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Updated references to spack module in the documentation.

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Massimiliano Culpo 2018-04-11 22:53:09 +02:00 committed by Todd Gamblin
parent 6ab57571c2
commit e81c0c3e2c
5 changed files with 46 additions and 55 deletions
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2
lib/spack/docs/developer_guide.rst
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@ -314,7 +314,7 @@ See the `Argparse documentation <https://docs.python.org/2.7/library/argparse.ht
for more details on how to add arguments.
Some commands have a set of subcommands, like ``spack compiler find`` or
``spack module refresh``. You can add subparsers to your parser to handle
``spack lmod refresh``. You can add subparsers to your parser to handle
this. Check out ``spack edit --command compiler`` for an example of this.
A lot of commands take the same arguments and flags. These arguments should

4
lib/spack/docs/getting_started.rst
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@ -816,7 +816,7 @@ This problem is related to OpenSSL, and in some cases might be solved
by installing a new version of ``git`` and ``openssl``:
#. Run ``spack install git``
#. Add the output of ``spack module loads git`` to your ``.bashrc``.
#. Add the output of ``spack tcl loads git`` to your ``.bashrc``.
If this doesn't work, it is also possible to disable checking of SSL
certificates by using:
@ -861,7 +861,7 @@ or alternately:
.. code-block:: console
$ spack module loads curl >>~/.bashrc
$ spack tcl loads curl >>~/.bashrc
or if environment modules don't work:

51
lib/spack/docs/module_file_support.rst
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@ -181,7 +181,7 @@ To identify just the one built with the Intel compiler.
.. _cmd-spack-module-loads:
^^^^^^^^^^^^^^^^^^^^^^
``spack module loads``
``spack tcl loads``
^^^^^^^^^^^^^^^^^^^^^^
In some cases, it is desirable to load not just a module, but also all
@ -195,21 +195,13 @@ Scripts to load modules recursively may be made with the command:
.. code-block:: console
$ spack module loads --dependencies <spec>
$ spack 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 loads --dependencies <spec> )
.. warning::
The ``spack load`` command does not currently accept the
``--dependencies`` flag. Use ``spack module loads`` instead, for
now.
.. See #1662
$ source <( spack tcl loads --dependencies <spec> )
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -219,12 +211,12 @@ 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 ``--shell`` flag,
``spack module find`` may also be used to generate code that can be
``spack tcl find`` may also be used to generate code that can be
cut-and-pasted into a shell script. For example:
.. code-block:: console
$ spack module loads --dependencies py-numpy git
$ spack 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
@ -264,9 +256,9 @@ Module Prefixes
^^^^^^^^^^^^^^^
On some systems, modules are automatically prefixed with a certain
string; ``spack module loads`` needs to know about that prefix when it
string; ``spack tcl loads`` needs to know about that prefix when it
issues ``module load`` commands. Add the ``--prefix`` option to your
``spack module loads`` commands if this is necessary.
``spack tcl loads`` commands if this is necessary.
For example, consider the following on one system:
@ -275,11 +267,11 @@ For example, consider the following on one system:
$ module avail
linux-SuSE11-x86_64/antlr-2.7.7-gcc-5.3.0-bdpl46y
$ spack module loads antlr # WRONG!
$ spack 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 loads --prefix linux-SuSE11-x86_64/ antlr
$ spack 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
@ -631,37 +623,36 @@ The allowed values for the ``autoload`` statement are either ``none``,
Maintaining Module Files
------------------------
Spack not only provides great flexibility in the generation of module files
and in the customization of both their layout and content, but also ships with
a tool to ease the burden of their maintenance in production environments.
This tool is the ``spack module`` command:
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 tcl`` command:
.. command-output:: spack tcl --help
.. _cmd-spack-module-refresh:
^^^^^^^^^^^^^^^^^^^^^^^^
``spack module refresh``
^^^^^^^^^^^^^^^^^^^^^^^^
^^^^^^^^^^^^^^^^^^^^^^^^^^
Refresh the set of modules
^^^^^^^^^^^^^^^^^^^^^^^^^^
The command that regenerates module files to update their content or
their layout is ``module refresh``:
The subcommand that regenerates module files to update their content or
their layout is ``refresh``:
.. command-output:: spack tcl refresh --help
A set of packages can be selected using anonymous specs for the optional
``constraint`` positional argument. The argument ``--module-type`` identifies
the type of module files to refresh. Optionally the entire tree can be deleted
``constraint`` positional argument. Optionally the entire tree can be deleted
before regeneration if the change in layout is radical.
.. _cmd-spack-module-rm:
^^^^^^^^^^^^^^^^^^^
``spack module rm``
Delete module files
^^^^^^^^^^^^^^^^^^^
If instead what you need is just to delete a few module files, then the right
command is ``module rm``:
subcommand is ``rm``:
.. command-output:: spack tcl rm --help

