I have recently performed various software updates as suggested by the "Software Center" on my Ubuntu machine (Ubuntu 18.04.5 LTS).
Now, when I try to import numba (numba==0.51.2) via
python3 -c 'import numba'
I get the following error
double free or corruption (top) Aborted (core dumped)
The same happens when I create a new conda environment with a fresh numba install.
I have looked at the core dump via
gdb -c core
with
thread apply all bt full
but I only get memory address information. I use python 3.6.9 on my machine, but I have also tried 3.8 in a new conda environment, where I get the same error.
I suspect that the software update is the reason for the error described above. But I might be mistaken and something else goes on here.
Is there any other way to get more info on where python crashes? I really don't want to go through the updated libraries one by one and roll them back to find the error.
At least I have now found the library that causes this error.
What I did were the following steps:
put import numba into a file, e.g. importNumba.py
locate python3.X-gdb.py via locate --regex python3.*-gdb.py. In my case it is in /usr/share/gdb/auto-load/usr/bin/python3.6-gdb.py
run python in debug mode via gdb python3 - the gdb console opens
execute source /usr/share/gdb/auto-load/usr/bin/python3.6-gdb.py in the gdb console - this will load the python extensions into gdb
execute run importNumba.py in the gdb console - this will produce above error
execute py-bt in the gdb console
This gives
Traceback (most recent call first):
File "/usr/local/lib/python3.6/dist-packages/llvmlite/binding/ffi.py", line 113, in __call__
return self._cfn(*args, **kwargs)
File "/usr/local/lib/python3.6/dist-packages/llvmlite/binding/dylib.py", line 29, in load_library_permanently
_encode_string(filename), outerr):
File "/usr/local/lib/python3.6/dist-packages/numba/__init__.py", line 151, in _try_enable_svml
llvmlite.binding.load_library_permanently("libsvml.so")
File "/usr/local/lib/python3.6/dist-packages/numba/__init__.py", line 201, in <module>
config.USING_SVML = _try_enable_svml()
<built-in method exec of module object at remote 0x7ffff7fb7638>
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "<frozen importlib._bootstrap_external>", line 678, in exec_module
File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 971, in _find_and_load
File "importNumba.py", line 1, in <module>
import numba
So it seems something is wrong with libsvml.so.
I found out that numba allows to disable SVML via
setting the environment flag NUMBA_DISABLE_INTEL_SVML to something other than 0, see https://numba.pydata.org/numba-doc/dev/reference/envvars.html
Changing importNumba.py to
import os
# note that this must be executed before 'import numba'
os.environ['NUMBA_DISABLE_INTEL_SVML'] = '1'
import numba
and running it via python3 importNumba.py now works without error.
These were a few useful resources that I used:
https://fedoraproject.org/wiki/Features/EasierPythonDebugging#New_gdb_commands
https://wiki.python.org/moin/DebuggingWithGdb
Related
I need a lldb python library to debug my python script. I made my python environment configuration following the lldb.llvm.org's instructions. But I got some errors as follow:
/Users/heping/Desktop/Scripts/.env/python-3.7.3/bin/python /Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/pydevd.py --multiproc --qt-support=auto --client 127.0.0.1 --port 57996 --file /Users/heping/Desktop/Scripts/RevealServerCommands.py
pydev debugger: process 59879 is connecting
Connected to pydev debugger (build 193.5662.61)
Traceback (most recent call last):
File "/Applications/Xcode.app/Contents/SharedFrameworks/LLDB.framework/Resources/Python/lldb/__init__.py", line 35, in <module>
import _lldb
ModuleNotFoundError: No module named '_lldb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<frozen importlib._bootstrap>", line 983, in _find_and_load
File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 728, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/Applications/Xcode.app/Contents/SharedFrameworks/LLDB.framework/Resources/Python/lldb/__init__.py", line 38, in <module>
from . import _lldb
ImportError: dynamic module does not define module export function (PyInit__lldb)
And the PyCharm project structure is as picture showing blow:
The lldb python module shipped with Xcode builds against a specific version of Python.
Prior to Xcode 11 lldb was built against the Python2.7.1 in /System/Library/Frameworks. Starting with Xcode 11, lldb is built against the version of Python 3 (currently 3.7.3) that ships with the Xcode from which you got your lldb. You can locate the proper python3 command line tool by running xcrun python3.
We haven't had much success getting the lldb module we build against this 3.7.3 Python to load into other hand-built Pythons. I'm not sure that this is particularly well supported by Python, though I don't know of anybody who has looked into what it would take to support this.
