Update versions for EasyBuild user install section

UNINETTSigma2 · Mar 6, 2024 · 14ba922 · 14ba922
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diff --git a/software/userinstallsw/easybuild.md b/software/userinstallsw/easybuild.md
@@ -13,7 +13,7 @@ already exists for the particular package you are interested in).
 With EasyBuild you might encounter a few different scenarios:
 
 1.  An easyconfig already exists for my software and can be used as is.
-2.  An easyconfig exists, but not for the compiler toolchain that I need.
+2.  An easyconfig exists, but not for the software version or compiler toolchain that I need.
 3.  An easyconfig does not exist for my software (not covered here, please
     refer to general EasyBuild tutorials).
 
@@ -35,9 +35,9 @@ load the software into your environment.
 EasyBuild is very explicit in the build specifications for each part in a
 software's chain of dependencies, and is very careful not to mix dependencies
 that are built using different compiler versions or toolchains. This is the
-reason for the long names, like ``rjags-4-6-intel-2017b-R-3.4.3``
-which means that the program ``rjags`` version 4.6 has been built using the
-``intel-2017b`` toolchain and aimed at ``R`` version 3.4.3. This in turn means
+reason for the long names, like ``rjags-4-12-foss-2021b-R-4.1.2``
+which means that the program ``rjags`` version 4.12 has been built using the
+``foss-2021b`` toolchain and aimed at ``R`` version 4.1.2. This in turn means
 that all other dependencies that ``rjags`` might have, or anything that want to
 *use* ``rjags`` as a dependency, will have to be compatible with these versions.
 
@@ -56,9 +56,9 @@ latest version you can find:
     $ module purge
     $ module avail easybuild
     ----------------------- /cluster/modulefiles/all ------------------------
-	EasyBuild/4.3.1
+	EasyBuild/4.9.0
 
-    $ module load EasyBuild/4.3.1
+    $ module load EasyBuild/4.9.0
 
 Say you want to install the already mentioned
 [rjags](http://cran.r-project.org/web/packages/rjags) package. Then you first
@@ -67,13 +67,13 @@ done with the `--search-filename` or `-S` option. So to display all rags
 version that can be installed use:
 
     $ eb --search-filename rjags
-    == found valid index for /cluster/software/EasyBuild/4.6.2/easybuild/easyconfigs, so using it...
+    == found valid index for /cluster/software/EasyBuild/4.9.0/easybuild/easyconfigs, so using it...
      * rjags-4-6-intel-2017a-R-3.4.0.eb
      * rjags-4-6-intel-2017b-R-3.4.3.eb
      * rjags-4-8-foss-2018b-R-3.5.1.eb
      * rjags-4-9-foss-2019a-R-3.6.0.eb
      * rjags-4-10-foss-2019b.eb
-     * rjags-4-10-foss-2020a-R-4.0.0.eb
+     * rjags-4-10-foss-2020a-R4.0.0.eb
      * rjags-4-10-foss-2020b-R-4.0.3.eb
      * rjags-4-10-foss-2020b-R-4.0.4.eb
      * rjags-4-10-foss-2020b-R-4.0.5.eb
@@ -82,12 +82,14 @@ version that can be installed use:
      * rjags-4-10-fosscuda-2020b-R-4.0.4.eb
      * rjags-4-10-fosscuda-2020b-R-4.0.5.eb
      * rjags-4-12-foss-2021b-R-4.1.2.eb
+     * rjags-4-13-foss-2022a-R-4.2.1.eb
+     * rjags-4-13-foss-2022b-R-4.2.2.eb
 
     Note: 1 matching archived easyconfig(s) found, use --consider-archived-easyconfigs to see them
 
 
 From this list we decide to go for ``rjags`` version mentioned above, i.e.
-``rjags-4-6-intel-2017b-R-3.4.3.eb``.
+``rjags-4-12-foss-2021b-R-4.1.2.eb``.
 
 Now, we advice to do an install in three steps, first download the sources of
 your software, then do a test run where you check what will be installed and
@@ -107,7 +109,7 @@ This will download a tarball into your local EB directory
 what will be installed with the command you are planning to use. This you get
 by the command:
 
-    $ eb rjags-4-6-intel-2017b-R-3.4.3.eb --dry-run
+    $ eb rjags-4-12-foss-2021b-R-4.1.2.eb --dry-run
 
 This will check that all the necessary dependencies are available in the current
 EB repository. If not, you will get an error message. It will also print the
@@ -116,7 +118,7 @@ dependency is already satisfied, and won't be re-installed.
 
