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Meanwhile I was digging a little bit further into the problem and I really think there is a bug in OpenCV.

In Mat::create the following code is executed

MatAllocator *a = allocator, *a0 = getStdAllocator();

which calls getStdAllocator. This is implemented as:

MatAllocator* Mat::getStdAllocator()
{
    static MatAllocator * allocator = new StdMatAllocator();
    return allocator;
}

i.e. returning a static local variable. When getStdAllocator() is executed in parallel this may crash (in my case it simply sometimes returns NULL).

I can get my example running by ensuring that the static local variable is initialized first, i.e.

cv::MatAllocator *a0 = cv::Mat::getStdAllocator();

#pragma omp parallel for
for(int i = 0; i < 100; i++)
{
    cv::Mat blub;
    blub.create(3456, 5184, 16);
    cout << ".";
}

But it seems to be fixed here already: http://code.opencv.org/issues/4189