We do use a lot of the Python C API's in the lldb bindings, so we are more bound to the Python version than pure Python modules. Anyway, at present if you need to load the lldb module into a python you have installed from elsewhere, you will most likely need to hand-build lldb against that python library.
On MacOS PyCharm go Preferences\Python Interpreter\ Then click on the Settings buttons and Show All.
Other answers said you need this:
import sys
sys.path.append('/Applications/Xcode.app/Contents/SharedFrameworks/LLDB.framework/Resources/Python3')
import lldb
With the above setting, it worked with just import lldb.
I'm running into an issue trying to get python-markdown to work in pyinstaller. I have this code to demonstrate the issue in file called test.py:
import markdown
testMarkdown = "blahdy blah blah"
print(markdown.markdown(testMarkdown))
print(markdown.markdown(testMarkdown, extensions=["extra"]))
When I run it using python3, I get as desired:
(venv) C:\Users\madgrizzle>python3 test.py
<p>blahdy blah blah</p>
<p>blahdy blah blah</p>
I run pyinstaller as follows:
(venv) C:\Users\madgrizzle>pyinstaller test.py
and run the resulting code, I get the following:
(venv) C:\Users\madgrizzle\dist\test>test
<p>blahdy blah blah</p>
Traceback (most recent call last):
File "test.py", line 5, in <module>
File "lib\site-packages\markdown\core.py", line 390, in markdown
File "lib\site-packages\markdown\core.py", line 100, in __init__
File "lib\site-packages\markdown\core.py", line 126, in registerExtensions
File "lib\site-packages\markdown\core.py", line 166, in build_extension
File "importlib\__init__.py", line 126, in import_module
File "<frozen importlib._bootstrap>", line 985, in _gcd_import
File "<frozen importlib._bootstrap>", line 968, in _find_and_load
File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
ImportError: No module named 'extra'
[14432] Failed to execute script test
I tried to rebuild using:
(venv) C:\Users\madgrizzle>pyinstaller --hidden-import="markdown.extensions.extra" test.py
but I get the same error message.
Is there something special that's needed for including markdown extensions?
Additional Information:
It appears that the 'extra' extension might be causing the problem. Per https://python-markdown.github.io/extensions/extra/, 'extra' is a compilation of multiple extensions, including fenced_code and tables. If I just try to use the tables extension by itself, pyinstaller works IF I use the full-name as follows:
markdown.markdown(testMarkdown, extensions=["markdown.extensions.tables"])
If instead of using 'markdown.extensions.tables' I use 'markdown.extensions.extra', compile using pyinstaller, and run it, it responds back with a missing "fenced_code" module. Basically, it seems I have to avoid 'extra' with pyinstaller.
Short names for extensions like extra and table are setuptools entrypoints. I expect that pyinstaller does not play nice with entrypoints. Therefore, you need to use the full importable string name for all extensions.
However, as extra uses the short names internally, that means you cannot use extra. You will need to call each of the nested extensions separately by their full importable string name:
markdown.markdown(
testMarkdown,
extensions=[
"markdown.extensions.abbr",
"markdown.extensions.attr_list",
"markdown.extensions.def_list",
"markdown.extensions.fenced_code",
"markdown.extensions.footnotes",
"markdown.extensions.tables"
]
)
The only problem with that is that you won't get any extra specific behavior. However, when version 3.2 is released, the changes here will be available and you can add markdown.extensions.md_in_html to the list of extensions. At that point, you will get all of extra without needing to include extra at all.
I am trying to set up python in Vim, but I failed to get it to work. It always throws an exception named UnicodeDecodeError.
I have installed gvim on windows 10. And also installed python 3 with the corresponding version.
Vim can find the python37.dll and the command
:echo has('python3')
returns 1 as expected.
My vim with python works only when no modules except for the builtin ones are imported.
For example:
:py3 print('a')
works pretty well.
:py3 import vim
or
:py3 import sys
are also working.
However, if I write a simple python script vim_test.py like this
print('This is for vim test')
then try to import it in vim as
:py3 import vim_test
it will give an exception:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "<frozen importlib._bootstrap>", line 983, in _find_and_load
File "<frozen importlib._bootstrap>", line 963, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 906, in _find_spec
File "<frozen importlib._bootstrap_external>", line 1280, in find_spec
File "<frozen importlib._bootstrap_external>", line 1252, in _get_spec
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb3 in position 9: invalid start byte
It cannot import any python module in Vim.
But it can run this script directly by
:py3file vim_test.py
if the script file vim_test.py is in the current directory.
What could be the reason for this problem?
And how can I solve it?
I expected to be able to use vim plugins written in python.
