Advanced packaging tutorial: reorganize for binary caches (#9804)
Update all examples that need an MPI provider to build with MPICH; reorganize so that fixing MPICH (as part of environment section) comes first in the tutorial (most examples in the tutorial use an MPI provider).
This commit is contained in:
Peter Scheibel
GitHub
parent
a8e8d80750
commit
2a5d5fda26
@ -38,6 +38,14 @@ in a separate package repository, which can be enabled with:
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$ spack repo add --scope=site var/spack/repos/tutorial
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This section of the tutorial may also require a newer version of gcc, which
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you can add with:
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.. code-block:: console
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$ spack install gcc@7.2.0
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$ spack compiler add --scope=site path/to/spack-installed-gcc/bin
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If you are using the tutorial docker image, all dependency packages
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will have been installed. Otherwise, to install these packages you can use
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the following commands:
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@ -47,24 +55,155 @@ the following commands:
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$ spack install openblas
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$ spack install netlib-lapack
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$ spack install mpich
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$ spack install openmpi
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$ spack install --only=dependencies armadillo ^openblas
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$ spack install --only=dependencies netcdf
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$ spack install --only=dependencies elpa
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Now, you are ready to set your preferred ``EDITOR`` and continue with
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the rest of the tutorial.
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.. note::
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Several of these packages depend on an MPI implementation. You can use
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OpenMPI if you install it from scratch, but this is slow (>10 min.).
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A binary cache of MPICH may be provided, in which case you can force
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the package to use it and install quickly. All tutorial examples with
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packages that depend on MPICH include the spec syntax for building with it
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.. _adv_pkg_tutorial_start:
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---------------------------------------
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Modifying a package's build environment
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---------------------------------------
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Spack sets up several environment variables like ``PATH`` by default to aid in
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building a package, but many packages make use of environment variables which
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convey specific information about their dependencies (e.g., ``MPICC``).
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This section covers how to update your Spack packages so that package-specific
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environment variables are defined at build-time.
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Set environment variables in dependent packages at build-time
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Dependencies can set environment variables that are required when their
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dependents build. For example, when a package depends on a python extension
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like py-numpy, Spack's ``python`` package will add it to ``PYTHONPATH``
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so it is available at build time; this is required because the default setup
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that spack does is not sufficient for python to import modules.
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To provide environment setup for a dependent, a package can implement the
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:py:func:`setup_dependent_environment <spack.package.PackageBase.setup_dependent_environment>`
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function. This function takes as a parameter a :py:class:`EnvironmentModifications <spack.util.environment.EnvironmentModifications>`
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object which includes convenience methods to update the environment. For
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example, an MPI implementation can set ``MPICC`` for packages that depend on it:
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.. code-block:: python
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def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
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spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
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In this case packages that depend on ``mpi`` will have ``MPICC`` defined in
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their environment when they build. This section is focused on modifying the
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build-time environment represented by ``spack_env``, but it's worth noting that
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modifications to ``run_env`` are included in Spack's automatically-generated
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module files.
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We can practice by editing the ``mpich`` package to set the ``MPICC``
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environment variable in the build-time environment of dependent packages.
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.. code-block:: console
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root@advanced-packaging-tutorial:/# spack edit mpich
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Once you're finished, the method should look like this:
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.. code-block:: python
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def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
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spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
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spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
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spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
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spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
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spack_env.set('MPICH_CC', spack_cc)
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spack_env.set('MPICH_CXX', spack_cxx)
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spack_env.set('MPICH_F77', spack_f77)
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spack_env.set('MPICH_F90', spack_fc)
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spack_env.set('MPICH_FC', spack_fc)
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At this point we can, for instance, install ``netlib-scalapack`` with
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``mpich``:
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.. code-block:: console
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root@advanced-packaging-tutorial:/# spack install netlib-scalapack ^mpich
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...
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==> Created stage in /usr/local/var/spack/stage/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z
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==> No patches needed for netlib-scalapack
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==> Building netlib-scalapack [CMakePackage]
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==> Executing phase: 'cmake'
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==> Executing phase: 'build'
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==> Executing phase: 'install'
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==> Successfully installed netlib-scalapack
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Fetch: 0.01s. Build: 3m 59.86s. Total: 3m 59.87s.
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[+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z
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and double check the environment logs to verify that every variable was
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set to the correct value.
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Set environment variables in your own package
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Packages can modify their own build-time environment by implementing the
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:py:func:`setup_environment <spack.package.PackageBase.setup_environment>` function.
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For ``qt`` this looks like:
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.. code-block:: python
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def setup_environment(self, spack_env, run_env):
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spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs))
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run_env.set('QTDIR', self.prefix)
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When ``qt`` builds, ``MAKEFLAGS`` will be defined in the environment.
