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##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import numbers
def is_integral(x):
"""Any integer value"""
try:
return isinstance(int(x), numbers.Integral) and not isinstance(x, bool)
except ValueError:
return False
class Netcdf(AutotoolsPackage):
"""NetCDF is a set of software libraries and self-describing,
machine-independent data formats that support the creation, access,
and sharing of array-oriented scientific data."""
homepage = "http://www.unidata.ucar.edu/software/netcdf"
url = "http://www.gfd-dennou.org/arch/netcdf/unidata-mirror/netcdf-4.3.3.tar.gz"
# Version 4.4.1.1 is having problems in tests
# https://github.com/Unidata/netcdf-c/issues/343
version('4.4.1.1', '503a2d6b6035d116ed53b1d80c811bda')
# netcdf@4.4.1 can crash on you (in real life and in tests). See:
# https://github.com/Unidata/netcdf-c/issues/282
version('4.4.1', '7843e35b661c99e1d49e60791d5072d8')
version('4.4.0', 'cffda0cbd97fdb3a06e9274f7aef438e')
version('4.3.3.1', '5c9dad3705a3408d27f696e5b31fb88c')
version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae')
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.
variant(
'maxdims',
default=1024,
description='Defines the maximum dimensions of NetCDF files.',
values=is_integral
)
variant(
'maxvars',
default=8192,
description='Defines the maximum variables of NetCDF files.',
values=is_integral
)
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='+parallel-netcdf')
# 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:")
# 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@:1.8.999', 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:
max_dims = int(self.spec.variants['maxdims'].value)
max_vars = int(self.spec.variants['maxvars'].value)
except (ValueError, TypeError):
raise TypeError('NetCDF variant values max[dims|vars] must be '
'integer values.')
ff = FileFilter(join_path('include', 'netcdf.h'))
ff.filter(r'^(#define\s+NC_MAX_DIMS\s+)\d+(.*)$',
r'\1{0}\2'.format(max_dims))
ff.filter(r'^(#define\s+NC_MAX_VARS\s+)\d+(.*)$',
r'\1{0}\2'.format(max_vars))
def configure_args(self):
CFLAGS = []
CPPFLAGS = []
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)
config_args += self.enable_or_disable('dap')
# config_args += self.enable_or_disable('cdmremote')
# 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
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')
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=' + ' '.join(CFLAGS))
config_args.append('CPPFLAGS=' + ' '.join(CPPFLAGS))
config_args.append('LDFLAGS=' + ' '.join(LDFLAGS))
config_args.append('LIBS=' + ' '.join(LIBS))
return config_args
def check(self):
# h5_test fails when run in parallel
make('check', parallel=False)
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