[petsc-users] Regarding P4est

[Dave May]

On Thu 18. Jun 2020 at 01:20, Mark Adams <mfadams at lbl.gov> wrote:

> PETSc does take pains to keep it clean in Valgrind, to make it more
> useful ...
>

Yes of course!

As I understood, the code being discussed was derived / based on ex11, and
not identical to ex11 (eg flux definitions have changed). Hence there’s
some user code in the mix which is not guaranteed to be valgrind clean.





> And yes there is tree structure to this error, and p4est is a tree code.
>
> Try with uniform bathymetry, maybe your mapping is messed up by some
> recording by p4est.
>
>
> On Wed, Jun 17, 2020 at 6:47 PM MUKKUND SUNJII <mukkundsunjii at gmail.com>
> wrote:
>
>> No, I have not checked it using Valgrind. Perhaps it will help me trace
>> the problem.
>>
>> Regards,
>>
>> Mukkund
>>
>> On 18 Jun 2020, at 00:43, Dave May <dave.mayhem23 at gmail.com> wrote:
>>
>> Is the code valgrind clean?
>>
>> On Wed, 17 Jun 2020 at 23:25, MUKKUND SUNJII <mukkundsunjii at gmail.com>
>> wrote:
>>
>>> I agree with the structured nature of the noise. I did play around with
>>> the PetscFV implementation a bit to allow for the computation of different
>>> fluxes left and right side of every interface.
>>>
>>> Nevertheless it is indeed strange that the problem disappears when I use
>>> a PLEX dm.
>>>
>>> Regards,
>>>
>>> Mukkund
>>>
>>> On 17 Jun 2020, at 22:53, Dave May <dave.mayhem23 at gmail.com> wrote:
>>>
>>>
>>>
>>> On Wed 17. Jun 2020 at 21:21, MUKKUND SUNJII <mukkundsunjii at gmail.com>
>>> wrote:
>>>
>>>> Yes, precisely! I am not sure how I can replicate using the original
>>>> version of ex11.c because it does not support bathymetry.
>>>>
>>>> Regardless, to demonstrate the discrepancy, I have uploaded three
>>>> plots. The scenario is a lake at rest. Essentially, you have a varying
>>>> bathymetry but a level water surface. If the model is well balanced, then
>>>> the water surface height must not change. The description of the files are
>>>> below
>>>>
>>>> 1) Bathymetry.png : It shows you the bathymetry profile (z(x)) and the
>>>> water surface height (H = h+z(x)) at t = 0.
>>>> <Bathymetry.png>
>>>>
>>>> 2) Plex.png : This is the water surface height after 1 time step (0.007055
>>>> sec)  and the dm type is Plex. As you can see, the water surface
>>>> height is undisturbed as expected.
>>>> <Plex.png>
>>>>
>>>> 3) P4est.png : This is the result after 1 time step (same final time)
>>>> if I set the dm type as p4est. The noise is in the order of 1e-3 to be a
>>>> little more specific. Since its not specifically at the boundaries and more
>>>> or less spread throughout, it could indeed be noise introduced. But of
>>>> course I could be wrong.
>>>> <p4est.png>
>>>>
>>>>
>>> The (wrong) result has seemingly a lot of structure. Have you verified
>>> your code using p4est is valgrind clean? This looks too much like a weird
>>> indexing bug for me to not ask this question.
>>>
>>> Thanks,
>>> Dave
>>>
>>>
>>> Maybe this paints a better picture.
>>>>
>>>> Regards,
>>>>
>>>> Mukkund
>>>>
>>>> For your reference, the Riemann Solver is a modified version of the HLL
>>>> solver: *A simple well-balanced and positive numerical scheme for the
>>>> shallow-water system by **Emmanuel Audusse, Christophe Chalons,
>>>> Philippe Ung. *
>>>> (
>>>> https://www.intlpress.com/site/pub/files/_fulltext/journals/cms/2015/0013/0005/CMS-2015-0013-0005-a011.pdf
>>>> )
>>>>
>>>> On 17 Jun 2020, at 20:47, Mark Adams <mfadams at lbl.gov> wrote:
>>>>
>>>> So you get this noise with a regular grid in p4est. So the same grid as
>>>> will Plex, and you are not getting the same results.
>>>>
>>>> I don't know of any difference from p4est on a non-adapted grid. Can
>>>> you reproduce this with ex11?
>>>>
>>>> Matt and Toby could answer this better.
>>>>
>>>>
>>>> On Wed, Jun 17, 2020 at 1:33 PM MUKKUND SUNJII <mukkundsunjii at gmail.com>
>>>> wrote:
>>>> Greetings,
>>>>
>>>> I am a master’s student working on the shallow water model of the TS
>>>> example 'ex11.c' as part of my thesis. Therefore, I am working with
>>>> DMForest for the implementation of adaptive grids. I have a question and an
>>>> observation.
>>>>
>>>> I am trying to find relevant information about interpolation that takes
>>>> place through the routine DMForestTransferVec. Perhaps it could be my
>>>> inability to find it, but I am unable to locate the implementation of the
>>>> routine
>>>>
>>>> (forest->transfervec)(dmIn,vecIn,dmOut,vecOut,useBCs,time).
>>>>
>>>> Any information on this particular routine is highly appreciated.
>>>>
>>>> Furthermore, I have developed a well balanced Riemann Solver that
>>>> includes topography in the model. In the process of testing both the
>>>> non-adaptive and adaptive version, I found that my results differed when I
>>>> changed the type of DM. For instance, when I run a scenario in a fixed,
>>>> non-adaptive grid  with a DM of type 'P4est', I find that the well balanced
>>>> nature is lost due to small perturbations all across the domain. However,
>>>> this does not occur when I use a DM of type ‘plex’. Is there a radical
>>>> change in the routines between the two DM’s? This is not as much of a
>>>> question as it is an observation.
>>>>
>>>> Thank you for all of your suggestions!
>>>>
>>>> Regards,
>>>>
>>>> Mukkund
>>>>
>>>>
>>>
>>
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