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Grouped all the module commands under spack module

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As requested in the review all the commands meant to manage module
files have been grouped under the `spack module` command.

Unit tests have been refactored to match the new command structure.
This commit is contained in:
Massimiliano Culpo
2018-07-20 10:30:36 +02:00
committed by Todd Gamblin
parent 7cbe1aedb7
commit 35cef16974
14 changed files with 272 additions and 396 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
lib/spack/docs/developer_guide.rst
View File

@@ -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 lmod refresh``. You can add subparsers to your parser to handle
``spack module 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
View File

@@ -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 tcl loads git`` to your ``.bashrc``.
#. Add the output of ``spack module 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 tcl loads curl >>~/.bashrc
$ spack module tcl loads curl >>~/.bashrc
or if environment modules don't work:

30
lib/spack/docs/module_file_support.rst
View File

@@ -180,9 +180,9 @@ To identify just the one built with the Intel compiler.
.. _cmd-spack-module-loads:
^^^^^^^^^^^^^^^^^^^^^^
``spack tcl loads``
^^^^^^^^^^^^^^^^^^^^^^
^^^^^^^^^^^^^^^^^^^^^^^^^^
``spack module tcl loads``
^^^^^^^^^^^^^^^^^^^^^^^^^^
In some cases, it is desirable to load not just a module, but also all
the modules it depends on. This is not required for most modules
@@ -195,13 +195,13 @@ Scripts to load modules recursively may be made with the command:
.. code-block:: console
$ spack tcl loads --dependencies <spec>
$ 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 tcl loads --dependencies <spec> )
$ source <( spack module tcl loads --dependencies <spec> )
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -211,12 +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 tcl find`` may also be used to generate code that can be
``spack module 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 tcl loads --dependencies py-numpy git
$ 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
@@ -256,9 +256,9 @@ Module Prefixes
^^^^^^^^^^^^^^^
On some systems, modules are automatically prefixed with a certain
string; ``spack tcl loads`` needs to know about that prefix when it
string; ``spack module tcl loads`` needs to know about that prefix when it
issues ``module load`` commands. Add the ``--prefix`` option to your
``spack tcl loads`` commands if this is necessary.
``spack module tcl loads`` commands if this is necessary.
For example, consider the following on one system:
@@ -267,11 +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 tcl loads antlr # WRONG!
$ 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 tcl loads --prefix linux-SuSE11-x86_64/ antlr
$ 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
@@ -626,9 +626,9 @@ 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 tcl`` command:
a sample of the features of the ``spack module tcl`` command:
.. command-output:: spack tcl --help
.. command-output:: spack module tcl --help
.. _cmd-spack-module-refresh:
@@ -639,7 +639,7 @@ Refresh the set of modules
The subcommand that regenerates module files to update their content or
their layout is ``refresh``:
.. command-output:: spack tcl refresh --help
.. 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
@@ -654,7 +654,7 @@ 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 tcl rm --help
.. command-output:: spack module tcl rm --help
.. note::
We care about your module files!

103
lib/spack/docs/tutorial_modules.rst
View File

@@ -166,7 +166,7 @@ The fastest way to set-up your environment is to :ref:`use a Docker image <workf
.. code-block:: console
$ docker pull alalazo/spack:module_tutorial
$ docker run --rm -h module-file-tutorial -it alalazo/spack:module_tutorial
$ docker run --rm -h module-file-tutorial -it spack/module-tutorial:latest
root@module-file-tutorial:/#
If you arrived at this point you should be ready to start, as all the software needed is
@@ -185,7 +185,7 @@ pre-installed in the image:
-- linux-ubuntu16.04-x86_64 / gcc@7.2.0 -------------------------
bzip2@1.0.6 mpich@3.2.1 netlib-scalapack@2.0.2 netlib-scalapack@2.0.2 openssl@1.0.2o py-scipy@1.1.0 readline@7.0
cmake@3.11.4 ncurses@6.1 netlib-scalapack@2.0.2 openblas@0.3.0 pkgconf@1.4.2 py-setuptools@39.2.0 sqlite@3.23.1
cmake@3.12.0 ncurses@6.1 netlib-scalapack@2.0.2 openblas@0.3.0 pkgconf@1.4.2 py-setuptools@39.2.0 sqlite@3.23.1
gdbm@1.14.1 netlib-lapack@3.8.0 netlib-scalapack@2.0.2 openmpi@1.10.2 py-numpy@1.14.3 python@2.7.15 zlib@1.2.11
Go to :ref:`module_file_tutorial_non_hierarchical` to proceed with the tutorial.
