Merge pull request #175 from zklaus/backport-fix-hdf5-diag

Backport fix for Unidata/netcdf-c#2674

.ci_support/linux_64_mpimpich.yaml

@@ -11,7 +11,7 @@ channel_sources:
 channel_targets:
 - conda-forge main
 curl:
-- '7'
+- '8'
 cxx_compiler:
 - gxx
 cxx_compiler_version:

.ci_support/linux_64_mpinompi.yaml

@@ -11,7 +11,7 @@ channel_sources:
 channel_targets:
 - conda-forge main
 curl:
-- '7'
+- '8'
 cxx_compiler:
 - gxx
 cxx_compiler_version:

.ci_support/linux_64_mpiopenmpi.yaml

@@ -11,7 +11,7 @@ channel_sources:
 channel_targets:
 - conda-forge main
 curl:
-- '7'
+- '8'
 cxx_compiler:
 - gxx
 cxx_compiler_version:

.ci_support/linux_aarch64_mpimpich.yaml

@@ -15,7 +15,7 @@ channel_sources:
 channel_targets:
 - conda-forge main
 curl:
-- '7'
+- '8'
 cxx_compiler:
 - gxx
 cxx_compiler_version:

.ci_support/linux_aarch64_mpinompi.yaml

@@ -15,7 +15,7 @@ channel_sources:
 channel_targets:
 - conda-forge main
 curl:
-- '7'
+- '8'
 cxx_compiler:
 - gxx
 cxx_compiler_version:

.ci_support/linux_aarch64_mpiopenmpi.yaml

@@ -15,7 +15,7 @@ channel_sources:
 channel_targets:
 - conda-forge main
 curl:
-- '7'
+- '8'
 cxx_compiler:
 - gxx
 cxx_compiler_version:

.ci_support/linux_ppc64le_mpimpich.yaml

@@ -11,7 +11,7 @@ channel_sources:
 channel_targets:
 - conda-forge main
 curl:
-- '7'
+- '8'
 cxx_compiler:
 - gxx
 cxx_compiler_version:

.ci_support/linux_ppc64le_mpinompi.yaml

@@ -11,7 +11,7 @@ channel_sources:
 channel_targets:
 - conda-forge main
 curl:
-- '7'
+- '8'
 cxx_compiler:
 - gxx
 cxx_compiler_version:

.ci_support/linux_ppc64le_mpiopenmpi.yaml

@@ -11,7 +11,7 @@ channel_sources:
 channel_targets:
 - conda-forge main
 curl:
-- '7'
+- '8'
 cxx_compiler:
 - gxx
 cxx_compiler_version:

.ci_support/osx_64_mpimpich.yaml

@@ -11,7 +11,7 @@ channel_sources:
 channel_targets:
 - conda-forge main
 curl:
-- '7'
+- '8'
 cxx_compiler:
 - clangxx
 cxx_compiler_version:

.ci_support/osx_64_mpinompi.yaml

@@ -11,7 +11,7 @@ channel_sources:
 channel_targets:
 - conda-forge main
 curl:
-- '7'
+- '8'
 cxx_compiler:
 - clangxx
 cxx_compiler_version:

.ci_support/osx_64_mpiopenmpi.yaml

@@ -11,7 +11,7 @@ channel_sources:
 channel_targets:
 - conda-forge main
 curl:
-- '7'
+- '8'
 cxx_compiler:
 - clangxx
 cxx_compiler_version:

.ci_support/osx_arm64_mpimpich.yaml

@@ -11,7 +11,7 @@ channel_sources:
 channel_targets:
 - conda-forge main
 curl:
-- '7'
+- '8'
 cxx_compiler:
 - clangxx
 cxx_compiler_version:

.ci_support/osx_arm64_mpinompi.yaml

@@ -11,7 +11,7 @@ channel_sources:
 channel_targets:
 - conda-forge main
 curl:
-- '7'
+- '8'
 cxx_compiler:
 - clangxx
 cxx_compiler_version:

.ci_support/osx_arm64_mpiopenmpi.yaml

@@ -11,7 +11,7 @@ channel_sources:
 channel_targets:
 - conda-forge main
 curl:
-- '7'
+- '8'
 cxx_compiler:
 - clangxx
 cxx_compiler_version:

.ci_support/win_64_.yaml

@@ -7,7 +7,7 @@ channel_sources:
 channel_targets:
 - conda-forge main
 curl:
-- '7'
+- '8'
 cxx_compiler:
 - vs2019
 hdf4:

recipe/build.sh

@@ -48,6 +48,7 @@ if [[ ${HOST} =~ .*darwin.* ]]; then
     #  or to fix ld64 so that it checks for symbols being used in this section).
     export LDFLAGS=$(echo "${LDFLAGS}" | sed "s/-Wl,-dead_strip_dylibs//g")
     export HDF5_PLUGIN_PATH=$(echo "H5_DEFAULT_PLUGINDIR" | clang-cpp -P -include $PREFIX/include/H5pubconf.h - | tr -d '"')
+    export CMAKE_ARGS="${CMAKE_ARGS} -DHAVE_CLOCK_GETTIME:BOOL=OFF"
 else
     export HDF5_PLUGIN_PATH=$(echo "H5_DEFAULT_PLUGINDIR" | $CPP -P -include $PREFIX/include/H5pubconf.h - | tr -d '"')
 fi

recipe/meta.yaml

@@ -1,5 +1,5 @@
 {% set version = "4.9.2" %}
-{% set build = 3 %}
+{% set build = 4 %}
 
 # recipe-lint fails if mpi is undefined
 {% set mpi = mpi or 'nompi' %}
@@ -20,6 +20,7 @@ source:
     - patches/0009-topsrcdir.patch
     - patches/prevent_MS_runtime_libs_being_installed_again.patch  # [win]
     - patches/do_not_use_16_processes_in_tests.patch  # [ppc64le]
+    - patches/0001-Fix-issue-2674.patch
 
 build:
   number: {{ build }}
@@ -107,3 +108,4 @@ extra:
     - msarahan
     - xylar
     - dopplershift
+    - zklaus

recipe/patches/0001-Fix-issue-2674.patch

@@ -0,0 +1,56 @@
+From b61e5cb9022b98312e6135bda859108352b531f0 Mon Sep 17 00:00:00 2001
+From: uweschulzweida <[email protected]>
+Date: Wed, 5 Apr 2023 18:05:53 +0200
+Subject: [PATCH] Fix issue #2674
+
+---
+ libhdf5/hdf5open.c | 16 ++++++++++------
+ 1 file changed, 10 insertions(+), 6 deletions(-)
+
+diff --git a/libhdf5/hdf5open.c b/libhdf5/hdf5open.c
+index cb2491ff..e00f426e 100644
+--- a/libhdf5/hdf5open.c
++++ b/libhdf5/hdf5open.c
+@@ -1205,12 +1205,14 @@ static int get_quantize_info(NC_VAR_INFO_T *var)
+ {
+     hid_t attid;
+     hid_t datasetid;
++    htri_t attr_exists;
+
+     /* Try to open an attribute of the correct name for quantize
+      * info. */
+     datasetid = ((NC_HDF5_VAR_INFO_T *)var->format_var_info)->hdf_datasetid;
+-    attid = H5Aopen_by_name(datasetid, ".", NC_QUANTIZE_BITGROOM_ATT_NAME,
+-			    H5P_DEFAULT, H5P_DEFAULT);
++    attr_exists = H5Aexists(datasetid, NC_QUANTIZE_BITGROOM_ATT_NAME);
++    attid = attr_exists ? H5Aopen_by_name(datasetid, ".", NC_QUANTIZE_BITGROOM_ATT_NAME,
++			    H5P_DEFAULT, H5P_DEFAULT) : 0;
+
+     if (attid > 0)
+       {
+@@ -1218,16 +1220,18 @@ static int get_quantize_info(NC_VAR_INFO_T *var)
+       }
+     else
+       {
+-	attid = H5Aopen_by_name(datasetid, ".", NC_QUANTIZE_GRANULARBR_ATT_NAME,
+-			    H5P_DEFAULT, H5P_DEFAULT);
++        attr_exists = H5Aexists(datasetid, NC_QUANTIZE_GRANULARBR_ATT_NAME);
++	attid = attr_exists ? H5Aopen_by_name(datasetid, ".", NC_QUANTIZE_GRANULARBR_ATT_NAME,
++			    H5P_DEFAULT, H5P_DEFAULT) : 0;
+ 	if (attid > 0)
+ 	  {
+ 	    var->quantize_mode = NC_QUANTIZE_GRANULARBR;
+ 	  }
+ 	else
+ 	  {
+-	    attid = H5Aopen_by_name(datasetid, ".", NC_QUANTIZE_BITROUND_ATT_NAME,
+-				    H5P_DEFAULT, H5P_DEFAULT);
++            attr_exists = H5Aexists(datasetid, NC_QUANTIZE_BITROUND_ATT_NAME);
++	    attid = attr_exists ? H5Aopen_by_name(datasetid, ".", NC_QUANTIZE_BITROUND_ATT_NAME,
++				    H5P_DEFAULT, H5P_DEFAULT) : 0;
+ 	    if (attid > 0)
+ 	      var->quantize_mode = NC_QUANTIZE_BITROUND;
+ 	  }
+-- 
+2.39.1
+