diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/netcdf/package.py | 217 |
1 files changed, 135 insertions, 82 deletions
diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py index 813b048bfc..1b3c9b7d48 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf/package.py @@ -53,12 +53,20 @@ class Netcdf(AutotoolsPackage): version('4.3.3.1', '5c9dad3705a3408d27f696e5b31fb88c') version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae') - variant('mpi', default=True, description='Enables MPI parallelism') - variant('hdf4', default=False, description='Enable HDF4 support') - variant('shared', default=True, description='Enable shared library') - variant('parallel-netcdf', default=False, description='Enable PnetCDF support') - variant('dap', default=False, description='Enable DAP support') - variant('cdmremote', default=False, description='Enable CDM Remote support') + variant('mpi', default=True, + description='Enable parallel I/O for netcdf-4') + variant('parallel-netcdf', default=False, + description='Enable parallel I/O for classic files') + variant('hdf4', default=False, description='Enable HDF4 support') + variant('shared', default=True, description='Enable shared library') + variant('dap', default=False, description='Enable DAP support') + + # It's unclear if cdmremote can be enabled if '--enable-netcdf-4' is passed + # to the configure script. Since netcdf-4 support is mandatory we comment + # this variant out. + # variant('cdmremote', default=False, + # description='Enable CDM Remote support') + # These variants control the number of dimensions (i.e. coordinates and # attributes) and variables (e.g. time, entity ID, number of coordinates) # that can be used in any particular NetCDF file. @@ -77,17 +85,57 @@ class Netcdf(AutotoolsPackage): depends_on("m4", type='build') depends_on("hdf", when='+hdf4') + + # curl 7.18.0 or later is required: + # http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html depends_on("curl@7.18.0:", when='+dap') - depends_on("curl@7.18.0:", when='+cdmremote') - depends_on('parallel-netcdf', when='@4.2.1.1:+parallel-netcdf') + # depends_on("curl@7.18.0:", when='+cdmremote') + + depends_on('parallel-netcdf', when='+parallel-netcdf') - # Required for NetCDF-4 support + # We need to build with MPI wrappers if any of the two + # parallel I/O features is enabled: + # http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html#build_parallel + depends_on('mpi', when='+mpi') + depends_on('mpi', when='+parallel-netcdf') + + # zlib 1.2.5 or later is required for netCDF-4 compression: + # http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html depends_on("zlib@1.2.5:") - depends_on('hdf5+hl') + + # High-level API of HDF5 1.8.9 or later is required for netCDF-4 support: + # http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html + depends_on('hdf5@1.8.9:+hl') + + # Starting version 4.4.0, it became possible to disable parallel I/O even + # if HDF5 supports it. For previous versions of the library we need + # HDF5 without mpi support to disable parallel I/O. + # The following doesn't work if hdf5+mpi by default and netcdf~mpi is + # specified in packages.yaml + # depends_on('hdf5~mpi', when='@:4.3~mpi') + # Thus, we have to introduce a conflict + conflicts('~mpi', when='@:4.3^hdf5+mpi', + msg='netcdf@:4.3~mpi requires hdf5~mpi') + + # We need HDF5 with mpi support to enable parallel I/O. + # The following doesn't work if hdf5~mpi by default and netcdf+mpi is + # specified in packages.yaml + # depends_on('hdf5+mpi', when='+mpi') + # Thus, we have to introduce a conflict + conflicts('+mpi', when='^hdf5~mpi', + msg='netcdf+mpi requires hdf5+mpi') # NetCDF 4.4.0 and prior have compatibility issues with HDF5 1.10 and later # https://github.com/Unidata/netcdf-c/issues/250 - depends_on('hdf5@:1.8', when='@:4.4.0') + depends_on('hdf5@:1.8.999', when='@:4.4.0') + + # The feature was introduced in version 4.1.2 + # and was removed in version 4.4.0 + # conflicts('+cdmremote', when='@:4.1.1,4.4:') + + # The features were introduced in version 4.1.0 + conflicts('+parallel-netcdf', when='@:4.0') + conflicts('+hdf4', when='@:4.0') def patch(self): try: @@ -104,91 +152,96 @@ class Netcdf(AutotoolsPackage): r'\1{0}\2'.format(max_vars)) def configure_args(self): - spec = self.spec - # Workaround until variant forwarding works properly - if '+mpi' in spec and spec.satisfies('^hdf5~mpi'): - raise RuntimeError('Invalid spec. Package netcdf requires ' - 'hdf5+mpi, but spec asked for hdf5~mpi.') - - # Environment variables - CFLAGS = [] + CFLAGS = [] CPPFLAGS = [] - LDFLAGS = [] - LIBS = [] - - config_args = [ - "--enable-fsync", - "--enable-v2", - "--enable-utilities", - "--enable-static", - "--enable-largefile", - # necessary for HDF5 support - "--enable-netcdf-4", - "--enable-dynamic-loading", - ] - - if '+shared' in spec: - config_args.append('--enable-shared') - else: - config_args.append('--disable-shared') + LDFLAGS = [] + LIBS = [] + + config_args = ['--enable-v2', + '--enable-utilities', + '--enable-static', + '--enable-largefile', + '--enable-netcdf-4'] + + # The flag was introduced in version 4.1.0 + if self.spec.satisfies('@4.1:'): + config_args.append('--enable-fsync') + + # The flag was introduced in version 4.3.1 + if self.spec.satisfies('@4.3.1:'): + config_args.append('--enable-dynamic-loading') + + config_args += self.enable_or_disable('shared') + + if '~shared' in self.spec: # We don't have shared libraries but we still want it to be # possible to use this library in shared builds CFLAGS.append(self.compiler.pic_flag) - if '+dap' in spec: - config_args.append('--enable-dap') - else: - config_args.append('--disable-dap') - - if '+cdmremote' in spec: - config_args.append('--enable-cdmremote') - else: - config_args.append('--disable-cdmremote') + config_args += self.enable_or_disable('dap') + # config_args += self.enable_or_disable('cdmremote') - if '+dap' in spec or '+cdmremote' in spec: + # if '+dap' in self.spec or '+cdmremote' in self.spec: + if '+dap' in self.spec: # Make sure Netcdf links against Spack's curl, otherwise it may # pick up system's curl, which can give link errors, e.g.: - # undefined reference to `SSL_CTX_use_certificate_chain_file` - LIBS.append("-lcurl") - CPPFLAGS.append("-I%s" % spec['curl'].prefix.include) - LDFLAGS.append("-L%s" % spec['curl'].prefix.lib) - - if '+mpi' in spec: - config_args.append('--enable-parallel4') - config_args.append('CC=%s' % spec['mpi'].mpicc) - - CPPFLAGS.append("-I%s/include" % spec['hdf5'].prefix) - LDFLAGS.append("-L%s/lib" % spec['hdf5'].prefix) - - # HDF4 support - # As of NetCDF 4.1.3, "--with-hdf4=..." is no longer a valid option - # You must use the environment variables CPPFLAGS and LDFLAGS - if '+hdf4' in spec: - config_args.append("--enable-hdf4") - CPPFLAGS.append("-I%s/include" % spec['hdf'].prefix) - LDFLAGS.append("-L%s/lib" % spec['hdf'].prefix) - LIBS.append("-l%s" % "jpeg") - - if '+szip' in spec: - CPPFLAGS.append("-I%s/include" % spec['szip'].prefix) - LDFLAGS.append("-L%s/lib" % spec['szip'].prefix) - LIBS.append("-l%s" % "sz") - - # PnetCDF support - if '+parallel-netcdf' in spec: + # undefined reference to `SSL_CTX_use_certificate_chain_file + curl = self.spec['curl'] + curl_libs = curl.libs + LIBS.append(curl_libs.link_flags) + LDFLAGS.append(curl_libs.search_flags) + # TODO: figure out how to get correct flags via headers.cpp_flags + CPPFLAGS.append('-I' + curl.prefix.include) + + if self.spec.satisfies('@4.4:'): + if '+mpi' in self.spec: + config_args.append('--enable-parallel4') + else: + config_args.append('--disable-parallel4') + + # Starting version 4.1.3, --with-hdf5= and other such configure options + # are removed. Variables CPPFLAGS, LDFLAGS, and LD_LIBRARY_PATH must be + # used instead. + hdf5_hl = self.spec['hdf5:hl'] + CPPFLAGS.append(hdf5_hl.headers.cpp_flags) + LDFLAGS.append(hdf5_hl.libs.search_flags) + + if '+parallel-netcdf' in self.spec: config_args.append('--enable-pnetcdf') - config_args.append('CC=%s' % spec['mpi'].mpicc) - CPPFLAGS.append("-I%s/include" % spec['parallel-netcdf'].prefix) - LDFLAGS.append("-L%s/lib" % spec['parallel-netcdf'].prefix) + pnetcdf = self.spec['parallel-netcdf'] + CPPFLAGS.append(pnetcdf.headers.cpp_flags) + # TODO: change to pnetcdf.libs.search_flags once 'parallel-netcdf' + # package gets custom implementation of 'libs' + LDFLAGS.append('-L' + pnetcdf.prefix.lib) + else: + config_args.append('--disable-pnetcdf') + + if '+mpi' in self.spec or '+parallel-netcdf' in self.spec: + config_args.append('CC=%s' % self.spec['mpi'].mpicc) + + config_args += self.enable_or_disable('hdf4') + if '+hdf4' in self.spec: + hdf4 = self.spec['hdf'] + CPPFLAGS.append(hdf4.headers.cpp_flags) + # TODO: change to hdf4.libs.search_flags once 'hdf' + # package gets custom implementation of 'libs' property. + LDFLAGS.append('-L' + hdf4.prefix.lib) + # TODO: change to self.spec['jpeg'].libs.link_flags once the + # implementations of 'jpeg' virtual package get 'jpeg_libs' + # property. + LIBS.append('-ljpeg') + if '+szip' in hdf4: + # This should also come from hdf4.libs + LIBS.append('-lsz') # Fortran support # In version 4.2+, NetCDF-C and NetCDF-Fortran have split. # Use the netcdf-fortran package to install Fortran support. - config_args.append('CFLAGS=%s' % ' '.join(CFLAGS)) - config_args.append('CPPFLAGS=%s' % ' '.join(CPPFLAGS)) - config_args.append('LDFLAGS=%s' % ' '.join(LDFLAGS)) - config_args.append('LIBS=%s' % ' '.join(LIBS)) + config_args.append('CFLAGS=' + ' '.join(CFLAGS)) + config_args.append('CPPFLAGS=' + ' '.join(CPPFLAGS)) + config_args.append('LDFLAGS=' + ' '.join(LDFLAGS)) + config_args.append('LIBS=' + ' '.join(LIBS)) return config_args |