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

[Smith, Barry F.]

   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
> > 
>