252 lines
10 KiB
Python
252 lines
10 KiB
Python
##############################################################################
|
|
# Copyright (c) 2013-2018, 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('4.6.1', 'ee81c593efc8a6229d9bcb350b6d7849')
|
|
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)
|