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spack/lib/spack/docs/tutorial_modules.rst
Massimiliano Culpo fe889124eb SC17: reworked module file tutorial section (#5657) 
* Reworked module file tutorial section

First draft for the SC17 update. This includes:

 - adding an introduction on module files + Spack's module
   generation blueprints
 - adding a set-up section and provide a docker image for easy set-up
 - updating all the relevant snippets
 - extending a bit some of the concepts that were already touched

* Added reference to #5582 + committed Dockerfiles

Also fixed a couple of typos spotted by Denis.

* module file tutorial: added section on template customization

* module file tutorial: fixed minor typos + rephrased a sentence

* module file tutorial: made explicit that Docker image comes with software

* module file tutorial: improved phrasing and layout.

Thanks Hartzell!

* module file tutorial: added vim and nano to editors

* module file tutorial: fixed typo

* Fixed typos

Thanks Adam!

* module file tutorial: updated Dockerfile + minor changes in introduction
2017-11-12 00:27:20 -08:00

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.. _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.
The best way to follow along is to use a Docker image, which comes
with Spack and all the software used in the following parts already
pre-installed. If you want to proceed this way, read :ref:`module_file_tutorial_use_docker`.
If you don't have Docker installed or for any other reason you
prefer to work locally, follow instead :ref:`module_file_tutorial_work_locally`
to know how to clone Spack and install the software.
Be aware that the set-up will take longer and that the details of the snippets
below assume the Docker image and may need changes to work in your particular
environment.
.. _module_file_tutorial_use_docker:
^^^^^^^^^^^^^^^^^^
Use a Docker image
^^^^^^^^^^^^^^^^^^
The fastest way to set-up your environment is to :ref:`use a Docker image <workflow_create_docker_image>`:
.. code-block:: console
$ docker pull alalazo/spack:module_tutorial
$ docker run --rm -h module-file-tutorial -it alalazo/spack:module_tutorial
root@module-file-tutorial:/#
If you arrived at this point you should be ready to start, as all the software needed is
pre-installed in the image:
.. code-block:: console
root@module-file-tutorial:/# which spack
/usr/local/bin/spack
root@module-file-tutorial:/# spack find
==> 46 installed packages.
-- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
autoconf@2.69 gcc@7.2.0 git@2.9.4 isl@0.18 libtool@2.4.6 lua@5.3.4 lua-luaposix@33.4.0 mpc@1.0.3 ncurses@6.0 pkg-config@0.29.2 tcl@8.6.6
automake@1.15.1 gdbm@1.13 gmp@6.1.2 libsigsegv@2.11 lmod@7.7 lua-luafilesystem@1_6_3 m4@1.4.18 mpfr@3.1.5 perl@5.24.1 readline@7.0 zlib@1.2.11
-- linux-ubuntu16.04-x86_64 / gcc@7.2.0 -------------------------
bzip2@1.0.6 ncurses@6.0 netlib-scalapack@2.0.2 openblas@0.2.20 pkg-config@0.29.2 py-packaging@16.8 py-setuptools@35.0.2 readline@7.0
cmake@3.9.4 netlib-lapack@3.6.1 netlib-scalapack@2.0.2 openmpi@1.10.2 py-appdirs@1.4.3 py-pyparsing@2.2.0 py-six@1.10.0 sqlite@3.20.0
mpich@3.2 netlib-scalapack@2.0.2 netlib-scalapack@2.0.2 openssl@1.0.2k py-numpy@1.13.1 py-scipy@0.19.1 python@2.7.14 zlib@1.2.11
Go to :ref:`module_file_tutorial_non_hierarchical` to proceed with the tutorial.
.. note::
Dockerfile for this image
Those of you that want to build a similar container themselves can find the
``Dockerfile`` and the other resources in Spack's ``share/spack/docs/docker``
folder.
.. _module_file_tutorial_work_locally:
^^^^^^^^^^^^^^^^^^^^^^
Work in a local folder
^^^^^^^^^^^^^^^^^^^^^^
If you don't feel like using a container, you can set-up your environment
locally. Let's start by cloning the Spack repository and moving to the directory
where it was checked out:
.. code-block:: console
$ git clone https://github.com/spack/spack.git
