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

[Austin Herrema]

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)

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
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