Just a little more context. I'm working on a machine learning project that
makes use of a lot of open source libraries for computation such as
tensorflow, sklearn, pandas, and xgboost. The versioning of each of the
libraries hasn't been closely tracked, unfortunately.
I've attached the output of the build procedure in this comment. In
particular, I'm also curious about these few lines:
ldd: warning: you do not have execution permission for
`/root/miniconda3/envs/rte/lib/python3.6/site-packages/cryptography-2.5-py3.6-linux-x86_64.egg/cryptography/hazmat/bindings/_constant_time.abi3.so'
ldd: warning: you do not have execution permission for
`/root/miniconda3/envs/rte/lib/python3.6/site-packages/cryptography-2.5-py3.6-linux-x86_64.egg/cryptography/hazmat/bindings/_openssl.abi3.so'
ldd: warning: you do not have execution permission for
`/root/miniconda3/envs/rte/lib/python3.6/site-packages/cryptography-2.5-py3.6-linux-x86_64.egg/cryptography/hazmat/bindings/_padding.abi3.so'
ldd: warning: you do not have execution permission for
`/root/miniconda3/envs/rte/lib/python3.6/site-packages/coverage-5.0a8-py3.6-linux-x86_64.egg/coverage/tracer.cpython-36m-x86_64-linux-gnu.so'
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/tbbpool.cpython-36m-x86_64-linux-gnu.so:
/lib64/libstdc++.so.6: version `CXXABI_1.3.11' not found (required by
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/tbbpool.cpython-36m-x86_64-linux-gnu.so:
/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/tbbpool.cpython-36m-x86_64-linux-gnu.so:
/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)
ldd: warning: you do not have execution permission for
`/root/miniconda3/envs/rte/plugins/imageformats/../../lib/libgcc_s.so.1'
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2:
/lib64/libstdc++.so.6: version `CXXABI_1.3.11' not found (required by
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2:
/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2:
/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)
I don't see any of these errors when building on MacOS.
On Thursday, October 31, 2019 at 7:33:11 AM UTC-5, James Loy wrote:
>
> Hi Folks-
>
> I have a situation that I'm having a tough time debugging. I'm new to
> PyInstaller, and I'm also dealing with a very hacked together code base
> with A LOT of dependencies.
>
> I am able to freeze my code on MacOS mojave, and run with no problem.
> However, when I freeze the code on CentOS 7.7 I encounter a seg fault.
> When I run the code straight from source (i.e., python myscript.py), the
> seg fault doesn't pop up and everything runs as expected (on both MacOS and
> CentOS 7.7).
>
> So my question is: what sort of things would cause an executable to seg
> fault, but not the python script? My first hunch is some binary
> compatibility issue with external libraries and the CentOS, but how does
> that explain that the python script works perfectly fine? I say this
> because, when I change some of the dependencies, I get errors about not
> being able to find the right version of GLIBCXX.
>
> Anyone have any thoughts? Thanks in advance.
> -James
>
>
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57 INFO: PyInstaller: 3.5
57 INFO: Python: 3.6.6
58 INFO: Platform:
Linux-3.10.0-1062.1.2.el7.x86_64-x86_64-with-centos-7.7.1908-Core
60 INFO: UPX is not available.
62 INFO: Extending PYTHONPATH with paths
['/home/jloy/amb-rte', '/home/jloy/amb-rte']
62 INFO: checking Analysis
62 INFO: Building Analysis because Analysis-00.toc is non existent
62 INFO: Initializing module dependency graph...
65 INFO: Initializing module graph hooks...
69 INFO: Analyzing base_library.zip ...
3833 INFO: Analyzing hidden import 'amb_pacman.settings.rte'
4862 INFO: Analyzing hidden import 'amb.settings.rte'
5161 INFO: Processing pre-find module path hook distutils
6538 INFO: Processing pre-safe import module hook six.moves
7696 INFO: Processing pre-safe import module hook setuptools.extern.six.moves
8283 INFO: Processing pre-find module path hook site
8284 INFO: site: retargeting to fake-dir
'/root/miniconda3/envs/rte/lib/python3.6/site-packages/PyInstaller/fake-modules'
