Expand the libMesh dependency list (#9642)

This commit overhauls the libMesh package script in a number of ways:

* We now inherit from AutotoolsPackage.
* libMesh contains about a dozen third-party dependencies that can
  only be provided by the copy bundled with libMesh. This  patch
  enumerates all such bundled dependencies and disables all of them
  by default.
* libMesh supports compilation with external installations of boost,
  eigen, hdf5, slepc, and tbb; this patch adds all of them to
  package.py.
* libMesh will look for a few system executables (xz, bzip, gdb) by
  default. This is now disabled.
* libMesh will now used a copy of perl installed by spack instead of
  trying to find the system copy.
* Compilation with non-system MPI installations requires an additional
  flag (--with-mpi=); this has been added.

var/spack/repos/builtin/packages/libmesh/package.py

@@ -6,7 +6,7 @@
 from spack import *
 
 
-class Libmesh(Package):
+class Libmesh(AutotoolsPackage):
     """The libMesh library provides a framework for the numerical simulation of
        partial differential equations using arbitrary unstructured
        discretizations on serial and parallel platforms."""
@@ -19,29 +19,194 @@ class Libmesh(Package):
     version('1.2.1', sha256='11c22c7d96874a17de6b8c74caa45d6745d40bf3610e88b2bd28fd3381f5ba70')
     version('1.0.0', 'cb464fc63ea0b71b1e69fa3f5d4f93a4')
 
+    # support for libraries that are only available through the bundled copies:
+    # TODO libMesh 1.2.1 gained the ability to specify a path to capnproto
+    variant('capnproto', default=False, description='Compile with the bundled capnproto serialization library')
+    variant('exodusii', default=False, description='Compile with the bundled ExodusII output library')
+    variant('fparser', default=False, description='Compile with the bundled fparser function parser library')
+    variant('gmv', default=False, description='Compile with the bundled gmv format IO library')
+    variant('laspack', default=False, description='Compile with the bundled laspack interative solver library')
+    variant('libhilbert', default=False, description='Compile with the bundled libHilbert partitioning library')
+    variant('metaphysicl', default=False, description='Compile with the bundled metaphysicl AD library')
+    variant('metis', default=False, description='Compile with the bundled METIS graph partitioning library')
+    variant('nanoflann', default=False, description='Compile with the bundled nanoflann graph library')
+    variant('nemesis', default=False, description='Compile with the bundled nemesis IO library')
+    variant('netcdf', default=False, description='Compile with the bundled NETCDF IO library')
+    # TODO the copy of parmetis bundled with libMesh assumes that we use the
+    # bundled copy of metis, but previous versions of this build script use an
+    # external metis installation. Be conservative and completely disable
+    # parmetis support to preserve the old behavior (and to prevent compiling
+    # with two different copies of metis).
+    #
+    # variant('parmetis', default=False,
+    #         description='Compile with the bundled PARMETIS graph library')
+    variant('qhull', default=False, description='Compile with the bundled qhull mesh generation library')
+    variant('sfc', default=False, description='Compile with the bundled sfcurves partitioning library')
+    variant('tetgen', default=False, description='Compile with the bundled tetgen mesh generation library')
+    variant('triangle', default=False, description='Compile with the bundled Triangle mesh generation library')
+
+    # support for libraries that may be externally installed:
+    variant('boost', default=False, description='Compile with components dependent on boost')
+    variant('eigen', default=False, description='support for dense linear algebra with Eigen')
+    variant('hdf5', default=False, description='Compile with support for HDF5 files')
+    variant('slepc', default=False, description='Compile with support for the SLEPc eigensolver')
+
+    # other features:
+    variant('debug', default=False, description='Compile with support for debugging')
     variant('mpi', default=True, description='Enables MPI parallelism')
-    variant('slepc', default=False, description='SLEPc eigensolver')
+    # While it is possible to configure libMesh to use openMP with neither
+    # pthreads nor TBB, no openMP code can actually be reached without enabling
+    # pthreads as well. Hence, since enabling openMP while disabling pthreads
+    # is not useful, we include openMP in the same variant to make it clear
+    # which scheduler is ultimately used.
+    variant('threads', default='none',
+            description='Enable threading support (with a particular '
+            'scheduler, in the case of openmp and tbb)',
+            values=('none', 'pthreads', 'tbb', 'openmp'), multi=False)
 
-    # Parallel version of libMesh needs MPI & parallel solvers
+    conflicts('+metaphysicl', when='@:1.2.999',
+              msg='The interface to metaphysicl is not available in libMesh '
+              'versions older than 1.3.0. Please explicitly disable this '
+              'variant.')
+
+    depends_on('boost', when='+boost')
+    # The Scotch dependency of Eigen is not used by libMesh. Since Scotch can
+    # only be used with certain versions of flex it conflicts with several
+    # versions of GCC, so explicitly disable it.
+    depends_on('eigen~scotch', when='+eigen')
+    depends_on('hdf5+mpi', when='+hdf5+mpi')
     depends_on('mpi', when='+mpi')
+    depends_on('mpi', when='+slepc')
+    # compilation dependencies depend on perl
+    depends_on('perl')
     depends_on('petsc+mpi', when='+mpi')
-
+    depends_on('petsc+metis', when='+metis')
-    # SLEPc version needs SLEPc and requires MPI
     depends_on('slepc', when='+slepc')
-    conflicts('~mpi', when='+slepc')
+    depends_on('tbb', when='threads=tbb')
 
