[yt-users] Performance when using derived fields

Daniel Fenn dsfenn at gmail.com
Fri Nov 28 08:19:33 PST 2014 

Thanks everyone for your help.

Nathan, I'm glad you were able to reproduce the behavior. I'm following the
issue that you created to keep updated.

Matt, I'll be sure to give periodic reminders if I don't hear anything for
a while. This functionality would be extremely helpful to me, but it's not
really feasible with the current speeds, so it's something I have a strong
incentive to keep on top of.

Thanks again,

Dan

2014-11-27 15:53 GMT-05:00 Nathan Goldbaum <nathan12343 at gmail.com>:

> I've reproduced similar timings using a FLASH dataset that I think is
> smaller than the one you're working with.  Follow the issue I've created to
> track this here:
>
>
> https://bitbucket.org/yt_analysis/yt/issue/944/slices-of-fields-that-need-ghost-zones-are
>
> Thanks for the report Dan!  Hopefully now that we have a test script that
> shows similar timings, we should be able to work on making this faster.
>
> On Thu, Nov 27, 2014 at 11:39 AM, Kacper Kowalik <xarthisius.kk at gmail.com>
> wrote:
>
>> On 11/27/2014 01:31 PM, Matthew Turk wrote:
>> > Hi Dan (and Nathan),
>> >
>> > I take that back, I was looking at the wrong file.  IO is a very small
>> > portion of the time -- a lot of it is spent in units-related
>> > activities.  I'm going to dig in to see what the time is spent in, but
>> > I think there is likely some location where a lot of teeny tiny unit
>> > operations are happening, over and over and over, and that's killing
>> > the performance.  Looks like it's in sanitize_units_add and
>> > sanitize_units_mul, which gets called in data_containers.py (line 549)
>> > in the selector creation.
>> >
>> > Following that further down, I believe the issue is inside the
>> > RegionSelector, which gets generated a ton of times, and which is
>> > doing all unitful operations even after converting the values to the
>> > units it knows they should be in.  I think this might be fixable by
>> > using the .d attributes inside the RegionSelector __init__.
>> >
>> > Dan, if you get an example of this working with the sample datasets on
>> > the website, that would be very useful to work on.
>> >
>> > Kacper, what do you think about adding speed tests to the CI system?
>>
>> It's already there, see for example [1]. There's one "but"... we would
>> need pretty decent box to make those kind of tests meaningful. I bet
>> that 99.99% of fluctuation in [1] are caused by buildbox load rather
>> code changes.
>>
>> Cheers,
>> Kacper
>>
>> [1]
>>
>> http://tests.yt-project.org/job/py2.7-yt-3.0_answer.enzo.moving7/lastCompletedBuild/testReport/history/
>>
>> > -Matt
>> >
>> > On Thu, Nov 27, 2014 at 2:17 PM, Matthew Turk <matthewturk at gmail.com>
>> wrote:
>> >> Hi Dan,
>> >>
>> >> Looking this over, I think the problem is definitely that the ghost
>> >> zone generation is currently quite stupid in 3.0.  We're revving up
>> >> for a 3.1 release, but I think for 3.2 or even within the 3.1 cycle we
>> >> can aim to have this fixed; I've implemented some simple caching that
>> >> should speed it up, but which has some issues presently that keep it
>> >> from being fully functional and effective.
>> >>
>> >> One issue that we've (well, I say "we" but I'm the most guilty) had
>> >> lately is keeping track of things and ensuring that blockers and
>> >> important new features are added with reasonable time.  This has come
>> >> up repeatedly in the user survey that's currently out.  You've been in
>> >> IRC lately and I wonder if maybe you could help us to keep track of
>> >> this, by reminding me once in a while if it slips off the radar?  It
