[yt-dev] Matching points to grids

[Matthew Turk]

Hi John,

I think this looks pretty good for now, certainly for 2.x.

In 3.0 I want to eventually transition FLASH to the Octree geometry
structure, which would mean that particle location could all occur directly
inside Cython.  We'd also have a number of much faster particle selection
routines, which could eventually make it not necessary to directly sort or
select particles too strongly in advance, as long as a coarse index could
be built.

I say push it and we can move on from there.  If you want, one thing you
could absolutely do right now is construct a Cython routine that accepted:

x,y,z
left_edges, right_edges, parent_index

and then construct an octree from that, assigning particles as they came.

-Matt

On Saturday, November 17, 2012, John ZuHone wrote:

> By the way, I certainly think that there is much room for improvement, so
> anyone that would like to take a look at it and make suggestions is most
> welcome.
>
> On Nov 17, 2012, at 6:09 PM, Christopher Moody <cemoody at ucsc.edu> wrote:
>
> Hi John,
> That speed is similar to what I found. Brute force collision check would
> make (3x2x7000x10^6) ~ 10^10 floating point operations, which should take a
> few seconds on a modern single core (3Ghz*10seconds). Making an actually
> intelligent depth-first search should drop the number of grids to check for
> every particle by an order of magnitude. So we should really be able to
> beat a 4-minute gridding time, we just need to figure out what the
> bottleneck is. And of course this is applicable to particles in yt-3.0.
>
> chris
>
>
> On Sat, Nov 17, 2012 at 6:30 AM, John ZuHone <jzuhone at gmail.com> wrote:
>
> Chris,
>
> Since last night I've developed a working depth-first approach which is
> *reasonably* fast, but I think it depends on your definition of reasonable.
> :) It just did a FLASH dataset with ~7000 blocks and 10^6 points in about 4
> minutes.
>
> I'm going to try it out on a few more datasets, and I'm hoping to issue a
> PR for it today or tomorrow.
>
> Best,
>
> John
>
> On Nov 16, 2012, at 6:21 PM, Christopher Moody <cemoody at ucsc.edu> wrote:
>
> Hi John,
> I tried writing a cython routine that matched particles to grids a while
> back. It works in the opposite order as a recursive octree-like gridding.
> It starts with the highest-level most-refined grids, recording the grid ID
> that each particle belongs to. It skips previously gridded particles as it
> progresses to coarser grids. It's likely not faster than depth-first
> approach.
>
> It could be helpful, but it's terribly slow, despite several attempts to
> speed it up.
> Check out  assign_particles_to_cell_lists()
> in yt-hg/yt/utilities/lib/CICDeposit.pyx
>
>  chris
>
>
> On Fri, Nov 16, 2012 at 11:30 AM, Matthew Turk <matthewturk at gmail.com>wrote:
>
> Hi John,
>
> I think that would work fine for Enzo, we'd just need to iterate over
> root grids.
>
> -Matt
>
> On Fri, Nov 16, 2012 at 2:28 PM, John ZuHone <jzuhone at gmail.com> wrote:
> > Hi Matt,
> >
> > Would it work just to start at the top-level grids and then work down
> the tree, checking the children as you go? I know this would work for
> FLASH, but I'm not certain it would work for Enzo.
> >
> > John
> >
> > On Nov 16, 2012, at 2:14 PM, Matthew Turk <matthewturk at gmail.com> wrote:
> >
> >> Hi John,
> >>
> >> That's the ideal way, but we don't yet have the code to do that.  I
> >> would like to do that.  The fastest method would be to create a new
> >> version of find_values_at_points (which accepts an array) and make itj
> >> ust return grid indices.  This would do the NxM collision check of
> >> particles in grids.
> >>
> >> Writing an octree-aware particle finder would be a good idea.
> >> Necessary, even...
> >>
> >> -Matt
> >>
> >> On Fri, Nov 16, 2012 at 1:07 PM, John ZuHone <jzuhone at gmail.com> wrote:
> >>> I did know about that, but given, say, a million points, would that be
> >>> *fast*? I need to look at what it does I guess.
> >>>
> >>> In FLASH, what'd we'd normally do is start at the top level and
> traverse
> >>> down the octree until we found the block.
> >>>
> >>> On Nov 16, 2012, at 1:02 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
> >>>
> >>> Hi John,
> >>>
> >>> Yes, you can use pf.h.find_point() to do that.  There's some
> documentation
> >>> on it here:
> >>>
> http://yt-project.org/doc/analyzing/low_level_inspection.html#finding-data-at-fixed-points
> >>>
> >>> -Nathan
> >>>
> >>> On Nov 16, 2012, at 10:00 AM, John ZuHone wrote:
> >>>
> >>> Hi all,
> >>>
> >>> Do we have anything in yt right now that, given a set of points,
> *quickly*
> >>> finds out which grids they belong to?
>
>
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