[petsc-users] How to access Vector data properly
Matthew Knepley
knepley at gmail.com
Mon Apr 9 11:42:11 CDT 2018
Did you build EXACTLY the code I sent back?
Thanks,
Matt
On Mon, Apr 9, 2018 at 12:13 PM, Songtao Chu <st.chu at outlook.com> wrote:
> The two output results are different in my test.
> If I use the way of assignment variables in current code. I got error
> output of VecView as below:
> Vec Object: 2 MPI processes
> type: mpi
> Vec Object: Vec_0x7fffd6895a90_0 2 MPI processes
> type: mpi
> Process [0]
> 0.
> 0.
> 0.
> Process [1]
> 0.
> 0.
>
> Or if I use the previous way (DMDANaturalToGlobal), I got error output
> of PetscSynchronizedPrintf:
> Rank=0
> 0 0 0
> Rank=1
> 0 0
>
> Both are fine if I run without mpiexec.
>
> Besides, my development environment is CLion + WSL + GCC 7.3.
>
>
> ------------------------------
> *From:* Matthew Knepley <knepley at gmail.com>
> *Sent:* Tuesday, April 10, 2018 0:01
> *To:* Songtao Chu
> *Cc:* Hong; petsc-users at mcs.anl.gov
> *Subject:* Re: [petsc-users] How to access Vector data properly
>
> This works fine for me:
>
> knepley/feature-pc-patch $:/PETSc3/petsc/petsc-pylith/tmp$
> ../arch-master-debug/bin/mpiexec -n 2 ./tester
>
> Vec Object: 2 MPI processes
>
> type: mpi
>
> Process [0]
>
> 0.
>
> 1.
>
> 2.
>
> Process [1]
>
> 3.
>
> 4.
>
> Rank=0
>
> 0 1 2
>
> Rank=1
>
> 3 4
>
> What is the problem?
>
> Matt
>
>
> On Mon, Apr 9, 2018 at 11:51 AM, Songtao Chu <st.chu at outlook.com> wrote:
>
> static char help[] = "\n\n";
> #include <petscdm.h>
> #include <petscdmda.h>
>
>
> int main(int argc,char **argv)
> {
> PetscMPIInt rank;
> PetscErrorCode ierr;
> Vec global,local,natural;
> DM da;
> PetscReal *val;
> PetscInt i,x,xm;
>
>
> ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
> ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
>
> ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,5,1,1,NULL,&da);CHKERRQ(ierr);
> ierr = DMSetUp(da);CHKERRQ(ierr);
> ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
>
> ierr = DMDAGetCorners(da,&x,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
> ierr = DMDAVecGetArray(da, global, &val);CHKERRQ(ierr);
> ierr = PetscSynchronizedPrintf(PETSC_COMM_SELF, "Rank=%d\n", rank);CHKERRQ(ierr);
> for (i = x; i < x + xm; ++i) {
> val[i] = i;
> }
> ierr = DMDAVecRestoreArray(da, global, &val);CHKERRQ(ierr);
>
> VecView(global,PETSC_VIEWER_STDOUT_WORLD);
>
> ierr = DMDAGetCorners(da,&x,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
> ierr = DMDAVecGetArray(da, global, &val);CHKERRQ(ierr);
> ierr = PetscSynchronizedPrintf(PETSC_COMM_SELF, "Rank=%d\n", rank);CHKERRQ(ierr);
> for (i = x; i < x + xm; ++i) {
> ierr = PetscSynchronizedPrintf(PETSC_COMM_SELF, "%4.f ", val[i]);CHKERRQ(ierr);
> }
> ierr = DMDAVecRestoreArray(da, global, &val);CHKERRQ(ierr);
> PetscSynchronizedFlush(PETSC_COMM_SELF, PETSC_STDOUT);
>
> ierr = PetscFinalize();
> return ierr;
> }
>
>
>
> ------------------------------
> *From:* Matthew Knepley <knepley at gmail.com>
> *Sent:* Monday, April 9, 2018 23:29
> *To:* Chu Songtao
> *Cc:* Hong; petsc-users at mcs.anl.gov
> *Subject:* Re: [petsc-users] How to access Vector data properly
>
> On Mon, Apr 9, 2018 at 11:19 AM, Chu Songtao <st.chu at outlook.com> wrote:
>
> Hong,
> I added the function to the end, but the results didn't change.
> Then I tested another thing, assigning global by Get(Restore)Array instead
> of DMDANaturalToGlobal. And the results switched. VecView outputs 0
> and PetscSynchronizedPrintf outputs correct values. Strange.
>
>
> Send the whole code. You have a logic error somewhere.
