Linux上的MATLAB MEX文件无法在libpython.2.7.so中找到符号

时间：2013-08-30 21:09:29

标签： python linux matlab shared-libraries mex

我一直在使用project将Python解释器作为MEX文件嵌入到MATLAB中，使用libpython2.7.so，但每当我尝试导入作为扩展模块实现的Python模块时都会遇到问题。例如，尝试导入itertools会导致以下错误：

>> py_import itertools
ImportError: /usr/lib64/python2.7/lib-dynload/itertoolsmodule.so: undefined symbol: PyTuple_Type
??? Error using ==> pymex_fns
Python exception inside py_import.

Error in ==> py_import at 24
    py_obj = pymex_fns(py_function_t.IMPORT, name);

无论是否在调用LD_LIBRARY_PATH之前清除Py_Initialize()，并且在MATLAB中调用ldd（对于此示例中为itertools.so），都会出现此问题不会产生任何(not found)条消息。下面，我用LD_DEBUG=libs集粘贴运行MATLAB的结果，首先用MATLAB的启动设置LD_LIBRARY_PATH，然后在尝试导入之前运行setenv('LD_LIBRARY_PATH', '')。

如何解决此问题，并允许动态加载扩展模块？

使用MATLAB-default LD_LIBRARY_PATH：

>> py_import itertools           
      3018: find library=libpython2.7.so.1.0 [0]; searching
      3018:  search path=/usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64:/usr/local/MATLAB/R2011a/bin/glnxa64:/usr/local/MATLAB/R2011a/bin/glnxa64/../../sys/os/glnxa64      (RPATH from file /usr/local/MATLAB/R2011a/bin/glnxa64/MATLAB)
      3018:   trying file=/usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libpython2.7.so.1.0
      3018:   trying file=/usr/local/MATLAB/R2011a/bin/glnxa64/libpython2.7.so.1.0
      3018:   trying file=/usr/local/MATLAB/R2011a/bin/glnxa64/../../sys/os/glnxa64/libpython2.7.so.1.0
      3018:  search path=/usr/local/MATLAB/R2011a/sys/os/glnxa64        (LD_LIBRARY_PATH)
      3018:   trying file=/usr/local/MATLAB/R2011a/sys/os/glnxa64/libpython2.7.so.1.0
      3018:  search path=/usr/local/MATLAB/R2011a/bin/glnxa64       (RPATH from file /usr/local/MATLAB/R2011a/bin/glnxa64/MATLAB)
      3018:   trying file=/usr/local/MATLAB/R2011a/bin/glnxa64/libpython2.7.so.1.0
      3018:  search path=/usr/local/MATLAB/R2011a/extern/lib/glnxa64:/usr/local/MATLAB/R2011a/runtime/glnxa64:/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64     (LD_LIBRARY_PATH)
      3018:   trying file=/usr/local/MATLAB/R2011a/extern/lib/glnxa64/libpython2.7.so.1.0
      3018:   trying file=/usr/local/MATLAB/R2011a/runtime/glnxa64/libpython2.7.so.1.0
      3018:   trying file=/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads/libpython2.7.so.1.0
      3018:   trying file=/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/server/libpython2.7.so.1.0
      3018:   trying file=/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/libpython2.7.so.1.0