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To contrast with ``qt``'s :py:func:`setup_dependent_environment <spack.package.PackageBase.setup_dependent_environment>`
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function:
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.. code-block:: python
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def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
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spack_env.set('QTDIR', self.prefix)
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Let's see how it works by completing the ``elpa`` package:
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.. code-block:: console
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root@advanced-packaging-tutorial:/# spack edit elpa
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In the end your method should look like:
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.. code-block:: python
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def setup_environment(self, spack_env, run_env):
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spec = self.spec
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spack_env.set('CC', spec['mpi'].mpicc)
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spack_env.set('FC', spec['mpi'].mpifc)
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spack_env.set('CXX', spec['mpi'].mpicxx)
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spack_env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined())
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spack_env.append_flags('LDFLAGS', spec['lapack'].libs.search_flags)
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spack_env.append_flags('LIBS', spec['lapack'].libs.link_flags)
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At this point it's possible to proceed with the installation of ``elpa ^mpich``
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------------------------------
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Retrieving library information
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------------------------------
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Although Spack attempts to help packages locate their dependency libraries
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automatically (e.g. by setting PKG_CONFIG_PATH and CMAKE_PREFIX_PATH), a
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package may have unique configuration options that are required to locate
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automatically (e.g. by setting ``PKG_CONFIG_PATH`` and ``CMAKE_PREFIX_PATH``),
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a package may have unique configuration options that are required to locate
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libraries. When a package needs information about dependency libraries, the
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general approach in Spack is to query the dependencies for the locations of
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their libraries and set configuration options accordingly. By default most
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@ -130,11 +269,11 @@ is as easy as accessing the their ``libs`` attribute. Furthermore, the interface
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remains the same whether you are querying regular or virtual dependencies.
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At this point you can complete the installation of ``armadillo`` using ``openblas``
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as a LAPACK provider:
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as a LAPACK provider (``armadillo ^openblas ^mpich``):
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.. code-block:: console
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root@advanced-packaging-tutorial:/# spack install armadillo ^openblas
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root@advanced-packaging-tutorial:/# spack install armadillo ^openblas ^mpich
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==> 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
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...
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==> superlu is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/superlu-5.2.1-q2mbtw2wo4kpzis2e2n227ip2fquxrno
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@ -179,12 +318,12 @@ follow this naming scheme must implement this function themselves, e.g.
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This issue is common for packages which implement an interface (i.e.
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virtual package providers in Spack). If we try to build another version of
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``armadillo`` tied to ``netlib-lapack`` we'll notice that this time the
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installation won't complete:
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``armadillo`` tied to ``netlib-lapack`` (``armadillo ^netlib-lapack ^mpich``)
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we'll notice that this time the installation won't complete:
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.. code-block:: console
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root@advanced-packaging-tutorial:/# spack install armadillo ^netlib-lapack
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root@advanced-packaging-tutorial:/# spack install armadillo ^netlib-lapack ^mpich
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==> 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
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...
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==> openmpi is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f
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@ -226,7 +365,7 @@ What we need to implement is:
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def lapack_libs(self):
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shared = True if '+shared' in self.spec else False
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return find_libraries(
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'liblapack', root=self.prefix, shared=shared, recurse=True
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'liblapack', root=self.prefix, shared=shared, recursive=True
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)
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i.e., a property that returns the correct list of libraries for the LAPACK interface.
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@ -236,11 +375,11 @@ We use the name ``lapack_libs`` rather than ``libs`` because
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as a separate library file. Using this name ensures that when
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dependents ask for ``lapack`` libraries, ``netlib-lapack`` will retrieve only
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the libraries associated with the ``lapack`` interface. Now we can finally
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install ``armadillo ^netlib-lapack``:
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install ``armadillo ^netlib-lapack ^mpich``:
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.. code-block:: console
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root@advanced-packaging-tutorial:/# spack install armadillo ^netlib-lapack
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root@advanced-packaging-tutorial:/# spack install armadillo ^netlib-lapack ^mpich
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...
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==> Building armadillo [CMakePackage]
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@ -256,133 +395,6 @@ libraries associated with the interfaces it provides, dependents do not need
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to include special-case logic for different implementations and for example
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need only ask for :code:`spec['blas'].libs`.
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---------------------------------------
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Modifying a package's build environment
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---------------------------------------
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Spack sets up several environment variables like PATH by default to aid in
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building a package, but many packages make use of environment variables which
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convey specific information about their dependencies (e.g., MPICC). This
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section covers how update your Spack packages so that package-specific
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environment variables are defined at build-time.
