C# is slow on arrays?

Question

I'm working with CT images, so I need to operate 3D arrays a lot, but found that C# deals with arrays extremely slow. I wrote a simple BFS test, based on https://stackoverflow.com/a/1056091:

struct Vector
{
    public int X, Y, Z;
}
int width = 512, height = 512, depth = 200;
public static int bfs(int[, ,] matrix)
{
    bool[, ,] visited = new bool[width, height, depth];
    int sum = 0;
    Queue<Vector> queue = new Queue<Vector>();
    queue.Enqueue(new Vector { X = 0, Y = 0, Z = 0 });
    while (queue.Count > 0)
    {
        Vector c = queue.Dequeue();
        int cx = c.X;
        int cy = c.Y;
        int cz = c.Z;
        sum += matrix[cx, cy, cz];
        int x, y, z;

        if ((x = cx - 1) >= 0 && !visited[x, cy, cz])
        { queue.Enqueue(new Vector { X = x, Y = cy, Z = cz }); visited[x, cy, cz] = true; }
        if ((y = cy - 1) >= 0 && !visited[cx, y, cz])
        { queue.Enqueue(new Vector { X = cx, Y = y, Z = cz }); visited[cx, y, cz] = true; }
        if ((z = cz - 1) >= 0 && !visited[cx, cy, z])
        { queue.Enqueue(new Vector { X = cx, Y = cy, Z = z }); visited[cx, cy, z] = true; }
        if ((x = cx + 1) < width && !visited[x, cy, cz])
        { queue.Enqueue(new Vector { X = x, Y = cy, Z = cz }); visited[x, cy, cz] = true; }
        if ((y = cy + 1) < height && !visited[cx, y, cz])
        { queue.Enqueue(new Vector { X = cx, Y = y, Z = cz }); visited[cx, y, cz] = true; }
        if ((z = cz + 1) < depth && !visited[cx, cy, z])
        { queue.Enqueue(new Vector { X = cx, Y = cy, Z = z }); visited[cx, cy, z] = true; }
    }
    return sum;
}
public static void TestTime<T, TR>(Func<T, TR> action, T obj, int iterations)
{
    Stopwatch stopwatch = Stopwatch.StartNew();
    for (int i = 0; i < iterations; ++i)
        action(obj);
    Console.WriteLine(action.Method.Name + " took " + stopwatch.Elapsed);
}
static void Main(string[] args)
{
    Random random = new Random();
    int[, ,] m1 = new int[width, height, depth];
    for (int x = 0; x < width; ++x)
        for (int y = 0; y < height; ++y)
            for (int z = 0; z < depth; ++z)
                m1[x, y, z] = random.Next();
    const int iterations = 1;
    TestTime<int[, ,], int>(bfs, m1, iterations);
    TestTime<int[, ,], int>(bfs, m1, iterations);
}

This takes ~23 secs (one iteration). Compiled with VS2012, "Release"d, optimized. Tried to write analogous C++ code (with stack allocated arrays), it takes ~0,08sec. DFS (with Stack instead of Queue) runs slower. 1D or jagged arrays give almost same results. I should note that continuous access (as in Why are multi-dimensional arrays in .NET slower than normal arrays?) runs fine, 100 iterations of [512x512x200] array in ~26 secs.

Why non-continuous array access is so slow in C#? Is there any way to speed it up?

Answer 1

I changed to using list+struct to see if it helped. It halved the time. I changed the multi-dimension array to to use a single dimension and hand-multiplied the indexer out. If anything, that made it worse.

struct Q
{
    public int X, Y, Z;
}
public static int bfs(int[, ,] matrix)
{
    int d1 = matrix.GetLength(0), d2 = matrix.GetLength(1), d3 = matrix.GetLength(2);
    var visited = new bool[d1, d2, d3];
    int sum = 0;
    var q = new List<Q>();
    q.Add(new Q());
    while (q.Count > 0)
    {
        var last = q[q.Count - 1];
        q.RemoveAt(q.Count - 1);
        int cx = last.X;
        int cy = last.Y;
        int cz = last.Z;
        sum += matrix[cx, cy, cz];
        int x, y, z;

        if ((x = cx - 1) >= 0 && !visited[x, cy, cz])
        { q.Add(new Q{X = x, Y = cy, Z = cz}); visited[x, cy, cz] = true; 
...