March 2012 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] redefine (or remove) MatPreallocateSymmetricInitialize to MatPreallocateInitialize
by Lisandro Dalcin 31 Mar '12

31 Mar '12

On 31 March 2012 18:59, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > Lisandro, > > What is the motivation? > > MatPreallocateSymmetricInitialize() is only trivially different than MatPreallocateInitialize() so why clutter the code with both? > Yea, that was my point too... But I was not sure about removing the #define for the MatPreallocateSymmetricInitialize. > > If it doesn't need to exist then remove it completely, don't keep it at all. > Thanks, I'll do that. -- Lisandro Dalcin --------------- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169

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Re: [petsc-dev] redefine (or remove) MatPreallocateSymmetricInitialize to MatPreallocateInitialize
by Barry Smith 31 Mar '12

31 Mar '12

Lisandro, What is the motivation? MatPreallocateSymmetricInitialize() is only trivially different than MatPreallocateInitialize() so why clutter the code with both? If it doesn't need to exist then remove it completely, don't keep it at all. Barry On Mar 31, 2012, at 7:45 AM, Lisandro Dalcin wrote: > The patch at the end is perhaps a little hard to read, but the basic > idea is to redefine (or eventually remove) > MatPreallocateSymmetricInitialize, and use MatPreallocateInitialize. > For this, all what is required is to somehow trick the C compiler to > not complain about unused-but-set-variable (the -W warning name for > GCC). That is the "__start = 0; __end = __start;" change in the first > hunk. > > If you agree, I'll like to push this change, and next I'll update the > code to use MatPreallocateInitialize() in all cases... What I'm not > sure is about removing MatPreallocateSymmetricInitialize, as it could > potentially break user code. > > > diff -r de0779566bd9 include/petscmat.h > --- a/include/petscmat.h Fri Mar 30 16:54:32 2012 -0500 > +++ b/include/petscmat.h Sat Mar 31 15:27:23 2012 +0300 > @@ -735,7 +735,7 @@ > PetscErrorCode _4_ierr; PetscInt __nrows = (nrows),__ctmp = > (ncols),__rstart,__start,__end; \ > _4_ierr = PetscMalloc2(__nrows,PetscInt,&dnz,__nrows,PetscInt,&onz);CHKERRQ(_4_ierr); > \ > _4_ierr = PetscMemzero(dnz,__nrows*sizeof(PetscInt));CHKERRQ(_4_ierr);\ > - _4_ierr = PetscMemzero(onz,__nrows*sizeof(PetscInt));CHKERRQ(_4_ierr);\ > + _4_ierr = PetscMemzero(onz,__nrows*sizeof(PetscInt));CHKERRQ(_4_ierr); > __start = 0; __end = __start; \ > _4_ierr = MPI_Scan(&__ctmp,&__end,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(_4_ierr); > __start = __end - __ctmp;\ > _4_ierr = MPI_Scan(&__nrows,&__rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(_4_ierr); > __rstart = __rstart - __nrows; > > @@ -772,14 +772,7 @@ > .seealso: MatPreallocateFinalize(), MatPreallocateSet(), > MatPreallocateSymmetricSet(), MatPreallocateSetLocal(), > MatPreallocateInitialize(), MatPreallocateSymmetricSetLocal() > M*/ > -#define MatPreallocateSymmetricInitialize(comm,nrows,ncols,dnz,onz) 0; \ > -{ \ > - PetscErrorCode _4_ierr; PetscInt __nrows = (nrows),__ctmp = > (ncols),__rstart,__end; \ > - _4_ierr = PetscMalloc2(__nrows,PetscInt,&dnz,__nrows,PetscInt,&onz);CHKERRQ(_4_ierr); > \ > - _4_ierr = PetscMemzero(dnz,__nrows*sizeof(PetscInt));CHKERRQ(_4_ierr);\ > - _4_ierr = PetscMemzero(onz,__nrows*sizeof(PetscInt));CHKERRQ(_4_ierr);\ > - _4_ierr = MPI_Scan(&__ctmp,&__end,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(_4_ierr);\ > - _4_ierr = MPI_Scan(&__nrows,&__rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(_4_ierr); > __rstart = __rstart - __nrows; > +#define MatPreallocateSymmetricInitialize(comm,nrows,ncols,dnz,onz) > MatPreallocateInitialize(comm,nrows,ncols,dnz,onz) > > /*MC > MatPreallocateSetLocal - Indicates the locations (rows and > columns) in the matrix where nonzeros will be > > > -- > Lisandro Dalcin > --------------- > CIMEC (INTEC/CONICET-UNL) > Predio CONICET-Santa Fe > Colectora RN 168 Km 472, Paraje El Pozo > 3000 Santa Fe, Argentina > Tel: +54-342-4511594 (ext 1011) > Tel/Fax: +54-342-4511169

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redefine (or remove) MatPreallocateSymmetricInitialize to MatPreallocateInitialize
by Lisandro Dalcin 31 Mar '12

31 Mar '12

The patch at the end is perhaps a little hard to read, but the basic idea is to redefine (or eventually remove) MatPreallocateSymmetricInitialize, and use MatPreallocateInitialize. For this, all what is required is to somehow trick the C compiler to not complain about unused-but-set-variable (the -W warning name for GCC). That is the "__start = 0; __end = __start;" change in the first hunk. If you agree, I'll like to push this change, and next I'll update the code to use MatPreallocateInitialize() in all cases... What I'm not sure is about removing MatPreallocateSymmetricInitialize, as it could potentially break user code. diff -r de0779566bd9 include/petscmat.h --- a/include/petscmat.h Fri Mar 30 16:54:32 2012 -0500 +++ b/include/petscmat.h Sat Mar 31 15:27:23 2012 +0300 @@ -735,7 +735,7 @@ PetscErrorCode _4_ierr; PetscInt __nrows = (nrows),__ctmp = (ncols),__rstart,__start,__end; \ _4_ierr = PetscMalloc2(__nrows,PetscInt,&dnz,__nrows,PetscInt,&onz);CHKERRQ(_4_ierr); \ _4_ierr = PetscMemzero(dnz,__nrows*sizeof(PetscInt));CHKERRQ(_4_ierr);\ - _4_ierr = PetscMemzero(onz,__nrows*sizeof(PetscInt));CHKERRQ(_4_ierr);\ + _4_ierr = PetscMemzero(onz,__nrows*sizeof(PetscInt));CHKERRQ(_4_ierr); __start = 0; __end = __start; \ _4_ierr = MPI_Scan(&__ctmp,&__end,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(_4_ierr); __start = __end - __ctmp;\ _4_ierr = MPI_Scan(&__nrows,&__rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(_4_ierr); __rstart = __rstart - __nrows; @@ -772,14 +772,7 @@ .seealso: MatPreallocateFinalize(), MatPreallocateSet(), MatPreallocateSymmetricSet(), MatPreallocateSetLocal(), MatPreallocateInitialize(), MatPreallocateSymmetricSetLocal() M*/ -#define MatPreallocateSymmetricInitialize(comm,nrows,ncols,dnz,onz) 0; \ -{ \ - PetscErrorCode _4_ierr; PetscInt __nrows = (nrows),__ctmp = (ncols),__rstart,__end; \ - _4_ierr = PetscMalloc2(__nrows,PetscInt,&dnz,__nrows,PetscInt,&onz);CHKERRQ(_4_ierr); \ - _4_ierr = PetscMemzero(dnz,__nrows*sizeof(PetscInt));CHKERRQ(_4_ierr);\ - _4_ierr = PetscMemzero(onz,__nrows*sizeof(PetscInt));CHKERRQ(_4_ierr);\ - _4_ierr = MPI_Scan(&__ctmp,&__end,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(_4_ierr);\ - _4_ierr = MPI_Scan(&__nrows,&__rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(_4_ierr); __rstart = __rstart - __nrows; +#define MatPreallocateSymmetricInitialize(comm,nrows,ncols,dnz,onz) MatPreallocateInitialize(comm,nrows,ncols,dnz,onz) /*MC MatPreallocateSetLocal - Indicates the locations (rows and columns) in the matrix where nonzeros will be -- Lisandro Dalcin --------------- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169

