module files tutorial : first complete draft (#2228)
* module files tutorial : first complete draft - first complete draft for module files tutorial - minor corrections to module file reference * module file tutorial : first batch of corrections - module avail spelled out fully - typos from @adamjstewart - rewording of a few sentences * module file tutorial : first batch of corrections - emphasized lines in yaml files * module file tutorial : fixes according to @citibeth and @adamjstewart reviews - used long format for command options - reworded unclear sentence on tokes - reworked table in reference manual to make it clearer * module file tutorial : implemented corrections collected on site from @schlyfts * module file tutorial : removed comment (@hartzell suggestion)
This commit is contained in:
Massimiliano Culpo
Todd Gamblin
parent
ee6eb508cb
commit
401b4cb137
3 changed files with 1009 additions and 27 deletions
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@ -46,6 +46,7 @@ or refer to the full manual below.
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getting_started
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basic_usage
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workflows
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module_file_tutorial
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.. toctree::
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:maxdepth: 2
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@ -1,8 +1,8 @@
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.. _modules:
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=====================================
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=======
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Modules
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=====================================
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=======
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The use of module systems to manage user environment in a controlled way
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is a common practice at HPC centers that is often embraced also by individual
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@ -24,6 +24,8 @@ directly with automatically generated module files.
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we advise you to use either Environment Modules or LMod. See :ref:`InstallEnvironmentModules`
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for more details.
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.. _shell_support:
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-------------
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Shell support
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-------------
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@ -110,9 +112,9 @@ you could type either of these commands to load the callpath module:
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.. _cmd-spack-load:
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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^^^^^^^^^^^^^^^^^^^^^^^
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``spack load / unload``
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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^^^^^^^^^^^^^^^^^^^^^^^
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Neither of these is particularly pretty, easy to remember, or
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easy to type. Luckily, Spack has its own interface for using modules
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@ -161,9 +163,9 @@ want to use a package, you can type unload or unuse similarly:
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only available if you have enabled Spack's shell support *and* you
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have dotkit or modules installed on your machine.
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^^^^^^^^^^^^^^^^^^^^^^^^^
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^^^^^^^^^^^^^^^^^^^^^^
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Ambiguous module names
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^^^^^^^^^^^^^^^^^^^^^^^^^
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^^^^^^^^^^^^^^^^^^^^^^
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If a spec used with load/unload or use/unuse is ambiguous (i.e. more
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than one installed package matches it), then Spack will warn you:
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@ -294,23 +296,24 @@ For example, consider the following on one system:
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# antlr@2.7.7%gcc@5.3.0~csharp+cxx~java~python arch=linux-SuSE11-x86_64
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module load linux-SuSE11-x86_64/antlr-2.7.7-gcc-5.3.0-bdpl46y
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-----------------------------
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----------------------------
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Auto-generating Module Files
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-----------------------------
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----------------------------
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Module files are generated by post-install hooks after the successful
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installation of a package. They are placed in the following directories
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under the Spack root:
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installation of a package. The following table summarizes the essential
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information associated with the different file formats
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that can be generated by Spack:
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+----------------------------------------+------------------------------------+------------------------+
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| | **Module Files Root directory** | **Compatible systems** |
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+========================================+====================================+========================+
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| **Dotkit Module Files** | share/spack/dotkit | DotKit |
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+----------------------------------------+------------------------------------+------------------------+
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| **Non-Hierarchical TCL Module Files** | share/spack/modules | Env. Modules/LMod |
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+----------------------------------------+------------------------------------+------------------------+
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| **Lua Hierarchical Module Files** | share/spack/lmod | LMod |
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+----------------------------------------+------------------------------------+------------------------+
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+-----------------------------+--------------------+-------------------------------+----------------------+
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| | **Hook name** | **Default root directory** | **Compatible tools** |
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+=============================+====================+===============================+======================+
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| **Dotkit** | ``dotkit`` | share/spack/dotkit | DotKit |
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+-----------------------------+--------------------+-------------------------------+----------------------+
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| **TCL - Non-Hierarchical** | ``tcl`` | share/spack/modules | Env. Modules/LMod |
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+-----------------------------+--------------------+-------------------------------+----------------------+
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| **Lua - Hierarchical** | ``lmod`` | share/spack/lmod | LMod |
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+-----------------------------+--------------------+-------------------------------+----------------------+
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Though Spack ships with sensible defaults for the generation of module files,
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@ -324,9 +327,9 @@ The former method fits best cases that are site independent, e.g. injecting vari
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from language interpreters into their extensions. The latter instead permits to
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fine tune the content, naming and creation of module files to meet site specific conventions.
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^^^^^^^^^^^^^^^^^^^^^^^^^^^
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^^^^^^^^^^^^^^^^^^^^
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``Package`` file API
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^^^^^^^^^^^^^^^^^^^^^^^^^^^
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^^^^^^^^^^^^^^^^^^^^
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There are two methods that can be overridden in any ``package.py`` to affect the
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content of generated module files. The first one is:
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@ -376,9 +379,9 @@ and has similar effects on module file of dependees. Even in this case
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.. _modules-yaml:
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----------------------------------
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---------------------------------
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Configuration in ``modules.yaml``
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----------------------------------
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---------------------------------
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The name of the configuration file that controls module generation behavior
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is ``modules.yaml``. The default configuration:
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@ -426,6 +429,8 @@ All these module sections allow for both:
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For the latter point in particular it is possible to use anonymous specs
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to select an appropriate set of packages on which the modifications should be applied.
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.. _anonymous_specs:
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Selection by anonymous specs
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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@ -544,7 +549,7 @@ most likely via the ``+blas`` variant specification.
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modules:
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tcl:
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naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVERSION}'
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naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVER}'
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all:
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conflict: ['${PACKAGE}', 'intel/14.0.1']
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@ -660,9 +665,9 @@ before regeneration if the change in layout is radical.
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.. _cmd-spack-module-rm:
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^^^^^^^^^^^^^^^^^^^^^^^^
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^^^^^^^^^^^^^^^^^^^
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``spack module rm``
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^^^^^^^^^^^^^^^^^^^^^^^^
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^^^^^^^^^^^^^^^^^^^
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If instead what you need is just to delete a few module files, then the right
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command is ``module rm``:
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@ -670,7 +675,8 @@ command is ``module rm``:
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.. command-output:: spack module rm --help
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.. note::
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We care about your module files! Every modification done on modules
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We care about your module files!