@@ -364,17 +364,17 @@ If you arrived to this point you should have an environment that looks similar t
autoconf-2.69-gcc-5.4.0-cbvv5rj lua-luaposix-33.4.0-gcc-5.4.0-i7w7ynf perl-5.26.2-gcc-5.4.0-n2k4mza
automake-1.16.1-gcc-5.4.0-lykrrr4 m4-1.4.18-gcc-5.4.0-3z33ecf pkgconf-1.4.2-gcc-5.4.0-fovrh7a
bzip2-1.0.6-gcc-7.2.0-mwamumj mpc-1.1.0-gcc-5.4.0-56lbd3h pkgconf-1.4.2-gcc-7.2.0-yoxwmgb
cmake-3.11.4-gcc-7.2.0-h24ofjs mpfr-4.0.1-gcc-5.4.0-dy5r7hi py-numpy-1.14.3-gcc-7.2.0-t3loxvu
cmake-3.12.0-gcc-7.2.0-6ovorxs mpfr-4.0.1-gcc-5.4.0-dy5r7hi py-numpy-1.14.3-gcc-7.2.0-t3loxvu
gcc-7.2.0-gcc-5.4.0-wwhgyej mpich-3.2.1-gcc-7.2.0-vt5xcat py-scipy-1.1.0-gcc-7.2.0-fdiryak
gdbm-1.14.1-gcc-5.4.0-q4fpyuo ncurses-6.1-gcc-5.4.0-3o765ou py-setuptools-39.2.0-gcc-7.2.0-jqhycal
gdbm-1.14.1-gcc-7.2.0-zk5lhob ncurses-6.1-gcc-7.2.0-xcgzqdv python-2.7.15-gcc-7.2.0-c7pnzul
git-2.9.4-gcc-5.4.0-mkaoyhz netlib-lapack-3.8.0-gcc-7.2.0-bcikpen readline-7.0-gcc-5.4.0-nxhwrg7
gmp-6.1.2-gcc-5.4.0-qc4qcfz netlib-scalapack-2.0.2-gcc-7.2.0-d3lertf readline-7.0-gcc-7.2.0-ccruj2i
isl-0.19-gcc-5.4.0-hsl7f52 netlib-scalapack-2.0.2-gcc-7.2.0-jae3ilo sqlite-3.23.1-gcc-7.2.0-5ltus3a
libsigsegv-2.11-gcc-5.4.0-fypapcp netlib-scalapack-2.0.2-gcc-7.2.0-lqfhvfh tcl-8.6.8-gcc-5.4.0-qhwyccy
libtool-2.4.6-gcc-5.4.0-o2pfwjf netlib-scalapack-2.0.2-gcc-7.2.0-uhzmwog zlib-1.2.11-gcc-5.4.0-5nus6kn
git-2.9.4-gcc-5.4.0-mkaoyhz netlib-lapack-3.8.0-gcc-7.2.0-7apabqu readline-7.0-gcc-5.4.0-nxhwrg7
gmp-6.1.2-gcc-5.4.0-qc4qcfz netlib-scalapack-2.0.2-gcc-7.2.0-3bz5rxx readline-7.0-gcc-7.2.0-ccruj2i
isl-0.19-gcc-5.4.0-hsl7f52 netlib-scalapack-2.0.2-gcc-7.2.0-6i5qsqx sqlite-3.23.1-gcc-7.2.0-5ltus3a
libsigsegv-2.11-gcc-5.4.0-fypapcp netlib-scalapack-2.0.2-gcc-7.2.0-uhzmwog tcl-8.6.8-gcc-5.4.0-qhwyccy
libtool-2.4.6-gcc-5.4.0-o2pfwjf netlib-scalapack-2.0.2-gcc-7.2.0-z52ltyy zlib-1.2.11-gcc-5.4.0-5nus6kn
lmod-7.7.29-gcc-5.4.0-wl6mywv openblas-0.3.0-gcc-7.2.0-pdatzbi zlib-1.2.11-gcc-7.2.0-ezuwp4p
lua-5.3.4-gcc-5.4.0-izvaota openmpi-1.10.2-gcc-7.2.0-2h6xmxh
lua-5.3.4-gcc-5.4.0-izvaota openmpi-1.10.2-gcc-7.2.0-6oewzwj
lua-luafilesystem-1_6_3-gcc-5.4.0-ywlmaou openssl-1.0.2o-gcc-7.2.0-cvldq3v
Use "module spider" to find all possible modules.