$ cd spack
From here we'll be building the required stack of software.
"""""""""""""""""""
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 source the setup file and activate the :ref:`shell support <shell-support>`:
.. 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. This is what you'll see
on Ubuntu 14.04:
.. code-block:: console
$ uname -a
Linux nuvolari 4.4.0-45-generic #66~14.04.1-Ubuntu SMP Wed Oct 19 15:05:38 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
$ spack compilers
==> Available compilers
-- gcc ----------------------------------------------------------
gcc@4.8
Let's bootstrap a more recent compiler with the one that was automatically detected:
.. 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) lmod-7.7-gcc-4.8-okcwjgw 2) gcc-7.2.0-gcc-4.8-twd5nqg
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 ~/.spack/linux/compilers.yaml
gcc@7.2.0
$ spack compilers
==> Available compilers
-- gcc ----------------------------------------------------------
gcc@7.2.0 gcc@4.8
""""""""""""""""""""""""""""""""""""""""""""""""""""
Build the software that will be used in the tutorial
""""""""""""""""""""""""""""""""""""""""""""""""""""
The last step is to install the software stack needed later on. To mimic
an external installation of an MPI provider we'll install ``openmpi`` on
the system we are working on. On Ubuntu 14.04 it boils down to:
.. code-block:: console
$ sudo apt-get install openmpi-bin openmpi-common libopenmpi-dev
...
but the exact command varies according to your OS. Then we need to prepare
a ``packages.yaml`` file that instructs Spack to use an externally provided MPI:
.. code-block:: yaml
packages:
openmpi:
buildable: False
paths:
openmpi@1.6: /usr
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
root@module-file-tutorial:/# module avail
----------------------------------------------------------------------------- /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------------------------------------
autoconf-2.69-gcc-5.4.0-bvabhji libtool-2.4.6-gcc-5.4.0-o2pfwjf ncurses-6.0-gcc-7.2.0-oh6pqty pkg-config-0.29.2-gcc-5.4.0-ae2hwm7 readline-7.0-gcc-5.4.0-gizxpch
automake-1.15.1-gcc-5.4.0-kaiefe4 lmod-7.7-gcc-5.4.0-okcwjgw netlib-lapack-3.6.1-gcc-7.2.0-5sywztc pkg-config-0.29.2-gcc-7.2.0-76z7ehw readline-7.0-gcc-7.2.0-eqos6rz
bzip2-1.0.6-gcc-7.2.0-mwamumj lua-5.3.4-gcc-5.4.0-ytxw2gq netlib-scalapack-2.0.2-gcc-7.2.0-5lb2j5p py-appdirs-1.4.3-gcc-7.2.0-7ncu7zr sqlite-3.20.0-gcc-7.2.0-hfmjilk
cmake-3.9.4-gcc-7.2.0-6bxdr6h lua-luafilesystem-1_6_3-gcc-5.4.0-5dzzlt4 netlib-scalapack-2.0.2-gcc-7.2.0-ax6aza6 py-numpy-1.13.1-gcc-7.2.0-22n5oub tcl-8.6.6-gcc-5.4.0-767ls4i
gcc-7.2.0-gcc-5.4.0-go3z4hb lua-luaposix-33.4.0-gcc-5.4.0-w5jpnwm netlib-scalapack-2.0.2-gcc-7.2.0-c4v5l7j py-packaging-16.8-gcc-7.2.0-c37cjmq zlib-1.2.11-gcc-5.4.0-swly52a
gdbm-1.13-gcc-5.4.0-vdhoris m4-1.4.18-gcc-5.4.0-r5envx3 netlib-scalapack-2.0.2-gcc-7.2.0-m7rzcmh py-pyparsing-2.2.0-gcc-7.2.0-ahdh5cx zlib-1.2.11-gcc-7.2.0-lv5fabl
git-2.9.4-gcc-5.4.0-atwjs4i mpc-1.0.3-gcc-5.4.0-tumbpsh openblas-0.2.20-gcc-7.2.0-kvddide py-scipy-0.19.1-gcc-7.2.0-7hi7r5j
gmp-6.1.2-gcc-5.4.0-qc4qcfz mpfr-3.1.5-gcc-5.4.0-mdi6irz openmpi-1.10.2-gcc-7.2.0-ufw7pdi py-setuptools-35.0.2-gcc-7.2.0-cvasi7i
isl-0.18-gcc-5.4.0-vttqout mpich-3.2-gcc-7.2.0-7gxffhv openssl-1.0.2k-gcc-7.2.0-pxv3dh4 py-six-1.10.0-gcc-7.2.0-3xk5mod
libsigsegv-2.11-gcc-5.4.0-fypapcp ncurses-6.0-gcc-5.4.0-ukq4tcc perl-5.24.1-gcc-5.4.0-mfzwy6y python-2.7.14-gcc-7.2.0-555u7ea
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
root@module-file-tutorial:/# module show gcc-7.2.0-gcc-5.4.0-go3z4hb
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/usr/local/share/spack/modules/linux-ubuntu16.04-x86_64/gcc-7.2.0-gcc-5.4.0-go3z4hb:
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/bin")
prepend_path("MANPATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/share/man")