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Every modification done on modules
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that are already existing will ask for a confirmation by default. If
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the command is used in a script it is possible though to pass the
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``-y`` argument, that will skip this safety measure.
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975
lib/spack/docs/module_file_tutorial.rst
Normal file
975
lib/spack/docs/module_file_tutorial.rst
Normal file
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@ -0,0 +1,975 @@
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.. _module_tutorial:
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=======
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Modules
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=======
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This tutorial will guide you through the customization of both
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content and naming of module files generated by Spack.
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Starting from the default Spack settings you will add an increasing
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number of directives to the ``modules.yaml`` configuration file to
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satisfy a number of constraints that mimic those that you may encounter
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in a typical production environment at HPC sites.
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Even though the focus will be for the most part on customizing
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TCL non-hierarchical module files, everything
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you'll see applies also to other kinds of module files generated by Spack.
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The generation of Lua hierarchical
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module files will be addressed at the end of the tutorial,
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and you'll see that with minor modifications
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to an existing ``modules.yaml`` written for TCL
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non-hierarchical modules you'll get almost
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for free the possibility to try a hierarchical layout.
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Let's start!
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.. _module_file_tutorial_prerequisites:
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-------------
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Prerequisites
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-------------
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Before proceeding further ensure:
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- you have LMod or Environment Modules available
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- have :ref:`shell support <shell_support>` activated in Spack
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If you need to install Lmod or Environment module you can refer
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to the documentation :ref:`here <InstallEnvironmentModules>`.
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^^^^^^^^^^^^^^^^^^
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Add a new compiler
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^^^^^^^^^^^^^^^^^^
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Spack automatically scans the environment to search for available
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compilers on first use. On a Ubuntu 14.04 a fresh clone will show
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something like this:
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.. code-block:: console
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$ uname -a
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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
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$ spack compilers
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==> Available compilers
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-- gcc ----------------------------------------------------------
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gcc@4.8
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For the purpose of building a limited set of packages with some features
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that will help showcasing the capabilities of
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module customization the first thing we need is to build a new compiler:
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.. code-block:: console
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$ spack install gcc@6.2.0
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# ...
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# Wait a long time
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# ...
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Then we can use shell support for modules to add it to the list of known compilers:
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.. code-block:: console
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# The name of the generated module may vary
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$ module load gcc-6.2.0-gcc-4.8-twd5nqg
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$ spack compiler add
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==> Added 1 new compiler to /home/mculpo/.spack/linux/compilers.yaml
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gcc@6.2.0
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$ spack compilers
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==> Available compilers
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-- gcc ----------------------------------------------------------
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gcc@6.2.0 gcc@4.8
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Note that the final 7 digits hash at the end of the generated module may vary depending
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on architecture or package version.
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Build software that will be used in the tutorial
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Next you should install a few modules that will be used in the tutorial:
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.. code-block:: console
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$ spack install netlib-scalapack ^openmpi ^openblas
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# ...
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The packages you need to install are:
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- ``netlib-scalapack ^openmpi ^openblas``
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- ``netlib-scalapack ^mpich ^openblas``
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- ``netlib-scalapack ^openmpi ^netlib-lapack``
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- ``netlib-scalapack ^mpich ^netlib-lapack``
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- ``py-scipy ^openblas``
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In the end your environment should look something like:
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.. code-block:: console
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$ module avail
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------------------------------------------------------------------------ /home/mculpo/wdir/spack/share/spack/modules/linux-Ubuntu14-x86_64 ------------------------------------------------------------------------
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binutils-2.27-gcc-4.8-dz3xevw libpciaccess-0.13.4-gcc-6.2.0-eo2siet lzo-2.09-gcc-6.2.0-jcngz72 netlib-scalapack-2.0.2-gcc-6.2.0-wnimqhw python-2.7.12-gcc-6.2.0-qu7rc5p
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bzip2-1.0.6-gcc-6.2.0-csoc2mq libsigsegv-2.10-gcc-4.8-avb6azw m4-1.4.17-gcc-4.8-iggewke netlib-scalapack-2.0.2-gcc-6.2.0-wojunhq sqlite-3.8.5-gcc-6.2.0-td3zfe7
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cmake-3.5.2-gcc-6.2.0-6poypqg libsigsegv-2.10-gcc-6.2.0-g3qpmbi m4-1.4.17-gcc-6.2.0-lhgqa6s nettle-3.2-gcc-6.2.0-djdthlh tcl-8.6.5-gcc-4.8-atddxu7
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curl-7.50.3-gcc-6.2.0-2ffacqm libtool-2.4.6-gcc-6.2.0-kiepac6 mpc-1.0.3-gcc-4.8-lylv7lk openblas-0.2.19-gcc-6.2.0-js33umc util-macros-1.19.0-gcc-6.2.0-uoukuqk
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expat-2.2.0-gcc-6.2.0-bxqnjar libxml2-2.9.4-gcc-6.2.0-3k4ykbe mpfr-3.1.4-gcc-4.8-bldfx3w openmpi-2.0.1-gcc-6.2.0-s3qbtby xz-5.2.2-gcc-6.2.0-t5lk6in
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gcc-6.2.0-gcc-4.8-twd5nqg lmod-6.4.5-gcc-4.8-7v7bh7b mpich-3.2-gcc-6.2.0-5n5xoep openssl-1.0.2j-gcc-6.2.0-hibnfda zlib-1.2.8-gcc-4.8-bds4ies
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gmp-6.1.1-gcc-4.8-uq52e2n lua-5.3.2-gcc-4.8-xozf2hx ncurses-6.0-gcc-4.8-u62fit4 pkg-config-0.29.1-gcc-6.2.0-rslsgcs zlib-1.2.8-gcc-6.2.0-asydrba
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gmp-6.1.1-gcc-6.2.0-3cfh3hi lua-luafilesystem-1_6_3-gcc-4.8-sbzejlz ncurses-6.0-gcc-6.2.0-7tb426s py-nose-1.3.7-gcc-6.2.0-4gl5c42
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hwloc-1.11.4-gcc-6.2.0-3ostwel lua-luaposix-33.4.0-gcc-4.8-xf7y2p5 netlib-lapack-3.6.1-gcc-6.2.0-mirer2l py-numpy-1.11.1-gcc-6.2.0-i3rpk4e
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isl-0.14-gcc-4.8-cq73t5m lz4-131-gcc-6.2.0-cagoem4 netlib-scalapack-2.0.2-gcc-6.2.0-6bqlxqy py-scipy-0.18.1-gcc-6.2.0-e6uljfi
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libarchive-3.2.1-gcc-6.2.0-2b54aos lzma-4.32.7-gcc-6.2.0-sfmeynw netlib-scalapack-2.0.2-gcc-6.2.0-hpqb3dp py-setuptools-25.2.0-gcc-6.2.0-hkqauaa
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------------------------------------------------
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Filter unwanted modifications to the environment
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------------------------------------------------
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The non-hierarchical TCL module files that have been generated so far
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follow the default rules for module generation, which are given
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:ref:`here <modules-yaml>` in the reference part of the manual. Taking a
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look at the ``gcc`` module you'll see something like:
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.. code-block:: console
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$ module show gcc-6.2.0-gcc-4.8-twd5nqg
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---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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/home/mculpo/wdir/spack/share/spack/modules/linux-Ubuntu14-x86_64/gcc-6.2.0-gcc-4.8-twd5nqg:
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---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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whatis("gcc @6.2.0 ")
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prepend_path("PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/bin")
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prepend_path("CMAKE_PREFIX_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/")
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prepend_path("MANPATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/share/man")
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prepend_path("PKG_CONFIG_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64/pkgconfig")
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prepend_path("LIBRARY_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64")
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prepend_path("LD_LIBRARY_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64")
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prepend_path("CPATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/include")
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help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
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Fortran, and Java.
