编译另一个库时出现 HDF5 错误

Posted 2023-03-11

【中文标题】编译另一个库时出现 HDF5 错误

【英文标题】：HDF5 error while compiling another library

【发布时间】：2017-02-23 04:40:13

【问题描述】：

我按照以下步骤编译了 HDF5：

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

但是，当我安装另一个请求 HDF5 的库 (OpenGM) 时，我给出了以下参数：

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

使用 CMake 并生成后，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“只是”警告，我可以编译我的 OpenGM 库：

make

但我因此最终出现以下错误：

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)

由于警告和错误都处理 HDF5，我想主要问题来自这个库。

如果有帮助，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)

【问题讨论】：

... where I provide the path to the HDF5 library ... - 看起来您将 directory 分配给了一个变量，该变量应该是一个 库文件。这就是你发出警告的原因。

查看我的编辑以查看我作为 CMake 参数给出的内容。

正如我之前所说的：您将目录分配给变量（HDF5_CORE_LIBRARY，HDF5_HL_LIBRARY），它应该是一个库文件。

你对库的定义是什么？我应该考虑哪些扩展？

您通过find_package(HDF5) 获得此变量列表，不是吗？与其手动填充这些变量，不如提示这个安装HDF5库的过程。 FindHDF5.cmake 脚本中的注释描述了如何提示它。跟着他们就行了。

【参考方案1】：

通过编译带有--with_cxx 标志的HDF5 库来构建C++ 接口解决了这个问题。另外我把HDF5库安装在/usr/local，这样安装opengm的时候就自动找到了。

【讨论】：

我遇到了类似的问题。问题是，尽管我可以成功编译 OpenGM，但我无法编译调用 opengm 库和 hdf5 的简单 c++ 文件。