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

4 files changed, 310 insertions, 232 deletions

diff --git a/var/spack/repos/builtin/packages/netcdf-c/4.7.3-spectrum-mpi-pnetcdf-detect.patch b/var/spack/repos/builtin/packages/netcdf-c/4.7.3-spectrum-mpi-pnetcdf-detect.patch
deleted file mode 100644
index 0e04164ff6..0000000000
--- a/var/spack/repos/builtin/packages/netcdf-c/4.7.3-spectrum-mpi-pnetcdf-detect.patch
+++ /dev/null
@@ -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
diff --git a/var/spack/repos/builtin/packages/netcdf-c/4.8.1-no-strict-aliasing-config.patch b/var/spack/repos/builtin/packages/netcdf-c/4.8.1-no-strict-aliasing-config.patch
deleted file mode 100644
index 3a2e0972c5..0000000000
--- a/var/spack/repos/builtin/packages/netcdf-c/4.8.1-no-strict-aliasing-config.patch
+++ /dev/null
@@ -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([
diff --git a/var/spack/repos/builtin/packages/netcdf-c/4.9.0-no-mpi-yes-pnetcdf.patch b/var/spack/repos/builtin/packages/netcdf-c/4.9.0-no-mpi-yes-pnetcdf.patch
deleted file mode 100644
index de4b34c986..0000000000
--- a/var/spack/repos/builtin/packages/netcdf-c/4.9.0-no-mpi-yes-pnetcdf.patch
+++ /dev/null
@@ -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
diff --git a/var/spack/repos/builtin/packages/netcdf-c/package.py b/var/spack/repos/builtin/packages/netcdf-c/package.py
index 25d93a52cf..b837eca71e 100644
--- a/var/spack/repos/builtin/packages/netcdf-c/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-c/package.py
@@ -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")
-
-    # See https://github.com/Unidata/netcdf-c/pull/2293
-    patch("4.8.1-no-strict-aliasing-config.patch", when="@4.8.1")
+    # 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(
+            "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")
+
+    # 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 features were introduced in version 4.1.0
-    conflicts("+parallel-netcdf", when="@:4.0")
-    conflicts("+hdf4", when="@:4.0")
+    # 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 @@ class Setup:
         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 @@ class BackupStep(metaclass=spack.builder.PhaseCallbacksMeta):
     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 @@ class CMakeBuilder(BackupStep, Setup, cmake.CMakeBuilder):
             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 @@ class AutotoolsBuilder(BackupStep, Setup, autotools.AutotoolsBuilder):
             "--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")
+
+        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 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")
 
-        config_args.extend(self.enable_or_disable("fsync"))
+        if self.spec.satisfies("@4.4:"):
+            config_args += self.enable_or_disable("parallel4", variant="mpi")
 
-        # The flag was introduced in version 4.3.1
-        if self.pkg.spec.satisfies("@4.3.1:"):
-            config_args.append("--enable-dynamic-loading")
+        config_args += self.enable_or_disable("pnetcdf", variant="parallel-netcdf")
 
-        config_args += self.enable_or_disable("shared")
+        config_args += self.enable_or_disable("hdf4")
 
-        if "+pic" in self.pkg.spec:
-            cflags.append(self.pkg.compiler.cc_pic_flag)
+        config_args += self.enable_or_disable("shared")
 
         config_args += self.enable_or_disable("dap")
-        # config_args += self.enable_or_disable('cdmremote')
-
-        # 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 self.spec.satisfies("@4.9.0:"):
+            # Prevent linking to system libxml2:
+            config_args += self.enable_or_disable("libxml2", variant="dap")
 
-        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 "+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("@4.3.2:"):
+        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)
-
-        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)
+        config_args += self.enable_or_disable("fsync")
+
+        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")
-
-        if "+mpi" in self.pkg.spec or "+parallel-netcdf" in self.pkg.spec:
-            config_args.append("CC=%s" % self.pkg.spec["mpi"].mpicc)
+            # Prevent overlinking to zlib:
+            config_args.append("ac_cv_search_deflate=")
+
+        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")
+
+        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 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")
 
-        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 "+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 "+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")
+
+        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))
+        )
 
-        config_args.append("CFLAGS=" + " ".join(cflags))
-        config_args.append("CPPFLAGS=" + " ".join(cppflags))
-        config_args.append("LDFLAGS=" + " ".join(ldflags))
-        config_args.append("LIBS=" + " ".join(libs))
+        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)