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]])
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As expected, a few environment variables representing paths will be modified
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by the modules according to the default prefix inspection rules.
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Consider now the case that your site has decided that e.g. ``CPATH`` and
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``LIBRARY_PATH`` modifications should not be present in module files. What you can
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do to abide by the rules is to create a configuration file ``~/.spack/modules.yaml``
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with the following content:
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.. code-block:: yaml
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modules:
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tcl:
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all:
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filter:
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environment_blacklist: ['CPATH', 'LIBRARY_PATH']
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Next you should regenerate all the module files:
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.. code-block:: console
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$ spack module refresh --module-type tcl
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==> You are about to regenerate tcl module files for:
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-- linux-Ubuntu14-x86_64 / gcc@4.8 ------------------------------
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dz3xevw binutils@2.27 uq52e2n gmp@6.1.1 avb6azw libsigsegv@2.10 xozf2hx lua@5.3.2 xf7y2p5 lua-luaposix@33.4.0 lylv7lk mpc@1.0.3 u62fit4 ncurses@6.0 bds4ies zlib@1.2.8
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twd5nqg gcc@6.2.0 cq73t5m isl@0.14 7v7bh7b lmod@6.4.5 sbzejlz lua-luafilesystem@1_6_3 iggewke m4@1.4.17 bldfx3w mpfr@3.1.4 atddxu7 tcl@8.6.5
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...
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==> Do you want to proceed ? [y/n]
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y
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==> Regenerating tcl module files
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If you take a look now at the module for ``gcc`` you'll see that the unwanted
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paths have disappeared:
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.. code-block:: console
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$ module show gcc-6.2.0-gcc-4.8-twd5nqg
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---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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/home/mculpo/wdir/spack/share/spack/modules/linux-Ubuntu14-x86_64/gcc-6.2.0-gcc-4.8-twd5nqg:
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---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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whatis("gcc @6.2.0 ")
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prepend_path("PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/bin")
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prepend_path("CMAKE_PREFIX_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/")
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prepend_path("MANPATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/share/man")
|
||||
prepend_path("PKG_CONFIG_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64/pkgconfig")
|
||||
prepend_path("LD_LIBRARY_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64")
|
||||
help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
|
||||
Fortran, and Java.
|
||||
]])
|
||||
|
||||
----------------------------------------------
|
||||
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@4.8`` (the OS provided compiler).
|
||||
|
||||
To do this you should add a ``blacklist`` keyword to the configuration file:
|
||||
|
||||
.. code-block:: yaml
|
||||
:emphasize-lines: 3,4
|
||||
|
||||
modules:
|
||||
tcl:
|
||||
blacklist:
|
||||
- '%gcc@4.8'
|
||||
all:
|
||||
filter:
|
||||
environment_blacklist: ['CPATH', 'LIBRARY_PATH']
|
||||
|
||||
and regenerate the module files:
|
||||
|
||||
.. code-block:: console
|
||||
|
||||
$ spack module refresh --module-type tcl --delete-tree
|
||||
==> You are about to regenerate tcl module files for:
|
||||
|
||||
-- linux-Ubuntu14-x86_64 / gcc@4.8 ------------------------------
|
||||
dz3xevw binutils@2.27 uq52e2n gmp@6.1.1 avb6azw libsigsegv@2.10 xozf2hx lua@5.3.2 xf7y2p5 lua-luaposix@33.4.0 lylv7lk mpc@1.0.3 u62fit4 ncurses@6.0 bds4ies zlib@1.2.8
