path: root/lib/spack/docs/tutorial_modules.rst

.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
   Spack Project Developers. See the top-level COPYRIGHT file for details.

   SPDX-License-Identifier: (Apache-2.0 OR MIT)

.. _modules-tutorial:

============
Module Files
============

In this tutorial, we'll introduce a few concepts that are fundamental
to the generation of module files with Spack, and we'll guide you through
the customization of both module files content and their layout on disk. In the end you
should have a clear understanding of:

  * What are module files and how they work
  * How Spack generates them
  * Which commands are available to ease their maintenance
  * How it is possible to customize them in all aspects

.. _module_file_tutorial_overview:

-------------------
Modules at a glance
-------------------

Let's start by summarizing what module files are and how you can use
them to modify your environment. The idea is to give enough information so that
people without any previous exposure to them will be able to follow the tutorial
later on. We'll also give a high-level view of how module files are generated
in Spack. If you are already familiar with these topics you can quickly skim
through this section or move directly to :ref:`module_file_tutorial_prerequisites`.

.. _module_file_tutorial_what_are_modules:

^^^^^^^^^^^^^^^^^^^^^^
What are module files?
^^^^^^^^^^^^^^^^^^^^^^

Module files are an easy way to modify your environment in a controlled manner
during a shell session. In general, they contain the information needed to run an
application or use a library, and they work in conjunction with a tool that
interprets them.
Typical module files instruct this tool to modify the environment variables when a
module file is loaded:

  .. code-block:: console

     $ module show zlib
     -------------------------------------------------------------------
     /home/mculpo/PycharmProjects/spack/share/spack/modules/linux-ubuntu14.04-x86_64/zlib/1.2.11-gcc-7.2.0-linux-ubuntu14.04-x86_64-co2px3k:

     module-whatis	 A free, general-purpose, legally unencumbered lossless data-compression library.
     prepend-path	 MANPATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/share/man
     prepend-path	 LIBRARY_PATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/lib
     prepend-path	 LD_LIBRARY_PATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/lib
     prepend-path	 CPATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/include
     prepend-path	 PKG_CONFIG_PATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/lib/pkgconfig
     prepend-path	 CMAKE_PREFIX_PATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/
     -------------------------------------------------------------------

     $ echo $LD_LIBRARY_PATH

     $ module load zlib
     $ echo $LD_LIBRARY_PATH
     /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/lib

and to undo the modifications when the same module file is unloaded:

  .. code-block:: console

     $ module unload zlib
     $ echo $LD_LIBRARY_PATH

     $

Different formats exist for module files, and different tools
provide various levels of support for them. Spack can natively generate:

1. Non-hierarchical module files written in TCL
2. Hierarchical module files written in Lua

and can build `environment-modules <http://modules.sourceforge.net/>`_
and `lmod <http://lmod.readthedocs.io/en/latest>`_ as support tools.
Which of the formats or tools best suits one's needs depends on each particular
use-case. For the sake of illustration, we'll be working on
both formats using ``lmod``.

.. seealso::
  Environment modules
    This is the original tool that provided modules support. Its first
    version was coded in C in the early '90s and was later substituted by a version
    completely coded in TCL - the one Spack is distributing. More details on
    its features are given in the `homepage of the project <http://modules.sourceforge.net/>`_
    or in its `github page <https://github.com/cea-hpc/modules>`_. The tool is able to
    interpret the non-hierarchical TCL modulefiles written by Spack.

  Lmod
    Lmod is a module system written in Lua, designed to easily handle hierarchies of
    module files. It's a drop-in replacement of Environment Modules and works with
    both of the module file formats generated by Spack.
    Despite being fully compatible with Environment Modules there are many features that
    are unique to Lmod. These features are either
    `targeted towards safety <http://lmod.readthedocs.io/en/latest/010_user.html#safety-features>`_
    or meant to
    `extend the module system functionality <http://lmod.readthedocs.io/en/latest/010_user.html#module-hierarchy>`_.


^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
How do we generate module files?
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Before  we dive into the hands-on sections it's worth spending a couple of words to explain how
module files are generated by Spack. The following diagram provides a high-level view
of the process:


.. image:: module_file_generation.*

The red dashed line above represents Spack's boundaries, the blue one Spack's dependencies [#f1]_.
Module files are generated by combining:

  * the configuration details in ``config.yaml`` and ``modules.yaml``
  * the information contained in Spack packages (and processed by the module subpackage)
  * a set of template files

with `Jinja2 <http://jinja.pocoo.org/docs/2.9/>`_, an external template engine
that stamps out each particular module file. As Spack serves very diverse needs
this process has many points of customization, and we'll explore most of
them in the next sections.

.. [#f1] Spack vendors its dependencies! This means that Spack comes with a copy of
         each one of its dependencies, including ``Jinja2``, and is already configured to use them.

.. _module_file_tutorial_prerequisites:

----------------------
Setup for the tutorial
----------------------

In order to showcase the capabilities of Spack's module file generation, we need
a representative set of software to work with. This set must include different
flavors of the same packages installed alongside each other and some
:ref:`external packages <sec-external-packages>`.

The purpose of this setup is not to make our life harder but to demonstrate
how Spack can help with similar situations, as they will happen on real HPC clusters.
For instance, it's often preferable for Spack to use vendor-provided MPI
implementations than to build one itself.

To keep the set of software we're dealing with manageable, we're going
to uninstall everything from earlier in the tutorial.

.. code-block: console

  $ spack uninstall -ay

^^^^^^^^^^^^^^^^^^^
Build a module tool
^^^^^^^^^^^^^^^^^^^

The first thing that we need is the module tool. In this case we
choose ``lmod`` as it can work with both hierarchical and non-hierarchical
module file layouts.

.. code-block:: console

  $ bin/spack install lmod

Once the module tool is installed we need to have it available in the
current shell. As the installation directories are definitely not easy
to remember, we'll employ the command ``spack location`` to retrieve the
``lmod`` prefix directly from Spack:

.. code-block:: console

  $ . $(spack location -i lmod)/lmod/lmod/init/bash

Now we can re-source the setup file and Spack modules will be put in
our module path.

.. code-block:: console

  $ . share/spack/setup_env.sh

.. FIXME: this needs bootstrap support for ``lmod``

.. FIXME: check the docs here, update them if necessary
  If you need to install Lmod or Environment module you can refer
  to the documentation :ref:`here <InstallEnvironmentModules>`.


^^^^^^^^^^^^^^^^^^
Add a new compiler
^^^^^^^^^^^^^^^^^^

The second step is to build a recent compiler. On first use, Spack
scans the environment and automatically locates the compiler(s)
already available on the system. For this tutorial, however, we want
to use ``gcc@7.2.0``.


.. code-block:: console

  $ spack install gcc@7.2.0
  ...
  Wait a long time
  ...

Once ``gcc`` is installed we can use shell support to load it and make
it readily available:

.. code-block:: console

  $ spack load gcc@7.2.0

It may not be apparent, but the last command employed the module files
generated automatically by Spack. What happens under the hood when you use
the ``spack load`` command is:

1. the spec passed as argument is translated into a module file name
2. the current module tool is used to load that module file

You can use this command to double check:

.. code-block:: console

  $ module list
  Currently Loaded Modules:
  1) gcc-7.2.0-gcc-5.4.0-b7smjjc

Note that the 7-digit hash at the end of the generated module may vary depending
on architecture or package version. Now that we have ``gcc@7.2.0`` in ``PATH`` we
can finally add it to the list of compilers known to Spack:

.. code-block:: console

  $ spack compiler add
  ==> Added 1 new compiler to /home/spack1/.spack/linux/compilers.yaml
      gcc@7.2.0
  ==> Compilers are defined in the following files:
      /home/spack1/.spack/linux/compilers.yaml

  $ spack compiler list
  ==> Available compilers
  -- clang ubuntu16.04-x86_64 -------------------------------------
  clang@3.8.0-2ubuntu4  clang@3.7.1-2ubuntu2

  -- gcc ubuntu16.04-x86_64 ---------------------------------------
  gcc@7.2.0  gcc@5.4.0  gcc@4.7


