From 514873948362f5828ba79a5bbd8bc30bf5dda9db Mon Sep 17 00:00:00 2001
From: Tim Heap <tim.heap@csiro.au>
Date: Mon, 4 Mar 2024 18:54:00 +1100
Subject: [PATCH 1/2] Backport fix for Unidata/netcdf-c#2674

---
 Dockerfile                                 |  2 +
 patches/netcdf-c/0001-Fix-issue-2674.patch | 53 ++++++++++++++++++++++
 2 files changed, 55 insertions(+)
 create mode 100644 patches/netcdf-c/0001-Fix-issue-2674.patch

diff --git a/Dockerfile b/Dockerfile
index 44e7e83..cb3f6cb 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -237,12 +237,14 @@ LABEL com.amazonaws.sdk.version=${AWS_SDK_CPP_REFSPEC}
 ARG NETCDF_VERSION
 ENV NETCDF_VERSION="${NETCDF_VERSION:-4.9.2}"
 ENV NETCDF_SRC_DIR="/usr/local/src/netcdf-c-${NETCDF_VERSION}"
+COPY ./patches/netcdf-c /tmp/netcdf-c/patches
 RUN --mount=target="${NETCDF_SRC_DIR}",type=cache,sharing=locked \
     if [ ! -f "${NETCDF_SRC_DIR}/configure" ]; then \
         wget -O - https://github.com/Unidata/netcdf-c/archive/refs/tags/v${NETCDF_VERSION}.tar.gz | tar -xz -C /usr/local/src/; \
     fi
 RUN --mount=target="${NETCDF_SRC_DIR}",type=cache,sharing=locked \
     cd "${NETCDF_SRC_DIR}" \
+    && patch -p1 < /tmp/netcdf-c/patches/0001-Fix-issue-2674.patch \
     && CPATH="${MPI_INCLUDE_PATH}" CC=mpicc LDFLAGS="-L/usr/local/lib -laws-cpp-sdk-s3" ./configure \
       --prefix=/usr/local \
       --enable-hdf5 \
diff --git a/patches/netcdf-c/0001-Fix-issue-2674.patch b/patches/netcdf-c/0001-Fix-issue-2674.patch
new file mode 100644
index 0000000..1ac328d
--- /dev/null
+++ b/patches/netcdf-c/0001-Fix-issue-2674.patch
@@ -0,0 +1,53 @@
+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
+

From 4e5c233d84ca4c4be5ef6e2d28c7a2c9f53c4b72 Mon Sep 17 00:00:00 2001
From: Tim Heap <tim.heap@csiro.au>
Date: Tue, 5 Mar 2024 13:32:23 +1100
Subject: [PATCH 2/2] Apply netcdf-c patch as part of the download step

It fails the second time around otherwise, due to the build cache.
---
 Dockerfile | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index cb3f6cb..1375cfe 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -237,14 +237,15 @@ LABEL com.amazonaws.sdk.version=${AWS_SDK_CPP_REFSPEC}
 ARG NETCDF_VERSION
 ENV NETCDF_VERSION="${NETCDF_VERSION:-4.9.2}"
 ENV NETCDF_SRC_DIR="/usr/local/src/netcdf-c-${NETCDF_VERSION}"
-COPY ./patches/netcdf-c /tmp/netcdf-c/patches
 RUN --mount=target="${NETCDF_SRC_DIR}",type=cache,sharing=locked \
+    --mount=target="${NETCDF_SRC_DIR}/patches",type=bind,source=./patches/netcdf-c \
     if [ ! -f "${NETCDF_SRC_DIR}/configure" ]; then \
         wget -O - https://github.com/Unidata/netcdf-c/archive/refs/tags/v${NETCDF_VERSION}.tar.gz | tar -xz -C /usr/local/src/; \
+        cd "${NETCDF_SRC_DIR}" ; \
+        patch -p1 < "./patches/0001-Fix-issue-2674.patch" ; \
     fi
 RUN --mount=target="${NETCDF_SRC_DIR}",type=cache,sharing=locked \
     cd "${NETCDF_SRC_DIR}" \
-    && patch -p1 < /tmp/netcdf-c/patches/0001-Fix-issue-2674.patch \
     && CPATH="${MPI_INCLUDE_PATH}" CC=mpicc LDFLAGS="-L/usr/local/lib -laws-cpp-sdk-s3" ./configure \
       --prefix=/usr/local \
       --enable-hdf5 \