* Build HDF5 with support for SZIP enabled (pull #1334)

bytedeco · Mar 20, 2023 · c62e06f · c62e06f
1 parent 9fc9006
commit c62e06f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,5 @@
 
+ * Build HDF5 with support for SZIP enabled ([pull #1334](https://github.com/bytedeco/javacpp-presets/pull/1334))
  * Map missing functions from `mkl_trans.h` in presets for MKL ([issue #1331](https://github.com/bytedeco/javacpp-presets/issues/1331))
  * Bundle the official Java API of HDF5 via the `hdf5_java` library ([pull #1327](https://github.com/bytedeco/javacpp-presets/pull/1327))
  * Map missing `cblas_?axpby()` functions in presets for MKL ([issue #1326](https://github.com/bytedeco/javacpp-presets/issues/1326))

diff --git a/hdf5/cppbuild.sh b/hdf5/cppbuild.sh
@@ -9,37 +9,69 @@ fi
 
 ZLIB=zlib-1.2.13
 HDF5_VERSION=1.14.0
+AEC_VERSION=1.0.6
 download "http://zlib.net/$ZLIB.tar.gz" $ZLIB.tar.gz
 download "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-$HDF5_VERSION/src/hdf5-$HDF5_VERSION.tar.bz2" hdf5-$HDF5_VERSION.tar.bz2
+# Use Github mirror repo rather than Gitlab repo for download speed
+#download "https://gitlab.dkrz.de/k202009/libaec/uploads/45b10e42123edd26ab7b3ad92bcf7be2/libaec-$AEC_VERSION.tar.gz" libaec-$AEC_VERSION.tar.gz
+download "https://github.com/MathisRosenhauer/libaec/releases/download/v$AEC_VERSION/libaec-$AEC_VERSION.tar.gz" libaec-$AEC_VERSION.tar.gz
 
 mkdir -p $PLATFORM
-cd $PLATFORM
+pushd $PLATFORM
 INSTALL_PATH=`pwd`
 echo "Decompressing archives..."
 tar --totals -xf ../hdf5-$HDF5_VERSION.tar.bz2
-cd hdf5-$HDF5_VERSION
+tar --totals -xf ../libaec-$AEC_VERSION.tar.gz
+pushd hdf5-$HDF5_VERSION
 
 #sedinplace '/cmake_minimum_required/d' $(find ./ -iname CMakeLists.txt)
 sedinplace 's/# *cmakedefine/#cmakedefine/g' config/cmake/H5pubconf.h.in
 sedinplace 's/COMPATIBILITY SameMinorVersion/COMPATIBILITY AnyNewerVersion/g' CMakeInstallation.cmake
 sedinplace '/C_RUN (/{N;N;d;}' config/cmake/ConfigureChecks.cmake
 
