diff options
| -rw-r--r-- | lib/spack/docs/index.rst | 1 | ||||
| -rw-r--r-- | lib/spack/docs/module_file_support.rst | 60 | ||||
| -rw-r--r-- | lib/spack/docs/module_file_tutorial.rst | 975 |
3 files changed, 1009 insertions, 27 deletions
diff --git a/lib/spack/docs/index.rst b/lib/spack/docs/index.rst index 3d1bd86c3e..daaeef1af6 100644 --- a/lib/spack/docs/index.rst +++ b/lib/spack/docs/index.rst @@ -46,6 +46,7 @@ or refer to the full manual below. getting_started basic_usage workflows + module_file_tutorial .. toctree:: :maxdepth: 2 diff --git a/lib/spack/docs/module_file_support.rst b/lib/spack/docs/module_file_support.rst index 19a8161477..f07bd31c2e 100644 --- a/lib/spack/docs/module_file_support.rst +++ b/lib/spack/docs/module_file_support.rst @@ -1,8 +1,8 @@ .. _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 @@ -24,6 +24,8 @@ directly with automatically generated module files. we advise you to use either Environment Modules or LMod. See :ref:`InstallEnvironmentModules` for more details. +.. _shell_support: + ------------- Shell support ------------- @@ -110,9 +112,9 @@ you could type either of these commands to load the callpath module: .. _cmd-spack-load: -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +^^^^^^^^^^^^^^^^^^^^^^^ ``spack load / unload`` -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +^^^^^^^^^^^^^^^^^^^^^^^ Neither of these is particularly pretty, easy to remember, or easy to type. Luckily, Spack has its own interface for using modules @@ -161,9 +163,9 @@ want to use a package, you can type unload or unuse similarly: only available if you have enabled Spack's shell support *and* you have dotkit or modules installed on your machine. -^^^^^^^^^^^^^^^^^^^^^^^^^ +^^^^^^^^^^^^^^^^^^^^^^ Ambiguous module names -^^^^^^^^^^^^^^^^^^^^^^^^^ +^^^^^^^^^^^^^^^^^^^^^^ If a spec used with load/unload or use/unuse is ambiguous (i.e. more than one installed package matches it), then Spack will warn you: @@ -294,23 +296,24 @@ For example, consider the following on one system: # 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 ------------------------------ +---------------------------- Auto-generating Module Files ------------------------------ +---------------------------- Module files are generated by post-install hooks after the successful -installation of a package. They are placed in the following directories -under the Spack root: +installation of a package. The following table summarizes the essential +information associated with the different file formats +that can be generated by Spack: - +----------------------------------------+------------------------------------+------------------------+ - | | **Module Files Root directory** | **Compatible systems** | - +========================================+====================================+========================+ - | **Dotkit Module Files** | share/spack/dotkit | DotKit | - +----------------------------------------+------------------------------------+------------------------+ - | **Non-Hierarchical TCL Module Files** | share/spack/modules | Env. Modules/LMod | - +----------------------------------------+------------------------------------+------------------------+ - | **Lua Hierarchical Module Files** | share/spack/lmod | LMod | - +----------------------------------------+------------------------------------+------------------------+ + +-----------------------------+--------------------+-------------------------------+----------------------+ + | | **Hook name** | **Default root directory** | **Compatible tools** | + +=============================+====================+===============================+======================+ + | **Dotkit** | ``dotkit`` | share/spack/dotkit | DotKit | + +-----------------------------+--------------------+-------------------------------+----------------------+ + | **TCL - Non-Hierarchical** | ``tcl`` | share/spack/modules | Env. Modules/LMod | + +-----------------------------+--------------------+-------------------------------+----------------------+ + | **Lua - Hierarchical** | ``lmod`` | share/spack/lmod | LMod | + +-----------------------------+--------------------+-------------------------------+----------------------+ Though Spack ships with sensible defaults for the generation of module files, @@ -324,9 +327,9 @@ The former method fits best cases that are site independent, e.g. injecting vari from language interpreters into their extensions. The latter instead permits to fine tune the content, naming and creation of module files to meet site specific conventions. -^^^^^^^^^^^^^^^^^^^^^^^^^^^ +^^^^^^^^^^^^^^^^^^^^ ``Package`` file API -^^^^^^^^^^^^^^^^^^^^^^^^^^^ +^^^^^^^^^^^^^^^^^^^^ There are two methods that can be overridden in any ``package.py`` to affect the content of generated module files. The first one is: @@ -376,9 +379,9 @@ and has similar effects on module file of dependees. Even in this case .. _modules-yaml: ----------------------------------- +--------------------------------- Configuration in ``modules.yaml`` ----------------------------------- +--------------------------------- The name of the configuration file that controls module generation behavior is ``modules.yaml``. The default configuration: @@ -426,6 +429,8 @@ All these module sections allow for both: For the latter point in particular it is possible to use anonymous specs to select an appropriate set of packages on which the modifications should be applied. +.. _anonymous_specs: + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Selection by anonymous specs ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -544,7 +549,7 @@ most likely via the ``+blas`` variant specification. modules: tcl: - naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVERSION}' + naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVER}' all: conflict: ['${PACKAGE}', 'intel/14.0.1'] @@ -660,9 +665,9 @@ before regeneration if the change in layout is radical. .. _cmd-spack-module-rm: -^^^^^^^^^^^^^^^^^^^^^^^^ +^^^^^^^^^^^^^^^^^^^ ``spack module rm`` -^^^^^^^^^^^^^^^^^^^^^^^^ +^^^^^^^^^^^^^^^^^^^ If instead what you need is just to delete a few module files, then the right command is ``module rm``: @@ -670,7 +675,8 @@ command is ``module rm``: .. command-output:: spack module rm --help .. note:: - We care about your module files! Every modification done on modules + 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. diff --git a/lib/spack/docs/module_file_tutorial.rst b/lib/spack/docs/module_file_tutorial.rst