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Caffe: a fast open framework for deep learning.
http://caffe.berkeleyvision.org/
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import pycaffe in local Mac OS 10.9 reports "segmentation fault: 11" #591

Closed liuxianming closed 10 years ago

liuxianming commented 10 years ago

I'm debuging on my local macbook. Before I tried to use the python lib "pycaffe" everything works well. While when I turn to attempt to write some python scripts relying on the "_caffe.so", the following error turns out:

python import _caffe

Segmentation fault: 11

This should be some problems in compiling the python lib.

Thanks.

nicodjimenez commented 10 years ago

I had the same error. You are probably compiling caffe with the default version of python on your mac (2.6) and are now trying to import caffe via python 2.7. Try upgrading and make sure that boost python is using 2.7. That fixed it for me.

shelhamer commented 10 years ago

@nicodjimenez is right.

You need to install Python 2.7 and our Python dependencies, for which Anaconda is a good choice, then build boost python and pycaffe with it and not the system Python.

kouohhashi commented 9 years ago

I had the same error. I can compile Caffe and "make runtest" generated no errors. But "import caffe" generate segmentation fault unfortunately.

I installed Python by using brew. OSX 10.10.2 Python 2.7.9 But since I set "cpu-only", I didn't changed fomuras to "-stdlib=libstdc++".

I tried to install Caffe many times. Any help is appreciated.

gp335 commented 9 years ago

I'm getting the same issue: "make runtest" is fine but "import caffe" in a python prompt results in "Segmentation fault: 11". Have tried to re-download and reinstall all components several times... please let me know what else I can share to be helpful? Any help is greatly appreciated.

Macbook Air, OSX 10.10.2, Homebrew and system-wide python are both 2.7.9 (system python symlinks to Homebrew python). Boost does appear as one of the last calls in the stack per the crash report.

pwais commented 9 years ago

Same issue with OSX 10.9.4, Python 2.7, libc++, CUDA 7, libs via macports. Built with cmake.

gp335 commented 9 years ago

Finally fixed it (painfuly). Problem (as has been indicated in a few other forum posts) was different versions of python: I had Python 2.7.9 (installed via homebrew in /usr/local/Cellar/python) which was newer than the system's python... and the system python's libraries (found in /System/Library/Frameworks) would "sneak in" during the linking stage and ultimately cause segfaults.

This is probably not the right way to fix it, but in hope of being helpful my work-around was: 1) Rename the system python libraries to something else so they wouldn't be found by ld. ("sudo mv /System/Library/Frameworks/Python.framework /System/Library/Frameworks/Python.framework_bak")

2) Explicitly add the correct library path in caffe's Makefile.config (e.g., "PYTHON_LIB := /usr/local/lib /usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/lib").

If you're not sure where your up-to-date python library is then in a shell run "locate updatedb; locate libpythonX.X" where X.X is your version of python... use the directory in the output that contains the .dylib and .a files referring to your preferred installation of Python.

If you're wondering if you suffer from the same problem I did, I was tipped of by a line in OSX's problem report that indicated an old version of python sneaking in. Under the "Binary Images" section there was a line that read, "0x108c69000 - 0x108d5aff7 org.python.python (2.7.6 - 2.7.6) /System/Library/Frameworks/Python.framework/Versions/2.7/Python)" ...indicating that the system version of python was being referenced.

NightFury13 commented 9 years ago

I'm facing similar issues for quite sometime now and still have not been able to solve it. Any solutions to this problem would really be appreciated. I've tried out most of the solutions posted on various forums across the internet.

System:

MacBook Pro
MAC OSX 10.10.3
Installed with CPU_ONLY:=1

Soln-1:

Generally, setting the PYTHONPATH is what most people forget and land in trouble. My PYTHONPATH variable looks like this.
export PYTHONPATH="<Caffe-Home>/caffe/python:$PYTHONPATH"

Error : 
The python command (on using 'import caffe') prompt freezes for a few seconds and returns with a "segmentation fault: 11" error message with the complete log as pasted below (at the bottom).

Soln-2:

I've also tried the distribute version.
export PYTHONPATH="<Caffe-home>/caffe/distribute/python:$PYTHONPATH"

Error : (on the python-command-prompt after using 'import caffe')
It is unable to find the _caffe.so file in the caffe directory however I have manually checked that this file is present in the directory.

