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