>> >> seems the bug tracker is not the best place, and making sure that we
>> >> have the underscoring that comes from mentioning and communicating can
>> >> really help to prioritize things.
>> >>
>> >> -Matt
>> >>
>> >> On Thu, Nov 27, 2014 at 10:26 AM, Daniel Fenn <dsfenn at gmail.com>
>> wrote:
>> >>> Hi Nathan,
>> >>>
>> >>> I've attached the html output of pyprof2html. I did it for two
>> cases--a
>> >>> large file on a fast disk, and a somewhat smaller file on a slower
>> disk. In
>> >>> both cases, I only used one processor. The output is not real
>> meaningful to
>> >>> me, since I'm not familiar with the code, and I'm not much of a python
>> >>> programmer.
>> >>>
>> >>> I'll work on doing this with one of the yt datasets, and let you know
>> how it
>> >>> goes.
>> >>>
>> >>> Thanks for your help.
>> >>>
>> >>> Dan
>> >>>
>> >>> 2014-11-27 0:08 GMT-05:00 Nathan Goldbaum <nathan12343 at gmail.com>:
>> >>>>
>> >>>>
>> >>>>
>> >>>> On Wed, Nov 26, 2014 at 8:09 PM, Daniel Fenn <dsfenn at gmail.com>
>> wrote:
>> >>>>>
>> >>>>> Hi everyone. Is it normal for slices to take substantially longer
>> to be
>> >>>>> created if they're made from a derived field rather than an
>> intrinsic one?
>> >>>>>
>> >>>>> Specifically, I'm having an issue creating an axis-aligned slice
>> using
>> >>>>> the divergence of the velocity field. It's taking around 6.5
>> minutes just to
>> >>>>> make the slice, whereas if I use temperature or density, it takes
>> around 10
>> >>>>> seconds or so for the same dataset.
>> >>>>
>> >>>>
>> >>>> Velocity divergence is particularly expensive because it needs ghost
>> >>>> zones, which must be filled in using cascading interpolation.
>> Depending on
>> >>>> the AMR structure in your data, this might be quite expensive.
>> >>>>
>> >>>> That said, 6.5 minutes for a slice is pretty bad.
>> >>>>
>> >>>> Is there any chance you can profile the execution of your script? If
>> you
>> >>>> run your script like so:
>> >>>>
>> >>>> $ python -m cProfile myscript.py
>> >>>>
>> >>>> you should get a summary printed to stdout of where the interpreter
>> is
>> >>>> spending most of its time. You can also visualize this in more depth
>> if you
>> >>>> dump the profile data to a file, and then use pyprof2html or
>> snakeviz to
>> >>>> load and display the data, e.g:
>> >>>>
>> >>>> $ python -m cProfile -o out.cprof myscript.py
>> >>>> $ pyprof2html out.cprof
>> >>>>
>> >>>> cProfile comes with pyhon, but pyp4orf2html and snakeviz must be
>> installed
>> >>>> separately using pip.
>> >>>>
>> >>>> It would be great if you could file an issue about this.  Even
>> better if
>> >>>> you can reproduce it using one of the test datasets on
>> yt-project.org/data
>> >>>> and attach a script that we can run ourselves.
>> >>>>
>> >>>>>
>> >>>>>
>> >>>>> I also notice that the amount of time it takes is not dependent on
>> the
>> >>>>> number of processors I'm using. I've used 1, 12, and 24 processors,
>> with
>> >>>>> identical results, even though I'm calling enable_parallelism(),
>> and I can
>> >>>>> see that all the processes are running.
>> >>>>>
>> >>>>>
>> >>>>> I read in the docs that slice operations aren't generally done in
>> >>>>> parallel, but in this case it seems that maybe it would be
>> beneficial. A
>> >>>>> similar operation in VisIt completes much faster, so I'm wondering
>> if I've
>> >>>>> misconfigured something, or if there is something I can do to speed
>> things
>> >>>>> up.
>> >>>>>
>> >>>>> I'd appreciate any thoughts anyone has on the subject.
>> >>>>>
>> >>>>> Thanks,
>> >>>>>
>> >>>>> Dan
>> >>>>>
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