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Update for 'netcdf'. (spack#5819)
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@skosukhin @tgamblin
skosukhin authored and tgamblin committed Oct 25, 2017
1 parent b430641 commit c9810f8
Showing 1 changed file with 135 additions and 82 deletions.
217 changes: 135 additions & 82 deletions var/spack/repos/builtin/packages/netcdf/package.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand All @@ -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("[email protected]:", when='+dap')
depends_on("[email protected]:", when='+cdmremote')
depends_on('parallel-netcdf', when='@4.2.1.1:+parallel-netcdf')
# depends_on("[email protected]:", 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("[email protected]:")
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('[email protected]:+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:
Expand All @@ -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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