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Set environment variables in dependent packages at build-time
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Dependencies can set environment variables that are required when their
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dependents build. For example, when a package depends on a python extension
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like py-numpy, Spack's ``python`` package will add it to ``PYTHONPATH``
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so it is available at build time; this is required because the default setup
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that spack does is not sufficient for python to import modules.
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To provide environment setup for a dependent, a package can implement the
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:py:func:`setup_dependent_environment <spack.package.PackageBase.setup_dependent_environment>`
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function. This function takes as a parameter a :py:class:`EnvironmentModifications <spack.util.environment.EnvironmentModifications>`
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object which includes convenience methods to update the environment. For
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example, an MPI implementation can set ``MPICC`` for packages that depend on it:
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.. code-block:: python
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def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
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spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
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In this case packages that depend on ``mpi`` will have ``MPICC`` defined in
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their environment when they build. This section is focused on modifying the
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build-time environment represented by ``spack_env``, but it's worth noting that
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modifications to ``run_env`` are included in Spack's automatically-generated
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module files.
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We can practice by editing the ``mpich`` package to set the ``MPICC``
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environment variable in the build-time environment of dependent packages.
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.. code-block:: console
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root@advanced-packaging-tutorial:/# spack edit mpich
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Once you're finished, the method should look like this:
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.. code-block:: python
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def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
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spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
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spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
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spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
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spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
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spack_env.set('MPICH_CC', spack_cc)
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spack_env.set('MPICH_CXX', spack_cxx)
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spack_env.set('MPICH_F77', spack_f77)
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spack_env.set('MPICH_F90', spack_fc)
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spack_env.set('MPICH_FC', spack_fc)
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At this point we can, for instance, install ``netlib-scalapack``:
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.. code-block:: console
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root@advanced-packaging-tutorial:/# spack install netlib-scalapack ^mpich
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...
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==> Created stage in /usr/local/var/spack/stage/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z
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==> No patches needed for netlib-scalapack
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==> Building netlib-scalapack [CMakePackage]
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==> Executing phase: 'cmake'
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==> Executing phase: 'build'
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==> Executing phase: 'install'
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==> Successfully installed netlib-scalapack
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Fetch: 0.01s. Build: 3m 59.86s. Total: 3m 59.87s.
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[+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z
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and double check the environment logs to verify that every variable was
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set to the correct value.
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Set environment variables in your own package
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Packages can modify their own build-time environment by implementing the
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:py:func:`setup_environment <spack.package.PackageBase.setup_environment>` function.
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For ``qt`` this looks like:
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.. code-block:: python
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def setup_environment(self, spack_env, run_env):
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spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs))
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run_env.set('QTDIR', self.prefix)
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When ``qt`` builds, ``MAKEFLAGS`` will be defined in the environment.
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To contrast with ``qt``'s :py:func:`setup_dependent_environment <spack.package.PackageBase.setup_dependent_environment>`
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function:
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.. code-block:: python
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def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
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spack_env.set('QTDIR', self.prefix)
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Let's see how it works by completing the ``elpa`` package:
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.. code-block:: console
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root@advanced-packaging-tutorial:/# spack edit elpa
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In the end your method should look like:
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.. code-block:: python
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def setup_environment(self, spack_env, run_env):
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spec = self.spec
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spack_env.set('CC', spec['mpi'].mpicc)
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spack_env.set('FC', spec['mpi'].mpifc)
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spack_env.set('CXX', spec['mpi'].mpicxx)
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spack_env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined())
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spack_env.append_flags('LDFLAGS', spec['lapack'].libs.search_flags)
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spack_env.append_flags('LIBS', spec['lapack'].libs.link_flags)
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At this point it's possible to proceed with the installation of ``elpa``.
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----------------------
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Other Packaging Topics
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----------------------
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@ -425,11 +437,11 @@ for extra parameters after the subscript key. In fact, any of the keys used in t
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can be followed by a comma-separated list of extra parameters which can be
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inspected by the package receiving the request to fine-tune a response.
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Let's look at an example and try to install ``netcdf``:
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Let's look at an example and try to install ``netcdf ^mpich``:
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.. code-block:: console
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root@advanced-packaging-tutorial:/# spack install netcdf
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root@advanced-packaging-tutorial:/# spack install netcdf ^mpich
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==> libsigsegv is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
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==> m4 is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a
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...
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@ -471,11 +483,11 @@ If you followed the instructions correctly, the code added to the
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)
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where we highlighted the line retrieving the extra parameters. Now we can successfully
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complete the installation of ``netcdf``:
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complete the installation of ``netcdf ^mpich``:
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.. code-block:: console
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root@advanced-packaging-tutorial:/# spack install netcdf
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root@advanced-packaging-tutorial:/# spack install netcdf ^mpich
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==> libsigsegv is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
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==> m4 is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a
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...
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Block a user