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authorDom Heinzeller <dom.heinzeller@icloud.com>2022-04-14 11:10:30 -0600
committerGitHub <noreply@github.com>2022-04-14 10:10:30 -0700
commitbb70e6ffcd6e6920b24677593a35987d1eb05ce1 (patch)
treec06aa12f79cba207dea41b67c59974d158d1c455
parentb09fb467f162e30903acf6ddc7a12a2969147b68 (diff)
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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>
-rw-r--r--var/spack/repos/builtin/packages/netcdf-cxx4/package.py133
-rw-r--r--var/spack/repos/builtin/packages/netcdf-fortran/package.py16
2 files changed, 103 insertions, 46 deletions
diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
index fc475be5ca..012ab9ace2 100644
--- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
@@ -3,6 +3,8 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+import os
+
from spack import *
@@ -19,61 +21,122 @@ class NetcdfCxx4(AutotoolsPackage):
version('4.3.1', sha256='6a1189a181eed043b5859e15d5c080c30d0e107406fbb212c8fb9814e90f3445')
version('4.3.0', sha256='e34fbc6aba243ec82c23e9ee99db2430555ada849c54c1f3ab081b0ddd0f5f30')
- # Usually the configure automatically inserts the pic flags, but we can
- # force its usage with this variant.
- variant('static', default=True, description='Enable building static libraries')
variant('shared', default=True, description='Enable shared library')
variant('pic', default=True, description='Produce position-independent code (for shared libs)')
- variant('doxygen', default=True, description='Enable doxygen docs')
+ variant('doc', default=False, description='Enable doxygen docs')
depends_on('netcdf-c')
- depends_on('automake', type='build')
- depends_on('autoconf', type='build')
- depends_on('libtool', type='build')
- depends_on('m4', type='build')
- depends_on('doxygen', when='+doxygen', type='build')
-
- conflicts('~shared', when='~static')
-
- force_autoreconf = True
+ depends_on('doxygen', when='+doc', type='build')
def flag_handler(self, name, flags):
if name == 'cflags' and '+pic' in self.spec:
flags.append(self.compiler.cc_pic_flag)
- elif name == 'cppflags':
- flags.append('-I' + self.spec['netcdf-c'].prefix.include)
-
- return (None, None, flags)
+ if name == 'cxxflags' and '+pic' in self.spec:
+ flags.append(self.compiler.cxx_pic_flag)
+ elif name == 'ldlibs':
+ # Address the underlinking problem reported in
+ # https://github.com/Unidata/netcdf-cxx4/issues/86, which also
+ # results into a linking error on macOS:
+ flags.append(self.spec['netcdf-c'].libs.link_flags)
+
+ # Note that cflags and cxxflags should be added by the compiler wrapper
+ # and not on the command line to avoid overriding the default
+ # compilation flags set by the configure script:
+ return flags, None, None
@property
def libs(self):
- shared = True
- return find_libraries(
- 'libnetcdf_c++4', root=self.prefix, shared=shared, recursive=True
- )
+ libraries = ['libnetcdf_c++4']
- def configure_args(self):
- config_args = []
+ query_parameters = self.spec.last_query.extra_parameters
- if '+static' in self.spec:
- config_args.append('--enable-static')
+ if 'shared' in query_parameters:
+ shared = True
+ elif 'static' in query_parameters:
+ shared = False
else:
- config_args.append('--disable-static')
+ shared = '+shared' in self.spec
- if '+shared' in self.spec:
- config_args.append('--enable-shared')
- else:
- config_args.append('--disable-shared')
+ libs = find_libraries(
+ libraries, root=self.prefix, shared=shared, recursive=True
+ )
- if '+pic' in self.spec:
- config_args.append('--with-pic')
- else:
- config_args.append('--without-pic')
+ if libs:
+ return libs
+
+ msg = 'Unable to recursively locate {0} {1} libraries in {2}'
+ raise spack.error.NoLibrariesError(
+ msg.format('shared' if shared else 'static',
+ self.spec.name,
+ self.spec.prefix))
+
+ @when('@4.3.1:+shared')
+ @on_package_attributes(run_tests=True)
+ def patch(self):
+ # We enable the filter tests only when the tests are requested by the
+ # user. This, however, has a side effect: an extra file 'libh5bzip2.so'
+ # gets installed (note that the file has .so extension even on darwin).
