From: Tuukka Lehtonen <tuukka.lehtonen@semantum.fi>
Date: Sun, 8 Apr 2018 22:01:52 +0000 (+0300)
Subject: Upgraded HDF5 library to 1.10.2 and added linux support
X-Git-Tag: v1.43.0~136^2~500
X-Git-Url: https://gerrit.simantics.org/r/gitweb?p=simantics%2Fplatform.git;a=commitdiff_plain;h=ce3c9f00e2cd5a41c668afb699f294897b6c4b66

Upgraded HDF5 library to 1.10.2 and added linux support

Amend by Miro:
Ran patchelf -set-rpath \$ORIGIN libhdf5_java.so and updated README

refs #7858

Change-Id: Ibe6d56443b8d02c4e2896adaed9b76f86e042f6e
---

diff --git a/bundles/hdf.hdf5lib/.classpath b/bundles/hdf.hdf5lib/.classpath
index 3d5627760..f0eb4b56a 100644
--- a/bundles/hdf.hdf5lib/.classpath
+++ b/bundles/hdf.hdf5lib/.classpath
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry exported="true" kind="lib" path="jarhdf5-1.10.0.jar" sourcepath="C:/work/hdf5/CMake-hdf5-1.10.0-patch1/hdf5-1.10.0-patch1/java/src"/>
+	<classpathentry exported="true" kind="lib" path="jarhdf5-1.10.2.jar" sourcepath="hdf5-src.zip"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
 	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
 	<classpathentry kind="src" path="src"/>
diff --git a/bundles/hdf.hdf5lib/META-INF/MANIFEST.MF b/bundles/hdf.hdf5lib/META-INF/MANIFEST.MF
index c7ef8a4da..91af25057 100644
--- a/bundles/hdf.hdf5lib/META-INF/MANIFEST.MF
+++ b/bundles/hdf.hdf5lib/META-INF/MANIFEST.MF
@@ -2,14 +2,15 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Java HDF5 Interface (JHI5)
 Bundle-SymbolicName: hdf.hdf5lib
-Bundle-Version: 1.10.0.patch1
+Bundle-Version: 1.10.2
 Bundle-Vendor: Semantum Oy
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Bundle-ClassPath: .,
- jarhdf5-1.10.0.jar
+ jarhdf5-1.10.2.jar
 Export-Package: hdf.hdf5lib,
  hdf.hdf5lib.callbacks,
  hdf.hdf5lib.exceptions,
  hdf.hdf5lib.structs
-Bundle-NativeCode: hdf5_java.dll; processor=x86_64; osname=win32
+Bundle-NativeCode: hdf5_java.dll; processor=x86_64; osname=win32,
+ libhdf5.so.101; libhdf5_java.so; processor=x86_64; osname=linux
 Require-Bundle: org.slf4j.api;bundle-version="1.7.2"
diff --git a/bundles/hdf.hdf5lib/README.md b/bundles/hdf.hdf5lib/README.md
index ea6445a44..a7a2b9aa7 100644
--- a/bundles/hdf.hdf5lib/README.md
+++ b/bundles/hdf.hdf5lib/README.md
@@ -1,4 +1,160 @@
 The Java HDF5 interface library and the accompanying hdf5_java.dll JNI library
 are built without both separately licensed ZLIB and SZIP open source libraries.
 The native library (DLL) has been compiled with Visual Studio 2015 and dynamic
-linking.
\ No newline at end of file
+linking.
+
+## Building HDF5 Linux native libraries
+
+Current libraries have been using the 1.10.2 source code release.
+
+* Get source code from https://www.hdfgroup.org/downloads/hdf5/source-code/
+  * The configure-version, not the CMake source
+
+* Extract source code package
+
+* According to the build instructions at
+  https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.2/src/unpacked/release_docs/INSTALL
+  configure the source using:
+
+      ./configure --enable-java --enable-build-mode=production --without-zlib --without-szlib --disable-sharedlib-rpath
+
+  and you'll get a listing like this in the end:
+
+~~~
+            SUMMARY OF THE HDF5 CONFIGURATION
+            =================================
+
+General Information:
+-------------------
+                   HDF5 Version: 1.10.2
+                  Configured on: Fri Apr  6 15:13:51 EEST 2018
+                  Configured by: lehtonen@dev2
+                    Host system: x86_64-unknown-linux-gnu
+              Uname information: Linux dev2 4.4.0-96-generic #119-Ubuntu SMP Tue Sep 12 14:59:54 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
+                       Byte sex: little-endian
+             Installation point: /home/lehtonen/hdf/hdf5-1.10.2/hdf5
+
+Compiling Options:
+------------------
+                     Build Mode: production
+              Debugging Symbols: no
+                        Asserts: no
+                      Profiling: no
+             Optimization Level: high
+
+Linking Options:
+----------------
+                      Libraries: static, shared
+  Statically Linked Executables:
+                        LDFLAGS:
+                     H5_LDFLAGS:
+                     AM_LDFLAGS:
+                Extra libraries: -ldl -lm
+                       Archiver: ar
+                       AR_FLAGS: cr
+                         Ranlib: ranlib
