add big-endian CI run and fix endian issues in test and hdf5var.c

.github/workflows/run_tests_bigendian.yml

@@ -0,0 +1,149 @@
+###
+# Build and test netCDF-C on a big-endian platform using QEMU emulation.
+#
+# Target: IBM s390x (z/Architecture), which is big-endian.
+# The job runs on a standard x86-64 GitHub Actions runner but uses
+# uraimo/run-on-arch-action to spin up a QEMU-emulated s390x container.
+# This lets us verify that netCDF-C builds and tests correctly on a
+# big-endian architecture without needing dedicated hardware.
+#
+# HDF5 is installed from the Ubuntu apt repository (libhdf5-dev) rather
+# than built from source, because building HDF5 from source inside QEMU
+# requires running compiled test binaries which fails under emulation.
+#
+# Triggered manually (workflow_dispatch) or on pull requests to main.
+###
+
+name: Run NON-REMOTE Big-Endian (s390x) netCDF Tests
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+jobs:
+
+  nc-bigendian-s390x:
+
+    name: Autotools build on s390x (big-endian)
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - uses: actions/checkout@v4
+
+      - name: Add swap space
+        # QEMU emulation is memory-intensive. The default GitHub Actions runner
+        # has limited swap, which can cause GCC's collect2 linker to segfault.
+        # Adding 16GB of swap reduces this risk. We also pass -Wl,--no-keep-memory
+        # to the linker to reduce its peak memory usage.
+        run: |
+          sudo swapoff -a || true
+          sudo dd if=/dev/zero of=/swapfile bs=1M count=16384
+          sudo chmod 600 /swapfile
+          sudo mkswap /swapfile
+          sudo swapon /swapfile
+          free -h
+
+      - name: Build and test on s390x via QEMU
+        uses: uraimo/run-on-arch-action@v2
+        with:
+          arch: s390x
+          distro: ubuntu22.04
+
+          # githubToken enables caching of the QEMU container image in the
+          # GitHub Container Registry, speeding up subsequent runs.
+          githubToken: ${{ github.token }}
+
+          install: |
+            apt-get update -q -y
+            # Print available HDF5 packages for debugging purposes
+            apt-cache search libhdf5 | sort
+            apt-get install -q -y \
+              libaec-dev \
+              zlib1g-dev \
+              automake \
+              autoconf \
+              libcurl4-openssl-dev \
+              libjpeg-dev \
+              wget \
+              curl \
+              bzip2 \
+              m4 \
+              flex \
+              bison \
+              cmake \
+              libzip-dev \
+              libhdf5-dev \
+              libhdf5-103-1 \
+              libtool \
+              gcc \
+              g++ \
+              clang \
+              binutils-gold
+
+          run: |
+            set -e
+            set -x
+
+            ###
+            # Regenerate the autotools build system from source.
+            # This is required because the checked-out tree may not include
+            # generated files (configure, Makefile.in, etc.).
+            ###
+            autoreconf -if
+
+            ###
+            # Configure netCDF-C against the apt-installed HDF5 serial library.
+            #
+            # The HDF5 serial library on Ubuntu s390x lives in a non-standard
+            # path (/usr/lib/s390x-linux-gnu/hdf5/serial), so we pass explicit
+            # CPPFLAGS, LDFLAGS, and LIBS to point configure there.
+            #
+            # Features disabled to avoid missing dependencies under emulation:
+            #   --disable-dap            : requires curl/libxml2 remote access
+            #   --disable-dap-remote-tests: requires a live DAP server
+            #   --disable-nczarr         : requires additional zip/cloud libs
+            #   --disable-libxml2        : not needed without DAP
+            #   --disable-shared         : simplifies linking under emulation
+            #   --enable-utilities       : builds ncgen/ncdump/etc. binaries
+            ###
+            CPPFLAGS="-I/usr/include/hdf5/serial" \
+            LDFLAGS="-L/usr/lib/s390x-linux-gnu/hdf5/serial -fuse-ld=gold -Wl,--no-keep-memory" \
+            LIBS="-lhdf5_serial -lz" \
+            CFLAGS="-O0 -g" \
+            CC=clang \
+            ./configure \
+              --enable-hdf5 \
+              --disable-dap \
+              --disable-dap-remote-tests \
+              --disable-nczarr \
+              --disable-libxml2 \
+              --disable-shared \
+              --enable-static \
+              --enable-utilities \
+              || { tail -200 config.log; exit 1; }
+
+            cat libnetcdf.settings
+
+            make -j 4
+
+            ###
+            # Build and run the test suite.
+            # make check TESTS="" builds the test binaries without running them,
+            # then make check runs the full suite.
+            ###
+            make check TESTS="" -j 4
+            make check -j 4
+
+      - name: Show test logs on failure
+        if: ${{ failure() }}
+        run: |
+          find /home/runner/work/netcdf-c/netcdf-c -name 'test-suite.log' | \
+            xargs -I{} sh -c 'echo "=== {} ==="; cat "{}"' || true
+          cat config.log || true