+# As of 1.14.0 the integrated cmake process for building aec/szip is broken
+# Revisit integrated szip build with 1.14.1
+
 case $PLATFORM in
 # HDF5 does not currently support cross-compiling:
 # https://support.hdfgroup.org/HDF5/faq/compile.html
 #    android-arm)
+#        # Build libaec for szip first
+#        mkdir -p ../libaec-$AEC_VERSION/build
+#        pushd ../libaec-$AEC_VERSION/build
+#        "$CMAKE" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH ..
+#        make -j $MAKEJ
+#        make install
+#        popd
+#
 #        patch -Np1 < ../../../hdf5-android.patch
 #        ./configure --prefix=$INSTALL_PATH --host="arm-linux-androideabi" --with-sysroot="$ANDROID_ROOT" AR="$ANDROID_BIN-ar" RANLIB="$ANDROID_BIN-ranlib" CPP="$ANDROID_BIN-cpp" CC="$ANDROID_BIN-gcc" CXX="$ANDROID_BIN-g++" STRIP="$ANDROID_BIN-strip" CPPFLAGS="--sysroot=$ANDROID_ROOT -DANDROID -I$ANDROID_CPP/include/ -I$ANDROID_CPP/include/backward/ -I$ANDROID_CPP/libs/armeabi/include/ -fPIC -ffunction-sections -funwind-tables -fstack-protector -march=armv7-a -mfloat-abi=softfp -mfpu=vfpv3-d16 -fomit-frame-pointer -fstrict-aliasing -funswitch-loops -finline-limit=300" LDFLAGS="-L$ANDROID_ROOT/usr/lib/ -L$ANDROID_CPP/libs/armeabi/ -nostdlib -Wl,--fix-cortex-a8 -z text -L./" LIBS="-lgnustl_static -lgcc -ldl -lz -lm -lc" --enable-cxx --enable-java
 #        make -j $MAKEJ
 #        make install-strip
 #        ;;
 #    android-x86)
+#        # Build libaec for szip first
+#        mkdir -p ../libaec-$AEC_VERSION/build
+#        pushd ../libaec-$AEC_VERSION/build
+#        "$CMAKE" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH ..
+#        make -j $MAKEJ
+#        make install
+#        popd
+#
 #        patch -Np1 < ../../../hdf5-android.patch
 #        ./configure --prefix=$INSTALL_PATH --host="i686-linux-android" --with-sysroot="$ANDROID_ROOT" AR="$ANDROID_BIN-ar" RANLIB="$ANDROID_BIN-ranlib" CPP="$ANDROID_BIN-cpp" CC="$ANDROID_BIN-gcc" CXX="$ANDROID_BIN-g++" STRIP="$ANDROID_BIN-strip" CPPFLAGS="--sysroot=$ANDROID_ROOT -DANDROID -I$ANDROID_CPP/include/ -I$ANDROID_CPP/include/backward/ -I$ANDROID_CPP/libs/x86/include/ -fPIC -ffunction-sections -funwind-tables -mssse3 -mfpmath=sse -fomit-frame-pointer -fstrict-aliasing -funswitch-loops -finline-limit=300" LDFLAGS="-L$ANDROID_ROOT/usr/lib/ -L$ANDROID_CPP/libs/x86/ -nostdlib -z text -L." LIBS="-lgnustl_static -lgcc -ldl -lz -lm -lc" --enable-cxx --enable-java
 #        make -j $MAKEJ
 #        make install-strip
 #        ;;
     linux-armhf)
+        # Build libaec for szip first
+        mkdir -p ../libaec-$AEC_VERSION/build
+        pushd ../libaec-$AEC_VERSION/build
+        "$CMAKE" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH ..
+        make -j $MAKEJ
+        make install
+        popd
+
         MACHINE_TYPE=$( uname -m )
         if [[ "$MACHINE_TYPE" =~ arm ]]; then
           ./configure --prefix=$INSTALL_PATH CC="gcc" CXX="g++" --enable-cxx --enable-java
@@ -57,6 +89,14 @@ case $PLATFORM in
         fi
         ;;
     linux-arm64)
+        # Build libaec for szip first
+        mkdir -p ../libaec-$AEC_VERSION/build
+        pushd ../libaec-$AEC_VERSION/build
+        "$CMAKE" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH ..
+        make -j $MAKEJ
+        make install
+        popd
+
         MACHINE_TYPE=$( uname -m )
         if [[ "$MACHINE_TYPE" =~ arm ]]; then
           ./configure --prefix=$INSTALL_PATH CC="gcc -m64" CXX="g++ -m64" --enable-cxx --enable-java
@@ -74,63 +114,112 @@ case $PLATFORM in