new file mode 100644 index 0000000000..c7c9f06bef --- /dev/null +++ b/lib/spack/docs/module_file_tutorial.rst @@ -0,0 +1,975 @@ +.. _module_tutorial: + +======= +Modules +======= + +This tutorial will guide you through the customization of both +content and naming of module files generated by Spack. + +Starting from the default Spack settings you will add an increasing +number of directives to the ``modules.yaml`` configuration file to +satisfy a number of constraints that mimic those that you may encounter +in a typical production environment at HPC sites. + +Even though the focus will be for the most part on customizing +TCL non-hierarchical module files, everything +you'll see applies also to other kinds of module files generated by Spack. + +The generation of Lua hierarchical +module files will be addressed at the end of the tutorial, +and you'll see that with minor modifications +to an existing ``modules.yaml`` written for TCL +non-hierarchical modules you'll get almost +for free the possibility to try a hierarchical layout. + +Let's start! + +.. _module_file_tutorial_prerequisites: + +------------- +Prerequisites +------------- + +Before proceeding further ensure: + +- you have LMod or Environment Modules available +- have :ref:`shell support <shell_support>` activated in Spack + +If you need to install Lmod or Environment module you can refer +to the documentation :ref:`here <InstallEnvironmentModules>`. + + +^^^^^^^^^^^^^^^^^^ +Add a new compiler +^^^^^^^^^^^^^^^^^^ + +Spack automatically scans the environment to search for available +compilers on first use. On a Ubuntu 14.04 a fresh clone will show +something like this: + +.. code-block:: console + + $ uname -a + Linux nuvolari 4.4.0-45-generic #66~14.04.1-Ubuntu SMP Wed Oct 19 15:05:38 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux + + $ spack compilers + ==> Available compilers + -- gcc ---------------------------------------------------------- + gcc@4.8 + +For the purpose of building a limited set of packages with some features +that will help showcasing the capabilities of +module customization the first thing we need is to build a new compiler: + +.. code-block:: console + + $ spack install gcc@6.2.0 + # ... + # Wait a long time + # ... + +Then we can use shell support for modules to add it to the list of known compilers: + +.. code-block:: console + + # The name of the generated module may vary + $ module load gcc-6.2.0-gcc-4.8-twd5nqg + + $ spack compiler add + ==> Added 1 new compiler to /home/mculpo/.spack/linux/compilers.yaml + gcc@6.2.0 + + $ spack compilers + ==> Available compilers + -- gcc ---------------------------------------------------------- + gcc@6.2.0 gcc@4.8 + +Note that the final 7 digits hash at the end of the generated module may vary depending +on architecture or package version. + +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Build software that will be used in the tutorial +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Next you should install a few modules that will be used in the tutorial: + +.. code-block:: console + + $ spack install netlib-scalapack ^openmpi ^openblas + # ... + +The packages you need to install are: + +- ``netlib-scalapack ^openmpi ^openblas`` +- ``netlib-scalapack ^mpich ^openblas`` +- ``netlib-scalapack ^openmpi ^netlib-lapack`` +- ``netlib-scalapack ^mpich ^netlib-lapack`` +- ``py-scipy ^openblas`` + +In the end your environment should look something like: + +.. code-block:: console + + $ module avail + + ------------------------------------------------------------------------ /home/mculpo/wdir/spack/share/spack/modules/linux-Ubuntu14-x86_64 ------------------------------------------------------------------------ + 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 + 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 + 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 + 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 + 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 + 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 + 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 + 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 + 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 + 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 + 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 + +------------------------------------------------ +Filter unwanted modifications to the environment +------------------------------------------------ + +The non-hierarchical TCL module files that have been generated so far +follow the default rules for module generation, which are given +:ref:`here <modules-yaml>` in the reference part of the manual. Taking a +look at the ``gcc`` module you'll see something like: + +.. code-block:: console + + $ module show 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: + --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + 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("LIBRARY_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64") + prepend_path("LD_LIBRARY_PATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64") + prepend_path("CPATH","/home/mculpo/wdir/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/include") + help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C, + Fortran, and Java. + ]]) + +As expected, a few environment variables representing paths will be modified +by the modules according to the default prefix inspection rules. + +Consider now the case that your site has decided that e.g. ``CPATH`` and +``LIBRARY_PATH`` modifications should not be present in module files. What you can +do to abide by the rules is to create a configuration file ``~/.spack/modules.yaml`` +with the following content: + +.. code-block:: yaml + + modules: + tcl: + all: + filter: + environment_blacklist: ['CPATH', 'LIBRARY_PATH'] + +Next you should regenerate all the module files: + +.. code-block:: console + + $ spack module refresh --module-type tcl + ==> 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 + + ... + + ==> Do you want to proceed ? [y/n] + y + ==> Regenerating tcl module files + +If you take a look now at the module for ``gcc`` you'll see that the unwanted +paths have disappeared: + +.. code-block:: console + + $ module show 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: + --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + 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") + 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! |