netcdf-cxx4 Package: updates to build on Mac OS (#29246)
Bug fixes for package netcdf-cxx4 so that it builds on macOS semi case-sensitive filesystems; this includes additional changes to build netcdf-cxx4 consistently with netcdf-fortran. * netcdf-fortran: remove unused config_flags * netcdf-fortran: avoid building without the optimization flags * netcdf-cxx4: do not enforce autoreconf. This was a rudiment from the times when the package was fetched with git, which broke timestamp order of the automatically generated Autoconf files. * netcdf-cxx4: inject PIC flags for C++ when '+pic' * netcdf-cxx4: inject C/CXXFLAGS via the wrapper * netcdf-cxx4: fix the underlinking problem for platforms other than darwin (add netcdf-c libs netcdf-cxx4 ldlibs flags) * netcdf-cxx4: remove redundant extension of CPPFLAGS * netcdf-cxx4: only need to use MPI compiler wrapper when building C (vs both C and C++) * netcdf-cxx4: remove variant 'static' This makes it consistent with other packages from the NetCDF constellation: always build the static libraries and additionally build the shared ones when '+shared'. * netcdf-cxx4: do not configure --with/--without-pic. This makes it consistent with other packages from the NetCDF constellation: build the shared libraries with the PIC flag and the static ones without it (the default for Autotools) when '~pic', and build the static libraries with PIC when '+pic' (to make them injectable into other shared libraries). * netcdf-cxx4: run the tests serially * netcdf-cxx4: build the plugins only when the tests are run Co-authored-by: Sergey Kosukhin <sergey.kosukhin@mpimet.mpg.de>
This commit is contained in:
Dom Heinzeller
GitHub
parent
b09fb467f1
commit
bb70e6ffcd
@ -3,6 +3,8 @@
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import os
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from spack import *
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@ -19,61 +21,122 @@ class NetcdfCxx4(AutotoolsPackage):
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version('4.3.1', sha256='6a1189a181eed043b5859e15d5c080c30d0e107406fbb212c8fb9814e90f3445')
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version('4.3.0', sha256='e34fbc6aba243ec82c23e9ee99db2430555ada849c54c1f3ab081b0ddd0f5f30')
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# Usually the configure automatically inserts the pic flags, but we can
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# force its usage with this variant.
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variant('static', default=True, description='Enable building static libraries')
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variant('shared', default=True, description='Enable shared library')
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variant('pic', default=True, description='Produce position-independent code (for shared libs)')
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variant('doxygen', default=True, description='Enable doxygen docs')
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variant('doc', default=False, description='Enable doxygen docs')
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depends_on('netcdf-c')
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depends_on('automake', type='build')
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depends_on('autoconf', type='build')
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depends_on('libtool', type='build')
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depends_on('m4', type='build')
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depends_on('doxygen', when='+doxygen', type='build')
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conflicts('~shared', when='~static')
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force_autoreconf = True
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depends_on('doxygen', when='+doc', type='build')
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def flag_handler(self, name, flags):
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if name == 'cflags' and '+pic' in self.spec:
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flags.append(self.compiler.cc_pic_flag)
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elif name == 'cppflags':
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flags.append('-I' + self.spec['netcdf-c'].prefix.include)
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if name == 'cxxflags' and '+pic' in self.spec:
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flags.append(self.compiler.cxx_pic_flag)
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elif name == 'ldlibs':
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# Address the underlinking problem reported in
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# https://github.com/Unidata/netcdf-cxx4/issues/86, which also
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# results into a linking error on macOS:
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flags.append(self.spec['netcdf-c'].libs.link_flags)
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return (None, None, flags)
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# Note that cflags and cxxflags should be added by the compiler wrapper
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# and not on the command line to avoid overriding the default
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# compilation flags set by the configure script:
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return flags, None, None
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@property
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def libs(self):
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shared = True
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return find_libraries(
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'libnetcdf_c++4', root=self.prefix, shared=shared, recursive=True
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libraries = ['libnetcdf_c++4']
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query_parameters = self.spec.last_query.extra_parameters
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if 'shared' in query_parameters:
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shared = True
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elif 'static' in query_parameters:
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shared = False
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else:
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shared = '+shared' in self.spec
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libs = find_libraries(
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libraries, root=self.prefix, shared=shared, recursive=True
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)
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if libs:
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return libs
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msg = 'Unable to recursively locate {0} {1} libraries in {2}'
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raise spack.error.NoLibrariesError(
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msg.format('shared' if shared else 'static',
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self.spec.name,
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self.spec.prefix))
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@when('@4.3.1:+shared')
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@on_package_attributes(run_tests=True)
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def patch(self):
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# We enable the filter tests only when the tests are requested by the
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# user. This, however, has a side effect: an extra file 'libh5bzip2.so'
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# gets installed (note that the file has .so extension even on darwin).
