编译另一个库时发生HDF5错误

Question

我按照以下步骤编译了HDF5：

untar hdf5-xxx.tar.gz
cd hdf5-xxx
make
make install

但是，在安装另一个请求OpenGM的库( HDF5 )时，我提供了以下参数：

HDF5_CORE_LIBRARY                /Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5                                                             
 HDF5_CPP_LIBRARY                 /Users/Florian/Documents/THESE/hdf5-1.8.7/c++                                                              
 HDF5_HL_LIBRARY                  /Users/Florian/Documents/THESE/hdf5-1.8.7/hl                                                               
 HDF5_INCLUDE_DIR                 /Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5/include                                                     
 HDF5_Z_LIBRARY                   /usr/lib/libz.dylib

在使用CMake和generate之后，我得到：

 WARNING: Target "example-io" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5".  Targets may link only to libraries.
  CMake is dropping the item.

 WARNING: Target "example-io" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hl".  Targets may link only to libraries.
 CMake is dropping the item.

 WARNING: Target "external-library-daoopt" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5".  Targets may link only
 to libraries.  CMake is dropping the item.

 WARNING: Target "external-library-daoopt" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hl".  Targets may link only to
 libraries.  CMake is dropping the item.

 WARNING: Target "external-library-daoopt-shared" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5".  Targets may
 link only to libraries.  CMake is dropping the item.

 WARNING: Target "external-library-daoopt-shared" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hl".  Targets may link
 only to libraries.  CMake is dropping the item.

 WARNING: Target "_opengmcore" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5".  Targets may link only to
 libraries.  CMake is dropping the item.

 WARNING: Target "_opengmcore" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5".  Targets may link only to
 libraries.  CMake is dropping the item.

 WARNING: Target "_opengmcore" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hl".  Targets may link only to libraries.
 CMake is dropping the item.

 WARNING: Target "_hdf5" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5".  Targets may link only to libraries.
 CMake is dropping the item.

 WARNING: Target "_hdf5" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hl".  Targets may link only to libraries.  CMake
 is dropping the item.

 WARNING: Target "modelIO" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5".  Targets may link only to libraries.
 CMake is dropping the item.

 WARNING: Target "modelIO" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hl".  Targets may link only to libraries.
 CMake is dropping the item.

 WARNING: Target "buildFoE" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5".  Targets may link only to libraries.
 CMake is dropping the item.

因为这些只是警告，所以我可以编译我的OpenGM库：

make

但是，我的结果是出现了以下错误：

Undefined symbols for architecture x86_64:
  "_H5Aclose", referenced from:
      void marray::hdf5::save<unsigned long>(int const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, marray::Marray<unsigned long, std::__1::allocator<unsigned long> > const&) in io_graphical_model.cxx.o
      void marray::hdf5::save<float>(int const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, marray::Marray<float, std::__1::allocator<unsigned long> > const&) in io_graphical_model.cxx.o
      void marray::hdf5::save<double>(int const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, marray::Marray<double, std::__1::allocator<unsigned long> > const&) in io_graphical_model.cxx.o
      void marray::hdf5::save<long>(int const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, marray::Marray<long, std::__1::allocator<unsigned long> > const&) in io_graphical_model.cxx.o
...
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

由于警告和错误处理都与HDF5有关，我认为主要问题来自于这个库。

如果可以的话，我正在使用MacOSX。

**编辑：**添加FindHDF5.cmake文件

# - Find HDF5, a library for reading and writing self describing array data.
#
FIND_PATH(HDF5_INCLUDE_DIR hdf5.h)

FIND_LIBRARY(HDF5_CORE_LIBRARY NAMES hdf5dll hdf5  )
FIND_LIBRARY(HDF5_HL_LIBRARY NAMES hdf5_hldll hdf5_hl  )
FIND_LIBRARY(HDF5_CPP_LIBRARY NAMES hdf5_cppdll hdf5_cpp )

IF(WIN32 AND HDF5_CORE_LIBRARY MATCHES "dll.lib$")
    SET(HDF5_CFLAGS "-D_HDF5USEDLL_")
    SET(HDF5_CPPFLAGS "-D_HDF5USEDLL_ -DHDF5CPP_USEDLL")
ELSE()
    SET(HDF5_CFLAGS)
    SET(HDF5_CPPFLAGS)
ENDIF()

