been removed.
```
If we try to build *git-2.11.1*, but we used easyconfig *git-2.11.0.eb* - change version command **--try-software-version=2.11.1**:
```console
$ eb git-2.11.0.eb -r --try-software-version=2.11.1
== temporary log file in case of crash /tmp/eb-oisi0q/easybuild-2rNh7I.log
== resolving dependencies ...
== processing EasyBuild easyconfig /tmp/eb-oisi0q/tweaked_easyconfigs/git-2.11.1.eb
== building and installing git/2.11.1...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully
== Results of the build can be found in the log file(s) /apps/all/git/2.11.1/easybuild/easybuild-git-2.11.1-20170221.111005.log
== Build succeeded for 1 out of 1
== Temporary log file(s) /tmp/eb-oisi0q/easybuild-2rNh7I.log\* have been removed.
== Temporary directory /tmp/eb-oisi0q has been removed.
```
and try to build *git-2.11.1-intel-2017a*, but we used easyconfig *git-2.11.0.eb* - change toolchains **--try-toolchain-name=intel --try-toolchain-version=2017a** or **--try-toolchain=intel,2017a**:
```console
$ eb git-2.11.0.eb -r --try-toolchain=intel,2017a
== temporary log file in case of crash /tmp/eb-oisi0q/easybuild-2Trh7I.log
== resolving dependencies ...
== processing EasyBuild easyconfig /tmp/eb-oisi0q/tweaked_easyconfigs/git-2.11.1-intel-2017a.eb
== building and installing git/2.11.1-intel-2017a...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully
== Results of the build can be found in the log file(s) /apps/all/git/2.11.1-intel-2017a/easybuild/easybuild-git-2.11.1-20170221.111005.log
== Build succeeded for 1 out of 1
== Temporary log file(s) /tmp/eb-oisi0q/easybuild-2Trh7I.log\* have been removed.
== Temporary directory /tmp/eb-oisi0q 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:
```console
$ module use $HOME/.local/easybuild/modules/all/
```
or modify your `.bash_profile`:
```console
$ 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 2.11.1 with *foss* toolchain. Open your favorite editor and create a file named *git-2.11.1-foss-2017a.eb* with the following content:
```console
$ vim git-2.11.1-foss-2017a.eb
```
```python
easyblock = 'ConfigureMake'
name = 'git'
version = '2.11.1'
homepage = 'http://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': '2017a'}
sources = ['v%(version)s.tar.gz']
source_urls = ['https://github.com/git/git/archive']
builddependencies = [('Autoconf', '2.69')]
dependencies = [
('cURL', '7.37.1'),
('expat', '2.1.0'),
('gettext', '0.19.2'),
('Perl', '5.20.2'),
]
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'"
sanity_check_paths = {
'files': ['bin/git'],
'dirs': [],
}
moduleclass = 'tools'
```
This is a simple EasyConfig. Most of the fields are self-descriptive. No build method is explicitely defined, so it uses by default the standard configure/make/make install approach.
Let's build Git with this EasyConfig file:
```console
$ eb ./git-2.11.1-foss-2017a.eb -r
== temporary log file in case of crash /tmp/eb-oisi0q/easybuild-2Tii7I.log
== resolving dependencies ...
== processing EasyBuild easyconfig /home/username/git-2.11.1-foss-2017a.eb
== building and installing git/2.11.1-foss-2017a...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully
== Results of the build can be found in the log file(s) /home/username/.local/easybuild/modules/all/git/2.11.1-foss-2017a/easybuild/easybuild-git-2.11.1-20170221.111005.log
== Build succeeded for 1 out of 1
== Temporary log file(s) /tmp/eb-oisi0q/easybuild-2Tii7I.log\* have been removed.
== Temporary directory /tmp/eb-oisi0q has been removed.
```
We can now check that our version of Git is available via the modules:
```console
$ ml av git
-------------------------------- /apps/modules/modulefiles/tools -------------------------
git/2.8.0-GNU-4.9.3-2.25 git/2.11.0-GNU-4.9.3-2.25 git/2.11.1-GNU-4.9.3-2.25 (D)
-------------------------------- /home/username/.local/easybuild/modules/all -------------
git/2.11.1-foss-2017a
Where:
D: Default Module
If you need software that is not listed, request it at support@it4i.cz.
```
## Submitting Build Jobs (Experimental)
Using the **--job** command line option, you can instruct EasyBuild to submit jobs for the installations that should be performed, rather than performing the installations locally on the system you are on.
```console
$ eb git-2.11.0-GNU-4.9.3-2.25.eb -r --job
== temporary log file in case of crash /tmp/eb-zeLzBb/easybuild-H_Z0fB.log
== resolving dependencies ...
== GC3Pie job overview: 1 submitted (total: 1)
== GC3Pie job overview: 1 running (total: 1)
== GC3Pie job overview: 1 running (total: 1)
== GC3Pie job overview: 1 running (total: 1)
== GC3Pie job overview: 1 running (total: 1)
== GC3Pie job overview: 1 running (total: 1)
== GC3Pie job overview: 1 running (total: 1)
== GC3Pie job overview: 1 running (total: 1)
== GC3Pie job overview: 1 running (total: 1)
== GC3Pie job overview: 1 terminated, 1 ok (total: 1)
== GC3Pie job overview: 1 terminated, 1 ok (total: 1)
== Done processing jobs
== GC3Pie job overview: 1 terminated, 1 ok (total: 1)
== Submitted parallel build jobs, exiting now
== Temporary log file(s) /tmp/eb-zeLzBb/easybuild-H_Z0fB.log* have been removed.
== Temporary directory /tmp/eb-zeLzBb has been removed.
```
!!! note ""
Salomon jobs ... XXXXX.isrv5
Anselm jobs ... XXXXX.dm2
```console
$ qstat -u username -w
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
------------------------------ --------------- --------------- --------------- -------- ---- ----- ------ ----- - -----
1319314.dm2 username qprod git-2.11.0-GNU- 85605 1 16 -- 24:00 R 00:00:17
```
docs.it4i/software/eb.md deleted 100644 → 0
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# EasyBuild
mkdocs.yml
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......@@ -64,6 +64,7 @@ pages:
- Lmod Environment: software/lmod.md
- Modules Matrix: modules-matrix.md
- Singularity Container: software/singularity.md
- EasyBuild: software/easybuild.md
- Salomon Software:
- Available Modules: modules-salomon.md
- Available Modules on UV: modules-salomon-uv.md
......
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