bundles/hdf.hdf5lib/README.md

   1 The Java HDF5 interface library and the accompanying hdf5_java.dll JNI library\r
   2 are built without both separately licensed ZLIB and SZIP open source libraries.\r
   3 The native library (DLL) has been compiled with Visual Studio 2015 and dynamic\r
   4 linking.\r
   5 \r
   6 ## Building HDF5 Linux native libraries\r
   7 \r
   8 Current libraries have been using the 1.10.2 source code release.\r
   9 \r
  10 * Get source code from https://www.hdfgroup.org/downloads/hdf5/source-code/\r
  11   * The configure-version, not the CMake source\r
  12 \r
  13 * Extract source code package\r
  14 \r
  15 * According to the build instructions at\r
  16   https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.2/src/unpacked/release_docs/INSTALL\r
  17   configure the source using:\r
  18 \r
  19       ./configure --enable-java --enable-build-mode=production --without-zlib --without-szlib --disable-sharedlib-rpath\r
  20 \r
  21   and you'll get a listing like this in the end:\r
  22 \r
  23 ~~~\r
  24             SUMMARY OF THE HDF5 CONFIGURATION\r
  25             =================================\r
  26 \r
  27 General Information:\r
  28 -------------------\r
  29                    HDF5 Version: 1.10.2\r
  30                   Configured on: Fri Apr  6 15:13:51 EEST 2018\r
  31                   Configured by: lehtonen@dev2\r
  32                     Host system: x86_64-unknown-linux-gnu\r
  33               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\r
  34                        Byte sex: little-endian\r
  35              Installation point: /home/lehtonen/hdf/hdf5-1.10.2/hdf5\r
  36 \r
  37 Compiling Options:\r
  38 ------------------\r
  39                      Build Mode: production\r
  40               Debugging Symbols: no\r
  41                         Asserts: no\r
  42                       Profiling: no\r
  43              Optimization Level: high\r
  44 \r
  45 Linking Options:\r
  46 ----------------\r
  47                       Libraries: static, shared\r
  48   Statically Linked Executables:\r
  49                         LDFLAGS:\r
  50                      H5_LDFLAGS:\r
  51                      AM_LDFLAGS:\r
  52                 Extra libraries: -ldl -lm\r
  53                        Archiver: ar\r
  54                        AR_FLAGS: cr\r
  55                          Ranlib: ranlib\r
  56                                                  \r
  57 Languages:\r
  58 ----------\r
  59                               C: yes\r
  60                      C Compiler: /usr/bin/gcc\r
  61                        CPPFLAGS:\r
  62                     H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L   -DNDEBUG -UH5_DEBUG_API\r
  63                     AM_CPPFLAGS:\r
  64                         C Flags:\r
  65                      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\r
  66                      AM C Flags:\r
  67                Shared C Library: yes\r
  68                Static C Library: yes\r
  69 \r
  70 \r
  71                         Fortran: no\r
  72 \r
  73                             C++: no\r
  74 \r
  75                            Java: yes\r
  76                   Java Compiler: /usr/bin/java (openjdk 1.8.0_162)\r
  77 \r
  78 \r
  79 Features:\r
  80 ---------\r
  81                   Parallel HDF5: no\r
  82              High-level library: yes\r
  83                    Threadsafety: no\r
  84             Default API mapping: v110\r
  85  With deprecated public symbols: yes\r
  86          I/O filters (external):\r
  87                             MPE: no\r
  88                      Direct VFD: no\r
  89                         dmalloc: no\r
  90  Packages w/ extra debug output: none\r
  91                     API tracing: no\r
  92            Using memory checker: no\r
  93 Memory allocation sanity checks: no\r
  94             Metadata trace file: no\r
  95          Function stack tracing: no\r
  96       Strict file format checks: no\r
  97    Optimization instrumentation: no\r
  98 \r
  99 ~~~\r
 100 \r
 101 * Build the library and utilities: `make -j -l6`\r
 102 \r
 103 * Copy the artifacts from the source tree into this directory:\r
 104   * Hdf5 library: `hdf5-1.10.2/src/.libs/libhdf5.so.101`\r
 105   * Hdf5 JNI library: `hdf5-1.10.2/java/src/jni/.libs/libhdf5_java.so`\r
 106 \r
 107 * IMPORTANT:\r
 108   * Linux .so files do not automatically look at the same directory they exist in for required .so files.\r
 109   * We can add this behaviour with the "patchelf" commandline tool:\r
 110   * apt-get update && apt-get install patchelf\r
 111   * patchelf --set-rpath \$ORIGIN libhdf5_java.so\r
 112 \r
 113 ## Building HDF5 Windows native libraries\r
 114 \r
 115 * Get CMake source code for Windows from https://www.hdfgroup.org/downloads/hdf5/source-code/#cmake\r
 116 * Build instructions are at https://portal.hdfgroup.org/display/support/Building+HDF5+with+CMake\r
 117   \r
 118 Here's our version in a nutshell:\r
 119   \r
 120 * Unpack CMake-hdf5-1.10.2.zip and step into the extracted directory \r
 121 * Edit HDF5options.cmake\r
 122   * Release build\r
 123     ~~~\r
 124     set(CTEST_BUILD_CONFIGURATION "Release")\r
 125     ~~~\r
 126   * Build shared libraries:\r
 127     ~~~\r
 128     set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_SHARED_LIBS:BOOL=ON")\r
 129     ~~~\r
 130   * Disable C++ library:\r
 131     ~~~\r
 132     set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=OFF")\r
 133     ~~~\r
 134   * Enable Java:\r
 135     ~~~\r
 136     #############################################################################################\r
 137     ####      java enabled      ####\r
 138     set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=ON")\r
 139     ####      java disabled      ####\r
 140     #set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=OFF")\r
 141     ~~~\r
 142   * Disable zlib and szip\r
 143     ~~~\r
 144         ### disable ext zlib building\r
 145     set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF")\r
 146     ### disable ext szip building\r
 147     set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF")\r
 148     set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_ENCODING:BOOL=OFF")\r
 149         ~~~\r
 150   * Disable packaging\r
 151     ~~~\r
 152     #############################################################################################\r
 153     ### disable packaging\r
 154 \r
 155     set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_NO_PACKAGES:BOOL=ON")\r
 156     ### Create install package with external libraries (szip, zlib)\r
 157     #set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACKAGE_EXTLIBS:BOOL=ON")\r
 158     ~~~\r
 159 * Run build-VS2015-64.bat and wait\r
 160 * Copy build\bin\hdf5_java.dll into this directory