I have two Anaconda environments I created, say A and B, plus the base env.
I have created environments A and B specific to what I do with them (different libraries).
Now I installed VScode. When I open VScode and set first the correct interpreter (A or B) in the lower part and run some python programs specific to A and B, the program does not run and error appears.
D:\Anaconda\envs\practica-mldl\lib\site-packages\numpy\__init__.py:138: UserWarning: mkl-service package failed to import, therefore Intel(R) MKL initialization ensuring its correct out-of-the box operation under condition when Gnu OpenMP had already been loaded by Python process is not assured. Please install mkl-service package, see http://github.com/IntelPython/mkl-service
from . import _distributor_init
Traceback (most recent call last):
File "D:\Anaconda\envs\practica-mldl\lib\site-packages\numpy\core\__init__.py", line 22, in <module>
from . import multiarray
File "D:\Anaconda\envs\practica-mldl\lib\site-packages\numpy\core\multiarray.py", line 12, in <module>
from . import overrides
File "D:\Anaconda\envs\practica-mldl\lib\site-packages\numpy\core\overrides.py", line 7, in <module>
from numpy.core._multiarray_umath import (
ImportError: DLL load failed while importing _multiarray_umath: The specified module could not be found.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "d:\Do\Python\ML practice\iris\own-knn.py", line 15, in <module>
import numpy as np
File "D:\Anaconda\envs\practica-mldl\lib\site-packages\numpy\__init__.py", line 140, in <module>
from . import core
File "D:\Anaconda\envs\practica-mldl\lib\site-packages\numpy\core\__init__.py", line 48, in <module>
raise ImportError(msg)
ImportError:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy C-extensions failed. This error can happen for
installed.
We have compiled some common reasons and troubleshooting tips at:
https://numpy.org/devdocs/user/troubleshooting-importerror.html
Please note and check the following:
* The Python version is: Python3.8 from "D:\Anaconda\envs\practica-mldl\python.exe"
* The NumPy version is: "1.19.2"
and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.
Original error was: DLL load failed while importing _multiarray_umath: The specified module could not be found.
PS D:\Do\Python\ML practice\iris> conda activate practica-mldl
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
If using 'conda activate' from a batch script, change your
invocation to 'CALL conda.bat activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- cmd.exe
- fish
- tcsh
- xonsh
- zsh
- powershell
See 'conda init --help' for more information and options.
IMPORTANT: You may need to close and restart your shell after running 'conda init'.
But when I open VScode through anaconda prompt by first activating the environment and opening VScode by typing code and running some programs, the program runs.
So from what I understand, simply changing the interpreter in VScode is not the same as opening VScode by activating first the environment. I thought by just changing the interpreter in VScode will work.
Is there a setup in VScode where I do not have to open VScode by activating the environments first so I can run python programs specific to that environment?
Thanks a lot!
Edit 1. Added error
Related
I have accessed Anaconda Prompt for the environment that I will be working.
Once there, I have changed the directory to the place where I have the grib files that I will be working with, in order to install cfgrib, I have used the following command:
conda install -c conda-forge cfgrib
As the Python module depends on ECMWF ecCodes binary library, in the same Anaconda Prompt, I ran the following command:
conda install -c conda-forge eccodes
Then, opened the file in Spyder, and tried to run this simple script:
import xarray as xr
ds = xr.open_dataset('download.grib', engine='cfgrib')
ds
But got the following error:
Can't read index file 'C:\Users\name\Desktop\data\download.grib.90c91.idx'
Traceback (most recent call last):
File "C:\Users\name\anaconda3\envs\Weather\lib\site-packages\cfgrib\messages.py", line 351, in from_indexpath_or_filestream
self = cls.from_indexpath(indexpath)
File "C:\Users\name\anaconda3\envs\Weather\lib\site-packages\cfgrib\messages.py", line 323, in from_indexpath
return pickle.load(file)
EOFError: Ran out of input
Then,
An error ocurred while starting the kernel
ECCODES ERROR : Unable to find boot.def. Context path=D:/bld/eccodes_1593015095851/_h_env/Library/share/eccodes/definitions
Possible causes:
‑ The software is not correctly installed
‑ The environment variable ECCODES_DEFINITION_PATH is defined but incorrect ecCodes assertion failed: `0' in D:\bld\eccodes_1593015095851\work\src\grib_context.c:226
What am I missing here?
