Update for 'netcdf'. (#5819)
This commit is contained in:
Sergey Kosukhin
Todd Gamblin
parent
b43064190c
commit
c9810f8088
@ -53,12 +53,20 @@ class Netcdf(AutotoolsPackage):
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version('4.3.3.1', '5c9dad3705a3408d27f696e5b31fb88c')
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version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae')
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variant('mpi', default=True, description='Enables MPI parallelism')
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variant('hdf4', default=False, description='Enable HDF4 support')
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variant('shared', default=True, description='Enable shared library')
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variant('parallel-netcdf', default=False, description='Enable PnetCDF support')
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variant('dap', default=False, description='Enable DAP support')
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variant('cdmremote', default=False, description='Enable CDM Remote support')
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variant('mpi', default=True,
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description='Enable parallel I/O for netcdf-4')
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variant('parallel-netcdf', default=False,
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description='Enable parallel I/O for classic files')
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variant('hdf4', default=False, description='Enable HDF4 support')
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variant('shared', default=True, description='Enable shared library')
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variant('dap', default=False, description='Enable DAP support')
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# It's unclear if cdmremote can be enabled if '--enable-netcdf-4' is passed
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# to the configure script. Since netcdf-4 support is mandatory we comment
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# this variant out.
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# variant('cdmremote', default=False,
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# description='Enable CDM Remote support')
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# These variants control the number of dimensions (i.e. coordinates and
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# attributes) and variables (e.g. time, entity ID, number of coordinates)
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# that can be used in any particular NetCDF file.
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@ -77,17 +85,57 @@ class Netcdf(AutotoolsPackage):
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depends_on("m4", type='build')
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depends_on("hdf", when='+hdf4')
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depends_on("curl@7.18.0:", when='+dap')
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depends_on("curl@7.18.0:", when='+cdmremote')
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depends_on('parallel-netcdf', when='@4.2.1.1:+parallel-netcdf')
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# Required for NetCDF-4 support
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# curl 7.18.0 or later is required:
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# http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html
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depends_on("curl@7.18.0:", when='+dap')
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# depends_on("curl@7.18.0:", when='+cdmremote')
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depends_on('parallel-netcdf', when='+parallel-netcdf')
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# We need to build with MPI wrappers if any of the two
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# parallel I/O features is enabled:
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# http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html#build_parallel
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depends_on('mpi', when='+mpi')
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depends_on('mpi', when='+parallel-netcdf')
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# zlib 1.2.5 or later is required for netCDF-4 compression:
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# http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html
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depends_on("zlib@1.2.5:")
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depends_on('hdf5+hl')
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# High-level API of HDF5 1.8.9 or later is required for netCDF-4 support:
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# http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html
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depends_on('hdf5@1.8.9:+hl')
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# Starting version 4.4.0, it became possible to disable parallel I/O even
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# if HDF5 supports it. For previous versions of the library we need
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# HDF5 without mpi support to disable parallel I/O.
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# The following doesn't work if hdf5+mpi by default and netcdf~mpi is
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# specified in packages.yaml
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# depends_on('hdf5~mpi', when='@:4.3~mpi')
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# Thus, we have to introduce a conflict
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conflicts('~mpi', when='@:4.3^hdf5+mpi',
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msg='netcdf@:4.3~mpi requires hdf5~mpi')
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# We need HDF5 with mpi support to enable parallel I/O.
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# The following doesn't work if hdf5~mpi by default and netcdf+mpi is
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# specified in packages.yaml
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# depends_on('hdf5+mpi', when='+mpi')
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# Thus, we have to introduce a conflict
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conflicts('+mpi', when='^hdf5~mpi',
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msg='netcdf+mpi requires hdf5+mpi')
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# NetCDF 4.4.0 and prior have compatibility issues with HDF5 1.10 and later
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# https://github.com/Unidata/netcdf-c/issues/250
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depends_on('hdf5@:1.8', when='@:4.4.0')
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depends_on('hdf5@:1.8.999', when='@:4.4.0')
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# The feature was introduced in version 4.1.2
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# and was removed in version 4.4.0
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# conflicts('+cdmremote', when='@:4.1.1,4.4:')
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# The features were introduced in version 4.1.0
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conflicts('+parallel-netcdf', when='@:4.0')
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conflicts('+hdf4', when='@:4.0')
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def patch(self):
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try:
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@ -104,91 +152,96 @@ def patch(self):
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r'\1{0}\2'.format(max_vars))
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def configure_args(self):
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spec = self.spec
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# Workaround until variant forwarding works properly
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if '+mpi' in spec and spec.satisfies('^hdf5~mpi'):
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raise RuntimeError('Invalid spec. Package netcdf requires '
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'hdf5+mpi, but spec asked for hdf5~mpi.')