prepend_path("LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib")
prepend_path("LD_LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib")
prepend_path("LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib64")
prepend_path("LD_LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib64")
prepend_path("CPATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/include")
prepend_path("CMAKE_PREFIX_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/")
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
root@module-file-tutorial:/# spack module refresh --module-type tcl
==> You are about to regenerate tcl module files for:
-- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
bvabhji autoconf@2.69 vdhoris gdbm@1.13 vttqout isl@0.18 okcwjgw lmod@7.7 w5jpnwm lua-luaposix@33.4.0 mdi6irz mpfr@3.1.5 ae2hwm7 pkg-config@0.29.2 swly52a zlib@1.2.11
kaiefe4 automake@1.15.1 atwjs4i git@2.9.4 fypapcp libsigsegv@2.11 ytxw2gq lua@5.3.4 r5envx3 m4@1.4.18 ukq4tcc ncurses@6.0 gizxpch readline@7.0
go3z4hb gcc@7.2.0 qc4qcfz gmp@6.1.2 o2pfwjf libtool@2.4.6 5dzzlt4 lua-luafilesystem@1_6_3 tumbpsh mpc@1.0.3 mfzwy6y perl@5.24.1 767ls4i tcl@8.6.6
-- linux-ubuntu16.04-x86_64 / gcc@7.2.0 -------------------------
mwamumj bzip2@1.0.6 5sywztc netlib-lapack@3.6.1 m7rzcmh netlib-scalapack@2.0.2 76z7ehw pkg-config@0.29.2 ahdh5cx py-pyparsing@2.2.0 555u7ea python@2.7.14
6bxdr6h cmake@3.9.4 ax6aza6 netlib-scalapack@2.0.2 kvddide openblas@0.2.20 7ncu7zr py-appdirs@1.4.3 7hi7r5j py-scipy@0.19.1 eqos6rz readline@7.0
7gxffhv mpich@3.2 c4v5l7j netlib-scalapack@2.0.2 ufw7pdi openmpi@1.10.2 22n5oub py-numpy@1.13.1 cvasi7i py-setuptools@35.0.2 hfmjilk sqlite@3.20.0
oh6pqty ncurses@6.0 5lb2j5p netlib-scalapack@2.0.2 pxv3dh4 openssl@1.0.2k c37cjmq py-packaging@16.8 3xk5mod py-six@1.10.0 lv5fabl zlib@1.2.11
==> 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
root@module-file-tutorial:/# module show gcc-7.2.0-gcc-5.4.0-go3z4hb
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/usr/local/share/spack/modules/linux-ubuntu16.04-x86_64/gcc-7.2.0-gcc-5.4.0-go3z4hb:
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/bin")
prepend_path("MANPATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/share/man")
prepend_path("LD_LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib")
prepend_path("LD_LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib64")
prepend_path("CMAKE_PREFIX_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/")
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:
.. code-block:: console
root@module-file-tutorial:/# spack module refresh --module-type tcl --delete-tree
==> You are about to regenerate tcl module files for:
-- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
bvabhji autoconf@2.69 vdhoris gdbm@1.13 vttqout isl@0.18 okcwjgw lmod@7.7 w5jpnwm lua-luaposix@33.4.0 mdi6irz mpfr@3.1.5 ae2hwm7 pkg-config@0.29.2 swly52a zlib@1.2.11
kaiefe4 automake@1.15.1 atwjs4i git@2.9.4 fypapcp libsigsegv@2.11 ytxw2gq lua@5.3.4 r5envx3 m4@1.4.18 ukq4tcc ncurses@6.0 gizxpch readline@7.0
go3z4hb gcc@7.2.0 qc4qcfz gmp@6.1.2 o2pfwjf libtool@2.4.6 5dzzlt4 lua-luafilesystem@1_6_3 tumbpsh mpc@1.0.3 mfzwy6y perl@5.24.1 767ls4i tcl@8.6.6
-- linux-ubuntu16.04-x86_64 / gcc@7.2.0 -------------------------
mwamumj bzip2@1.0.6 5sywztc netlib-lapack@3.6.1 m7rzcmh netlib-scalapack@2.0.2 76z7ehw pkg-config@0.29.2 ahdh5cx py-pyparsing@2.2.0 555u7ea python@2.7.14
6bxdr6h cmake@3.9.4 ax6aza6 netlib-scalapack@2.0.2 kvddide openblas@0.2.20 7ncu7zr py-appdirs@1.4.3 7hi7r5j py-scipy@0.19.1 eqos6rz readline@7.0
7gxffhv mpich@3.2 c4v5l7j netlib-scalapack@2.0.2 ufw7pdi openmpi@1.10.2 22n5oub py-numpy@1.13.1 cvasi7i py-setuptools@35.0.2 hfmjilk sqlite@3.20.0
oh6pqty ncurses@6.0 5lb2j5p netlib-scalapack@2.0.2 pxv3dh4 openssl@1.0.2k c37cjmq py-packaging@16.8 3xk5mod py-six@1.10.0 lv5fabl zlib@1.2.11
==> Do you want to proceed? [y/n] y
==> Regenerating tcl module files
