Calling a bash script which uses python and opencv

Hello,

I am trying to call a bash script on Ubuntu from Matlab. The script is itself a call to some python code in the form of

mpiexec -n 4 python $PY_SCRIPT_PATH $1 $2 $3 $4

The python code uses opencv, cuda, ...:

from sys import argv
import numpy as np
import time
import colorsys

import matplotlib.image as img
import matplotlib.pyplot as plt
import scipy.misc as scipy
import cv2

from Cheetah.Template import Template

import pycuda.compiler as nvcc
import pycuda.gpuarray as gpu
import pycuda.driver as cu

import pycuda.autoinit

from mpi4py import MPI
import math

The matlab terminal outputs

ImportError: /usr/lib/python2.7/dist-packages/cv2.so: undefined symbol: _ZTIN2cv5BRISKE

when I try to run the command. I tried reloading the .bashrc from the script to reset the environment variables with no luck. Does anyone know how to fix it?

Thanks

Answer 1

[Erik]

i ran into a possible explanation from this SO question that references trying to import opencv:

dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cv2.so, 2): Library not loaded: /opt/local/lib/libtiff.5.dylib
    Referenced from: /opt/local/lib/libopencv_highgui.2.4.dylib
    Reason: Incompatible library version: libopencv_highgui.2.4.dylib requires version 8.0.0 or later, but libtiff.5.dylib provides version 6.0.0

perhaps matlab executes system calls in some way that links against its old versions of libraries rather than the up to date ones you have installed?

you don't say whether the script runs fine when executed from a regular shell?

[Garoe Dorta]

The script runs fine in a regular shell. Thanks for your answer.

[Erik]

and do you use !, system(), unix(), or what? do these (or their outputs) differ?

[Erik]

did you get it running? i'm still trying to find a solution

Answer 2

[Erik]

forcing matlab to use your preferred libtiff may work -- on osx:

$ DYLD_INSERT_LIBRARIES=/opt/local/lib/libtiff.5.dylib /Applications/MATLAB_R2015a.app/bin/matlab

on linux i think it's LD_PRELOAD