+ # It's unclear whether that is intended but given the description of the
+ # configure option --disable-filter-testing (Do not run filter test and
+ # example; requires shared libraries and netCDF-4), we currently assume
+ # that the file is not really meant for the installation. To make all
+ # installations consistent and independent of whether the shared
+ # libraries or the tests are requested, we prevent installation of
+ # 'libh5bzip2.so':
+ filter_file(r'(^\s*)lib(_LTLIBRARIES\s*)(=\s*libh5bzip2\.la\s*$)',
+ r'\1noinst\2+\3', join_path(self.stage.source_path,
+ 'plugins', 'Makefile.in'))
+
+ def configure_args(self):
+ config_args = self.enable_or_disable('shared')
- if '+doxygen' in self.spec:
+ if '+doc' in self.spec:
config_args.append('--enable-doxygen')
else:
config_args.append('--disable-doxygen')
+ if self.spec.satisfies('@4.3.1:'):
+ if self.run_tests and '+shared' in self.spec:
+ config_args.append('--enable-filter-testing')
+ if self.spec.satisfies('^hdf5+mpi'):
+ # The package itself does not need the MPI libraries but
+ # includes <hdf5.h> in the filter test C code, which
+ # requires <mpi.h> when HDF5 is built with the MPI support.
+ # Using the MPI wrapper introduces overlinking to MPI
+ # libraries and we would prefer not to use it but it is the
+ # only reliable way to provide the compiler with the correct
+ # path to <mpi.h>. For example, <mpi.h> of a MacPorts-built
+ # MPICH might reside in /opt/local/include/mpich-gcc10,
+ # which Spack does not know about and cannot inject with its
+ # compiler wrapper.
+ config_args.append('CC={0}'.format(self.spec['mpi'].mpicc))
+ else:
+ config_args.append('--disable-filter-testing')
+
return config_args
+
+ @run_after('configure')
+ def rename_version(self):
+ # See https://github.com/Unidata/netcdf-cxx4/issues/109
+ # The issue is fixed upstream:
+ # https://github.com/Unidata/netcdf-cxx4/commit/e7cc5bab02cf089dc79616456a0a951fee979fe9
+ # We do not apply the upstream patch because we want to avoid running
+ # autoreconf and introduce additional dependencies. We do not generate a
+ # patch for the configure script because the patched string contains the
+ # version and we would need a patch file for each supported version of
+ # the library. We do not implement the patching with filter_file in the
+ # patch method because writing a robust regexp seems to be more
+ # difficult that simply renaming the file if exists. It also looks like
+ # we can simply remove the file since it is not used anywhere.
+ if not self.spec.satisfies('@:4.3.1 platform=darwin'):
+ return
+
+ with working_dir(self.build_directory):
+ fname = 'VERSION'
+ if os.path.exists(fname):
+ os.rename(fname, '{0}.txt'.format(fname))
+
+ def check(self):
+ with working_dir(self.build_directory):
+ make('check', parallel=False)
diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
index d3843ccd0b..c79c8af46a 100644
--- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
@@ -62,8 +62,6 @@ class NetcdfFortran(AutotoolsPackage):
patch('no_parallel_build.patch', when='@4.5.2')
def flag_handler(self, name, flags):
- config_flags = None
-
if name == 'cflags':
if '+pic' in self.spec:
flags.append(self.compiler.cc_pic_flag)
@@ -81,15 +79,11 @@ class NetcdfFortran(AutotoolsPackage):
# The following flag forces the compiler to produce module
# files with lowercase names.
flags.append('-ef')
- elif name == 'ldflags':
- # We need to specify LDFLAGS to get correct dependency_libs
- # in libnetcdff.la, so packages that use libtool for linking
- # could correctly link to all the dependencies even when the
- # building takes place outside of Spack environment, i.e.
- # without Spack's compiler wrappers.
- config_flags = [self.spec['netcdf-c'].libs.search_flags]
-
- return flags, None, config_flags
+
+ # Note that cflags and fflags should be added by the compiler wrapper
+ # and not on the command line to avoid overriding the default
+ # compilation flags set by the configure script:
+ return flags, None, None
@property
def libs(self):