      3018:  search cache=/etc/ld.so.cache
      3018:   trying file=/lib64/libpython2.7.so.1.0
      3018: 
      3018: find library=libutil.so.1 [0]; searching
      3018:  search path=/usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64:/usr/local/MATLAB/R2011a/bin/glnxa64:/usr/local/MATLAB/R2011a/bin/glnxa64/../../sys/os/glnxa64      (RPATH from file /usr/local/MATLAB/R2011a/bin/glnxa64/MATLAB)
      3018:   trying file=/usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libutil.so.1
      3018:   trying file=/usr/local/MATLAB/R2011a/bin/glnxa64/libutil.so.1
      3018:   trying file=/usr/local/MATLAB/R2011a/bin/glnxa64/../../sys/os/glnxa64/libutil.so.1
      3018:  search path=/usr/local/MATLAB/R2011a/sys/os/glnxa64        (LD_LIBRARY_PATH)
      3018:   trying file=/usr/local/MATLAB/R2011a/sys/os/glnxa64/libutil.so.1
      3018:  search path=/usr/local/MATLAB/R2011a/bin/glnxa64       (RPATH from file /usr/local/MATLAB/R2011a/bin/glnxa64/MATLAB)
      3018:   trying file=/usr/local/MATLAB/R2011a/bin/glnxa64/libutil.so.1
      3018:  search path=/usr/local/MATLAB/R2011a/extern/lib/glnxa64:/usr/local/MATLAB/R2011a/runtime/glnxa64:/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64     (LD_LIBRARY_PATH)
      3018:   trying file=/usr/local/MATLAB/R2011a/extern/lib/glnxa64/libutil.so.1
      3018:   trying file=/usr/local/MATLAB/R2011a/runtime/glnxa64/libutil.so.1
      3018:   trying file=/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads/libutil.so.1
      3018:   trying file=/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/server/libutil.so.1
      3018:   trying file=/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/libutil.so.1
      3018:  search cache=/etc/ld.so.cache
      3018:   trying file=/lib64/libutil.so.1
      3018: 
      3018: 
      3018: calling init: /lib64/libutil.so.1
      3018: 
      3018: 
      3018: calling init: /lib64/libpython2.7.so.1.0
      3018: 
      3018: 
      3018: calling init: /home/cgranade/academics/software-projects/pymex-embed/src/pymex_fns.mexa64
      3018: 
      3018: /home/cgranade/academics/software-projects/pymex-embed/src/pymex_fns.mexa64: error: symbol lookup error: undefined symbol: mexLibrary (fatal)
      3018: /usr/lib64/python2.7/lib-dynload/itertoolsmodule.so: error: symbol lookup error: undefined symbol: PyTuple_Type (fatal)
??? Error using ==> pymex_fns
Python exception inside py_import.

