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netcdf-c: major refactoring, new variants and versions (#36485)

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This commit is contained in:
Sergey Kosukhin 2023-04-17 17:59:10 +02:00 committed by GitHub
parent 036695ac94
commit 275bfc15b4
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GPG Key ID: 4AEE18F83AFDEB23
4 changed files with 305 additions and 227 deletions
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44
var/spack/repos/builtin/packages/netcdf-c/4.7.3-spectrum-mpi-pnetcdf-detect.patch
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@ -1,44 +0,0 @@
--- a/configure 2019-11-20 18:59:25.000000000 -0500
+++ b/configure 13:20:48.088873402 -0500
@@ -18459,12 +18459,12 @@
$as_echo_n "checking Is libpnetcdf version 1.6.0 or later?... " >&6; }
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
+#include <pnetcdf.h>
int
main ()
{
-#include <pnetcdf.h>
#if (PNETCDF_VERSION_MAJOR*1000 + PNETCDF_VERSION_MINOR < 1006)
choke me
#endif
@@ -18584,12 +18584,12 @@
$as_echo_n "checking if erange-fill is enabled in PnetCDF... " >&6; }
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
+#include <pnetcdf.h>
int
main ()
{
-#include <pnetcdf.h>
#if !defined(PNETCDF_ERANGE_FILL) || PNETCDF_ERANGE_FILL == 0
choke me
#endif
@@ -18619,12 +18619,12 @@
$as_echo_n "checking if relax-coord-bound is enabled in PnetCDF... " >&6; }
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
+#include <pnetcdf.h>
int
main ()
{
-#include <pnetcdf.h>
#if !defined(PNETCDF_RELAX_COORD_BOUND) || PNETCDF_RELAX_COORD_BOUND == 0
choke me
#endif

31
var/spack/repos/builtin/packages/netcdf-c/4.8.1-no-strict-aliasing-config.patch
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@ -1,31 +0,0 @@
--- a/configure
+++ b/configure
@@ -3307,8 +3307,6 @@ ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu
-CFLAGS="${CFLAGS} -fno-strict-aliasing"
-
# Expand $ac_aux_dir to an absolute path.
am_aux_dir=`cd "$ac_aux_dir" && pwd`
@@ -4161,6 +4159,9 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+CFLAGS="${CFLAGS} -fno-strict-aliasing"
+
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
--- a/configure.ac
+++ b/configure.ac
@@ -61,6 +61,7 @@ AC_CONFIG_HEADERS([config.h])
##
SAVE_CFLAGS="${CFLAGS}"
AC_LANG_PUSH([C])
+AC_LANG_COMPILER_REQUIRE
CFLAGS="${CFLAGS} -fno-strict-aliasing"
AC_COMPILE_IFELSE([AC_LANG_PROGRAM([

11
var/spack/repos/builtin/packages/netcdf-c/4.9.0-no-mpi-yes-pnetcdf.patch
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@ -1,11 +0,0 @@
--- a/libhdf5/hdf5internal.c
+++ b/libhdf5/hdf5internal.c
@@ -163,7 +163,7 @@ find_var_dim_max_length(NC_GRP_INFO_T *grp, int varid, int dimid,
if (var->dimids[d] == dimid)
*maxlen = *maxlen > h5dimlen[d] ? *maxlen : h5dimlen[d];
-#ifdef USE_PARALLEL
+#ifdef USE_PARALLEL4
/* If we are doing parallel I/O in collective mode (with
* either pnetcdf or HDF5), then communicate with all
* other tasks in the collective and find out which has

446
var/spack/repos/builtin/packages/netcdf-c/package.py
View File

@ -3,12 +3,16 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import itertools
import os
import sys
from llnl.util.lang import dedupe
import spack.builder
from spack.build_systems import autotools, cmake
from spack.package import *
from spack.util.environment import filter_system_paths
class NetcdfC(CMakePackage, AutotoolsPackage):
@ -23,6 +27,7 @@ class NetcdfC(CMakePackage, AutotoolsPackage):
maintainers("skosukhin", "WardF")
version("main", branch="main")
version("4.9.2", sha256="bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7")
version("4.9.0", sha256="9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6")
version("4.8.1", sha256="bc018cc30d5da402622bf76462480664c6668b55eb16ba205a0dfb8647161dd0")
version("4.8.0", sha256="aff58f02b1c3e91dc68f989746f652fe51ff39e6270764e484920cb8db5ad092")
@ -46,36 +51,53 @@ class NetcdfC(CMakePackage, AutotoolsPackage):
version("4.3.3.1", sha256="f2ee78eb310637c007f001e7c18e2d773d23f3455242bde89647137b7344c2e2")
version("4.3.3", sha256="3f16e21bc3dfeb3973252b9addf5defb48994f84fc9c9356081f871526a680e7")