+						 
+Languages:
+----------
+                              C: yes
+                     C Compiler: /usr/bin/gcc
+                       CPPFLAGS:
+                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L   -DNDEBUG -UH5_DEBUG_API
+                    AM_CPPFLAGS:
+                        C Flags:
+                     H5 C Flags:   -std=c99 -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-arith -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-default -Wswitch-enum -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -fstdarg-opt -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-suggest-attribute=const -Wno-suggest-attribute=pure -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=format -O3
+                     AM C Flags:
+               Shared C Library: yes
+               Static C Library: yes
+
+
+                        Fortran: no
+
+                            C++: no
+
+                           Java: yes
+                  Java Compiler: /usr/bin/java (openjdk 1.8.0_162)
+
+
+Features:
+---------
+                  Parallel HDF5: no
+             High-level library: yes
+                   Threadsafety: no
+            Default API mapping: v110
+ With deprecated public symbols: yes
+         I/O filters (external):
+                            MPE: no
+                     Direct VFD: no
+                        dmalloc: no
+ Packages w/ extra debug output: none
+                    API tracing: no
+           Using memory checker: no
+Memory allocation sanity checks: no
+            Metadata trace file: no
+         Function stack tracing: no
+      Strict file format checks: no
+   Optimization instrumentation: no
+
+~~~
+
+* Build the library and utilities: `make -j -l6`
+
+* Copy the artifacts from the source tree into this directory:
+  * Hdf5 library: `hdf5-1.10.2/src/.libs/libhdf5.so.101`
+  * Hdf5 JNI library: `hdf5-1.10.2/java/src/jni/.libs/libhdf5_java.so`
+
+* IMPORTANT:
+  * Linux .so files do not automatically look at the same directory they exist in for required .so files.
+  * We can add this behaviour with the "patchelf" commandline tool:
+  * apt-get update && apt-get install patchelf
+  * patchelf --set-rpath \$ORIGIN libhdf5_java.so
+
+## Building HDF5 Windows native libraries
+
+* Get CMake source code for Windows from https://www.hdfgroup.org/downloads/hdf5/source-code/#cmake
+* Build instructions are at https://portal.hdfgroup.org/display/support/Building+HDF5+with+CMake
+  
+Here's our version in a nutshell:
+  
+* Unpack CMake-hdf5-1.10.2.zip and step into the extracted directory 
+* Edit HDF5options.cmake
+  * Release build
+    ~~~
+    set(CTEST_BUILD_CONFIGURATION "Release")
+    ~~~
+  * Build shared libraries:
+    ~~~
+    set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_SHARED_LIBS:BOOL=ON")
+    ~~~
+  * Disable C++ library:
+    ~~~
+    set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=OFF")
+    ~~~
+  * Enable Java:
+    ~~~
+    #############################################################################################
+    ####      java enabled      ####
+    set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=ON")
+    ####      java disabled      ####
+    #set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=OFF")
+    ~~~
+  * Disable zlib and szip
+    ~~~
+	### disable ext zlib building
+    set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF")
+    ### disable ext szip building
+    set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF")
+    set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_ENCODING:BOOL=OFF")
+	~~~
+  * Disable packaging
+    ~~~
+    #############################################################################################
+    ### disable packaging
+
+    set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_NO_PACKAGES:BOOL=ON")
+    ### Create install package with external libraries (szip, zlib)
+    #set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACKAGE_EXTLIBS:BOOL=ON")
+    ~~~
+* Run build-VS2015-64.bat and wait
+* Copy build\bin\hdf5_java.dll into this directory
\ No newline at end of file
diff --git a/bundles/hdf.hdf5lib/about.html b/bundles/hdf.hdf5lib/about.html
index 80b486768..af353e432 100644
--- a/bundles/hdf.hdf5lib/about.html
+++ b/bundles/hdf.hdf5lib/about.html
@@ -7,16 +7,16 @@
 <body lang="EN-US">
 <h2>About This Content</h2>
  