|
||||
twd5nqg gcc@6.2.0 cq73t5m isl@0.14 7v7bh7b lmod@6.4.5 sbzejlz lua-luafilesystem@1_6_3 iggewke m4@1.4.17 bldfx3w mpfr@3.1.4 atddxu7 tcl@8.6.5
|
||||
|
||||
-- linux-Ubuntu14-x86_64 / gcc@6.2.0 ----------------------------
|
||||
csoc2mq bzip2@1.0.6 2b54aos libarchive@3.2.1 sfmeynw lzma@4.32.7 wnimqhw netlib-scalapack@2.0.2 s3qbtby openmpi@2.0.1 hkqauaa py-setuptools@25.2.0
|
||||
6poypqg cmake@3.5.2 eo2siet libpciaccess@0.13.4 jcngz72 lzo@2.09 6bqlxqy netlib-scalapack@2.0.2 hibnfda openssl@1.0.2j qu7rc5p python@2.7.12
|
||||
2ffacqm curl@7.50.3 g3qpmbi libsigsegv@2.10 lhgqa6s m4@1.4.17 wojunhq netlib-scalapack@2.0.2 rslsgcs pkg-config@0.29.1 td3zfe7 sqlite@3.8.5
|
||||
bxqnjar expat@2.2.0 kiepac6 libtool@2.4.6 5n5xoep mpich@3.2 hpqb3dp netlib-scalapack@2.0.2 4gl5c42 py-nose@1.3.7 uoukuqk util-macros@1.19.0
|
||||
3cfh3hi gmp@6.1.1 3k4ykbe libxml2@2.9.4 7tb426s ncurses@6.0 djdthlh nettle@3.2 i3rpk4e py-numpy@1.11.1 t5lk6in xz@5.2.2
|
||||
3ostwel hwloc@1.11.4 cagoem4 lz4@131 mirer2l netlib-lapack@3.6.1 js33umc openblas@0.2.19 e6uljfi py-scipy@0.18.1 asydrba zlib@1.2.8
|
||||
|
||||
==> Do you want to proceed ? [y/n]
|
||||
y
|
||||
|
||||
$ module avail
|
||||
|
||||
------------------------------------------------------------------------ /home/mculpo/wdir/spack/share/spack/modules/linux-Ubuntu14-x86_64 ------------------------------------------------------------------------
|
||||
bzip2-1.0.6-gcc-6.2.0-csoc2mq libsigsegv-2.10-gcc-6.2.0-g3qpmbi ncurses-6.0-gcc-6.2.0-7tb426s openmpi-2.0.1-gcc-6.2.0-s3qbtby sqlite-3.8.5-gcc-6.2.0-td3zfe7
|
||||
cmake-3.5.2-gcc-6.2.0-6poypqg libtool-2.4.6-gcc-6.2.0-kiepac6 netlib-lapack-3.6.1-gcc-6.2.0-mirer2l openssl-1.0.2j-gcc-6.2.0-hibnfda util-macros-1.19.0-gcc-6.2.0-uoukuqk
|
||||
curl-7.50.3-gcc-6.2.0-2ffacqm libxml2-2.9.4-gcc-6.2.0-3k4ykbe netlib-scalapack-2.0.2-gcc-6.2.0-6bqlxqy pkg-config-0.29.1-gcc-6.2.0-rslsgcs xz-5.2.2-gcc-6.2.0-t5lk6in
|
||||
expat-2.2.0-gcc-6.2.0-bxqnjar lz4-131-gcc-6.2.0-cagoem4 netlib-scalapack-2.0.2-gcc-6.2.0-hpqb3dp py-nose-1.3.7-gcc-6.2.0-4gl5c42 zlib-1.2.8-gcc-6.2.0-asydrba
|
||||
gmp-6.1.1-gcc-6.2.0-3cfh3hi lzma-4.32.7-gcc-6.2.0-sfmeynw netlib-scalapack-2.0.2-gcc-6.2.0-wnimqhw py-numpy-1.11.1-gcc-6.2.0-i3rpk4e
|
||||
hwloc-1.11.4-gcc-6.2.0-3ostwel lzo-2.09-gcc-6.2.0-jcngz72 netlib-scalapack-2.0.2-gcc-6.2.0-wojunhq py-scipy-0.18.1-gcc-6.2.0-e6uljfi
|
||||
libarchive-3.2.1-gcc-6.2.0-2b54aos m4-1.4.17-gcc-6.2.0-lhgqa6s nettle-3.2-gcc-6.2.0-djdthlh py-setuptools-25.2.0-gcc-6.2.0-hkqauaa
|
||||
libpciaccess-0.13.4-gcc-6.2.0-eo2siet mpich-3.2-gcc-6.2.0-5n5xoep openblas-0.2.19-gcc-6.2.0-js33umc python-2.7.12-gcc-6.2.0-qu7rc5p
|
||||
|
||||
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 pay careful attention you'll see though that we went too far in blacklisting modules:
|
||||
the module for ``gcc@6.2.0`` disappeared as it was bootstrapped with ``gcc@4.8``. To specify
|
||||
exceptions to the blacklist rules you can use ``whitelist``:
|
||||
|
||||
.. code-block:: yaml
|
||||
:emphasize-lines: 3,4
|
||||
|
||||
modules:
|
||||
tcl:
|
||||
whitelist:
|
||||
- gcc
|
||||
blacklist:
|
||||
- '%gcc@4.8'
|
||||
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 refresh --module-type tcl -y
|
||||
|
||||
you'll see that now the module for ``gcc@6.2.0`` has reappeared:
|
||||
|
||||
.. code-block:: console
|
||||
|
||||
$ module avail gcc-6.2.0-gcc-4.8-twd5nqg
|
||||
|
||||
------------------------------------------------------------------------ /home/mculpo/wdir/spack/share/spack/modules/linux-Ubuntu14-x86_64 ------------------------------------------------------------------------
|
||||
gcc-6.2.0-gcc-4.8-twd5nqg
|
||||
|
||||
-------------------------
|
||||
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@4.8'
|
||||
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 refresh --module-type tcl --delete-tree -y
|
||||
==> Error: Name clashes detected in module files:
|
||||
|
||||
file : /home/mculpo/wdir/spack/share/spack/modules/linux-Ubuntu14-x86_64/netlib-scalapack-2.0.2-gcc-6.2.0
|
||||
spec : netlib-scalapack@2.0.2%gcc@6.2.0~fpic+shared arch=linux-Ubuntu14-x86_64
|
||||
spec : netlib-scalapack@2.0.2%gcc@6.2.0~fpic+shared arch=linux-Ubuntu14-x86_64
|
||||
spec : netlib-scalapack@2.0.2%gcc@6.2.0~fpic+shared arch=linux-Ubuntu14-x86_64
|
||||
spec : netlib-scalapack@2.0.2%gcc@6.2.0~fpic+shared arch=linux-Ubuntu14-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 have the possibility to add suffixes to differentiate them:
|
||||
|
||||
.. code-block:: yaml
|
||||
:emphasize-lines: 9-11,14-17
|
||||
|
||||
modules:
|
||||
tcl:
|
||||
hash_length: 0
|
||||
whitelist:
|
||||
- gcc
|
||||
blacklist:
|
||||
- '%gcc@4.8'
|
||||
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 applies only to a
|
||||
restricted set of packages using :ref:`anonymous specs <anonymous_specs>`.