# configure fails if curl is not installed.
# See https://github.com/Unidata/netcdf-c/issues/1390
patch(
"https://github.com/Unidata/netcdf-c/commit/e5315da1e748dc541d50796fb05233da65e86b6b.patch?full_index=1",
sha256="c551ca2f5b6bcefa07dd7f8b7bac426a5df9861e091df1ab99167d8d401f963f",
when="@4.7.0",
)
# fix headers
patch(
"https://github.com/Unidata/netcdf-c/pull/1505.patch?full_index=1",
sha256="495b3e5beb7f074625bcec2ca76aebd339e42719e9c5ccbedbdcc4ffb81a7450",
when="@4.7.2",
)
patch(
"https://github.com/Unidata/netcdf-c/pull/1508.patch?full_index=1",
sha256="19e7f31b96536928621b1c29bb6d1a57bcb7aa672cea8719acf9ac934cdd2a3e",
when="@4.7.2",
)
with when("build_system=cmake"):
# TODO: document why we need to revert https://github.com/Unidata/netcdf-c/pull/1731
# with the following patch:
patch("4.8.1-win-hdf5-with-zlib.patch", when="@4.8.1: platform=windows")
patch("4.8.1-win-hdf5-with-zlib.patch", when="@4.8.1: platform=windows")
# TODO: fetch from the upstream repo once https://github.com/Unidata/netcdf-c/pull/2595
# is accepted:
patch("netcdfc-mpi-win-support.patch", when="platform=windows")
patch("netcdfc-mpi-win-support.patch", when="platform=windows")
# See https://github.com/Unidata/netcdf-c/pull/1752
patch("4.7.3-spectrum-mpi-pnetcdf-detect.patch", when="@4.7.3:4.7.4 +parallel-netcdf")
# Some of the patches touch configure.ac and, therefore, require forcing the autoreconf stage:
_force_autoreconf_when = []
with when("build_system=autotools"):
# See https://github.com/Unidata/netcdf-c/pull/1752
patch(
"https://github.com/Unidata/netcdf-c/commit/386e2695286702156eba27ab7c68816efb192230.patch?full_index=1",
sha256="cb928a91f87c1615a0788f95b95d7a2e3df91dc16822f8b8a34a85d4e926c0de",
when="@4.7.3:4.7.4 +parallel-netcdf",
)
_force_autoreconf_when.append("@4.7.3:4.7.4 +parallel-netcdf")
# See https://github.com/Unidata/netcdf-c/pull/2293
patch("4.8.1-no-strict-aliasing-config.patch", when="@4.8.1")
# See https://github.com/Unidata/netcdf-c/pull/2293
patch(
"https://github.com/Unidata/netcdf-c/commit/a7ea050ebb3c412a99cc352859d5176a9b5ef986.patch?full_index=1",
sha256="38d34de38bad99737d3308867071196f20a3fb39b936de7bfcfbc85eb0c7ef54",
when="@4.8.1",
)
_force_autoreconf_when.append("@4.8.1")
with when("@4.7.2"):
# Fix headers
# See https://github.com/Unidata/netcdf-c/pull/1505
patch(
"https://github.com/Unidata/netcdf-c/pull/1505.patch?full_index=1",
sha256="495b3e5beb7f074625bcec2ca76aebd339e42719e9c5ccbedbdcc4ffb81a7450",
)
# See https://github.com/Unidata/netcdf-c/pull/1508
patch(
"https://github.com/Unidata/netcdf-c/pull/1508.patch?full_index=1",
sha256="19e7f31b96536928621b1c29bb6d1a57bcb7aa672cea8719acf9ac934cdd2a3e",
)
# See https://github.com/Unidata/netcdf-c/pull/2618
patch("4.9.0-no-mpi-yes-pnetcdf.patch", when="@4.9.0: ~mpi+parallel-netcdf")
patch(
"https://github.com/Unidata/netcdf-c/commit/00a722b253bae186bba403d0f92ff1eba719591f.patch?full_index=1",
sha256="25b83de1e081f020efa9e21c94c595220849f78c125ad43d8015631d453dfcb9",
when="@4.9.0:4.9.1~mpi+parallel-netcdf",
)
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")
@ -83,31 +105,58 @@ class NetcdfC(CMakePackage, AutotoolsPackage):
variant("pic", default=True, description="Produce position-independent code (for shared libs)")
variant("shared", default=True, description="Enable shared library")
variant("dap", default=False, description="Enable DAP support")
variant("byterange", default=False, description="Enable byte-range I/O")
variant("jna", default=False, description="Enable JNA support")
variant("fsync", default=False, description="Enable fsync support")
variant("zstd", default=True, description="Enable ZStandard compression", when="@4.9.0:")
variant("nczarr_zip", default=False, description="Enable NCZarr zipfile format storage")
