Does maint also need this fix? Satish
On Thu, 21 Mar 2019, Stefano Zampini via petsc-users wrote: > Derek > > I have fixed the optimized plan few weeks ago > > https://bitbucket.org/petsc/petsc/commits/c3caad8634d376283f7053f3b388606b45b3122c > > Maybe this will fix your problem too? > > Stefano > > > Il Gio 21 Mar 2019, 04:21 Zhang, Junchao via petsc-users < > petsc-users@mcs.anl.gov> ha scritto: > > > Hi, Derek, > > Try to apply this tiny (but dirty) patch on your version of PETSc to > > disable the VecScatterMemcpyPlan optimization to see if it helps. > > Thanks. > > --Junchao Zhang > > > > On Wed, Mar 20, 2019 at 6:33 PM Junchao Zhang <jczh...@mcs.anl.gov> wrote: > > > >> Did you see the warning with small scale runs? Is it possible to provide > >> a test code? > >> You mentioned "changing PETSc now would be pretty painful". Is it because > >> it will affect your performance (but not your code)? If yes, could you try > >> PETSc master and run you code with or without -vecscatter_type sf. I want > >> to isolate the problem and see if it is due to possible bugs in VecScatter. > >> If the above suggestion is not feasible, I will disable VecScatterMemcpy. > >> It is an optimization I added. Sorry I did not have an option to turn off > >> it because I thought it was always useful:) I will provide you a patch > >> later to disable it. With that you can run again to isolate possible bugs > >> in VecScatterMemcpy. > >> Thanks. > >> --Junchao Zhang > >> > >> > >> On Wed, Mar 20, 2019 at 5:40 PM Derek Gaston via petsc-users < > >> petsc-users@mcs.anl.gov> wrote: > >> > >>> Trying to track down some memory corruption I'm seeing on larger scale > >>> runs (3.5B+ unknowns). Was able to run Valgrind on it... and I'm seeing > >>> quite a lot of uninitialized value errors coming from ghost updating. > >>> Here > >>> are some of the traces: > >>> > >>> ==87695== Conditional jump or move depends on uninitialised value(s) > >>> ==87695== at 0x73236D3: PetscMallocAlign (mal.c:28) > >>> ==87695== by 0x7323C70: PetscMallocA (mal.c:390) > >>> ==87695== by 0x739048E: VecScatterMemcpyPlanCreate_Index (vscat.c:284) > >>> ==87695== by 0x73A5D97: VecScatterMemcpyPlanCreate_PtoP > >>> (vpscat_mpi1.c:312) > >>> ==64730== by 0x7393E8A: VecScatterSetUp_vectype_private (vscat.c:857) > >>> ==64730== by 0x7395E5D: VecScatterSetUp_MPI1 (vpscat_mpi1.c:2543) > >>> ==64730== by 0x73DDD39: VecScatterSetUp (vscatfce.c:212) > >>> ==64730== by 0x73DCD73: VecScatterCreateWithData (vscreate.c:333) > >>> ==64730== by 0x7444232: VecCreateGhostWithArray (pbvec.c:685) > >>> ==64730== by 0x744490D: VecCreateGhost (pbvec.c:741) > >>> > >>> ==133582== Conditional jump or move depends on uninitialised value(s) > >>> ==133582== at 0x4030384: memcpy@@GLIBC_2.14 > >>> (vg_replace_strmem.c:1034) > >>> ==133582== by 0x739E4F9: PetscMemcpy (petscsys.h:1649) > >>> ==133582== by 0x739E4F9: VecScatterMemcpyPlanExecute_Pack > >>> (vecscatterimpl.h:150) > >>> ==133582== by 0x739E4F9: VecScatterBeginMPI1_1 (vpscat_mpi1.h:69) > >>> ==133582== by 0x73DD964: VecScatterBegin (vscatfce.c:110) > >>> ==133582== by 0x744E195: VecGhostUpdateBegin (commonmpvec.c:225) > >>> > >>> This is from a Git checkout of PETSc... the hash I branched from is: > >>> 0e667e8fea4aa from December 23rd (updating would be really hard at this > >>> point as I've completed 90% of my dissertation with this version... and > >>> changing PETSc now would be pretty painful!). > >>> > >>> Any ideas? Is it possible it's in my code? Is it possible that there > >>> are later PETSc commits that already fix this? > >>> > >>> Thanks for any help, > >>> Derek > >>> > >>> >