Edit 1
The problem also happens if I use Visual Studio Code.
In the terminal, if I am inside the directory that the GRIB files are stored, and I activate the environment that I am working with:
conda activate Weather
And then:
& C:/Users/name/anaconda3/envs/Weather/python.exe c:/Users/name/Desktop/data/3_climate/2mtemp_open.py
It gives the same error as above.
As the error says, ECCODES_DEFINITION_PATH was not set.
As I am using Anaconda on Windows 10, the path is the following
C:/Users/[USER]/Anaconda3/envs/envgeo/Library/share/eccodes/definitions
In order to set the environment variable, one can simply run
setx ECCODES_DEFINITION_PATH "[ECCODES definition path/directory]"
This should solve the problem.
However, a new one may emerge. As the .grib file may take a lot to run, consider using the data in the format NetCDF.
I want to call my Anaconda Python from the Windows shell. The goal is to eventually call it from MATLAB using a system call, so I have to use the plain Windows shell, and not the "Anaconda prompt".
I have a simple Python script that I want to run, but it doesn't get past the import statements:
> "C:\ProgramData\Anaconda3\python.exe" lhs.py
Traceback (most recent call last):
File "lhs.py", line 8, in <module>
import numpy
File "C:\ProgramData\Anaconda3\lib\site-packages\numpy\__init__.py", line 140, in <module>
from . import _distributor_init
File "C:\ProgramData\Anaconda3\lib\site-packages\numpy\_distributor_init.py", line 34, in <module>
from . import _mklinit
ImportError: DLL load failed: The specified module could not be found.
EDIT
I made a simplified Python script (error.py) containing only one line:
import numpy
I then call it as:
"C:\ProgramData\Anaconda3\python.exe" error.py
TL;DR
C:\ProgramData\Anaconda3\condabin\activate.bat YOURENVIRONMENTNAME && python N:\Temp\lhs.py
Long Answer
There is a similar issue reported on github. I found this by searching for the last few lines of your message. It is about this:
File "C:\Users\hanna\Anaconda3\lib\site-packages\tensorflow\python_init.py",
line 47, in
import numpy as np
File "C:\Users\hanna\Anaconda3\lib\site-packages\numpy_init_.py", line 140, in
from . import _distributor_init
File "C:\Users\hanna\Anaconda3\lib\site-packages\numpy_distributor_init.py",
line 34, in
from . import _mklinit
There, they link to a conda troubleshooting page:
Error messages like
Intel MKL FATAL ERROR: Cannot load mkl_intel_thread.dll
Cause
NumPy is unable to load the correct MKL or Intel OpenMP runtime
libraries. This is almost always caused by one of two things:
The environment with NumPy has not been activated.
Another software vendor has installed MKL or Intel OpenMP
(libiomp5md.dll) files into the C:\Windows\System32 folder. These
files are being loaded before Anaconda's and they're not compatible.
If you are not activating your environments, start with doing that.
So let us try this first:
C:\\ProgramData\\Anaconda3\\condabin\\activate.bat
conda run -n yourenvironment C:\\path\\to\\your\\pythonfile\\lhs.py
(Yes, from a normal cmd terminal)
If that seems to work, you should be able to chain the two commands using &&. My own example looks like this:
F:\Programme\Programme\Anaconda3\condabin\activate.bat && conda run -n textrecognition N:\Temp\temp.py
This can be simplified further to
F:\Programme\Programme\Anaconda3\condabin\activate.bat textrecognition && python N:\Temp\temp.py
In case of the problem being number two, you have the option to load conda things before system32. This is supported in anaconda starting the following versions:
Python 2.7.15 build 14
Python 3.6.8 build 7
Python 3.7.2 build 8
To activate that, you need to set some environment variables to 1:
Control environment variables:
CONDA_DLL_SEARCH_MODIFICATION_ENABLE
CONDA_DLL_SEARCH_MODIFICATION_DEBUG
CONDA_DLL_SEARCH_MODIFICATION_NEVER_ADD_WINDOWS_DIRECTORY
CONDA_DLL_SEARCH_MODIFICATION_NEVER_ADD_CWD
To set variables on Windows, you may use either the CLI (Anaconda
Prompt, for example) or a Windows GUI.