@@ -433,7 +433,7 @@ Next you should regenerate all the module files:
.. code-block:: console
root@module-file-tutorial:/# spack tcl refresh
root@module-file-tutorial:/# spack module tcl refresh
==> You are about to regenerate tcl module files for:
-- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
@@ -444,11 +444,11 @@ Next you should regenerate all the module files:
mkaoyhz git@2.9.4 wl6mywv lmod@7.7.29 56lbd3h mpc@1.1.0 nxhwrg7 readline@7.0
-- linux-ubuntu16.04-x86_64 / gcc@7.2.0 -------------------------
mwamumj bzip2@1.0.6 bcikpen netlib-lapack@3.8.0 pdatzbi openblas@0.3.0 fdiryak py-scipy@1.1.0 ezuwp4p zlib@1.2.11
h24ofjs cmake@3.11.4 d3lertf netlib-scalapack@2.0.2 2h6xmxh openmpi@1.10.2 jqhycal py-setuptools@39.2.0
mwamumj bzip2@1.0.6 7apabqu netlib-lapack@3.8.0 pdatzbi openblas@0.3.0 fdiryak py-scipy@1.1.0 ezuwp4p zlib@1.2.11
6ovorxs cmake@3.12.0 6i5qsqx netlib-scalapack@2.0.2 6oewzwj openmpi@1.10.2 jqhycal py-setuptools@39.2.0
zk5lhob gdbm@1.14.1 uhzmwog netlib-scalapack@2.0.2 cvldq3v openssl@1.0.2o c7pnzul python@2.7.15
vt5xcat mpich@3.2.1 lqfhvfh netlib-scalapack@2.0.2 yoxwmgb pkgconf@1.4.2 ccruj2i readline@7.0
xcgzqdv ncurses@6.1 jae3ilo netlib-scalapack@2.0.2 t3loxvu py-numpy@1.14.3 5ltus3a sqlite@3.23.1
vt5xcat mpich@3.2.1 3bz5rxx netlib-scalapack@2.0.2 yoxwmgb pkgconf@1.4.2 ccruj2i readline@7.0
xcgzqdv ncurses@6.1 z52ltyy netlib-scalapack@2.0.2 t3loxvu py-numpy@1.14.3 5ltus3a sqlite@3.23.1
==> Do you want to proceed? [y/n] y
==> Regenerating tcl module files
@@ -503,7 +503,7 @@ and regenerate the module files:
.. code-block:: console
root@module-file-tutorial:/# spack tcl refresh --delete-tree
root@module-file-tutorial:/# spack module tcl refresh --delete-tree
==> You are about to regenerate tcl module files for:
-- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
@@ -514,11 +514,11 @@ and regenerate the module files:
mkaoyhz git@2.9.4 wl6mywv lmod@7.7.29 56lbd3h mpc@1.1.0 nxhwrg7 readline@7.0
-- linux-ubuntu16.04-x86_64 / gcc@7.2.0 -------------------------
mwamumj bzip2@1.0.6 bcikpen netlib-lapack@3.8.0 pdatzbi openblas@0.3.0 fdiryak py-scipy@1.1.0 ezuwp4p zlib@1.2.11
h24ofjs cmake@3.11.4 d3lertf netlib-scalapack@2.0.2 2h6xmxh openmpi@1.10.2 jqhycal py-setuptools@39.2.0
mwamumj bzip2@1.0.6 7apabqu netlib-lapack@3.8.0 pdatzbi openblas@0.3.0 fdiryak py-scipy@1.1.0 ezuwp4p zlib@1.2.11
6ovorxs cmake@3.12.0 6i5qsqx netlib-scalapack@2.0.2 6oewzwj openmpi@1.10.2 jqhycal py-setuptools@39.2.0
zk5lhob gdbm@1.14.1 uhzmwog netlib-scalapack@2.0.2 cvldq3v openssl@1.0.2o c7pnzul python@2.7.15
vt5xcat mpich@3.2.1 lqfhvfh netlib-scalapack@2.0.2 yoxwmgb pkgconf@1.4.2 ccruj2i readline@7.0
xcgzqdv ncurses@6.1 jae3ilo netlib-scalapack@2.0.2 t3loxvu py-numpy@1.14.3 5ltus3a sqlite@3.23.1
vt5xcat mpich@3.2.1 3bz5rxx netlib-scalapack@2.0.2 yoxwmgb pkgconf@1.4.2 ccruj2i readline@7.0
xcgzqdv ncurses@6.1 z52ltyy netlib-scalapack@2.0.2 t3loxvu py-numpy@1.14.3 5ltus3a sqlite@3.23.1
==> Do you want to proceed? [y/n] y
==> Regenerating tcl module files
@@ -526,13 +526,13 @@ and regenerate the module files:
root@module-file-tutorial:/# module avail