         fi
         ;;
     linux-x86)
-        ./configure --prefix=$INSTALL_PATH CC="gcc -m32" CXX="g++ -m32" --enable-cxx --enable-java
+        # Build libaec for szip first
+        mkdir -p ../libaec-$AEC_VERSION/build
+        pushd ../libaec-$AEC_VERSION/build
+        "$CMAKE" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH ..
+        make -j $MAKEJ
+        make install
+        popd
+
+        ./configure --prefix=$INSTALL_PATH CC="gcc -m32" CXX="g++ -m32" --enable-cxx --enable-java --with-szlib
         make -j $MAKEJ
         make install-strip
         ;;
     linux-x86_64)
-        ./configure --prefix=$INSTALL_PATH CC="gcc -m64" CXX="g++ -m64" --enable-cxx --enable-java
+        # Build libaec for szip first
+        mkdir -p ../libaec-$AEC_VERSION/build
+        pushd ../libaec-$AEC_VERSION/build
+        "$CMAKE" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH ..
+        make -j $MAKEJ
+        make install
+        popd
+
+        ./configure --prefix=$INSTALL_PATH CC="gcc -m64" CXX="g++ -m64" --enable-cxx --enable-java --with-szlib
         make -j $MAKEJ
         make install-strip
         ;;
     linux-ppc64le)
         MACHINE_TYPE=$( uname -m )
         if [[ "$MACHINE_TYPE" =~ ppc64 ]]; then
-          ./configure --prefix=$INSTALL_PATH CC="gcc -m64" CXX="g++ -m64" --enable-cxx --enable-java
+          # Build libaec for szip first
+          mkdir -p ../libaec-$AEC_VERSION/build
+          pushd ../libaec-$AEC_VERSION/build
+          "$CMAKE" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH ..
+          make -j $MAKEJ
+          make install
+          popd
+
+          ./configure --prefix=$INSTALL_PATH CC="gcc -m64" CXX="g++ -m64" --enable-cxx --enable-java --with-szlib
           make -j $MAKEJ
           make install-strip
         else
           echo "Not native ppc so assume cross compiling"
           patch -Np1 < ../../../hdf5-linux-ppc64le.patch || true
           #need this to run twice, first run fails so we fake the exit code too
           for x in 1 2; do
-              "$CMAKE" -DCMAKE_TOOLCHAIN_FILE=`pwd`/ppc.cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH -DBUILD_TESTING=false -DHDF5_BUILD_EXAMPLES=false -DHDF5_BUILD_TOOLS=false -DCMAKE_CXX_FLAGS="-D_GNU_SOURCE" -DCMAKE_C_FLAGS="-D_GNU_SOURCE" -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ" -DZLIB_TGZ_NAME:STRING="$ZLIB.tar.gz" -DTGZPATH:STRING="$INSTALL_PATH/.." -DHDF5_ENABLE_Z_LIB_SUPPORT=ON -DHDF5_BUILD_CPP_LIB=ON -DHDF5_BUILD_JAVA=ON . || true
+              "$CMAKE" -DCMAKE_TOOLCHAIN_FILE=`pwd`/ppc.cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH -DBUILD_TESTING=false -DHDF5_BUILD_EXAMPLES=false -DHDF5_BUILD_TOOLS=false -DCMAKE_CXX_FLAGS="-D_GNU_SOURCE" -DCMAKE_C_FLAGS="-D_GNU_SOURCE" -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ" -DZLIB_TGZ_NAME:STRING="$ZLIB.tar.gz" -DTGZPATH:STRING="$INSTALL_PATH/.." -DHDF5_ENABLE_Z_LIB_SUPPORT=ON -DSZAEC_TGZ_NAME:STRING="libaec-$AEC_VERSION.tar.gz" -DHDF5_ENABLE_SZIP_SUPPORT=ON -DHDF5_ENABLE_SZIP_ENCODING=ON -DUSE_LIBAEC=ON -DHDF5_BUILD_CPP_LIB=ON -DHDF5_BUILD_JAVA=ON . || true
           done
           make -j $MAKEJ
           make install
         fi
         ;;
     macosx-*)
+        # Build libaec for szip first
+        mkdir -p ../libaec-$AEC_VERSION/build
+        pushd ../libaec-$AEC_VERSION/build
+        "$CMAKE" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH ..
+        make -j $MAKEJ
+        make install
+        popd
+
         patch -Np1 < ../../../hdf5-macosx.patch
