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I just did some small test. The following code performs exactly what you want, creating a large sized matrix:

#include "opencv2\opencv.hpp";

using namespace std;
using namespace cv;

int _tmain(int argc, _TCHAR* argv[])
{
    Mat test_matrix = Mat::zeros(100000, 5000, CV_8UC1);
    cout << "It works!" << endl;

    return 0;
}

It creates a matrix of zeros (with possible integer values as descriptor value) the size of the descriptor has been arbitrarily set to 5000 which is large, but could even be larger.

I guess you are running in problems with your clustering? Care to explain in more detail?