variant("optimize", default=True, description="Enable -O2 for a more optimized lib")
# 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')
variant("szip", default=True, description="Enable Szip compression plugin")
variant("blosc", default=True, description="Enable Blosc compression plugin")
variant("zstd", default=True, description="Enable Zstandard compression plugin")
with when("build_system=cmake"):
# Based on the versions required by the root CMakeLists.txt:
depends_on("cmake@2.8.12:", type="build", when="@4.3.3:4.3")
depends_on("cmake@2.8.11:", type="build", when="@4.4.0:")
depends_on("cmake@3.6.1:", type="build", when="@4.5.0:")
depends_on("cmake@3.12:", type="build", when="@4.9.0:")
# Starting version 4.9.1, nczarr_test/CMakeLists.txt relies on the FILE_PERMISSIONS feature
# of the configure_file command, which is only available starting CMake 3.20:
depends_on("cmake@3.20:", type="test", when="@4.9.1:")
# The patch for 4.7.0 touches configure.ac. See force_autoreconf below.
with when("build_system=autotools"):
depends_on("autoconf", type="build", when="@4.7.0,main")
depends_on("automake", type="build", when="@4.7.0,main")
depends_on("libtool", type="build", when="@4.7.0,main")
# CMake system can use m4, but Windows does not yet support
depends_on("m4", type="build", when=sys.platform != "win32")
for __s in itertools.chain(["@main"], _force_autoreconf_when):
with when(__s):
depends_on("autoconf", type="build")
depends_on("automake", type="build")
depends_on("libtool", type="build")
depends_on("m4", type="build")
del __s
# M4 is also needed for the source and man file generation. All the generated source files are
# included in the release tarballs starting at least the oldest supported version:
depends_on("m4", type="build", when="@main")
# The man files are included in the release tarballs starting version 4.5.0 but they are not
# needed for the Windows platform:
for __p in ["darwin", "cray", "linux"]:
with when("platform={0}".format(__p)):
# It is possible to install the package with CMake and without M4 on a non-Windows
# platform but some of the man files will not be installed in that case (even if they
# are in the release tarball):
depends_on("m4", type="build", when="build_system=cmake")
# Apart from the redundant configure-time check, which we suppress below, M4 is not
# needed when building with Autotools if the man files are in the release tarball:
depends_on("m4", type="build", when="@:4.4 build_system=autotools")
del __p
depends_on("hdf~netcdf", when="+hdf4")
# curl 7.18.0 or later is required:
# http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html
# https://docs.unidata.ucar.edu/nug/current/getting_and_building_netcdf.html
depends_on("curl@7.18.0:", when="+dap")
# depends_on("curl@7.18.0:", when='+cdmremote')
depends_on("curl@7.18.0:", when="+byterange")
# Need to include libxml2 when using DAP in 4.9.0 and newer to build
# https://github.com/Unidata/netcdf-c/commit/53464e89635a43b812b5fec5f7abb6ff34b9be63
@ -117,16 +166,15 @@ class NetcdfC(CMakePackage, AutotoolsPackage):
# 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
# https://docs.unidata.ucar.edu/nug/current/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:")
# We also need to use MPI wrappers when building against static MPI-enabled HDF5:
depends_on("mpi", when="^hdf5+mpi~shared")
# 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
# https://docs.unidata.ucar.edu/nug/current/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
@ -141,31 +189,94 @@ class NetcdfC(CMakePackage, AutotoolsPackage):
# https://github.com/Unidata/netcdf-c/issues/250
depends_on("hdf5@:1.8", when="@:4.4.0")
# NetCDF 4.7.4 and prior require HDF5 1.10 or older
# https://github.com/Unidata/netcdf-c/pull/1671
depends_on("hdf5@:1.10", when="@:4.7.3")