|
||||
Regenerating module files now we obtain:
|
||||
|
||||
.. code-block:: console
|
||||
|
||||
$ spack module refresh --module-type tcl --delete-tree -y
|
||||
==> Regenerating tcl module files
|
||||
$ module avail
|
||||
|
||||
------------------------------------------------------------------------ /home/mculpo/wdir/spack/share/spack/modules/linux-Ubuntu14-x86_64 ------------------------------------------------------------------------
|
||||
bzip2-1.0.6-gcc-6.2.0 libpciaccess-0.13.4-gcc-6.2.0 mpich-3.2-gcc-6.2.0 openblas-0.2.19-gcc-6.2.0 python-2.7.12-gcc-6.2.0
|
||||
cmake-3.5.2-gcc-6.2.0 libsigsegv-2.10-gcc-6.2.0 ncurses-6.0-gcc-6.2.0 openmpi-2.0.1-gcc-6.2.0 sqlite-3.8.5-gcc-6.2.0
|
||||
curl-7.50.3-gcc-6.2.0 libtool-2.4.6-gcc-6.2.0 netlib-lapack-3.6.1-gcc-6.2.0 openssl-1.0.2j-gcc-6.2.0 util-macros-1.19.0-gcc-6.2.0
|
||||
expat-2.2.0-gcc-6.2.0 libxml2-2.9.4-gcc-6.2.0 netlib-scalapack-2.0.2-gcc-6.2.0-netlib-mpich pkg-config-0.29.1-gcc-6.2.0 xz-5.2.2-gcc-6.2.0
|
||||
gcc-6.2.0-gcc-4.8 lz4-131-gcc-6.2.0 netlib-scalapack-2.0.2-gcc-6.2.0-netlib-openmpi py-nose-1.3.7-gcc-6.2.0 zlib-1.2.8-gcc-6.2.0
|
||||
gmp-6.1.1-gcc-6.2.0 lzma-4.32.7-gcc-6.2.0 netlib-scalapack-2.0.2-gcc-6.2.0-openblas-mpich py-numpy-1.11.1-gcc-6.2.0-openblas
|
||||
hwloc-1.11.4-gcc-6.2.0 lzo-2.09-gcc-6.2.0 netlib-scalapack-2.0.2-gcc-6.2.0-openblas-openmpi py-scipy-0.18.1-gcc-6.2.0-openblas
|
||||
libarchive-3.2.1-gcc-6.2.0 m4-1.4.17-gcc-6.2.0 nettle-3.2-gcc-6.2.0 py-setuptools-25.2.0-gcc-6.2.0
|
||||
|
||||
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@4.8'
|
||||
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
|
||||
|
||||
$ module avail
|
||||
|
||||
------------------------------------------------------------------------ /home/mculpo/wdir/spack/share/spack/modules/linux-Ubuntu14-x86_64 ------------------------------------------------------------------------
|
||||
bzip2/1.0.6-gcc-6.2.0 libpciaccess/0.13.4-gcc-6.2.0 mpich/3.2-gcc-6.2.0 openblas/0.2.19-gcc-6.2.0 python/2.7.12-gcc-6.2.0
|
||||
cmake/3.5.2-gcc-6.2.0 libsigsegv/2.10-gcc-6.2.0 ncurses/6.0-gcc-6.2.0 openmpi/2.0.1-gcc-6.2.0 sqlite/3.8.5-gcc-6.2.0
|
||||
curl/7.50.3-gcc-6.2.0 libtool/2.4.6-gcc-6.2.0 netlib-lapack/3.6.1-gcc-6.2.0 openssl/1.0.2j-gcc-6.2.0 util-macros/1.19.0-gcc-6.2.0
|
||||
expat/2.2.0-gcc-6.2.0 libxml2/2.9.4-gcc-6.2.0 netlib-scalapack/2.0.2-gcc-6.2.0-netlib-mpich pkg-config/0.29.1-gcc-6.2.0 xz/5.2.2-gcc-6.2.0
|
||||
gcc/6.2.0-gcc-4.8 lz4/131-gcc-6.2.0 netlib-scalapack/2.0.2-gcc-6.2.0-netlib-openmpi py-nose/1.3.7-gcc-6.2.0 zlib/1.2.8-gcc-6.2.0
|
||||
gmp/6.1.1-gcc-6.2.0 lzma/4.32.7-gcc-6.2.0 netlib-scalapack/2.0.2-gcc-6.2.0-openblas-mpich py-numpy/1.11.1-gcc-6.2.0-openblas
|
||||
hwloc/1.11.4-gcc-6.2.0 lzo/2.09-gcc-6.2.0 netlib-scalapack/2.0.2-gcc-6.2.0-openblas-openmpi (D) py-scipy/0.18.1-gcc-6.2.0-openblas
|
||||
libarchive/3.2.1-gcc-6.2.0 m4/1.4.17-gcc-6.2.0 nettle/3.2-gcc-6.2.0 py-setuptools/25.2.0-gcc-6.2.0
|
||||
|
||||
.. note::
|
||||
TCL specific directive
|
||||
The directives ``naming_scheme`` and ``conflict`` are TCL specific and do not apply
|
||||
to the ``dotkit`` or ``lmod`` sections in the configuration file.
|
||||
|
||||
------------------------------------
|
||||
Add custom environment modifications
|
||||
------------------------------------
|
||||
|
||||
At many sites it is customary to set in module file for packages
|
||||
an environment variable that points to the root folder where the package
|
||||
is installed. You can achieve this using 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@4.8'
|
||||
all:
|
||||
conflict:
|
||||
- '${PACKAGE}'
|
||||
suffixes:
|
||||
'^openblas': openblas
|
||||
'^netlib-lapack': netlib
|
||||
filter:
|
||||
environment_blacklist: ['CPATH', 'LIBRARY_PATH']
|
||||
environment:
|
||||
set:
|
||||
'${PACKAGE}_ROOT': '${PREFIX}'
|
||||
netlib-scalapack:
|
||||
suffixes:
|
||||
'^openmpi': openmpi
|
||||
'^mpich': mpich
|
||||
|
||||
There are many variable tokens available to use in the ``environment``
|
||||
and ``naming_scheme`` directives, such as ``${PACKAGE}``,
|
||||
``${VERSION}``, etc. (see :meth:`~spack.spec.Spec.format` API documentation
|
||||
for the complete list).
