[petsc-dev] DACreate3d should work for 1 node in Z

[Jed Brown]

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)

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