CLI:
https://superuser.com/questions/79612/setting-and-getting-windows-environment-variables-from-the-command-prompt/79614
GUI:
http://www.dowdandassociates.com/blog/content/howto-set-an-environment-variable-in-windows-gui/
These should be set to a value of 1 to enable them. For example, in an
anaconda prompt terminal:
set CONDA_DLL_SEARCH_MODIFICATION_ENABLE=1
you need to activate your conda base in cmd before calling the script
call <path>\anaconda\Scripts\activate base
<path>\anaconda\python.exe <path>\scriptname.py
I am trying to create an executable file (exe) for a Python script that I written in PyCharm.
When I run the script from the PyCharm is working fine but when I try to run it as an individual .py or try to run the exe I am getting an error.
The issue I believe is with the "from infi.devicemanager import DeviceManager" library.
from infi.devicemanager import DeviceManager # Used for the retrievement of Device manager information
dm = DeviceManager()
dm.root.rescan()
devs = dm.all_devices # Get all the devices to a list called devs
for d in devs:
print (d.description)
I get following error:
PS C:\Python> python.exe .\tests.py
Traceback (most recent call last):
File ".\tests.py", line 1, in <module>
import infi.devicemanager # Used for the retrievement of Device manager information
ModuleNotFoundError: No module named 'infi'
PS C:\Python> pyinstaller -F .\tests.py
PS C:\Python\dist> .\tests.exe
Traceback (most recent call last):
File "tests.py", line 1, in <module>
ModuleNotFoundError: No module named 'infi'
[15072] Failed to execute script tests
Is there a way to include this library to the exe file so anyone without python can run this script?
I am open to suggestions.
Thank you in advance!
=== UPDATE ===
Full script can be found here
https://github.com/elessargr/k9-serial
My answer assumes that the interpreter that has infi.devicemanager is C:\Python\venv\Scripts\python.exe as stated by OP in the comments
So there is virtual environment named venv. You need to activate the virtual environment and install PyInstaller in it.
C:\Python>venv\Scripts\activate
(venv)C:\Python>
Note (venv) in front of your shell - that means virtual environment venv is activated
Now install PyInstaller
(venv)C:\Python>pip install pyinstaller
-- here it will install pyinstaller --
now you can test that both pyinstaller and infi.devicemanager are installed in venv
(venv)C:\Python>pip list
it should list both packages among some others. now
(venv)C:\Python>pyinstaller -F C:\Python\tests.py --hidden-import=infi.devicemanager
--here it will create the exe --
if I was right it should work now
EDIT: It looks like infi is using __import__(pkg_resources), so the command should be
(venv)C:\Python>pyinstaller -F C:\Python\tests.py --hidden-import=infi.devicemanager --hiden-import=pkg_resources
I have an annoying problem with PyCharm CE and naoqi. Following the installation instructions in Aldebaran Guide, I have configured my environment to work with this one.
I have installed the version of python (python 2.7.13) suggested by Aldebaran, I have written the .bash_profile using:
# Setting PATH for Python 2.7
# The original version is saved in .bash_profile.pysave
PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}"
export PATH
#NaoQI 2.5.5
export PYTHONPATH=${PYTHONPATH}:/Users/francesco/Documents/PyLibs/pynaoqi-python2.7-2.5.5.5-mac64/lib/python2.7/site-packages
export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/Users/francesco/Documents/PyLibs/pynaoqi-python2.7-2.5.5.5-mac64/lib
after that, I launch my code in python from Terminal (making sure that the right version of python is called when I type
$ python my_code.py
and all is working (I tried also with virtualenv and all works fine if I launch all from terminal).
