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

(Rebecca) Xuefei YUAN xy2102 at columbia.edu
Wed Apr 28 01:37:33 CDT 2010 

Dear Satish,

After I use this env set, it is right and no error comes out.

Thanks very much!

Rebecca


Quoting Satish Balay <balay at mcs.anl.gov>:

> It should be used at runtime. For ex on our bgl - we use qsub as:
>
> qsub --env BG_MAXALIGNEXP=-1 -t 00:15:00 -n 4 ./ex2
>
> Satish
>
>
> On Tue, 27 Apr 2010, (Rebecca) Xuefei YUAN wrote:
>
>> Dear Satish,
>>
>> I think it is the latest petsc-dev, but I can check.
>>
>> How could I use the env variable?
>>
>> Do I need to put this
>>
>> 'BG_MAXALIGNEXP=-1'
>>
>> in the configure.py?
>>
>> Thanks a lot!
>>
>> Rebecca
>>
>>
>> Quoting Satish Balay <balay at mcs.anl.gov>:
>>
>> > Is this latest petsc-dev?
>> >
>> > Can you try using the following env variable and see if the error message
>> > goes away?
>> >
>> > 'BG_MAXALIGNEXP=-1'
>> >
>> >
>> > We still have to find the source of the problem..
>> >
>> > Satish
>> >
>> > On Tue, 27 Apr 2010, Aron Ahmadia wrote:
>> >
>> > > 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
>> > > >
>> > > >
>> > > >
>> > > >
>> > >
>> >
>>
>>
>>
>>
>



-- 
(Rebecca) Xuefei YUAN
Department of Applied Physics and Applied Mathematics
Columbia University
Tel:917-399-8032
www.columbia.edu/~xy2102

More information about the petsc-users mailing list