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adding netcdf4 to main (emscripten-forge#2255)
* adding * pinning
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‎recipes/recipes_emscripten/libnetcdf/build.sh‎

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emconfigure ./configure --host=none --disable-parallel4 --disable-dap --disable-dap-remote-tests --disable-nczarr --prefix=$PREFIX
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emmake make
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emmake make install

‎recipes/recipes_emscripten/libnetcdf/hdf5-parallel-disable.patch‎

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From 4957785c768d6f2816ae989a6acf6e6e84055da8 Mon Sep 17 00:00:00 2001
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From: Sam Gardner <sam@wx4stg.com>
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Date: Mon, 17 Mar 2025 03:27:16 -0500
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Subject: [PATCH] disable hdf5 parallelism
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---
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libhdf5/hdf5create.c | 16 ++++++++--------
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libhdf5/hdf5open.c | 12 ++++++------
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2 files changed, 14 insertions(+), 14 deletions(-)
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diff --git a/libhdf5/hdf5create.c b/libhdf5/hdf5create.c
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index 02cd1b92ed..9a46c5192c 100644
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--- a/libhdf5/hdf5create.c
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+++ b/libhdf5/hdf5create.c
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@@ -198,14 +198,14 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
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H5P_CRT_ORDER_INDEXED)) < 0)
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BAIL(NC_EHDFERR);
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}
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-#ifdef HDF5_HAS_COLL_METADATA_OPS
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- /* If HDF5 supports collective metadata operations, turn them
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- * on. This is only relevant for parallel I/O builds of HDF5. */
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- if (H5Pset_all_coll_metadata_ops(fapl_id, 1) < 0)
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- BAIL(NC_EHDFERR);
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- if (H5Pset_coll_metadata_write(fapl_id, 1) < 0)
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- BAIL(NC_EHDFERR);
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-#endif
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+// #ifdef HDF5_HAS_COLL_METADATA_OPS
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+// /* If HDF5 supports collective metadata operations, turn them
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+// * on. This is only relevant for parallel I/O builds of HDF5. */
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+// if (H5Pset_all_coll_metadata_ops(fapl_id, 1) < 0)
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+// BAIL(NC_EHDFERR);
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+// if (H5Pset_coll_metadata_write(fapl_id, 1) < 0)
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+// BAIL(NC_EHDFERR);
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+// #endif
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if (cmode & NC_NODIMSCALE_ATTACH) {
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/* See https://github.com/Unidata/netcdf-c/issues/2128 */
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diff --git a/libhdf5/hdf5open.c b/libhdf5/hdf5open.c
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index 082d528a0a..e2126cf4c6 100644
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--- a/libhdf5/hdf5open.c
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+++ b/libhdf5/hdf5open.c
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@@ -810,12 +810,12 @@ nc4_open_file(const char *path, int mode, void* parameters, int ncid)
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}
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}
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-#ifdef HDF5_HAS_COLL_METADATA_OPS
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- /* If collective metadata operations are available in HDF5, turn
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- * them on. */
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- if (H5Pset_all_coll_metadata_ops(fapl_id, 1) < 0)
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- BAIL(NC_EPARINIT);
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-#endif /* HDF5_HAS_COLL_METADATA_OPS */
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+// #ifdef HDF5_HAS_COLL_METADATA_OPS
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+// /* If collective metadata operations are available in HDF5, turn
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+// * them on. */
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+// if (H5Pset_all_coll_metadata_ops(fapl_id, 1) < 0)
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+// BAIL(NC_EPARINIT);
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+// #endif /* HDF5_HAS_COLL_METADATA_OPS */
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#endif /* USE_PARALLEL4 */
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/* Only set cache for non-parallel opens. */