^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Build the software that will be used in the tutorial
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Finally, we should use Spack to install the packages used in the examples:

.. code-block:: console

   $ spack install netlib-scalapack ^openmpi ^openblas
   $ spack install netlib-scalapack ^mpich ^openblas
   $ spack install netlib-scalapack ^openmpi ^netlib-lapack
   $ spack install netlib-scalapack ^mpich ^netlib-lapack
   $ spack install py-scipy ^openblas


.. _module_file_tutorial_non_hierarchical:

-----------------------------
Non-hierarchical module files
-----------------------------

If you arrived to this point you should have an environment that looks similar to:

.. code-block:: console

  $ module avail

  ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------
     autoconf-2.69-gcc-5.4.0-3sx2gxe              libsigsegv-2.11-gcc-7.2.0-g67xpfd            openssl-1.0.2o-gcc-5.4.0-b4y3w3b
     autoconf-2.69-gcc-7.2.0-yb2makb              libtool-2.4.6-gcc-5.4.0-o2pfwjf              openssl-1.0.2o-gcc-7.2.0-cvldq3v
     automake-1.16.1-gcc-5.4.0-rymw7im            libtool-2.4.6-gcc-7.2.0-kt2udm6              pcre-8.42-gcc-5.4.0-gt5lgzi
     automake-1.16.1-gcc-7.2.0-qoowd5q            libxml2-2.9.8-gcc-5.4.0-wpexsph              perl-5.26.2-gcc-5.4.0-ic2kyoa
     bzip2-1.0.6-gcc-5.4.0-ufczdvs                libxml2-2.9.8-gcc-7.2.0-47gf5kk              perl-5.26.2-gcc-7.2.0-fdwz5yu
     bzip2-1.0.6-gcc-7.2.0-mwamumj                lmod-7.8-gcc-5.4.0-kmhks3p                   pkgconf-1.4.2-gcc-5.4.0-fovrh7a
     cmake-3.12.3-gcc-7.2.0-obqgn2v               lua-5.3.4-gcc-5.4.0-cpfeo2w                  pkgconf-1.4.2-gcc-7.2.0-yoxwmgb
     curl-7.60.0-gcc-5.4.0-vzqreb2                lua-luafilesystem-1_6_3-gcc-5.4.0-alakjim    py-numpy-1.15.2-gcc-7.2.0-wbwtcxf
     diffutils-3.6-gcc-5.4.0-2rhuivg              lua-luaposix-33.4.0-gcc-5.4.0-7wqhwoc        py-scipy-1.1.0-gcc-7.2.0-d5n3cph
     diffutils-3.6-gcc-7.2.0-eauxwi7              m4-1.4.18-gcc-5.4.0-suf5jtc                  py-setuptools-40.4.3-gcc-7.2.0-5dbwfwn
     expat-2.2.5-gcc-5.4.0-emyv67q                m4-1.4.18-gcc-7.2.0-wdzvagl                  python-2.7.15-gcc-7.2.0-ucmr2mn
     findutils-4.6.0-gcc-7.2.0-ca4b7zq            mpc-1.1.0-gcc-5.4.0-iuf3gc3                  readline-7.0-gcc-5.4.0-nxhwrg7
     gcc-7.2.0-gcc-5.4.0-b7smjjc           (L)    mpfr-3.1.6-gcc-5.4.0-jnt2nnp                 readline-7.0-gcc-7.2.0-ccruj2i
     gdbm-1.14.1-gcc-5.4.0-q4fpyuo                mpich-3.2.1-gcc-7.2.0-vt5xcat                sqlite-3.23.1-gcc-7.2.0-5ltus3a
     gdbm-1.14.1-gcc-7.2.0-zk5lhob                ncurses-6.1-gcc-5.4.0-3o765ou                tar-1.30-gcc-5.4.0-dk7lrpo
     gettext-0.19.8.1-gcc-5.4.0-tawgous           ncurses-6.1-gcc-7.2.0-xcgzqdv                tcl-8.6.8-gcc-5.4.0-qhwyccy
     git-2.19.1-gcc-5.4.0-p3gjnfa                 netlib-lapack-3.8.0-gcc-7.2.0-fj7nayd        texinfo-6.5-gcc-7.2.0-cuqnfgf
     gmp-6.1.2-gcc-5.4.0-qc4qcfz                  netlib-scalapack-2.0.2-gcc-7.2.0-67nmj7g     unzip-6.0-gcc-5.4.0-ba23fbg
     hwloc-1.11.9-gcc-7.2.0-gbyc65s               netlib-scalapack-2.0.2-gcc-7.2.0-6jgjbyg     util-macros-1.19.1-gcc-7.2.0-t62kozq
     isl-0.18-gcc-5.4.0-vttqout                   netlib-scalapack-2.0.2-gcc-7.2.0-prgo67d     xz-5.2.4-gcc-5.4.0-teneqii
     libbsd-0.8.6-gcc-5.4.0-f4qkkwm               netlib-scalapack-2.0.2-gcc-7.2.0-zxpt252     xz-5.2.4-gcc-7.2.0-rql5kog
     libiconv-1.15-gcc-5.4.0-u2x3umv              numactl-2.0.11-gcc-7.2.0-rifwktk             zlib-1.2.11-gcc-5.4.0-5nus6kn
     libpciaccess-0.13.5-gcc-7.2.0-riipwi2        openblas-0.3.3-gcc-7.2.0-xxoxfh4             zlib-1.2.11-gcc-7.2.0-ezuwp4p
     libsigsegv-2.11-gcc-5.4.0-fypapcp            openmpi-3.1.3-gcc-7.2.0-do5xfer

    Where:
     L:  Module is loaded

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

The non-hierarchical module files that have been generated so far
follow :ref:`the default rules for module generation <modules-yaml>`.
Taking a look at the ``gcc`` module you'll see, for example:

.. code-block:: console

  $ module show gcc-7.2.0-gcc-5.4.0-b7smjjc
  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
     /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/gcc-7.2.0-gcc-5.4.0-b7smjjc:
  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
  whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ")
  prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin")
  prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/share/man")
  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib")
  prepend_path("LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib")
  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64")
  prepend_path("LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64")
  prepend_path("CPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/include")
  prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/")
  setenv("CC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gcc")
  setenv("CXX","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/g++")
  setenv("FC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
  setenv("F77","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
  setenv("F90","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
  help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
  Fortran, Ada, and Go, as well as libraries for these languages.
  ]])

As expected, a few environment variables representing paths will be modified
by the module file according to the default prefix inspection rules.


^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Filter unwanted modifications to the environment
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Now consider the case that your site has decided that ``CPATH`` and
``LIBRARY_PATH`` modifications should not be present in module files. What you can
do to abide by the rules is to create a configuration file ``~/.spack/modules.yaml``
with the following content:

.. code-block:: yaml

  modules:
    tcl:
      all:
        filter:
          environment_blacklist: ['CPATH', 'LIBRARY_PATH']

Next you should regenerate all the module files:

.. code-block:: console

  $ spack module tcl refresh
  ==> You are about to regenerate tcl module files for:

  -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
  3sx2gxe autoconf@2.69    b7smjjc gcc@7.2.0         f4qkkwm libbsd@0.8.6     cpfeo2w lua@5.3.4                3o765ou ncurses@6.1     dk7lrpo tar@1.30
  rymw7im automake@1.16.1  q4fpyuo gdbm@1.14.1       u2x3umv libiconv@1.15    alakjim lua-luafilesystem@1_6_3  b4y3w3b openssl@1.0.2o  qhwyccy tcl@8.6.8
  ufczdvs bzip2@1.0.6      tawgous gettext@0.19.8.1  fypapcp libsigsegv@2.11  7wqhwoc lua-luaposix@33.4.0      gt5lgzi pcre@8.42       ba23fbg unzip@6.0
  vzqreb2 curl@7.60.0      p3gjnfa git@2.19.1        o2pfwjf libtool@2.4.6    suf5jtc m4@1.4.18                ic2kyoa perl@5.26.2     teneqii xz@5.2.4
  2rhuivg diffutils@3.6    qc4qcfz gmp@6.1.2         wpexsph libxml2@2.9.8    iuf3gc3 mpc@1.1.0                fovrh7a pkgconf@1.4.2   5nus6kn zlib@1.2.11
  emyv67q expat@2.2.5      vttqout isl@0.18          kmhks3p lmod@7.8         jnt2nnp mpfr@3.1.6               nxhwrg7 readline@7.0

