[Users] Problem with CarpetRegrid2/AMR

[Ian Hawke]

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?