root@module-file-tutorial:/# module avail
----------------------------------------------------------------------------- /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------------------------------------
bzip2-1.0.6-gcc-7.2.0-mwamumj netlib-scalapack-2.0.2-gcc-7.2.0-5lb2j5p openmpi-1.10.2-gcc-7.2.0-ufw7pdi py-packaging-16.8-gcc-7.2.0-c37cjmq python-2.7.14-gcc-7.2.0-555u7ea
cmake-3.9.4-gcc-7.2.0-6bxdr6h netlib-scalapack-2.0.2-gcc-7.2.0-ax6aza6 openssl-1.0.2k-gcc-7.2.0-pxv3dh4 py-pyparsing-2.2.0-gcc-7.2.0-ahdh5cx readline-7.0-gcc-7.2.0-eqos6rz
mpich-3.2-gcc-7.2.0-7gxffhv netlib-scalapack-2.0.2-gcc-7.2.0-c4v5l7j pkg-config-0.29.2-gcc-7.2.0-76z7ehw py-scipy-0.19.1-gcc-7.2.0-7hi7r5j sqlite-3.20.0-gcc-7.2.0-hfmjilk
ncurses-6.0-gcc-7.2.0-oh6pqty netlib-scalapack-2.0.2-gcc-7.2.0-m7rzcmh py-appdirs-1.4.3-gcc-7.2.0-7ncu7zr py-setuptools-35.0.2-gcc-7.2.0-cvasi7i zlib-1.2.11-gcc-7.2.0-lv5fabl
netlib-lapack-3.6.1-gcc-7.2.0-5sywztc openblas-0.2.20-gcc-7.2.0-kvddide py-numpy-1.13.1-gcc-7.2.0-22n5oub py-six-1.10.0-gcc-7.2.0-3xk5mod
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 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.
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
root@module-file-tutorial:/# spack module refresh --module-type tcl -y
==> Regenerating tcl module files
you'll see that now the module for ``gcc@7.2.0`` has reappeared:
.. code-block:: console
root@module-file-tutorial:/# module avail gcc-7.2.0-gcc-5.4.0-go3z4hb
----------------------------------------------------------------------------- /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------------------------------------
gcc-7.2.0-gcc-5.4.0-go3z4hb
Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
^^^^^^^^^^^^^^^^^^^^^^^^^
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:
.. TODO: give reasons to remove hashes if they are not evident enough?
.. 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
root@module-file-tutorial:/# spack module refresh --module-type tcl --delete-tree -y
==> Error: Name clashes detected in module files:
file: /usr/local/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
root@module-file-tutorial:/# spack module refresh --module-type tcl --delete-tree -y
==> Regenerating tcl module files
root@module-file-tutorial:/# module avail
----------------------------------------------------------------------------- /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------------------------------------
bzip2-1.0.6-gcc-7.2.0 netlib-lapack-3.6.1-gcc-7.2.0 openblas-0.2.20-gcc-7.2.0 py-numpy-1.13.1-gcc-7.2.0-openblas py-six-1.10.0-gcc-7.2.0
cmake-3.9.4-gcc-7.2.0 netlib-scalapack-2.0.2-gcc-7.2.0-netlib-mpich openmpi-1.10.2-gcc-7.2.0 py-packaging-16.8-gcc-7.2.0 python-2.7.14-gcc-7.2.0
gcc-7.2.0-gcc-5.4.0 netlib-scalapack-2.0.2-gcc-7.2.0-netlib-openmpi openssl-1.0.2k-gcc-7.2.0 py-pyparsing-2.2.0-gcc-7.2.0 readline-7.0-gcc-7.2.0
mpich-3.2-gcc-7.2.0 netlib-scalapack-2.0.2-gcc-7.2.0-openblas-mpich pkg-config-0.29.2-gcc-7.2.0 py-scipy-0.19.1-gcc-7.2.0-openblas sqlite-3.20.0-gcc-7.2.0
ncurses-6.0-gcc-7.2.0 netlib-scalapack-2.0.2-gcc-7.2.0-openblas-openmpi py-appdirs-1.4.3-gcc-7.2.0 py-setuptools-35.0.2-gcc-7.2.0 zlib-1.2.11-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
root@module-file-tutorial:/# spack module refresh --module-type tcl --delete-tree -y
==> Regenerating tcl module files
root@module-file-tutorial:/# module avail
----------------------------------------------------------------------------- /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------------------------------------
bzip2/1.0.6-gcc-7.2.0 netlib-lapack/3.6.1-gcc-7.2.0 openblas/0.2.20-gcc-7.2.0 py-numpy/1.13.1-gcc-7.2.0-openblas py-six/1.10.0-gcc-7.2.0
cmake/3.9.4-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-netlib-mpich openmpi/1.10.2-gcc-7.2.0 py-packaging/16.8-gcc-7.2.0 python/2.7.14-gcc-7.2.0
