フィルターのクリア

Importing custom python module fails

16 ビュー (過去 30 日間)
Fernando Bechtelar
Fernando Bechtelar 2016 年 1 月 26 日
コメント済み: Ronan Fleming 2021 年 4 月 12 日
I am using Matlab2014b and try to import python packages. I am on a linux computer and executing the command py.numpy.* works and py.importlib.import_module('numpy') gives me the correct output. However, numpy lives in my /usr/lib/pymodules/python2.7/ directory, which according to the output of py.sys.path is in the search directory, so the import should work.
However, I have another package that I would like to include, which is in /usr/lib/python2.7/dist-packages/. Again, according to py.sys.path, this directory is included in the search path, however, importing the package fails ("Import argument 'py.fabio' cannot be found or cannot be imported."). I hope someone has an advice how to solve this problem.
PS: pyversion returns my current installation (2.7) and shows isloaded: 1
PPS: Adding the directory to the search path, as outlined in http://www.mathworks.com/help/matlab/matlab_external/call-python-from-matlab.html has failed.
PPPS: When I try to get feedback from py.importlib.import_module, Matlab crashes.
  4 件のコメント
Robert Snoeberger
Robert Snoeberger 2016 年 1 月 27 日
/usr/bin/python2.7.so is the shared library for Python. It might be helpful to attach the stack trace.
Fernando Bechtelar
Fernando Bechtelar 2016 年 1 月 27 日
This is the stack trace when I try to include the fabio package. I tried to skim it a bit to make to post not too cluttered.
Stack Trace (from fault):
[ 0] /lib/x86_64-linux-gnu/libc.so.6+00205157 gsignal+00000053
[ 1] /lib/x86_64-linux-gnu/libc.so.6+00218080 abort+00000384
[ 2] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libhdf5.so.8+00224629 H5check_version+00000325
[ 3] /usr/lib/python2.7/dist-packages/h5py/h5f.so+00042095 inith5f+00006975
[ 4] /usr/lib/libpython2.7.so+01579985 _PyImport_LoadDynamicModule+00000193
[ 5] /usr/lib/libpython2.7.so+01109372
[ 6] /usr/lib/libpython2.7.so+01110002
[ 7] /usr/lib/libpython2.7.so+01110925 PyImport_ImportModuleLevel+00000605
[ 8] /usr/lib/libpython2.7.so+00666527
[ 9] /usr/lib/libpython2.7.so+01269118 PyObject_Call+00000078
[ 10] /usr/lib/libpython2.7.so+01271431 PyEval_CallObjectWithKeywords+00000071
[ 11] /usr/lib/libpython2.7.so+00306307 PyEval_EvalFrameEx+00004915
[ 12] /usr/lib/libpython2.7.so+00328424 PyEval_EvalCodeEx+00002120
[ 13] /usr/lib/libpython2.7.so+00328738 PyEval_EvalCode+00000050
[ 14] /usr/lib/libpython2.7.so+00685773 PyImport_ExecCodeModuleEx+00000173
...
[ 19] /usr/lib/libpython2.7.so+01110685 PyImport_ImportModuleLevel+00000365
[ 20] /usr/lib/libpython2.7.so+00666527
[ 21] /usr/lib/libpython2.7.so+01269118 PyObject_Call+00000078
[ 22] /usr/lib/libpython2.7.so+01271431 PyEval_CallObjectWithKeywords+00000071
[ 23] /usr/lib/libpython2.7.so+00306307 PyEval_EvalFrameEx+00004915
[ 24] /usr/lib/libpython2.7.so+00328424 PyEval_EvalCodeEx+00002120
[ 25] /usr/lib/libpython2.7.so+00328738 PyEval_EvalCode+00000050
[ 26] /usr/lib/libpython2.7.so+00685773 PyImport_ExecCodeModuleEx+00000173
...
[ 30] /usr/lib/libpython2.7.so+01110925 PyImport_ImportModuleLevel+00000605
[ 31] /usr/lib/libpython2.7.so+00666527
[ 32] /usr/lib/libpython2.7.so+01269118 PyObject_Call+00000078
[ 33] /usr/lib/libpython2.7.so+01271431 PyEval_CallObjectWithKeywords+00000071
[ 34] /usr/lib/libpython2.7.so+00306307 PyEval_EvalFrameEx+00004915
[ 35] /usr/lib/libpython2.7.so+00328424 PyEval_EvalCodeEx+00002120
[ 36] /usr/lib/libpython2.7.so+00328738 PyEval_EvalCode+00000050
[ 37] /usr/lib/libpython2.7.so+00685773 PyImport_ExecCodeModuleEx+00000173
...
[ 41] /usr/lib/libpython2.7.so+01110925 PyImport_ImportModuleLevel+00000605
[ 42] /usr/lib/libpython2.7.so+00666527
[ 43] /usr/lib/libpython2.7.so+01269118 PyObject_Call+00000078
[ 44] /usr/lib/libpython2.7.so+01271431 PyEval_CallObjectWithKeywords+00000071
[ 45] /usr/lib/libpython2.7.so+00306307 PyEval_EvalFrameEx+00004915
[ 46] /usr/lib/libpython2.7.so+00328424 PyEval_EvalCodeEx+00002120
[ 47] /usr/lib/libpython2.7.so+00328738 PyEval_EvalCode+00000050
[ 48] /usr/lib/libpython2.7.so+00685773 PyImport_ExecCodeModuleEx+00000173
...
[ 53] /usr/lib/libpython2.7.so+01110685 PyImport_ImportModuleLevel+00000365
[ 54] /usr/lib/libpython2.7.so+00666527
[ 55] /usr/lib/libpython2.7.so+00324642 PyEval_EvalFrameEx+00023250
[ 56] /usr/lib/libpython2.7.so+00328424 PyEval_EvalCodeEx+00002120
[ 57] /usr/lib/libpython2.7.so+00682263
[ 58] /usr/lib/libpython2.7.so+01269118 PyObject_Call+00000078
[ 59] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwpycli.so+00299020
[ 60] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwpycli.so+00289121
[ 61] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwpycli.so+00425954
[ 62] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwmcos_impl.so+01540515
...
[ 66] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwmcos_impl.so+02046678
[ 67] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwm_lxe.so+09159856
...
[ 81] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwbridge.so+00168636
[ 82] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwbridge.so+00171767 _Z8mnParserv+00000823
[ 83] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwmcr.so+00686927 _ZN11mcrInstance30mnParser_on_interpreter_threadEv+00000031
[ 84] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwmcr.so+00607299
[ 85] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwmcr.so+00608825 _ZN5boost6detail11task_objectIvNS_3_bi6bind_tIvPFvRKNS_8functionIFvvEEEENS2_5list1INS2_5valueIS6_EEEEEEE6do_runEv+00000025
[ 86] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwmcr.so+00614215 _ZN5boost6detail9task_baseIvE3runEv+00000071
[ 87] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwmcr.so+00614311
[ 88] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwmcr.so+00594682
[ 89] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwuix.so+00313014
[ 90] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwuix.so+00206946
[ 91] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwservices.so+03002591
...
[ 94] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwservices.so+03012684 _Z25svWS_ProcessPendingEventsiib+00000092
...
[ 97] /mntdirect/_sware/com/matlab_2015b/bin/glnxa64/libmwmcr.so+00516077
[ 98] /lib/x86_64-linux-gnu/libpthread.so.0+00027472
[ 99] /lib/x86_64-linux-gnu/libc.so.6+00899421 clone+00000109

