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spack/lib/spack/docs/module_file_support.rst
Harmen Stoppels e72f87ec64
Switch lmod default all:autoload from none to direct (#28357) 
* Switch lmod module all autoload default from none to direct

* Fix the docs
2022-01-18 09:06:41 -08:00

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.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
.. _modules:
=======
Modules
=======
The use of module systems to manage user environment in a controlled way
is a common practice at HPC centers that is often embraced also by
individual programmers on their development machines. To support this
common practice Spack integrates with `Environment Modules
<http://modules.sourceforge.net/>`_ and `LMod
<http://lmod.readthedocs.io/en/latest/>`_ by providing post-install hooks
that generate module files and commands to manipulate them.
Modules are one of several ways you can use Spack packages. For other
options that may fit your use case better, you should also look at
:ref:`spack load <spack-load>` and :ref:`environments <environments>`.
----------------------------
Using module files via Spack
----------------------------
If you have installed a supported module system you should be able to
run either ``module avail`` or ``use -l spack`` to see what module
files have been installed. Here is sample output of those programs,
showing lots of installed packages:
.. code-block:: console
$ module avail
--------------------------------------------------------------- ~/spack/share/spack/modules/linux-ubuntu14-x86_64 ---------------------------------------------------------------
autoconf-2.69-gcc-4.8-qextxkq hwloc-1.11.6-gcc-6.3.0-akcisez m4-1.4.18-gcc-4.8-ev2znoc openblas-0.2.19-gcc-6.3.0-dhkmed6 py-setuptools-34.2.0-gcc-6.3.0-fadur4s
automake-1.15-gcc-4.8-maqvukj isl-0.18-gcc-4.8-afi6taq m4-1.4.18-gcc-6.3.0-uppywnz openmpi-2.1.0-gcc-6.3.0-go2s4z5 py-six-1.10.0-gcc-6.3.0-p4dhkaw
binutils-2.28-gcc-4.8-5s7c6rs libiconv-1.15-gcc-4.8-at46wg3 mawk-1.3.4-gcc-4.8-acjez57 openssl-1.0.2k-gcc-4.8-dkls5tk python-2.7.13-gcc-6.3.0-tyehea7
bison-3.0.4-gcc-4.8-ek4luo5 libpciaccess-0.13.4-gcc-6.3.0-gmufnvh mawk-1.3.4-gcc-6.3.0-ostdoms openssl-1.0.2k-gcc-6.3.0-gxgr5or readline-7.0-gcc-4.8-xhufqhn
bzip2-1.0.6-gcc-4.8-iffrxzn libsigsegv-2.11-gcc-4.8-pp2cvte mpc-1.0.3-gcc-4.8-g5mztc5 pcre-8.40-gcc-4.8-r5pbrxb readline-7.0-gcc-6.3.0-zzcyicg
bzip2-1.0.6-gcc-6.3.0-bequudr libsigsegv-2.11-gcc-6.3.0-7enifnh mpfr-3.1.5-gcc-4.8-o7xm7az perl-5.24.1-gcc-4.8-dg5j65u sqlite-3.8.5-gcc-6.3.0-6zoruzj
cmake-3.7.2-gcc-6.3.0-fowuuby libtool-2.4.6-gcc-4.8-7a523za mpich-3.2-gcc-6.3.0-dmvd3aw perl-5.24.1-gcc-6.3.0-6uzkpt6 tar-1.29-gcc-4.8-wse2ass
curl-7.53.1-gcc-4.8-3fz46n6 libtool-2.4.6-gcc-6.3.0-n7zmbzt ncurses-6.0-gcc-4.8-dcpe7ia pkg-config-0.29.2-gcc-4.8-ib33t75 tcl-8.6.6-gcc-4.8-tfxzqbr
expat-2.2.0-gcc-4.8-mrv6bd4 libxml2-2.9.4-gcc-4.8-ryzxnsu ncurses-6.0-gcc-6.3.0-ucbhcdy pkg-config-0.29.2-gcc-6.3.0-jpgubk3 util-macros-1.19.1-gcc-6.3.0-xorz2x2
flex-2.6.3-gcc-4.8-yf345oo libxml2-2.9.4-gcc-6.3.0-rltzsdh netlib-lapack-3.6.1-gcc-6.3.0-js33dog py-appdirs-1.4.0-gcc-6.3.0-jxawmw7 xz-5.2.3-gcc-4.8-mew4log