gcc/7.2.0-gcc-5.4.0 netlib-scalapack/2.0.2-gcc-7.2.0-netlib-openmpi openssl/1.0.2k-gcc-7.2.0 py-pyparsing/2.2.0-gcc-7.2.0 readline/7.0-gcc-7.2.0
mpich/3.2-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-openblas-mpich pkg-config/0.29.2-gcc-7.2.0 py-scipy/0.19.1-gcc-7.2.0-openblas sqlite/3.20.0-gcc-7.2.0
ncurses/6.0-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-openblas-openmpi (D) py-appdirs/1.4.3-gcc-7.2.0 py-setuptools/35.0.2-gcc-7.2.0 zlib/1.2.11-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
root@module-file-tutorial:/# spack module refresh -y --module-type tcl
==> Regenerating tcl module files
root@module-file-tutorial:/# module show gcc
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/usr/local/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","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/bin")
prepend_path("MANPATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/share/man")
prepend_path("LD_LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib")
prepend_path("LD_LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib64")
prepend_path("CMAKE_PREFIX_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/")
setenv("GCC_ROOT","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd")
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
root@module-file-tutorial:/# spack module refresh -y --module-type tcl gcc
==> Regenerating tcl module files
root@module-file-tutorial:/# spack module refresh -y --module-type tcl openmpi
==> Regenerating tcl module files
root@module-file-tutorial:/# module show gcc
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/usr/local/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","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/bin")
prepend_path("MANPATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/share/man")
prepend_path("LD_LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib")
prepend_path("LD_LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib64")
prepend_path("CMAKE_PREFIX_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/")
setenv("GCC_ROOT","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd")
setenv("CC","gcc")
setenv("CXX","g++")
setenv("FC","gfortran")
setenv("F90","gfortran")
setenv("F77","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.
]])
root@module-file-tutorial:/# module show openmpi
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/usr/local/share/spack/modules/linux-ubuntu16.04-x86_64/openmpi/1.10.2-gcc-7.2.0:
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
whatis("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 t
o 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. ")
conflict("openmpi")
prepend_path("MANPATH","/usr/share/man")
prepend_path("ACLOCAL_PATH","/usr/share/aclocal")
prepend_path("PKG_CONFIG_PATH","/usr/lib/pkgconfig")
setenv("OPENMPI_ROOT","/usr")
setenv("SLURM_MPI_TYPE","pmi2")
setenv("OMPI_MCA_btl_openib_warn_default_gid_prefix","0")
help([[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 refresh -y --module-type tcl ^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 2017-10-07 15:02:14.974937
##
## py-scipy@0.19.1%gcc@7.2.0 arch=linux-ubuntu16.04-x86_64 /7hi7r5j
##
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 ![ is-loaded python/2.7.14-gcc-7.2.0 ] {
puts stderr "Autoloading python/2.7.14-gcc-7.2.0"
module load python/2.7.14-gcc-7.2.0
}
if ![ is-loaded openblas/0.2.20-gcc-7.2.0 ] {
puts stderr "Autoloading openblas/0.2.20-gcc-7.2.0"
module load openblas/0.2.20-gcc-7.2.0
}
if ![ is-loaded py-numpy/1.13.1-gcc-7.2.0-openblas ] {
puts stderr "Autoloading py-numpy/1.13.1-gcc-7.2.0-openblas"
module load py-numpy/1.13.1-gcc-7.2.0-openblas
}
conflict py-scipy
prepend-path LD_LIBRARY_PATH "/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-0.19.1-7hi7r5jri7bmohh4oontvfxo7rgj4hef/lib"
prepend-path CMAKE_PREFIX_PATH "/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-0.19.1-7hi7r5jri7bmohh4oontvfxo7rgj4hef/"
