I want to
import pybel
in jupyter-notebook and it says
The kernel appears to have died. It will restart automatically.
When I use it in python3, I get:
Python 3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:53:17)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel
terminate called after throwing an instance of 'std::logic_error'
what(): basic_string::_M_construct null not valid
Aborted (core dumped)
Installing using pip3 instead of conda
pip3 install pybel
works
Related
I I'm trying to use python with conda environment.
I create an environment using
conda create -n new_env3 python=3.9
Then when I start python terminal (just running 'python') I get:
Python 3.9.12 (main, Apr 5 2022, 06:56:58)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
Segmentation fault
I tried multiple python versions and sub-versions, but all resulted in the same error
i met the same problem, and conda clean -a didn't solve the problem
$ python
Python 3.10.6 (main, Oct 24 2022, 16:07:47) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
Segmentation fault
Try running conda clean -a.
This will remove all unused packages.
I am trying to start a vagrant vm and provision it using its ansible provisioner;
config.vm.provision "ansible" do |ansible|
ansible.limit = "all"
ansible.compatibility_mode = "2.0"
ansible.playbook = "ansible/install.yml"
end
the box is ubuntu/xenial64
Provisioning fails as follows:
==> default: Running provisioner: ansible...
default: Running ansible-playbook...
ImportError: No module named site
Ansible failed to complete successfully. Any error output should be
visible above. Please fix these errors and try again.
Host is Ubuntu 16.04.05 with ansible 2.7.0
I even tried to run a shell provisioner that installs python-minimal on the guest before executing ansible, but with no luck.
edit: in the mean time, on my controller:
/home/pkara/Desktop
$ python
Python 2.7.12 (default, Dec 4 2017, 14:50:18)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import site
>>>
/home/pkara/Desktop
$ python3
Python 3.5.2 (default, Nov 23 2017, 16:37:01)
[GCC 5.4.0 20160609] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import site
>>>
Actually I already installed tensorflow by using
$ pip install tensorflow
and it works well when I use
$ python
Python 2.7.15 (default, Jul 23 2018, 21:27:06)
[GCC 4.2.1 Compatible Apple LLVM 9.1.0 (clang-902.0.39.2)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>import tensorflow
>>>
but when I use python3 on command line
Python 3.7.0 (v3.7.0:1bf9cc5093, Jun 26 2018, 23:26:24)
[Clang 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import tensorflow
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'tensorflow'
>>>
it shows an error, and it shows the same error when I use IDLE
use
pip3 install tensorflow
pip installs to default python directory. pip3 installs to python3
I've successfully compiled the caffe library and the python module.
I can do this:
Jamess-Air:~ james$ python2 -V
Python 2.7.10
Jamess-Air:~ james$ python2
Python 2.7.10 (default, Jul 13 2015, 12:05:58)
[GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import caffe
>>>
But, bizarrely, this fails:
Jamess-Air:~ james$ python2.7 -V
Python 2.7.10
Jamess-Air:~ james$ python2.7
Python 2.7.10 (default, Jun 19 2015, 15:39:31)
[GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import caffe
Segmentation fault: 11
Jamess-Air:~ james$
I cannot understand this at all! Whenever I try to run using iPython notebook I get the same crash.
Any ideas as to what may be causing this, and how I might fix it, or at least get iPython Notebook to use the different python version so I can run this thing?
Thanks!
I have installed numpy and opencv using macports as per these instructions, but when I try import cv or import cv2 I just get the segfault and I have no idea why.
Any suggestions?
$ python
Python 2.7.6 (default, Sep 9 2014, 15:04:36)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import cv
Segmentation fault: 11
$ python
Python 2.7.6 (default, Sep 9 2014, 15:04:36)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import cv2
Segmentation fault: 11
Sorry there are so few details, but this is a new computer and I installed macports on it just for this, and these are the only things I've installed with macports, so I have no idea why this isn't working.
Edit: Now I'm More Confused.
Looking through the crash report I found this:
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000000
So, as a shot in the dark, I ran python as super user:
$ sudo python
Python 2.7.9 (default, Dec 13 2014, 15:13:49)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import cv
>>>
As super user, everything appears to run fine. How is this possible?
If you look closely to the info message of your python command, you will see the difference.
From the buggy one:
$ python
Python 2.7.6 (default, Sep 9 2014, 15:04:36)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import cv2
Segmentation fault: 11
From the working one:
$ sudo python
Python 2.7.9 (default, Dec 13 2014, 15:13:49)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import cv
>>>
You have two different versions of Python on your machine which might explain the behaviors you got.
After hitting this problem on OSX 10.11 and trawling through several cases of this problem in various contexts, I realized that this problem happens due to following independent reasons mostly:
conflicting python versions (more than one pythons); solution - uninstall one of them, get the one thats compatible with opencv ("Segmentation fault" during "import cv" on Mac OS)
opencv version issue; solution - get the right version for you Python opencv feature detector causes segmentation fault
issue with your numpy version; solution - uninstall and install numpy again (OpenCV - cannot find module cv2)
I tried all 3 but number 3 solved my issue.
Using
cv2.ocl.setUseOpenCL(False)
at the beginning of the code solved the problem for me.
For me the solution was simply
sudo apt install python3-opencv
and then install pip opencv package
sudo pip3 install opencv-python
or
sudo pip install opencv-python
Note: This was because I have launched a new Aws instance.
I encountered the similar problem.
➜ ~ ✗ python
Python 3.6.0 |Continuum Analytics, Inc.| (default, Dec 23 2016, 13:19:00)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import cv2
[1] 41233 segmentation fault python
But if I import numpy first, the problem will go away.
➜ ~ ✗ python
Python 3.6.0 |Continuum Analytics, Inc.| (default, Dec 23 2016, 13:19:00)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> import cv2
>>>