I'm trying to install mpi4py and have followed the installation instructions using pip found here: http://mpi4py.scipy.org/docs/usrman/install.html#using-pip-or-easy-install
I'm running a virtualenv with python 2.7.10 on Mac OS 10.11.6, and have installed mpich3 using homebrew.
This is the error when I attempt to run a test:
Lorens-MBP:mpi4py-mpi4py-b9fccf29258a lorensheets$ ../bin/python test/runtests.py
Traceback (most recent call last):
File "test/runtests.py", line 257, in <module>
sys.exit(main())
File "test/runtests.py", line 244, in main
package = import_package(options, pkgname)
File "test/runtests.py", line 109, in import_package
import mpi4py.MPI
ImportError: dlopen(/Users/lorensheets/Desktop/fresh/virtual/lib/python2.7/site-packages/mpi4py/MPI.so, 2): Library not loaded: /
Users/lorensheets/opt/usr/local/lib/libmpi.20.dylib
Referenced from: /Users/lorensheets/Desktop/fresh/virtual/lib/python2.7/site-packages/mpi4py/MPI.so
Reason: image not found
Try installing openmpi instead of mpich3
Related
I'm using my company's VM which already has Python 2.7 (comes with the OS) and Python 3.6.13 (Installed by the company)
Recently, there is a need to upgrade an application to latest version of Python ie: 3.10.2
So, I installed Python 3.10.2 in a local directory inside my $HOME. I referred to this link for the installation link.
While 2.7 & 3.6 are already there in the system.
Now, when I try to create a VENV with this python version (3.10.2), I see this error:
Traceback (most recent call last):
File "/export/home/sdc/python_versions/python310/python/lib/python3.10/subprocess.py", line 69, in <module>
import msvcrt
ModuleNotFoundError: No module named 'msvcrt'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/export/home/sdc/python_versions/python310/python/lib/python3.10/runpy.py", line 187, in _run_module_as_main
mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
File "/export/home/sdc/python_versions/python310/python/lib/python3.10/runpy.py", line 146, in _get_module_details
return _get_module_details(pkg_main_name, error)
File "/export/home/sdc/python_versions/python310/python/lib/python3.10/runpy.py", line 110, in _get_module_details
__import__(pkg_name)
File "/export/home/sdc/python_versions/python310/python/lib/python3.10/venv/__init__.py", line 10, in <module>
import subprocess
File "/export/home/sdc/python_versions/python310/python/lib/python3.10/subprocess.py", line 74, in <module>
import _posixsubprocess
ModuleNotFoundError: No module named '_posixsubprocess'
I found some solutions like this one: link but I cannot figure out how it will translate in my case since my installation directory is not /usr/local/... It is $HOME/path/to/dir
Python on Linux does not have the msvcrt module at all. It's strictly Windows only. You seem to have miscompiled your Python somehow, since it also doesn't have the _posixsubprocess module (and msvcrt is used for Windows detection in subprocess.py).
May I recommend using pyenv or asdf for custom Python versions? They're less likely to miscompile Python.
My environment specs
python --version
Python 3.7.6
anaconda --version
anaconda Command line client (version 1.7.2)
sw_vers
ProductName: Mac OS X
ProductVersion: 10.15.2
BuildVersion: 19C57
I installed camelot from conda-forge
using the command below.
conda install -c conda-forge camelot-py
Attaching the logs when I try to import camelot for pdf parsing and text extraction purposes.
Traceback (most recent call last):
File "/~/PycharmProjects/Utilities/rosblancos/pdf-utilities/pdf-element-extractor.py", line 1, in <module>
import camelot
File "/~/.conda/envs/Utilities/lib/python3.7/site-packages/camelot/__init__.py", line 6, in <module>
from .io import read_pdf
File "/~/.conda/envs/Utilities/lib/python3.7/site-packages/camelot/io.py", line 5, in <module>
from .handlers import PDFHandler
File "/~/.conda/envs/Utilities/lib/python3.7/site-packages/camelot/handlers.py", line 9, in <module>
from .parsers import Stream, Lattice
File "/~/.conda/envs/Utilities/lib/python3.7/site-packages/camelot/parsers/__init__.py", line 4, in <module>
from .lattice import Lattice
File "/~/.conda/envs/Utilities/lib/python3.7/site-packages/camelot/parsers/lattice.py", line 27, in <module>
from ..image_processing import (
File "/~/.conda/envs/Utilities/lib/python3.7/site-packages/camelot/image_processing.py", line 5, in <module>
import cv2
ImportError: dlopen(/~/.conda/envs/Utilities/lib/python3.7/site-packages/cv2.cpython-37m-darwin.so, 2): Library not loaded: #rpath/libglib-2.0.0.dylib
Referenced from: /~/.conda/envs/Utilities/lib/libharfbuzz.0.dylib
Reason: Incompatible library version: libharfbuzz.0.dylib requires version 5601.0.0 or later, but libglib-2.0.0.dylib provides version 0.0.0
Process finished with exit code 1
I googled the error above and found this issue. However, I am unable to solve this issue as I am not able to find out what I need to do with the file named libglib.