>
> Matt
>
>
> ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,5,1,1,NULL,&da);CHKERRQ(ierr);
> ierr = DMSetUp(da);CHKERRQ(ierr);
> ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
>
> ierr = DMDAGetCorners(da,&x,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
> ierr = DMDAVecGetArray(da, global, &val);CHKERRQ(ierr);
> ierr = PetscSynchronizedPrintf(PETSC_COMM_SELF, "Rank=%d\n", rank);CHKERRQ(ierr);
> for (i = x; i < x + xm; ++i) {
> val[i] = i;
> }
> ierr = DMDAVecRestoreArray(da, global, &val);CHKERRQ(ierr);
>
> VecView(global,PETSC_VIEWER_STDOUT_WORLD);
>
> ierr = DMDAGetCorners(da,&x,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
> ierr = DMDAVecGetArray(da, global, &val);CHKERRQ(ierr);
> ierr = PetscSynchronizedPrintf(PETSC_COMM_SELF, "Rank=%d\n", rank);CHKERRQ(ierr);
> for (i = x; i < x + xm; ++i) {
> ierr = PetscSynchronizedPrintf(PETSC_COMM_SELF, "%4.f ", val[i]);CHKERRQ(ierr);
> }
> ierr = DMDAVecRestoreArray(da, global, &val);CHKERRQ(ierr);
> PetscSynchronizedFlush(PETSC_COMM_SELF, PETSC_STDOUT);
>
> $ mpiexec -n 2 ./test0
> Rank=0
> Rank=1
> Vec Object: 2 MPI processes
> type: mpi
> Vec Object: Vec_0x7fffd6629a90_0 2 MPI processes
> type: mpi
> Rank=1
> 3 4 Process [0]
> 0.
> 0.
> 0.
> Process [1]
> 0.
> 0.
> Rank=0
> 0 1 2
>
>
> ------------------------------
>
> Songtao :
> You may need adding PetscSynchronizedFlush() to the end.
> See petsc/src/dm/examples/tests/ex43.c
> Hong
>
> Hello,
> I am just a beginner. Now I get confused on how to correctly use Vec
> and DMDA.
> I set 1D DMDA global vector with natural values for a test. Then use
> VecView and DMDAVecGetArray to view the data, but the results are
> different. I don't know why.
>
> this is the code:
>
> PetscMPIInt rank;
> PetscErrorCode ierr;
> Vec global,local,natural;
> DM da;
> PetscReal *xnatural,*val;
> PetscInt i,start,end,x,xm;
>
>
> ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
> ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
>
> ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,5,1,1,NULL,&da);CHKERRQ(ierr);
> ierr = DMSetUp(da);CHKERRQ(ierr);
> ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
>
> ierr = DMDACreateNaturalVector(da,&natural);CHKERRQ(ierr);
> ierr = VecGetOwnershipRange(natural,&start,&end);CHKERRQ(ierr);
> ierr = VecGetArray(natural,&xnatural);CHKERRQ(ierr);
> for (i=start; i<end; i++) {
> xnatural[i-start] = i;
> }
> ierr = VecRestoreArray(natural,&xnatural);CHKERRQ(ierr);
> ierr = DMDANaturalToGlobalBegin(da,natural,INSERT_VALUES,global);CHKERRQ(ierr);
> ierr = DMDANaturalToGlobalEnd(da,natural,INSERT_VALUES,global);CHKERRQ(ierr);
> ierr = VecDestroy(&natural);CHKERRQ(ierr);
>
> VecView(global,PETSC_VIEWER_STDOUT_WORLD);
>
> ierr = DMDAGetCorners(da,&x,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
> ierr = DMDAVecGetArray(da, global, &val);CHKERRQ(ierr);
> ierr = PetscSynchronizedPrintf(PETSC_COMM_SELF, "Rank=%d\n", rank);CHKERRQ(ierr);
> for (i = x; i < x + xm; ++i) {
> ierr = PetscSynchronizedPrintf(PETSC_COMM_SELF, "%4.f ", val[i]);CHKERRQ(ierr);
> }
> ierr = DMDAVecRestoreArray(da, global, &val);CHKERRQ(ierr);
>
> and the results are:
>
> $ ./test0
> Vec Object: 1 MPI processes
> type: seq
> Vec Object: Vec_0x7ffff3cbc500_0 1 MPI processes
> type: mpi
> Process [0]
> 0.
> 1.
> 2.
> 3.
> 4.
> Rank=0
> 0 1 2 3 4
>
> $ mpiexec -n 2 ./test0
> Vec Object: 2 MPI processes
> type: mpi
> Vec Object: Vec_0x7fffcf948a90_0 2 MPI processes
> type: mpi
> Process [0]
> 0.
> 1.
> 2.
> Process [1]
> 3.
> 4.
> Rank=0
> 0 0 0 Rank=1
> 0 0
>
>
> the seq version is correct, but the mpi version is wrong. Every element in
> val is 0.
>
>
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
>
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
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