38655 INFO: Analyzing hidden import 'amb.evolve.neat.core.indexer'
38734 INFO: Analyzing hidden import 'amb_utils.settings.rte'
40367 INFO: Analyzing hidden import 'sklearn.utils._cython_blas'
40368 INFO: Analyzing hidden import 'sklearn.neighbors.typedefs'
40369 INFO: Analyzing hidden import 'sklearn.neighbors.quad_tree'
40369 INFO: Analyzing hidden import 'sklearn.tree._utils'
40455 INFO: Analyzing hidden import 'multiprocessing.forking'
40455 ERROR: Hidden import 'multiprocessing.forking' not found
40455 INFO: Analyzing hidden import 'multiprocessing.freeze_support'
40456 ERROR: Hidden import 'multiprocessing.freeze_support' not found
40456 INFO: Analyzing hidden import 'numpy.type'
40456 ERROR: Hidden import 'numpy.type' not found
40456 INFO: running Analysis Analysis-00.toc
40476 INFO: Caching module hooks...
40480 INFO: Analyzing /home/jloy/amb-rte/runtime_engine.py
52047 INFO: Processing pre-safe import module hook win32com
68834 INFO: Processing pre-safe import module hook urllib3.packages.six.moves
104147 INFO: Loading module hooks...
104147 INFO: Loading module hook "hook-IPython.py"...
104161 INFO: Excluding import 'matplotlib'
104174 INFO: Removing import of matplotlib._pylab_helpers from module
IPython.core.pylabtools
104174 INFO: Removing import of matplotlib.pyplot from module
IPython.core.pylabtools
104174 INFO: Removing import of matplotlib from module IPython.core.pylabtools
104174 INFO: Removing import of matplotlib.figure from module
IPython.core.pylabtools
104176 INFO: Excluding import 'PyQt5'
104190 INFO: Excluding import 'gtk'
104204 INFO: Excluding import 'PySide'
104218 INFO: Excluding import 'PyQt4'
104232 INFO: Loading module hook "hook-PIL.Image.py"...
104660 INFO: Loading module hook "hook-PIL.SpiderImagePlugin.py"...
104679 INFO: Excluding import 'tkinter'
104689 INFO: Import to be excluded not found: 'FixTk'
104690 INFO: Loading module hook "hook-PIL.py"...
104700 INFO: Excluding import 'PyQt5'
104711 INFO: Removing import of PyQt5.QtCore from module PIL.ImageQt
104711 INFO: Removing import of PyQt5.QtGui from module PIL.ImageQt
104712 INFO: Import to be excluded not found: 'FixTk'
104713 INFO: Excluding import 'tkinter'
104724 INFO: Removing import of tkinter from module PIL.ImageTk
104724 INFO: Excluding import 'PySide'
104735 INFO: Removing import of PySide from module PIL.ImageQt
104737 INFO: Excluding import 'PyQt4'
104748 INFO: Removing import of PyQt4 from module PIL.ImageQt
104749 INFO: Loading module hook "hook-PyQt5.QtCore.py"...
104898 INFO: Loading module hook "hook-PyQt5.QtGui.py"...
105000 INFO: Loading module hook "hook-PyQt5.QtWidgets.py"...
105168 INFO: Loading module hook "hook-PyQt5.py"...
105620 WARNING: Hidden import "PyQt5.sip" not found!
105621 INFO: Loading module hook "hook-_tkinter.py"...
105792 INFO: checking Tree
105792 INFO: Building Tree because Tree-00.toc is non existent
105792 INFO: Building Tree Tree-00.toc
105801 INFO: checking Tree
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105801 INFO: Building Tree Tree-01.toc
105806 INFO: Loading module hook "hook-certifi.py"...
105807 INFO: Loading module hook "hook-cryptography.py"...
106345 INFO: Loading module hook "hook-distutils.py"...
106346 INFO: Loading module hook "hook-encodings.py"...
106461 INFO: Loading module hook "hook-h5py.py"...
106462 INFO: Loading module hook "hook-importlib_metadata.py"...
106465 INFO: Loading module hook "hook-jedi.py"...
106510 INFO: Loading module hook "hook-jinja2.py"...
106540 INFO: Loading module hook "hook-lib2to3.py"...
106541 INFO: Loading module hook "hook-llvmlite.py"...
106544 INFO: Loading module hook "hook-matplotlib.backends.py"...
107358 INFO: Matplotlib backend "GTK": ignored
Gtk* backend requires pygtk to be installed.
107923 INFO: Matplotlib backend "GTKAgg": ignored
Gtk* backend requires pygtk to be installed.
108296 INFO: Matplotlib backend "GTKCairo": ignored
No module named 'gtk'
108884 INFO: Matplotlib backend "GTK3Agg": ignored
The Gtk3 backend requires PyGObject or pgi
109270 INFO: Matplotlib backend "GTK3Cairo": ignored
cairo backend requires that cairocffi or pycairo is installed
109830 INFO: Matplotlib backend "MacOSX": ignored
cannot import name '_macosx'
/root/miniconda3/envs/rte/lib/python3.6/site-packages/IPython/kernel/__init__.py:13:
ShimWarning: The `IPython.kernel` package has been deprecated since IPython
4.0.You should import from ipykernel or jupyter_client instead.