-------------------------------------------- /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64 ---------------------------------------------
bzip2-1.0.6-gcc-7.2.0-mwamumj netlib-scalapack-2.0.2-gcc-7.2.0-jae3ilo py-numpy-1.14.3-gcc-7.2.0-t3loxvu
cmake-3.11.4-gcc-7.2.0-h24ofjs netlib-scalapack-2.0.2-gcc-7.2.0-lqfhvfh py-scipy-1.1.0-gcc-7.2.0-fdiryak
gdbm-1.14.1-gcc-7.2.0-zk5lhob netlib-scalapack-2.0.2-gcc-7.2.0-uhzmwog py-setuptools-39.2.0-gcc-7.2.0-jqhycal
bzip2-1.0.6-gcc-7.2.0-mwamumj netlib-scalapack-2.0.2-gcc-7.2.0-6i5qsqx py-numpy-1.14.3-gcc-7.2.0-t3loxvu
cmake-3.12.0-gcc-7.2.0-6ovorxs netlib-scalapack-2.0.2-gcc-7.2.0-uhzmwog py-scipy-1.1.0-gcc-7.2.0-fdiryak
gdbm-1.14.1-gcc-7.2.0-zk5lhob netlib-scalapack-2.0.2-gcc-7.2.0-z52ltyy py-setuptools-39.2.0-gcc-7.2.0-jqhycal
mpich-3.2.1-gcc-7.2.0-vt5xcat openblas-0.3.0-gcc-7.2.0-pdatzbi python-2.7.15-gcc-7.2.0-c7pnzul
ncurses-6.1-gcc-7.2.0-xcgzqdv openmpi-1.10.2-gcc-7.2.0-2h6xmxh readline-7.0-gcc-7.2.0-ccruj2i
netlib-lapack-3.8.0-gcc-7.2.0-bcikpen openssl-1.0.2o-gcc-7.2.0-cvldq3v sqlite-3.23.1-gcc-7.2.0-5ltus3a
netlib-scalapack-2.0.2-gcc-7.2.0-d3lertf pkgconf-1.4.2-gcc-7.2.0-yoxwmgb zlib-1.2.11-gcc-7.2.0-ezuwp4p
ncurses-6.1-gcc-7.2.0-xcgzqdv openmpi-1.10.2-gcc-7.2.0-6oewzwj readline-7.0-gcc-7.2.0-ccruj2i
netlib-lapack-3.8.0-gcc-7.2.0-7apabqu openssl-1.0.2o-gcc-7.2.0-cvldq3v sqlite-3.23.1-gcc-7.2.0-5ltus3a
netlib-scalapack-2.0.2-gcc-7.2.0-3bz5rxx pkgconf-1.4.2-gcc-7.2.0-yoxwmgb zlib-1.2.11-gcc-7.2.0-ezuwp4p
Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
@@ -562,7 +562,7 @@ exceptions to the blacklist rules you can use ``whitelist``:
.. code-block:: console
root@module-file-tutorial:/# spack tcl refresh -y
root@module-file-tutorial:/# spack module tcl refresh -y
==> Regenerating tcl module files
@@ -626,7 +626,7 @@ If you try to regenerate the module files now you will get an error:
.. code-block:: console
root@module-file-tutorial:/# spack tcl refresh --delete-tree -y
root@module-file-tutorial:/# spack module 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
@@ -673,14 +673,14 @@ Regenerating module files now we obtain:
.. code-block:: console
root@module-file-tutorial:/# spack tcl refresh --delete-tree -y
root@module-file-tutorial:/# spack module tcl refresh --delete-tree -y
==> Regenerating tcl module files
root@module-file-tutorial:/# module av
-------------------------------------------- /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64 ---------------------------------------------
bzip2-1.0.6-gcc-7.2.0 netlib-lapack-3.8.0-gcc-7.2.0 openmpi-1.10.2-gcc-7.2.0 python-2.7.15-gcc-7.2.0
cmake-3.11.4-gcc-7.2.0 netlib-scalapack-2.0.2-gcc-7.2.0-netlib-mpich openssl-1.0.2o-gcc-7.2.0 readline-7.0-gcc-7.2.0
cmake-3.12.0-gcc-7.2.0 netlib-scalapack-2.0.2-gcc-7.2.0-netlib-mpich openssl-1.0.2o-gcc-7.2.0 readline-7.0-gcc-7.2.0
gcc-7.2.0-gcc-5.4.0 netlib-scalapack-2.0.2-gcc-7.2.0-netlib-openmpi pkgconf-1.4.2-gcc-7.2.0 sqlite-3.23.1-gcc-7.2.0
gdbm-1.14.1-gcc-7.2.0 netlib-scalapack-2.0.2-gcc-7.2.0-openblas-mpich py-numpy-1.14.3-gcc-7.2.0-openblas zlib-1.2.11-gcc-7.2.0