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/Home/research/virginia/CloudCV/caffe/distribute/python/caffe/__init__.py", line 1, in <module>
    from .pycaffe import Net, SGDSolver
  File "/Users/Home/research/virginia/CloudCV/caffe/distribute/python/caffe/pycaffe.py", line 13, in <module>
    from ._caffe import Net, SGDSolver
ImportError: dlopen(/Users/Home/research/virginia/CloudCV/caffe/distribute/python/caffe/_caffe.so, 2): Library not loaded: @rpath/libcaffe.so
  Referenced from: /Users/Home/research/virginia/CloudCV/caffe/distribute/python/caffe/_caffe.so
  Reason: image not found

@gp335 : I might not be on the same issue as yours as I don't see any "/System/Library/Frameworks/Python.framework/Versions/2.7/Python" calls being made in my error-log. To be precise, here it is.... (error-log on using /caffe/python in PYTHONPATH)

Process:               Python [761]
Path:                  /usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier:            Python
Version:               2.7.9 (2.7.9)
Code Type:             X86-64 (Native)
Parent Process:        bash [710]
Responsible:           iTerm [635]
User ID:               501

Date/Time:             2015-05-28 00:28:36.361 +0530
OS Version:            Mac OS X 10.10.3 (14D136)
Report Version:        11
Anonymous UUID:        4D1E2216-6A20-E2AC-00A1-758B0B4AF821

Sleep/Wake UUID:       5F600EBD-9CB0-4BD5-A304-C45F57351EEE

Time Awake Since Boot: 18000 seconds
Time Since Wake:       6800 seconds

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x0000000000000000

VM Regions Near 0:
--> 
    __TEXT                 0000000106592000-0000000106594000 [    8K] r-x/rwx SM=COW  /usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   ???                             000000000000000000 0 + 0
1   org.python.python               0x00000001080770dd PyEval_GetGlobals + 23
2   org.python.python               0x000000010808662b PyImport_Import + 137
3   org.python.python               0x0000000108084d27 PyImport_ImportModule + 31
4   _caffe.so                       0x00000001072edcf8 caffe::init_module__caffe() + 4328
5   libboost_python.dylib           0x0000000107f98391 boost::python::handle_exception_impl(boost::function0<void>) + 81
6   libboost_python.dylib           0x0000000107f993b9 boost::python::detail::init_module(char const*, void (*)()) + 121
7   org.python.python               0x00000001066332cf _PyImport_LoadDynamicModule + 140
8   org.python.python               0x0000000106632fb7 import_submodule + 270
9   org.python.python               0x0000000106632b81 load_next + 280
10  org.python.python               0x0000000106630d89 PyImport_ImportModuleLevel + 1135
11  org.python.python               0x00000001066163db builtin___import__ + 135
12  org.python.python               0x00000001065a10ea PyObject_Call + 99
13  org.python.python               0x0000000106620d8b PyEval_CallObjectWithKeywords + 93
14  org.python.python               0x000000010661d065 PyEval_EvalFrameEx + 8375
15  org.python.python               0x000000010661ad7a PyEval_EvalCodeEx + 1409
16  org.python.python               0x000000010661a7f3 PyEval_EvalCode + 54
17  org.python.python               0x000000010662f836 PyImport_ExecCodeModuleEx + 241
18  org.python.python               0x0000000106632516 load_source_module + 1091
19  org.python.python               0x0000000106632fb7 import_submodule + 270
20  org.python.python               0x0000000106632b81 load_next + 280
21  org.python.python               0x0000000106630d89 PyImport_ImportModuleLevel + 1135
22  org.python.python               0x00000001066163db builtin___import__ + 135
23  org.python.python               0x00000001065a10ea PyObject_Call + 99
24  org.python.python               0x0000000106620d8b PyEval_CallObjectWithKeywords + 93
25  org.python.python               0x000000010661d065 PyEval_EvalFrameEx + 8375
26  org.python.python               0x000000010661ad7a PyEval_EvalCodeEx + 1409
27  org.python.python               0x000000010661a7f3 PyEval_EvalCode + 54
28  org.python.python               0x000000010662f836 PyImport_ExecCodeModuleEx + 241
29  org.python.python               0x0000000106632516 load_source_module + 1091
30  org.python.python               0x00000001066327d7 load_package + 303
31  org.python.python               0x0000000106632fb7 import_submodule + 270
32  org.python.python               0x0000000106632b81 load_next + 280
33  org.python.python               0x0000000106630d89 PyImport_ImportModuleLevel + 1135
34  org.python.python               0x00000001066163db builtin___import__ + 135
35  org.python.python               0x00000001065a10ea PyObject_Call + 99
36  org.python.python               0x0000000106620d8b PyEval_CallObjectWithKeywords + 93
37  org.python.python               0x000000010661d065 PyEval_EvalFrameEx + 8375
38  org.python.python               0x000000010661ad7a PyEval_EvalCodeEx + 1409
39  org.python.python               0x000000010661a7f3 PyEval_EvalCode + 54
40  org.python.python               0x000000010663a8a2 run_mod + 53
41  org.python.python               0x000000010663a6be PyRun_InteractiveOneFlags + 353
42  org.python.python               0x000000010663a1cd PyRun_InteractiveLoopFlags + 192
43  org.python.python               0x000000010663a077 PyRun_AnyFileExFlags + 60
44  org.python.python               0x000000010664bc5b Py_Main + 3051
45  libdyld.dylib                   0x00007fff98d525c9 start + 1

