[MOAB-dev] iMesh_stepIter

[Steve Jackson]

On Feb 29, 2012, at 12:42 , James Porter wrote:

> On Wed, 2012-02-29 at 10:33 -0600, Steve Jackson wrote:
>> After using pytaps to build a structured mesh of size 100x100x100, I
>> walked over the whole mesh in a non-standard iteration order.  My
>> iteration algorithm works as follows:
>> 
>> * Find the i,j,k coordinates of the next mesh element.
>> * Compute N, the offset from the zeroth hexahedron in the mesh, based
>> on i, j, and k.
>> * Advance a pytaps array iterator N steps using a single call to
>> stepIter.
>> * Return the first item from this pytaps iterator, and reset the
>> iterator.
>> 
>> The bad news: while a standard pytaps iterator can walk over a 1
>> million element mesh in under a second, this customized approach takes
>> more than ten minutes.
> 
> Do you know where the bottleneck in your algorithm is?

I believe it's in the iterator functions:

* If I only compute each N, the algorithm takes 15 seconds for 1M elements.  (Slow, but not beyond reason.)
* But if I use each computed N to access the pytaps iterator, resetting the iterator each time, it takes 800 seconds.

I'm not sure which of the iterator functions (stepIter, next, or reset) is the slowest.   My system, unfortunately, doesn't seem to have the python profile package installed.  I can get you the code if you're interested in trying it.

(I realize there's a more efficient algorithm that only calls reset() when N is smaller than the previous N, and advances by (N - last_N) otherwise.  But I can't imagine that'd give me any better than a 2x speedup, and I need at least a 30x speedup.)
~S