gcc-6.3.0-gcc-4.8-24puqve lmod-7.4.1-gcc-4.8-je4srhr netlib-scalapack-2.0.2-gcc-6.3.0-5aidk4l py-numpy-1.12.0-gcc-6.3.0-oemmoeu xz-5.2.3-gcc-6.3.0-3vqeuvb
gettext-0.19.8.1-gcc-4.8-yymghlh lua-5.3.4-gcc-4.8-im75yaz netlib-scalapack-2.0.2-gcc-6.3.0-hjsemcn py-packaging-16.8-gcc-6.3.0-i2n3dtl zip-3.0-gcc-4.8-rwar22d
gmp-6.1.2-gcc-4.8-5ub2wu5 lua-luafilesystem-1_6_3-gcc-4.8-wkey3nl netlib-scalapack-2.0.2-gcc-6.3.0-jva724b py-pyparsing-2.1.10-gcc-6.3.0-tbo6gmw zlib-1.2.11-gcc-4.8-pgxsxv7
help2man-1.47.4-gcc-4.8-kcnqmau lua-luaposix-33.4.0-gcc-4.8-mdod2ry netlib-scalapack-2.0.2-gcc-6.3.0-rgqfr6d py-scipy-0.19.0-gcc-6.3.0-kr7nat4 zlib-1.2.11-gcc-6.3.0-7cqp6cj
The names should look familiar, as they resemble the output from ``spack find``.
You *can* use the modules here directly. For example, you could type either of these commands
to load the ``cmake`` module:
.. code-block:: console
$ use cmake-3.7.2-gcc-6.3.0-fowuuby
.. code-block:: console
$ module load cmake-3.7.2-gcc-6.3.0-fowuuby
Neither of these is particularly pretty, easy to remember, or easy to
type. Luckily, Spack offers many facilities for customizing the module
scheme used at your site.
-------------------------
Module file customization
-------------------------
Module files are generated by post-install hooks after the successful
installation of a package.
.. note::
Spack only generates modulefiles when a package is installed. If
you attempt to install a package and it is already installed, Spack
will not regenerate modulefiles for the package. This may to
inconsistent modulefiles if the Spack module configuration has
changed since the package was installed, either by editing a file
or changing scopes or environments.
Later in this section there is a subsection on :ref:`regenerating
modules <cmd-spack-module-refresh>` that will allow you to bring
your modules to a consistent state.
The table below summarizes the essential information associated with
the different file formats that can be generated by Spack:
+-----------------------------+--------------------+-------------------------------+----------------------------------------------+----------------------+
| | **Hook name** | **Default root directory** | **Default template file** | **Compatible tools** |
+=============================+====================+===============================+==============================================+======================+
| **TCL - Non-Hierarchical** | ``tcl`` | share/spack/modules | share/spack/templates/modules/modulefile.tcl | Env. Modules/LMod |
+-----------------------------+--------------------+-------------------------------+----------------------------------------------+----------------------+
| **Lua - Hierarchical** | ``lmod`` | share/spack/lmod | share/spack/templates/modules/modulefile.lua | LMod |
+-----------------------------+--------------------+-------------------------------+----------------------------------------------+----------------------+
Spack ships with sensible defaults for the generation of module files, but
you can customize many aspects of it to accommodate package or site specific needs.