-        ./configure --prefix=$INSTALL_PATH --enable-cxx --enable-java
+        ./configure --prefix=$INSTALL_PATH --enable-cxx --enable-java --with-szlib
         make -j $MAKEJ
         make install-strip
         ;;
     windows-x86)
-        mkdir -p build
-        cd build
         export CC="cl.exe"
         export CXX="cl.exe"
-        "$CMAKE" -G "Ninja" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH -DBUILD_TESTING=false -DHDF5_BUILD_EXAMPLES=false -DHDF5_BUILD_TOOLS=false -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ" -DZLIB_TGZ_NAME:STRING="$ZLIB.tar.gz" -DTGZPATH:STRING="$INSTALL_PATH/.." -DHDF5_ENABLE_Z_LIB_SUPPORT=ON -DHDF5_BUILD_CPP_LIB=ON -DHDF5_BUILD_JAVA=ON ..
+
+        mkdir -p ../libaec-$AEC_VERSION/build
+        pushd ../libaec-$AEC_VERSION/build
+        "$CMAKE" -G "Ninja" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH ..
+        ninja -j $MAKEJ
+        ninja install
+        popd
+
+        mkdir -p build
+        pushd build
+        "$CMAKE" -G "Ninja" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH -DBUILD_TESTING=false -DHDF5_BUILD_EXAMPLES=false -DHDF5_BUILD_TOOLS=false -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ" -DZLIB_TGZ_NAME:STRING="$ZLIB.tar.gz" -DTGZPATH:STRING="$INSTALL_PATH/.." -DHDF5_ENABLE_Z_LIB_SUPPORT=ON -DHDF5_ENABLE_SZIP_SUPPORT=ON -DHDF5_ENABLE_SZIP_ENCODING=ON -DUSE_LIBAEC=ON -DSZIP_LIBRARY:FILEPATH="$INSTALL_PATH/lib/szip_static.lib" -DSZIP_INCLUDE_DIR="$INSTALL_PATH/include" -DSZIP_USE_EXTERNAL:BOOL=OFF -DHDF5_BUILD_CPP_LIB=ON -DHDF5_BUILD_JAVA=ON ..
         sedinplace 's/Release\\libz.lib/zlibstatic.lib/g' build.ninja
         ninja -j $MAKEJ HDF5_ZLIB
         ninja -j $MAKEJ
         ninja install
         cp bin/zlib* ../../lib/
-        cd ..
+        popd
         ;;
     windows-x86_64)
-        mkdir -p build
-        cd build
         export CC="cl.exe"
         export CXX="cl.exe"
-        "$CMAKE" -G "Ninja" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH -DBUILD_TESTING=false -DHDF5_BUILD_EXAMPLES=false -DHDF5_BUILD_TOOLS=false -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ" -DZLIB_TGZ_NAME:STRING="$ZLIB.tar.gz" -DTGZPATH:STRING="$INSTALL_PATH/.." -DHDF5_ENABLE_Z_LIB_SUPPORT=ON -DHDF5_BUILD_CPP_LIB=ON -DHDF5_BUILD_JAVA=ON ..
+
+        mkdir -p ../libaec-$AEC_VERSION/build
+        pushd ../libaec-$AEC_VERSION/build
+        "$CMAKE" -G "Ninja" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH ..
+        ninja -j $MAKEJ
+        ninja install
+        popd
+
+        mkdir -p build
+        pushd build
+        "$CMAKE" -G "Ninja" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH -DBUILD_TESTING=false -DHDF5_BUILD_EXAMPLES=false -DHDF5_BUILD_TOOLS=false -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ" -DZLIB_TGZ_NAME:STRING="$ZLIB.tar.gz" -DTGZPATH:STRING="$INSTALL_PATH/.." -DHDF5_ENABLE_Z_LIB_SUPPORT=ON -DHDF5_ENABLE_SZIP_SUPPORT=ON -DHDF5_ENABLE_SZIP_ENCODING=ON -DUSE_LIBAEC=ON -DSZIP_LIBRARY:FILEPATH="$INSTALL_PATH/lib/szip_static.lib" -DSZIP_INCLUDE_DIR="$INSTALL_PATH/include" -DSZIP_USE_EXTERNAL:BOOL=OFF -DHDF5_BUILD_CPP_LIB=ON -DHDF5_BUILD_JAVA=ON ..
+
         sedinplace 's/Release\\libz.lib/zlibstatic.lib/g' build.ninja
         ninja -j $MAKEJ HDF5_ZLIB
         ninja -j $MAKEJ
         ninja install
         cp bin/zlib* ../../lib/
-        cd ..
+        popd
         ;;
     *)
         echo "Error: Platform \"$PLATFORM\" is not supported"
@@ -140,4 +229,5 @@ esac
 [ -d "../java" ] && rm -r ../java
 cp -r java/src ../java
 