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Re: [petsc-dev] DMCreateComposition crash in tests
by Dmitry Karpeev 30 Mar '12

30 Mar '12

I don't think so. On Fri, Mar 30, 2012 at 9:39 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > Do I have to rerun configure ? > > On Mar 30, 2012, at 9:35 PM, Dmitry Karpeev wrote: > > > Maybe that arch didn't get rebuilt? The HG time stamp in your stack > trace says 'March 23'. > > Hong alerted me to this bug today and the fix is here: > > http://petsc.cs.iit.edu/petsc/petsc-dev/rev/de0779566bd9 > > > > Dmitry. > > On Fri, Mar 30, 2012 at 9:27 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > > > I will try again. But I just pulled before the test. Will see. > > > > Barry > > > > On Mar 30, 2012, at 9:21 PM, Dmitry Karpeev wrote: > > > > > Barry, > > > This looks like petsc-dev from about a week ago -- I fixed this bug > today. > > > It runs on my laptop right now. > > > > > > Dmitry. > > > > > > On Fri, Mar 30, 2012 at 9:00 PM, Barry Smith <bsmith(a)mcs.anl.gov> > wrote: > > > > > > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > > > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation > Violation, probably memory access out of range > > > > [0]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > > > > [0]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSCERROR: 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] DMCreateDecomposition line 854 > /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > > > [0]PETSC ERROR: [0] PCSetUp_ASM line 161 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > > > [0]PETSC ERROR: [0] PCSetUp line 810 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > > > [0]PETSC ERROR: [0] KSPSetUp line 182 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > > [0]PETSC ERROR: [0] KSPSolve line 339 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > > [0]PETSC ERROR: [0] SNES_KSPSolve line 4169 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > > [0]PETSC ERROR: [0] SNESSolve_LS line 143 > /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > > > [0]PETSC ERROR: [0] SNESSolve line 3345 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > > > > [0]PETSC ERROR: Signal received! > > > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > > > > [0]PETSC ERROR: Petsc Development HG revision: > ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 > -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: ./ex50 on a arch-gnu named > barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > > > [0]PETSC ERROR: Libraries linked from > /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > > > [0]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > > > [0]PETSC ERROR: Configure options --download-blacs --download-fftw > --download-hypre --download-metis --download-mpich --download-mumps > --download-parmetis --download-ptscotch --download-scalapack > --download-superlu --download-superlu_dist --download-yaml > --with-shared-libraries PETSC_ARCH=arch-gnu > > > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > > > > [0]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > > > [cli_0]: aborting job: > > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > > > [1]PETSC ERROR: > ------------------------------------------------------------------------ > > > > [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation > Violation, probably memory access out of range > > > > [1]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > > > > [1]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSCERROR: or try > http://valgrind.org on GNU/linux and Apple Mac OS X to find memory > corruption errors > > > > [1]PETSC ERROR: likely location of problem given in stack below > > > > [1]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > > > > [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > > > > [1]PETSC ERROR: INSTEAD the line number of the start of the > function > > > > [1]PETSC ERROR: is given. > > > > [1]PETSC ERROR: [1] DMCreateDecomposition line 854 > /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > > > [1]PETSC ERROR: [1] PCSetUp_ASM line 161 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > > > [1]PETSC ERROR: [1] PCSetUp line 810 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > > > [1]PETSC ERROR: [1] KSPSetUp line 182 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > > [1]PETSC ERROR: [1] KSPSolve line 339 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > > [1]PETSC ERROR: [1] SNES_KSPSolve line 4169 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > > [1]PETSC ERROR: [1] SNESSolve_LS line 143 > /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > > > [1]PETSC ERROR: [1] SNESSolve line 3345 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > > [1]PETSC ERROR: --------------------- Error Message > ------------------------------------ > > > > [1]PETSC ERROR: Signal received! > > > > [1]PETSC ERROR: > ------------------------------------------------------------------------ > > > > [1]PETSC ERROR: Petsc Development HG revision: > ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 > -0500 > > > > [1]PETSC ERROR: See docs/changes/index.html for recent updates. > > > > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > > > [1]PETSC ERROR: See docs/index.html for manual pages. > > > > [1]PETSC ERROR: > ------------------------------------------------------------------------ > > > > [1]PETSC ERROR: ./ex50 on a arch-gnu named > barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > > > [1]PETSC ERROR: Libraries linked from > /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > > > [1]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > > > [1]PETSC ERROR: Configure options --download-blacs --download-fftw > --download-hypre --download-metis --download-mpich --download-mumps > --download-parmetis --download-ptscotch --download-scalapack > --download-superlu --download-superlu_dist --download-yaml > --with-shared-libraries PETSC_ARCH=arch-gnu > > > > [1]PETSC ERROR: > ------------------------------------------------------------------------ > > > > [1]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1 > > > > [cli_1]: aborting job: > > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1 > > > > [2]PETSC ERROR: > ------------------------------------------------------------------------ > > > > [2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation > Violation, probably memory access out of range > > > > [2]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > > > > [2]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[2]PETSCERROR: or try > http://valgrind.org on GNU/linux and Apple Mac OS X to find memory > corruption errors > > > > [2]PETSC ERROR: likely location of problem given in stack below > > > > [2]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > > > > [2]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > > > > [2]PETSC ERROR: INSTEAD the line number of the start of the > function > > > > [2]PETSC ERROR: is given. > > > > [2]PETSC ERROR: [2] DMCreateDecomposition line 854 > /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > > > [2]PETSC ERROR: [2] PCSetUp_ASM line 161 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > > > [2]PETSC ERROR: [2] PCSetUp line 810 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > > > [2]PETSC ERROR: [2] KSPSetUp line 182 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > > [2]PETSC ERROR: [2] KSPSolve line 339 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > > [2]PETSC ERROR: [2] SNES_KSPSolve line 4169 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > > [2]PETSC ERROR: [2] SNESSolve_LS line 143 > /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > > > [2]PETSC ERROR: [2] SNESSolve line 3345 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > > [2]PETSC ERROR: --------------------- Error Message > ------------------------------------ > > > > [2]PETSC ERROR: Signal received! > > > > [2]PETSC ERROR: > ------------------------------------------------------------------------ > > > > [2]PETSC ERROR: Petsc Development HG revision: > ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 > -0500 > > > > [2]PETSC ERROR: See docs/changes/index.html for recent updates. > > > > [2]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > > > [2]PETSC ERROR: See docs/index.html for manual pages. > > > > [2]PETSC ERROR: > ------------------------------------------------------------------------ > > > > [2]PETSC ERROR: ./ex50 on a arch-gnu named > barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > > > [2]PETSC ERROR: Libraries linked from > /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > > > [2]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > > > [2]PETSC ERROR: Configure options --download-blacs --download-fftw > --download-hypre --download-metis --download-mpich --download-mumps > --download-parmetis --download-ptscotch --download-scalapack > --download-superlu --download-superlu_dist --download-yaml > --with-shared-libraries PETSC_ARCH=arch-gnu > > > > [2]PETSC ERROR: > ------------------------------------------------------------------------ > > > > [2]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2 > > > > [cli_2]: aborting job: > > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2 > > > > [3]PETSC ERROR: > ------------------------------------------------------------------------ > > > > [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation > Violation, probably memory access out of range > > > > [3]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > > > > [3]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[3]PETSCERROR: or try > http://valgrind.org on GNU/linux and Apple Mac OS X to find memory > corruption errors > > > > [3]PETSC ERROR: likely location of problem given in stack below > > > > [3]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > > > > [3]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > > > > [3]PETSC ERROR: INSTEAD the line number of the start of the > function > > > > [3]PETSC ERROR: is given. > > > > [3]PETSC ERROR: [3] DMCreateDecomposition line 854 > /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > > > [3]PETSC ERROR: [3] PCSetUp_ASM line 161 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > > > [3]PETSC ERROR: [3] PCSetUp line 810 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > > > [3]PETSC ERROR: [3] KSPSetUp line 182 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > > [3]PETSC ERROR: [3] KSPSolve line 339 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > > [3]PETSC ERROR: [3] SNES_KSPSolve line 4169 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > > [3]PETSC ERROR: [3] SNESSolve_LS line 143 > /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > > > [3]PETSC ERROR: [3] SNESSolve line 3345 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > > [3]PETSC ERROR: --------------------- Error Message > ------------------------------------ > > > > [3]PETSC ERROR: Signal received! > > > > [3]PETSC ERROR: > ------------------------------------------------------------------------ > > > > [3]PETSC ERROR: Petsc Development HG revision: > ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 > -0500 > > > > [3]PETSC ERROR: See docs/changes/index.html for recent updates. > > > > [3]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > > > [3]PETSC ERROR: See docs/index.html for manual pages. > > > > [3]PETSC ERROR: > ------------------------------------------------------------------------ > > > > [3]PETSC ERROR: ./ex50 on a arch-gnu named > barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > > > [3]PETSC ERROR: Libraries linked from > /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > > > [3]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > > > [3]PETSC ERROR: Configure options --download-blacs --download-fftw > --download-hypre --download-metis --download-mpich --download-mumps > --download-parmetis --download-ptscotch --download-scalapack > --download-superlu --download-superlu_dist --download-yaml > --with-shared-libraries PETSC_ARCH=arch-gnu > > > > [3]PETSC ERROR: > ------------------------------------------------------------------------ > > > > [3]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3 > > > > [cli_3]: aborting job: > > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3 > > > /Users/barrysmith/Src/petsc-dev/src/snes/examples/tutorials > > > Possible problem with ex50_6, diffs above > > > > > > > > > > > >

