[petsc-users] questions regarding simple petsc matrix vector operation

[Karl Lin]

Sure thank you.

On Thu, Apr 25, 2019 at 10:32 AM Smith, Barry F. <bsmith at mcs.anl.gov> wrote:

>
>    Thanks for letting us know. The latest PETSc release automatically
> detects this issue at ./configure time. You might consider upgrading just
> to get the most stable software as we keep improving PETSc.
>
>    Barry
>
>
> > On Apr 25, 2019, at 9:35 AM, Karl Lin <karl.linkui at gmail.com> wrote:
> >
> > Thanks for tip, I figured out the issue. I was linking to ilp64 instead
> of lp64.
> >
> > On Thu, Apr 25, 2019 at 12:34 AM Smith, Barry F. <bsmith at mcs.anl.gov>
> wrote:
> >
> >   I ran your problem fine on one process. no errors.
> >
> >    Suggest you run under valgrind on your system:
> https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind  or if that
> is not useful
> >
> >    Run in the debugger with the option -start_in_debugger noxterm
> >
> >   Good luck,
> >
> > Barry
> >
> >
> >
> > > On Apr 24, 2019, at 10:36 PM, Zhang, Junchao via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
> > >
> > > How many MPI ranks do you use? The following line is suspicious.  I
> guess you do not want a vector of global length 1.
> > > 66   VecSetSizes(b,PETSC_DECIDE,1);
> > >
> > > --Junchao Zhang
> > >
> > >
> > > On Wed, Apr 24, 2019 at 4:14 PM Karl Lin via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
> > > Hi, there
> > >
> > > I have been trying to get a simple program run with the following code:
> > >
> > >  12 int main(int argc,char **args)
> > >  13 {
> > >  14   PetscErrorCode ierr;
> > >  15   Mat            A;
> > >  16   Mat           AT;
> > >  17   Mat            N;
> > >  18   char           name[1024];
> > >  19   char           vname[1024];
> > >  20   char           pass[1024];
> > >  21   PetscBool      flg;
> > >  22   Vec            b,x,u,Ab,Au;
> > >  23   PetscViewer    viewer;                        /* viewer */
> > >  24   PetscMPIInt    rank,size;
> > >  25
> > >  26   KSP            QRsolver;
> > >  27   PC             pc;
> > >  28   PetscInt       its;
> > >  29   PetscReal      norm;
> > >  30
> > >  31   PetscInt       n1, n2, n3, np1, np2, np3, p, jj;
> > >  32
> > >  33   PetscInt       *cols, *dnz, *onz;
> > >  34   PetscScalar    *vals;
> > >  35
> > >  36   ierr = PetscInitialize(&argc,&args,0,help);if (ierr) return ierr;
> > >  37
> > >  38   ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
> > >  39   ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
> > >  40
> > >  41   PetscMalloc1(1, &dnz);
> > >  42   PetscMalloc1(1, &onz);
> > >  43
> > >  44   dnz[0]=2;
> > >  45   onz[0]=1;
> > >  46
> > >  47   MatCreateMPIAIJMKL(PETSC_COMM_WORLD, 1, 2, 1, 2, 2, dnz, 2, onz,
> &A); CHKERRQ(ierr);
> > >  48
> > >  49   PetscMalloc1(2, &cols);
> > >  50   PetscMalloc1(2, &vals);
> > >  51
> > >  52   jj = rank;
> > >  53   cols[0]=0; cols[1]=1;
> > >  54   vals[0]=1.0;vals[1]=1.0;
> > >  55
> > >  56   MatSetValues(A, 1, &jj, 2, cols, vals, INSERT_VALUES);
> > >  57
> > >  58   MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);
> > >  59   MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
> > >  60
> > >  61   VecCreate(PETSC_COMM_WORLD,&x);
> > >  62   VecSetSizes(x,PETSC_DECIDE,2);
> > >  63   VecSetFromOptions(x);
> > >  64
> > >  65   VecCreate(PETSC_COMM_WORLD,&b);
> > >  66   VecSetSizes(b,PETSC_DECIDE,1);
> > >  67   VecSetFromOptions(b);
> > >  68
> > >  69   VecCreate(PETSC_COMM_WORLD,&u);
> > >  70   VecSetSizes(u,PETSC_DECIDE,1);
> > >  71   VecSetFromOptions(u);
> > >  72
> > >  73   VecSet(b, 2.0);
> > >  74   VecSet(u, 0.0);
> > >  75   VecSet(x, 0.0);
> > >  76
> > >  77   MatMult(A, x, u);
> > >  78
> > >  79   VecView(x, PETSC_VIEWER_STDOUT_WORLD);
> > >  80   VecView(b, PETSC_VIEWER_STDOUT_WORLD);
> > >  81   VecView(u, PETSC_VIEWER_STDOUT_WORLD);
> > >  82
> > >  83   VecAXPY(u,-1.0,b);
> > >
> > > However, it always crashes at line 83 even with single process saying:
> > > [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: configure using --with-debugging=yes, recompile, link,
> and run
> > > [0]PETSC ERROR: to get more information on the crash.
> > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > [0]PETSC ERROR: Signal received
> > > [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > > [0]PETSC ERROR: Petsc Release Version 3.10.4, Feb, 26, 2019
> > >
> > > I can't figure out why this would happen. The printout from VecView
> shows every vec value is correct. I will greatly appreciate any tips.
> > >
> > > Regards,
> > > Karl
> > >
> >
>
>
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