upate build_hdf5 with patches from conda-forge for cross-compiling

Author: Jeff Whitaker

config.sh

@@ -77,6 +77,63 @@ function build_curl2 {
     touch curl-stamp
 }
 
+function build_hdf5 {
+    if [ -e hdf5-stamp ]; then return; fi
+    build_zlib
+    # libaec is a drop-in replacement for szip
+    build_libaec
+    local hdf5_url=https://support.hdfgroup.org/ftp/HDF5/releases
+    local short=$(echo $HDF5_VERSION | awk -F "." '{printf "%d.%d", $1, $2}')
+    fetch_unpack $hdf5_url/hdf5-$short/hdf5-$HDF5_VERSION/src/hdf5-$HDF5_VERSION.tar.gz
+    
+    if [[ ! -z "IS_OSX"  && "$PLAT" = "arm64" ]] && [[ "$CROSS_COMPILING" = "1" ]]; then
+    pushd hdf5-$HDF5_VERSION
+    # from https://github.com/conda-forge/hdf5-feedstock/commit/2cb83b63965985fa8795b0a13150bf0fd2525ebd
+    export ac_cv_sizeof_long_double=8
+    export hdf5_cv_ldouble_to_long_special=no
+    export hdf5_cv_long_to_ldouble_special=no
+    export hdf5_cv_ldouble_to_llong_accurate=yes
+    export hdf5_cv_llong_to_ldouble_correct=yes
+    export hdf5_cv_disable_some_ldouble_conv=no
+    export hdf5_cv_system_scope_threads=yes
+    export hdf5_cv_printf_ll="l"
+    export PAC_FC_MAX_REAL_PRECISION=15
+    export PAC_C_MAX_REAL_PRECISION=17
+    export PAC_FC_ALL_INTEGER_KINDS="{1,2,4,8,16}"
+    export PAC_FC_ALL_REAL_KINDS="{4,8}"
+    export H5CONFIG_F_NUM_RKIND="INTEGER, PARAMETER :: num_rkinds = 2"
+    export H5CONFIG_F_NUM_IKIND="INTEGER, PARAMETER :: num_ikinds = 5"
+    export H5CONFIG_F_RKIND="INTEGER, DIMENSION(1:num_rkinds) :: rkind = (/4,8/)"
+    export H5CONFIG_F_IKIND="INTEGER, DIMENSION(1:num_ikinds) :: ikind = (/1,2,4,8,16/)"
+    export PAC_FORTRAN_NATIVE_INTEGER_SIZEOF="                    4"
+    export PAC_FORTRAN_NATIVE_INTEGER_KIND="           4"
+    export PAC_FORTRAN_NATIVE_REAL_SIZEOF="                    4"
+    export PAC_FORTRAN_NATIVE_REAL_KIND="           4"
+    export PAC_FORTRAN_NATIVE_DOUBLE_SIZEOF="                    8"
+    export PAC_FORTRAN_NATIVE_DOUBLE_KIND="           8"
+    export PAC_FORTRAN_NUM_INTEGER_KINDS="5"
+    export PAC_FC_ALL_REAL_KINDS_SIZEOF="{4,8}"
+    export PAC_FC_ALL_INTEGER_KINDS_SIZEOF="{1,2,4,8,16}"
+    curl -sLO https://github.com/conda-forge/hdf5-feedstock/raw/2cb83b63965985fa8795b0a13150bf0fd2525ebd/recipe/patches/osx_cross_configure.patch
+    curl -sLO https://github.com/conda-forge/hdf5-feedstock/raw/2cb83b63965985fa8795b0a13150bf0fd2525ebd/recipe/patches/osx_cross_fortran_src_makefile.patch
+    curl -sLO https://github.com/conda-forge/hdf5-feedstock/raw/2cb83b63965985fa8795b0a13150bf0fd2525ebd/recipe/patches/osx_cross_hl_fortran_src_makefile.patch
+    curl -sLO https://github.com/conda-forge/hdf5-feedstock/raw/2cb83b63965985fa8795b0a13150bf0fd2525ebd/recipe/patches/osx_cross_src_makefile.patch
+    patch -p0 < osx_cross_configure.patch
+    patch -p0 < osx_cross_fortran_src_makefile.patch
+    patch -p0 < osx_cross_hl_fortran_src_makefile.patch
+    patch -p0 < osx_cross_src_makefile.patch
+    popd
+    fi
+    
+    (cd hdf5-$HDF5_VERSION \
+        && export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$BUILD_PREFIX/lib \
+        && ./configure --with-szlib=$BUILD_PREFIX --prefix=$BUILD_PREFIX \
+        --enable-threadsafe --enable-unsupported --with-pthread=yes \
+        && make -j4 \
+        && make install)
+    touch hdf5-stamp
+}
+
 function build_libs {
     build_hdf5
     build_curl2