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Backport fix for Unidata/netcdf-c#2674 #175

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merged 3 commits into from
Apr 18, 2023
Merged

Backport fix for Unidata/netcdf-c#2674 #175

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01433a8
Backport fix for Unidata/netcdf-c#2674
Apr 18, 2023
db6017d
MNT: Re-rendered with conda-build 3.24.0, conda-smithy 3.23.1, and co…
Apr 18, 2023
dbcf8d0
Deactivate clock_gettime on Osx
Apr 18, 2023
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2 changes: 1 addition & 1 deletion .ci_support/linux_64_mpimpich.yaml
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Expand Up @@ -11,7 +11,7 @@ channel_sources:
channel_targets:
- conda-forge main
curl:
- '7'
- '8'
cxx_compiler:
- gxx
cxx_compiler_version:
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2 changes: 1 addition & 1 deletion .ci_support/linux_64_mpinompi.yaml
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Expand Up @@ -11,7 +11,7 @@ channel_sources:
channel_targets:
- conda-forge main
curl:
- '7'
- '8'
cxx_compiler:
- gxx
cxx_compiler_version:
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2 changes: 1 addition & 1 deletion .ci_support/linux_64_mpiopenmpi.yaml
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Expand Up @@ -11,7 +11,7 @@ channel_sources:
channel_targets:
- conda-forge main
curl:
- '7'
- '8'
cxx_compiler:
- gxx
cxx_compiler_version:
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2 changes: 1 addition & 1 deletion .ci_support/linux_aarch64_mpimpich.yaml
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Expand Up @@ -15,7 +15,7 @@ channel_sources:
channel_targets:
- conda-forge main
curl:
- '7'
- '8'
cxx_compiler:
- gxx
cxx_compiler_version:
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2 changes: 1 addition & 1 deletion .ci_support/linux_aarch64_mpinompi.yaml
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Expand Up @@ -15,7 +15,7 @@ channel_sources:
channel_targets:
- conda-forge main
curl:
- '7'
- '8'
cxx_compiler:
- gxx
cxx_compiler_version:
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2 changes: 1 addition & 1 deletion .ci_support/linux_aarch64_mpiopenmpi.yaml
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Expand Up @@ -15,7 +15,7 @@ channel_sources:
channel_targets:
- conda-forge main
curl:
- '7'
- '8'
cxx_compiler:
- gxx
cxx_compiler_version:
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2 changes: 1 addition & 1 deletion .ci_support/linux_ppc64le_mpimpich.yaml
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Expand Up @@ -11,7 +11,7 @@ channel_sources:
channel_targets:
- conda-forge main
curl:
- '7'
- '8'
cxx_compiler:
- gxx
cxx_compiler_version:
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2 changes: 1 addition & 1 deletion .ci_support/linux_ppc64le_mpinompi.yaml
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Expand Up @@ -11,7 +11,7 @@ channel_sources:
channel_targets:
- conda-forge main
curl:
- '7'
- '8'
cxx_compiler:
- gxx
cxx_compiler_version:
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2 changes: 1 addition & 1 deletion .ci_support/linux_ppc64le_mpiopenmpi.yaml
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Expand Up @@ -11,7 +11,7 @@ channel_sources:
channel_targets:
- conda-forge main
curl:
- '7'
- '8'
cxx_compiler:
- gxx
cxx_compiler_version:
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2 changes: 1 addition & 1 deletion .ci_support/osx_64_mpimpich.yaml
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Expand Up @@ -11,7 +11,7 @@ channel_sources:
channel_targets:
- conda-forge main
curl:
- '7'
- '8'
cxx_compiler:
- clangxx
cxx_compiler_version:
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2 changes: 1 addition & 1 deletion .ci_support/osx_64_mpinompi.yaml
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Expand Up @@ -11,7 +11,7 @@ channel_sources:
channel_targets:
- conda-forge main
curl:
- '7'
- '8'
cxx_compiler:
- clangxx
cxx_compiler_version:
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2 changes: 1 addition & 1 deletion .ci_support/osx_64_mpiopenmpi.yaml
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Expand Up @@ -11,7 +11,7 @@ channel_sources:
channel_targets:
- conda-forge main
curl:
- '7'
- '8'
cxx_compiler:
- clangxx
cxx_compiler_version:
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2 changes: 1 addition & 1 deletion .ci_support/osx_arm64_mpimpich.yaml
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Expand Up @@ -11,7 +11,7 @@ channel_sources:
channel_targets:
- conda-forge main
curl:
- '7'
- '8'
cxx_compiler:
- clangxx
cxx_compiler_version:
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2 changes: 1 addition & 1 deletion .ci_support/osx_arm64_mpinompi.yaml
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Expand Up @@ -11,7 +11,7 @@ channel_sources:
channel_targets:
- conda-forge main
curl:
- '7'
- '8'
cxx_compiler:
- clangxx
cxx_compiler_version:
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2 changes: 1 addition & 1 deletion .ci_support/osx_arm64_mpiopenmpi.yaml
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Expand Up @@ -11,7 +11,7 @@ channel_sources:
channel_targets:
- conda-forge main
curl:
- '7'
- '8'
cxx_compiler:
- clangxx
cxx_compiler_version:
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2 changes: 1 addition & 1 deletion .ci_support/win_64_.yaml
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Expand Up @@ -7,7 +7,7 @@ channel_sources:
channel_targets:
- conda-forge main
curl:
- '7'
- '8'
cxx_compiler:
- vs2019
hdf4:
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2 changes: 1 addition & 1 deletion .github/CODEOWNERS
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1 change: 1 addition & 0 deletions README.md
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1 change: 1 addition & 0 deletions recipe/build.sh
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Expand Up @@ -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
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4 changes: 3 additions & 1 deletion recipe/meta.yaml
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@@ -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' %}
Expand All @@ -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 }}
Expand Down Expand Up @@ -107,3 +108,4 @@ extra:
- msarahan
- xylar
- dopplershift
- zklaus
56 changes: 56 additions & 0 deletions recipe/patches/0001-Fix-issue-2674.patch
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@@ -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