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Re: [petsc-dev] DMCreateComposition crash in tests
by Barry Smith 30 Mar '12

30 Mar '12

Do I have to rerun configure ? On Mar 30, 2012, at 9:35 PM, Dmitry Karpeev wrote: > Maybe that arch didn't get rebuilt? The HG time stamp in your stack trace says 'March 23'. > Hong alerted me to this bug today and the fix is here: > http://petsc.cs.iit.edu/petsc/petsc-dev/rev/de0779566bd9 > > Dmitry. > On Fri, Mar 30, 2012 at 9:27 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > I will try again. But I just pulled before the test. Will see. > > Barry > > On Mar 30, 2012, at 9:21 PM, Dmitry Karpeev wrote: > > > Barry, > > This looks like petsc-dev from about a week ago -- I fixed this bug today. > > It runs on my laptop right now. > > > > Dmitry. > > > > On Fri, Mar 30, 2012 at 9:00 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > > > > [0]PETSC ERROR: ------------------------------------------------------------------------ > > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > > [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/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] DMCreateDecomposition line 854 /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > > [0]PETSC ERROR: [0] PCSetUp_ASM line 161 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > > [0]PETSC ERROR: [0] PCSetUp line 810 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > > [0]PETSC ERROR: [0] KSPSetUp line 182 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > [0]PETSC ERROR: [0] KSPSolve line 339 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > [0]PETSC ERROR: [0] SNES_KSPSolve line 4169 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > [0]PETSC ERROR: [0] SNESSolve_LS line 143 /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > > [0]PETSC ERROR: [0] SNESSolve line 3345 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > [0]PETSC ERROR: --------------------- Error Message ------------------------------------ > > > [0]PETSC ERROR: Signal received! > > > [0]PETSC ERROR: ------------------------------------------------------------------------ > > > [0]PETSC ERROR: Petsc Development HG revision: ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 -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: ./ex50 on a arch-gnu named barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > > [0]PETSC ERROR: Libraries linked from /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > > [0]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > > [0]PETSC ERROR: Configure options --download-blacs --download-fftw --download-hypre --download-metis --download-mpich --download-mumps --download-parmetis --download-ptscotch --download-scalapack --download-superlu --download-superlu_dist --download-yaml --with-shared-libraries PETSC_ARCH=arch-gnu > > > [0]PETSC ERROR: ------------------------------------------------------------------------ > > > [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > > [cli_0]: aborting job: > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > > [1]PETSC ERROR: ------------------------------------------------------------------------ > > > [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > > [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > > [1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors > > > [1]PETSC ERROR: likely location of problem given in stack below > > > [1]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > > > [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > > > [1]PETSC ERROR: INSTEAD the line number of the start of the function > > > [1]PETSC ERROR: is given. > > > [1]PETSC ERROR: [1] DMCreateDecomposition line 854 /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > > [1]PETSC ERROR: [1] PCSetUp_ASM line 161 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > > [1]PETSC ERROR: [1] PCSetUp line 810 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > > [1]PETSC ERROR: [1] KSPSetUp line 182 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > [1]PETSC ERROR: [1] KSPSolve line 339 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > [1]PETSC ERROR: [1] SNES_KSPSolve line 4169 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > [1]PETSC ERROR: [1] SNESSolve_LS line 143 /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > > [1]PETSC ERROR: [1] SNESSolve line 3345 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > [1]PETSC ERROR: --------------------- Error Message ------------------------------------ > > > [1]PETSC ERROR: Signal received! > > > [1]PETSC ERROR: ------------------------------------------------------------------------ > > > [1]PETSC ERROR: Petsc Development HG revision: ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 -0500 > > > [1]PETSC ERROR: See docs/changes/index.html for recent updates. > > > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > > [1]PETSC ERROR: See docs/index.html for manual pages. > > > [1]PETSC ERROR: ------------------------------------------------------------------------ > > > [1]PETSC ERROR: ./ex50 on a arch-gnu named barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > > [1]PETSC ERROR: Libraries linked from /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > > [1]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > > [1]PETSC ERROR: Configure options --download-blacs --download-fftw --download-hypre --download-metis --download-mpich --download-mumps --download-parmetis --download-ptscotch --download-scalapack --download-superlu --download-superlu_dist --download-yaml --with-shared-libraries PETSC_ARCH=arch-gnu > > > [1]PETSC ERROR: ------------------------------------------------------------------------ > > > [1]PETSC ERROR: User provided function() line 0 in unknown directory unknown file > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1 > > > [cli_1]: aborting job: > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1 > > > [2]PETSC ERROR: ------------------------------------------------------------------------ > > > [2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > > [2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > > [2]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors > > > [2]PETSC ERROR: likely location of problem given in stack below > > > [2]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > > > [2]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > > > [2]PETSC ERROR: INSTEAD the line number of the start of the function > > > [2]PETSC ERROR: is given. > > > [2]PETSC ERROR: [2] DMCreateDecomposition line 854 /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > > [2]PETSC ERROR: [2] PCSetUp_ASM line 161 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > > [2]PETSC ERROR: [2] PCSetUp line 810 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > > [2]PETSC ERROR: [2] KSPSetUp line 182 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > [2]PETSC ERROR: [2] KSPSolve line 339 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > [2]PETSC ERROR: [2] SNES_KSPSolve line 4169 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > [2]PETSC ERROR: [2] SNESSolve_LS line 143 /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > > [2]PETSC ERROR: [2] SNESSolve line 3345 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > [2]PETSC ERROR: --------------------- Error Message ------------------------------------ > > > [2]PETSC ERROR: Signal received! > > > [2]PETSC ERROR: ------------------------------------------------------------------------ > > > [2]PETSC ERROR: Petsc Development HG revision: ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 -0500 > > > [2]PETSC ERROR: See docs/changes/index.html for recent updates. > > > [2]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > > [2]PETSC ERROR: See docs/index.html for manual pages. > > > [2]PETSC ERROR: ------------------------------------------------------------------------ > > > [2]PETSC ERROR: ./ex50 on a arch-gnu named barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > > [2]PETSC ERROR: Libraries linked from /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > > [2]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > > [2]PETSC ERROR: Configure options --download-blacs --download-fftw --download-hypre --download-metis --download-mpich --download-mumps --download-parmetis --download-ptscotch --download-scalapack --download-superlu --download-superlu_dist --download-yaml --with-shared-libraries PETSC_ARCH=arch-gnu > > > [2]PETSC ERROR: ------------------------------------------------------------------------ > > > [2]PETSC ERROR: User provided function() line 0 in unknown directory unknown file > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2 > > > [cli_2]: aborting job: > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2 > > > [3]PETSC ERROR: ------------------------------------------------------------------------ > > > [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > > [3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > > [3]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors > > > [3]PETSC ERROR: likely location of problem given in stack below > > > [3]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > > > [3]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > > > [3]PETSC ERROR: INSTEAD the line number of the start of the function > > > [3]PETSC ERROR: is given. > > > [3]PETSC ERROR: [3] DMCreateDecomposition line 854 /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > > [3]PETSC ERROR: [3] PCSetUp_ASM line 161 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > > [3]PETSC ERROR: [3] PCSetUp line 810 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > > [3]PETSC ERROR: [3] KSPSetUp line 182 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > [3]PETSC ERROR: [3] KSPSolve line 339 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > [3]PETSC ERROR: [3] SNES_KSPSolve line 4169 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > [3]PETSC ERROR: [3] SNESSolve_LS line 143 /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > > [3]PETSC ERROR: [3] SNESSolve line 3345 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > [3]PETSC ERROR: --------------------- Error Message ------------------------------------ > > > [3]PETSC ERROR: Signal received! > > > [3]PETSC ERROR: ------------------------------------------------------------------------ > > > [3]PETSC ERROR: Petsc Development HG revision: ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 -0500 > > > [3]PETSC ERROR: See docs/changes/index.html for recent updates. > > > [3]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > > [3]PETSC ERROR: See docs/index.html for manual pages. > > > [3]PETSC ERROR: ------------------------------------------------------------------------ > > > [3]PETSC ERROR: ./ex50 on a arch-gnu named barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > > [3]PETSC ERROR: Libraries linked from /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > > [3]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > > [3]PETSC ERROR: Configure options --download-blacs --download-fftw --download-hypre --download-metis --download-mpich --download-mumps --download-parmetis --download-ptscotch --download-scalapack --download-superlu --download-superlu_dist --download-yaml --with-shared-libraries PETSC_ARCH=arch-gnu > > > [3]PETSC ERROR: ------------------------------------------------------------------------ > > > [3]PETSC ERROR: User provided function() line 0 in unknown directory unknown file > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3 > > > [cli_3]: aborting job: > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3 > > /Users/barrysmith/Src/petsc-dev/src/snes/examples/tutorials > > Possible problem with ex50_6, diffs above > > > > > >