mpich-3.2.1-gcc-7.2.0 netlib-scalapack-2.0.2-gcc-7.2.0-openblas-openmpi py-scipy-1.1.0-gcc-7.2.0-openblas
@@ -720,13 +720,13 @@ The final result should look like:
.. code-block:: console
root@module-file-tutorial:/# spack tcl refresh --delete-tree -y
root@module-file-tutorial:/# spack module tcl refresh --delete-tree -y
==> Regenerating tcl module files
root@module-file-tutorial:/# module av
-------------------------------------------- /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64 ---------------------------------------------
bzip2/1.0.6-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-netlib-openmpi py-scipy/1.1.0-gcc-7.2.0-openblas
cmake/3.11.4-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-openblas-mpich py-setuptools/39.2.0-gcc-7.2.0
cmake/3.12.0-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-openblas-mpich py-setuptools/39.2.0-gcc-7.2.0
gcc/7.2.0-gcc-5.4.0 netlib-scalapack/2.0.2-gcc-7.2.0-openblas-openmpi (D) python/2.7.15-gcc-7.2.0
gdbm/1.14.1-gcc-7.2.0 openblas/0.3.0-gcc-7.2.0 readline/7.0-gcc-7.2.0
mpich/3.2.1-gcc-7.2.0 openmpi/1.10.2-gcc-7.2.0 sqlite/3.23.1-gcc-7.2.0
@@ -794,7 +794,7 @@ Regenerating the module files results in something like:
.. code-block:: console
:emphasize-lines: 15
root@module-file-tutorial:/# spack tcl refresh -y
root@module-file-tutorial:/# spack module tcl refresh -y
==> Regenerating tcl module files
root@module-file-tutorial:/# module show gcc
@@ -870,10 +870,10 @@ This time we will be more selective and regenerate only the ``gcc`` and
.. code-block:: console
root@module-file-tutorial:/# spack tcl refresh -y gcc
root@module-file-tutorial:/# spack module tcl refresh -y gcc
==> Regenerating tcl module files
root@module-file-tutorial:/# spack tcl refresh -y openmpi
root@module-file-tutorial:/# spack module tcl refresh -y openmpi
==> Regenerating tcl module files
root@module-file-tutorial:/# module show gcc
@@ -981,7 +981,7 @@ and regenerating the module files for every package that depends on ``python``:
.. code-block:: console
root@module-file-tutorial:/# spack tcl refresh -y ^python
root@module-file-tutorial:/# spack module tcl refresh -y ^python
==> Regenerating tcl module files
Now the ``py-scipy`` module will be:
@@ -1165,7 +1165,7 @@ If we now regenerate the module files:
.. code-block:: console
root@module-file-tutorial:/# spack lmod refresh --delete-tree -y
root@module-file-tutorial:/# spack module lmod refresh --delete-tree -y
==> Regenerating lmod module files
and update ``MODULEPATH`` to point to the ``Core``:
@@ -1198,7 +1198,7 @@ the ``Compiler`` part of the hierarchy:
----------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 -----------------------------------------
bzip2/1.0.6 mpich/3.2.1 openblas/0.3.0 pkgconf/1.4.2 py-setuptools/39.2.0 sqlite/3.23.1
cmake/3.11.4 ncurses/6.1 openmpi/1.10.2 py-numpy/1.14.3-openblas python/2.7.15 zlib/1.2.11
cmake/3.12.0 ncurses/6.1 openmpi/1.10.2 py-numpy/1.14.3-openblas python/2.7.15 zlib/1.2.11
gdbm/1.14.1 netlib-lapack/3.8.0 openssl/1.0.2o py-scipy/1.1.0-openblas readline/7.0
