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

Question

我一直在一个项目中，使用libpython2.7.so将Python解释器作为MEX文件嵌入到MATLAB中，但是每当我尝试导入实现为扩展模块的Python模块时，都会遇到问题。 例如，尝试导入itertools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);

无论我是否在调用Py_Initialize()之前清除LD_LIBRARY_PATH以及从MATLAB内部对ldd的调用（对于本示例中为itertools.so ）都不会导致任何(not found)消息，都会发生此行为。 下面，我粘贴了使用LD_DEBUG=libs设置运行MATLAB的结果，首先通过MATLAB的启动设置了LD_LIBRARY_PATH ，然后在尝试导入之前运行setenv('LD_LIBRARY_PATH', '')之后粘贴了结果。

如何解决此问题，并允许动态加载扩展模块？

使用MATLAB默认的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)

Answer 1

尝试从MATLAB内部和系统外壳上运行常规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（也许all信息all太多了！）。 注意我改为导入numpy因为itertools在安装中没有相应的共享库。

---

一种想法是尝试在调用Py_Initialize()之前在MEX函数中手动加载共享库：

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

---

我在Windows计算机上，但是上一次我玩这个游戏时，我也遇到了一些问题。 我记得，一旦导入，某些C扩展模块就无法在同一会话中卸载和重新加载（在嵌入Python的托管过程的生存期内）。 请参阅这些说明和相关的PEP 。