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| -rw-r--r-- | lib/spack/docs/tutorial_advanced_packaging.rst | 505 |
1 files changed, 227 insertions, 278 deletions
diff --git a/lib/spack/docs/tutorial_advanced_packaging.rst b/lib/spack/docs/tutorial_advanced_packaging.rst index 901e75bfd7..23e04082af 100644 --- a/lib/spack/docs/tutorial_advanced_packaging.rst +++ b/lib/spack/docs/tutorial_advanced_packaging.rst @@ -4,18 +4,17 @@ Advanced Topics in Packaging ============================ -While you can quickly accomplish most common tasks with what -was covered in :ref:`packaging-tutorial`, there are times when such -knowledge won't suffice. Usually this happens for libraries that provide -more than one API and need to let dependents decide which one to use -or for packages that provide tools that are invoked at build-time, -or in other similar situations. - -In the following we'll dig into some of the details of package -implementation that help us deal with these rare, but important, -occurrences. You can rest assured that in every case Spack remains faithful to -its philosophy: keep simple things simple, but be flexible enough when -complex requests arise! +Spack tries to automatically configure packages with information from +dependencies such that all you need to do is to list the dependencies +(i.e. with the ``depends_on`` directive) and the build system (for example +by deriving from :code:`CmakePackage`). + +However, there are many special cases. Often you need to retrieve details +about dependencies to set package-specific configuration options, or to +define package-specific environment variables used by the package's build +system. This tutorial covers how to retrieve build information from +dependencies, and how you can automatically provide important information to +dependents in your package. ---------------------- Setup for the tutorial @@ -37,7 +36,7 @@ which comes with Spack and various packages pre-installed: If you already started the image, you can set the ``EDITOR`` environment variable to your preferred editor (``vi``, ``emacs``, and ``nano`` are included in the image) -and move directly to :ref:`specs_build_interface_tutorial`. +and move directly to :ref:`adv_pkg_tutorial_start`. If you choose not to use the Docker image, you can clone the Spack repository and build the necessary bits yourself: @@ -76,29 +75,44 @@ Now, you are ready to set your preferred ``EDITOR`` and continue with the rest of the tutorial. -.. _specs_build_interface_tutorial: +.. _adv_pkg_tutorial_start: ----------------------- -Spec's build interface ----------------------- +------------------------------ +Retrieving library information +------------------------------ -Spack is designed with an emphasis on assigning responsibilities -to the appropriate entities, as this results in a clearer and more intuitive interface -for the users. -When it comes to packaging, one of the most fundamental guideline that -emerged from this tenet is that: +Although Spack attempts to help packages locate their dependency libraries +automatically (e.g. by setting PKG_CONFIG_PATH and CMAKE_PREFIX_PATH), a +package may have unique configuration options that are required to locate +libraries. When a package needs information about dependency libraries, the +general approach in Spack is to query the dependencies for the locations of +their libraries and set configuration options accordingly. By default most +Spack packages know how to automatically locate their libraries. This section +covers how to retrieve library information from dependencies and how to locate +libraries when the default logic doesn't work. - *It is a package's responsibility to know - every software it directly depends on and to expose to others how to - use the services it provides*. +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Accessing dependency libraries +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Spec's build interface is a protocol-like implementation of this guideline -that allows packages to easily query their dependencies, -and prescribes how they should expose their own build information. +If you need to access the libraries of a dependency, you can do so +via the ``libs`` property of the spec, for example in the ``arpack-ng`` +package: + +.. code-block:: python -^^^^^^^^^^^^^^^^^^^^ -A motivating example -^^^^^^^^^^^^^^^^^^^^ + def install(self, spec, prefix): + lapack_libs = spec['lapack'].libs.joined(';') + blas_libs = spec['blas'].libs.joined(';') + + cmake(*[ + '-DLAPACK_LIBRARIES={0}'.format(lapack_libs), + '-DBLAS_LIBRARIES={0}'.format(blas_libs) + ], '.') + +Note that ``arpack-ng`` is querying virtual dependencies, which Spack +automatically resolves to the installed implementation (e.g. ``openblas`` +for ``blas``). We've started work on a package for ``armadillo``. You should open it, read through the comment that starts with ``# TUTORIAL:`` and complete @@ -160,8 +174,32 @@ Hopefully the installation went fine and the code we added