"You should import from ipykernel or jupyter_client instead.", ShimWarning)
110641 INFO: Matplotlib backend "nbAgg": ignored
No module named 'ipykernel'
111318 INFO: Matplotlib backend "Qt4Agg": added
111715 INFO: Matplotlib backend "Qt4Cairo": ignored
cairo backend requires that cairocffi or pycairo is installed
112389 INFO: Matplotlib backend "Qt5Agg": added
112780 INFO: Matplotlib backend "Qt5Cairo": ignored
cairo backend requires that cairocffi or pycairo is installed
113374 INFO: Matplotlib backend "TkAgg": added
113756 INFO: Matplotlib backend "TkCairo": ignored
cairo backend requires that cairocffi or pycairo is installed
114432 INFO: Matplotlib backend "WebAgg": added
115124 INFO: Matplotlib backend "WX": ignored
Matplotlib backend_wx and backend_wxagg require wxPython>=2.9
115551 INFO: Matplotlib backend "WXAgg": ignored
No module named 'wx'
115986 INFO: Matplotlib backend "WXCairo": ignored
No module named 'wx'
116561 INFO: Matplotlib backend "agg": added
116937 INFO: Matplotlib backend "cairo": ignored
cairo backend requires that cairocffi or pycairo is installed
117338 INFO: Matplotlib backend "gdk": ignored
No module named 'gobject'
117915 INFO: Matplotlib backend "pdf": added
118809 INFO: Matplotlib backend "pgf": added
119491 INFO: Matplotlib backend "ps": added
120148 INFO: Matplotlib backend "svg": added
120824 INFO: Matplotlib backend "template": added
121378 INFO: Loading module hook "hook-matplotlib.py"...
121744 INFO: Loading module hook "hook-numba.py"...
121771 INFO: Excluding import 'IPython'
121788 INFO: Removing import of IPython.utils.path from module numba.caching
121788 INFO: Removing import of IPython.paths from module numba.caching
121795 INFO: Excluding import 'scipy'
121813 INFO: Removing import of scipy.linalg.cython_blas from module
numba.targets.linalg
121814 INFO: Removing import of scipy.linalg.cython_lapack from module
numba.targets.linalg
121828 INFO: Loading module hook "hook-numpy.core.py"...
121996 INFO: MKL libraries found when importing numpy. Adding MKL to binaries
121997 INFO: Loading module hook "hook-numpy.py"...
121998 INFO: Loading module hook "hook-pandas.py"...
123523 INFO: Loading module hook "hook-patsy.py"...
123525 INFO: Loading module hook "hook-pkg_resources.py"...
124490 INFO: Loading module hook "hook-pycparser.py"...
124490 INFO: Loading module hook "hook-pydoc.py"...
124491 INFO: Loading module hook "hook-pygments.py"...
127052 INFO: Loading module hook "hook-pytest.py"...
128099 INFO: Loading module hook "hook-pytz.py"...
128117 INFO: Loading module hook "hook-scipy.io.matlab.py"...
128118 INFO: Loading module hook "hook-scipy.linalg.py"...
128119 INFO: Loading module hook "hook-scipy.py"...
128120 INFO: Loading module hook "hook-scipy.sparse.csgraph.py"...
128123 INFO: Loading module hook "hook-scipy.special._ellip_harm_2.py"...
128124 INFO: Loading module hook "hook-scipy.special._ufuncs.py"...
128124 INFO: Loading module hook "hook-setuptools.py"...
129122 INFO: Loading module hook "hook-shelve.py"...
129123 INFO: Loading module hook "hook-sklearn.metrics.cluster.py"...
129152 WARNING: Hidden import "sklearn.utils.sparsetools._graph_validation" not
found!
129152 WARNING: Hidden import "sklearn.utils.sparsetools._graph_tools" not
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129153 INFO: Loading module hook "hook-sqlite3.py"...