1 0

Re: [petsc-dev] DMCreateComposition crash in tests
by Dmitry Karpeev 30 Mar '12

30 Mar '12

Maybe that arch didn't get rebuilt? The HG time stamp in your stack trace says 'March 23'. Hong alerted me to this bug today and the fix is here: http://petsc.cs.iit.edu/petsc/petsc-dev/rev/de0779566bd9 Dmitry. On Fri, Mar 30, 2012 at 9:27 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > I will try again. But I just pulled before the test. Will see. > > Barry > > On Mar 30, 2012, at 9:21 PM, Dmitry Karpeev wrote: > > > Barry, > > This looks like petsc-dev from about a week ago -- I fixed this bug > today. > > It runs on my laptop right now. > > > > Dmitry. > > > > On Fri, Mar 30, 2012 at 9:00 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > > > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > > [0]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > > > [0]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSCERROR: 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] DMCreateDecomposition line 854 > /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > > [0]PETSC ERROR: [0] PCSetUp_ASM line 161 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > > [0]PETSC ERROR: [0] PCSetUp line 810 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > > [0]PETSC ERROR: [0] KSPSetUp line 182 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > [0]PETSC ERROR: [0] KSPSolve line 339 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > [0]PETSC ERROR: [0] SNES_KSPSolve line 4169 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > [0]PETSC ERROR: [0] SNESSolve_LS line 143 > /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > > [0]PETSC ERROR: [0] SNESSolve line 3345 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > > > [0]PETSC ERROR: Signal received! > > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > > > [0]PETSC ERROR: Petsc Development HG revision: > ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 > -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: ./ex50 on a arch-gnu named > barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > > [0]PETSC ERROR: Libraries linked from > /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > > [0]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > > [0]PETSC ERROR: Configure options --download-blacs --download-fftw > --download-hypre --download-metis --download-mpich --download-mumps > --download-parmetis --download-ptscotch --download-scalapack > --download-superlu --download-superlu_dist --download-yaml > --with-shared-libraries PETSC_ARCH=arch-gnu > > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > > > [0]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > > [cli_0]: aborting job: > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > > [1]PETSC ERROR: > ------------------------------------------------------------------------ > > > [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > > [1]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > > > [1]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSCERROR: or try > http://valgrind.org on GNU/linux and Apple Mac OS X to find memory > corruption errors > > > [1]PETSC ERROR: likely location of problem given in stack below > > > [1]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > > > [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > > > [1]PETSC ERROR: INSTEAD the line number of the start of the > function > > > [1]PETSC ERROR: is given. > > > [1]PETSC ERROR: [1] DMCreateDecomposition line 854 > /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > > [1]PETSC ERROR: [1] PCSetUp_ASM line 161 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > > [1]PETSC ERROR: [1] PCSetUp line 810 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > > [1]PETSC ERROR: [1] KSPSetUp line 182 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > [1]PETSC ERROR: [1] KSPSolve line 339 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > [1]PETSC ERROR: [1] SNES_KSPSolve line 4169 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > [1]PETSC ERROR: [1] SNESSolve_LS line 143 > /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > > [1]PETSC ERROR: [1] SNESSolve line 3345 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > [1]PETSC ERROR: --------------------- Error Message > ------------------------------------ > > > [1]PETSC ERROR: Signal received! > > > [1]PETSC ERROR: > ------------------------------------------------------------------------ > > > [1]PETSC ERROR: Petsc Development HG revision: > ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 > -0500 > > > [1]PETSC ERROR: See docs/changes/index.html for recent updates. > > > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > > [1]PETSC ERROR: See docs/index.html for manual pages. > > > [1]PETSC ERROR: > ------------------------------------------------------------------------ > > > [1]PETSC ERROR: ./ex50 on a arch-gnu named > barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > > [1]PETSC ERROR: Libraries linked from > /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > > [1]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > > [1]PETSC ERROR: Configure options --download-blacs --download-fftw > --download-hypre --download-metis --download-mpich --download-mumps > --download-parmetis --download-ptscotch --download-scalapack > --download-superlu --download-superlu_dist --download-yaml > --with-shared-libraries PETSC_ARCH=arch-gnu > > > [1]PETSC ERROR: > ------------------------------------------------------------------------ > > > [1]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1 > > > [cli_1]: aborting job: > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1 > > > [2]PETSC ERROR: > ------------------------------------------------------------------------ > > > [2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > > [2]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > > > [2]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[2]PETSCERROR: or try > http://valgrind.org on GNU/linux and Apple Mac OS X to find memory > corruption errors > > > [2]PETSC ERROR: likely location of problem given in stack below > > > [2]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > > > [2]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > > > [2]PETSC ERROR: INSTEAD the line number of the start of the > function > > > [2]PETSC ERROR: is given. > > > [2]PETSC ERROR: [2] DMCreateDecomposition line 854 > /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > > [2]PETSC ERROR: [2] PCSetUp_ASM line 161 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > > [2]PETSC ERROR: [2] PCSetUp line 810 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > > [2]PETSC ERROR: [2] KSPSetUp line 182 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > [2]PETSC ERROR: [2] KSPSolve line 339 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > [2]PETSC ERROR: [2] SNES_KSPSolve line 4169 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > [2]PETSC ERROR: [2] SNESSolve_LS line 143 > /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > > [2]PETSC ERROR: [2] SNESSolve line 3345 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > [2]PETSC ERROR: --------------------- Error Message > ------------------------------------ > > > [2]PETSC ERROR: Signal received! > > > [2]PETSC ERROR: > ------------------------------------------------------------------------ > > > [2]PETSC ERROR: Petsc Development HG revision: > ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 > -0500 > > > [2]PETSC ERROR: See docs/changes/index.html for recent updates. > > > [2]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > > [2]PETSC ERROR: See docs/index.html for manual pages. > > > [2]PETSC ERROR: > ------------------------------------------------------------------------ > > > [2]PETSC ERROR: ./ex50 on a arch-gnu named > barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > > [2]PETSC ERROR: Libraries linked from > /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > > [2]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > > [2]PETSC ERROR: Configure options --download-blacs --download-fftw > --download-hypre --download-metis --download-mpich --download-mumps > --download-parmetis --download-ptscotch --download-scalapack > --download-superlu --download-superlu_dist --download-yaml > --with-shared-libraries PETSC_ARCH=arch-gnu > > > [2]PETSC ERROR: > ------------------------------------------------------------------------ > > > [2]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2 > > > [cli_2]: aborting job: > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2 > > > [3]PETSC ERROR: > ------------------------------------------------------------------------ > > > [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > > [3]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > > > [3]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[3]PETSCERROR: or try > http://valgrind.org on GNU/linux and Apple Mac OS X to find memory > corruption errors > > > [3]PETSC ERROR: likely location of problem given in stack below > > > [3]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > > > [3]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > > > [3]PETSC ERROR: INSTEAD the line number of the start of the > function > > > [3]PETSC ERROR: is given. > > > [3]PETSC ERROR: [3] DMCreateDecomposition line 854 > /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > > [3]PETSC ERROR: [3] PCSetUp_ASM line 161 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > > [3]PETSC ERROR: [3] PCSetUp line 810 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > > [3]PETSC ERROR: [3] KSPSetUp line 182 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > [3]PETSC ERROR: [3] KSPSolve line 339 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > > [3]PETSC ERROR: [3] SNES_KSPSolve line 4169 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > [3]PETSC ERROR: [3] SNESSolve_LS line 143 > /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > > [3]PETSC ERROR: [3] SNESSolve line 3345 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > > [3]PETSC ERROR: --------------------- Error Message > ------------------------------------ > > > [3]PETSC ERROR: Signal received! > > > [3]PETSC ERROR: > ------------------------------------------------------------------------ > > > [3]PETSC ERROR: Petsc Development HG revision: > ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 > -0500 > > > [3]PETSC ERROR: See docs/changes/index.html for recent updates. > > > [3]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > > [3]PETSC ERROR: See docs/index.html for manual pages. > > > [3]PETSC ERROR: > ------------------------------------------------------------------------ > > > [3]PETSC ERROR: ./ex50 on a arch-gnu named > barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > > [3]PETSC ERROR: Libraries linked from > /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > > [3]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > > [3]PETSC ERROR: Configure options --download-blacs --download-fftw > --download-hypre --download-metis --download-mpich --download-mumps > --download-parmetis --download-ptscotch --download-scalapack > --download-superlu --download-superlu_dist --download-yaml > --with-shared-libraries PETSC_ARCH=arch-gnu > > > [3]PETSC ERROR: > ------------------------------------------------------------------------ > > > [3]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3 > > > [cli_3]: aborting job: > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3 > > /Users/barrysmith/Src/petsc-dev/src/snes/examples/tutorials > > Possible problem with ex50_6, diffs above > > > > > >