|
||||
|
||||
Regenerating the module files should result in:
|
||||
|
||||
.. code-block:: console
|
||||
:emphasize-lines: 14
|
||||
|
||||
$ spack module refresh -y --module-type tcl
|
||||
==> Regenerating tcl module files
|
||||
|
||||
$ module show gcc
|
||||
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|
||||
/home/mculpo/wdir/spack/share/spack/modules/linux-Ubuntu14-x86_64/gcc/6.2.0-gcc-4.8:
|
||||
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|
||||
whatis("gcc @6.2.0 ")
|
||||
prepend_path("PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/bin")
|
||||
prepend_path("CMAKE_PREFIX_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/")
|
||||
prepend_path("MANPATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/share/man")
|
||||
prepend_path("PKG_CONFIG_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64/pkgconfig")
|
||||
prepend_path("LD_LIBRARY_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64")
|
||||
setenv("GCC_ROOT","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u")
|
||||
conflict("gcc")
|
||||
help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
|
||||
Fortran, and Java.
|
||||
]])
|
||||
|
||||
As you 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@4.8'
|
||||
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 refresh -y --module-type tcl gcc
|
||||
==> Regenerating tcl module files
|
||||
|
||||
$ spack module refresh -y --module-type tcl openmpi
|
||||
==> Regenerating tcl module files
|
||||
|
||||
$ module show gcc
|
||||
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|
||||
/home/mculpo/wdir/spack/share/spack/modules/linux-Ubuntu14-x86_64/gcc/6.2.0-gcc-4.8:
|
||||
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|
||||
whatis("gcc @6.2.0 ")
|
||||
prepend_path("PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/bin")
|
||||
prepend_path("CMAKE_PREFIX_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/")
|
||||
prepend_path("MANPATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/share/man")
|
||||
prepend_path("PKG_CONFIG_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64/pkgconfig")
|
||||
prepend_path("LD_LIBRARY_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64")
|
||||
setenv("GCC_ROOT","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u")
|
||||
setenv("CC","gcc")
|
||||
setenv("CXX","g++")
|
||||
setenv("F90","gfortran")
|
||||
setenv("FC","gfortran")
|
||||
setenv("F77","gfortran")
|
||||
conflict("gcc")
|
||||
help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
|
||||
Fortran, and Java.
|
||||
]])
|
||||
|
||||
$ module show openmpi
|
||||
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|
||||
/home/mculpo/wdir/spack/share/spack/modules/linux-Ubuntu14-x86_64/openmpi/2.0.1-gcc-6.2.0:
|
||||
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|
||||
whatis("openmpi @2.0.1 ")
|
||||
prepend_path("PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/openmpi-2.0.1-s3qbtbyh3y5y4gkchmhcuak7th44l53w/bin")
|
||||
prepend_path("CMAKE_PREFIX_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/openmpi-2.0.1-s3qbtbyh3y5y4gkchmhcuak7th44l53w/")
|
||||
prepend_path("LD_LIBRARY_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/openmpi-2.0.1-s3qbtbyh3y5y4gkchmhcuak7th44l53w/lib")
|
||||
prepend_path("PKG_CONFIG_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/openmpi-2.0.1-s3qbtbyh3y5y4gkchmhcuak7th44l53w/lib/pkgconfig")
|
||||
prepend_path("MANPATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/openmpi-2.0.1-s3qbtbyh3y5y4gkchmhcuak7th44l53w/share/man")
|
||||
setenv("SLURM_MPI_TYPE","pmi2")
|
||||
setenv("OMPI_MCA_BTL_OPENIB_WARN_DEFAULT_GID_PREFIX","0")
|
||||
setenv("OPENMPI_ROOT","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/openmpi-2.0.1-s3qbtbyh3y5y4gkchmhcuak7th44l53w")
|
||||
conflict("openmpi")
|
||||
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:
|
||||
|
||||
.. code-block:: yaml
|
||||
:emphasize-lines: 37,38
|
||||
|
||||
modules:
|
||||
tcl:
|
||||
hash_length: 0
|
||||
naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVER}'
|
||||
whitelist:
|
||||
- gcc
|
||||
blacklist:
|
||||
- '%gcc@4.8'
|
||||
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
|
||||
|
||||
$ 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/LLNL/spack) on 2016-11-02 20:53:21.283547
|
||||
##
|
||||
## py-scipy@0.18.1%gcc@6.2.0 arch=linux-Ubuntu14-x86_64-e6uljfi
|
||||
##
|
||||
module-whatis "py-scipy @0.18.1"
|
||||
|
||||
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/2.7.12-gcc-6.2.0 ] {
|
||||
puts stderr "Autoloading python/2.7.12-gcc-6.2.0"
|
||||
module load python/2.7.12-gcc-6.2.0
|
||||
}
|
||||
|
||||
if ![ is-loaded openblas/0.2.19-gcc-6.2.0 ] {
|
||||
puts stderr "Autoloading openblas/0.2.19-gcc-6.2.0"
|
||||
module load openblas/0.2.19-gcc-6.2.0
|
||||
}
|
||||
|
||||
if ![ is-loaded py-numpy/1.11.1-gcc-6.2.0-openblas ] {
|
||||
puts stderr "Autoloading py-numpy/1.11.1-gcc-6.2.0-openblas"
|
||||
module load py-numpy/1.11.1-gcc-6.2.0-openblas
|
||||
}
|
||||
|
||||
prepend-path CMAKE_PREFIX_PATH "/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/py-scipy-0.18.1-e6uljfiffgym4xvj6wveevqxfqnfb3gh/"
|
||||
prepend-path LD_LIBRARY_PATH "/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/py-scipy-0.18.1-e6uljfiffgym4xvj6wveevqxfqnfb3gh/lib"
|
||||
prepend-path PYTHONPATH "/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/py-scipy-0.18.1-e6uljfiffgym4xvj6wveevqxfqnfb3gh/lib/python2.7/site-packages"
|
||||
setenv PY_SCIPY_ROOT "/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/py-scipy-0.18.1-e6uljfiffgym4xvj6wveevqxfqnfb3gh"
|
||||
conflict py-scipy
|
||||
|
||||
and will contain code to autoload all the dependencies:
|
||||
|
||||
.. code-block:: console
|
||||
|
||||
$ module load py-scipy
|
||||
Autoloading python/2.7.12-gcc-6.2.0
|
||||
Autoloading openblas/0.2.19-gcc-6.2.0
|
||||
Autoloading py-numpy/1.11.1-gcc-6.2.0-openblas
|
||||
|
||||
-----------------------------
|
||||
Lua hierarchical module files
|
||||
-----------------------------
|
||||
|
||||
In the final part of this tutorial you will modify ``modules.yaml`` to generate
|
||||
Lua hierarchical module files. You will see that most of the directives used before
|
||||
are also valid in the ``lmod`` context.
