Migrate JHDF5 to HDF5 1.10.

A big 'thank you' goes to Gerd Heber from the HDF Group for doing a lot of the porting work to 1.10.

.gitignore

@@ -5,3 +5,4 @@
 /.project
 /.settings
 /test-output
+/source/c/build

build.gradle

@@ -46,7 +46,6 @@ task nativeJarLinuxIntel(type: Jar) {
     archiveName 'hdf5-linux-intel.jar'
     from ("libs") {
         include 'native/jhdf5/amd64-Linux/**/*'
-        include 'native/jhdf5/i386-Linux/**/*'
         include 'native/jhdf5/arm-Linux/**/*'
     }
     
@@ -58,7 +57,6 @@ task nativeJarLinuxIntel(type: Jar) {
 task nativeJarMacIntel(type: Jar) {
     archiveName 'hdf5-macosx-intel.jar'
     from ("libs") {
-        include 'native/jhdf5/i386-Mac OS X/**/*'
         include 'native/jhdf5/x86_64-Mac OS X/**/*'
     }
     
@@ -71,7 +69,6 @@ task nativeJarWindowsIntel(type: Jar) {
     archiveName 'hdf5-windows-intel.jar'
     from ("libs") {
         include 'native/jhdf5/amd64-Windows/**/*'
-        include 'native/jhdf5/x86-Windows/**/*'
     }
     
     from('targets/dist') {
@@ -150,8 +147,10 @@ task myJavadoc(type: Javadoc) {
 	options.memberLevel = JavadocMemberLevel.PUBLIC
 	options.overview = "overview.html"
 	include "ch/systemsx/cisd/hdf5/**"
-	include "ncsa/hdf/hdf5lib/exceptions/**"
+	include "ch/ethz/sis/hdf5/**"
+	include "hdf/hdf5lib/exceptions/**"
 	exclude "ch/systemsx/cisd/hdf5/hdf5lib/**"
+	exclude "ch/ethz/sis/hdf5/hdf5lib/**"
 	exclude "ch/systemsx/cisd/hdf5/cleanup/**"
 	exclude "ch/systemsx/cisd/hdf5/BitSetConversionUtils.java"
 	exclude "ch/systemsx/cisd/hdf5/MatrixUtils.java"
@@ -202,7 +201,7 @@ task distributionZip(type: Zip, dependsOn: [jar, toolsJar, allJar, nativeJarLinu
     }
     
     from (zipTree(batteriesIncluded.archivePath)) {
-        into "${project.group}-jhdf5/lib/native"
+        into "${project.group}-jhdf5/lib"
         include 'native/**'
     }
     

javaproject.gradle

@@ -226,7 +226,7 @@ test {
     systemProperty "ant.project.name", project.name
 
     maxHeapSize = "6144m"
-    jvmArgs '-XX:MaxPermSize=1024m', '-Duser.timezone=Europe/Zurich'
+    jvmArgs '-Duser.timezone=Europe/Zurich'
     