1 0

Re: [petsc-dev] DMCreateComposition crash in tests
by Barry Smith 30 Mar '12

30 Mar '12

I will try again. But I just pulled before the test. Will see. Barry On Mar 30, 2012, at 9:21 PM, Dmitry Karpeev wrote: > Barry, > This looks like petsc-dev from about a week ago -- I fixed this bug today. > It runs on my laptop right now. > > Dmitry. > > On Fri, Mar 30, 2012 at 9:00 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > > [0]PETSC ERROR: ------------------------------------------------------------------------ > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/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] DMCreateDecomposition line 854 /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > [0]PETSC ERROR: [0] PCSetUp_ASM line 161 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > [0]PETSC ERROR: [0] PCSetUp line 810 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > [0]PETSC ERROR: [0] KSPSetUp line 182 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > [0]PETSC ERROR: [0] KSPSolve line 339 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > [0]PETSC ERROR: [0] SNES_KSPSolve line 4169 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > [0]PETSC ERROR: [0] SNESSolve_LS line 143 /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > [0]PETSC ERROR: [0] SNESSolve line 3345 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > [0]PETSC ERROR: --------------------- Error Message ------------------------------------ > > [0]PETSC ERROR: Signal received! > > [0]PETSC ERROR: ------------------------------------------------------------------------ > > [0]PETSC ERROR: Petsc Development HG revision: ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 -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: ./ex50 on a arch-gnu named barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > [0]PETSC ERROR: Libraries linked from /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > [0]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > [0]PETSC ERROR: Configure options --download-blacs --download-fftw --download-hypre --download-metis --download-mpich --download-mumps --download-parmetis --download-ptscotch --download-scalapack --download-superlu --download-superlu_dist --download-yaml --with-shared-libraries PETSC_ARCH=arch-gnu > > [0]PETSC ERROR: ------------------------------------------------------------------------ > > [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > [cli_0]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > [1]PETSC ERROR: ------------------------------------------------------------------------ > > [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors > > [1]PETSC ERROR: likely location of problem given in stack below > > [1]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > > [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > > [1]PETSC ERROR: INSTEAD the line number of the start of the function > > [1]PETSC ERROR: is given. > > [1]PETSC ERROR: [1] DMCreateDecomposition line 854 /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > [1]PETSC ERROR: [1] PCSetUp_ASM line 161 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > [1]PETSC ERROR: [1] PCSetUp line 810 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > [1]PETSC ERROR: [1] KSPSetUp line 182 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > [1]PETSC ERROR: [1] KSPSolve line 339 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > [1]PETSC ERROR: [1] SNES_KSPSolve line 4169 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > [1]PETSC ERROR: [1] SNESSolve_LS line 143 /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > [1]PETSC ERROR: [1] SNESSolve line 3345 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > [1]PETSC ERROR: --------------------- Error Message ------------------------------------ > > [1]PETSC ERROR: Signal received! > > [1]PETSC ERROR: ------------------------------------------------------------------------ > > [1]PETSC ERROR: Petsc Development HG revision: ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 -0500 > > [1]PETSC ERROR: See docs/changes/index.html for recent updates. > > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [1]PETSC ERROR: See docs/index.html for manual pages. > > [1]PETSC ERROR: ------------------------------------------------------------------------ > > [1]PETSC ERROR: ./ex50 on a arch-gnu named barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > [1]PETSC ERROR: Libraries linked from /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > [1]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > [1]PETSC ERROR: Configure options --download-blacs --download-fftw --download-hypre --download-metis --download-mpich --download-mumps --download-parmetis --download-ptscotch --download-scalapack --download-superlu --download-superlu_dist --download-yaml --with-shared-libraries PETSC_ARCH=arch-gnu > > [1]PETSC ERROR: ------------------------------------------------------------------------ > > [1]PETSC ERROR: User provided function() line 0 in unknown directory unknown file > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1 > > [cli_1]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1 > > [2]PETSC ERROR: ------------------------------------------------------------------------ > > [2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > [2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [2]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors > > [2]PETSC ERROR: likely location of problem given in stack below > > [2]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > > [2]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > > [2]PETSC ERROR: INSTEAD the line number of the start of the function > > [2]PETSC ERROR: is given. > > [2]PETSC ERROR: [2] DMCreateDecomposition line 854 /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > [2]PETSC ERROR: [2] PCSetUp_ASM line 161 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > [2]PETSC ERROR: [2] PCSetUp line 810 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > [2]PETSC ERROR: [2] KSPSetUp line 182 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > [2]PETSC ERROR: [2] KSPSolve line 339 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > [2]PETSC ERROR: [2] SNES_KSPSolve line 4169 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > [2]PETSC ERROR: [2] SNESSolve_LS line 143 /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > [2]PETSC ERROR: [2] SNESSolve line 3345 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > [2]PETSC ERROR: --------------------- Error Message ------------------------------------ > > [2]PETSC ERROR: Signal received! > > [2]PETSC ERROR: ------------------------------------------------------------------------ > > [2]PETSC ERROR: Petsc Development HG revision: ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 -0500 > > [2]PETSC ERROR: See docs/changes/index.html for recent updates. > > [2]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [2]PETSC ERROR: See docs/index.html for manual pages. > > [2]PETSC ERROR: ------------------------------------------------------------------------ > > [2]PETSC ERROR: ./ex50 on a arch-gnu named barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > [2]PETSC ERROR: Libraries linked from /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > [2]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > [2]PETSC ERROR: Configure options --download-blacs --download-fftw --download-hypre --download-metis --download-mpich --download-mumps --download-parmetis --download-ptscotch --download-scalapack --download-superlu --download-superlu_dist --download-yaml --with-shared-libraries PETSC_ARCH=arch-gnu > > [2]PETSC ERROR: ------------------------------------------------------------------------ > > [2]PETSC ERROR: User provided function() line 0 in unknown directory unknown file > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2 > > [cli_2]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2 > > [3]PETSC ERROR: ------------------------------------------------------------------------ > > [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > [3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [3]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors > > [3]PETSC ERROR: likely location of problem given in stack below > > [3]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > > [3]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > > [3]PETSC ERROR: INSTEAD the line number of the start of the function > > [3]PETSC ERROR: is given. > > [3]PETSC ERROR: [3] DMCreateDecomposition line 854 /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > [3]PETSC ERROR: [3] PCSetUp_ASM line 161 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > [3]PETSC ERROR: [3] PCSetUp line 810 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > [3]PETSC ERROR: [3] KSPSetUp line 182 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > [3]PETSC ERROR: [3] KSPSolve line 339 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > [3]PETSC ERROR: [3] SNES_KSPSolve line 4169 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > [3]PETSC ERROR: [3] SNESSolve_LS line 143 /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > [3]PETSC ERROR: [3] SNESSolve line 3345 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > [3]PETSC ERROR: --------------------- Error Message ------------------------------------ > > [3]PETSC ERROR: Signal received! > > [3]PETSC ERROR: ------------------------------------------------------------------------ > > [3]PETSC ERROR: Petsc Development HG revision: ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 -0500 > > [3]PETSC ERROR: See docs/changes/index.html for recent updates. > > [3]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [3]PETSC ERROR: See docs/index.html for manual pages. > > [3]PETSC ERROR: ------------------------------------------------------------------------ > > [3]PETSC ERROR: ./ex50 on a arch-gnu named barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > [3]PETSC ERROR: Libraries linked from /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > [3]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > [3]PETSC ERROR: Configure options --download-blacs --download-fftw --download-hypre --download-metis --download-mpich --download-mumps --download-parmetis --download-ptscotch --download-scalapack --download-superlu --download-superlu_dist --download-yaml --with-shared-libraries PETSC_ARCH=arch-gnu > > [3]PETSC ERROR: ------------------------------------------------------------------------ > > [3]PETSC ERROR: User provided function() line 0 in unknown directory unknown file > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3 > > [cli_3]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3 > /Users/barrysmith/Src/petsc-dev/src/snes/examples/tutorials > Possible problem with ex50_6, diffs above > >