-cd ../..
+# Return to cppbuild directory
+popd
diff --git a/hdf5/src/gen/java/org/bytedeco/hdf5/global/hdf5.java b/hdf5/src/gen/java/org/bytedeco/hdf5/global/hdf5.java
@@ -136,7 +136,7 @@ public class hdf5 extends org.bytedeco.hdf5.presets.hdf5 {
 public static final int H5_HAVE_FILTER_DEFLATE = 1;
 
 /* Define if support for szip filter is enabled */
-/* #undef H5_HAVE_FILTER_SZIP */
+public static final int H5_HAVE_FILTER_SZIP = 1;
 
 /* Determine if __float128 is available */
 /* #undef H5_HAVE_FLOAT128 */
@@ -207,7 +207,7 @@ public class hdf5 extends org.bytedeco.hdf5.presets.hdf5 {
 /* #undef H5_HAVE_LIBPTHREAD */
 
 /* Define to 1 if you have the `sz' library (-lsz). */
-/* #undef H5_HAVE_LIBSZ */
+public static final int H5_HAVE_LIBSZ = 1;
 
 /* Define to 1 if you have the `ws2_32' library (-lws2_32). */
 /* #undef H5_HAVE_LIBWS2_32 */
@@ -352,7 +352,7 @@ public class hdf5 extends org.bytedeco.hdf5.presets.hdf5 {
 public static final int H5_HAVE_SYS_TYPES_H = 1;
 
 /* Define to 1 if you have the <szlib.h> header file. */
-/* #undef H5_HAVE_SZLIB_H */
+public static final int H5_HAVE_SZLIB_H = 1;
 
 /* Define if we have thread safe support */
 /* #undef H5_HAVE_THREADSAFE */

diff --git a/hdf5/src/main/java/org/bytedeco/hdf5/presets/hdf5.java b/hdf5/src/main/java/org/bytedeco/hdf5/presets/hdf5.java
@@ -51,7 +51,7 @@
         "H5FaccProp.h", "H5FcreatProp.h", "H5AtomType.h", "H5PredType.h", "H5EnumType.h", "H5IntType.h", "H5FloatType.h", "H5StrType.h", "H5CompType.h",
         "H5ArrayType.h", "H5VarLenType.h", "H5DataSet.h", "H5Group.h", "H5File.h", "H5Library.h"},
             link = {"hdf5@.310", "hdf5_cpp@.310", "hdf5_hl@.310", "hdf5_hl_cpp@.310"}, resource = {"include", "lib"}),
-    @Platform(value = "windows", link = {"zlibstatic", "libhdf5", "libhdf5_cpp", "libhdf5_hl", "libhdf5_hl_cpp"}) })
+    @Platform(value = "windows", link = {"zlibstatic", "libhdf5", "libhdf5_cpp", "libhdf5_hl", "libhdf5_hl_cpp", "szip_static"}) })
 public class hdf5 implements InfoMapper {
     static { Loader.checkVersion("org.bytedeco", "hdf5"); }