在 Matlab 中启动 python 脚本时模块导入错误
Module ImportError when launching python script in Matlab
我在 Matlab 中使用操作系统命令来启动 python 脚本。直到最近一切都运行良好，事实上我怀疑问题出在最近将 Matlab 升级到 R2017b 和 Fedora 到 FC27。
事实：如果我在 shell 中启动脚本 python 一切正常。但是如果我在 Matlab 中启动相同的脚本，很少会引发 ImportError 异常：
Traceback (most recent call last):
File "/usr/lib64/python3.6/xml/etree/ElementTree.py", line 1448, in __init__
from xml.parsers import expat
File "/usr/lib64/python3.6/xml/parsers/expat.py", line 4, in <module>
from pyexpat import *
ImportError: /usr/lib64/python3.6/lib-dynload/pyexpat.cpython-36m-x86_64-linux-gnu.so: undefined symbol: XML_SetHashSalt
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib64/python3.6/xml/etree/ElementTree.py", line 1451, in __init__
import pyexpat as expat
ImportError: /usr/lib64/python3.6/lib-dynload/pyexpat.cpython-36m-x86_64-linux-gnu.so: undefined symbol: XML_SetHashSalt
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data_1/IRM/amigo/src/IRMAGE_python_scripts/IRMAGE_report.py", line 1409, in <module>
outFormat = 'png')
File "/data_1/IRM/amigo/src/IRMAGE_python_modules/IRMAGE_reporting.py", line 1576, in plotPatVsRef
bookRef = xlrd.open_workbook(refFile)
File "/usr/lib/python3.6/site-packages/xlrd/__init__.py", line 422, in open_workbook
ragged_rows=ragged_rows,
File "/usr/lib/python3.6/site-packages/xlrd/xlsx.py", line 784, in open_workbook_2007_xml
ensure_elementtree_imported(verbosity, logfile)
File "/usr/lib/python3.6/site-packages/xlrd/xlsx.py", line 48, in ensure_elementtree_imported
ET.iterparse(_dummy_stream)
File "/usr/lib64/python3.6/xml/etree/ElementTree.py", line 1217, in iterparse
pullparser = XMLPullParser(events=events, _parser=parser)
File "/usr/lib64/python3.6/xml/etree/ElementTree.py", line 1256, in __init__
self._parser = _parser or XMLParser(target=TreeBuilder())
File "/usr/lib64/python3.6/xml/etree/ElementTree.py", line 1454, in __init__
"No module named expat; use SimpleXMLTreeBuilder instead"
ImportError: No module named expat; use SimpleXMLTreeBuilder instead
从昨天开始面对这个问题我有点迷茫，我承认我没有解决这个问题的新想法......非常欢迎有关这个问题的所有想法，信息和帮助
我只是想检查有关 /usr/lib64/python3.6/lib-dynload/pyexpat.cpython-36m-x86_64-linux-gnu. 的共享对象依赖关系，因此引发了 ImportError 异常！ !!