1 0

Re: [petsc-dev] DMCreateComposition crash in tests
by Dmitry Karpeev 30 Mar '12

30 Mar '12

Barry, This looks like petsc-dev from about a week ago -- I fixed this bug today. It runs on my laptop right now. Dmitry. On Fri, Mar 30, 2012 at 9:00 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > > [0]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSCERROR: 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] DMCreateDecomposition line 854 > /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > [0]PETSC ERROR: [0] PCSetUp_ASM line 161 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > [0]PETSC ERROR: [0] PCSetUp line 810 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > [0]PETSC ERROR: [0] KSPSetUp line 182 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > [0]PETSC ERROR: [0] KSPSolve line 339 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > [0]PETSC ERROR: [0] SNES_KSPSolve line 4169 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > [0]PETSC ERROR: [0] SNESSolve_LS line 143 > /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > [0]PETSC ERROR: [0] SNESSolve line 3345 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > > [0]PETSC ERROR: Signal received! > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > > [0]PETSC ERROR: Petsc Development HG revision: > ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 > -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: ./ex50 on a arch-gnu named > barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > [0]PETSC ERROR: Libraries linked from > /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > [0]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > [0]PETSC ERROR: Configure options --download-blacs --download-fftw > --download-hypre --download-metis --download-mpich --download-mumps > --download-parmetis --download-ptscotch --download-scalapack > --download-superlu --download-superlu_dist --download-yaml > --with-shared-libraries PETSC_ARCH=arch-gnu > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > > [0]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > [cli_0]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > [1]PETSC ERROR: > ------------------------------------------------------------------------ > > [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > [1]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > > [1]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSCERROR: or try > http://valgrind.org on GNU/linux and Apple Mac OS X to find memory > corruption errors > > [1]PETSC ERROR: likely location of problem given in stack below > > [1]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > > [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > > [1]PETSC ERROR: INSTEAD the line number of the start of the > function > > [1]PETSC ERROR: is given. > > [1]PETSC ERROR: [1] DMCreateDecomposition line 854 > /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > [1]PETSC ERROR: [1] PCSetUp_ASM line 161 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > [1]PETSC ERROR: [1] PCSetUp line 810 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > [1]PETSC ERROR: [1] KSPSetUp line 182 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > [1]PETSC ERROR: [1] KSPSolve line 339 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > [1]PETSC ERROR: [1] SNES_KSPSolve line 4169 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > [1]PETSC ERROR: [1] SNESSolve_LS line 143 > /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > [1]PETSC ERROR: [1] SNESSolve line 3345 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > [1]PETSC ERROR: --------------------- Error Message > ------------------------------------ > > [1]PETSC ERROR: Signal received! > > [1]PETSC ERROR: > ------------------------------------------------------------------------ > > [1]PETSC ERROR: Petsc Development HG revision: > ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 > -0500 > > [1]PETSC ERROR: See docs/changes/index.html for recent updates. > > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [1]PETSC ERROR: See docs/index.html for manual pages. > > [1]PETSC ERROR: > ------------------------------------------------------------------------ > > [1]PETSC ERROR: ./ex50 on a arch-gnu named > barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > [1]PETSC ERROR: Libraries linked from > /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > [1]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > [1]PETSC ERROR: Configure options --download-blacs --download-fftw > --download-hypre --download-metis --download-mpich --download-mumps > --download-parmetis --download-ptscotch --download-scalapack > --download-superlu --download-superlu_dist --download-yaml > --with-shared-libraries PETSC_ARCH=arch-gnu > > [1]PETSC ERROR: > ------------------------------------------------------------------------ > > [1]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1 > > [cli_1]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1 > > [2]PETSC ERROR: > ------------------------------------------------------------------------ > > [2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > [2]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > > [2]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[2]PETSCERROR: or try > http://valgrind.org on GNU/linux and Apple Mac OS X to find memory > corruption errors > > [2]PETSC ERROR: likely location of problem given in stack below > > [2]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > > [2]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > > [2]PETSC ERROR: INSTEAD the line number of the start of the > function > > [2]PETSC ERROR: is given. > > [2]PETSC ERROR: [2] DMCreateDecomposition line 854 > /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > [2]PETSC ERROR: [2] PCSetUp_ASM line 161 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > [2]PETSC ERROR: [2] PCSetUp line 810 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > [2]PETSC ERROR: [2] KSPSetUp line 182 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > [2]PETSC ERROR: [2] KSPSolve line 339 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > [2]PETSC ERROR: [2] SNES_KSPSolve line 4169 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > [2]PETSC ERROR: [2] SNESSolve_LS line 143 > /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > [2]PETSC ERROR: [2] SNESSolve line 3345 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > [2]PETSC ERROR: --------------------- Error Message > ------------------------------------ > > [2]PETSC ERROR: Signal received! > > [2]PETSC ERROR: > ------------------------------------------------------------------------ > > [2]PETSC ERROR: Petsc Development HG revision: > ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 > -0500 > > [2]PETSC ERROR: See docs/changes/index.html for recent updates. > > [2]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [2]PETSC ERROR: See docs/index.html for manual pages. > > [2]PETSC ERROR: > ------------------------------------------------------------------------ > > [2]PETSC ERROR: ./ex50 on a arch-gnu named > barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > [2]PETSC ERROR: Libraries linked from > /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > [2]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > [2]PETSC ERROR: Configure options --download-blacs --download-fftw > --download-hypre --download-metis --download-mpich --download-mumps > --download-parmetis --download-ptscotch --download-scalapack > --download-superlu --download-superlu_dist --download-yaml > --with-shared-libraries PETSC_ARCH=arch-gnu > > [2]PETSC ERROR: > ------------------------------------------------------------------------ > > [2]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2 > > [cli_2]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2 > > [3]PETSC ERROR: > ------------------------------------------------------------------------ > > [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > [3]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > > [3]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[3]PETSCERROR: or try > http://valgrind.org on GNU/linux and Apple Mac OS X to find memory > corruption errors > > [3]PETSC ERROR: likely location of problem given in stack below > > [3]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > > [3]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > > [3]PETSC ERROR: INSTEAD the line number of the start of the > function > > [3]PETSC ERROR: is given. > > [3]PETSC ERROR: [3] DMCreateDecomposition line 854 > /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > > [3]PETSC ERROR: [3] PCSetUp_ASM line 161 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > > [3]PETSC ERROR: [3] PCSetUp line 810 > /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > > [3]PETSC ERROR: [3] KSPSetUp line 182 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > [3]PETSC ERROR: [3] KSPSolve line 339 > /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > > [3]PETSC ERROR: [3] SNES_KSPSolve line 4169 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > [3]PETSC ERROR: [3] SNESSolve_LS line 143 > /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > > [3]PETSC ERROR: [3] SNESSolve line 3345 > /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > > [3]PETSC ERROR: --------------------- Error Message > ------------------------------------ > > [3]PETSC ERROR: Signal received! > > [3]PETSC ERROR: > ------------------------------------------------------------------------ > > [3]PETSC ERROR: Petsc Development HG revision: > ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 > -0500 > > [3]PETSC ERROR: See docs/changes/index.html for recent updates. > > [3]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [3]PETSC ERROR: See docs/index.html for manual pages. > > [3]PETSC ERROR: > ------------------------------------------------------------------------ > > [3]PETSC ERROR: ./ex50 on a arch-gnu named > barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > > [3]PETSC ERROR: Libraries linked from > /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > > [3]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > > [3]PETSC ERROR: Configure options --download-blacs --download-fftw > --download-hypre --download-metis --download-mpich --download-mumps > --download-parmetis --download-ptscotch --download-scalapack > --download-superlu --download-superlu_dist --download-yaml > --with-shared-libraries PETSC_ARCH=arch-gnu > > [3]PETSC ERROR: > ------------------------------------------------------------------------ > > [3]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3 > > [cli_3]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3 > /Users/barrysmith/Src/petsc-dev/src/snes/examples/tutorials > Possible problem with ex50_6, diffs above > >