‎recipes/recipes_emscripten/libnetcdf/parallel-disable.patch‎

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From c471b9ce6f726101563f7738844e4dbb7bd6fd7b Mon Sep 17 00:00:00 2001
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From: Sam Gardner <sam@wx4stg.com>
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Date: Sun, 16 Mar 2025 16:32:35 -0500
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Subject: [PATCH] dont use hdf5 parallel if available but not requested
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---
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configure | 4 +++-
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1 file changed, 3 insertions(+), 1 deletion(-)
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diff --git a/configure b/configure
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index ae48feca8d..7d7f45f85f 100755
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--- a/configure
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+++ b/configure
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@@ -27628,7 +27628,9 @@ printf "%s\n" "#define HDF5_HAS_COLL_METADATA_OPS 1" >>confdefs.h
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# If parallel is available in hdf5, enable it in the C code. Also add some stuff to netcdf.h.
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if test "x$ac_cv_func_H5Pget_fapl_mpio" = xyes -o "x$ac_cv_func_H5Pget_fapl_mpiposix" = xyes; then
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- hdf5_parallel=yes
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+ if test "x$enable_parallel" = xyes; then
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+ hdf5_parallel=yes
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+ fi
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fi
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{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking whether parallel io is enabled in hdf5" >&5
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printf %s "checking whether parallel io is enabled in hdf5... " >&6; }

‎recipes/recipes_emscripten/libnetcdf/recipe.yaml‎

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context:
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version: "4.9.3"
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name: "libnetcdf"
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package:
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name: ${{ name }}
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version: ${{ version }}
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source:
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url: https://github.com/Unidata/netcdf-c/archive/refs/tags/v${{ version }}.tar.gz
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sha256: 990f46d49525d6ab5dc4249f8684c6deeaf54de6fec63a187e9fb382cc0ffdff
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patches:
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- parallel-disable.patch
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- hdf5-parallel-disable.patch
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build:
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number: 0
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requirements:
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build:
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- python
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- cross-python_${{ target_platform }}
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- ${{ compiler('c') }}
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- pip
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- m4
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- make
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host:
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- python
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- libxml2
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- hdf5
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- zlib
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run:
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- python

‎recipes/recipes_emscripten/netcdf4/build.sh‎

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#!/bin/bash
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# remove the emcc symlink in the $BUILD_PREFIX/bin
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rm $BUILD_PREFIX/bin/emcc
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# make callable
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chmod +x $RECIPE_DIR/emcc_wrapper.sh
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# create symlink to $RECIPE_DIR/emcc_wrapper.sh
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ln -s $RECIPE_DIR/emcc_wrapper.sh $BUILD_PREFIX/bin/emcc
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${PYTHON} -m pip install .

‎recipes/recipes_emscripten/netcdf4/emcc_wrapper.sh‎

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#!/bin/bash
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set -e
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$BUILD_PREFIX/bin/python3 $RECIPE_DIR/py_emcc_wrapper.py $BUILD_PREFIX/opt/emsdk/upstream/emscripten/emcc "$@"
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exit $?

‎recipes/recipes_emscripten/netcdf4/py_emcc_wrapper.py‎

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import sys
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import subprocess
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if __name__ == '__main__':
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args = sys.argv[2:]
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filtered_args = []
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for arg in args:
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if ("-Wl,-R$PREFIX/lib" in arg )or ("-R" in arg):
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print("removed arg:", arg)
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else:
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filtered_args.append(arg)
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# run the actual command in argv[1]
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subprocess.run([sys.argv[1]] + filtered_args, check=True)
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‎recipes/recipes_emscripten/netcdf4/recipe.yaml‎

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context:
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version: "1.7.2"
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name: "netcdf4"
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package:
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name: ${{ name }}
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version: ${{ version }}
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source:
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url: https://github.com/Unidata/netcdf4-python/archive/refs/tags/v${{ version }}rel.tar.gz
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sha256: cce7d42a83f84b6ce6288bb2fb171d5ffd294f1a1ba2650807d238ae961e9629
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build:
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number: 0
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requirements:
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build:
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- python
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- cross-python_${{ target_platform }}
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- ${{ compiler("c") }}
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- pip
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- pkg-config
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- numpy
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- cython
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host:
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- python
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- hdf5
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- libnetcdf
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run:
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- python
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- numpy
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- hdf5
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- cftime
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- certifi
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tests:
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- script: pytester
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requirements:
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build:
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- pytester
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run:
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- pytester-run
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files:
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recipe:
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- test_netcdf4.py

‎recipes/recipes_emscripten/netcdf4/test_netcdf4.py‎

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def test_netcdf4():
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from netCDF4 import Dataset
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rootgrp = Dataset("test.nc", "w", format="NETCDF4")
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rootgrp.data_model == "NETCDF4"
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rootgrp.close()
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‎variant.yaml‎

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@@ -443,7 +443,7 @@ libmatio:
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libmicrohttpd:
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- 0.9
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libnetcdf:
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- 4.8.1
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- 4.9.3
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libopencv:
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- 4.5.5
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libpcap:

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