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x00000001081252d8  rbx: 0x0000000108406030  rcx: 0x0800bf453c5d2274  rdx: 0x0000000108409050
  rdi: 0x0000000000000000  rsi: 0x00000001080b90d7  rbp: 0x00007fff5966c050  rsp: 0x00007fff5966c048
   r8: 0x2000000000000200   r9: 0x0800000000000100  r10: 0x0000000004001049  r11: 0x000000000034dfe4
  r12: 0x0000000108406030  r13: 0x0000000000000000  r14: 0x0000000000000000  r15: 0x0000000000000000
  rip: 0x0000000000000000  rfl: 0x0000000000010206  cr2: 0x0000000000000000

Logical CPU:     2
Error Code:      0x00000014
Trap Number:     14

Binary Images:
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@shelhamer : any inputs would be of great value.

Thanks! :)

gp335 commented 9 years ago

I am seeing two different version of python in your error log: You're predominantly referencing the one from home-brew: 0x106592000 - 0x106593fff +org.python.python (2.7.9 - 2.7.9) /usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python

But further down the system version of python is still sneaking in (and it seems to be version 2.7.6 instead of the 2.7.9 that's used by home-brew): 0x107fed000 - 0x1080deff7 org.python.python (2.7.6 - 2.7.6) /System/Library/Frameworks/Python.framework/Versions/2.7/Python

I'd suggest trying the steps above and recompiling everything?

Having lived with the work-around for a few weeks, it did cause a headache when I updated my command line tools, so I'd probably suggest rather than moving the framework in step #1 to maybe just symlinking it appropriately to the home-brew directory...but for now the original post should still hopefully fix your problems :)

Good luck and hope it starts working!

NightFury13 commented 9 years ago

@gp335 : Thanks for that point out! The different versions on my system python and brewed python was the root of the problem. I fixed the error by changing the PYTHON_LIB variable in my Makefile.config.

PYTHON_LIB := /usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/lib/

This got me through importing caffe in python. I've also written a small Wiki page to get people through the problems that I faced. http://installing-caffe-the-right-way.wikidot.com/ @gp335 : your suggestions would hold great value :D

christopher5106 commented 9 years ago

created my tutorial as well : http://christopher5106.github.io/big/data/2015/07/16/deep-learning-install-caffe-cudnn-cuda-for-digits-python-on-mac-osx.html

aniryou commented 8 years ago

For me the error log indicated references to /usr/lib/libpython2.7.dylib which links to /System/Library/Frameworks/Python.framework/Versions/2.7/Python.I wanted to use anaconda distribution. Fix: issue got resolved by linking /usr/lib/libpython2.7.dylib to $ANACONDA_HOME/lib/libpython2.7.dylib. Note: I'm using OSX El Captain and had to disable system integrity protection to do same.

junwenchen commented 8 years ago

@aniryou :I want to use anaconda too. could you please explain how to link the /usr/lib/libpython2.7.dylib to $ANACONDA_HOME/lib/libpython2.7.dylib. Thank you.

stgzr commented 8 years ago

@junwenchen For my case, I tried to modify ../cmake/Dependencies.cmake, add corresponding path of PYTHON_LIBRARY and PYTHON_INCLUDE_DIR before find_package(PythonLibs 2.7). Then it works:)