So far so good but then comes the poison arrow. I use PyCharm CE like IDE, I have created a new project that use the same environment that works fine in terminal and the magic happens..
The first issue is:
/Users/francesco/Documents/PyEnv/pynaoqi255_python2713/bin/python /Users/francesco/PycharmProjects/PepperRobot/PepperRobot.py
Traceback (most recent call last):
File "/Users/francesco/PycharmProjects/PepperRobot/PepperRobot.py", line 5, in
import qi
ImportError: No module named qi
(Ok seriuosly this is the same environment that in terminal works)
I try to bypass the problem, adding the content of naoqi sdk in the virtualenv's site-package. Ok, the problem is bypassed.. But there is another problem:
/Users/francesco/Documents/PyEnv/pynaoqi255_python2713/bin/python /Users/francesco/PycharmProjects/PepperRobot/PepperRobot.py
Traceback (most recent call last):
File "/Users/francesco/PycharmProjects/PepperRobot/PepperRobot.py", line 5, in
import qi
File "/Users/francesco/Documents/PyEnv/pynaoqi255_python2713/lib/python2.7/site-packages/qi/init.py", line 88, in
from _qi import Application as _Application
ImportError: dlopen(/Users/francesco/Documents/PyEnv/pynaoqi255_python2713/lib/python2.7/site-packages/_qi.so, 2): Library not loaded: #loader_path/libqipython.dylib
Referenced from: /Users/francesco/Documents/PyEnv/pynaoqi255_python2713/lib/python2.7/site-packages/_qi.so
Reason: image not found
Process finished with exit code 1
I did not understand why...
I have also include in
Preferences -> console -> Python Console -> Environment Variables
the same variables included in .bash_profile but to no avail.
How can I solve this tedious problem ?
I have solved my problem editing run/debug configuration and putting here the environment variable DYLD_LIBRARY_PATH. All works fine.
After I broke my Ubuntu precise with a Cython compilation I like to keep the system Python clean. I like to have 2.7.x & 3.4.x besides each other and used Pyenv to have a global default interpreter independent from the system python. Now I also want to define local interpreters on a per project basis, usually done with pyenv local. Unfortunately my favorite IDE PyCharm does only support pyenv global, the local .python-version files are obviously not recognized by PyCharm.
So I tried to use the pyenv global interpreter in PyCharm with ~/.pyenv/bin/python-local-exec which works but unfortunately is already deprecated. When I then tried to create a virtualenv from the pyenv Python 3 global interpreter, it throwed the follwing error:
The following command was executed:
virtualenv.py /home/barrios/code/so/venv
The error output of the command:
pyenv: `python-local-exec' is deprecated and will be removed in the next release.
To upgrade: https://github.com/yyuu/pyenv/wiki/python-local-exec
Failed to import the site module
Traceback (most recent call last):
File "/home/barrios/code/so/venv/lib/python3.4/site.py", line 67, in <module>
import os
File "/home/barrios/code/so/venv/lib/python3.4/os.py", line 634, in <module>
from _collections_abc import MutableMapping
ImportError: No module named '_collections_abc'
Using base prefix '/home/barrios/.pyenv/versions/3.4.0b3'
New python executable in /home/barrios/code/so/venv/bin/python
ERROR: The executable /home/barrios/code/so/venv/bin/python is not functioning
ERROR: It thinks sys.prefix is '/home/barrios/.pyenv/bin' (should be '/home/barrios/code/so/venv')
ERROR: virtualenv is not compatible with this system or executable
As mentioned before, I don't want to install Python 3 into my Ubuntu system folders. Any ideas how to achieve that?
TNX a lot!
I'd suggest to use https://github.com/yyuu/pyenv-virtualenv to create virtualenv for a desired interpreter and then add it as a Python interpreter in PyCharm.