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# Environment variables
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CFLAGS = []
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CFLAGS = []
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CPPFLAGS = []
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LDFLAGS = []
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LIBS = []
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LDFLAGS = []
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LIBS = []
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config_args = [
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"--enable-fsync",
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"--enable-v2",
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"--enable-utilities",
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"--enable-static",
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"--enable-largefile",
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# necessary for HDF5 support
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"--enable-netcdf-4",
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"--enable-dynamic-loading",
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]
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config_args = ['--enable-v2',
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'--enable-utilities',
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'--enable-static',
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'--enable-largefile',
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'--enable-netcdf-4']
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if '+shared' in 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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# The flag was introduced in version 4.1.0
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if self.spec.satisfies('@4.1:'):
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config_args.append('--enable-fsync')
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# The flag was introduced in version 4.3.1
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if self.spec.satisfies('@4.3.1:'):
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config_args.append('--enable-dynamic-loading')
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config_args += self.enable_or_disable('shared')
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if '~shared' in self.spec:
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# We don't have shared libraries but we still want it to be
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# possible to use this library in shared builds
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CFLAGS.append(self.compiler.pic_flag)
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if '+dap' in spec:
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config_args.append('--enable-dap')
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else:
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config_args.append('--disable-dap')
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config_args += self.enable_or_disable('dap')
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# config_args += self.enable_or_disable('cdmremote')
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if '+cdmremote' in spec:
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config_args.append('--enable-cdmremote')
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else:
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config_args.append('--disable-cdmremote')
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if '+dap' in spec or '+cdmremote' in spec:
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# if '+dap' in self.spec or '+cdmremote' in self.spec:
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if '+dap' in self.spec:
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# Make sure Netcdf links against Spack's curl, otherwise it may
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# pick up system's curl, which can give link errors, e.g.:
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# undefined reference to `SSL_CTX_use_certificate_chain_file`
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LIBS.append("-lcurl")
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CPPFLAGS.append("-I%s" % spec['curl'].prefix.include)
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LDFLAGS.append("-L%s" % spec['curl'].prefix.lib)
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# undefined reference to `SSL_CTX_use_certificate_chain_file
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curl = self.spec['curl']
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curl_libs = curl.libs
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LIBS.append(curl_libs.link_flags)
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LDFLAGS.append(curl_libs.search_flags)
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# TODO: figure out how to get correct flags via headers.cpp_flags
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CPPFLAGS.append('-I' + curl.prefix.include)
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if '+mpi' in spec:
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config_args.append('--enable-parallel4')
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config_args.append('CC=%s' % spec['mpi'].mpicc)
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if self.spec.satisfies('@4.4:'):
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if '+mpi' in self.spec:
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config_args.append('--enable-parallel4')
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else:
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config_args.append('--disable-parallel4')
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CPPFLAGS.append("-I%s/include" % spec['hdf5'].prefix)
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LDFLAGS.append("-L%s/lib" % spec['hdf5'].prefix)
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# Starting version 4.1.3, --with-hdf5= and other such configure options
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# are removed. Variables CPPFLAGS, LDFLAGS, and LD_LIBRARY_PATH must be
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# used instead.
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hdf5_hl = self.spec['hdf5:hl']
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CPPFLAGS.append(hdf5_hl.headers.cpp_flags)
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LDFLAGS.append(hdf5_hl.libs.search_flags)
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# HDF4 support
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# As of NetCDF 4.1.3, "--with-hdf4=..." is no longer a valid option
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# You must use the environment variables CPPFLAGS and LDFLAGS
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if '+hdf4' in spec:
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config_args.append("--enable-hdf4")
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CPPFLAGS.append("-I%s/include" % spec['hdf'].prefix)
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LDFLAGS.append("-L%s/lib" % spec['hdf'].prefix)
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LIBS.append("-l%s" % "jpeg")
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if '+szip' in spec:
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CPPFLAGS.append("-I%s/include" % spec['szip'].prefix)
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LDFLAGS.append("-L%s/lib" % spec['szip'].prefix)
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LIBS.append("-l%s" % "sz")
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# PnetCDF support
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if '+parallel-netcdf' in spec:
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if '+parallel-netcdf' in self.spec:
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config_args.append('--enable-pnetcdf')
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config_args.append('CC=%s' % spec['mpi'].mpicc)
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CPPFLAGS.append("-I%s/include" % spec['parallel-netcdf'].prefix)
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LDFLAGS.append("-L%s/lib" % spec['parallel-netcdf'].prefix)
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pnetcdf = self.spec['parallel-netcdf']
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CPPFLAGS.append(pnetcdf.headers.cpp_flags)
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# TODO: change to pnetcdf.libs.search_flags once 'parallel-netcdf'
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# package gets custom implementation of 'libs'
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LDFLAGS.append('-L' + pnetcdf.prefix.lib)
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else:
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config_args.append('--disable-pnetcdf')
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if '+mpi' in self.spec or '+parallel-netcdf' in self.spec:
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config_args.append('CC=%s' % self.spec['mpi'].mpicc)
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config_args += self.enable_or_disable('hdf4')
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if '+hdf4' in self.spec:
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hdf4 = self.spec['hdf']
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CPPFLAGS.append(hdf4.headers.cpp_flags)
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# TODO: change to hdf4.libs.search_flags once 'hdf'
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# package gets custom implementation of 'libs' property.
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LDFLAGS.append('-L' + hdf4.prefix.lib)
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# TODO: change to self.spec['jpeg'].libs.link_flags once the
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# implementations of 'jpeg' virtual package get 'jpeg_libs'
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# property.
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LIBS.append('-ljpeg')
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if '+szip' in hdf4:
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# This should also come from hdf4.libs
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LIBS.append('-lsz')
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# Fortran support
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# In version 4.2+, NetCDF-C and NetCDF-Fortran have split.
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# Use the netcdf-fortran package to install Fortran support.
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config_args.append('CFLAGS=%s' % ' '.join(CFLAGS))
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config_args.append('CPPFLAGS=%s' % ' '.join(CPPFLAGS))
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config_args.append('LDFLAGS=%s' % ' '.join(LDFLAGS))
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config_args.append('LIBS=%s' % ' '.join(LIBS))
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config_args.append('CFLAGS=' + ' '.join(CFLAGS))
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config_args.append('CPPFLAGS=' + ' '.join(CPPFLAGS))
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config_args.append('LDFLAGS=' + ' '.join(LDFLAGS))
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config_args.append('LIBS=' + ' '.join(LIBS))
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return config_args
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