1 0

DMCreateComposition crash in tests
by Barry Smith 30 Mar '12

30 Mar '12

> [0]PETSC ERROR: ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/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] DMCreateDecomposition line 854 /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > [0]PETSC ERROR: [0] PCSetUp_ASM line 161 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > [0]PETSC ERROR: [0] PCSetUp line 810 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > [0]PETSC ERROR: [0] KSPSetUp line 182 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: [0] KSPSolve line 339 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: [0] SNES_KSPSolve line 4169 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > [0]PETSC ERROR: [0] SNESSolve_LS line 143 /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > [0]PETSC ERROR: [0] SNESSolve line 3345 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > [0]PETSC ERROR: --------------------- Error Message ------------------------------------ > [0]PETSC ERROR: Signal received! > [0]PETSC ERROR: ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Development HG revision: ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 -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: ./ex50 on a arch-gnu named barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > [0]PETSC ERROR: Libraries linked from /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > [0]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > [0]PETSC ERROR: Configure options --download-blacs --download-fftw --download-hypre --download-metis --download-mpich --download-mumps --download-parmetis --download-ptscotch --download-scalapack --download-superlu --download-superlu_dist --download-yaml --with-shared-libraries PETSC_ARCH=arch-gnu > [0]PETSC ERROR: ------------------------------------------------------------------------ > [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > [cli_0]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > [1]PETSC ERROR: ------------------------------------------------------------------------ > [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors > [1]PETSC ERROR: likely location of problem given in stack below > [1]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > [1]PETSC ERROR: INSTEAD the line number of the start of the function > [1]PETSC ERROR: is given. > [1]PETSC ERROR: [1] DMCreateDecomposition line 854 /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > [1]PETSC ERROR: [1] PCSetUp_ASM line 161 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > [1]PETSC ERROR: [1] PCSetUp line 810 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > [1]PETSC ERROR: [1] KSPSetUp line 182 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > [1]PETSC ERROR: [1] KSPSolve line 339 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > [1]PETSC ERROR: [1] SNES_KSPSolve line 4169 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > [1]PETSC ERROR: [1] SNESSolve_LS line 143 /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > [1]PETSC ERROR: [1] SNESSolve line 3345 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > [1]PETSC ERROR: --------------------- Error Message ------------------------------------ > [1]PETSC ERROR: Signal received! > [1]PETSC ERROR: ------------------------------------------------------------------------ > [1]PETSC ERROR: Petsc Development HG revision: ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 -0500 > [1]PETSC ERROR: See docs/changes/index.html for recent updates. > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [1]PETSC ERROR: See docs/index.html for manual pages. > [1]PETSC ERROR: ------------------------------------------------------------------------ > [1]PETSC ERROR: ./ex50 on a arch-gnu named barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > [1]PETSC ERROR: Libraries linked from /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > [1]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > [1]PETSC ERROR: Configure options --download-blacs --download-fftw --download-hypre --download-metis --download-mpich --download-mumps --download-parmetis --download-ptscotch --download-scalapack --download-superlu --download-superlu_dist --download-yaml --with-shared-libraries PETSC_ARCH=arch-gnu > [1]PETSC ERROR: ------------------------------------------------------------------------ > [1]PETSC ERROR: User provided function() line 0 in unknown directory unknown file > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1 > [cli_1]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1 > [2]PETSC ERROR: ------------------------------------------------------------------------ > [2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > [2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [2]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors > [2]PETSC ERROR: likely location of problem given in stack below > [2]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > [2]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > [2]PETSC ERROR: INSTEAD the line number of the start of the function > [2]PETSC ERROR: is given. > [2]PETSC ERROR: [2] DMCreateDecomposition line 854 /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > [2]PETSC ERROR: [2] PCSetUp_ASM line 161 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > [2]PETSC ERROR: [2] PCSetUp line 810 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > [2]PETSC ERROR: [2] KSPSetUp line 182 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > [2]PETSC ERROR: [2] KSPSolve line 339 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > [2]PETSC ERROR: [2] SNES_KSPSolve line 4169 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > [2]PETSC ERROR: [2] SNESSolve_LS line 143 /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > [2]PETSC ERROR: [2] SNESSolve line 3345 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > [2]PETSC ERROR: --------------------- Error Message ------------------------------------ > [2]PETSC ERROR: Signal received! > [2]PETSC ERROR: ------------------------------------------------------------------------ > [2]PETSC ERROR: Petsc Development HG revision: ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 -0500 > [2]PETSC ERROR: See docs/changes/index.html