 **Step 3:** If the test build was successful, you can perform the build with:
 
-    $ eb rjags-4-6-intel-2017b-R-3.4.3.eb --robot --parallel=2
+    $ eb rjags-4-12-foss-2021b-R-4.1.2.eb --robot --parallel=2
 
 where ``--robot`` means that EasyBuild should automatically resolve and install
 all necessary dependencies, and ``--parallel`` will set the number of CPU
@@ -136,7 +138,7 @@ login node.
 You can now confirm that the package has been installed under
 ``.local/easybuild/software``:
 
-    $ ls $HOME/.local/easybuild/software/rjags/4-6-intel-2017b-R-3.4.3/rjags/
+    $ ls $HOME/.local/easybuild/software/rjags/4-12-foss-2021b-R-4.1.2/rjags/
     data  DESCRIPTION  help  html  INDEX  libs  Meta  NAMESPACE  R
 
 
@@ -147,7 +149,7 @@ folder under ``.local/easybuild/software``. At the same time, EasyBuild
 created a new module file under ``.local/easybuild/modules``:
 
     $ ls .local/easybuild/modules/all/rjags/
-    4-6-intel-2017b-R-3.4.3.lua
+    4-12-foss-2021b-R-4.1.2.lua
 
 which can now be loaded and used alongside any other globally installed
 software. In order to do so you need to tell the module system to look for
@@ -156,14 +158,14 @@ modules in this directory, which is done with the ``module use`` command:
     $ module use $HOME/.local/easybuild/modules/all
     $ module avail rjags
     ------------------------------------ .local/easybuild/modules/all -------------------------------------
-        rjags/4-6-intel-2017b-R-3.4.3
+        rjags/4-12-foss-2021b-R-4.1.2
 
     Use "module spider" to find all possible modules.
     Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
 
 You can now load and use the package just like any other module:
 
-    $ module load rjags/4-6-intel-2017b-R-3.4.3
+    $ module load rjags/4-12-foss-2021b-R-4.1.2
 
 **For more information about the module system, please see:**
 <https://lmod.readthedocs.io/en/latest>
@@ -176,9 +178,9 @@ following changes to the above procedure.
 
     $ my_path=/cluster/projects/nnXXXXk/easybuild
     $ mkdir -p $my_path
-    $ eb rjags-4-6-intel-2017b-R-3.4.3.eb --prefix=$my_path --fetch
-    $ eb rjags-4-6-intel-2017b-R-3.4.3.eb --prefix=$my_path --dry-run
-    $ eb rjags-4-6-intel-2017b-R-3.4.3.eb --prefix=$my_path
+    $ eb rjags-4-12-foss-2021b-R-4.1.2.eb --prefix=$my_path --fetch
+    $ eb rjags-4-12-foss-2021b-R-4.1.2.eb --prefix=$my_path --dry-run
+    $ eb rjags-4-12-foss-2021b-R-4.1.2.eb --prefix=$my_path
 
 where XXXX is your project id number. Note the easybuild folder in the path,
 this is a tip for housekeeping and not strictly required. This will give the
@@ -193,15 +195,17 @@ Now the ``rjags`` installation is available to everyone associated with the
 
 ## Writing your own easyconfigs
 
-Let's say that for some reason you need to use ``rjags`` with the
-``intel/2018b`` toolchain, instead of ``2017b`` which we already installed.
+Let's say that for some reason you need to use ``rjags-4-12`` with the
+``foss/2022a`` toolchain, instead of ``2021b`` which we already installed.
 A quick look into the EB repo tells you that this particular version is not
 available, which means that simply substituting the toolchain version will
 *not* work:
 
-    $ eb rjags-4-6-intel-2018b-R-3.4.3.eb --fetch
-    == temporary log file in case of crash /tmp/eb-hZoghE/easybuild-2YC1pX.log
-    ERROR: Can't find path /cluster/home/$USER/rjags-4-6-intel-2018b-R-3.4.3.eb
+    $ eb rjags-4-12-foss-2022a-R-4.1.2.eb --fetch
+    == Temporary log file in case of crash /tmp/eb-bliwuikc/easybuild-2a9dc17d.log
+    == found valid index for /cluster/software/EasyBuild/4.9.0/easybuild/easyconfigs, so using it...
+    ERROR: One or more files not found: rjags-4-12-foss-2022a-R-4.1.2.eb (search paths:
+    /cluster/software/EasyBuild/4.9.0/easybuild/easyconfigs)
 
 In this case what you need to do is to write your own easyconfig file and use
 that for your easy build. Depending on the package this can be either really
@@ -215,80 +219,80 @@ already become available on the
 so please check this out first. In that case you can simply download or copy
 the easyconfig file from there, otherwise it's a good idea to start from an
 easyconfig that is similar to the one you are trying to make. In our case we
-will copy the ``rjags-4-6-intel-2017b-R-3.4.3.eb`` file and work from there.
+will copy the ``rjags-4-12-foss-2021b-R-4.1.2.eb`` file and work from there.
 