24
lib/spack/docs/tutorial_modules.rst
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@ -422,7 +422,7 @@ Next you should regenerate all the module files:
.. code-block:: console
root@module-file-tutorial:/# spack module refresh --module-type tcl
root@module-file-tutorial:/# spack tcl refresh
==> You are about to regenerate tcl module files for:
-- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
@ -484,7 +484,7 @@ and regenerate the module files:
.. code-block:: console
root@module-file-tutorial:/# spack module refresh --module-type tcl --delete-tree
root@module-file-tutorial:/# spack tcl refresh --delete-tree
==> You are about to regenerate tcl module files for:
-- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
@ -538,7 +538,7 @@ exceptions to the blacklist rules you can use ``whitelist``:
.. code-block:: console
root@module-file-tutorial:/# spack module refresh --module-type tcl -y
root@module-file-tutorial:/# spack tcl refresh -y
==> Regenerating tcl module files
@ -584,7 +584,7 @@ If you try to regenerate the module files now you will get an error:
.. code-block:: console
root@module-file-tutorial:/# spack module refresh --module-type tcl --delete-tree -y
root@module-file-tutorial:/# spack tcl refresh --delete-tree -y
==> Error: Name clashes detected in module files:
file: /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64/netlib-scalapack-2.0.2-gcc-7.2.0
@ -631,7 +631,7 @@ Regenerating module files now we obtain:
.. code-block:: console
root@module-file-tutorial:/# spack module refresh --module-type tcl --delete-tree -y
root@module-file-tutorial:/# spack tcl refresh --delete-tree -y
==> Regenerating tcl module files
root@module-file-tutorial:/# module avail
@ -677,7 +677,7 @@ The final result should look like:
.. code-block:: console
root@module-file-tutorial:/# spack module refresh --module-type tcl --delete-tree -y
root@module-file-tutorial:/# spack tcl refresh --delete-tree -y
==> Regenerating tcl module files
root@module-file-tutorial:/# module avail
@ -748,7 +748,7 @@ Regenerating the module files results in something like:
.. code-block:: console
:emphasize-lines: 15
root@module-file-tutorial:/# spack module refresh -y --module-type tcl
root@module-file-tutorial:/# spack tcl refresh -y
==> Regenerating tcl module files
root@module-file-tutorial:/# module show gcc
@ -819,10 +819,10 @@ This time we will be more selective and regenerate only the ``gcc`` and
.. code-block:: console
root@module-file-tutorial:/# spack module refresh -y --module-type tcl gcc
root@module-file-tutorial:/# spack tcl refresh -y gcc
==> Regenerating tcl module files
root@module-file-tutorial:/# spack module refresh -y --module-type tcl openmpi
root@module-file-tutorial:/# spack tcl refresh -y openmpi
==> Regenerating tcl module files
root@module-file-tutorial:/# module show gcc
@ -926,7 +926,7 @@ and regenerating the module files for every package that depends on ``python``:
.. code-block:: console
root@module-file-tutorial:/# spack module refresh -y --module-type tcl ^python
root@module-file-tutorial:/# spack tcl refresh -y ^python
==> Regenerating tcl module files
Now the ``py-scipy`` module will be:
@ -1102,7 +1102,7 @@ If we now regenerate the module files:
.. code-block:: console
root@module-file-tutorial:/# spack module refresh --module-type lmod --delete-tree -y
root@module-file-tutorial:/# spack lmod refresh --delete-tree -y
==> Regenerating lmod module files
and update ``MODULEPATH`` to point to the ``Core``:
@ -1293,7 +1293,7 @@ After module files have been regenerated as usual:
root@module-file-tutorial:/# module purge
root@module-file-tutorial:/# spack module refresh --delete-tree -y -m lmod
root@module-file-tutorial:/# spack lmod refresh --delete-tree -y
==> Regenerating lmod module files
we can see that now we have additional components in the hierarchy:

20
lib/spack/docs/workflows.rst
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@ -276,11 +276,11 @@ have some drawbacks:
2. The ``spack spec`` and ``spack install`` commands use a
sophisticated concretization algorithm that chooses the "best"
among several options, taking into account ``packages.yaml`` file.
The ``spack load`` and ``spack module loads`` commands, on the
The ``spack load`` and ``spack tcl loads`` commands, on the
other hand, are not very smart: if the user-supplied spec matches
more than one installed package, then ``spack module loads`` will
more than one installed package, then ``spack tcl loads`` will
fail. This may change in the future. For now, the workaround is to
be more specific on any ``spack module loads`` lines that fail.
be more specific on any ``spack tcl loads`` lines that fail.
""""""""""""""""""""""
@ -290,7 +290,7 @@ Generated Load Scripts
Another problem with using `spack load` is, it is slow; a typical user
environment could take several seconds to load, and would not be
appropriate to put into ``.bashrc`` directly. It is preferable to use
a series of ``spack module loads`` commands to pre-compute which
a series of ``spack tcl loads`` commands to pre-compute which
modules to load. These can be put in a script that is run whenever
installed Spack packages change. For example:
@ -301,7 +301,7 @@ installed Spack packages change. For example:
# Generate module load commands in ~/env/spackenv
cat <<EOF | /bin/sh >$HOME/env/spackenv
FIND='spack module loads --prefix linux-SuSE11-x86_64/'
FIND='spack tcl loads --prefix linux-SuSE11-x86_64/'
\$FIND modele-utils
\$FIND emacs
@ -346,14 +346,14 @@ Users may now put ``source ~/env/spackenv`` into ``.bashrc``.
Some module systems put a prefix on the names of modules created
by Spack. For example, that prefix is ``linux-SuSE11-x86_64/`` in
the above case. If a prefix is not needed, you may omit the
``--prefix`` flag from ``spack module loads``.
``--prefix`` flag from ``spack tcl loads``.
"""""""""""""""""""""""
Transitive Dependencies
"""""""""""""""""""""""
In the script above, each ``spack module loads`` command generates a
In the script above, each ``spack tcl loads`` command generates a
*single* ``module load`` line. Transitive dependencies do not usually
need to be loaded, only modules the user needs in ``$PATH``. This is
because Spack builds binaries with RPATH. Spack's RPATH policy has
@ -394,13 +394,13 @@ Unfortunately, Spack's RPATH support does not work in all case. For example:
In cases where RPATH support doesn't make things "just work," it can
be necessary to load a module's dependencies as well as the module
itself. This is done by adding the ``--dependencies`` flag to the
``spack module loads`` command. For example, the following line,
``spack tcl loads`` command. For example, the following line,
added to the script above, would be used to load SciPy, along with
Numpy, core Python, BLAS/LAPACK and anything else needed:
.. code-block:: sh
spack module loads --dependencies py-scipy
spack tcl loads --dependencies py-scipy
^^^^^^^^^^^^^^
Dummy Packages
@ -630,7 +630,7 @@ environments:
and extension packages.
* Views and activated extensions maintain state that is semantically
equivalent to the information in a ``spack module loads`` script.
equivalent to the information in a ``spack tcl loads`` script.
Administrators might find things easier to maintain without the
added "heavyweight" state of a view.