  -- linux-ubuntu16.04-x86_64 / gcc@7.2.0 -------------------------
  yb2makb autoconf@2.69    riipwi2 libpciaccess@0.13.5  6jgjbyg netlib-scalapack@2.0.2  fdwz5yu perl@5.26.2           cuqnfgf texinfo@6.5
  qoowd5q automake@1.16.1  g67xpfd libsigsegv@2.11      zxpt252 netlib-scalapack@2.0.2  yoxwmgb pkgconf@1.4.2         t62kozq util-macros@1.19.1
  mwamumj bzip2@1.0.6      kt2udm6 libtool@2.4.6        67nmj7g netlib-scalapack@2.0.2  wbwtcxf py-numpy@1.15.2       rql5kog xz@5.2.4
  obqgn2v cmake@3.12.3     47gf5kk libxml2@2.9.8        prgo67d netlib-scalapack@2.0.2  d5n3cph py-scipy@1.1.0        ezuwp4p zlib@1.2.11
  eauxwi7 diffutils@3.6    wdzvagl m4@1.4.18            rifwktk numactl@2.0.11          5dbwfwn py-setuptools@40.4.3
  ca4b7zq findutils@4.6.0  vt5xcat mpich@3.2.1          xxoxfh4 openblas@0.3.3          ucmr2mn python@2.7.15
  zk5lhob gdbm@1.14.1      xcgzqdv ncurses@6.1          do5xfer openmpi@3.1.3           ccruj2i readline@7.0
  gbyc65s hwloc@1.11.9     fj7nayd netlib-lapack@3.8.0  cvldq3v openssl@1.0.2o          5ltus3a sqlite@3.23.1

  ==> Do you want to proceed? [y/n] y
  ==> Regenerating tcl module files

If you take a look now at the module for ``gcc`` you'll see that the unwanted
paths have disappeared:

.. code-block:: console

  $ module show gcc-7.2.0-gcc-5.4.0-b7smjjc
  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
     /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/gcc-7.2.0-gcc-5.4.0-b7smjjc:
  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
  whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ")
  prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin")
  prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/share/man")
  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib")
  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64")
  prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/")
  setenv("CC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gcc")
  setenv("CXX","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/g++")
  setenv("FC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
  setenv("F77","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
  setenv("F90","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
  help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
  Fortran, Ada, and Go, as well as libraries for these languages.
  ]])

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Prevent some module files from being generated
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Another common request at many sites is to avoid exposing software that
is only needed as an intermediate step when building a newer stack.
Let's try to prevent the generation of
module files for anything that is compiled with ``gcc@5.4.0`` (the OS provided compiler).

To do this you should add a ``blacklist`` keyword to ``~/.spack/modules.yaml``:

.. code-block:: yaml
  :emphasize-lines: 3,4

  modules:
    tcl:
      blacklist:
        -  '%gcc@5.4.0'
      all:
        filter:
          environment_blacklist: ['CPATH', 'LIBRARY_PATH']

and regenerate the module files:

This time it is convenient to pass the option ``--delete-tree`` to the command that
regenerates the module files to instruct it to delete the existing tree and regenerate
a new one instead of overwriting the files in the existing directory.

.. code-block:: console

  $ spack module tcl refresh --delete-tree
  ==> You are about to regenerate tcl module files for:

  -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
  3sx2gxe autoconf@2.69    b7smjjc gcc@7.2.0         f4qkkwm libbsd@0.8.6     cpfeo2w lua@5.3.4                3o765ou ncurses@6.1     dk7lrpo tar@1.30
  rymw7im automake@1.16.1  q4fpyuo gdbm@1.14.1       u2x3umv libiconv@1.15    alakjim lua-luafilesystem@1_6_3  b4y3w3b openssl@1.0.2o  qhwyccy tcl@8.6.8
  ufczdvs bzip2@1.0.6      tawgous gettext@0.19.8.1  fypapcp libsigsegv@2.11  7wqhwoc lua-luaposix@33.4.0      gt5lgzi pcre@8.42       ba23fbg unzip@6.0
  vzqreb2 curl@7.60.0      p3gjnfa git@2.19.1        o2pfwjf libtool@2.4.6    suf5jtc m4@1.4.18                ic2kyoa perl@5.26.2     teneqii xz@5.2.4
  2rhuivg diffutils@3.6    qc4qcfz gmp@6.1.2         wpexsph libxml2@2.9.8    iuf3gc3 mpc@1.1.0                fovrh7a pkgconf@1.4.2   5nus6kn zlib@1.2.11
  emyv67q expat@2.2.5      vttqout isl@0.18          kmhks3p lmod@7.8         jnt2nnp mpfr@3.1.6               nxhwrg7 readline@7.0

  -- linux-ubuntu16.04-x86_64 / gcc@7.2.0 -------------------------
  yb2makb autoconf@2.69    riipwi2 libpciaccess@0.13.5  6jgjbyg netlib-scalapack@2.0.2  fdwz5yu perl@5.26.2           cuqnfgf texinfo@6.5
  qoowd5q automake@1.16.1  g67xpfd libsigsegv@2.11      zxpt252 netlib-scalapack@2.0.2  yoxwmgb pkgconf@1.4.2         t62kozq util-macros@1.19.1
  mwamumj bzip2@1.0.6      kt2udm6 libtool@2.4.6        67nmj7g netlib-scalapack@2.0.2  wbwtcxf py-numpy@1.15.2       rql5kog xz@5.2.4
  obqgn2v cmake@3.12.3     47gf5kk libxml2@2.9.8        prgo67d netlib-scalapack@2.0.2  d5n3cph py-scipy@1.1.0        ezuwp4p zlib@1.2.11
  eauxwi7 diffutils@3.6    wdzvagl m4@1.4.18            rifwktk numactl@2.0.11          5dbwfwn py-setuptools@40.4.3
  ca4b7zq findutils@4.6.0  vt5xcat mpich@3.2.1          xxoxfh4 openblas@0.3.3          ucmr2mn python@2.7.15
  zk5lhob gdbm@1.14.1      xcgzqdv ncurses@6.1          do5xfer openmpi@3.1.3           ccruj2i readline@7.0
  gbyc65s hwloc@1.11.9     fj7nayd netlib-lapack@3.8.0  cvldq3v openssl@1.0.2o          5ltus3a sqlite@3.23.1

  ==> Do you want to proceed? [y/n] y
  ==> Regenerating tcl module files

  $ module avail

  ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------
     autoconf-2.69-gcc-7.2.0-yb2makb          m4-1.4.18-gcc-7.2.0-wdzvagl                 perl-5.26.2-gcc-7.2.0-fdwz5yu
     automake-1.16.1-gcc-7.2.0-qoowd5q        mpich-3.2.1-gcc-7.2.0-vt5xcat               pkgconf-1.4.2-gcc-7.2.0-yoxwmgb
     bzip2-1.0.6-gcc-7.2.0-mwamumj            ncurses-6.1-gcc-7.2.0-xcgzqdv               py-numpy-1.15.2-gcc-7.2.0-wbwtcxf
     cmake-3.12.3-gcc-7.2.0-obqgn2v           netlib-lapack-3.8.0-gcc-7.2.0-fj7nayd       py-scipy-1.1.0-gcc-7.2.0-d5n3cph
     diffutils-3.6-gcc-7.2.0-eauxwi7          netlib-scalapack-2.0.2-gcc-7.2.0-67nmj7g    py-setuptools-40.4.3-gcc-7.2.0-5dbwfwn
     findutils-4.6.0-gcc-7.2.0-ca4b7zq        netlib-scalapack-2.0.2-gcc-7.2.0-6jgjbyg    python-2.7.15-gcc-7.2.0-ucmr2mn
     gdbm-1.14.1-gcc-7.2.0-zk5lhob            netlib-scalapack-2.0.2-gcc-7.2.0-prgo67d    readline-7.0-gcc-7.2.0-ccruj2i
     hwloc-1.11.9-gcc-7.2.0-gbyc65s           netlib-scalapack-2.0.2-gcc-7.2.0-zxpt252    sqlite-3.23.1-gcc-7.2.0-5ltus3a
     libpciaccess-0.13.5-gcc-7.2.0-riipwi2    numactl-2.0.11-gcc-7.2.0-rifwktk            texinfo-6.5-gcc-7.2.0-cuqnfgf
     libsigsegv-2.11-gcc-7.2.0-g67xpfd        openblas-0.3.3-gcc-7.2.0-xxoxfh4            util-macros-1.19.1-gcc-7.2.0-t62kozq
     libtool-2.4.6-gcc-7.2.0-kt2udm6          openmpi-3.1.3-gcc-7.2.0-do5xfer             xz-5.2.4-gcc-7.2.0-rql5kog
     libxml2-2.9.8-gcc-7.2.0-47gf5kk          openssl-1.0.2o-gcc-7.2.0-cvldq3v            zlib-1.2.11-gcc-7.2.0-ezuwp4p