# Although NetCDF 4.8.0 builds and passes the respective tests against HDF5 1.12.0 with the
# default API (i.e. the problem reported in https://github.com/Unidata/netcdf-c/issues/1965 is
# not reproducible), the configure script fails if HDF5 1.12.0 is built without api=v18
# (according to the error message emitted by the configure script) or api=v110 (according to
# the comments in the configure script and its implementation). The check that led to the
# failure was removed in version 4.8.1 (https://github.com/Unidata/netcdf-c/pull/2044). To
# keep it simple, we require HDF5 1.10.x or older:
depends_on("hdf5@:1.10", when="@4.8.0")
with when("+byterange"):
# HDF5 implements H5allocate_memory starting version 1.8.15:
depends_on("hdf5@1.8.15:")
# HDF5 defines H5FD_FEAT_DEFAULT_VFD_COMPATIBLE (required when version 1.10.x is used)
# starting version 1.10.2:
depends_on("hdf5@:1.9,1.10.2:")
# The macro usage was adjusted (required when versions 1.8.23+, 1.10.8+, 1.12.1+ and
# 1.13.0+ of HDF5 are used) in NetCDF 4.8.1
# (see https://github.com/Unidata/netcdf-c/pull/2034):
depends_on("hdf5@:1.8.22,1.10.0:1.10.7,1.12.0,1.13:", when="@:4.8.0")
# Compatibility with HDF5 1.14.x was introduced in NetCDF 4.9.2
# (see https://github.com/Unidata/netcdf-c/pull/2615):
depends_on("hdf5@:1.12", when="@:4.9.1")
depends_on("libzip", when="+nczarr_zip")
# According to the documentation (see
# https://docs.unidata.ucar.edu/nug/current/getting_and_building_netcdf.html), zlib 1.2.5 or
# later is required for netCDF-4 compression. However, zlib became a direct dependency only
# starting NetCDF 4.9.0 (for the deflate plugin):
depends_on("zlib@1.2.5:", when="@4.9.0:+shared")
# Use the vendored bzip2 on Windows:
for __p in ["darwin", "cray", "linux"]:
depends_on("bzip2", when="@4.9.0:+shared platform={0}".format(__p))
del __p
depends_on("szip", when="+szip")
depends_on("c-blosc", when="+blosc")
depends_on("zstd", when="+zstd")
# 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:')
# Byte-range I/O was added in version 4.7.0:
conflicts("+byterange", when="@:4.6")
# The features were introduced in version 4.1.0
conflicts("+parallel-netcdf", when="@:4.0")
conflicts("+hdf4", when="@:4.0")
# NCZarr was added in version 4.8.0 as an experimental feature and became a supported one in
# version 4.8.1:
conflicts("+nczarr_zip", when="@:4.8.0")
# The features were introduced in version 4.9.0:
with when("@:4.8"):
conflicts("+szip")
conflicts("+blosc")
conflicts("+zstd")
# The plugins are not built when the shared libraries are disabled:
with when("~shared"):
conflicts("+szip")
conflicts("+blosc")
conflicts("+zstd")
default_build_system = "cmake" if sys.platform == "win32" else "autotools"
build_system("cmake", "autotools", default=default_build_system)
def setup_run_environment(self, env):
if "+zstd" in self.spec:
if self.spec.satisfies("@4.9.0:+shared"):
# Both HDF5 and NCZarr backends honor the same environment variable:
env.append_path("HDF5_PLUGIN_PATH", self.prefix.plugins)
def flag_handler(self, name, flags):
if self.builder.build_system == "autotools":
if name == "cflags":
if "+pic" in self.spec:
flags.append(self.compiler.cc_pic_flag)
if "+optimize" in self.spec:
flags.append("-O2")
return flags, None, None
@property
def libs(self):
shared = "+shared" in self.spec
return find_libraries("libnetcdf", root=self.prefix, shared=shared, recursive=True)
class Setup:
class BaseBuilder(metaclass=spack.builder.PhaseCallbacksMeta):
def setup_dependent_build_environment(self, env, dependent_spec):
self.pkg.setup_run_environment(env)
# Some packages, e.g. ncview, refuse to build if the compiler path returned by nc-config
@ -175,8 +286,6 @@ def setup_dependent_build_environment(self, env, dependent_spec):
if os.path.exists(self._nc_config_backup_dir):
env.prepend_path("PATH", self._nc_config_backup_dir)