In general you can override or extend the default behavior by:
1. overriding certain callback APIs in the Python packages
2. writing specific rules in the ``modules.yaml`` configuration file
3. writing your own templates to override or extend the defaults
The former method let you express changes in the run-time environment
that are needed to use the installed software properly, e.g. injecting variables
from language interpreters into their extensions. The latter two instead permit to
fine tune the filesystem layout, content and creation of module files to meet
site specific conventions.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Override API calls in ``package.py``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
There are two methods that you can override in any ``package.py`` to affect the
content of the module files generated by Spack. The first one:
.. code-block:: python
def setup_run_environment(self, env):
pass
can alter the content of the module file associated with the same package where it is overridden.
The second method:
.. code-block:: python
def setup_dependent_run_environment(self, env, dependent_spec):
pass
can instead inject run-time environment modifications in the module files of packages
that depend on it. In both cases you need to fill ``run_env`` with the desired
list of environment modifications.
.. admonition:: The ``r`` package and callback APIs
An example in which it is crucial to override both methods
is given by the ``r`` package. This package installs libraries and headers
in non-standard locations and it is possible to prepend the appropriate directory
to the corresponding environment variables:
================== =================================
LD_LIBRARY_PATH ``self.prefix/rlib/R/lib``
PKG_CONFIG_PATH ``self.prefix/rlib/pkgconfig``
================== =================================
with the following snippet:
.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/r/package.py
:pyobject: R.setup_run_environment
The ``r`` package also knows which environment variable should be modified
to make language extensions provided by other packages available, and modifies
it appropriately in the override of the second method:
.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/r/package.py
:pyobject: R.setup_dependent_run_environment
.. _modules-yaml:
^^^^^^^^^^^^^^^^^^^^^^^^^^
Write a configuration file
^^^^^^^^^^^^^^^^^^^^^^^^^^
The configuration files that control module generation behavior
are named ``modules.yaml``. The default configuration:
.. literalinclude:: _spack_root/etc/spack/defaults/modules.yaml
:language: yaml
activates the hooks to generate ``tcl`` module files and inspects
the installation folder of each package for the presence of a set of subdirectories
(``bin``, ``man``, ``share/man``, etc.). If any is found its full path is prepended
to the environment variables listed below the folder name.
Spack modules can be configured for multiple module sets. The default
module set is named ``default``. All Spack commands which operate on
modules default to apply the ``default`` module set, but can be
applied to any module set in the configuration. Settings applied at
the root of the configuration (e.g. ``modules:enable`` rather than
``modules:default:enable``) are applied to the default module set for
backwards compatibility.
"""""""""""""""""""""""""
Changing the modules root
"""""""""""""""""""""""""
As shown in the table above, the default module root for ``lmod`` is
``$spack/share/spack/lmod`` and the default root for ``tcl`` is
``$spack/share/spack/modules``. This can be overridden for any module
set by changing the ``roots`` key of the configuration.
.. code-block:: yaml
modules:
default:
roots:
tcl: /path/to/install/tcl/modules
my_custom_lmod_modules:
roots:
lmod: /path/to/install/custom/lmod/modules
...
This configuration will create two module sets. The default module set
will install its ``tcl`` modules to ``/path/to/install/tcl/modules``
(and still install its lmod modules, if any, to the default
location). The set ``my_custom_lmod_modules`` will install its lmod
modules to ``/path/to/install/custom/lmod/modules`` (and still install
its tcl modules, if any, to the default location).
By default, an architecture-specific directory is added to the root
directory. A module set may override that behavior by setting the
``arch_folder`` config value to ``False``.
.. code-block:: yaml
modules:
default:
roots:
tcl: /path/to/install/tcl/modules
arch_folder: false
Obviously, having multiple module sets install modules to the default
location could be confusing to users of your modules. In the next
section, we will discuss enabling and disabling module types (module
file generators) for each module set.
""""""""""""""""""""
Activate other hooks
""""""""""""""""""""
Any other module file generator shipped with Spack can be activated adding it to the
list under the ``enable`` key in the module file. Currently the only generator that
is not active by default is ``lmod``, which produces hierarchical lua module files.