|
||||
|
||||
^^^^^^^^^^^^^^^^^
|
||||
Core/Compiler/MPI
|
||||
^^^^^^^^^^^^^^^^^
|
||||
|
||||
.. warning::
|
||||
Only LMod supports Lua hierarchical module files
|
||||
For this part of the tutorial you need to have LMod as a tool to
|
||||
manage your environment.
|
||||
|
||||
The most common hierarchy is the so called ``Core/Compiler/MPI``. To have an idea
|
||||
how a hierarchy is organized you may refer to the
|
||||
`Lmod guide <https://www.tacc.utexas.edu/research-development/tacc-projects/lmod/user-guide/module-hierarchy>`_.
|
||||
Since ``lmod`` is not enabled by default, you need to add it to the list of
|
||||
enabled module file generators. The other things you need to do are:
|
||||
|
||||
- change the ``tcl`` tag to ``lmod``
|
||||
- remove ``tcl`` specific directives (``naming_scheme`` and ``conflict``)
|
||||
- set which compilers are considered ``core``
|
||||
- remove the ``mpi`` related suffixes (as they will be substituted by hierarchies)
|
||||
|
||||
After modifications the configuration file will be:
|
||||
|
||||
.. code-block:: yaml
|
||||
:emphasize-lines: 2-6
|
||||
|
||||
modules:
|
||||
enable::
|
||||
- lmod
|
||||
lmod:
|
||||
core_compilers:
|
||||
- 'gcc@4.8'
|
||||
hash_length: 0
|
||||
whitelist:
|
||||
- gcc
|
||||
blacklist:
|
||||
- '%gcc@4.8'
|
||||
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'
|
||||
|
||||
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:`the reference manual<config-overrides>` for a more detailed explanation
|
||||
of config scopes).
|
||||
|
||||
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. It is
|
||||
common practice to put OS provided compilers in the list and only build common utilities
|
||||
and other compilers in ``Core``.
|
||||
|
||||
You can now regenerate the module files
|
||||
|
||||
.. code-block:: console
|
||||
|
||||
$ spack module refresh --module-type lmod --delete-tree -y
|
||||
|
||||
and update ``MODULEPATH`` to point to the ``Core`` folder:
|
||||
|
||||
.. code-block:: console
|
||||
|
||||
$ module unuse /home/mculpo/wdir/spack/share/spack/modules/linux-Ubuntu14-x86_64
|
||||
$ module use /home/mculpo/wdir/spack/share/spack/lmod/linux-Ubuntu14-x86_64/Core
|
||||
$ module avail
|
||||
|
||||
----------------------------------------------------------------------- /home/mculpo/wdir/spack/share/spack/lmod/linux-Ubuntu14-x86_64/Core -----------------------------------------------------------------------
|
||||
gcc/6.2.0
|
||||
|
||||
As you see the only module visible now is ``gcc``. Loading that you will make
|
||||
visible the ``Compiler`` part of the software stack that was built with ``gcc/6.2.0``:
|
||||
|
||||
.. code-block:: console
|
||||
|
||||
$ module load gcc
|
||||
$ module avail
|
||||
|
||||
-------------------------------------------------------------------- /home/mculpo/wdir/spack/share/spack/lmod/linux-Ubuntu14-x86_64/gcc/6.2.0 ---------------------------------------------------------------------
|
||||
binutils/2.27 curl/7.50.3 hwloc/1.11.4 libtool/2.4.6 lzo/2.09 netlib-lapack/3.6.1 openssl/1.0.2j py-scipy/0.18.1-openblas util-macros/1.19.0
|
||||
bison/3.0.4 expat/2.2.0 libarchive/3.2.1 libxml2/2.9.4 m4/1.4.17 nettle/3.2 pkg-config/0.29.1 py-setuptools/25.2.0 xz/5.2.2
|
||||
bzip2/1.0.6 flex/2.6.0 libpciaccess/0.13.4 lz4/131 mpich/3.2 openblas/0.2.19 py-nose/1.3.7 python/2.7.12 zlib/1.2.8
|
||||
cmake/3.6.1 gmp/6.1.1 libsigsegv/2.10 lzma/4.32.7 ncurses/6.0 openmpi/2.0.1 py-numpy/1.11.1-openblas sqlite/3.8.5
|
||||
|
||||
----------------------------------------------------------------------- /home/mculpo/wdir/spack/share/spack/lmod/linux-Ubuntu14-x86_64/Core -----------------------------------------------------------------------
|
||||
gcc/6.2.0 (L)
|
||||
|
||||
The same holds true for the ``MPI`` part of the stack, that you can enable by loading
|
||||
either ``mpich`` or ``openmpi``. The nice features of LMod will become evident
|
||||
once you'll try switching among different stacks:
|
||||
|
||||
.. code-block:: console
|
||||
|
||||
$ module load mpich
|
||||
$ module avail
|
||||
|
||||
----------------------------------------------------------- /home/mculpo/wdir/spack/share/spack/lmod/linux-Ubuntu14-x86_64/mpich/3.2-5n5xoep/gcc/6.2.0 ------------------------------------------------------------
|
||||
netlib-scalapack/2.0.2-netlib netlib-scalapack/2.0.2-openblas (D)
|
||||
|
||||
-------------------------------------------------------------------- /home/mculpo/wdir/spack/share/spack/lmod/linux-Ubuntu14-x86_64/gcc/6.2.0 ---------------------------------------------------------------------
|
||||
binutils/2.27 curl/7.50.3 hwloc/1.11.4 libtool/2.4.6 lzo/2.09 netlib-lapack/3.6.1 openssl/1.0.2j py-scipy/0.18.1-openblas util-macros/1.19.0
|
||||
bison/3.0.4 expat/2.2.0 libarchive/3.2.1 libxml2/2.9.4 m4/1.4.17 nettle/3.2 pkg-config/0.29.1 py-setuptools/25.2.0 xz/5.2.2
|
||||
bzip2/1.0.6 flex/2.6.0 libpciaccess/0.13.4 lz4/131 mpich/3.2 (L) openblas/0.2.19 py-nose/1.3.7 python/2.7.12 zlib/1.2.8
|
||||
cmake/3.6.1 gmp/6.1.1 libsigsegv/2.10 lzma/4.32.7 ncurses/6.0 openmpi/2.0.1 py-numpy/1.11.1-openblas sqlite/3.8.5
|
||||
|
||||
----------------------------------------------------------------------- /home/mculpo/wdir/spack/share/spack/lmod/linux-Ubuntu14-x86_64/Core -----------------------------------------------------------------------
|
||||
gcc/6.2.0 (L)
|
||||
|
||||
$ module load openblas netlib-scalapack/2.0.2-openblas
|
||||
$ module list
|
||||
|
||||
Currently Loaded Modules:
|
||||
1) gcc/6.2.0 2) mpich/3.2 3) openblas/0.2.19 4) netlib-scalapack/2.0.2-openblas
|
||||
|
||||
$ module load openmpi
|
||||
|
||||
Lmod is automatically replacing "mpich/3.2" with "openmpi/2.0.1"
|
||||
|
||||
|
||||
Due to MODULEPATH changes the following have been reloaded:
|
||||
1) netlib-scalapack/2.0.2-openblas
|
||||
|
||||
This layout is already a great improvement over the usual non-hierarchical layout,
|
||||
but it still has an asymmetry: ``LAPACK`` providers are semantically the same as ``MPI``
|
||||
providers, but they are still not part of the hierarchy. One possible solution is shown next.