expanded to the right of semicolon separated libraries (you are encouraged to open ``armadillo``'s build logs to double check). -If we try to build another version tied to ``netlib-lapack`` we'll -notice that this time the installation won't complete: +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Providing libraries to dependents +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Spack provides a default implementation for ``libs`` which often works +out of the box. A user can write a package definition without having to +implement a ``libs`` property and dependents can retrieve its libraries +as shown in the above section. However, the default implementation assumes that +libraries follow the naming scheme ``lib<package name>.so`` (or e.g. +``lib<package name>.a`` for static libraries). Packages which don't +follow this naming scheme must implement this function themselves, e.g. +``opencv``: + +.. code-block:: python + + @property + def libs(self): + shared = "+shared" in self.spec + return find_libraries( + "libopencv_*", root=self.prefix, shared=shared, recurse=True + ) + +This issue is common for packages which implement an interface (i.e. +virtual package providers in Spack). If we try to build another version of +``armadillo`` tied to ``netlib-lapack`` we'll notice that this time the +installation won't complete: .. code-block:: console @@ -190,8 +228,9 @@ notice that this time the installation won't complete: See build log for details: /usr/local/var/spack/stage/arpack-ng-3.5.0-bloz7cqirpdxj33pg7uj32zs5likz2un/arpack-ng-3.5.0/spack-build.out -This is because ``netlib-lapack`` requires extra work, compared to ``openblas``, -to expose its build information to other packages. Let's edit it: +Unlike ``openblas`` which provides a library named ``libopenblas.so``, +``netlib-lapack`` provides ``liblapack.so``, so it needs to implement +customized library search logic. Let's edit it: .. code-block:: console @@ -210,7 +249,13 @@ What we need to implement is: ) i.e. a property that returns the correct list of libraries for the LAPACK interface. -Now we can finally install ``armadillo ^netlib-lapack``: + +We use the name ``lapack_libs`` rather than ``libs`` because +``netlib-lapack`` can also provide ``blas``, and when it does it is provided +as a separate library file. Using this name ensures that when +dependents ask for ``lapack`` libraries, ``netlib-lapack`` will retrieve only +the libraries associated with the ``lapack`` interface. Now we can finally +install ``armadillo ^netlib-lapack``: .. code-block:: console @@ -225,62 +270,170 @@ Now we can finally install ``armadillo ^netlib-lapack``: Fetch: 0.01s. Build: 3.75s. Total: 3.76s. [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/armadillo-8.100.1-sxmpu5an4dshnhickh6ykchyfda7jpyn -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -What happens at subscript time? -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Since each implementation of a virtual package is responsible for locating the +libraries associated with the interfaces it provides, dependents do not need +to include special-case logic for different implementations and for example +need only ask for :code:`spec['blas'].libs`. + +--------------------------------------- +Modifying a package's build environment +--------------------------------------- + +Spack sets up several environment variables like PATH by default to aid in +building a package, but many packages make use of environment variables which +convey specific information about their dependencies, for example MPICC. This +section covers how update your Spack packages so that package-specific +environment variables are defined at build-time. + +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Set environment variables in dependent packages at build-time +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Dependencies can set environment variables that are required when their +dependents build. For example, when a package depends on a python extension +like py-numpy, Spack's ``python`` package will add it to ``PYTHONPATH`` +so it is available at build time; this is required because the default setup +that spack does is not sufficient for python to import modules. + +To provide environment setup for a dependent, a package can implement the +:py:func:`setup_dependent_environment <spack.package.PackageBase.setup_dependent_environment>` +function. This function takes as a parameter a :py:class:`EnvironmentModifications <spack.environment.EnvironmentModifications>` +object which includes convenience methods to update the environment. For +example an MPI implementation can set ``MPICC`` for packages that depend on it: + +.. code-block:: python + + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) + +In this case packages which depend on ``mpi`` will have ``MPICC`` defined in +their environment when they build. This section is focused on modifying the +build-time environment represented by ``spack_env``, but it's worth