[Users] Problem with CarpetRegrid2/AMR

Tue Sep 13 17:45:16 CDT 2011

Hal

Were you running with multiple processes?

-erik

On Tue, Sep 13, 2011 at 12:00 PM, Hal Finkel <hfinkel at anl.gov> wrote:
> Ian,
>
> I'd not found the problem yet. Hopefully this will be the hint we need
> to get this fixed.
>
> Thanks again,
> Hal
>
> On Tue, 2011-09-13 at 15:31 +0100, Ian Hawke wrote:
>> Erik, Hal,
>>
>> Did you have any luck tracking down this error? I've just come back to
>> this and am seeing the same error message; it appears to arise when two
>> grids on a refined level merge, as in:
>>
>>     [3][0][0]   exterior: [-0.010000,-0.020000,-0.020000] :
>> [0.000000,0.020000,0.020000] : [0.001250,0.001250,0.001250]
>>     [3][0][1]   exterior: [0.010000,-0.020000,-0.020000] :
>> [0.040000,0.020000,0.020000] : [0.001250,0.001250,0.001250]
>>
>> becomes
>>
>>   [3][0][0]   exterior: [-0.010000,-0.020000,-0.020000] :
>> [0.040000,0.020000,0.020000] : [0.001250,0.001250,0.001250]
>>
>> It seems that the old grids are destroyed before the data is
>> copied/populated in Recompose (either that or the old grid structure is
>> not referred to in the data transfer).
>>
>> Ian
>>
>> On 07/09/11 01:03, Erik Schnetter wrote:
>> > Hal
>> >
>> > This is where numbers are assigned to components. The communication
>> > schedule decides which component needs to send data to which other
>> > component (which may be located on another process or not); this
>> > schedule is created for each refinement level independently, and may
>> > (if there is an error) refer to component numbers that don't exist.
>> > This schedule is set up in dh.cc.
>> >
>> > Can you send me the example you are currently running (your source
>> > code and parameter file)? I will try to give it a try.
>> >
>> > -erik
>> >
>> > On Tue, Sep 6, 2011 at 7:44 PM, Hal Finkel<hfinkel at anl.gov>  wrote:
>> >> On Thu, 2011-09-01 at 15:16 -0400, Erik Schnetter wrote:
>> >>> On Thu, Sep 1, 2011 at 3:05 PM, Hal Finkel<hfinkel at anl.gov>  wrote:
>> >>>> On Thu, 2011-09-01 at 14:25 -0400, Erik Schnetter wrote:
>> >>>>> On Thu, Sep 1, 2011 at 11:51 AM, Hal Finkel<hfinkel at anl.gov>  wrote:
>> >>>>>> On Thu, 2011-09-01 at 11:37 -0400, Erik Schnetter wrote:
>> >>>>>>> On Thu, Sep 1, 2011 at 10:53 AM, Hal Finkel<hfinkel at anl.gov>  wrote:
>> >>>>>>>> On Tue, 2011-08-30 at 21:06 -0400, Erik Schnetter wrote:
>> >>>>>>>>> On Tue, Aug 30, 2011 at 5:28 PM, Hal Finkel<hfinkel at anl.gov>  wrote:
>> >>>>>>>>>> Could I also decrease the block size? I currently have
>> >>>>>>>>>> CarpetRegrid2::adaptive_block_size = 4, could it be smaller than that?
>> >>>>>>>>>> Is there a restriction based on the number of ghost points?
>> >>>>>>>>> Yes, you can reduce the block size. I assume that both the regridding
>> >>>>>>>>> operation and the time evolution will become slower if you do that,
>> >>>>>>>>> because more blocks will have to be handled.
>> >>>>>>>> Regardless of what I do, once we get past the first coarse time step,
>> >>>>>>>> the program seems to "hang" at "INFO (Carpet): [ml=0][rl=0][m=0][tl=0]
>> >>>>>>>> Regridding map 0...".
>> >>>>>>>>
>> >>>>>>>> Overall, it is in dh::regrid(do_init=true). It spends most of its time
>> >>>>>>>> in bboxset<int, 3>::normalize() and, specifically, mostly in the loop:
>> >>>>>>>> for (typename bset::iterator nsi = nbs.begin(); nsi != nbs.end(); ++
>> >>>>>>>> nsi). The normalize() function does exit, however, so it is not hanging
>> >>>>>>>> in that function.
>> >>>>>>>>
>> >>>>>>>> The core problem seems to be that it takes a long time to execute:
>> >>>>>>>> boxes  = boxes .shift(-dir) - boxes;
>> >>>>>>>> in dh::regrid(do_init=true). Probably because boxes has 129064 elements.
>> >>>>>>>> The coarse grid is now only 30^3 and I've left the regrid box size at 4.