SET(HDF5_VERSION_MAJOR 1)
SET(HDF5_VERSION_MINOR 8)

set(HDF5_SUFFICIENT_VERSION FALSE)

TRY_COMPILE(HDF5_SUFFICIENT_VERSION
            ${CMAKE_BINARY_DIR} ${CMAKE_MODULE_PATH}/checkHDF5version.c
            COMPILE_DEFINITIONS "-I\"${HDF5_INCLUDE_DIR}\" -DMIN_MAJOR=${HDF5_VERSION_MAJOR} -DMIN_MINOR=${HDF5_VERSION_MINOR}")

if(HDF5_SUFFICIENT_VERSION)
    MESSAGE(STATUS
           "Checking HDF5 version (at least ${HDF5_VERSION_MAJOR}.${HDF5_VERSION_MINOR}): ok")
else()
    MESSAGE( STATUS "HDF5: need at least version ${HDF5_VERSION_MAJOR}.${HDF5_VERSION_MINOR}" )
endif()

set(HDF5_USES_ZLIB FALSE)
TRY_COMPILE(HDF5_USES_ZLIB
           ${CMAKE_BINARY_DIR} ${CMAKE_MODULE_PATH}/checkHDF5usesCompression.c
           COMPILE_DEFINITIONS "-I\"${HDF5_INCLUDE_DIR}\" -DH5_SOMETHING=H5_HAVE_FILTER_DEFLATE")

if(HDF5_USES_ZLIB)
    FIND_LIBRARY(HDF5_Z_LIBRARY NAMES zlib1 zlib z )
    set(HDF5_ZLIB_OK ${HDF5_Z_LIBRARY})
else()
    set(HDF5_ZLIB_OK TRUE)
    set(HDF5_Z_LIBRARY "")
endif()

set(HDF5_USES_SZLIB FALSE)
TRY_COMPILE(HDF5_USES_SZLIB 
            ${CMAKE_BINARY_DIR} ${CMAKE_MODULE_PATH}/checkHDF5usesCompression.c
            COMPILE_DEFINITIONS "-I\"${HDF5_INCLUDE_DIR}\" -DH5_SOMETHING=H5_HAVE_FILTER_SZIP")

if(HDF5_USES_SZLIB)
    FIND_LIBRARY(HDF5_SZ_LIBRARY NAMES szlibdll sz )
    set(HDF5_SZLIB_OK ${HDF5_SZ_LIBRARY})
else()
    set(HDF5_SZLIB_OK TRUE)
    set(HDF5_SZ_LIBRARY "")
endif()

# handle the QUIETLY and REQUIRED arguments and set HDF5_FOUND to TRUE if 
# all listed variables are TRUE
INCLUDE(FindPackageHandleStandardArgs)

FIND_PACKAGE_HANDLE_STANDARD_ARGS(HDF5 DEFAULT_MSG HDF5_CORE_LIBRARY 
        HDF5_HL_LIBRARY HDF5_ZLIB_OK HDF5_SZLIB_OK HDF5_INCLUDE_DIR)

IF(HDF5_FOUND)
    SET(HDF5_LIBRARIES ${HDF5_CORE_LIBRARY} ${HDF5_HL_LIBRARY} ${HDF5_Z_LIBRARY} ${HDF5_SZ_LIBRARY})
ELSE()
    SET(HDF5_CORE_LIBRARY HDF5_CORE_LIBRARY-NOTFOUND)
    SET(HDF5_HL_LIBRARY   HDF5_HL_LIBRARY-NOTFOUND)
    SET(HDF5_Z_LIBRARY    HDF5_Z_LIBRARY-NOTFOUND)
    SET(HDF5_SZ_LIBRARY   HDF5_SZ_LIBRARY-NOTFOUND)
ENDIF(HDF5_FOUND)

Answer 1

通过编译带有HDF5标志的--with_cxx库来构建C++接口，解决了这个问题。此外，我在HDF5中安装了/usr/local库，以便在安装opengm时自动找到它。