JPaulMora commented 8 years ago

@aniryou I can confirm this fixes the issue :D

digitizdat commented 8 years ago

For posterity, I will note that I also ran into this problem, but from a different error:

In [1]: import caffe
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-1cca3aa1f8c5> in <module>()
----> 1 import caffe

/opt/caffe/python/caffe/__init__.py in <module>()
----> 1 from .pycaffe import Net, SGDSolver, NesterovSolver, AdaGradSolver, RMSPropSolver, AdaDeltaSolver, AdamSolver
      2 from ._caffe import set_mode_cpu, set_mode_gpu, set_device, Layer, get_solver, layer_type_list
      3 from ._caffe import __version__
      4 from .proto.caffe_pb2 import TRAIN, TEST
      5 from .classifier import Classifier

/opt/caffe/python/caffe/pycaffe.py in <module>()
     11 import numpy as np
     12 
---> 13 from ._caffe import Net, SGDSolver, NesterovSolver, AdaGradSolver, \
     14         RMSPropSolver, AdaDeltaSolver, AdamSolver
     15 import caffe.io

ImportError: No module named _caffe

I had to first rename the file that was installed as _caffe.dylib to _caffe.so before I could even get the system to recognize it. Then once that was done, I ran into a SIGSEGV:

# mv /opt/caffe/python/caffe/_caffe.dylib /opt/caffe/python/caffe/_caffe.so

...
In [1]: import caffe
Segmentation fault: 11

I could see by looking at the dynamic linker information for the library that it was linked to the system Python, which did not seem right:

# otool -L /opt/caffe/python/caffe/_caffe.so  |grep -i python

...
/opt/caffe/python/caffe/_caffe.so:
    /System/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.10)
    /usr/local/opt/boost-python/lib/libboost_python-mt.dylib (compatibility version 0.0.0, current version 0.0.0)

Then I found this thread, which further advanced the notion that it might be a python version mismatch. I was using Anaconda for my Python env and using the cmake method for Caffe compilation, so I checked the output I had from cmake:

# cmake -D CMAKE_CXX_FLAGS="-I/System/Library/Frameworks/Accelerate.framework/Versions/Current/Frameworks/vecLib.framework/Versions/Current/Headers -Wl,-framework,Accelerate" -D OpenCV_DIR=/usr/local/opt/opencv3/share/OpenCV ..

...
-- Python:
--   Interpreter       :   /Users/martin/anaconda3/envs/dev27/bin/python2.7 (ver. 2.7.10)
--   Libraries         :   /usr/lib/libpython2.7.dylib (ver 2.7.10)
...

This indeed confirmed that the problem was a conflict between Python distributions, so I changed my cmake flags like so:

# cmake -D PYTHON_INCLUDE_DIR=/Users/martin/anaconda3/envs/dev27/include/python2.7 -D PYTHON_LIBRARY=/Users/martin/anaconda3/envs/dev27/lib/libpython2.7.dylib -D CMAKE_CXX_FLAGS="-I/System/Library/Frameworks/Accelerate.framework/Versions/Current/Frameworks/vecLib.framework/Versions/Current/Headers -Wl,-framework,Accelerate" -D OpenCV_DIR=/usr/local/opt/opencv3/share/OpenCV ..

...
-- Python:
--   Interpreter       :   /Users/martin/anaconda3/envs/dev27/bin/python2.7 (ver. 2.7.10)
--   Libraries         :   /Users/martin/anaconda3/envs/dev27/lib/libpython2.7.dylib (ver 2.7.10)

And rebuilt.

Now, looking at the linker information for the library, I can see that it is no longer linked to the system Python: 

# otool -L install/python/caffe/_caffe.dylib  |grep -i python

...
install/python/caffe/_caffe.dylib:
    libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0)
    /usr/local/opt/boost-python/lib/libboost_python-mt.dylib (compatibility version 0.0.0, current version 0.0.0)

Then the next problem was that the libpython2.7.dylib from the Anaconda env could not be found at runtime:

In [1]: import _caffe
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-8f34565b13c7> in <module>()
----> 1 import _caffe

ImportError: dlopen(./_caffe.so, 2): Library not loaded: libpython2.7.dylib
  Referenced from: /opt/caffe/python/caffe/_caffe.dylib
  Reason: image not found

So I next had to update the 

# export DYLD_FALLBACK_LIBRARY_PATH=/Users/martin/anaconda3/envs/dev27/lib:$DYLD_FALLBACK_LIBRARY_PATH
# ipy
Python 2.7.10 |Continuum Analytics, Inc.| (default, Oct 19 2015, 18:31:17) 
Type "copyright", "credits" or "license" for more information.

