[petsc-users] [Supercomputing Lab #847] VecView() error in BlueGene

Tue Apr 27 05:55:51 CDT 2010

I'll take a look at this and report back Rebecca.  I was seeing
similar bus errors on some PETSc example code calling VecView and we
haven't tracked it down yet.

A

On Tue, Apr 27, 2010 at 5:20 AM, Xuefei YUAN via RT
<shaheen-help at kaust.edu.sa> wrote:
>
> Tue Apr 27 12:20:11 2010: Request 847 was acted upon.
>  Transaction: Ticket created by xy2102 at columbia.edu
>       Queue: Shaheen
>     Subject: VecView() error in BlueGene
>       Owner: Nobody
>  Requestors: xy2102 at columbia.edu
>      Status: new
>  Ticket <URL: http://www.hpc.kaust.edu.sa/rt/Ticket/Display.html?id=847 >
>
>
> Hi,
>
> I tried the example code /petsc-dev/src/snes/examples/tutorials/ex5.c
> on bluegene, but get the following message about the VecView().
>
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 7 BUS: Bus Error, possibly
> illegal memory access
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#valgrind[0]PETSC
> ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to
> find memory corruption errors
> [0]PETSC ERROR: likely location of problem given in stack below
> [0]PETSC ERROR: ---------------------  Stack Frames
> ------------------------------------
> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> [0]PETSC ERROR:       INSTEAD the line number of the start of the function
> [0]PETSC ERROR:       is given.
> [0]PETSC ERROR: [0] VecView_MPI line 801 src/vec/vec/impls/mpi/pdvec.c
> [0]PETSC ERROR: [0] VecView line 690 src/vec/vec/interface/vector.c
> [0]PETSC ERROR: [0] DAView_VTK line 129 src/dm/da/src/daview.c
> [0]PETSC ERROR: [0] DAView line 227 src/dm/da/src/daview.c
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Development HG revision: unknown HG Date: unknown
> [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: ./ex5.exe on a arch-bgp- named ionode37 by Unknown Thu
> Jan  1 03:03:12 1970
> [0]PETSC ERROR: Libraries linked from
> /scratch/rebeccaxyf/petsc-dev/arch-bgp-ibm-dbg/lib
> [0]PETSC ERROR: Configure run at Mon Apr 26 15:37:29 2010
> [0]PETSC ERROR: Configure options --with-cc=mpixlc_r
> --with-cxx=mpixlcxx_r --with-fc=mpixlf90_r --with-clanguage=cxx
> --with-blas-lapack-lib="-L/opt/share/math_libraries/lapack/ppc64/IBM/
> -llapack -lblas" --with-x=0 --with-is-color-value-type=short
> --with-shared=0 -CFLAGS="-qmaxmem=-1 -g" -CXXFLAGS="-qmaxmem=-1 -g"
> -FFLAGS="-qmaxmem=-1 -g" --with-debugging=1 --with-fortran-kernels=1
> --with-batch=1 --known-mpi-shared=0 --known-memcmp-ok
> --known-sizeof-char=1 --known-sizeof-void-p=4 --known-sizeof-short=2
> --known-sizeof-int=4 --known-sizeof-long=4 --known-sizeof-size_t=4
> --known-sizeof-long-long=8 --known-sizeof-float=4
> --known-sizeof-double=8 --known-bits-per-byte=8
> --known-sizeof-MPI_Comm=4 --known-sizeof-MPI_Fint=4
> --known-mpi-long-double=1 --known-level1-dcache-assoc=0
> --known-level1-dcache-linesize=32 --known-level1-dcache-size=32768
> --petsc-arch=bgp-dbg PETSC_ARCH=arch-bgp-ibm-dbg
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> Abort(59) on node 0 (rank 0 in comm 1140850688): application called
> MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
>
> Also, my code is not working for calling VecView() with error message:
>
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 7 BUS: Bus Error, possibly
> illegal memory access
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#valgrind[0]PETSC
> ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to
> find memory corruption errors
> [0]PETSC ERROR: likely location of problem given in stack below
> [0]PETSC ERROR: ---------------------  Stack Frames
> ------------------------------------
> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> [0]PETSC ERROR:       INSTEAD the line number of the start of the function
> [0]PETSC ERROR:       is given.
> [0]PETSC ERROR: [0] VecView_MPI_DA line 508 src/dm/da/src/gr2.c
> [0]PETSC ERROR: [0] VecView line 690 src/vec/vec/interface/vector.c
> [0]PETSC ERROR: [0] DumpSolutionToMatlab line 1052 twqt2ff.c
> [0]PETSC ERROR: [0] Solve line 235 twqt2ff.c
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Development HG revision: unknown HG Date: unknown
> [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: ./twqt2ff.exe on a arch-bgp- named ionode132 by
> Unknown Fri Jan  2 00:44:26 1970
> [0]PETSC ERROR: Libraries linked from
> /scratch/rebeccaxyf/petsc-dev/arch-bgp-ibm-dbg/lib
> [0]PETSC ERROR: Configure run at Mon Apr 26 15:37:29 2010
> [0]PETSC ERROR: Configure options --with-cc=mpixlc_r
> --with-cxx=mpixlcxx_r --with-fc=mpixlf90_r --with-clanguage=cxx
> --with-blas-lapack-lib="-L/opt/share/math_libraries/lapack/ppc64/IBM/
> -llapack -lblas" --with-x=0 --with-is-color-value-type=short
> --with-shared=0 -CFLAGS="-qmaxmem=-1 -g" -CXXFLAGS="-qmaxmem=-1 -g"
> -FFLAGS="-qmaxmem=-1 -g" --with-debugging=1 --with-fortran-kernels=1
> --with-batch=1 --known-mpi-shared=0 --known-memcmp-ok
> --known-sizeof-char=1 --known-sizeof-void-p=4 --known-sizeof-short=2
> --known-sizeof-int=4 --known-sizeof-long=4 --known-sizeof-size_t=4
> --known-sizeof-long-long=8 --known-sizeof-float=4
> --known-sizeof-double=8 --known-bits-per-byte=8
> --known-sizeof-MPI_Comm=4 --known-sizeof-MPI_Fint=4
> --known-mpi-long-double=1 --known-level1-dcache-assoc=0
> --known-level1-dcache-linesize=32 --known-level1-dcache-size=32768
> --petsc-arch=bgp-dbg PETSC_ARCH=arch-bgp-ibm-dbg
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> Abort(59) on node 0 (rank 0 in comm 1140850688): application called
> MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
>
> Am I wrong at configure?
>
> Thanks a lot!
>
> Rebecca
>
>
> --
> (Rebecca) Xuefei YUAN
> Department of Applied Physics and Applied Mathematics
> Columbia University
> Tel:917-399-8032
> www.columbia.edu/~xy2102
>
>
>
>