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

If you look closely you'll see though that we went too far in blacklisting modules:
the module for ``gcc@7.2.0`` disappeared as it was bootstrapped with ``gcc@5.4.0``. To specify
exceptions to the blacklist rules you can use ``whitelist``:

.. code-block:: yaml
  :emphasize-lines: 3,4

  modules:
    tcl:
      whitelist:
        -  gcc
      blacklist:
        -  '%gcc@5.4.0'
      all:
        filter:
          environment_blacklist: ['CPATH', 'LIBRARY_PATH']

``whitelist`` rules always have precedence over ``blacklist`` rules. If you regenerate the modules again:

.. code-block:: console

  $ spack module tcl refresh -y
  ==> Regenerating tcl module files


you'll see that now the module for ``gcc@7.2.0`` has reappeared:

.. code-block:: console

  $ module avail gcc-7.2.0-gcc-5.4.0-b7smjjc

  -------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 ---------------------------------------------
     gcc-7.2.0-gcc-5.4.0-b7smjjc

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

An additional possibility that you can leverage to unclutter the environment
is that of preventing the generation of module files for implicitly installed
packages. In this case all one needs to do is to add the following line:

.. code-block:: yaml
  :emphasize-lines: 3

  modules:
    tcl:
      blacklist_implicits: true
      whitelist:
        -  gcc
      blacklist:
        -  '%gcc@5.4.0'
      all:
        filter:
          environment_blacklist: ['CPATH', 'LIBRARY_PATH']

to ``modules.yaml`` and regenerate the module file tree as above.

^^^^^^^^^^^^^^^^^^^^^^^^^
Change module file naming
^^^^^^^^^^^^^^^^^^^^^^^^^

The next step in making  module files more user-friendly is to
improve their naming scheme.
To reduce the length of the hash or remove it altogether you can
use the ``hash_length`` keyword in the configuration file:

.. code-block:: yaml
  :emphasize-lines: 3

  modules:
    tcl:
      hash_length: 0
      whitelist:
        -  gcc
      blacklist:
        -  '%gcc@5.4.0'
      all:
        filter:
          environment_blacklist: ['CPATH', 'LIBRARY_PATH']

If you try to regenerate the module files now you will get an error:

.. code-block:: console

  $ spack module tcl refresh --delete-tree -y
  ==> Error: Name clashes detected in module files:

  file: /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/netlib-scalapack-2.0.2-gcc-7.2.0
  spec: netlib-scalapack@2.0.2%gcc@7.2.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64
  spec: netlib-scalapack@2.0.2%gcc@7.2.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64
  spec: netlib-scalapack@2.0.2%gcc@7.2.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64
  spec: netlib-scalapack@2.0.2%gcc@7.2.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64

  ==> Error: Operation aborted

.. note::
  We try to check for errors upfront!
   In Spack we check for errors upfront whenever possible, so don't worry about your module files:
   as a name clash was detected nothing has been changed on disk.

The problem here is that without
the hashes the four different flavors of ``netlib-scalapack`` map to the same module file
name. We can add suffixes to differentiate them:

.. code-block:: yaml
 :emphasize-lines: 9-11,14-17

  modules:
    tcl:
      hash_length: 0
      whitelist:
        -  gcc
      blacklist:
        -  '%gcc@5.4.0'
      all:
        suffixes:
          '^openblas': openblas
          '^netlib-lapack': netlib
        filter:
          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
      netlib-scalapack:
        suffixes:
          '^openmpi': openmpi
          '^mpich': mpich

As you can see it is possible to specify rules that apply only to a
restricted set of packages using :ref:`anonymous specs <anonymous_specs>`.
Regenerating module files now we obtain:

.. code-block:: console

  $ spack module tcl refresh --delete-tree -y
  ==> Regenerating tcl module files
  $ module avail

  ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------
     autoconf-2.69-gcc-7.2.0          m4-1.4.18-gcc-7.2.0                                  pkgconf-1.4.2-gcc-7.2.0
     automake-1.16.1-gcc-7.2.0        mpich-3.2.1-gcc-7.2.0                                py-numpy-1.15.2-gcc-7.2.0-openblas
     bzip2-1.0.6-gcc-7.2.0            ncurses-6.1-gcc-7.2.0                                py-scipy-1.1.0-gcc-7.2.0-openblas
     cmake-3.12.3-gcc-7.2.0           netlib-lapack-3.8.0-gcc-7.2.0                        py-setuptools-40.4.3-gcc-7.2.0
     diffutils-3.6-gcc-7.2.0          netlib-scalapack-2.0.2-gcc-7.2.0-netlib-mpich        python-2.7.15-gcc-7.2.0
     findutils-4.6.0-gcc-7.2.0        netlib-scalapack-2.0.2-gcc-7.2.0-netlib-openmpi      readline-7.0-gcc-7.2.0
     gcc-7.2.0-gcc-5.4.0              netlib-scalapack-2.0.2-gcc-7.2.0-openblas-mpich      sqlite-3.23.1-gcc-7.2.0
     gdbm-1.14.1-gcc-7.2.0            netlib-scalapack-2.0.2-gcc-7.2.0-openblas-openmpi    texinfo-6.5-gcc-7.2.0
     hwloc-1.11.9-gcc-7.2.0           numactl-2.0.11-gcc-7.2.0                             util-macros-1.19.1-gcc-7.2.0
     libpciaccess-0.13.5-gcc-7.2.0    openblas-0.3.3-gcc-7.2.0                             xz-5.2.4-gcc-7.2.0
     libsigsegv-2.11-gcc-7.2.0        openmpi-3.1.3-gcc-7.2.0                              zlib-1.2.11-gcc-7.2.0
     libtool-2.4.6-gcc-7.2.0          openssl-1.0.2o-gcc-7.2.0
     libxml2-2.9.8-gcc-7.2.0          perl-5.26.2-gcc-7.2.0

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

Finally we can set a ``naming_scheme`` to prevent users from loading
modules that refer to different flavors of the same library/application:

.. code-block:: yaml
  :emphasize-lines: 4,10,11

  modules:
    tcl:
      hash_length: 0
      naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVER}'
      whitelist:
        -  gcc
      blacklist:
        -  '%gcc@5.4.0'
      all:
        conflict:
          - '${PACKAGE}'
        suffixes:
          '^openblas': openblas
          '^netlib-lapack': netlib
        filter:
          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
      netlib-scalapack:
        suffixes:
          '^openmpi': openmpi
          '^mpich': mpich

The final result should look like:

.. code-block:: console

  $ spack module tcl refresh --delete-tree -y
  ==> Regenerating tcl module files
  $ module avail

  ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------
     autoconf/2.69-gcc-7.2.0          m4/1.4.18-gcc-7.2.0                                      pkgconf/1.4.2-gcc-7.2.0
     automake/1.16.1-gcc-7.2.0        mpich/3.2.1-gcc-7.2.0                                    py-numpy/1.15.2-gcc-7.2.0-openblas
     bzip2/1.0.6-gcc-7.2.0            ncurses/6.1-gcc-7.2.0                                    py-scipy/1.1.0-gcc-7.2.0-openblas
     cmake/3.12.3-gcc-7.2.0           netlib-lapack/3.8.0-gcc-7.2.0                            py-setuptools/40.4.3-gcc-7.2.0
     diffutils/3.6-gcc-7.2.0          netlib-scalapack/2.0.2-gcc-7.2.0-netlib-mpich            python/2.7.15-gcc-7.2.0
     findutils/4.6.0-gcc-7.2.0        netlib-scalapack/2.0.2-gcc-7.2.0-netlib-openmpi          readline/7.0-gcc-7.2.0
     gcc/7.2.0-gcc-5.4.0              netlib-scalapack/2.0.2-gcc-7.2.0-openblas-mpich          sqlite/3.23.1-gcc-7.2.0
     gdbm/1.14.1-gcc-7.2.0            netlib-scalapack/2.0.2-gcc-7.2.0-openblas-openmpi (D)    texinfo/6.5-gcc-7.2.0
     hwloc/1.11.9-gcc-7.2.0           numactl/2.0.11-gcc-7.2.0                                 util-macros/1.19.1-gcc-7.2.0
     libpciaccess/0.13.5-gcc-7.2.0    openblas/0.3.3-gcc-7.2.0                                 xz/5.2.4-gcc-7.2.0
     libsigsegv/2.11-gcc-7.2.0        openmpi/3.1.3-gcc-7.2.0                                  zlib/1.2.11-gcc-7.2.0
     libtool/2.4.6-gcc-7.2.0          openssl/1.0.2o-gcc-7.2.0
     libxml2/2.9.8-gcc-7.2.0          perl/5.26.2-gcc-7.2.0

    Where:
     D:  Default Module

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

.. note::
  TCL specific directive
    The directives ``naming_scheme`` and ``conflict`` are TCL specific and
    can't be used in the ``lmod`` section of the configuration file.

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Add custom environment modifications
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

At many sites it is customary to set an environment variable in a
package's module file that points to the folder in which the package
is installed. You can achieve this with Spack by adding an
``environment`` directive to the configuration file:

.. code-block:: yaml
  :emphasize-lines: 17-19

  modules:
    tcl:
      hash_length: 0
      naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVER}'
      whitelist:
        -  gcc
      blacklist:
        -  '%gcc@5.4.0'
      all:
        conflict:
          - '${PACKAGE}'
        suffixes:
          '^openblas': openblas
          '^netlib-lapack': netlib
        filter:
          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
        environment:
          set:
            '${PACKAGE}_ROOT': '${PREFIX}'
      netlib-scalapack:
        suffixes:
          '^openmpi': openmpi
          '^mpich': mpich

Under the hood Spack uses the :meth:`~spack.spec.Spec.format` API to substitute
tokens in either environment variable names or values. There are two caveats though:

- The set of allowed tokens in variable names is restricted to ``PACKAGE``,
  ``VERSION``, ``COMPILER``, ``COMPILERNAME``, ``COMPILERVER``, ``ARCHITECTURE``
- Any token expanded in a variable name is made uppercase, but other than that
  case sensitivity is preserved

Regenerating the module files results in something like:

.. code-block:: console
  :emphasize-lines: 15

  $ spack module tcl refresh -y
  ==> Regenerating tcl module files

  $ module show gcc
  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
     /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/gcc/7.2.0-gcc-5.4.0:
  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
  whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ")
  conflict("gcc")
  prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin")
  prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/share/man")
  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib")
  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64")
  prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/")
  setenv("CC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gcc")
  setenv("CXX","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/g++")
  setenv("FC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
  setenv("F77","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
  setenv("F90","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
  setenv("GCC_ROOT","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs")
  help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
  Fortran, Ada, and Go, as well as libraries for these languages.
  ]])

As you can see, the ``gcc`` module has the environment variable ``GCC_ROOT`` set.

Sometimes it's also useful to apply environment modifications selectively and target
only certain packages. You can, for instance set the common variables ``CC``, ``CXX``,
etc. in the ``gcc`` module file and apply other custom modifications to the
``openmpi`` modules as follows:

.. code-block:: yaml
  :emphasize-lines: 20-32

  modules:
    tcl:
      hash_length: 0
      naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVER}'
      whitelist:
        - gcc
      blacklist:
        - '%gcc@5.4.0'
      all:
        conflict:
          - '${PACKAGE}'
        suffixes:
          '^openblas': openblas
          '^netlib-lapack': netlib
        filter:
          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
        environment:
          set:
            '${PACKAGE}_ROOT': '${PREFIX}'
      gcc:
        environment:
          set:
            CC: gcc
            CXX: g++
            FC: gfortran
            F90: gfortran
            F77: gfortran
      openmpi:
        environment:
          set:
            SLURM_MPI_TYPE: pmi2
            OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
      netlib-scalapack:
        suffixes:
          '^openmpi': openmpi
          '^mpich': mpich

This time we will be more selective and regenerate only the ``gcc`` and
``openmpi`` module files:

.. code-block:: console

  $ spack module tcl refresh -y gcc
  ==> Regenerating tcl module files

  $ spack module tcl refresh -y openmpi
  ==> Regenerating tcl module files

  $ module show gcc
  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
     /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/gcc/7.2.0-gcc-5.4.0:
  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
  whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ")
  conflict("gcc")
  prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin")
  prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/share/man")
  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib")
  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64")
  prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/")
  setenv("CC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gcc")
  setenv("CXX","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/g++")
  setenv("FC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
  setenv("F77","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
  setenv("F90","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
  setenv("GCC_ROOT","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs")
  setenv("CC","gcc")
  setenv("CXX","g++'")
  setenv("FC","gfortran")
  setenv("F77","gfortran")
  setenv("F90","gfortran")
  help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
  Fortran, Ada, and Go, as well as libraries for these languages.
  ]])

  $ module show openmpi
  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
    /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/openmpi/3.1.3-gcc-7.2.0:
  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
  whatis("An open source Message Passing Interface implementation. ")
  conflict("openmpi")
  prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/bin")
  prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/share/man")
  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/lib")
  prepend_path("PKG_CONFIG_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/lib/pkgconfig")
  prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/")
  setenv("OPENMPI_ROOT","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4")
  setenv("SLURM_MPI_TYPE","pmi2")
  setenv("OMPI_MCA_btl_openib_warn_default_gid_prefix","0")
  help([[An open source Message Passing Interface implementation. The Open MPI
  Project is an open source Message Passing Interface implementation that
  is developed and maintained by a consortium of academic, research, and
  industry partners. Open MPI is therefore able to combine the expertise,
  technologies, and resources from all across the High Performance
  Computing community in order to build the best MPI library available.
  Open MPI offers advantages for system and software vendors, application
  developers and computer science researchers.
  ]])


^^^^^^^^^^^^^^^^^^^^^
Autoload dependencies
^^^^^^^^^^^^^^^^^^^^^

Spack can also generate module files that contain code to load the
dependencies automatically. You can, for instance generate python
modules that load their dependencies by adding the ``autoload``
directive and assigning it the value ``direct``:

.. code-block:: yaml
  :emphasize-lines: 3,38,39

  modules:
    tcl:
      verbose: True
      hash_length: 0
      naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVER}'
      whitelist:
        - gcc
      blacklist:
        - '%gcc@5.4.0'
      all:
        conflict:
          - '${PACKAGE}'
        suffixes:
          '^openblas': openblas
          '^netlib-lapack': netlib
        filter:
          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
        environment:
          set:
            '${PACKAGE}_ROOT': '${PREFIX}'
      gcc:
        environment:
          set:
            CC: gcc
            CXX: g++
            FC: gfortran
            F90: gfortran
            F77: gfortran
      openmpi:
        environment:
          set:
            SLURM_MPI_TYPE: pmi2
            OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
      netlib-scalapack:
        suffixes:
          '^openmpi': openmpi
          '^mpich': mpich
      ^python:
        autoload:  'direct'

and regenerating the module files for every package that depends on ``python``:

.. code-block:: console

  root@module-file-tutorial:/# spack module tcl refresh -y ^python
  ==> Regenerating tcl module files

Now the ``py-scipy`` module will be:

.. code-block:: tcl

  #%Module1.0
  ## Module file created by spack (https://github.com/spack/spack) on 2018-11-11 22:10:48.834221
  ##
  ## py-scipy@1.1.0%gcc@7.2.0 arch=linux-ubuntu16.04-x86_64 /d5n3cph
  ##


  module-whatis "SciPy (pronounced 'Sigh Pie') is a Scientific Library for Python. It provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization."

  proc ModulesHelp { } {
  puts stderr "SciPy (pronounced "Sigh Pie") is a Scientific Library for Python. It"
  puts stderr "provides many user-friendly and efficient numerical routines such as"
  puts stderr "routines for numerical integration and optimization."
  }

  if { [ module-info mode load ] && ![ is-loaded python/2.7.15-gcc-7.2.0 ] } {
      puts stderr "Autoloading python/2.7.15-gcc-7.2.0"
      module load python/2.7.15-gcc-7.2.0
  }
  if { [ module-info mode load ] && ![ is-loaded openblas/0.3.3-gcc-7.2.0 ] } {
      puts stderr "Autoloading openblas/0.3.3-gcc-7.2.0"
      module load openblas/0.3.3-gcc-7.2.0
  }
  if { [ module-info mode load ] && ![ is-loaded py-numpy/1.15.2-gcc-7.2.0-openblas ] } {
      puts stderr "Autoloading py-numpy/1.15.2-gcc-7.2.0-openblas"
      module load py-numpy/1.15.2-gcc-7.2.0-openblas
  }
  conflict py-scipy

  prepend-path LD_LIBRARY_PATH "/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-1.1.0-d5n3cphk2lx2v74ypwb6h7tna7vvgdyn/lib"
  prepend-path CMAKE_PREFIX_PATH "/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-1.1.0-d5n3cphk2lx2v74ypwb6h7tna7vvgdyn/"
  prepend-path PYTHONPATH "/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-1.1.0-d5n3cphk2lx2v74ypwb6h7tna7vvgdyn/lib/python2.7/site-packages"
  setenv PY_SCIPY_ROOT "/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-1.1.0-d5n3cphk2lx2v74ypwb6h7tna7vvgdyn"

and will contain code to autoload all the dependencies:

.. code-block:: console

  $ module load py-scipy
  Autoloading python/2.7.15-gcc-7.2.0
  Autoloading openblas/0.3.3-gcc-7.2.0
  Autoloading py-numpy/1.15.2-gcc-7.2.0-openblas

In case messages are unwanted during the autoload procedure, it will be
sufficient to omit the line setting ``verbose: True`` in the configuration file above.

-------------------------
Hierarchical module files
-------------------------

So far we worked with non-hierarchical module files, i.e. with module files
that are all generated in the same root directory and don't attempt to
dynamically modify the ``MODULEPATH``. This results in a flat module structure where
all the software is visible at the same time:

.. code-block:: console

  $ module avail

  ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------
     autoconf/2.69-gcc-7.2.0          m4/1.4.18-gcc-7.2.0                                      pkgconf/1.4.2-gcc-7.2.0
     automake/1.16.1-gcc-7.2.0        mpich/3.2.1-gcc-7.2.0                                    py-numpy/1.15.2-gcc-7.2.0-openblas (L)
     bzip2/1.0.6-gcc-7.2.0            ncurses/6.1-gcc-7.2.0                                    py-scipy/1.1.0-gcc-7.2.0-openblas  (L)
     cmake/3.12.3-gcc-7.2.0           netlib-lapack/3.8.0-gcc-7.2.0                            py-setuptools/40.4.3-gcc-7.2.0
     diffutils/3.6-gcc-7.2.0          netlib-scalapack/2.0.2-gcc-7.2.0-netlib-mpich           python/2.7.15-gcc-7.2.0            (L)
     findutils/4.6.0-gcc-7.2.0        netlib-scalapack/2.0.2-gcc-7.2.0-netlib-openmpi         readline/7.0-gcc-7.2.0
     gcc/7.2.0-gcc-5.4.0              netlib-scalapack/2.0.2-gcc-7.2.0-openblas-mpich          sqlite/3.23.1-gcc-7.2.0
     gdbm/1.14.1-gcc-7.2.0            netlib-scalapack/2.0.2-gcc-7.2.0-openblas-openmpi (D)    texinfo/6.5-gcc-7.2.0
     hwloc/1.11.9-gcc-7.2.0           numactl/2.0.11-gcc-7.2.0                                 util-macros/1.19.1-gcc-7.2.0
     libpciaccess/0.13.5-gcc-7.2.0    openblas/0.3.3-gcc-7.2.0                          (L)    xz/5.2.4-gcc-7.2.0
     libsigsegv/2.11-gcc-7.2.0        openmpi/3.1.3-gcc-7.2.0                                  zlib/1.2.11-gcc-7.2.0
     libtool/2.4.6-gcc-7.2.0          openssl/1.0.2o-gcc-7.2.0
     libxml2/2.9.8-gcc-7.2.0          perl/5.26.2-gcc-7.2.0

    Where:
     L:  Module is loaded
     D:  Default Module

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

This layout is quite simple to deploy, but you can see from the above snippet
that nothing prevents users from loading incompatible sets of modules:

.. code-block:: console

  $ module purge
  $ module load netlib-lapack/3.8.0-gcc-7.2.0 openblas/0.3.3-gcc-7.2.0
  $ module list

  Currently Loaded Modules:
    1) netlib-lapack/3.8.0-gcc-7.2.0   2) openblas/0.3.3-gcc-7.2.0

Even if ``conflicts`` directives are carefully placed in module files, they:

  - won't enforce a consistent environment, but will just report an error
  - need constant updates, for instance as soon as a new compiler or MPI library is installed

`Hierarchical module files <http://lmod.readthedocs.io/en/latest/080_hierarchy.html>`_ try to
overcome these shortcomings by showing at start-up only a restricted view of what is
available on the system: more specifically only the software that has been installed with
OS provided compilers. Among this software there will be other - usually more recent - compilers
that, once loaded, will prepend new directories to ``MODULEPATH`` unlocking all the software
that was compiled with them. This "unlocking" idea can then be extended arbitrarily to
virtual dependencies, as we'll see in the following section.

^^^^^^^^^^^^^^^^^
Core/Compiler/MPI
^^^^^^^^^^^^^^^^^

The most widely used hierarchy is the so called ``Core/Compiler/MPI`` where, on top
of the compilers, different MPI libraries also unlock software linked to them.
There are just a few steps needed to adapt the ``modules.yaml`` file we used previously:

  #. enable the ``lmod`` file generator
  #. change the ``tcl`` tag to ``lmod``
  #. remove ``tcl`` specific directives (``naming_scheme`` and ``conflict``)
  #. declare which compilers are considered ``core_compilers``
  #. remove the ``mpi`` related suffixes (as they will be substituted by hierarchies)

After these modifications your configuration file should look like:

.. code-block:: yaml
  :emphasize-lines: 2-8

  modules:
    enable::
      - lmod
    lmod:
      core_compilers:
        - 'gcc@5.4.0'
      hierarchy:
        - mpi
      hash_length: 0
      whitelist:
        - gcc
      blacklist:
        - '%gcc@5.4.0'
      all:
        suffixes:
          '^openblas': openblas
          '^netlib-lapack': netlib
        filter:
          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
        environment:
          set:
            '${PACKAGE}_ROOT': '${PREFIX}'
      gcc:
        environment:
          set:
            CC: gcc
            CXX: g++
            FC: gfortran
            F90: gfortran
            F77: gfortran
      openmpi:
        environment:
          set:
            SLURM_MPI_TYPE: pmi2
            OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'


.. note::
  Double colon in configuration files
    The double colon after ``enable`` is intentional and it serves the
    purpose of overriding the default list of enabled generators so
    that only ``lmod`` will be active (see :ref:`config-overrides` for more
    details).