class BackupStep(metaclass=spack.builder.PhaseCallbacksMeta):
@property
def _nc_config_backup_dir(self):
return join_path(self.pkg.metadata_dir, "spack-nc-config")
@ -192,14 +301,14 @@ def backup_nc_config(self):
filter_compiler_wrappers("nc-config", relative_root="bin")
class CMakeBuilder(BackupStep, Setup, cmake.CMakeBuilder):
class CMakeBuilder(BaseBuilder, cmake.CMakeBuilder):
def cmake_args(self):
base_cmake_args = [
self.define_from_variant("BUILD_SHARED_LIBS", "shared"),
self.define_from_variant("ENABLE_BYTERANGE", "byterange"),
self.define("BUILD_UTILITIES", True),
self.define("ENABLE_NETCDF_4", True),
self.define_from_variant("ENABLE_DAP", "dap"),
self.define("CMAKE_INSTALL_PREFIX", self.prefix),
self.define_from_variant("ENABLE_HDF4", "hdf4"),
self.define("ENABLE_PARALLEL_TESTS", False),
self.define_from_variant("ENABLE_FSYNC", "fsync"),
@ -209,25 +318,23 @@ def cmake_args(self):
base_cmake_args.append(self.define("ENABLE_PNETCDF", True))
if self.pkg.spec.satisfies("@4.3.1:"):
base_cmake_args.append(self.define("ENABLE_DYNAMIC_LOADING", True))
if "platform=windows" in self.pkg.spec:
# Enforce the usage of the vendored version of bzip2 on Windows:
base_cmake_args.append(self.define("Bz2_INCLUDE_DIRS", ""))
return base_cmake_args
class AutotoolsBuilder(BackupStep, Setup, autotools.AutotoolsBuilder):
class AutotoolsBuilder(BaseBuilder, autotools.AutotoolsBuilder):
@property
def force_autoreconf(self):
# The patch for 4.7.0 touches configure.ac.
return self.pkg.spec.satisfies("@4.7.0")
return any(self.spec.satisfies(s) for s in self.pkg._force_autoreconf_when)
@when("@4.6.3:")
def autoreconf(self, pkg, spec, prefix):
if not os.path.exists(self.configure_abs_path):
Executable("./bootstrap")()
def configure_args(self):
cflags = []
cppflags = []
ldflags = []
libs = []
config_args = [
"--enable-v2",
"--enable-utilities",
@ -236,105 +343,162 @@ def configure_args(self):
"--enable-netcdf-4",
]
if "+optimize" in self.pkg.spec:
cflags.append("-O2")
# NCZarr was added in version 4.8.0 as an experimental feature and became a supported one
# in version 4.8.1:
if self.spec.satisfies("@4.8.1:"):
config_args.append("--enable-nczarr")
elif self.spec.satisfies("@4.8.0"):
config_args.append("--disable-nczarr")
config_args.extend(self.enable_or_disable("fsync"))
if self.spec.satisfies("@4.9.0:+shared"):
# The plugins are not built when the shared libraries are disabled:
config_args.extend(
["--enable-plugins", "--with-plugin-dir={0}".format(self.prefix.plugins)]
)
# The flag was introduced in version 4.3.1
if self.pkg.spec.satisfies("@4.3.1:"):
# The option was introduced in version 4.3.1 and does nothing starting version 4.6.1:
if self.spec.satisfies("@4.3.1:4.6.0"):
config_args.append("--enable-dynamic-loading")
if self.spec.satisfies("@4.4:"):
config_args += self.enable_or_disable("parallel4", variant="mpi")
config_args += self.enable_or_disable("pnetcdf", variant="parallel-netcdf")
config_args += self.enable_or_disable("hdf4")
config_args += self.enable_or_disable("shared")
if "+pic" in self.pkg.spec:
cflags.append(self.pkg.compiler.cc_pic_flag)
config_args += self.enable_or_disable("dap")
# config_args += self.enable_or_disable('cdmremote')
if self.spec.satisfies("@4.9.0:"):
# Prevent linking to system libxml2:
config_args += self.enable_or_disable("libxml2", variant="dap")
# if '+dap' in self.pkg.spec or '+cdmremote' in self.pkg.spec:
if "+dap" in self.pkg.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.pkg.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)
elif self.pkg.spec.satisfies("@4.8.0:"):
# Prevent overlinking to a system installation of libcurl:
config_args.append("ac_cv_lib_curl_curl_easy_setopt=no")
if "+byterange" in self.spec:
config_args.append("--enable-byterange")
elif self.spec.satisfies("@4.7.0:"):
config_args.append("--disable-byterange")