------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/Core --------------------------------------------
@@ -1223,7 +1223,7 @@ either ``mpich`` or ``openmpi``. Let's start by loading ``mpich``:
----------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 -----------------------------------------
bzip2/1.0.6 mpich/3.2.1 (L) openblas/0.3.0 pkgconf/1.4.2 py-setuptools/39.2.0 sqlite/3.23.1
cmake/3.11.4 ncurses/6.1 openmpi/1.10.2 py-numpy/1.14.3-openblas python/2.7.15 zlib/1.2.11
cmake/3.12.0 ncurses/6.1 openmpi/1.10.2 py-numpy/1.14.3-openblas python/2.7.15 zlib/1.2.11
gdbm/1.14.1 netlib-lapack/3.8.0 openssl/1.0.2o py-scipy/1.1.0-openblas readline/7.0
------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/Core --------------------------------------------
@@ -1357,7 +1357,7 @@ After module files have been regenerated as usual:
root@module-file-tutorial:/# module purge
root@module-file-tutorial:/# spack lmod refresh --delete-tree -y
root@module-file-tutorial:/# spack module lmod refresh --delete-tree -y
==> Regenerating lmod module files
we can see that now we have additional components in the hierarchy:
@@ -1369,11 +1369,11 @@ we can see that now we have additional components in the hierarchy:
root@module-file-tutorial:/# module avail
----------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/openblas/0.3.0-pdatzbi/gcc/7.2.0 ------------------------------
py-numpy/1.14.3-openblas py-scipy/1.1.0-openblas
py-numpy/1.14.3 py-scipy/1.1.0
----------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 -----------------------------------------
bzip2/1.0.6 mpich/3.2.1 openblas/0.3.0 (L) pkgconf/1.4.2 readline/7.0
cmake/3.11.4 ncurses/6.1 openmpi/1.10.2 py-setuptools/39.2.0 sqlite/3.23.1
cmake/3.12.0 ncurses/6.1 openmpi/1.10.2 py-setuptools/39.2.0 sqlite/3.23.1
gdbm/1.14.1 netlib-lapack/3.8.0 openssl/1.0.2o python/2.7.15 zlib/1.2.11
------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/Core --------------------------------------------
@@ -1389,11 +1389,11 @@ we can see that now we have additional components in the hierarchy:
root@module-file-tutorial:/# module load openmpi
root@module-file-tutorial:/# module avail
------------------ /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/openmpi/1.10.2-2h6xmxh/openblas/0.3.0-pdatzbi/gcc/7.2.0 ------------------
netlib-scalapack/2.0.2-openblas
------------------ /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/openmpi/1.10.2-6oewzwj/openblas/0.3.0-pdatzbi/gcc/7.2.0 ------------------
netlib-scalapack/2.0.2
----------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/openblas/0.3.0-pdatzbi/gcc/7.2.0 ------------------------------
py-numpy/1.14.3-openblas py-scipy/1.1.0-openblas
py-numpy/1.14.3 py-scipy/1.1.0
----------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 -----------------------------------------
bzip2/1.0.6 mpich/3.2.1 openblas/0.3.0 (L) pkgconf/1.4.2 readline/7.0
@@ -1420,18 +1420,15 @@ Both ``MPI`` and ``LAPACK`` providers will now benefit from the same safety feat
Due to MODULEPATH changes, the following have been reloaded:
1) netlib-scalapack/2.0.2-openblas