Each module system can then be configured separately. In fact, you should list configuration
options that affect a particular type of module files under a top level key corresponding
to the generator being customized:
.. code-block:: yaml
modules:
default:
enable:
- tcl
- lmod
tcl:
# contains environment modules specific customizations
lmod:
# contains lmod specific customizations
In general, the configuration options that you can use in ``modules.yaml`` will
either change the layout of the module files on the filesystem, or they will affect
their content. For the latter point it is possible to use anonymous specs
to fine tune the set of packages on which the modifications should be applied.
.. _anonymous_specs:
""""""""""""""""""""""""""""
Selection by anonymous specs
""""""""""""""""""""""""""""
In the configuration file you can use *anonymous specs* (i.e. specs
that **are not required to have a root package** and are thus used just
to express constraints) to apply certain modifications on a selected set
of the installed software. For instance, in the snippet below:
.. code-block:: yaml
modules:
default:
tcl:
# The keyword `all` selects every package
all:
environment:
set:
BAR: 'bar'
# This anonymous spec selects any package that
# depends on openmpi. The double colon at the
# end clears the set of rules that matched so far.
^openmpi::
environment:
set:
BAR: 'baz'
# Selects any zlib package
zlib:
environment:
prepend_path:
LD_LIBRARY_PATH: 'foo'
# Selects zlib compiled with gcc@4.8
zlib%gcc@4.8:
environment:
unset:
- FOOBAR
you are instructing Spack to set the environment variable ``BAR=bar`` for every module,
unless the associated spec satisfies ``^openmpi`` in which case ``BAR=baz``.
In addition in any spec that satisfies ``zlib`` the value ``foo`` will be
prepended to ``LD_LIBRARY_PATH`` and in any spec that satisfies ``zlib%gcc@4.8``
the variable ``FOOBAR`` will be unset.
.. note::
Order does matter
The modifications associated with the ``all`` keyword are always evaluated
first, no matter where they appear in the configuration file. All the other
spec constraints are instead evaluated top to bottom.
""""""""""""""""""""""""""""""""""""""""""""
Blacklist or whitelist specific module files
""""""""""""""""""""""""""""""""""""""""""""
You can use anonymous specs also to prevent module files from being written or
to force them to be written. Consider the case where you want to hide from users
all the boilerplate software that you had to build in order to bootstrap a new
compiler. Suppose for instance that ``gcc@4.4.7`` is the compiler provided by
your system. If you write a configuration file like:
.. code-block:: yaml
modules:
default:
tcl:
whitelist: ['gcc', 'llvm'] # Whitelist will have precedence over blacklist
blacklist: ['%gcc@4.4.7'] # Assuming gcc@4.4.7 is the system compiler
you will prevent the generation of module files for any package that
is compiled with ``gcc@4.4.7``, with the only exception of any ``gcc``
or any ``llvm`` installation.
.. _modules-projections:
"""""""""""""""""""""""""""""""
Customize the naming of modules
"""""""""""""""""""""""""""""""
The names of environment modules generated by spack are not always easy to
fully comprehend due to the long hash in the name. There are three module
configuration options to help with that. The first is a global setting to
adjust the hash length. It can be set anywhere from 0 to 32 and has a default
length of 7. This is the representation of the hash in the module file name and
does not affect the size of the package hash. Be aware that the smaller the
hash length the more likely naming conflicts will occur. The following snippet
shows how to set hash length in the module file names:
.. code-block:: yaml
modules:
default:
tcl:
hash_length: 7
To help make module names more readable, and to help alleviate name conflicts
with a short hash, one can use the ``suffixes`` option in the modules
configuration file. This option will add strings to modules that match a spec.
For instance, the following config options,
.. code-block:: yaml
modules:
default:
tcl:
all:
suffixes:
^python@2.7.12: 'python-2.7.12'
^openblas: 'openblas'
will add a ``python-2.7.12`` version string to any packages compiled with
python matching the spec, ``python@2.7.12``. This is useful to know which
version of python a set of python extensions is associated with. Likewise, the
``openblas`` string is attached to any program that has openblas in the spec,
most likely via the ``+blas`` variant specification.