noting that +modifications to ``run_env`` are included in Spack's automatically-generated +module files. + +We can practice by editing the ``mpich`` package to set the ``MPICC`` +environment variable in the build-time environment of dependent packages. + +.. code-block:: console + + root@advanced-packaging-tutorial:/# spack edit mpich + +Once you're finished the method should look like this: + +.. code-block:: python + + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) + spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++')) + spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) + spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) + + spack_env.set('MPICH_CC', spack_cc) + spack_env.set('MPICH_CXX', spack_cxx) + spack_env.set('MPICH_F77', spack_f77) + spack_env.set('MPICH_F90', spack_fc) + spack_env.set('MPICH_FC', spack_fc) + +At this point we can, for instance, install ``netlib-scalapack``: + +.. code-block:: console + + root@advanced-packaging-tutorial:/# spack install netlib-scalapack ^mpich + ... + ==> Created stage in /usr/local/var/spack/stage/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z + ==> No patches needed for netlib-scalapack + ==> Building netlib-scalapack [CMakePackage] + ==> Executing phase: 'cmake' + ==> Executing phase: 'build' + ==> Executing phase: 'install' + ==> Successfully installed netlib-scalapack + Fetch: 0.01s. Build: 3m 59.86s. Total: 3m 59.87s. + [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z + + +and double check the environment logs to verify that every variable was +set to the correct value. + +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Set environment variables in your own package +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Packages can modify their own build-time environment by implementing the +:py:func:`setup_environment <spack.package.PackageBase.setup_environment>` function. +For ``qt`` this looks like: + +.. code-block:: python + + def setup_environment(self, spack_env, run_env): + spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs)) + run_env.set('QTDIR', self.prefix) + +When ``qt`` builds, ``MAKEFLAGS`` will be defined in the environment. -The example above leaves us with a few questions. How could it be that the -attribute: +To contrast with ``qt``'s :py:func:`setup_dependent_environment <spack.package.PackageBase.setup_dependent_environment>` +function: .. code-block:: python - spec['lapack'].libs + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + spack_env.set('QTDIR', self.prefix) -stems from a property of the ``netlib-lapack`` package that has a different name? -How is it even computed for ``openblas``, given that in its package there's no code -that deals with finding libraries? -The answer is that ``libs`` is one of the few properties of specs that follow the -*build-interface protocol*. The others are currently ``command`` and ``headers``. -These properties exist only on concrete specs that have been retrieved via the -subscript notation. +Let's see how it works by completing the ``elpa`` package: -What happens is that, whenever you retrieve a spec using subscripts: +.. code-block:: console + + root@advanced-packaging-tutorial:/# spack edit elpa + +In the end your method should look like: .. code-block:: python - lapack = spec['lapack'] + def setup_environment(self, spack_env, run_env): + spec = self.spec + + spack_env.set('CC', spec['mpi'].mpicc) + spack_env.set('FC', spec['mpi'].mpifc) + spack_env.set('CXX', spec['mpi'].mpicxx) + spack_env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined()) + + spack_env.append_flags('LDFLAGS', spec['lapack'].libs.search_flags) + spack_env.append_flags('LIBS', spec['lapack'].libs.link_flags) + +At this point it's possible to proceed with the installation of ``elpa``. -the key that appears in the query (in this case ``'lapack'``) is attached to the -returned item. When, later on, you access any of the build-interface attributes, this -key is used to compute the result according to the following algorithm: +---------------------- +Other Packaging Topics +---------------------- -.. code-block:: none +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Attach attributes to other packages +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Given any pair of <query-key> and <build-attribute>: +Build tools usually also provide a set of executables that can be used +when another package is being installed. Spack gives the opportunity +to monkey-patch dependent modules and attach attributes to them. This +helps make the packager experience as similar as possible to what would +have been the manual installation of the same package. - 1. If <query-key> is the name of a virtual spec and the package - providing it has an attribute named '<query-key>_<build-attribute>' - return it +An example here is the ``automake`` package, which overrides +:py:func:`setup_dependent_package <spack.package.PackageBase.setup_dependent_package>`: - 2. Otherwise if the package