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# It's unclear whether that is intended but given the description of the
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# configure option --disable-filter-testing (Do not run filter test and
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# example; requires shared libraries and netCDF-4), we currently assume
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# that the file is not really meant for the installation. To make all
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# installations consistent and independent of whether the shared
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# libraries or the tests are requested, we prevent installation of
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# 'libh5bzip2.so':
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filter_file(r'(^\s*)lib(_LTLIBRARIES\s*)(=\s*libh5bzip2\.la\s*$)',
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r'\1noinst\2+\3', join_path(self.stage.source_path,
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'plugins', 'Makefile.in'))
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def configure_args(self):
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config_args = []
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config_args = self.enable_or_disable('shared')
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if '+static' in self.spec:
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config_args.append('--enable-static')
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else:
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config_args.append('--disable-static')
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if '+shared' in self.spec:
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config_args.append('--enable-shared')
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else:
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config_args.append('--disable-shared')
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if '+pic' in self.spec:
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config_args.append('--with-pic')
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else:
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config_args.append('--without-pic')
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if '+doxygen' in self.spec:
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if '+doc' in self.spec:
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config_args.append('--enable-doxygen')
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else:
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config_args.append('--disable-doxygen')
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if self.spec.satisfies('@4.3.1:'):
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if self.run_tests and '+shared' in self.spec:
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config_args.append('--enable-filter-testing')
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if self.spec.satisfies('^hdf5+mpi'):
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# The package itself does not need the MPI libraries but
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# includes <hdf5.h> in the filter test C code, which
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# requires <mpi.h> when HDF5 is built with the MPI support.
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# Using the MPI wrapper introduces overlinking to MPI
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# libraries and we would prefer not to use it but it is the
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# only reliable way to provide the compiler with the correct
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# path to <mpi.h>. For example, <mpi.h> of a MacPorts-built
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# MPICH might reside in /opt/local/include/mpich-gcc10,
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# which Spack does not know about and cannot inject with its
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# compiler wrapper.
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config_args.append('CC={0}'.format(self.spec['mpi'].mpicc))
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else:
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config_args.append('--disable-filter-testing')
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return config_args
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@run_after('configure')
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def rename_version(self):
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# See https://github.com/Unidata/netcdf-cxx4/issues/109
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# The issue is fixed upstream:
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# https://github.com/Unidata/netcdf-cxx4/commit/e7cc5bab02cf089dc79616456a0a951fee979fe9
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# We do not apply the upstream patch because we want to avoid running
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# autoreconf and introduce additional dependencies. We do not generate a
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# patch for the configure script because the patched string contains the
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# version and we would need a patch file for each supported version of
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# the library. We do not implement the patching with filter_file in the
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# patch method because writing a robust regexp seems to be more
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# difficult that simply renaming the file if exists. It also looks like
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# we can simply remove the file since it is not used anywhere.
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if not self.spec.satisfies('@:4.3.1 platform=darwin'):
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return
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with working_dir(self.build_directory):
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fname = 'VERSION'
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if os.path.exists(fname):
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os.rename(fname, '{0}.txt'.format(fname))
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def check(self):
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with working_dir(self.build_directory):
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make('check', parallel=False)
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@ -62,8 +62,6 @@ class NetcdfFortran(AutotoolsPackage):
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patch('no_parallel_build.patch', when='@4.5.2')
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def flag_handler(self, name, flags):
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config_flags = None
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if name == 'cflags':
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if '+pic' in self.spec:
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flags.append(self.compiler.cc_pic_flag)
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@ -81,15 +79,11 @@ def flag_handler(self, name, flags):
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# The following flag forces the compiler to produce module
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# files with lowercase names.
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flags.append('-ef')
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elif name == 'ldflags':
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# We need to specify LDFLAGS to get correct dependency_libs
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# in libnetcdff.la, so packages that use libtool for linking
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# could correctly link to all the dependencies even when the
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# building takes place outside of Spack environment, i.e.
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# without Spack's compiler wrappers.
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config_flags = [self.spec['netcdf-c'].libs.search_flags]
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return flags, None, config_flags
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# Note that cflags and fflags should be added by the compiler wrapper
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# and not on the command line to avoid overriding the default
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# compilation flags set by the configure script:
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return flags, None, None
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@property
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def libs(self):
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