The directive ``core_compilers`` accepts a list of compilers. Everything built
using these compilers will create a module in the ``Core`` part of the hierarchy,
which is the entry point for hierarchical module files. It is
common practice to put the OS provided compilers in the list and only build common utilities
and other compilers with them.

If we now regenerate the module files:

.. code-block:: console

  $ spack module lmod refresh --delete-tree -y
  ==> Regenerating lmod module files

and update ``MODULEPATH`` to point to the ``Core``:

.. code-block:: console

  $ module purge
  $ module unuse /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64
  $ module use /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/Core

asking for the available modules will return:

.. code-block:: console

  $ module avail

  ----------------------------------------------------------- share/spack/lmod/linux-ubuntu16.04-x86_64/Core ------------------------------------------------------------
     gcc/7.2.0

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

Unsurprisingly, the only visible module is ``gcc``. Loading that we'll unlock
the ``Compiler`` part of the hierarchy:

.. code-block:: console

  $ module load gcc
  $ module avail

  ------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------
     autoconf/2.69      findutils/4.6.0        libtool/2.4.6    netlib-lapack/3.8.0    perl/5.26.2                 python/2.7.15         xz/5.2.4
     automake/1.16.1    gdbm/1.14.1            libxml2/2.9.8    numactl/2.0.11         pkgconf/1.4.2               readline/7.0          zlib/1.2.11
     bzip2/1.0.6        hwloc/1.11.9           m4/1.4.18        openblas/0.3.3         py-numpy/1.15.2-openblas    sqlite/3.23.1
     cmake/3.12.3       libpciaccess/0.13.5    mpich/3.2.1      openmpi/3.1.3          py-scipy/1.1.0-openblas     texinfo/6.5
     diffutils/3.6      libsigsegv/2.11        ncurses/6.1      openssl/1.0.2o         py-setuptools/40.4.3        util-macros/1.19.1

  ----------------------------------------------------------- share/spack/lmod/linux-ubuntu16.04-x86_64/Core ------------------------------------------------------------
     gcc/7.2.0 (L)

    Where:
     L:  Module is loaded

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

The same holds true also for the ``MPI`` part, that you can enable by loading
either ``mpich`` or ``openmpi``. Let's start by loading ``mpich``:

.. code-block:: console

  $ module load mpich
  $ module avail

  --------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/mpich/3.2.1-vt5xcat/gcc/7.2.0 ----------------------------------
     netlib-scalapack/2.0.2-netlib    netlib-scalapack/2.0.2-openblas (D)

  ------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------
     autoconf/2.69      findutils/4.6.0        libtool/2.4.6        netlib-lapack/3.8.0    perl/5.26.2                 python/2.7.15         xz/5.2.4
     automake/1.16.1    gdbm/1.14.1            libxml2/2.9.8        numactl/2.0.11         pkgconf/1.4.2               readline/7.0          zlib/1.2.11
     bzip2/1.0.6        hwloc/1.11.9           m4/1.4.18            openblas/0.3.3         py-numpy/1.15.2-openblas    sqlite/3.23.1
     cmake/3.12.3       libpciaccess/0.13.5    mpich/3.2.1   (L)    openmpi/3.1.3          py-scipy/1.1.0-openblas     texinfo/6.5
     diffutils/3.6      libsigsegv/2.11        ncurses/6.1          openssl/1.0.2o         py-setuptools/40.4.3        util-macros/1.19.1

  ----------------------------------------------------------- share/spack/lmod/linux-ubuntu16.04-x86_64/Core ------------------------------------------------------------
     gcc/7.2.0 (L)

    Where:
     L:  Module is loaded
     D:  Default Module

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


  root@module-file-tutorial:/# module load openblas netlib-scalapack/2.0.2-openblas
  root@module-file-tutorial:/# module list

  Currently Loaded Modules:
    1) gcc/7.2.0   2) mpich/3.2.1   3) openblas/0.3.3   4) netlib-scalapack/2.0.2-openblas

At this point we can showcase the improved consistency that a hierarchical layout provides
over a non-hierarchical one:

.. code-block:: console

  $ module load openmpi

  Lmod is automatically replacing "mpich/3.2.1" with "openmpi/3.1.3".


  Due to MODULEPATH changes, the following have been reloaded:
    1) netlib-scalapack/2.0.2-openblas

``Lmod`` took care of swapping the MPI provider for us, and it also substituted the
``netlib-scalapack`` module to conform to the change in the MPI.
In this way we can't accidentally pull-in two different MPI providers at the
same time or load a module file for a package linked to ``openmpi`` when ``mpich`` is also loaded.
Consistency for compilers and MPI is ensured by the tool.


^^^^^^^^^^^^^^^^^^^^^^^^^^^
Add LAPACK to the hierarchy
^^^^^^^^^^^^^^^^^^^^^^^^^^^

The hierarchy just shown is already a great improvement over non-hierarchical layouts,
but it still has an asymmetry: ``LAPACK`` providers cover the same semantic role
as ``MPI`` providers, but yet they are not part of the hierarchy.

To be more practical, this means that although we have gained an improved consistency in
our environment when it comes to ``MPI``, we still have the same problems as we had before
for ``LAPACK`` implementations:

.. code-block:: console

  root@module-file-tutorial:/# module list

  Currently Loaded Modules:
    1) gcc/7.2.0   2) openblas/0.3.3   3) openmpi/3.1.3   4) netlib-scalapack/2.0.2-openblas

  root@module-file-tutorial:/# module load netlib-scalapack/2.0.2-netlib

  The following have been reloaded with a version change:
    1) netlib-scalapack/2.0.2-openblas => netlib-scalapack/2.0.2-netlib

  root@module-file-tutorial:/# module list

  Currently Loaded Modules:
    1) gcc/7.2.0   2) openblas/0.3.3   3) openmpi/3.1.3   4) netlib-scalapack/2.0.2-netlib

Hierarchies that are deeper than ``Core``/``Compiler``/``MPI`` are
probably still considered "unusual" or "impractical" at many sites, mainly because
module files are written manually and keeping track of the combinations
among multiple providers quickly becomes quite involved.

For instance, having both ``MPI`` and ``LAPACK`` in the hierarchy
means we must classify software into one of four categories:

  #. Software that doesn't depend on ``MPI`` or ``LAPACK``
  #. Software that depends only on ``MPI``
  #. Software that depends only on ``LAPACK``
  #. Software that depends on both

to decide when to show it to the user. The situation becomes more involved as the number of virtual
dependencies in the hierarchy increases.

We can take advantage of the DAG that Spack maintains for the installed software and solve
this combinatorial problem in a clean and automated way.
In some sense Spack's ability to manage this combinatorial complexity makes deeper
hierarchies feasible.

Coming back to our example, let's add ``lapack`` to the hierarchy and remove any remaining suffix:

.. code-block:: yaml
  :emphasize-lines: 9

  modules:
    enable::
      - lmod
    lmod:
      core_compilers:
        - 'gcc@5.4.0'
      hierarchy:
        - mpi
        - lapack
      hash_length: 0
      whitelist:
        - gcc
      blacklist:
        - '%gcc@5.4.0'
      all:
        filter:
          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
        environment:
          set:
            '${PACKAGE}_ROOT': '${PREFIX}'
      gcc:
        environment:
          set:
            CC: gcc
            CXX: g++
            FC: gfortran
            F90: gfortran
            F77: gfortran
      openmpi:
        environment:
          set:
            SLURM_MPI_TYPE: pmi2
            OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'

After module files have been regenerated as usual:

.. code-block:: console

  root@module-file-tutorial:/# module purge

  root@module-file-tutorial:/# spack module lmod refresh --delete-tree -y
  ==> Regenerating lmod module files

we can see that now we have additional components in the hierarchy:

.. code-block:: console

  $ module load gcc
  $ module load openblas
  $ module avail

  -------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/openblas/0.3.3-xxoxfh4/gcc/7.2.0 --------------------------------
     py-numpy/1.15.2    py-scipy/1.1.0