.gitignore

@@ -64,3 +64,4 @@ build_llvm
 .vagrant
 Vagrantfile
 netcdf-fortran
+.windsurf

configure.ac

@@ -2032,6 +2032,7 @@ AM_CONDITIONAL(HAVE_H5Z_SZIP, [test "x$enable_hdf5_szip" = xyes])
 AM_CONDITIONAL(HAVE_BLOSC, [test "x$have_blosc" = xyes])
 AM_CONDITIONAL(HAVE_BZ2, [test "x$have_bz2" = xyes])
 AM_CONDITIONAL(HAVE_ZSTD, [test "x$have_zstd" = xyes])
+AM_CONDITIONAL(ENABLE_SHARED, [test "x$enable_shared" = xyes])
 
 # If the machine doesn't have a long long, and we want netCDF-4, then
 # we've got problems!

libhdf5/hdf5var.c

@@ -1810,7 +1810,7 @@ NC4_put_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
     LOG((4, "about to H5Dwrite datasetid 0x%x mem_spaceid 0x%x "
          "file_spaceid 0x%x", hdf5_var->hdf_datasetid, mem_spaceid, file_spaceid));
     if (H5Dwrite(hdf5_var->hdf_datasetid,
-                 ((NC_HDF5_TYPE_INFO_T *)var->type_info->format_type_info)->hdf_typeid,
+                 ((NC_HDF5_TYPE_INFO_T *)var->type_info->format_type_info)->native_hdf_typeid,
                  mem_spaceid, file_spaceid, xfer_plistid, bufr) < 0)
         BAIL(NC_EHDFERR);
 

libsrc/ncx.m4

@@ -3204,7 +3204,7 @@ APIPrefix`x_getn_'NC_TYPE(float)_float(const void **xpp, IntType nelems, float *
 
 	for( ; nelems != 0; nelems--, xp += X_SIZEOF_FLOAT, tp++)
 	{
-		const int lstatus = APIPrefix`x_get_'NC_TYPE(float)_float(xp, tp, fillp);
+		const int lstatus = APIPrefix`x_get_'NC_TYPE(float)_float(xp, tp, NULL);
 		if (status == NC_NOERR) /* report the first encountered error */
 			status = lstatus;
 	}
@@ -3314,7 +3314,7 @@ APIPrefix`x_getn_'NC_TYPE(double)_double(const void **xpp, IntType nelems, doubl
 
 	for( ; nelems != 0; nelems--, xp += X_SIZEOF_DOUBLE, tp++)
 	{
-		const int lstatus = APIPrefix`x_get_'NC_TYPE(double)_double(xp, tp, fillp);
+		const int lstatus = APIPrefix`x_get_'NC_TYPE(double)_double(xp, tp, NULL);
 		if (status == NC_NOERR) /* report the first encountered error */
 			status = lstatus;
 	}

nc_test4/Makefile.am

@@ -35,7 +35,7 @@ tst_h_scalar tst_rename tst_rename2 tst_rename3 tst_h5_endians		\
 tst_atts_string_rewrite tst_hdf5_file_compat tst_fill_attr_vanish	\
 tst_rehash tst_filterparser tst_bug324 tst_types tst_atts3		\
 tst_put_vars tst_elatefill tst_udf tst_put_vars_two_unlim_dim		\
-tst_bug1442 tst_quantize tst_h_transient_types tst_udf_self_load
+tst_bug1442 tst_quantize tst_h_transient_types
 
 if HAS_PAR_FILTERS
 NC4_TESTS += tst_alignment
@@ -44,6 +44,10 @@ endif
 NC4_TESTS += tst_h_strbug tst_h_refs
 
 # UDF self-registration plugin loading test.
+# Requires a shared library build: the test dlopen()s a .so plugin.
+# Skip entirely when built with --disable-shared.
+if ENABLE_SHARED
+NC4_TESTS += tst_udf_self_load
 # Build the test plugin as a shared library (libtool module).
 check_LTLIBRARIES = tst_udf_self_load_plugin.la
 tst_udf_self_load_plugin_la_SOURCES = tst_udf_self_load_plugin.c
@@ -59,6 +63,7 @@ tst_udf_self_load_plugin_la_LIBADD = ${top_builddir}/liblib/libnetcdf.la
 # by configure.ac (see the case $host_os block after LT_INIT) so the
 # compiled-in TEST_PLUGIN_PATH always points to the correct filename.
 tst_udf_self_load_CPPFLAGS = $(AM_CPPFLAGS) -DTEST_PLUGIN_PATH=\"$(abs_builddir)/.libs/tst_udf_self_load_plugin@MODULE_EXT@\"
+endif # ENABLE_SHARED
 
 # Build test programs plus programs used in test scripts.
 check_PROGRAMS = $(NC4_TESTS) tst_empty_vlen_unlim tst_charvlenbug \