prepend-path PYTHONPATH "/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-0.19.1-7hi7r5jri7bmohh4oontvfxo7rgj4hef/lib/python2.7/site-packages"
setenv PY_SCIPY_ROOT "/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-0.19.1-7hi7r5jri7bmohh4oontvfxo7rgj4hef"
and will contain code to autoload all the dependencies:
.. code-block:: console
root@module-file-tutorial:/# module load py-scipy
Autoloading python/2.7.14-gcc-7.2.0
Autoloading openblas/0.2.20-gcc-7.2.0
Autoloading py-numpy/1.13.1-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
root@module-file-tutorial:/# module avail
----------------------------------------------------------------------------- /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------------------------------------
bzip2/1.0.6-gcc-7.2.0 netlib-lapack/3.6.1-gcc-7.2.0 openblas/0.2.20-gcc-7.2.0 py-numpy/1.13.1-gcc-7.2.0-openblas py-six/1.10.0-gcc-7.2.0
cmake/3.9.4-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-netlib-mpich openmpi/1.10.2-gcc-7.2.0 py-packaging/16.8-gcc-7.2.0 python/2.7.14-gcc-7.2.0
gcc/7.2.0-gcc-5.4.0 netlib-scalapack/2.0.2-gcc-7.2.0-netlib-openmpi openssl/1.0.2k-gcc-7.2.0 py-pyparsing/2.2.0-gcc-7.2.0 readline/7.0-gcc-7.2.0
mpich/3.2-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-openblas-mpich pkg-config/0.29.2-gcc-7.2.0 py-scipy/0.19.1-gcc-7.2.0-openblas sqlite/3.20.0-gcc-7.2.0
ncurses/6.0-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-openblas-openmpi (D) py-appdirs/1.4.3-gcc-7.2.0 py-setuptools/35.0.2-gcc-7.2.0 zlib/1.2.11-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".
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
root@module-file-tutorial:/# module load netlib-lapack/3.6.1-gcc-7.2.0 openblas/0.2.20-gcc-7.2.0
root@module-file-tutorial:/# module list
Currently Loaded Modules:
1) netlib-lapack/3.6.1-gcc-7.2.0 2) openblas/0.2.20-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
root@module-file-tutorial:/# spack module refresh --module-type lmod --delete-tree -y
==> Regenerating lmod module files
and update ``MODULEPATH`` to point to the ``Core``:
.. code-block:: console
root@module-file-tutorial:/# module unuse /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64
root@module-file-tutorial:/# module use /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/Core
asking for the available modules will return:
.. code-block:: console
root@module-file-tutorial:/# module avail
---------------------------------------------------------------------------- /usr/local/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
root@module-file-tutorial:/# module load gcc
root@module-file-tutorial:/# module avail
------------------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------------------------------------
bzip2/1.0.6 mpich/3.2 netlib-lapack/3.6.1 openmpi/1.10.2 pkg-config/0.29.2 py-numpy/1.13.1-openblas py-pyparsing/2.2.0 py-setuptools/35.0.2 python/2.7.14 sqlite/3.20.0
cmake/3.9.4 ncurses/6.0 openblas/0.2.20 openssl/1.0.2k py-appdirs/1.4.3 py-packaging/16.8 py-scipy/0.19.1-openblas py-six/1.10.0 readline/7.0 zlib/1.2.11
---------------------------------------------------------------------------- /usr/local/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
root@module-file-tutorial:/# module load mpich
root@module-file-tutorial:/# module avail
---------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/mpich/3.2-7gxffhv/gcc/7.2.0 -----------------------------------------------------------------
netlib-scalapack/2.0.2-netlib netlib-scalapack/2.0.2-openblas (D)
------------------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------------------------------------
bzip2/1.0.6 mpich/3.2 (L) netlib-lapack/3.6.1 openmpi/1.10.2 pkg-config/0.29.2 py-numpy/1.13.1-openblas py-pyparsing/2.2.0 py-setuptools/35.0.2 python/2.7.14 sqlite/3.20.0