|
||||
|
||||
.. Activate lmod and turn the previous modifications into lmod:
|
||||
Add core compilers
|
||||
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
Extend the hierarchy to other virtual providers
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
.. warning::
|
||||
This is an experimental feature
|
||||
Having a hierarchy deeper than ``Core``/``Compiler``/``MPI`` is an experimental
|
||||
feature, still not fully supported by ``module spider``,
|
||||
see `here <https://github.com/TACC/Lmod/issues/114>`_. Furthermore its use
|
||||
with hierarchies more complex than ``Core``/``Compiler``/``MPI``/``LAPACK``
|
||||
has not been thoroughly tested in production environments.
|
||||
|
||||
Spack permits you to generate Lua hierarchical module files where users
|
||||
can add an arbitrary list of virtual providers to the triplet
|
||||
``Core``/``Compiler``/``MPI``. A configuration file like:
|
||||
|
||||
.. code-block:: yaml
|
||||
:emphasize-lines: 7,8
|
||||
|
||||
modules:
|
||||
enable::
|
||||
- lmod
|
||||
lmod:
|
||||
core_compilers:
|
||||
- 'gcc@4.8'
|
||||
hierarchical_scheme:
|
||||
- lapack
|
||||
hash_length: 0
|
||||
whitelist:
|
||||
- gcc
|
||||
blacklist:
|
||||
- '%gcc@4.8'
|
||||
- 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'
|
||||
|
||||
will add ``lapack`` providers to the mix. After the usual regeneration of module files:
|
||||
|
||||
.. code-block:: console
|
||||
|
||||
$ module purge
|
||||
$ spack module refresh --module-type lmod --delete-tree -y
|
||||
==> Regenerating lmod module files
|
||||
|
||||
you will have something like:
|
||||
|
||||
.. code-block:: console
|
||||
|
||||
$ module load gcc
|
||||
$ module load openblas
|
||||
$ module load openmpi
|
||||
$ module avail
|
||||
|
||||
--------------------------------------------- /home/mculpo/wdir/spack/share/spack/lmod/linux-Ubuntu14-x86_64/openblas/0.2.19-js33umc/openmpi/2.0.1-s3qbtby/gcc/6.2.0 ----------------------------------------------
|
||||
netlib-scalapack/2.0.2
|
||||
|
||||
-------------------------------------------------------- /home/mculpo/wdir/spack/share/spack/lmod/linux-Ubuntu14-x86_64/openblas/0.2.19-js33umc/gcc/6.2.0 ---------------------------------------------------------
|
||||
py-numpy/1.11.1 py-scipy/0.18.1
|
||||
|
||||
-------------------------------------------------------------------- /home/mculpo/wdir/spack/share/spack/lmod/linux-Ubuntu14-x86_64/gcc/6.2.0 ---------------------------------------------------------------------
|
||||
binutils/2.27 curl/7.50.3 hwloc/1.11.4 libtool/2.4.6 lzo/2.09 netlib-lapack/3.6.1 openssl/1.0.2j python/2.7.12 zlib/1.2.8
|
||||
bison/3.0.4 expat/2.2.0 libarchive/3.2.1 libxml2/2.9.4 m4/1.4.17 nettle/3.2 pkg-config/0.29.1 sqlite/3.8.5
|
||||
bzip2/1.0.6 flex/2.6.0 libpciaccess/0.13.4 lz4/131 mpich/3.2 openblas/0.2.19 (L) py-nose/1.3.7 util-macros/1.19.0
|
||||
cmake/3.6.1 gmp/6.1.1 libsigsegv/2.10 lzma/4.32.7 ncurses/6.0 openmpi/2.0.1 (L) py-setuptools/25.2.0 xz/5.2.2
|
||||
|
||||
----------------------------------------------------------------------- /home/mculpo/wdir/spack/share/spack/lmod/linux-Ubuntu14-x86_64/Core -----------------------------------------------------------------------
|
||||
gcc/6.2.0 (L)
|
||||
|
||||
Now both the ``MPI`` and the ``LAPACK`` providers are handled by LMod as hierarchies:
|
||||
|
||||
.. code-block:: console
|
||||
|
||||
$ module load py-numpy netlib-scalapack
|
||||
$ module load mpich
|
||||
|
||||
Lmod is automatically replacing "openmpi/2.0.1" with "mpich/3.2"
|
||||
|
||||
|
||||
Due to MODULEPATH changes the following have been reloaded:
|
||||
1) netlib-scalapack/2.0.2
|
||||
|
||||
$ module load netlib-lapack
|
||||
|
||||
Lmod is automatically replacing "openblas/0.2.19" 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
|
||||
|
||||
making the use of tags to differentiate them unnecessary.
|
||||
Note that as we compiled ``py-numpy`` only with ``openblas`` the module
|
||||
is made inactive when we switch the ``LAPACK`` provider. The user
|
||||
environment will now be consistent by design!
|
||||
Loading…
Reference in a new issue