Which version of petsc you tested? With petsc 3.18.4, median duan volume gives the same value with petsc from DMPlexComputeCellGeometryFVM().
> On Sat, Feb 25, 2023 at 3:11 PM Mike Michell <[email protected]> > wrote: > >> My apologies for the late follow-up. There was a time conflict. >> >> A simple example code related to the issue I mentioned is attached here. >> The sample code does: (1) load grid on dm, (2) compute vertex-wise control >> volume for each node in a median-dual way, (3) halo exchange among procs to >> have complete control volume values, and (4) print out its field as a .vtu >> file. To make sure, the computed control volume is also compared with >> PETSc-computed control volume via DMPlexComputeCellGeometryFVM() (see lines >> 771-793). >> >> Back to the original problem, I can get a proper control volume field >> with PETSc 3.18.4, which is the latest stable release. However, if I use >> PETSc from the main repo, it gives a strange control volume field. >> Something is certainly strange around the parallel boundaries, thus I think >> something went wrong with halo communication. To help understand, a >> comparing snapshot is also attached. I guess a certain part of my code is >> no longer compatible with PETSc unless there is a bug in the library. Could >> I get comments on it? >> > > I can run your example. The numbers I get for "median-dual volume" do not > match the "PETSc volume", and the PETSc volume is correct. Moreover, the > median-dual numbers change, which suggests a memory fault. I compiled it > using address sanitizer, and it found an error: > > Number of physical boundary edge ... 4 0 > Number of physical and parallel boundary edge ... 4 > 0 > Number of parallel boundary edge ... 0 0 > Number of physical boundary edge ... 4 1 > Number of physical and parallel boundary edge ... 4 > 1 > Number of parallel boundary edge ... 0 1 > ================================================================= > ==36587==ERROR: AddressSanitizer: heap-buffer-overflow on address > 0x603000022d40 at pc 0x0001068e12a8 bp 0x7ffee932cfd0 sp 0x7ffee932cfc8 > READ of size 8 at 0x603000022d40 thread T0 > ================================================================= > ==36588==ERROR: AddressSanitizer: heap-buffer-overflow on address > 0x60300000f0f0 at pc 0x00010cf702a8 bp 0x7ffee2c9dfd0 sp 0x7ffee2c9dfc8 > READ of size 8 at 0x60300000f0f0 thread T0 > #0 0x10cf702a7 in MAIN__ test.F90:657 > #1 0x10cf768ee in main test.F90:43 > #0 0x1068e12a7 in MAIN__ test.F90:657 > #1 0x1068e78ee in main test.F90:43 > #2 0x7fff6b80acc8 in start (libdyld.dylib:x86_64+0x1acc8) > > 0x60300000f0f0 is located 0 bytes to the right of 32-byte region > [0x60300000f0d0,0x60300000f0f0) > allocated by thread T0 here: > #2 0x7fff6b80acc8 in start (libdyld.dylib:x86_64+0x1acc8) > > 0x603000022d40 is located 0 bytes to the right of 32-byte region > [0x603000022d20,0x603000022d40) > allocated by thread T0 here: > #0 0x114a7457f in wrap_malloc (libasan.5.dylib:x86_64+0x7b57f) > #1 0x1068dba71 in MAIN__ test.F90:499 > #2 0x1068e78ee in main test.F90:43 > #3 0x7fff6b80acc8 in start (libdyld.dylib:x86_64+0x1acc8) > > SUMMARY: AddressSanitizer: heap-buffer-overflow test.F90:657 in MAIN__ > Shadow bytes around the buggy address: > > which corresponds to > > ! midpoint of median-dual face for inner face > axrf(ifa,1) = 0.5d0*(yc(nc1)+yfc(ifa)) ! for nc1 cell > axrf(ifa,2) = 0.5d0*(yc(nc2)+yfc(ifa)) ! for nc2 cell > > and these were allocated here > > allocate(xc(ncell)) > allocate(yc(ncell)) > > Hopefully the error is straightforward to see now. > > Thanks, > > Matt > > >> Thanks, >> Mike >> >> >>> On Mon, Feb 20, 2023 at 12:05 PM Matthew Knepley <[email protected]> >>> wrote: >>> >>>> On Sat, Feb 18, 2023 at 12:00 PM Mike Michell <[email protected]> >>>> wrote: >>>> >>>>> As a follow-up, I tested: >>>>> >>>>> (1) Download tar for v3.18.4 from petsc gitlab ( >>>>> https://gitlab.com/petsc/petsc/-/tree/v3.18.4) has no issue on DMPlex >>>>> halo exchange. This version works as I expect. >>>>> (2) Clone main branch (git clone https://gitlab.com/petsc/petsc.git) >>>>> has issues with DMPlex halo exchange. Something is suspicious about this >>>>> main branch, related to DMPlex halo. The solution field I got is not >>>>> correct. But it works okay with 1-proc. >>>>> >>>>> Does anyone have any comments on this issue? I am curious if other >>>>> DMPlex users have no problem regarding halo exchange. FYI, I do not >>>>> declare ghost layers for halo exchange. >>>>> >>>> >>>> There should not have been any changes there and there are definitely >>>> tests for this. >>>> >>>> It would be great if you could send something that failed. I could fix >>>> it and add it as a test. >>>> >>> >>> Just to follow up, we have tests of the low-level communication (Plex >>> tests ex1, ex12, ex18, ex29, ex31), and then we have >>> tests that use halo exchange for PDE calculations, for example SNES >>> tutorial ex12, ex13, ex62. THe convergence rates >>> should be off if the halo exchange were wrong. Is there any example >>> similar to your code that is failing on your installation? >>> Or is there a way to run your code? >>> >>> Thanks, >>> >>> Matt >>> >>> >>>> Thanks, >>>> >>>> Matt >>>> >>>> >>>>> Thanks, >>>>> Mike >>>>> >>>>> >>>>>> Dear PETSc team, >>>>>> >>>>>> I am using PETSc for Fortran with DMPlex. I have been using this >>>>>> version of PETSc: >>>>>> >>git rev-parse origin >>>>>> >>995ec06f924a86c4d28df68d1fdd6572768b0de1 >>>>>> >>git rev-parse FETCH_HEAD >>>>>> >>9a04a86bf40bf893fb82f466a1bc8943d9bc2a6b >>>>>> >>>>>> There has been no issue, before the one with VTK viewer, which Jed >>>>>> fixed today ( >>>>>> https://gitlab.com/petsc/petsc/-/merge_requests/6081/diffs?commit_id=27ba695b8b62ee2bef0e5776c33883276a2a1735 >>>>>> ). >>>>>> >>>>>> Since that MR has been merged into the main repo, I pulled the latest >>>>>> version of PETSc (basically I cloned it from scratch). But if I use the >>>>>> same configure option with before, and run my code, then there is an >>>>>> issue >>>>>> with halo exchange. The code runs without error message, but it gives >>>>>> wrong >>>>>> solution field. I guess the issue I have is related to graph partitioner >>>>>> or >>>>>> halo exchange part. This is because if I run the code with 1-proc, the >>>>>> solution is correct. I only updated the version of PETSc and there was no >>>>>> change in my own code. Could I get any comments on the issue? I was >>>>>> wondering if there have been many changes in halo exchange or graph >>>>>> partitioning & distributing part related to DMPlex. >>>>>> >>>>>> Thanks, >>>>>> Mike >>>>>> >>>>> >>>> >>>> -- >>>> 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/> >>>> >>> >>> >>> -- >>> 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/> >>> >> > > -- > 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/> >