在 shell:
% ldd /usr/lib64/python3.6/lib-dynload/pyexpat.cpython-36m-x86_64-linux-gnu.so
linux-vdso.so.1 (0x00007ffd8f7c5000)
libexpat.so.1 => /lib64/libexpat.so.1 (0x00007ff82fae8000)
libpython3.6m.so.1.0 => /lib64/libpython3.6m.so.1.0 (0x00007ff82f588000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007ff82f369000)
libc.so.6 => /lib64/libc.so.6 (0x00007ff82ef86000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007ff82ed82000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007ff82eb7f000)
libm.so.6 => /lib64/libm.so.6 (0x00007ff82e82a000)
/lib64/ld-linux-x86-64.so.2 (0x00007ff82ff2c000)
在 Matlab 中：
! ldd /usr/lib64/python3.6/lib-dynload/pyexpat.cpython-36m-x86_64-linux-gnu.so
linux-vdso.so.1 (0x00007ffeec596000)
libexpat.so.1 => /usr/local/MATLAB/R2017b/bin/glnxa64/libexpat.so.1 (0x00007fcd2931e000)
libpython3.6m.so.1.0 => /lib64/libpython3.6m.so.1.0 (0x00007fcd28dbe000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fcd28b9f000)
libc.so.6 => /lib64/libc.so.6 (0x00007fcd287bc000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007fcd285b8000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007fcd283b5000)
libm.so.6 => /lib64/libm.so.6 (0x00007fcd28060000)
/lib64/ld-linux-x86-64.so.2 (0x00007fcd29758000)
所以很明显，问题出在 Matlab 发行版 (libexpat.so.1.5.0) 中的 libexpat.so.1 共享对象，比系统 ( libexpat.so.1.6.7)!!!:
% ls -l /usr/local/MATLAB/R2017b/bin/glnxa64/libexpat.so*
lrwxrwxrwx. 1 root root 17 Feb 22 12:41 libexpat.so.1 -> libexpat.so.1.5.0
-r-xr-xr-x. 1 root root 182222 Jul 24 2017 libexpat.so.1.5.0
% ls -l /usr/lib64/libexpat.so*
lrwxrwxrwx. 1 root root 17 Nov 6 18:00 /usr/lib64/libexpat.so -> l ibexpat.so.1.6.7
lrwxrwxrwx. 1 root root 17 Nov 6 18:00 /usr/lib64/libexpat.so.1 -> libexpat.so.1.6.7
-rwxr-xr-x. 1 root root 206000 Nov 6 18:00 /usr/lib64/libexpat.so.1.6.7
我通过将 Matlab distrib 的共享对象移动到排除目录来解决问题，以强制使用系统之一！！！
# cd /usr/local/MATLAB/R2017b/bin/glnxa64
# mkdir exclude
# mv libexpat.so* exclude/
现在一切正常！！！
P.S。在升级 Matlab 和 Fedora 后，我遇到了一些其他问题 运行 正确地使用 Matlab，我在这里没有详细说明。但是，如果有人对 Matlab 和 FC26 或 FC27 有其他问题，我可以根据要求提供我所做的所有更改（所有更改都与 Matlab 发行版中太旧的共享对象有关！！！）
我在 Matlab 中使用操作系统命令来启动 python 脚本。直到最近一切都运行良好，事实上我怀疑问题出在最近将 Matlab 升级到 R2017b 和 Fedora 到 FC27。
事实：如果我在 shell 中启动脚本 python 一切正常。但是如果我在 Matlab 中启动相同的脚本，很少会引发 ImportError 异常：
Traceback (most recent call last):
File "/usr/lib64/python3.6/xml/etree/ElementTree.py", line 1448, in __init__
from xml.parsers import expat
File "/usr/lib64/python3.6/xml/parsers/expat.py", line 4, in <module>
from pyexpat import *
ImportError: /usr/lib64/python3.6/lib-dynload/pyexpat.cpython-36m-x86_64-linux-gnu.so: undefined symbol: XML_SetHashSalt
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib64/python3.6/xml/etree/ElementTree.py", line 1451, in __init__
import pyexpat as expat
ImportError: /usr/lib64/python3.6/lib-dynload/pyexpat.cpython-36m-x86_64-linux-gnu.so: undefined symbol: XML_SetHashSalt
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data_1/IRM/amigo/src/IRMAGE_python_scripts/IRMAGE_report.py", line 1409, in <module>
outFormat = 'png')
File "/data_1/IRM/amigo/src/IRMAGE_python_modules/IRMAGE_reporting.py", line 1576, in plotPatVsRef
bookRef = xlrd.open_workbook(refFile)
File "/usr/lib/python3.6/site-packages/xlrd/__init__.py", line 422, in open_workbook
ragged_rows=ragged_rows,
File "/usr/lib/python3.6/site-packages/xlrd/xlsx.py", line 784, in open_workbook_2007_xml
ensure_elementtree_imported(verbosity, logfile)
File "/usr/lib/python3.6/site-packages/xlrd/xlsx.py", line 48, in ensure_elementtree_imported
ET.iterparse(_dummy_stream)
File "/usr/lib64/python3.6/xml/etree/ElementTree.py", line 1217, in iterparse
pullparser = XMLPullParser(events=events, _parser=parser)
File "/usr/lib64/python3.6/xml/etree/ElementTree.py", line 1256, in __init__
self._parser = _parser or XMLParser(target=TreeBuilder())
File "/usr/lib64/python3.6/xml/etree/ElementTree.py", line 1454, in __init__
"No module named expat; use SimpleXMLTreeBuilder instead"
ImportError: No module named expat; use SimpleXMLTreeBuilder instead
从昨天开始面对这个问题我有点迷茫，我承认我没有解决这个问题的新想法......非常欢迎有关这个问题的所有想法，信息和帮助
我只是想检查有关 /usr/lib64/python3.6/lib-dynload/pyexpat.cpython-36m-x86_64-linux-gnu. 的共享对象依赖关系，因此引发了 ImportError 异常！ !!