The most heavyweight solution to module naming is to change the entire
naming convention for module files. This uses the projections format
covered in :ref:`adding_projections_to_views`.
.. code-block:: yaml
modules:
default:
tcl:
projections:
all: '{name}/{version}-{compiler.name}-{compiler.version}-module'
^mpi: '{name}/{version}-{^mpi.name}-{^mpi.version}-{compiler.name}-{compiler.version}-module'
will create module files that are nested in directories by package
name, contain the version and compiler name and version, and have the
word ``module`` before the hash for all specs that do not depend on
mpi, and will have the same information plus the MPI implementation
name and version for all packages that depend on mpi.
When specifying module names by projection for Lmod modules, we
recommend NOT including names of dependencies (e.g., MPI, compilers)
that are already in the LMod hierarchy.
.. note::
TCL modules
TCL modules also allow for explicit conflicts between modulefiles.
.. code-block:: yaml
modules:
default:
enable:
- tcl
tcl:
projections:
all: '{name}/{version}-{compiler.name}-{compiler.version}'
all:
conflict:
- '{name}'
- 'intel/14.0.1'
will create module files that will conflict with ``intel/14.0.1`` and with the
base directory of the same module, effectively preventing the possibility to
load two or more versions of the same software at the same time. The tokens
that are available for use in this directive are the same understood by
the :meth:`~spack.spec.Spec.format` method.
.. note::
LMod hierarchical module files
When ``lmod`` is activated Spack will generate a set of hierarchical lua module
files that are understood by LMod. The hierarchy will always contain the
two layers ``Core`` / ``Compiler`` but can be further extended to
any of the virtual dependencies present in Spack. A case that could be useful in
practice is for instance:
.. code-block:: yaml
modules:
default:
enable:
- lmod
lmod:
core_compilers:
- 'gcc@4.8'
core_specs:
- 'python'
hierarchy:
- 'mpi'
- 'lapack'
that will generate a hierarchy in which the ``lapack`` and ``mpi`` layer can be switched
independently. This allows a site to build the same libraries or applications against different
implementations of ``mpi`` and ``lapack``, and let LMod switch safely from one to the
other.
All packages built with a compiler in ``core_compilers`` and all
packages that satisfy a spec in ``core_specs`` will be put in the
``Core`` hierarchy of the lua modules.
.. warning::
Consistency of Core packages
The user is responsible for maintining consistency among core packages, as ``core_specs``
bypasses the hierarchy that allows LMod to safely switch between coherent software stacks.
.. warning::
Deep hierarchies and ``lmod spider``
For hierarchies that are deeper than three layers ``lmod spider`` may have some issues.
See `this discussion on the LMod project <https://github.com/TACC/Lmod/issues/114>`_.
""""""""""""""""""""""
Select default modules
""""""""""""""""""""""
By default, when multiple modules of the same name share a directory,
the highest version number will be the default module. This behavior
of the ``module`` command can be overridden with a symlink named
``default`` to the desired default module. If you wish to configure
default modules with Spack, add a ``defaults`` key to your modules
configuration:
.. code-block:: yaml
modules:
my-module-set:
tcl:
defaults:
- gcc@10.2.1
- hdf5@1.2.10+mpi+hl%gcc
These defaults may be arbitrarily specific. For any package that
satisfies a default, Spack will generate the module file in the
appropriate path, and will generate a default symlink to the module
file as well.
.. warning::
If Spack is configured to generate multiple default packages in the
same directory, the last modulefile to be generated will be the
default module.
.. _customize-env-modifications:
"""""""""""""""""""""""""""""""""""
Customize environment modifications
"""""""""""""""""""""""""""""""""""
You can control which prefixes in a Spack package are added to
environment variables with the ``prefix_inspections`` section; this
section maps relative prefixes to the list of environment variables
which should be updated with those prefixes.