 **Step 1:** Copy similar easyconfig to somewhere in your ``$HOME``, here
 ``eb-sandbox``:
 
     $ cd eb-sandbox
-    $ cp $EBROOTEASYBUILD/easybuild/easyconfigs/r/rjags/rjags-4-6-intel-2017b-R-3.4.3.eb .
+    $ eb --copy-ec rjags-4-12-foss-2021b-R-4.1.2.eb
 
 **Step 2:** Inspect the easyconfig file and check for dependencies; in this
 case there are two, ``R`` and ``JAGS``. Next you need to check if any of the
 dependencies are available with the toolchain that you want. Here we see that
-``R-3.5.1`` *is* available with ``intel-2018b``:
+``R-4.2.1`` *is* available with ``foss-2022a``:
 
-    $ ls $EBROOTEASYBUILD/easybuild/easyconfigs/r/R/*intel-2018b*
-    /cluster/software/EasyBuild/4.3.1/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb
+    $ ls $EBROOTEASYBUILD/easybuild/easyconfigs/r/R/*foss-2022a*
+    /cluster/software/EasyBuild/4.9.0/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
 
-but ``JAGS`` is not:
+Also a never version of ``JAGS``is available, but if we assume that we need to keep the version at 4.3.0 it is not available for the new toolchain
 
-    $ ls $EBROOTEASYBUILD/easybuild/easyconfigs/j/JAGS/*intel-2018b*
+    $ ls $EBROOTEASYBUILD/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-foss-2022a*
     No such file or directory
 
-However, we do have a version with ``intel/2017b`` (which of course is the one
+However, we do have a version with ``foss/2021b`` (which of course is the one
 used by our original ``rjags``), so we'll copy that one as well and adapt it to
 our target toolchain:
 
-    $ cp $EBROOTEASYBUILD/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-intel-2017b.eb .
+    $ eb --copy-ec JAGS-4.3.0-foss-2021b.eb
 
 You can see that this procedure gets exponentially more complicated when you
 have to recursively update all dependencies of your original package, but
 thankfully in our case it stops here.
 
 ```{note}
-The versions do not necessarily have to match *literally*, they just need to
-not be *conflicting*. For instance, ``intel/2018b`` includes the compiler
-``GCCcore/7.3.0``, so any easyconfig with the ``GCCcore-7.3.0`` suffix would
-also be compatible.
+The toolchains do not necessarily have to match *literally*, they just need to
+not be *conflicting*. For instance, ``foss/2022a`` includes the compiler
+``GCCcore/11.3.0``, so any easyconfig with the ``GCCcore-11.3.0`` suffix would
+also be compatible. For more information about common toolchains: <https://docs.easybuild.io/common-toolchains/>
 ```
 
 **Step 3:** Starting with your deepest dependency, edit your new easyconfigs
 and change the version specifications. In ``JAGS`` it's just a matter of
 changing the toolchain to:
 
-    toolchain = {'name': 'intel', 'version': '2018b'}
+    toolchain = {'name': 'foss', 'version': '2022a'}
 
-and at the same time remove the checksum line. For ``rjags`` you do exactly the
+If the software version is changed you also need to update the checksum line. 
+For ``rjags`` you do exactly the
 same, but you should also update the versions of the dependencies. The ``JAGS``
 entry does not have to be changed, because we're still using version 4.3.0, but
-``R`` has to be changed to version 3.5.1, which was the one we found in **Step
-2** to be available for our toolchain. Note that the version suffix ``-X11...``
-is no longer applicable for this version of ``R``, so it should be removed.
+``R`` has to be changed to version 4.2.1, which was the one we found in **Step
+2** to be available for our toolchain.
 
