On Thu 18. Jun 2020 at 01:20, Mark Adams <mfad...@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 <mukkundsun...@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.mayhe...@gmail.com> wrote: >> >> Is the code valgrind clean? >> >> On Wed, 17 Jun 2020 at 23:25, MUKKUND SUNJII <mukkundsun...@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.mayhe...@gmail.com> wrote: >>> >>> >>> >>> On Wed 17. Jun 2020 at 21:21, MUKKUND SUNJII <mukkundsun...@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 <mfad...@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 <mukkundsun...@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 >>>> >>>> >>> >>