-    def install(self, spec, prefix):
+    def configure_args(self):
-        config_args = ["--prefix=%s" % prefix]
+        options = []
 
-        if '+mpi' in spec:
+        # GLIBCXX debugging is not, by default, supported by other libraries,
-            config_args.append('CC=%s' % spec['mpi'].mpicc)
+        # so unconditionally disable it for libmesh
-            config_args.append('CXX=%s' % spec['mpi'].mpicxx)
+        options.append('--enable-glibcxx-debugging=no')
-            config_args.append('PETSC_DIR=%s' % spec['petsc'].prefix)
 
-            if '+slepc' in spec:
+        # All bundled dependencies are explicitly disabled, so we do not need
-                config_args.append('SLEPC_DIR=%s' % spec['slepc'].prefix)
+        # to perform this check:
+        options.append('--disable-strict-lgpl')
 
-        configure(*config_args)
+        # The Hinnant unique pointer implementation is incompatible with boost
+        # (and not necessary with C++11 support), so unconditionally disable
+        # it:
+        options.append('--disable-hinnant-unique-ptr')
+        # libMesh does not allow for us to specify an installation location for
+        # zlib, an undocumented dependency of gzstreams: hence we must
+        # unconditionally disable gzstreams.
+        options.append('--enable-gzstreams=no')
+        # Similarly, since we cannot specify a location for bzip2 or xz, so
+        # disable them to avoid picking up system installations:
+        options.append('--disable-bzip2')
+        options.append('--disable-xz')
+        # TODO enable GDB backtracing. Disable for now to avoid picking up the
+        # system gdb installation:
+        options.append('--without-gdb-command')
 
-        make()
+        # TODO add X11 as a dependency to get tecplot working
-        make('install')
+        options.append('--enable-tecio=no')
+        options.append('--enable-tecplot=no')
+
+        # handle the bundled libraries that are not themselves dependencies of
+        # other bundled libaries:
+        for bundled_library in ['capnproto', 'exodusii', 'fparser', 'gmv',
+                                'laspack', 'libHilbert', 'metaphysicl',
+                                'nanoflann', 'nemesis', 'parmetis', 'qhull',
+                                'sfc', 'tetgen', 'triangle']:
+            if '+' + bundled_library.lower() in self.spec:
+                options.append('--enable-' + bundled_library + "=yes")
+            else:
+                options.append('--enable-' + bundled_library + "=no")
+
+        # and the ones which are dependencies of other bundled libraries:
+        if '+exodusii' in self.spec or '+netcdf' in self.spec:
+            options.append('--enable-netcdf=yes')
+        else:
+            options.append('--enable-netcdf=no')
+
+        # handle external library dependencies:
+        if '+boost' in self.spec:
+            options.append('--with-boost=%s' % self.spec['boost'].prefix)
+        else:
+            options.append('--enable-boost=no')
+
+        if '+eigen' in self.spec:
+            options.append('--with-eigen=%s' % self.spec['eigen'].prefix)
+        else:
+            options.append('--enable-eigen=no')
+
+        if '+hdf5' in self.spec:
+            options.append('--with-hdf5=%s' % self.spec['hdf5'].prefix)
+        else:
+            options.append('--enable-hdf5=no')
+            # This is necessary with libMesh 1.2.1 to prevent a configure
+            # error:
+            if '+netcdf' not in self.spec:
+                options.append('--disable-netcdf-4')
+
+        if '+metis' in self.spec:
+            options.append('--with-metis=PETSc')
+
+        if '+petsc' in self.spec:
+            options.append('--enable-petsc=yes')
+            options.append('PETSC_DIR=%s' % self.spec['petsc'].prefix)
+        else:
+            options.append('--enable-petsc=no')
+
+        if '+slepc' in self.spec:
+            options.append('SLEPC_DIR=%s' % self.spec['slepc'].prefix)
+        else:
+            options.append('--enable-slepc=no')
+
+        # and, finally, other things:
+        if '+debug' in self.spec:
+            options.append('--with-methods=dbg')
+        else:
+            options.append('--with-methods=opt')
+
+        if '+mpi' in self.spec:
+            options.append('CC=%s' % self.spec['mpi'].mpicc)
+            options.append('CXX=%s' % self.spec['mpi'].mpicxx)
+            options.append('--with-mpi=%s' % self.spec['mpi'].prefix)
+        else:
+            options.append('--disable-mpi')
+            # libMesh will try to link with the system MPI library unless we
+            # provide explicit overrides
+            options.append('CC=%s' % self.compiler.cc)
+            options.append('CXX=%s' % self.compiler.cxx)
+
+        if 'threads=openmp' in self.spec:
+            # OpenMP cannot be used if pthreads is not available: see
+            # parallel/threads_pthread.h and parallel/threads.h
+            options.append('--enable-openmp=yes')
+            options.append('--with-thread-model=pthread')
+            options.append('--enable-pthreads=yes')
+        else:
+            options.append('--enable-openmp=no')
+
+        if 'threads=pthreads' in self.spec:
+            options.append('--with-thread-model=pthread')
+            options.append('--enable-pthreads=yes')
+        else:
+            if 'threads=openmp' not in self.spec:
+                options.append('--enable-pthreads=no')
+
+        if 'threads=tbb' in self.spec:
+            options.append('--with-thread-model=tbb')
+            options.append('--enable-tbb=yes')
+            options.append('--with-tbb=%s' % self.spec['tbb'].prefix)
+        else:
+            options.append('--enable-tbb=no')
+
+        return options
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.append_flags('PERL', self.spec['perl'].command.path)