Update to HDF5 1.8.16 with the HDFFV-9670 patch (btree2 code guard against...

Update to HDF5 1.8.16 with the HDFFV-9670 patch (btree2 code guard against corrupt HDF5 files) (merge from 14.12.x).

SVN: 35714

libs/native/jhdf5/version.txt

-1.8.13
+1.8.16-HDFFV-9670

source/c/compile_hdf5_gcc.sh

@@ -6,17 +6,22 @@ PATCHES="$2"
 
 if [ "$PLATFORM" != "i386" -a "$PLATFORM" != "x86" -a "$PLATFORM" != "amd64" -a "$PLATFORM" != "x86_64" -a "$PLATFORM" != "armv6l" ]; then
   echo "Syntax: compile_hdf5.sh <platform>"
-  echo "where <platform> is one of i386, x86, amd64, or x86_64"
+  echo "where <platform> is one of i386, x86, amd64, x86_64, or armv6l"
   exit 1
 fi
 
 tar xvf hdf5-$VERSION.tar
 
+if [ -n "$POSTFIX" ]; then
+  mv hdf5-$VERSION hdf5-$VERSION-$POSTFIX
+  VERSION="$VERSION-$POSTFIX"
+fi
+
 cd hdf5-$VERSION
 
 if [ -n "$PATCHES" ]; then
   for p in $PATCHES; do
-    patch -p0 < ../$p
+    patch -p1 < ../$p
   done
 fi
 

source/c/compile_hdf5_linux_amd64.sh

 #! /bin/bash
 
-CFLAGS='-fPIC -m64' ./compile_hdf5_gcc.sh amd64 "gcc-4.678-optimizations-config.patch"
+CFLAGS='-fPIC -m64' ./compile_hdf5_gcc.sh amd64 "HDFFV-9670-1.8.16.patch gcc-4+-optimizations-config.patch"

source/c/compile_hdf5_linux_arm.sh

 #! /bin/bash
 
-./compile_hdf5_gcc.sh armv6l
+./compile_hdf5_gcc.sh armv6l "HDFFV-9670-1.8.16.patch"

source/c/compile_hdf5_linux_i386.sh

 #! /bin/bash
 
-CFLAGS='-m32' ./compile_hdf5_gcc.sh i386 "gcc-4.678-optimizations-config.patch"
+CFLAGS='-m32' ./compile_hdf5_gcc.sh i386 "HDFFV-9670-1.8.16.patch gcc-4+-optimizations-config.patch"

source/c/compile_hdf5_macosx_i386.sh

 #! /bin/bash
 
-CFLAGS='-m32 -mmacosx-version-min=10.6' ./compile_hdf5_gcc.sh i386
+CFLAGS='-m32 -mmacosx-version-min=10.6' ./compile_hdf5_gcc.sh i386 "HDFFV-9670-1.8.16.patch"

source/c/compile_hdf5_macosx_x86_64.sh

 #! /bin/bash
 
-CFLAGS='-m64 -mmacosx-version-min=10.6' ./compile_hdf5_gcc.sh x86_64
+CFLAGS='-m64 -mmacosx-version-min=10.6' ./compile_hdf5_gcc.sh x86_64 "HDFFV-9670-1.8.16.patch"

source/c/compile_hdf5_sunstudio_64.sh

@@ -5,10 +5,17 @@ export PATH
 
 source version.sh
 
-tar xf hdf5-$VERSION.tar
+tar xvf hdf5-$VERSION.tar
+
+if [ -n "$POSTFIX" ]; then
+  mv hdf5-$VERSION hdf5-$VERSION-$POSTFIX
+  VERSION="$VERSION-$POSTFIX"
+fi
 
 cd hdf5-$VERSION
 
+patch -p1 < ../HDFFV-9670-1.8.16.patch
+
 CFLAGS='-fast -m64 -KPIC' ./configure --prefix=/opt/hdf5-$VERSION-64 --enable-shared --enable-debug=none --enable-production
 
 make > make.log 2>&1