cmake/3.9.4 ncurses/6.0 openblas/0.2.20 openssl/1.0.2k py-appdirs/1.4.3 py-packaging/16.8 py-scipy/0.19.1-openblas py-six/1.10.0 readline/7.0 zlib/1.2.11
---------------------------------------------------------------------------- /usr/local/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 3) openblas/0.2.20 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
root@module-file-tutorial:/# module load openmpi
Lmod is automatically replacing "mpich/3.2" with "openmpi/1.10.2".
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/0.2.20 3) openmpi/1.10.2 4) netlib-scalapack/2.0.2-openblas
root@module-file-tutorial:/# module load netlib-scalapack/2.0.2-netlib
Autoloading netlib-lapack/3.6.1
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/0.2.20 3) openmpi/1.10.2 4) netlib-lapack/3.6.1 5) 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'
- 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'
After module files have been regenerated as usual:
.. code-block:: console
root@module-file-tutorial:/# module purge
root@module-file-tutorial:/# spack module refresh --delete-tree -y -m lmod
==> Regenerating lmod module files
we can see that now we have additional components in the hierarchy:
.. code-block:: console
root@module-file-tutorial:/# module load gcc
root@module-file-tutorial:/# module load openblas
root@module-file-tutorial:/# module avail
------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/openblas/0.2.20-kvddide/gcc/7.2.0 --------------------------------------------------------------
py-numpy/1.13.1 py-scipy/0.19.1
------------------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------------------------------------
bzip2/1.0.6 mpich/3.2 netlib-lapack/3.6.1 openmpi/1.10.2 pkg-config/0.29.2 py-packaging/16.8 py-setuptools/35.0.2 python/2.7.14 sqlite/3.20.0
cmake/3.9.4 ncurses/6.0 openblas/0.2.20 (L) openssl/1.0.2k py-appdirs/1.4.3 py-pyparsing/2.2.0 py-six/1.10.0 readline/7.0 zlib/1.2.11
---------------------------------------------------------------------------- /usr/local/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".
root@module-file-tutorial:/# module load openmpi
root@module-file-tutorial:/# module avail
-------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/openmpi/1.10.2-ufw7pdi/openblas/0.2.20-kvddide/gcc/7.2.0 --------------------------------------------------
netlib-scalapack/2.0.2
------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/openblas/0.2.20-kvddide/gcc/7.2.0 --------------------------------------------------------------
py-numpy/1.13.1 py-scipy/0.19.1
------------------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------------------------------------
bzip2/1.0.6 mpich/3.2 netlib-lapack/3.6.1 openmpi/1.10.2 (L) pkg-config/0.29.2 py-packaging/16.8 py-setuptools/35.0.2 python/2.7.14 sqlite/3.20.0
cmake/3.9.4 ncurses/6.0 openblas/0.2.20 (L) openssl/1.0.2k py-appdirs/1.4.3 py-pyparsing/2.2.0 py-six/1.10.0 readline/7.0 zlib/1.2.11
---------------------------------------------------------------------------- /usr/local/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
root@module-file-tutorial:/# module load py-numpy netlib-scalapack
root@module-file-tutorial:/# module load mpich
Lmod is automatically replacing "openmpi/1.10.2" with "mpich/3.2".
Due to MODULEPATH changes, the following have been reloaded:
1) netlib-scalapack/2.0.2
root@module-file-tutorial:/# module load netlib-lapack
Lmod is automatically replacing "openblas/0.2.20" with "netlib-lapack/3.6.1".
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
``templates/module`` directory, 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:: ../../../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:: ../../../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 refresh -y -m lmod 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-ax6aza6vyepceyr3fihewp7rbr2vp7ym") 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!
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