for recent updates. > [2]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [2]PETSC ERROR: See docs/index.html for manual pages. > [2]PETSC ERROR: ------------------------------------------------------------------------ > [2]PETSC ERROR: ./ex50 on a arch-gnu named barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > [2]PETSC ERROR: Libraries linked from /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > [2]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > [2]PETSC ERROR: Configure options --download-blacs --download-fftw --download-hypre --download-metis --download-mpich --download-mumps --download-parmetis --download-ptscotch --download-scalapack --download-superlu --download-superlu_dist --download-yaml --with-shared-libraries PETSC_ARCH=arch-gnu > [2]PETSC ERROR: ------------------------------------------------------------------------ > [2]PETSC ERROR: User provided function() line 0 in unknown directory unknown file > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2 > [cli_2]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2 > [3]PETSC ERROR: ------------------------------------------------------------------------ > [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > [3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [3]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors > [3]PETSC ERROR: likely location of problem given in stack below > [3]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > [3]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > [3]PETSC ERROR: INSTEAD the line number of the start of the function > [3]PETSC ERROR: is given. > [3]PETSC ERROR: [3] DMCreateDecomposition line 854 /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c > [3]PETSC ERROR: [3] PCSetUp_ASM line 161 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c > [3]PETSC ERROR: [3] PCSetUp line 810 /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c > [3]PETSC ERROR: [3] KSPSetUp line 182 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > [3]PETSC ERROR: [3] KSPSolve line 339 /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c > [3]PETSC ERROR: [3] SNES_KSPSolve line 4169 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > [3]PETSC ERROR: [3] SNESSolve_LS line 143 /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c > [3]PETSC ERROR: [3] SNESSolve line 3345 /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c > [3]PETSC ERROR: --------------------- Error Message ------------------------------------ > [3]PETSC ERROR: Signal received! > [3]PETSC ERROR: ------------------------------------------------------------------------ > [3]PETSC ERROR: Petsc Development HG revision: ebfd90d136e614e3f7e877dc536ab77f25382894 HG Date: Fri Mar 23 21:43:17 2012 -0500 > [3]PETSC ERROR: See docs/changes/index.html for recent updates. > [3]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [3]PETSC ERROR: See docs/index.html for manual pages. > [3]PETSC ERROR: ------------------------------------------------------------------------ > [3]PETSC ERROR: ./ex50 on a arch-gnu named barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012 > [3]PETSC ERROR: Libraries linked from /Users/barrysmith/Src/petsc-dev/arch-gnu/lib > [3]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012 > [3]PETSC ERROR: Configure options --download-blacs --download-fftw --download-hypre --download-metis --download-mpich --download-mumps --download-parmetis --download-ptscotch --download-scalapack --download-superlu --download-superlu_dist --download-yaml --with-shared-libraries PETSC_ARCH=arch-gnu > [3]PETSC ERROR: ------------------------------------------------------------------------ > [3]PETSC ERROR: User provided function() line 0 in unknown directory unknown file > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3 > [cli_3]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3 /Users/barrysmith/Src/petsc-dev/src/snes/examples/tutorials Possible problem with ex50_6, diffs above

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Re: [petsc-dev] Weird interaction between VecDuplicate and VecSetBlockSize
by Lisandro Dalcin 30 Mar '12

30 Mar '12

On 30 March 2012 19:34, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > On Mar 30, 2012, at 11:07 AM, Lisandro Dalcin wrote: > >> On 30 March 2012 19:00, Lisandro Dalcin <dalcinl(a)gmail.com> wrote: >>> On 30 March 2012 18:20, Blaise Bourdin <bourdin(a)lsu.edu> wrote: >>>> >>>> On Mar 30, 2012, at 10:13 AM, Jed Brown wrote: >>>> >>>> The PetscLayout is shared. It should probably not be allowed to change block >>>> size after duplicating. >>>> >> >> Actually, reading my previous reply, I did not expressed it well. I DO >> AGREE with you that blocksizes should not be allowed to change once >> set for first time. However, I think PETSc do have some code around >> (in PC?) relying on this and unashamedly changing the bs of an INPUT >> vector! If that was fixed, then we can disable changing bs for Vec. >> But as long as we need to support this misfeature, at least let's try >> to do better around the lines of my patch (BTW, I'm not sure how to >> handle the blocked local to global mapping.... perhaps we can >> reconstruct another one?) > > > Let's locate all the code that changes the block size (after it is set) and eradicate it, then we won't need this bad patch. > I think I complained about this long, long ago: $ grep VecSetBlockSize -nR src/ksp/pc/ src/ksp/pc/impls/fieldsplit/fieldsplit.c:637: ierr = VecSetBlockSize(x,jac->bs);CHKERRQ(ierr); src/ksp/pc/impls/fieldsplit/fieldsplit.c:638: ierr = VecSetBlockSize(y,jac->bs);CHKERRQ(ierr); src/ksp/pc/impls/fieldsplit/fieldsplit.c:710: ierr = VecSetBlockSize(x,jac->bs);CHKERRQ(ierr); src/ksp/pc/impls/fieldsplit/fieldsplit.c:711: ierr = VecSetBlockSize(y,jac->bs);CHKERRQ(ierr); > > I think this can be done by having VecSetBlockSize() simple error out it if the map->bs != -1 and new block size not equals current block size. > Are you sure? How are we going to support the usage below?: VecCreateSeq(comm,n,&vec) VecSetBlockSize(vec,bs) We cannot certainly have a long-living vec with bs=-1, right? -- Lisandro Dalcin --------------- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169

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