The ``prefix_inspections`` configuration is different from other
settings in that a ``prefix_inspections`` configuration at the
``modules`` level of the configuration file applies to all module
sets. This allows users to make general overrides to the default
inspections and customize them per-module-set.
.. code-block:: yaml
modules:
prefix_inspections:
bin:
- PATH
lib:
- LIBRARY_PATH
'':
- CMAKE_PREFIX_PATH
Prefix inspections are only applied if the relative path inside the
installation prefix exists. In this case, for a Spack package ``foo``
installed to ``/spack/prefix/foo``, if ``foo`` installs executables to
``bin`` but no libraries in ``lib``, the generated module file for
``foo`` would update ``PATH`` to contain ``/spack/prefix/foo/bin`` and
``CMAKE_PREFIX_PATH`` to contain ``/spack/prefix/foo``, but would not
update ``LIBRARY_PATH``.
There is a special case for prefix inspections relative to environment
views. If all of the following conditions hold for a module set
configuration:
#. The configuration is for an :ref:`environment <environments>` and
will never be applied outside the environment,
#. The environment in question is configured to use a :ref:`view
<filesystem-views>`,
#. The :ref:`environment view is configured
<configuring_environment_views>` with a projection that ensures
every package is linked to a unique directory,
then the module set may be configured to create modules relative to
the environment view. This is specified by the ``use_view``
configuration option in the module set. If ``True``, the module set is
constructed relative to the default view of the
environment. Otherwise, the value must be the name of the environment
view relative to which to construct modules, or ``False-ish`` to
disable the feature explicitly (the default is ``False``).
If the ``use_view`` value is set in the config, then the prefix
inspections for the package are done relative to the package's path in
the view.
.. code-block:: yaml
spack:
modules:
view_relative_modules:
use_view: my_view
prefix_inspections:
bin:
- PATH
view:
my_view:
projections:
root: /path/to/my/view
all: '{name}-{hash}'
The ``spack`` key is relevant to :ref:`environment <environments>`
configuration, and the view key is discussed in detail in the section
on :ref:`Configuring environment views
<configuring_environment_views>`. With this configuration the
generated module for package ``foo`` would set ``PATH`` to include
``/path/to/my/view/foo-<hash>/bin`` instead of
``/spack/prefix/foo/bin``.
The ``use_view`` option is useful when deploying a large software
stack to users who are likely to inspect the modules to find full
paths to software, when it is desirable to present the users with a
simpler set of paths than those generated by the Spack install tree.
""""""""""""""""""""""""""""""""""""
Filter out environment modifications
""""""""""""""""""""""""""""""""""""
Modifications to certain environment variables in module files are there by
default, for instance because they are generated by prefix inspections.
If you want to prevent modifications to some environment variables, you can
do so by using the environment blacklist:
.. code-block:: yaml
modules:
default:
tcl:
all:
filter:
# Exclude changes to any of these variables
environment_blacklist: ['CPATH', 'LIBRARY_PATH']
The configuration above will generate module files that will not contain
modifications to either ``CPATH`` or ``LIBRARY_PATH``.
.. _autoloading-dependencies:
"""""""""""""""""""""
Autoload dependencies
"""""""""""""""""""""
Often it is required for a module to have its (transient) dependencies loaded as well.
One example where this is useful is when one package needs to use executables provided
by its dependency; when the dependency is autoloaded, the executable will be in the
PATH. Similarly for scripting languages such as Python, packages and their dependencies
have to be loaded together.
Autoloading is enabled by default for LMod, as it has great builtin support for through
the ``depends_on`` function. For Environment Modules it is disabled by default.
Autoloading can also be enabled conditionally:
.. code-block:: yaml
modules:
default:
tcl:
all:
autoload: none
^python:
autoload: direct
The configuration file above will produce module files that will
load their direct dependencies if the package installed depends on ``python``.
The allowed values for the ``autoload`` statement are either ``none``,
``direct`` or ``all``.
