[petsc-users] questions regarding simple petsc matrix vector operation
Karl Lin
karl.linkui at gmail.com
Thu Apr 25 11:07:10 CDT 2019
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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