 **Step 4:** Rename the easyconfig files to match the new versions:
 
-    $ mv JAGS-4.3.0-intel-2017b.eb JAGS-4.3.0-intel-2018b.eb
-    $ mv rjags-4-6-intel-2017b-R-3.4.3.eb rjags-4-6-intel-2018b-R-3.5.1.eb
+    $ mv JAGS-4.3.0-foss-2021b.eb JAGS-4.3.0-foss-2022a.eb
+    $ mv rjags-4-12-foss-2021b-R-4.1.2.eb rjags-4-12-foss-2022a-R-4.2.1.eb
 
 Our new easyconfigs should now look like this:
 
-**JAGS-4.3.0-intel-2018b.eb:**
+**JAGS-4.3.0-foss-2022a.eb:**
 ```{eval-rst}
-.. literalinclude:: files/JAGS-4.3.0-intel-2018b.eb
+.. literalinclude:: files/JAGS-4.3.0-foss-2022a.eb
   :language: bash
 ```
 
-**rjags-4-6-intel-2018b-R-3.5.1.eb:**
+**rjags-4-6-foss-2022a-R-3.5.1.eb:**
 ```{eval-rst}
-.. literalinclude:: files/rjags-4-6-intel-2018b-R-3.5.1.eb
+.. literalinclude:: files/rjags-4-12-foss-2022a-R-4.2.1.eb
   :language: bash
 ```
 
 **Step 5:** Build your new module while adding the current directory to
 ``--robot`` so that your new `.eb` files are picked up:
 
-    $ eb rjags-4-6-intel-2018b-R-3.5.1.eb --robot=. --parallel=2
+    $ eb rjags-4-12-foss-2022a-R-4.2.1.eb --robot=. --parallel=2
 
 Again, please don't use too many ``--parallel`` threads on login!
 
@@ -297,9 +301,9 @@ Again, please don't use too many ``--parallel`` threads on login!
     $ module use $HOME/.local/easybuild/modules/all
     $ module avail rjags
     --------------------------- $HOME/.local/easybuild/modules/all ---------------------------
-        rjags/4-6-intel-2017b-R-3.4.3    rjags/4-6-intel-2018b-R-3.5.1
+        rjags/4-12-foss-2021b-R-4.1.2    rjags/4-12-foss-2022a-R-4.2.1
 
-    $ module load rjags/4-6-intel-2018b-R-3.5.1
+    $ module load rjags/4-12-foss-2022a-R-4.2.1
 
 **For more information on how to write easyconfigs:**
 <https://easybuild.readthedocs.io/en/latest/Writing_easyconfig_files.html>
diff --git a/software/userinstallsw/files/JAGS-4.3.0-foss-2022a.eb b/software/userinstallsw/files/JAGS-4.3.0-foss-2022a.eb
@@ -0,0 +1,36 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics
+# Biozentrum - University of Basel
+
+easyblock = 'ConfigureMake'
+
+name = 'JAGS'
+version = '4.3.0'
+
+homepage = 'http://mcmc-jags.sourceforge.net/'
+description = """JAGS is Just Another Gibbs Sampler.  It is a program for analysis
+ of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation  """
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = [
+    ('https://sourceforge.net/projects/mcmc-%(namelower)s/files/%(name)s/%(version_major)s.x/Source/', 'download')
+]
+sources = [SOURCE_TAR_GZ]
+checksums = ['8ac5dd57982bfd7d5f0ee384499d62f3e0bb35b5f1660feb368545f1186371fc']
+
+configopts = ' --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
+
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s', 'libexec/%(namelower)s-terminal', 'lib/libjags.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+modextrapaths = {
+    'JAGS_INCLUDE': 'include/%(name)s',
+    'JAGS_LIB': 'lib',
+}
+
+moduleclass = 'math'
diff --git a/software/userinstallsw/files/rjags-4-12-foss-2022a-R-4.2.1.eb b/software/userinstallsw/files/rjags-4-12-foss-2022a-R-4.2.1.eb
@@ -0,0 +1,29 @@
+easyblock = 'RPackage'
+
+name = 'rjags'
+version = '4-12'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://cran.r-project.org/web/packages/rjags'
+description = """The rjags package is an interface to the JAGS library."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = [
+    'https://cran.r-project.org/src/contrib/',
+    'https://cran.r-project.org/src/contrib/Archive/rjags/',
+]
+sources = ['%(name)s_%(version)s.tar.gz']
+checksums = ['b91f34c3f9ebf78fa44bd661346fbb6f28a01693a7203ac133c98392dd273e10']
+
+dependencies = [
+    ('R', '4.2.1'),
+    ('JAGS', '4.3.0'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['rjags'],
+}
+
+moduleclass = 'math'