     testLogging.showStandardStreams = true
     ignoreFailures = true

libs/native/jhdf5/version.txt

-1.8.16-HDFFV-9670

source/c/COPYING

-Copyright Notice and Statement for NCSA Hierarchical Data Format (HDF)
-Java Software Library and Utilities
-
-NCSA Hierarchical Data Format (HDF) Software Library and Utilities 
-Copyright 1988-2004, the Board of Trustees of the University of Illinois.
-Copyright 2007-2009, Center for Information Sciences and Databases, ETH Zurich, Switzerland.  
-All rights reserved.
-
-Contributors to the library: National Center for Supercomputing 
-Applications (NCSA) at the University of Illinois, Lawrence 
-Livermore Nationall Laboratory (LLNL), Sandia National Laboratories (SNL), 
-Los Alamos National Laboratory (LANL). Fortner Software, Unidata 
-Program Center (netCDF), The Independent JPEG Group (JPEG), 
-Jean-loup Gailly and Mark Adler (gzip), and Digital Equipment 
-Corporation (DEC). Macintosh support contributed by Gregory L. Guerin.
-
-The package 'glguerin':
-Copyright 1998, 1999 by Gregory L. Guerin.
-Redistribute or reuse only as described below.
-These files are from the MacBinary Toolkit for Java:
-   <http://www.amug.org/~glguerin/sw/#macbinary>
-and are redistributed by NCSA with permission of the author.
-
-This work was supported in part by a Cooperative Agreement with 
-NASA under NASA grant NAG 5-2040 and NAG NCC5-599.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted for any purpose (including commercial purposes)
-provided that the following conditions are met:
-
-1.  Redistributions of source code must retain the above copyright notice,
-    this list of conditions and the following disclaimer.
-
-2.  Redistributions in binary form must reproduce the above copyright notice,
-    this list of conditions and the following disclaimer in the documentation
-    and/or materials provided with the distribution.
-
-3.  In addition, redistributions of modified forms of the source or binary
-    code must carry prominent notices stating that the original code was
-    changed and the date of the change.
-
-4.  All publications or advertising materials mentioning features or use of
-    this software must acknowledge that it was developed by the National
-    Center for Supercomputing Applications at the University of Illinois, and
-    credit the Contributors.
-
-5.  Neither the name of the University nor the names of the Contributors may
-    be used to endorse or promote products derived from this software without
-    specific prior written permission from the University or the Contributors.
-
-6.  THIS SOFTWARE IS PROVIDED BY THE UNIVERSITY AND THE CONTRIBUTORS "AS IS"
-    WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED.  In no event
-    shall the University or the Contributors be liable for any damages
-    suffered by the users arising out of the use of this software, even if
-    advised of the possibility of such damage.
-
---------------------------------------------------------------------------
-Portions of HDF5 were developed with support from the University of 
-California, Lawrence Livermore National Laboratory (UC LLNL).
-The following statement applies to those portions of the product
-and must be retained in any redistribution of source code, binaries,
-documentation, and/or accompanying materials:
-
-    This work was partially produced at the University of California,
-    Lawrence Livermore National Laboratory (UC LLNL) under contract no.
-    W-7405-ENG-48 (Contract 48) between the U.S. Department of Energy 
-    (DOE) and The Regents of the University of California (University) 
-    for the operation of UC LLNL.
-
-    DISCLAIMER:
-    This work was prepared as an account of work sponsored by an agency 
-    of the United States Government.  Neither the United States 
-    Government nor the University of California nor any of their 
-    employees, makes any warranty, express or implied, or assumes any 
-    liability or responsibility for the accuracy, completeness, or 
-    usefulness of any information, apparatus, product, or process 
-    disclosed, or represents that its use would not infringe privately-
-    owned rights.  Reference herein to any specific commercial products, 
-    process, or service by trade name, trademark, manufacturer, or 
-    otherwise, does not necessarily constitute or imply its endorsement, 
-    recommendation, or favoring by the United States Government or the 
-    University of California.  The views and opinions of authors 
-    expressed herein do not necessarily state or reflect those of the 
-    United States Government or the University of California, and shall 
-    not be used for advertising or product endorsement purposes.
---------------------------------------------------------------------------
-

source/c/compile_hdf5_gcc.sh

@@ -10,7 +10,13 @@ if [ "$PLATFORM" != "i386" -a "$PLATFORM" != "x86" -a "$PLATFORM" != "amd64" -a
   exit 1
 fi
 
-tar xvf hdf5-$VERSION.tar
+rm -fR build
+mkdir build
+
+cd build
+BUILD_ROOT=`pwd`
+
+tar xvf ../hdf5-$VERSION.tar*
 
 if [ -n "$POSTFIX" ]; then
   mv hdf5-$VERSION hdf5-$VERSION-$POSTFIX
@@ -21,12 +27,15 @@ cd hdf5-$VERSION
 
 if [ -n "$PATCHES" ]; then
   for p in $PATCHES; do
-    patch -p1 < ../$p
+    patch -p1 < ../../$p
   done
 fi
 
-CFLAGS=$CFLAGS ./configure --prefix=/opt/hdf5-$VERSION-$PLATFORM --enable-debug=none --enable-production $ADDITIONAL &> configure.log
+CFLAGS=$CFLAGS ./configure --prefix=$BUILD_ROOT/hdf5-$VERSION-$PLATFORM --enable-build-mode=production $ADDITIONAL &> configure.log
+
+make -j 4 &> build.log
+make install &> install.log
+#make test &> test.log
+
 
-make &> make.log
 
-make test &> test.log

source/c/compile_hdf5_linux_amd64.sh

 #! /bin/bash
 
-CFLAGS='-fPIC -m64' ./compile_hdf5_gcc.sh amd64 "HDFFV-9670-1.8.16.patch gcc-4+-optimizations-config.patch"
+CFLAGS='-fPIC -m64' ./compile_hdf5_gcc.sh amd64 "hdf5-1.10.3-pre1-jhdf5-h5dImp.patch hdf5-1.10.3-pre1-jhdf5-exceptionImp.patch"

source/c/compile_hdf5_linux_arm.sh

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