On Thu, Dec 22, 2022 at 3:08 PM Matteo Semplice < [email protected]> wrote:
> > Il 22/12/22 20:06, Dave May ha scritto: > > > > On Thu 22. Dec 2022 at 10:27, Matteo Semplice < > [email protected]> wrote: > >> Dear Dave and Matt, >> >> I am really dealing with two different use cases in a code that will >> compute a levelset function passing through a large set of points. If I had >> DMSwarmSetMigrateType() and if it were safe to switch the migration mode >> back and forth in the same swarm, this would cover all my use cases here. >> Is it safe to add it back to petsc? Details below if you are curious. >> >> 1) During preprocessing I am loading a point cloud from disk (in whatever >> order it comes) and need to send the particles to the right ranks. Since >> the background DM is a DMDA I can easily figure out the destination rank. >> This would be covered by your suggestion not to attach the DM, except that >> later I need to locate these points with respect to the background cells in >> order to initialize data on the Vecs associated to the DMDA. >> >> 2) Then I need to implement a semilagrangian time evolution scheme. For >> this I'd like to send particles around at the "foot of characteristic", >> collect data there and then send them back to the originating point. The >> first migration would be based on particle coordinates >> (DMSwarmMigrate_DMNeighborScatter and the restriction to only neighbouring >> ranks is perfect), while for the second move it would be easier to just >> send them back to the originating rank, which I can easily store in an Int >> field in the swarm. Thus at each timestep I'd need to swap migrate types in >> this swarm (DMScatter for moving them to the feet and BASIC to send them >> back). >> > > When you use BASIC, you would have to explicitly call the point location > routine from your code as BASIC does not interact with the DM. > > Based on what I see in the code, switching migrate modes between basic > and dmneighbourscatter should be safe. > > If you are fine calling the point location from your side then what you > propose should work. > > If I understood the code correctly, BASIC will just migrate particles > sending them to what is stored in DMSwarmField_rank, right? That'd be easy > since I can create a SWARM with all the data I need and an extra int field > (say "original_rank") and copy those values into DMSwarmField_rank before > calling migrate for the "going back" step. After this backward migration I > do not need to locate particles again (e.g. I do not need > DMSwarmSortGetAccess after the BASIC migration, but only after the > DMNeighborScatter one). > > Thus having back DMSwarmSetMigrateType() should be enough for me. > > Hi Matteo, I have done this in https://gitlab.com/petsc/petsc/-/merge_requests/5941 I also hope to get the fix for your DMDA issue in there. Thanks, Matt > Thanks > > Matteo > > > Cheers > Dave > > > >> Thanks >> >> Matteo >> Il 22/12/22 18:40, Dave May ha scritto: >> >> Hey Matt, >> >> On Thu 22. Dec 2022 at 05:02, Matthew Knepley <[email protected]> wrote: >> >>> On Thu, Dec 22, 2022 at 6:28 AM Matteo Semplice < >>> [email protected]> wrote: >>> >>>> Dear all >>>> >>>> please ignore my previous email and read this one: I have better >>>> localized the problem. Maybe DMSwarmMigrate is designed to migrate >>>> particles only to first neighbouring ranks? >>>> >>> Yes, I believe that was the design. >>> >>> Dave, is this correct? >>> >> >> Correct. DMSwarmMigrate_DMNeighborScatter() only scatter points to the >> neighbour ranks - where neighbours are defined by the DM provided to >> represent the mesh. >> >> DMSwarmMigrate_DMNeighborScatter() Is selected by default if you attach >> a DM. >> >> The scatter method should be over ridden with >> >> DMSwarmSetMigrateType() >> >> however it appears this method no longer exists. >> >> If one can determine the exact rank where points should should be sent >> and it is not going to be the neighbour rank (given by the DM), I would >> suggest not attaching the DM at all. >> >> However if this is not possible and one wanted to scatter to say the >> neighbours neighbours, we will have to add a new interface and refactor >> things a little bit. >> >> Cheers >> Dave >> >> >> >>> Thanks, >>> >>> Matt >>> >>> >>>> Il 22/12/22 11:44, Matteo Semplice ha scritto: >>>> >>>> Dear everybody, >>>> >>>> I have bug a bit into the code and I am able to add more >>>> information. >>>> Il 02/12/22 12:48, Matteo Semplice ha scritto: >>>> >>>> Hi. >>>> I am sorry to take this up again, but further tests show that it's not >>>> right yet. >>>> >>>> Il 04/11/22 12:48, Matthew Knepley ha scritto: >>>> >>>> On Fri, Nov 4, 2022 at 7:46 AM Matteo Semplice < >>>> [email protected]> wrote: >>>> >>>>> On 04/11/2022 02:43, Matthew Knepley wrote: >>>>> >>>>> On Thu, Nov 3, 2022 at 8:36 PM Matthew Knepley <[email protected]> >>>>> wrote: >>>>> >>>>>> On Thu, Oct 27, 2022 at 11:57 AM Semplice Matteo < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> Dear Petsc developers, >>>>>>> I am trying to use a DMSwarm to locate a cloud of points with >>>>>>> respect to a background mesh. In the real application the points will be >>>>>>> loaded from disk, but I have