-<p>August 29th, 2016</p>
+<p>April 9th, 2018</p>
 <h3>License</h3>
 
 		<h3>Third Party Content</h3>
 		<p>The Content includes items that have been sourced from third parties as set out below.</p>
 		<p><em>
-		<strong>Java HDF5 Interface (JHI5), version 1.10.0-patch1</strong> <br><br>
+		<strong>Java HDF5 Interface (JHI5), version 1.10.2</strong> <br><br>
 			This library has been obtained from the HDF Group
-			(https://www.hdfgroup.org/HDF5/release/obtain5110.html) unmodified.
+			(https://www.hdfgroup.org/downloads/hdf5/) unmodified.
 			See file COPYING for more information on the license.
 		</em></p>
 
-</body></html>
\ No newline at end of file
+</body></html>
diff --git a/bundles/hdf.hdf5lib/build.properties b/bundles/hdf.hdf5lib/build.properties
index 4a873ef6e..391232811 100644
--- a/bundles/hdf.hdf5lib/build.properties
+++ b/bundles/hdf.hdf5lib/build.properties
@@ -2,8 +2,10 @@ source.. = src/
 output.. = bin/
 bin.includes = META-INF/,\
                .,\
-               jarhdf5-1.10.0.jar,\
+               jarhdf5-1.10.2.jar,\
                hdf5_java.dll,\
+               libhdf5.so.101,\
+               libhdf5_java.so,\
                COPYING,\
                README.md,\
                about.html
diff --git a/bundles/hdf.hdf5lib/hdf5-src.zip b/bundles/hdf.hdf5lib/hdf5-src.zip
new file mode 100644
index 000000000..8004458fd
Binary files /dev/null and b/bundles/hdf.hdf5lib/hdf5-src.zip differ
diff --git a/bundles/hdf.hdf5lib/hdf5_java.dll b/bundles/hdf.hdf5lib/hdf5_java.dll
index aed8a7705..915096b8e 100644
Binary files a/bundles/hdf.hdf5lib/hdf5_java.dll and b/bundles/hdf.hdf5lib/hdf5_java.dll differ
diff --git a/bundles/hdf.hdf5lib/jarhdf5-1.10.0.jar b/bundles/hdf.hdf5lib/jarhdf5-1.10.0.jar
deleted file mode 100644
index 1fcdb3261..000000000
Binary files a/bundles/hdf.hdf5lib/jarhdf5-1.10.0.jar and /dev/null differ
diff --git a/bundles/hdf.hdf5lib/jarhdf5-1.10.2.jar b/bundles/hdf.hdf5lib/jarhdf5-1.10.2.jar
new file mode 100644
index 000000000..780a5c1d5
Binary files /dev/null and b/bundles/hdf.hdf5lib/jarhdf5-1.10.2.jar differ
diff --git a/bundles/hdf.hdf5lib/libhdf5.so.101 b/bundles/hdf.hdf5lib/libhdf5.so.101
new file mode 100755
index 000000000..7f0641ee9
Binary files /dev/null and b/bundles/hdf.hdf5lib/libhdf5.so.101 differ
diff --git a/bundles/hdf.hdf5lib/libhdf5_java.so b/bundles/hdf.hdf5lib/libhdf5_java.so
new file mode 100755
index 000000000..1ce6a1f82
Binary files /dev/null and b/bundles/hdf.hdf5lib/libhdf5_java.so differ
diff --git a/bundles/hdf.hdf5lib/pom.xml b/bundles/hdf.hdf5lib/pom.xml
index 5c00b7ab1..a64ceb4bc 100644
--- a/bundles/hdf.hdf5lib/pom.xml
+++ b/bundles/hdf.hdf5lib/pom.xml
@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>hdf.hdf5lib</artifactId>
 	<packaging>eclipse-plugin</packaging>
-	<version>1.10.0.patch1</version>
+	<version>1.10.2</version>
 
 	<parent>
 		<groupId>org.simantics</groupId>
@@ -23,10 +23,14 @@
 							<os>win32</os>
 							<arch>x86_64</arch>
 						</environment>
+						<environment>
+							<os>linux</os>
+							<arch>x86_64</arch>
+						</environment>
 					</environments>
 				</configuration>
 			</plugin>
 		</plugins>
 	</build>
 
-</project>
\ No newline at end of file
+</project>
diff --git a/features/hdf.hdf5.feature/feature.xml b/features/hdf.hdf5.feature/feature.xml
index d0cd9a1d5..0e47915d1 100644
--- a/features/hdf.hdf5.feature/feature.xml
+++ b/features/hdf.hdf5.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="hdf.hdf5"
       label="HDF5 for Java"
-      version="1.10.0.patch1"
+      version="1.10.2"
       provider-name="Semantum Oy">
 
    <description>
@@ -118,7 +118,7 @@ in HDF Products” (www.hdfgroup.org/doc_resource/SZIP/) for further details.
 
    <plugin
          id="hdf.hdf5lib"
-         os="win32"
+         os="linux,win32"
          arch="x86_64"
          download-size="0"
          install-size="0"