From c9810f8088ad2511ed02e5d3891bd8ed0742adbc Mon Sep 17 00:00:00 2001
From: Sergey Kosukhin <skosukhin@gmail.com>
Date: Wed, 25 Oct 2017 14:30:58 +0200
Subject: [PATCH] Update for 'netcdf'. (#5819)
---
.../repos/builtin/packages/netcdf/package.py | 217 +++++++++++-------
1 file 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 @@ def patch(self):
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
--
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