has an attribute named '<build-attribute>' - return that +.. code-block:: python - 3. Otherwise use the default handler for <build-attribute> + def setup_dependent_package(self, module, dependent_spec): + # Automake is very likely to be a build dependency, + # so we add the tools it provides to the dependent module + executables = ['aclocal', 'automake'] + for name in executables: + setattr(module, name, self._make_executable(name)) -Going back to our concrete case this means that, if the spec providing LAPACK -is ``netlib-lapack``, we are returning the value computed in the ``lapack_libs`` -property. If it is ``openblas``, we are instead resorting to the default handler -for ``libs`` (which searches for the presence of ``libopenblas`` in the -installation prefix). +so that every other package that depends on it can use directly ``aclocal`` +and ``automake`` with the usual function call syntax of :py:class:`Executable <spack.util.executable.Executable>`: -.. note:: +.. code-block:: python - Types commonly returned by build-interface attributes - Even though there's no enforcement on it, the type of the objects returned most often when - asking for the ``libs`` attributes is :py:class:`LibraryList <llnl.util.filesystem.LibraryList>`. - Similarly the usual type returned for ``headers`` is :py:class:`HeaderList <llnl.util.filesystem.HeaderList>`, - while for ``command`` is :py:class:`Executable <spack.util.executable.Executable>`. You can refer to - these objects' API documentation to discover more about them. + aclocal('--force') ^^^^^^^^^^^^^^^^^^^^^^^ Extra query parameters @@ -357,207 +510,3 @@ complete the installation of ``netcdf``: ==> Successfully installed netcdf Fetch: 0.01s. Build: 24.61s. Total: 24.62s. [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj - - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Single package providing multiple virtual specs -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -At the close of this tutorial's subsection, it may be useful to see where the -build-interface protocol shines the most i.e. when it comes to manage packages -that provide more than one virtual spec. An example of a package of this kind is -``intel-parallel-studio``, and due to its complexity we'll limit our discussion -here to just a few considerations (without any hands-on). You can open -the related ``package.py`` in the usual way: - -.. code-block:: console - - root@advanced-packaging-tutorial:/# spack edit intel-parallel-studio - -As you can see this package provides a lot of virtual specs, and thus it has -more than one function that enters into the build-interface protocol. These -functions will be invoked for *exactly the same spec* according to the key used -by its dependents in the subscript query. - -So, for instance, the ``blas_libs`` property will be returned when -``intel-parallel-studio`` is the BLAS provider in the current DAG and -is retrieved by a dependent with: - -.. code-block:: python - - blas = self.spec['blas'] - blas_libs = blas.libs - -Within the property we inspect various aspects of the current spec: - -.. code-block:: python - - @property - def blas_libs(self): - spec = self.spec - prefix = self.prefix - shared = '+shared' in spec - - if '+ilp64' in spec: - mkl_integer = ['libmkl_intel_ilp64'] - else: - mkl_integer = ['libmkl_intel_lp64'] - ... - -and construct the list of library we need to return accordingly. - -What we achieved is that the complexity of dealing with ``intel-parallel-studio`` -is now gathered in the package itself, instead of being spread -all over its possible dependents. -Thus, a package that uses MPI or LAPACK doesn't care which implementation it uses, -as each virtual dependency has -*a uniform interface* to ask for libraries or headers and manipulate them. -The packages that provide this virtual spec, on the other hand, have a clear -way to differentiate their answer to the query [#uniforminterface]_. - -.. [#uniforminterface] Before this interface was added, each package that - depended on MPI or LAPACK had dozens of lines of code copied from other - packages telling it where to find the libraries and what they are called. - With the addition of this interface, the virtual dependency itself tells - other packages that depend on it where it can find its libraries. - ---------------------------- -Package's build environment ---------------------------- - -Besides Spec's build interface, Spack provides means to set environment -variables, either for yourself or for your dependent packages, and to -attach attributes to your dependents. We'll see them next with the help -of a few real use cases. - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Set variables at build-time for yourself -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Spack provides a way to manipulate a package's build time and -run time environments using the -:py:func:`setup_environment <spack.package.PackageBase.setup_environment>` function. -Let's try to see how it works