.. note::
TCL prerequisites
In the ``tcl`` section of the configuration file it is possible to use
the ``prerequisites`` directive that accepts the same values as
``autoload``. It will produce module files that have a ``prereq``
statement, which can be used to autoload dependencies in some versions
of Environment Modules.
------------------------
Maintaining Module Files
------------------------
Each type of module file has a command with the same name associated
with it. The actions these commands permit are usually associated
with the maintenance of a production environment. Here's, for instance,
a sample of the features of the ``spack module tcl`` command:
.. command-output:: spack module tcl --help
.. _cmd-spack-module-refresh:
^^^^^^^^^^^^^^^^^^^^^^^^^^
Refresh the set of modules
^^^^^^^^^^^^^^^^^^^^^^^^^^
The subcommand that regenerates module files to update their content or
their layout is ``refresh``:
.. command-output:: spack module tcl refresh --help
A set of packages can be selected using anonymous specs for the optional
``constraint`` positional argument. Optionally the entire tree can be deleted
before regeneration if the change in layout is radical.
.. _cmd-spack-module-rm:
^^^^^^^^^^^^^^^^^^^
Delete module files
^^^^^^^^^^^^^^^^^^^
If instead what you need is just to delete a few module files, then the right
subcommand is ``rm``:
.. command-output:: spack module tcl rm --help
.. note::
We care about your module files!
Every modification done on modules
that are already existing will ask for a confirmation by default. If
the command is used in a script it is possible though to pass the
``-y`` argument, that will skip this safety measure.
.. _modules-in-shell-scripts:
------------------------------------
Using Spack modules in shell scripts
------------------------------------
The easiest To enable additional Spack commands for loading and unloading
module files, and to add the correct path to ``MODULEPATH``, you need to
source the appropriate setup file. Assuming Spack is installed in
``$SPACK_ROOT``, run the appropriate command for your shell:
.. code-block:: console
# For bash/zsh/sh
$ . $SPACK_ROOT/share/spack/setup-env.sh
# For tcsh/csh
$ source $SPACK_ROOT/share/spack/setup-env.csh
# For fish
$ . $SPACK_ROOT/share/spack/setup-env.fish
If you want to have Spack's shell support available on the command line
at any login you can put this source line in one of the files that are
sourced at startup (like ``.profile``, ``.bashrc`` or ``.cshrc``). Be
aware that the shell startup time may increase slightly as a result.
.. _cmd-spack-module-loads:
^^^^^^^^^^^^^^^^^^^^^^^^^^
``spack module tcl loads``
^^^^^^^^^^^^^^^^^^^^^^^^^^
In some cases, it is desirable to use a Spack-generated module, rather
than relying on Spack's built-in user-environment modification
capabilities. To translate a spec into a module name, use ``spack
module tcl loads`` or ``spack module lmod loads`` depending on the
module system desired.
To load not just a module, but also all the modules it depends on, use
the ``--dependencies`` option. This is not required for most modules
because Spack builds binaries with RPATH support. However, not all
packages use RPATH to find their dependencies: this can be true in
particular for Python extensions, which are currently *not* built with
RPATH.
Scripts to load modules recursively may be made with the command:
.. code-block:: console
$ spack module tcl loads --dependencies <spec>
An equivalent alternative using `process substitution <http://tldp.org/LDP/abs/html/process-sub.html>`_ is:
.. code-block:: console
$ source <( spack module tcl loads --dependencies <spec> )
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Module Commands for Shell Scripts
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Although Spack is flexible, the ``module`` command is much faster.