  ------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------
     autoconf/2.69      findutils/4.6.0        libtool/2.4.6    netlib-lapack/3.8.0        perl/5.26.2             sqlite/3.23.1
     automake/1.16.1    gdbm/1.14.1            libxml2/2.9.8    numactl/2.0.11             pkgconf/1.4.2           texinfo/6.5
     bzip2/1.0.6        hwloc/1.11.9           m4/1.4.18        openblas/0.3.3      (L)    py-setuptools/40.4.3    util-macros/1.19.1
     cmake/3.12.3       libpciaccess/0.13.5    mpich/3.2.1      openmpi/3.1.3              python/2.7.15           xz/5.2.4
     diffutils/3.6      libsigsegv/2.11        ncurses/6.1      openssl/1.0.2o             readline/7.0            zlib/1.2.11

  ----------------------------------------------------------- share/spack/lmod/linux-ubuntu16.04-x86_64/Core ------------------------------------------------------------
     gcc/7.2.0 (L)

    Where:
     L:  Module is loaded

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


  $ module load openmpi
  $ module avail

  --------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/openmpi/3.1.3-do5xfer/openblas/0.3.3-xxoxfh4/gcc/7.2.0 ---------------------
     netlib-scalapack/2.0.2

  -------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/openblas/0.3.3-xxoxfh4/gcc/7.2.0 --------------------------------
     py-numpy/1.15.2    py-scipy/1.1.0

  ------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------
     autoconf/2.69      findutils/4.6.0        libtool/2.4.6    netlib-lapack/3.8.0        perl/5.26.2             sqlite/3.23.1
     automake/1.16.1    gdbm/1.14.1            libxml2/2.9.8    numactl/2.0.11             pkgconf/1.4.2           texinfo/6.5
     bzip2/1.0.6        hwloc/1.11.9           m4/1.4.18        openblas/0.3.3      (L)    py-setuptools/40.4.3    util-macros/1.19.1
     cmake/3.12.3       libpciaccess/0.13.5    mpich/3.2.1      openmpi/3.1.3       (L)    python/2.7.15           xz/5.2.4
     diffutils/3.6      libsigsegv/2.11        ncurses/6.1      openssl/1.0.2o             readline/7.0            zlib/1.2.11

  ---------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/Core ----------------------------------------------
     gcc/7.2.0 (L)

    Where:
     L:  Module is loaded

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

Both ``MPI`` and ``LAPACK`` providers will now benefit from the same safety features:

.. code-block:: console

  $ module load py-numpy netlib-scalapack
  $ module load mpich

  Lmod is automatically replacing "openmpi/3.1.3" with "mpich/3.2.1".


  Due to MODULEPATH changes, the following have been reloaded:
    1) netlib-scalapack/2.0.2

  $ module load netlib-lapack

  Lmod is automatically replacing "openblas/0.3.3" with "netlib-lapack/3.8.0".


  Inactive Modules:
    1) py-numpy

  Due to MODULEPATH changes, the following have been reloaded:
    1) netlib-scalapack/2.0.2

Because we only compiled ``py-numpy`` with ``openblas`` the module
is made inactive when we switch the ``LAPACK`` provider. The user
environment is now consistent by design!

----------------------
Working with templates
----------------------

As briefly mentioned in the introduction, Spack uses `Jinja2 <http://jinja.pocoo.org/docs/2.9/>`_
to generate each individual module file.
This means that you have all of its flexibility and power when it comes to
customizing what gets generated!

^^^^^^^^^^^^^^^^^^^^^
Module file templates
^^^^^^^^^^^^^^^^^^^^^

The templates that Spack uses to generate module files are stored in the
``share/spack/templates/module`` directory within the Spack prefix, and
they all share the same common structure.  Usually, they start with a
header that identifies the type of module being generated. In the case of
hierarchical module files it's:

.. literalinclude:: ../../../share/spack/templates/modules/modulefile.lua
  :language: jinja
  :lines: 1-6

The statements within double curly brackets ``{{ ... }}`` denote
`expressions <http://jinja.pocoo.org/docs/2.9/templates/#expressions>`_
that will be evaluated and substituted at module generation time.
The rest of the file is then divided into
`blocks <http://jinja.pocoo.org/docs/2.9/templates/#template-inheritance>`_
that can be overridden or extended by users, if need be.
`Control structures <http://jinja.pocoo.org/docs/2.9/templates/#list-of-control-structures>`_
, delimited by ``{% ... %}``,
are also permitted in the template language:

.. literalinclude:: ../../../share/spack/templates/modules/modulefile.lua
  :language: jinja
  :lines: 73-88

The locations where Spack looks for templates are specified
in ``config.yaml``:

.. literalinclude:: ../../../etc/spack/defaults/config.yaml
  :language: yaml
  :lines: 21-24

and can be extended by users to employ custom templates, as we'll see next.

^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Extend the default templates
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Let's assume one of our software is protected by group membership:
allowed users belong to the same linux group, and access is granted at group level.
Wouldn't it be nice if people that are not
yet entitled to use it could receive a helpful message at module load time
that tells them who to contact in your organization to be inserted in the group?

To automate the generation of module files with such site-specific behavior
we'll start by extending the list of locations where Spack looks for module
files. Let's create the file ``~/.spack/config.yaml`` with the content:

.. code-block:: yaml

  config:
    template_dirs:
      - $HOME/.spack/templates

This tells Spack to also search another location when looking for template files.
Next, we need to create our custom template extension in the folder listed above:

.. code-block:: jinja

  {% extends "modules/modulefile.lua" %}
  {% block footer %}
  -- Access is granted only to specific groups
  if not isDir("{{ spec.prefix }}") then
      LmodError (
          "You don't have the necessary rights to run \"{{ spec.name }}\".\n\n",
          "\tPlease write an e-mail to 1234@foo.com if you need further information on how to get access to it.\n"
      )
  end
  {% endblock %}

Let's name this file ``group-restricted.lua``. The line:

.. code-block:: jinja

  {% extends "modules/modulefile.lua" %}

tells Jinja2 that we are reusing the standard template for hierarchical module files.
The section:

.. code-block:: jinja

  {% block footer %}
  -- Access is granted only to specific groups
  if not isDir("{{ spec.prefix }}") then
      LmodError (
          "You don't have the necessary rights to run \"{{ spec.name }}\".\n\n",
          "\tPlease write an e-mail to 1234@foo.com if you need further information on how to get access to it.\n"
      )
  end
  {% endblock %}

overrides the ``footer`` block.
Finally, we need to add a couple of lines in ``modules.yaml`` to tell Spack which specs
need to use the new custom template. For the sake of illustration let's assume
it's ``netlib-scalapack``:

.. code-block:: yaml
  :emphasize-lines: 35-36

  modules:
    enable::
      - lmod
    lmod:
      core_compilers:
        - 'gcc@5.4.0'
      hierarchy:
        - mpi
        - lapack
      hash_length: 0
      whitelist:
        - gcc
      blacklist:
        - '%gcc@5.4.0'
        - readline
      all:
        filter:
          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
        environment:
          set:
            '${PACKAGE}_ROOT': '${PREFIX}'
      gcc:
        environment:
          set:
            CC: gcc
            CXX: g++
            FC: gfortran
            F90: gfortran
            F77: gfortran
      openmpi:
        environment:
          set:
            SLURM_MPI_TYPE: pmi2
            OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
      netlib-scalapack:
        template: 'group-restricted.lua'

If we regenerate the module files one last time:

.. code-block:: console

  root@module-file-tutorial:/# spack module lmod refresh -y netlib-scalapack
  ==> Regenerating lmod module files

we'll find the following at the end of each ``netlib-scalapack`` module file:

.. code-block:: lua

  -- Access is granted only to specific groups
  if not isDir("/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/netlib-scalapack-2.0.2-d3lertflood3twaor44eam2kcr4l72ag") then
      LmodError (
          "You don't have the necessary rights to run \"netlib-scalapack\".\n\n",
          "\tPlease write an e-mail to 1234@foo.com if you need further information on how to get access to it.\n"
      )
  end

and every user that doesn't have access to the software will now be redirected to
the right e-mail address where to ask for it!