[petsc-dev] DACreate3d should work for 1 node in Z
Ethan Coon
ecoon at lanl.gov
Tue Apr 19 14:47:58 CDT 2011
Hmm, crap. I don't get your valgrind error but I do get the crash with
stencil size 2. Will get back to you, thanks,
Ethan
On Tue, 2011-04-19 at 21:25 +0200, Jed Brown wrote:
> On Tue, 19 Apr 2011 09:18:44 -0600, Ethan Coon <ecoon at lanl.gov> wrote:
> > Can you shoot me your example? I run 1-node z direction both with and
> > without periodic BCs, and with and without ghost nodes, without a
> > valgrind complaint in DMDACreate3D.
>
> See attached very simple test case. It only crashes for stencil width
> greater than 1 (the original support request needs stencil width of 2
> for TVD FV methods),
>
> mpiexec -n 1 ./a.out # stencil width 2 in code
>
> [0]PETSC ERROR: --------------------- Error Message ------------------------------------
> [0]PETSC ERROR: Argument out of range!
> [0]PETSC ERROR: Negative index -100 at 0 location!
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Development HG revision: 335e836c7798747e6242df554ae58fe4db9f803f HG Date: Fri Apr 15 16:04:07 2011 -0500
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: ./a.out on a ompi named kunyang by jed Tue Apr 19 21:22:07 2011
> [0]PETSC ERROR: Libraries linked from /home/jed/petsc/ompi/lib
> [0]PETSC ERROR: Configure run at Sat Apr 16 13:36:39 2011
> [0]PETSC ERROR: Configure options --download-blacs --download-chaco --download-hypre=externalpackages/hypre-2.7.0b.tar.gz --download-ml --download-mum
> ps --download-parms --download-scalapack --download-scotch --download-spai --download-spooles --download-sundials --download-superlu --download-superl
> u_dist --with-blas-lapack-dir=/usr --with-c2html --with-cholmod-dir=/usr --with-clib-autodetect=0 --with-cxxlib-autodetect=0 --with-fortranlib-autodet
> ect=0 --with-hdf5-dir=/usr --with-java-dir=/usr --with-lgrind --with-mpi-dir=/usr --with-parmetis-dir=/usr --with-shared-libraries --with-single-libra
> ry=0 --with-sowing --with-umfpack-dir=/usr -LIBS="-L/usr/lib/openmpi -lmpi_f90 -lmpi_f77 -lmpi_cxx -lstdc++ -lgfortran" PETSC_ARCH=ompi
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: VecScatterCheckIndices_Private() line 26 in /home/jed/petsc/src/vec/vec/utils/vscat.c
> [0]PETSC ERROR: VecScatterCreate() line 1106 in /home/jed/petsc/src/vec/vec/utils/vscat.c
> [0]PETSC ERROR: DMSetUp_DA_3D() line 953 in /home/jed/petsc/src/dm/impls/da/da3.c
> [0]PETSC ERROR: DMSetUp_DA() line 22 in /home/jed/petsc/src/dm/impls/da/dareg.c
> [0]PETSC ERROR: DMSetUp() line 189 in /home/jed/petsc/src/dm/interface/dm.c
> [0]PETSC ERROR: DMDACreate3d() line 1366 in /home/jed/petsc/src/dm/impls/da/da3.c
> [0]PETSC ERROR: main() line 14 in "unknowndirectory/"da3d.c
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 63.
>
>
> I still see Valgrind noise for stencil width of 1:
>
> mpiexec -n 2 valgind ./a.out # stencil width 1 in code
>
> ==26044== Invalid read of size 2
> ==26044== at 0x4C26C2C: memcpy (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
> ==26044== by 0x71D8D01: opal_convertor_pack (in /usr/lib/openmpi/libmpi.so.1.0.1)
> ==26044== by 0x117600C8: ??? (in /usr/lib/openmpi/openmpi/mca_btl_sm.so)
> ==26044== by 0x10F421B7: ??? (in /usr/lib/openmpi/openmpi/mca_pml_ob1.so)
> ==26044== by 0x10F30C0C: ??? (in /usr/lib/openmpi/openmpi/mca_pml_ob1.so)
> ==26044== by 0x7127650: PMPI_Isend (in /usr/lib/openmpi/libmpi.so.1.0.1)
> ==26044== by 0x6C5A103: PetscGatherMessageLengths (mpimesg.c:127)
> ==26044== by 0x697A90A: VecScatterCreate_PtoS (vpscat.c:1623)
> ==26044== by 0x69564FD: VecScatterCreate (vscat.c:1334)
> ==26044== by 0x7CB339A: DMSetUp_DA_3D (da3.c:953)
> ==26044== by 0x7D044BF: DMSetUp_DA (dareg.c:22)
> ==26044== by 0x7C76A6C: DMSetUp (dm.c:189)
> ==26044== Address 0xdfeda02 is 2 bytes inside a block of size 8 alloc'd
> ==26044== at 0x4C23918: memalign (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
> ==26044== by 0x6CC9DEF: PetscMallocAlign (mal.c:30)
> ==26044== by 0x697A5EA: VecScatterCreate_PtoS (vpscat.c:1603)
> ==26044== by 0x69564FD: VecScatterCreate (vscat.c:1334)
> ==26044== by 0x7CB339A: DMSetUp_DA_3D (da3.c:953)
> ==26044== by 0x7D044BF: DMSetUp_DA (dareg.c:22)
> ==26044== by 0x7C76A6C: DMSetUp (dm.c:189)
> ==26044== by 0x7CB6D8D: DMDACreate3d (da3.c:1366)
> ==26044== by 0x400938: main (in /home/jed/lang/c/petsc/a.out)
>
> C source code attachment (da3d.c)
> #include <petscdmda.h>
>
> int main(int argc, char *argv[])
> {
> DM da;
> PetscErrorCode ierr;
>
> PetscInitialize(&argc,&argv,0,0);
> ierr = DMDACreate3d(PETSC_COMM_WORLD,
> DMDA_BOUNDARY_PERIODIC, DMDA_BOUNDARY_PERIODIC, DMDA_BOUNDARY_PERIODIC,
> DMDA_STENCIL_STAR,
> 10, 10, 1,
> PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE, 1, 1, /* Stencil width of 2 in original request */
> PETSC_NULL, PETSC_NULL, PETSC_NULL, &da);CHKERRQ(ierr);
> ierr = DMDestroy(da);CHKERRQ(ierr);
> PetscFinalize();
> return 0;
> }
--
------------------------------------
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
------------------------------------
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