Commit 20212c5f authored by brinn's avatar brinn
Browse files

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.
parent eb715b2c
......@@ -5,3 +5,4 @@
......@@ -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/"
exclude "ch/systemsx/cisd/hdf5/"
......@@ -202,7 +201,7 @@ task distributionZip(type: Zip, dependsOn: [jar, toolsJar, allJar, nativeJarLinu
from (zipTree(batteriesIncluded.archivePath)) {
into "${}-jhdf5/lib/native"
into "${}-jhdf5/lib"
include 'native/**'
......@@ -226,7 +226,7 @@ test {
systemProperty "",
maxHeapSize = "6144m"
jvmArgs '-XX:MaxPermSize=1024m', '-Duser.timezone=Europe/Zurich'
jvmArgs '-Duser.timezone=Europe/Zurich'
testLogging.showStandardStreams = true
ignoreFailures = true
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:
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.
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.
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.
This diff is collapsed.
......@@ -10,7 +10,13 @@ if [ "$PLATFORM" != "i386" -a "$PLATFORM" != "x86" -a "$PLATFORM" != "amd64" -a
exit 1
tar xvf hdf5-$VERSION.tar
rm -fR build
mkdir build
cd build
tar xvf ../hdf5-$VERSION.tar*
if [ -n "$POSTFIX" ]; then
......@@ -21,12 +27,15 @@ cd hdf5-$VERSION
if [ -n "$PATCHES" ]; then
for p in $PATCHES; do
patch -p1 < ../$p
patch -p1 < ../../$p
CFLAGS=$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
#! /bin/bash
CFLAGS='-fPIC -m64' ./ amd64 "HDFFV-9670-1.8.16.patch gcc-4+-optimizations-config.patch"
CFLAGS='-fPIC -m64' ./ amd64 "hdf5-1.10.3-pre1-jhdf5-h5dImp.patch hdf5-1.10.3-pre1-jhdf5-exceptionImp.patch"
#! /bin/bash
./ armv6l "HDFFV-9670-1.8.16.patch"
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