if self.pkg.spec.satisfies("@4.4:"):
if "+mpi" in self.pkg.spec:
config_args.append("--enable-parallel4")
else:
config_args.append("--disable-parallel4")
if self.pkg.spec.satisfies("@4.3.2:"):
if self.spec.satisfies("@4.3.2:"):
config_args += self.enable_or_disable("jna")
# 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.pkg.spec["hdf5:hl"]
cppflags.append(hdf5_hl.headers.cpp_flags)
ldflags.append(hdf5_hl.libs.search_flags)
config_args += self.enable_or_disable("fsync")
if "+parallel-netcdf" in self.pkg.spec:
config_args.append("--enable-pnetcdf")
pnetcdf = self.pkg.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)
if any(self.spec.satisfies(s) for s in ["+mpi", "+parallel-netcdf", "^hdf5+mpi~shared"]):
config_args.append("CC={0}".format(self.spec["mpi"].mpicc))
# In general, we rely on the compiler wrapper to inject the required CPPFLAGS and LDFLAGS.
# However, the injected LDFLAGS are invisible for the configure script and are added
# neither to the pkg-config nor to the nc-config files. Therefore, we generate LDFLAGS
# based on the contents of the following list and pass them to the configure script:
lib_search_dirs = []
# In general, we rely on the configure script to generate the required linker flags in the
# right order. However, the configure script does not know and does not check for several
# possible transitive dependencies and we have to pass them as the LIBS argument. The list
# is generated based on the contents of the following list:
extra_libs = []
if "+parallel-netcdf" in self.spec:
lib_search_dirs.extend(self.spec["parallel-netcdf"].libs.directories)
if "+hdf4" in self.spec:
hdf = self.spec["hdf"]
lib_search_dirs.extend(hdf.libs.directories)
# The configure script triggers unavoidable overlinking to jpeg:
lib_search_dirs.extend(hdf["jpeg"].libs.directories)
if "~shared" in hdf:
# We do not use self.spec["hdf:transitive"].libs to avoid even more duplicates
# introduced by the configure script:
if "+szip" in hdf:
extra_libs.append(hdf["szip"].libs)
if "+external-xdr" in hdf:
extra_libs.append(hdf["rpc"].libs)
extra_libs.append(hdf["zlib"].libs)
hdf5 = self.spec["hdf5:hl"]
lib_search_dirs.extend(hdf5.libs.directories)
if "~shared" in hdf5:
if "+szip" in hdf5:
extra_libs.append(hdf5["szip"].libs)
extra_libs.append(hdf5["zlib"].libs)
if self.spec.satisfies("@4.9.0:+shared"):
lib_search_dirs.extend(self.spec["zlib"].libs.directories)
else:
config_args.append("--disable-pnetcdf")
# Prevent overlinking to zlib:
config_args.append("ac_cv_search_deflate=")
if "+mpi" in self.pkg.spec or "+parallel-netcdf" in self.pkg.spec:
config_args.append("CC=%s" % self.pkg.spec["mpi"].mpicc)
if "+nczarr_zip" in self.spec:
lib_search_dirs.extend(self.spec["libzip"].libs.directories)
elif self.spec.satisfies("@4.9.2:"):
# Prevent linking to libzip to disable the feature:
config_args.append("ac_cv_search_zip_open=no")
elif self.spec.satisfies("@4.8.0:"):
# Prevent linking to libzip to disable the feature:
config_args.append("ac_cv_lib_zip_zip_open=no")
config_args += self.enable_or_disable("hdf4")
if "+hdf4" in self.pkg.spec:
hdf4 = self.pkg.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.pkg.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")
if "+external-xdr" in hdf4 and hdf4["rpc"].name != "libc":
libs.append(hdf4["rpc"].libs.link_flags)
if "+szip" in self.spec:
lib_search_dirs.extend(self.spec["szip"].libs.directories)
elif self.spec.satisfies("@4.9.0:"):
# Prevent linking to szip to disable the plugin:
config_args.append("ac_cv_lib_sz_SZ_BufftoBuffCompress=no")
if "+zstd" in self.pkg.spec:
zstd = self.pkg.spec["zstd"]
cppflags.append(zstd.headers.cpp_flags)
ldflags.append(zstd.libs.search_flags)
config_args.append("--with-plugin-dir={}".format(self.prefix.plugins))
elif "~zstd" in self.pkg.spec:
# Prevent linking to system zstd.
# There is no explicit option to disable zstd.
if self.spec.satisfies("@4.9.0:"):
if "+shared" in self.spec:
lib_search_dirs.extend(self.spec["bzip2"].libs.directories)
else:
# Prevent redundant entries mentioning system bzip2 in nc-config and pkg-config
# files:
config_args.append("ac_cv_lib_bz2_BZ2_bzCompress=no")
if "+zstd" in self.spec:
lib_search_dirs.extend(self.spec["zstd"].libs.directories)
elif self.spec.satisfies("@4.9.0:"):
# Prevent linking to system zstd:
config_args.append("ac_cv_lib_zstd_ZSTD_compress=no")
# Fortran support
# In version 4.2+, NetCDF-C and NetCDF-Fortran have split.
# Use the netcdf-fortran package to install Fortran support.
if "+blosc" in self.spec:
lib_search_dirs.extend(self.spec["c-blosc"].libs.directories)
elif self.spec.satisfies("@4.9.0:"):
# Prevent linking to system c-blosc:
config_args.append("ac_cv_lib_blosc_blosc_init=no")
config_args.append("CFLAGS=" + " ".join(cflags))
config_args.append("CPPFLAGS=" + " ".join(cppflags))
config_args.append("LDFLAGS=" + " ".join(ldflags))
config_args.append("LIBS=" + " ".join(libs))
if self.spec.satisfies("@:4.7~dap+byterange"):
extra_libs.append(self.spec["curl"].libs)
elif "+dap" in self.spec or "+byterange" in self.spec:
lib_search_dirs.extend(self.spec["curl"].libs.directories)
elif self.spec.satisfies("@4.7.0"):
# This particular version fails if curl is not found, even if it is not needed
# (see https://github.com/Unidata/netcdf-c/issues/1390). Note that the following does
# not trigger linking to system curl for this version because DAP support is disabled:
config_args.append("ac_cv_lib_curl_curl_easy_setopt=yes")
else:
# Prevent linking to system curl (for versions 4.8.0 and newer) and the redundant check
# for curl (for older versions):
config_args.append("ac_cv_lib_curl_curl_easy_setopt=no")
if not self.spec.satisfies("@:4.4,main"):
# Suppress the redundant check for m4:
config_args.append("ac_cv_prog_NC_M4=false")
lib_search_dirs.extend(d for libs in extra_libs for d in libs.directories)
# Remove duplicates and system prefixes:
lib_search_dirs = filter_system_paths(dedupe(lib_search_dirs))
config_args.append(
"LDFLAGS={0}".format(" ".join("-L{0}".format(d) for d in lib_search_dirs))
)
extra_lib_names = [n for libs in extra_libs for n in libs.names]
# Remove duplicates in the reversed order:
extra_lib_names = reversed(list(dedupe(reversed(extra_lib_names))))
config_args.append("LIBS={0}".format(" ".join("-l{0}".format(n) for n in extra_lib_names)))
return config_args
# It looks like the issues with running the tests in parallel were fixed around version 4.6.0
# (see https://github.com/Unidata/netcdf-c/commit/812c2fd4d108cca927582c0d84049c0f271bb9e0):
@when("@:4.5.0")
def check(self):
# h5_test fails when run in parallel
make("check", parallel=False)