This could become an issue when emitting a series of ``spack load``
commands inside a shell script. By adding the ``--dependencies`` flag,
``spack module tcl loads`` may also be used to generate code that can be
cut-and-pasted into a shell script. For example:
.. code-block:: console
$ spack module tcl loads --dependencies py-numpy git
# bzip2@1.0.6%gcc@4.9.3=linux-x86_64
module load bzip2-1.0.6-gcc-4.9.3-ktnrhkrmbbtlvnagfatrarzjojmkvzsx
# ncurses@6.0%gcc@4.9.3=linux-x86_64
module load ncurses-6.0-gcc-4.9.3-kaazyneh3bjkfnalunchyqtygoe2mncv
# zlib@1.2.8%gcc@4.9.3=linux-x86_64
module load zlib-1.2.8-gcc-4.9.3-v3ufwaahjnviyvgjcelo36nywx2ufj7z
# sqlite@3.8.5%gcc@4.9.3=linux-x86_64
module load sqlite-3.8.5-gcc-4.9.3-a3eediswgd5f3rmto7g3szoew5nhehbr
# readline@6.3%gcc@4.9.3=linux-x86_64
module load readline-6.3-gcc-4.9.3-se6r3lsycrwxyhreg4lqirp6xixxejh3
# python@3.5.1%gcc@4.9.3=linux-x86_64
module load python-3.5.1-gcc-4.9.3-5q5rsrtjld4u6jiicuvtnx52m7tfhegi
# py-setuptools@20.5%gcc@4.9.3=linux-x86_64
module load py-setuptools-20.5-gcc-4.9.3-4qr2suj6p6glepnedmwhl4f62x64wxw2
# py-nose@1.3.7%gcc@4.9.3=linux-x86_64
module load py-nose-1.3.7-gcc-4.9.3-pwhtjw2dvdvfzjwuuztkzr7b4l6zepli
# openblas@0.2.17%gcc@4.9.3+shared=linux-x86_64
module load openblas-0.2.17-gcc-4.9.3-pw6rmlom7apfsnjtzfttyayzc7nx5e7y
# py-numpy@1.11.0%gcc@4.9.3+blas+lapack=linux-x86_64
module load py-numpy-1.11.0-gcc-4.9.3-mulodttw5pcyjufva4htsktwty4qd52r
# curl@7.47.1%gcc@4.9.3=linux-x86_64
module load curl-7.47.1-gcc-4.9.3-ohz3fwsepm3b462p5lnaquv7op7naqbi
# autoconf@2.69%gcc@4.9.3=linux-x86_64
module load autoconf-2.69-gcc-4.9.3-bkibjqhgqm5e3o423ogfv2y3o6h2uoq4
# cmake@3.5.0%gcc@4.9.3~doc+ncurses+openssl~qt=linux-x86_64
module load cmake-3.5.0-gcc-4.9.3-x7xnsklmgwla3ubfgzppamtbqk5rwn7t
# expat@2.1.0%gcc@4.9.3=linux-x86_64
module load expat-2.1.0-gcc-4.9.3-6pkz2ucnk2e62imwakejjvbv6egncppd
# git@2.8.0-rc2%gcc@4.9.3+curl+expat=linux-x86_64
module load git-2.8.0-rc2-gcc-4.9.3-3bib4hqtnv5xjjoq5ugt3inblt4xrgkd
The script may be further edited by removing unnecessary modules.
^^^^^^^^^^^^^^^
Module Prefixes
^^^^^^^^^^^^^^^
On some systems, modules are automatically prefixed with a certain
string; ``spack module tcl loads`` needs to know about that prefix when it
issues ``module load`` commands. Add the ``--prefix`` option to your
``spack module tcl loads`` commands if this is necessary.
For example, consider the following on one system:
.. code-block:: console
$ module avail
linux-SuSE11-x86_64/antlr-2.7.7-gcc-5.3.0-bdpl46y
$ spack module tcl loads antlr # WRONG!
# antlr@2.7.7%gcc@5.3.0~csharp+cxx~java~python arch=linux-SuSE11-x86_64
module load antlr-2.7.7-gcc-5.3.0-bdpl46y
$ spack module tcl loads --prefix linux-SuSE11-x86_64/ antlr
# antlr@2.7.7%gcc@5.3.0~csharp+cxx~java~python arch=linux-SuSE11-x86_64
module load linux-SuSE11-x86_64/antlr-2.7.7-gcc-5.3.0-bdpl46y
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