[petsc-users] Segmentation violation issue when using MatSetVals in Fortran

[Stefano Zampini]

> On Feb 2, 2017, at 10:25 PM, Austin Herrema <aherrema at iastate.edu> wrote:
> 
> Hello all,
> 
> I'm having a strange issue when using the MatSetVals function in Fortran. The code is quite large, but relevant snippets of what I'm trying to do are below.
> 
>   ! PETSc variable declaration
>   Mat LHS
>   PetscErrorCode ier
>   PetscInt idx1(nsd*nsd*nshl*nshl), idx2(nsd*nsd*nshl*nshl)
>   PetscScalar vals(nsd*nsd*nshl*nshl)
> 
>   ! Code for filling in index and value arrays... I've verified that there are 2304 elements in each array.
> 
>   ! Fill in values
>   call MatSetValues(LHS, nvals, idx1, nvals, idx2, vals, ADD_VALUES, ier)
> 
> Upon executing this, I get a general segmentation violation error. Running in Valgrind I get:
> 
> ==87676== Invalid read of size 8
> ==87676==    at 0x1008D1F45: MatSetValues_SeqAIJ (aij.c:461)
> ==87676==    by 0x1004C523C: MatSetValues (matrix.c:1190)
> ==87676==    by 0x10053F1A5: matsetvalues_ (matrixf.c:696)
> ==87676==    by 0x10005F47D: petsc_fillmat_ (petsc_fillMat.F90:78)
> ==87676==    by 0x10005E5C9: intelmass_shell_ (shell_IntElmAss.F90:330)
> ==87676==    by 0x100057259: solflowgmres_ (solflow.F90:125)
> ==87676==    by 0x100051051: MAIN__ (driver.F90:140)
> ==87676==    by 0x1000545C4: main (driver.F90:7)
> ==87676==  Address 0x10a4dac60 is 0 bytes after a block of size 18,432 alloc'd
> ==87676==    at 0x100088681: malloc (in /usr/local/Cellar/valgrind/3.12.0/lib/valgrind/vgpreload_memcheck-amd64-darwin.so)
> ==87676==    by 0x10005EF47: petsc_fillmat_ (petsc_fillMat.F90:23)
> ==87676==    by 0x10005E5C9: intelmass_shell_ (shell_IntElmAss.F90:330)
> ==87676==    by 0x100057259: solflowgmres_ (solflow.F90:125)
> ==87676==    by 0x100051051: MAIN__ (driver.F90:140)
> ==87676==    by 0x1000545C4: main (driver.F90:7)
> ==87676==
> ==87676== Conditional jump or move depends on uninitialised value(s)
> ==87676==    at 0x1008D1F57: MatSetValues_SeqAIJ (aij.c:463)
> ==87676==    by 0x1004C523C: MatSetValues (matrix.c:1190)
> ==87676==    by 0x10053F1A5: matsetvalues_ (matrixf.c:696)
> ==87676==    by 0x10005F47D: petsc_fillmat_ (petsc_fillMat.F90:78)
> ==87676==    by 0x10005E5C9: intelmass_shell_ (shell_IntElmAss.F90:330)
> ==87676==    by 0x100057259: solflowgmres_ (solflow.F90:125)
> ==87676==    by 0x100051051: MAIN__ (driver.F90:140)
> ==87676==    by 0x1000545C4: main (driver.F90:7)
> ==87676==
> ==87676== Conditional jump or move depends on uninitialised value(s)
> ==87676==    at 0x1008D1F62: MatSetValues_SeqAIJ (aij.c:463)
> ==87676==    by 0x1004C523C: MatSetValues (matrix.c:1190)
> ==87676==    by 0x10053F1A5: matsetvalues_ (matrixf.c:696)
> ==87676==    by 0x10005F47D: petsc_fillmat_ (petsc_fillMat.F90:78)
> ==87676==    by 0x10005E5C9: intelmass_shell_ (shell_IntElmAss.F90:330)
> ==87676==    by 0x100057259: solflowgmres_ (solflow.F90:125)
> ==87676==    by 0x100051051: MAIN__ (driver.F90:140)
> ==87676==    by 0x1000545C4: main (driver.F90:7)
> ==87676==
> 
> I'm not terribly experienced with Valgrind but I can't find anything too helpful in that output. It shows the traceback but I still cannot understand why the error is being produced. Strangely, if I try to set the matrix values in a few smaller chunks, i.e.
> 
>   call MatSetValues(LHS, 500, idx1(1:500), 500, idx2(1:500), vals(1:500), ADD_VALUES, ier)
>   call MatSetValues(LHS, 500, idx1(501:1000), 500, idx2(501:1000), vals(501:1000), ADD_VALUES, ier)
>   call MatSetValues(LHS, 500, idx1(1001:1500), 500, idx2(1001:1500), vals(1001:1500), ADD_VALUES, ier)
>   call MatSetValues(LHS, 500, idx1(1501:2000), 500, idx2(1501:2000), vals(1501:2000), ADD_VALUES, ier)
>   call MatSetValues(LHS, 304, idx1(2001:2304), 304, idx2(2001:2304), vals(2001:2304), ADD_VALUES, ier)
> 

vals is supposed to be a 2D array of size nvals*nvals; it seems to me that the size of your vals is nvals (supposedly, nsd*nsd*nshl*nshl)


> Then everything works with no errors. Is there some kind of limitation to how many values you can insert into a matrix at once? Would strike me as strange. I can assign elements one at a time but reducing the number of calls to MatSetVals by a factor of 2000 would be fantastic. I would be happy to provide more details of the matrix setup if necessary.
> 
> Thank you for any help!
> Austin
> 
> 
> -- 
> Austin Herrema
> PhD Student | Graduate Research Assistant | Iowa State University
> Wind Energy Science, Engineering, and Policy | Mechanical Engineering

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20170202/75418c80/attachment.html>