在 shell:
% ldd /usr/lib64/python3.6/lib-dynload/pyexpat.cpython-36m-x86_64-linux-gnu.so
linux-vdso.so.1 (0x00007ffd8f7c5000)
libexpat.so.1 => /lib64/libexpat.so.1 (0x00007ff82fae8000)
libpython3.6m.so.1.0 => /lib64/libpython3.6m.so.1.0 (0x00007ff82f588000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007ff82f369000)
libc.so.6 => /lib64/libc.so.6 (0x00007ff82ef86000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007ff82ed82000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007ff82eb7f000)
libm.so.6 => /lib64/libm.so.6 (0x00007ff82e82a000)
/lib64/ld-linux-x86-64.so.2 (0x00007ff82ff2c000)
在 Matlab 中：
! ldd /usr/lib64/python3.6/lib-dynload/pyexpat.cpython-36m-x86_64-linux-gnu.so
linux-vdso.so.1 (0x00007ffeec596000)
libexpat.so.1 => /usr/local/MATLAB/R2017b/bin/glnxa64/libexpat.so.1 (0x00007fcd2931e000)
libpython3.6m.so.1.0 => /lib64/libpython3.6m.so.1.0 (0x00007fcd28dbe000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fcd28b9f000)
libc.so.6 => /lib64/libc.so.6 (0x00007fcd287bc000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007fcd285b8000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007fcd283b5000)
libm.so.6 => /lib64/libm.so.6 (0x00007fcd28060000)
/lib64/ld-linux-x86-64.so.2 (0x00007fcd29758000)
所以很明显，问题出在 Matlab 发行版 (libexpat.so.1.5.0) 中的 libexpat.so.1 共享对象，比系统 ( libexpat.so.1.6.7)!!!:
% ls -l /usr/local/MATLAB/R2017b/bin/glnxa64/libexpat.so*
lrwxrwxrwx. 1 root root 17 Feb 22 12:41 libexpat.so.1 -> libexpat.so.1.5.0
-r-xr-xr-x. 1 root root 182222 Jul 24 2017 libexpat.so.1.5.0
% ls -l /usr/lib64/libexpat.so*
lrwxrwxrwx. 1 root root 17 Nov 6 18:00 /usr/lib64/libexpat.so -> l ibexpat.so.1.6.7
lrwxrwxrwx. 1 root root 17 Nov 6 18:00 /usr/lib64/libexpat.so.1 -> libexpat.so.1.6.7
-rwxr-xr-x. 1 root root 206000 Nov 6 18:00 /usr/lib64/libexpat.so.1.6.7
我通过将 Matlab distrib 的共享对象移动到排除目录来解决问题，以强制使用系统之一！！！
# cd /usr/local/MATLAB/R2017b/bin/glnxa64
# mkdir exclude
# mv libexpat.so* exclude/
现在一切正常！！！
P.S。在升级 Matlab 和 Fedora 后，我遇到了一些其他问题 运行 正确地使用 Matlab，我在这里没有详细说明。但是，如果有人对 Matlab 和 FC26 或 FC27 有其他问题，我可以根据要求提供我所做的所有更改（所有更改都与 Matlab 发行版中太旧的共享对象有关！！！）