サインインしてコメントする。

採用された回答

Robert Snoeberger
Robert Snoeberger 2016 年 1 月 28 日
編集済み: Robert Snoeberger 2016 年 1 月 28 日
Based on the stack trace, your issue looks like a library conflict with libhdf5.so. It seems like the libhdf5 that is in the stack trace is a library that is installed with MATLAB; I am assuming this based on the '/matlab_2015b/bin/glnxa64/' in the path to the library. I would guess that the appropriate version of libhdf5.so for Python should be located at /usr/lib/libhdf5.so. Try the following command to look for the correct libhdf5.so.
ldd /usr/lib/python2.7/dist-packages/h5py/h5f.so | grep libhdf5
My hunch about the library conflict is further confirmed by the fact that the libhdf5.so function that is executing is called H5check_version (line [2] of the stack trace). The documentation I found for that function says, "If this check fails, H5check_version causes the application to abort (by means of a standard C abort() call)..." [1].
Assuming you aren't using MATLAB's interface to HDF5, you should be able to use LD_PRELOAD to load the correct version of libhdf5.so [2,3].
References
  1. https://www.hdfgroup.org/HDF5/doc1.6/RM_H5.html#Library-VersCheck
  2. http://man7.org/linux/man-pages/man8/ld.so.8.html -- Search for "LD_PRELOAD". It should say, "A list of additional, user-specified, ELF shared objects to be loaded before all others..."
  3. http://stackoverflow.com/questions/426230/what-is-the-ld-preload-trick
  6 件のコメント
Michael Thieme
Michael Thieme 2018 年 10 月 18 日
I'm also having this issue on Windows 10, it would be great if someone is able to find a workaround!
Michael Thieme
Michael Thieme 2018 年 10 月 18 日
編集済み: Michael Thieme 2018 年 10 月 18 日
All,
I found a solution to this problem. My problem was related to tensorflow/keras rather than fabio. This thread (https://github.com/NeurodataWithoutBorders/api-python/issues/28) led me to the solution. Basically my order of operations was:
  • conda uninstall hdf5
  • conda uninstall h5py
  • pip uninstall hdf5
  • pip uninstall h5py
  • conda install hdf5=1.8.12 h5py=2.7.0 -c jonc
  • pip install keras
  • pip install tensorflow-gpu

サインインしてコメントする。

その他の回答 (1 件)

Rafael Rebouças
Rafael Rebouças 2021 年 1 月 19 日
編集済み: Rafael Rebouças 2021 年 1 月 19 日
My solution:
% Simple way to load your library
copyfile(my_library_file_path, pwd, 'f');
% It's necessary to load library
py.my_library.any_method_or_function();
delete 'my_library.py';
Now, your Python library is loaded to use in any directory.
  1 件のコメント
Ronan Fleming
Ronan Fleming 2021 年 4 月 12 日
https://nl.mathworks.com/help/releases/R2021a/matlab/matlab_external/out-of-process-execution-of-python-functionality.html

サインインしてコメントする。

カテゴリ

Help Center および File ExchangeCall Python from MATLAB についてさらに検索

タグ

製品

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

Translated by