Doing this worked for me:
pip install opencv-python
I am trying to import igraph but it keeps throwing this error at me:
>>> import igraph
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.6/site-packages/igraph/__init__.py",
line 36, in <module>
from igraph.clustering import *
File "/usr/local/lib/python3.6/site-packages/igraph/clustering.py",
line 36, in <module>
from igraph.drawing.colors import ClusterColoringPalette
File "/usr/local/lib/python3.6/site-
packages/igraph/drawing/__init__.py", line 27, in <module>
from igraph.drawing.graph import DefaultGraphDrawer
File "/usr/local/lib/python3.6/site-
packages/igraph/drawing/graph.py", line 27, in <module>
from igraph.drawing.edge import ArrowEdgeDrawer
File "/usr/local/lib/python3.6/site-packages/igraph/drawing/edge.py",
line 17, in <module>
cairo = find_cairo()
File "/usr/local/lib/python3.6/site-
packages/igraph/drawing/utils.py", line 413, in find_cairo
module = __import__(module_name)
File "/usr/local/lib/python3.6/site-packages/cairocffi/__init__.py",
line 41, in <module>
cairo = dlopen(ffi, 'cairo', 'cairo-2')
File "/usr/local/lib/python3.6/site-packages/cairocffi/__init__.py",
line 38, in dlopen
raise OSError("dlopen() failed to load a library: %s" % ' /
'.join(names))
OSError: dlopen() failed to load a library: cairo / cairo-2
I have tried to follow this guide to install cairo but it throws this error and doesn't solve the igraph import issue: error: mandatory image surface backend feature could not be enabled
I have also tried to install pycairo but that resulted in no module founds: cairo, which brought me back to square one.
I tried running sudo port install cairo as per https://cairographics.org/download/ instructions. But that results in Error: Port cairo not found
My sys config:
MacOS High Sierra 10.13.1
Python 3.6
python-igraph 0.7.1
I am clueless as to what can be the issue. Any help would be highly appreciated. Thank you :)
Thanks to #Aiven I have managed to solve my issue. If anyone ever comes across the same problem, this have done the trick for me:
brew install cairo
brew install py2cairo
brew install igraph (install C-core)
sudo pip install python-igraph (install igraph for python)
I had some problems with upgrading matplotlib recently so I ended up installing different versions of Python on my Mac (Sierra) via brew, and then uninstalled afterwards. However, now matplotlib works (2.0.2) but whenever I run a particular python script that used to work I get an error which I didn't have before:
Traceback (most recent call last):
File "sim.py", line 254, in <module>
main()
File "sim.py", line 118, in main
db = shelve.open('.sim_balance', 'c')
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shelve.py", line 243, in open
return DbfilenameShelf(filename, flag, protocol, writeback)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shelve.py", line 227, in __init__
Shelf.__init__(self, anydbm.open(filename, flag), protocol, writeback)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/anydbm.py", line 84, in open
mod = __import__(result)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/dbhash.py", line 7, in <module>
import bsddb
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/bsddb/__init__.py", line 67, in <module>
import _bsddb
ImportError: No module named _bsddb
According to my searches online this has something to do with my brew installed python interfering? I also deleted all my files in /Library/Python/2.7/site-packages yesterday which may have caused this as well.
I have tried homebrew brew install berkeley-db but then pip install bsddb3 yields:
Terrys-MBP:site-packages Terry$ pip install bsddb3
Collecting bsddb3
Using cached bsddb3-6.2.4.tar.gz
Complete output from command python setup.py egg_info:
Can't find a local Berkeley DB installation.
(suggestion: try the --berkeley-db=/path/to/bsddb option)
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/m5/1fg5rnj11_9cz5pntlqlwzyc0000gn/T/pip-build-elBAFK/bsddb3/
EDIT: Solved. Installed anaconda, installed bsddb via conda install and everything is working now.
Solved. I Installed anaconda, installed bsddb via conda install and everything is working now.
I am tyying to install anaconda on my mac but at the last step of installtion it gives me following error:
installing: conda-env-2.4.5-py27_0 ...
Python 2.7.11 :: Continuum Analytics, Inc.
creating default environment...
Traceback (most recent call last):
File "/Users/sdb99/anaconda2/pkgs/conda-4.0.5-py27_0/lib/python2.7/site-packages/conda/install.py", line 37, in <module>
import subprocess
File "/Users/sdb99/anaconda2/pkgs/python-2.7.11-0/lib/python2.7/subprocess.py", line 430, in <module>
import pickle
File "/Users/sdb99/anaconda2/pkgs/python-2.7.11-0/lib/python2.7/pickle.py", line 1272, in <module>
import binascii as _binascii
ImportError: dlopen(/Users/sdb99/anaconda2/pkgs/python-2.7.11-0/lib/python2.7/lib-dynload/binascii.so, 2): Library not loaded: #loader_path/../../libz.1.dylib
Referenced from: /Users/sdb99/anaconda2/pkgs/python-2.7.11-0/lib/python2.7/lib-dynload/binascii.so
Reason: image not found
Any idea how i can get ahead from here?
Thanks!
Just update python to the next version and try installing Anaconda again.
I had python 2.7 and then I updated it to python 3 and I was able to install Anaconda graphical installer successfully.