129258 INFO: Loading module hook "hook-sysconfig.py"...
129270 INFO: Loading module hook "hook-torch.py"...
129302 INFO: Loading module hook "hook-xml.dom.domreg.py"...
129303 INFO: Loading module hook "hook-xml.etree.cElementTree.py"...
129304 INFO: Loading module hook "hook-xml.py"...
129304 INFO: Loading module hook "hook-xgboost.py"...
129440 INFO: Determining a mapping of distributions to packages...
159204 INFO: Packages required by xgboost:
['numpy', 'scipy']
159461 INFO: checking Tree
159461 INFO: Building Tree because Tree-02.toc is non existent
159461 INFO: Building Tree Tree-02.toc
159463 INFO: checking Tree
159463 INFO: Building Tree because Tree-03.toc is non existent
159463 INFO: Building Tree Tree-03.toc
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159463 INFO: Building Tree because Tree-04.toc is non existent
159463 INFO: Building Tree Tree-04.toc
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159464 INFO: Building Tree because Tree-05.toc is non existent
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159499 INFO: Building Tree because Tree-20.toc is non existent
159499 INFO: Building Tree Tree-20.toc
159499 INFO: Looking for ctypes DLLs
159962 WARNING: library user32 required via ctypes not found
161955 INFO: Analyzing run-time hooks ...
162065 INFO: Including run-time hook 'pyi_rth_traitlets.py'
162069 INFO: Including run-time hook 'pyi_rth__tkinter.py'
162072 INFO: Including run-time hook 'pyi_rth_mplconfig.py'
162076 INFO: Including run-time hook 'pyi_rth_mpldata.py'
162080 INFO: Including run-time hook 'pyi_rth_pyqt5.py'
162086 INFO: Including run-time hook 'pyi_rth_pkgres.py'
162092 INFO: Including run-time hook 'pyi_rth_certifi.py'
162099 INFO: Including run-time hook 'pyi_rth_multiprocessing.py'
162316 INFO: Looking for dynamic libraries
ldd: warning: you do not have execution permission for
`/root/miniconda3/envs/rte/lib/python3.6/site-packages/cryptography-2.5-py3.6-linux-x86_64.egg/cryptography/hazmat/bindings/_constant_time.abi3.so'
ldd: warning: you do not have execution permission for
`/root/miniconda3/envs/rte/lib/python3.6/site-packages/cryptography-2.5-py3.6-linux-x86_64.egg/cryptography/hazmat/bindings/_openssl.abi3.so'
ldd: warning: you do not have execution permission for
`/root/miniconda3/envs/rte/lib/python3.6/site-packages/cryptography-2.5-py3.6-linux-x86_64.egg/cryptography/hazmat/bindings/_padding.abi3.so'
ldd: warning: you do not have execution permission for
`/root/miniconda3/envs/rte/lib/python3.6/site-packages/coverage-5.0a8-py3.6-linux-x86_64.egg/coverage/tracer.cpython-36m-x86_64-linux-gnu.so'
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/tbbpool.cpython-36m-x86_64-linux-gnu.so:
/lib64/libstdc++.so.6: version `CXXABI_1.3.11' not found (required by
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/tbbpool.cpython-36m-x86_64-linux-gnu.so:
/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/tbbpool.cpython-36m-x86_64-linux-gnu.so:
/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)
ldd: warning: you do not have execution permission for
`/root/miniconda3/envs/rte/plugins/imageformats/../../lib/libgcc_s.so.1'
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2:
/lib64/libstdc++.so.6: version `CXXABI_1.3.11' not found (required by
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2:
/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2:
/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by
/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)
176012 INFO: Looking for eggs
176012 INFO: Using Python library
/root/miniconda3/envs/rte/lib/python3.6/site-packages/PIL/../../../libpython3.6m.so.1.0
176239 INFO: Warnings written to
/home/jloy/amb-rte/pydist/build/runtime_engine/warn-runtime_engine.txt
177110 INFO: Graph cross-reference written to
/home/jloy/amb-rte/pydist/build/runtime_engine/xref-runtime_engine.html
177431 INFO: Appending 'datas' from .spec
177454 INFO: checking PYZ
177454 INFO: Building PYZ because PYZ-00.toc is non existent
177454 INFO: Building PYZ (ZlibArchive)
/home/jloy/amb-rte/pydist/build/runtime_engine/PYZ-00.pyz
190344 INFO: Building PYZ (ZlibArchive)
/home/jloy/amb-rte/pydist/build/runtime_engine/PYZ-00.pyz completed
successfully.
190521 INFO: checking PKG
190521 INFO: Building PKG because PKG-00.toc is non existent
190521 INFO: Building PKG (CArchive) PKG-00.pkg
190594 INFO: Building PKG (CArchive) PKG-00.pkg completed successfully.
190596 INFO: Bootloader
/root/miniconda3/envs/rte/lib/python3.6/site-packages/PyInstaller/bootloader/Linux-64bit/run_d
190596 INFO: checking EXE
190596 INFO: Building EXE because EXE-00.toc is non existent
190596 INFO: Building EXE from EXE-00.toc
190597 INFO: Appending archive to ELF section in EXE
/home/jloy/amb-rte/pydist/build/runtime_engine/runtime_engine
190674 INFO: Building EXE from EXE-00.toc completed successfully.
190685 INFO: checking COLLECT
190685 INFO: Building COLLECT because COLLECT-00.toc is non existent
190686 INFO: Building COLLECT COLLECT-00.toc
196525 INFO: Building COLLECT COLLECT-00.toc completed successfully.