With this problem, I cannot achieve that.
I'm on Windows 10.
I tried to install channels to use websockets with Django but it doesn't work. I got the following error :
Failed building wheel for Twisted
I have still not succeeded to install channels.
But now I have a new problem, I can no anymore access Python shell from my virtual environment that I use for Django.
(myproject) D:\Django\mysite>py manage.py shell
Traceback (most recent call last):
File "manage.py", line 15, in <module>
execute_from_command_line(sys.argv)
File "C:\Users\kevin\Envs\myproject\lib\site-packages\django\core\management\__init__.py", line 381, in execute_from_command_line
utility.execute()
File "C:\Users\kevin\Envs\myproject\lib\site-packages\django\core\management\__init__.py", line 357, in execute
django.setup()
File "C:\Users\kevin\Envs\myproject\lib\site-packages\django\__init__.py", line 24, in setup
apps.populate(settings.INSTALLED_APPS)
File "C:\Users\kevin\Envs\myproject\lib\site-packages\django\apps\registry.py", line 89, in populate
app_config = AppConfig.create(entry)
File "C:\Users\kevin\Envs\myproject\lib\site-packages\django\apps\config.py", line 90, in create
module = import_module(entry)
File "C:\Users\kevin\Envs\myproject\lib\importlib\__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
File "<frozen importlib._bootstrap>", line 983, in _find_and_load
File "<frozen importlib._bootstrap>", line 965, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'channels'
I have no idea to solve my problem ... Someone could bring me help ?
Try install channels by using pip install channels
then run shell again
Seems like you broke something when you tried to install channels. From the spares information I guess that easiest course of action is to simply use a new virtual environment. After all that is the point of a virtual environment, if it breaks you can just rebuild it.
Manually fixing the virtual environment usually (this is my personal experience) takes more time then just setting up a new one.
For your installation trouble we need more info and you should open a new question.
So just deactivate your current environment (this might help), delete it and set up a new one.
Keep in mind that this will only bring the shell back and give you a "fresh start". Your installation problem will usually not disappear!
After installing Anaconda for Python 3.4 on my Mac I get constant messages saying:
Error in sitecustomize; set PYTHONVERBOSE for traceback:
KeyError: 'PYTHONPATH'
As suggested by a user on another question, I used
PYTHONVERBOSE=1 conda update --all
And received the traceback:
Traceback (most recent call last):
File "/Users/user/anaconda/lib/python3.4/site.py", line 506, in execsitecustomize
import sitecustomize
File "<frozen importlib._bootstrap>", line 2237, in _find_and_load
File "<frozen importlib._bootstrap>", line 2226, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 1200, in _load_unlocked
File "<frozen importlib._bootstrap>", line 1129, in _exec
File "<frozen importlib._bootstrap>", line 1471, in exec_module
File "<frozen importlib._bootstrap>", line 321, in _call_with_frames_removed
File "/usr/local/lib/python2.7/site-packages/sitecustomize.py", line 15, in <module>
str(sys.version_info[0]) + '.x!\n PYTHONPATH is currently: "' + str(os.environ['PYTHONPATH']) + '"\n' +
File "/Users/user/anaconda/lib/python3.4/os.py", line 633, in __getitem__
raise KeyError(key) from None
KeyError: 'PYTHONPATH'
# destroy sitecustomize
I have looked around and found that 'PYTHONPATH' does not exist as a key in os.environ.
If your PYTHONPATH environment variable is set, unset it. You can check with echo $PYTHONPATH. If it is set it is probably coming from something in ~/.profile or ~/.bash_profile.
The issue is the file /usr/local/lib/python2.7/site-packages/sitecustomize.py. You may want to check what that file is and where it comes from, but removing it should fix the problem.
Going to necro-answer here with more detail for folks that might hit this page after searching for the error shown…
If your Mac has messages referencing /usr/local/, I'm going to go ahead and assume you've used homebrew to install something. In this case, Python.
When Anaconda's Python distribution is installed, one of the things it'll check is if there are any site customizations applied to your existing Python installation. If you installed any version of Python using Homebrew, you likely have such a site customization.
Running conda info -a | grep dirs will get your Anaconda install info and look for a line with dirs included. Only one should match, if it exists:
user site dirs: ~/.local/lib/python3.5
If it does exist, cd to that directory (whatever it is), and get a directory listing (ls). You'll then (likely) find a file called homebrew.pth.
Remove that file, and the error goes away.
Reason: Anaconda is referencing that homebrew.pth file, which then goes on to include the sitecustomize.py from your earlier homebrew-installed version of Python.