by completing the ``elpa`` package: - -.. code-block:: console - - root@advanced-packaging-tutorial:/# spack edit elpa - -In the end your method should look like: - -.. code-block:: python - - def setup_environment(self, spack_env, run_env): - spec = self.spec - - spack_env.set('CC', spec['mpi'].mpicc) - spack_env.set('FC', spec['mpi'].mpifc) - spack_env.set('CXX', spec['mpi'].mpicxx) - spack_env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined()) - - spack_env.append_flags('LDFLAGS', spec['lapack'].libs.search_flags) - spack_env.append_flags('LIBS', spec['lapack'].libs.link_flags) - -The two arguments, ``spack_env`` and ``run_env``, are both instances of -:py:class:`EnvironmentModifications <spack.environment.EnvironmentModifications>` and -permit you to register modifications to either the build-time or the run-time -environment of the package, respectively. -At this point it's possible to proceed with the installation of ``elpa``: - -.. code-block:: console - - root@advanced-packaging-tutorial:/# spack install elpa - ==> pkg-config is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj - ==> ncurses is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.0-ukq4tccptm2rxd56d2bumqthnpcjzlez - ... - ==> Executing phase: 'build' - ==> Executing phase: 'install' - ==> Successfully installed elpa - Fetch: 3.94s. Build: 41.93s. Total: 45.87s. - [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/elpa-2016.05.004-sdbfhwcexg7s2zqf52vssb762ocvklbu - -If you had modifications to ``run_env``, those would have appeared e.g. in the module files -generated for the package. - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Set variables in dependencies at build-time -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Another common occurrence, particularly for packages like ``r`` and ``python`` -that support extensions and for packages that provide build tools, -is to require *their dependents* to have some environment variables set. - -The mechanism is similar to what we just saw, except that we override the -:py:func:`setup_dependent_environment <spack.package.PackageBase.setup_dependent_environment>` -function, which takes one additional argument, i.e. the dependent spec that needs the modified -environment. Let's practice completing the ``mpich`` package: - -.. code-block:: console - - root@advanced-packaging-tutorial:/# spack edit mpich - -Once you're finished the method should look like this: - -.. code-block:: python - - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) - spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++')) - spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) - spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) - - spack_env.set('MPICH_CC', spack_cc) - spack_env.set('MPICH_CXX', spack_cxx) - spack_env.set('MPICH_F77', spack_f77) - spack_env.set('MPICH_F90', spack_fc) - spack_env.set('MPICH_FC', spack_fc) - -At this point we can, for instance, install ``netlib-scalapack``: - -.. code-block:: console - - root@advanced-packaging-tutorial:/# spack install netlib-scalapack ^mpich - ... - ==> Created stage in /usr/local/var/spack/stage/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z - ==> No patches needed for netlib-scalapack - ==> Building netlib-scalapack [CMakePackage] - ==> Executing phase: 'cmake' - ==> Executing phase: 'build' - ==> Executing phase: 'install' - ==> Successfully installed netlib-scalapack - Fetch: 0.01s. Build: 3m 59.86s. Total: 3m 59.87s. - [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z - - -and double check the environment logs to verify that every variable was -set to the correct value. More complicated examples of the use of this function -may be found in the ``r`` and ``python`` package. - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Attach attributes to other packages -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Build tools usually also provide a set of executables that can be used -when another package is being installed. Spack gives the opportunity -to monkey-patch dependent modules and attach attributes to them. This -helps make the packager experience as similar as possible to what would -have been the manual installation of the same package. - -An example here is the ``automake`` package, which overrides -:py:func:`setup_dependent_package <spack.package.PackageBase.setup_dependent_package>`: - -.. code-block:: python - - def setup_dependent_package(self, module, dependent_spec): - # Automake is very likely to be a build dependency, - # so we add the tools it provides to the dependent module - executables = ['aclocal', 'automake'] - for name in executables: - setattr(module, name, self._make_executable(name)) - -so that every other package that depends on it can use directly ``aclocal`` -and ``automake`` with the usual function call syntax of :py:class:`Executable <spack.util.executable.Executable>`: - -.. code-block:: python - - aclocal('--force')
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