Error in ==> py_import at 24
    py_obj = pymex_fns(py_function_t.IMPORT, name);

清除LD_LIBRARY_PATH：

>> py_import itertools           
      3125: find library=libpython2.7.so.1.0 [0]; searching
      3125:  search path=/usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64:/usr/local/MATLAB/R2011a/bin/glnxa64:/usr/local/MATLAB/R2011a/bin/glnxa64/../../sys/os/glnxa64      (RPATH from file /usr/local/MATLAB/R2011a/bin/glnxa64/MATLAB)
      3125:   trying file=/usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libpython2.7.so.1.0
      3125:   trying file=/usr/local/MATLAB/R2011a/bin/glnxa64/libpython2.7.so.1.0
      3125:   trying file=/usr/local/MATLAB/R2011a/bin/glnxa64/../../sys/os/glnxa64/libpython2.7.so.1.0
      3125:  search path=/usr/local/MATLAB/R2011a/sys/os/glnxa64        (LD_LIBRARY_PATH)
      3125:   trying file=/usr/local/MATLAB/R2011a/sys/os/glnxa64/libpython2.7.so.1.0
      3125:  search path=/usr/local/MATLAB/R2011a/bin/glnxa64       (RPATH from file /usr/local/MATLAB/R2011a/bin/glnxa64/MATLAB)
      3125:   trying file=/usr/local/MATLAB/R2011a/bin/glnxa64/libpython2.7.so.1.0
      3125:  search path=/usr/local/MATLAB/R2011a/extern/lib/glnxa64:/usr/local/MATLAB/R2011a/runtime/glnxa64:/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64     (LD_LIBRARY_PATH)
      3125:   trying file=/usr/local/MATLAB/R2011a/extern/lib/glnxa64/libpython2.7.so.1.0
      3125:   trying file=/usr/local/MATLAB/R2011a/runtime/glnxa64/libpython2.7.so.1.0
      3125:   trying file=/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads/libpython2.7.so.1.0
      3125:   trying file=/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/server/libpython2.7.so.1.0
      3125:   trying file=/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/libpython2.7.so.1.0
      3125:  search cache=/etc/ld.so.cache
      3125:   trying file=/lib64/libpython2.7.so.1.0
      3125: 
      3125: find library=libutil.so.1 [0]; searching
      3125:  search path=/usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64:/usr/local/MATLAB/R2011a/bin/glnxa64:/usr/local/MATLAB/R2011a/bin/glnxa64/../../sys/os/glnxa64      (RPATH from file /usr/local/MATLAB/R2011a/bin/glnxa64/MATLAB)
      3125:   trying file=/usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libutil.so.1
      3125:   trying file=/usr/local/MATLAB/R2011a/bin/glnxa64/libutil.so.1
      3125:   trying file=/usr/local/MATLAB/R2011a/bin/glnxa64/../../sys/os/glnxa64/libutil.so.1
      3125:  search path=/usr/local/MATLAB/R2011a/sys/os/glnxa64        (LD_LIBRARY_PATH)
      3125:   trying file=/usr/local/MATLAB/R2011a/sys/os/glnxa64/libutil.so.1
      3125:  search path=/usr/local/MATLAB/R2011a/bin/glnxa64       (RPATH from file /usr/local/MATLAB/R2011a/bin/glnxa64/MATLAB)
      3125:   trying file=/usr/local/MATLAB/R2011a/bin/glnxa64/libutil.so.1
      3125:  search path=/usr/local/MATLAB/R2011a/extern/lib/glnxa64:/usr/local/MATLAB/R2011a/runtime/glnxa64:/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64     (LD_LIBRARY_PATH)
      3125:   trying file=/usr/local/MATLAB/R2011a/extern/lib/glnxa64/libutil.so.1
      3125:   trying file=/usr/local/MATLAB/R2011a/runtime/glnxa64/libutil.so.1
      3125:   trying file=/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads/libutil.so.1
      3125:   trying file=/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/server/libutil.so.1
      3125:   trying file=/usr/local/MATLAB/R2011a/sys/java/jre/glnxa64/jre/lib/amd64/libutil.so.1
      3125:  search cache=/etc/ld.so.cache
      3125:   trying file=/lib64/libutil.so.1
      3125: 
      3125: 
      3125: calling init: /lib64/libutil.so.1
      3125: 
      3125: 
      3125: calling init: /lib64/libpython2.7.so.1.0
      3125: 
      3125: 
      3125: calling init: /home/cgranade/academics/software-projects/pymex-embed/src/pymex_fns.mexa64
      3125: 
      3125: /home/cgranade/academics/software-projects/pymex-embed/src/pymex_fns.mexa64: error: symbol lookup error: undefined symbol: mexLibrary (fatal)
      3125: /usr/lib64/python2.7/lib-dynload/itertoolsmodule.so: error: symbol lookup error: undefined symbol: PyTuple_Type (fatal)

1 个答案:

答案 0 :(得分：1)

尝试从MATLAB内部和系统shell上运行常规python：

贝壳

$ LD_DEBUG_OUTPUT=./ld_debug_out LD_DEBUG=all python -c 'import numpy'

MATLAB 

>> !LD_DEBUG_OUTPUT=./ld_debug_out LD_DEBUG=all python -c 'import numpy'

并检查输出文件（可能all有点太多信息！）。注意我导入了numpy，因为itertools在我的安装中没有相应的共享库..

一个想法是在调用Py_Initialize()之前尝试手动加载MEX函数中的共享库：

dlopen('libpython2.7.so', RTLD_GLOBAL|RTLD_LAZY);

我在Windows机器上，但上次我玩这个时我也遇到了一些问题。我记得一旦导入，一些C扩展模块无法在同一个会话中卸载和重新加载（在嵌入Python的托管过程的生命周期中）。请参阅这些remarks和相关的PEP。

相关问题
最新问题