1) netlib-scalapack/2.0.2
root@module-file-tutorial:/# module load netlib-lapack
root@module-file-tutorial:/# module load mpich
Lmod is automatically replacing "openblas/0.3.0" with "netlib-lapack/3.8.0".
Lmod is automatically replacing "openmpi/1.10.2" with "mpich/3.2.1".
Inactive Modules:
1) py-numpy
The following have been reloaded with a version change:
1) netlib-scalapack/2.0.2-openblas => netlib-scalapack/2.0.2-netlib
Due to MODULEPATH changes, the following have been reloaded:
1) netlib-scalapack/2.0.2
Because we only compiled ``py-numpy`` with ``openblas`` the module
is made inactive when we switch the ``LAPACK`` provider. The user
@@ -1589,7 +1586,7 @@ If we regenerate the module files one last time:
.. code-block:: console
root@module-file-tutorial:/# spack lmod refresh -y netlib-scalapack
root@module-file-tutorial:/# spack module lmod refresh -y netlib-scalapack
==> Regenerating lmod module files
we'll find the following at the end of each ``netlib-scalapack`` module file:

20
lib/spack/docs/workflows.rst
View File

@@ -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 tcl loads`` commands, on the
The ``spack load`` and ``spack module tcl loads`` commands, on the
other hand, are not very smart: if the user-supplied spec matches
more than one installed package, then ``spack tcl loads`` will
more than one installed package, then ``spack module tcl loads`` will
fail. This may change in the future. For now, the workaround is to
be more specific on any ``spack tcl loads`` lines that fail.
be more specific on any ``spack module 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 tcl loads`` commands to pre-compute which
a series of ``spack module 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 >$HOME/env/spackenv
FIND='spack tcl loads --prefix linux-SuSE11-x86_64/'
FIND='spack module tcl loads --prefix linux-SuSE11-x86_64/'
\$FIND modele-utils
\$FIND emacs
@@ -346,14 +346,14 @@ Users may now put ``source ~/env/spackenv`` into ``.bashrc``.
Some module systems put a prefix on the names of modules created
by Spack. For example, that prefix is ``linux-SuSE11-x86_64/`` in
the above case. If a prefix is not needed, you may omit the
``--prefix`` flag from ``spack tcl loads``.
``--prefix`` flag from ``spack module tcl loads``.
"""""""""""""""""""""""
Transitive Dependencies
"""""""""""""""""""""""
In the script above, each ``spack tcl loads`` command generates a
In the script above, each ``spack module tcl loads`` command generates a
*single* ``module load`` line. Transitive dependencies do not usually
need to be loaded, only modules the user needs in ``$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 tcl loads`` command. For example, the following line,
``spack module 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 tcl loads --dependencies py-scipy
spack module 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 tcl loads`` script.
equivalent to the information in a ``spack module tcl loads`` script.
Administrators might find things easier to maintain without the
added "heavyweight" state of a view.