IPython 4.0.1 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: import _caffe

In [2]:

Now finally everything is working.

dozyc commented 8 years ago

Similar to lots of people here I had a mix of system Python and Anaconda Python being linked together. I used install_name_tool to force _caffe.so to use the Anaconda Python, without disabling system integrity protection (I'm also on El Capitan).

You can use otool to see which libraries are linked in:

otool -L python/caffe/_caffe.so

There should be one line that links a bare "libpython2.7.lib" without any path, I think this is why the system python gets pulled in at runtime.

I used this command to change it:

install_name_tool -change "libpython2.7.dylib" "$HOME/anaconda/lib/libpython2.7.dylib" python/caffe/_caffe.so

No more seg fault!!

I learned about this strategy from issue #3227

samyouxyz commented 8 years ago

If you use Anaconda, try this in terminal before import caffe in Python interactive session:

export DYLD_FALLBACK_LIBRARY_PATH=$HOME/anaconda/lib

It works for me. Hope it helps!

drewfarris commented 8 years ago

What @dozyc said worked for me as well, but with slightly different invocations.

I was hitting SIGSEGV when calling import caffe on OSX 10.11.6 (El Capitan) with python 2.7.12 installed via Homebrew.

I ran:

otool -L ./python/caffe/_caffe.so

And observed:

/usr/local/opt/boost-python/lib/libboost_python.dylib (compatibility version 0.0.0, current version 0.0.0)
/System/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.10)
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib (compatibility version 1.0.0, current version 1.0.0)

The dependency on Python from /System/Library/Frameworks is bad - this is the OS version of Python, not the version installed via homebrew, hence incompatibility.

I fixed this with:

install_name_tool -change /System/Library/Frameworks/Python.framework/Versions/2.7/Python /usr/local/Cellar/python/2.7.12/Frameworks/Python.framework/Versions/2.7/Python ./python/caffe/_caffe.so

One one system I had to also do the same for the caffe library because I built it with Python layer support:

install_name_tool -change /System/Library/Frameworks/Python.framework/Versions/2.7/Python /usr/local/Cellar/python/2.7.12/Frameworks/Python.framework/Versions/2.7/Python ../distribute/lib/libcaffe.so.1.0.0-rc3

Hope this helps.

jurastm commented 8 years ago

If you use MacOS El capitan, uncomment this line in MakeConfig file WITH_PYTHON_LAYER := 1

alanwangmodify commented 8 years ago

I'm facing similar issues. And can not fix it by the above ways。 Mac OS X 10.11.13

jurastm commented 8 years ago

I had many issues while installation. In my case the real solution was:

  1. Uninstall homebrew, all dependencies, brewed Python and all content in usr/local
  2. Install homebrew, Python and all dependencies from scratch
  3. Note: I didn't change args DPYTHON in opencv file.
  4. Clone caffe
  5. Modify makefile.config - you have carefully provide PYTHON_PATHs - make sure twice that your pathways are correct. Don't forget to uncomment WITH_PYTHON_LAYER := 1 Don't forget to provide correct pathways in your ~/.bash_profile
  6. Make clean, make all, make test, make runtest. Be aware that you could face some errors about abcence opencv3 while compilation. In this case brew opencv3.
  7. Make pycaffe. In command line: cd //python
  8. Cross your fingers and input "import caffe"

My configuration: Mac OS X 10.11.6 CPU only No anaconda, no cudnn

Tutorials that I used: https://frankzliu.com/installing-caffe-on-os-x-el-capitan/ http://installing-caffe-the-right-way.wikidot.com/start

On Friday, 30 September 2016, 王小树 notifications@github.com wrote:

I'm facing similar issues. And can not fix it by the above ways。 Mac OS X 10.11.13

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/BVLC/caffe/issues/591#issuecomment-250650500, or mute the thread https://github.com/notifications/unsubscribe-auth/AF9YWqWr5A49Ho_xBi-YsND7emEncAgAks5qvIKQgaJpZM4CJyGp .

Sincerely, Yura Vasiliuk

ShangxuanWu commented 7 years ago

@NightFury13 Your solution just works!