created a small demo in which >>>>>>> >>>>>>> - each processor creates Npart particles, all within the domain >>>>>>> covered by the mesh, but not all in the local portion of the mesh >>>>>>> - migrate the particles >>>>>>> >>>>>>> After migration most particles are not any more in the DMSwarm (how >>>>>>> many and which ones seems to depend on the number of cpus, but it never >>>>>>> happens that all particle survive the migration process). >>>>>>> >>>>>>> Thanks for sending this. I found the problem. Someone has some >>>>>> overly fancy code inside DMDA to figure out the local bounding box from >>>>>> the >>>>>> coordinates. >>>>>> It is broken for DM_BOUNDARY_GHOSTED, but we never tested with this. >>>>>> I will fix it. >>>>>> >>>>> >>>>> Okay, I think this fix is correct >>>>> >>>>> https://gitlab.com/petsc/petsc/-/merge_requests/5802 >>>>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgitlab.com%2Fpetsc%2Fpetsc%2F-%2Fmerge_requests%2F5802&data=05%7C01%7Cmatteo.semplice%40uninsubria.it%7C94569ac2a32a4838103608dae44f9c46%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C638073327837332509%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=9yKNH0%2FbepSLU2PO5S%2B2GkYSmjjFIDGHpapy%2FUb43D4%3D&reserved=0> >>>>> >>>>> I incorporated your test as src/dm/impls/da/tests/ex1.c. Can you take >>>>> a look and see if this fixes your issue? >>>>> >>>>> Yes, we have tested 2d and 3d, with various combinations of >>>>> DM_BOUNDARY_* along different directions and it works like a charm. >>>>> >>>>> On a side note, neither DMSwarmViewXDMF nor DMSwarmMigrate seem to be >>>>> implemented for 1d: I get >>>>> >>>>> [0]PETSC ERROR: No support for this operation for this object type >>>>> >>>>> [0]PETSC >>>>> ERROR: Support not provided for 1D >>>>> >>>>> However, currently I have no need for this feature. >>>>> >>>>> Finally, if the test is meant to stay in the source, you may remove >>>>> the call to DMSwarmRegisterPetscDatatypeField as in the attached >>>>> patch. >>>>> >>>>> Thanks a lot!! >>>>> >>>> Thanks! Glad it works. >>>> >>>> Matt >>>> >>>> There are still problems when not using 1,2 or 4 cpus. Any other number >>>> of cpus that I've tested does not work corectly. >>>> >>>> I have now modified private_DMDALocatePointsIS_2D_Regular to print out >>>> some debugging information. I see that this is called twice during >>>> migration, once before and once after DMSwarmMigrate_DMNeighborScatter. If >>>> I understand correctly, the second call to >>>> private_DMDALocatePointsIS_2D_Regular should be able to locate all >>>> particles owned by the rank but it fails for some of them because they have >>>> been sent to the wrong rank (despite being well away from process >>>> boundaries). >>>> >>>> For example, running the example src/dm/impls/da/tests/ex1.c with Nx=21 >>>> (20x20 Q1 elements on [-1,1]X[-1,1]) with 3 processors, >>>> >>>> - the particles (-0.191,-0.462) and (0.191,-0.462) are sent cpu2 >>>> instead of cpu0 >>>> >>>> - those at (-0.287,-0.693)and (0.287,-0.693) are sent to cpu1 instead >>>> of cpu0 >>>> >>>> - those at (0.191,0.462) and (-0.191,0.462) are sent to cpu0 instead of >>>> cpu2 >>>> >>>> (This is 2d and thus not affected by the 3d issue mentioned yesterday >>>> on petsc-dev. Tests were made based on the release branch pulled out this >>>> morning, i.e. on commit bebdc8d016f). >>>> >>>> I see: particles are sent "all around" and not only to the destination >>>> rank. >>>> >>>> Still however, running the example src/dm/impls/da/tests/ex1.c with >>>> Nx=21 (20x20 Q1 elements on [-1,1]X[-1,1]) with 3 processors, there are 2 >>>> particles initially owned by rank2 (at y=-0.6929 and x=+/-0.2870) that are >>>> sent only to rank1 and never make it to rank0 and are thus lost in the end >>>> since rank1, correctly, discards them. >>>> >>>> Thanks >>>> >>>> Matteo >>>> >>> >>> >>> -- >>> What most experimenters take for granted before they begin their >>> experiments is infinitely more interesting than any results to which their >>> experiments lead. >>> -- Norbert Wiener >>> >>> https://www.cse.buffalo.edu/~knepley/ >>> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7Cmatteo.semplice%40uninsubria.it%7C94569ac2a32a4838103608dae44f9c46%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C638073327837332509%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LEmGbachok2Z3m9SyCASEcTWytkpxw%2FnHCIXjYXPTa8%3D&reserved=0> >>> >> -- >> --- >> Professore Associato in Analisi Numerica >> Dipartimento di Scienza e Alta Tecnologia >> Università degli Studi dell'InsubriaVia Valleggio, 11 - Como >> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.google.com%2Fmaps%2Fsearch%2FVia%2BValleggio%2C%2B11%2B-%2BComo%3Fentry%3Dgmail%26source%3Dg&data=05%7C01%7Cmatteo.semplice%40uninsubria.it%7C94569ac2a32a4838103608dae44f9c46%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C638073327837332509%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=0MwkPJb5hslcrFhqrLCaN4OKs%2FoylMR3dOib2MYsNOY%3D&reserved=0> >> >> -- > --- > Professore Associato in Analisi Numerica > Dipartimento di Scienza e Alta Tecnologia > Università degli Studi dell'Insubria > Via Valleggio, 11 - Como > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