>> >>>>>>>> I'd think, then, that the coarse grid should have a maximum of 30^3/4^3
>> >>>>>>>> ~ 420 refinement regions.
>> >>>>>>>>
>> >>>>>>>> What is the best way to figure out what is going on?
>> >>>>>>> Hal
>> >>>>>>>
>> >>>>>>> Yes, this function is very slow. I did not expect it to be
>> >>>>>>> prohibitively slow. Are you compiling with optimisation enabled?
>> >>>>>> I've tried with optimizations enabled (and without for debugging).
>> >>>>>>
>> >>>>>>> The bboxset represents the set of refined regions, and it is
>> >>>>>>> internally represented as a list of bboxes (regions). Carpet performs
>> >>>>>>> set operations on these (intersection, union, complement, etc.) to
>> >>>>>>> determine the communication schedule, i.e. which ghost zones of which
>> >>>>>>> bbox need to be filled from which other bbox. Unfortunately, the
>> >>>>>>> algorithm used for this is O(n^2) in the number of refined regions,
>> >>>>>>> and set operations when implemented via lists themselves are O(n^2) in
>> >>>>>>> the set size, leading to a rather unfortunate overall complexity. The
>> >>>>>>> only cure is to reduce the number of bboxes (make them larger) and to
>> >>>>>>> regrid fewer times.
>> >>>>>> This is what I suspected, but nevertheless, is there something wrong?
>> >>>>>> How many boxes do you expect that I should have? The reason that it does
>> >>>>>> not finish, even with optimizations, is that there are 129K boxes in the
>> >>>>>> loop (that's at least 16 billion box normalizations?).
>> >>>>>>
>> >>>>>> The coarse grid is only 30^3, and the regrid box size is 4, so at
>> >>>>>> maximum, there should be ~400 level one boxes. Even if some of those
>> >>>>>> have level 2 boxes, I don't understand how there could be 129K boxes.
>> >>>>> The refinement structure itself should have one bbox per refined 4^3
>> >>>>> box, and both CarpetRegrid2 and CarpetLib would try to combine these
>> >>>>> into fewer boxes where possible, i.e. where one can form rectangles or
>> >>>>> larger cubes. I would thus expect no more than (30/4)^2 = 64 bboxes on
>> >>>>> level one.
>> >>>> That makes sense. I think that there is a bug somewhere which is causing
>> >>>> the box set to be much too big. Furthermore, it does not happen on every
>> >>>> run, only sometimes. When it does not happen, I hit another bug after a
>> >>>> few coarse timesteps:
>> >>>>
>> >>>> I get a range-check exception from std::vector in a call to:
>> >>>> gh::get_local_component (rl=1, c=8)
>> >>>> the problem is that this returns:
>> >>>> local_components_.AT(rl).AT(c);
>> >>>> and local_components_[1].size() is 8
>> >>>> The call to get_local_component is coming from ggf::transfer_from_all
>> >>>> at:
>> >>>> int const lc2 = h.get_local_component(rl2,c2);
>> >>>> where c2 is from psend.component.
>> >>>> So it looks like there is an off-by-one error somewhere.
>> >>> Very strange. This code should be quite solid by now. psend is set in
>> >>> the file dh.cc in thorn Carpet/CarpetLib; there is one (large) routine
>> >>> that calculates the communication schedule. Some of the indexing
>> >>> errors there in the past included confusing the number of components
>> >>> on different refinement levels, which led to indexing errors such as
>> >>> the one you describe.
>> >> The bad component numbers are not coming from:
>> >> preg.component = tmpncomps.AT(m)++;
>> >> in Carpet/src/Recompose.cc
>> >>
>> >> Where else are the component numbers assigned?
>>
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>
> --
> Hal Finkel
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
> 1-630-252-0023
> hfinkel at anl.gov
>
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-- 
Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/