[petsc-users] KSPSetUp with PETSc/MUMPS

Satish Balay balay at mcs.anl.gov
Thu May 26 11:23:52 CDT 2016 

Mat Object: 1 MPI processes
  type: mpiaij
row 0: (0, 0.)  (1, 0.486111) 
row 1: (0, 0.486111)  (1, 0.) 
row 2: (2, 0.)  (3, 0.486111) 
row 3: (4, 0.486111)  (5, -0.486111) 
row 4:
row 5:

The matrix created is funny (empty rows at the end) - so perhaps its
exposing bugs in Mat code? [is that a valid matrix for this code?]

==21091== Use of uninitialised value of size 8
==21091==    at 0x57CA16B: MatGetRowIJ_SeqAIJ_Inode_Symmetric (inode.c:101)
==21091==    by 0x57CBA1C: MatGetRowIJ_SeqAIJ_Inode (inode.c:241)
==21091==    by 0x537C0B5: MatGetRowIJ (matrix.c:7274)
==21091==    by 0x53072FD: MatGetOrdering_ND (spnd.c:18)
==21091==    by 0x530BC39: MatGetOrdering (sorder.c:260)
==21091==    by 0x530A72D: MatGetOrdering (sorder.c:202)
==21091==    by 0x5DDD764: PCSetUp_LU (lu.c:124)
==21091==    by 0x5EBFE60: PCSetUp (precon.c:968)
==21091==    by 0x5FDA1B3: KSPSetUp (itfunc.c:390)
==21091==    by 0x601C17D: kspsetup_ (itfuncf.c:252)
==21091==    by 0x4028B9: MAIN__ (ex1f.F90:104)
==21091==    by 0x403535: main (ex1f.F90:185)


This goes away if  I add:

   call PCFactorSetMatOrderingType(pc,MATORDERINGNATURAL,ierr)

And then there is also:

==21275== Invalid read of size 8
==21275==    at 0x584DE93: MatGetBrowsOfAoCols_MPIAIJ (mpiaij.c:4734)
==21275==    by 0x58970A8: MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable (mpimatmatmult.c:198)
==21275==    by 0x5894A54: MatMatMult_MPIAIJ_MPIAIJ (mpimatmatmult.c:34)
==21275==    by 0x539664E: MatMatMult (matrix.c:9510)
==21275==    by 0x53B3201: matmatmult_ (matrixf.c:1157)
==21275==    by 0x402FC9: MAIN__ (ex1f.F90:149)
==21275==    by 0x4035B9: main (ex1f.F90:186)
==21275==  Address 0xa3d20f0 is 0 bytes after a block of size 48 alloc'd
==21275==    at 0x4C2DF93: memalign (vg_replace_malloc.c:858)
==21275==    by 0x4FDE05E: PetscMallocAlign (mal.c:28)
==21275==    by 0x5240240: VecScatterCreate (vscat.c:1220)
==21275==    by 0x5857708: MatSetUpMultiply_MPIAIJ (mmaij.c:116)
==21275==    by 0x581C31E: MatAssemblyEnd_MPIAIJ (mpiaij.c:747)
==21275==    by 0x53680F2: MatAssemblyEnd (matrix.c:5187)
==21275==    by 0x53B24D2: matassemblyend_ (matrixf.c:926)
==21275==    by 0x40262C: MAIN__ (ex1f.F90:60)
==21275==    by 0x4035B9: main (ex1f.F90:186)


Satish

-----------

$ diff build_nullbasis_petsc_mumps.F90 ex1f.F90
3,7c3
< #include <petsc/finclude/petscsys.h>
< #include "petsc/finclude/petscvec.h"
< #include "petsc/finclude/petscmat.h"
< #include "petsc/finclude/petscpc.h"
< #include "petsc/finclude/petscksp.h"
---
> #include "petsc/finclude/petsc.h"
40,41c36,37
<    call PetscViewerBinaryOpen(PETSC_COMM_WORLD, "mat_c_bin.txt", 0, viewer, ierr) 
<    call MatLoad(mat_c, viewer)
---
>    call PetscViewerBinaryOpen(PETSC_COMM_WORLD, "mat_c_bin.txt", FILE_MODE_READ, viewer, ierr) 
>    call MatLoad(mat_c, viewer,ierr)
75a72
>    call PCFactorSetMatOrderingType(pc,MATORDERINGNATURAL,ierr)
150c147
<    call MatConvert(x, MATMPIAIJ, MAT_REUSE_MATRIX, x, ierr)
---
>    call MatConvert(x, MATMPIAIJ, MAT_INPLACE_MATRIX, x, ierr)


On Thu, 26 May 2016, Matthew Knepley wrote:

> Usually this means you have an uninitialized variable that is causing you
> to overwrite memory. Fortran
> is so lax in checking this, its one reason to switch to C.
> 
>   Thanks,
> 
>     Matt
> 
> On Thu, May 26, 2016 at 1:46 AM, Constantin Nguyen Van <
> constantin.nguyen.van at openmailbox.org> wrote:
> 
> > Thanks for all your answers.
> > I'm sorry for the syntax mistake in MatLoad, it was done afterwards.
> >
> > I recompile PETSC --with-debugging=yes and run my code again.
> > Now, I also have this strange behaviour. When I run the code without
> > valgrind and with one proc, I have this error message:
> >
> >  BEGIN PROC           0
> >  ITERATION           1
> >  ECHO 1
> >  ECHO 2
> >  INFOG(28):           2
> >  BASIS OK           0
> >  END PROC             0
> >  BEGIN PROC           0
> >  ITERATION           2
> >  ECHO 1
> >  ECHO 2
> >  INFOG(28):           2
> >  BASIS OK           0
> >  END PROC             0
> >  BEGIN PROC           0
> >  ITERATION           3
> >  ECHO 1
> > [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: likely location of problem given in stack below
> > [0]PETSC ERROR: ---------------------  Stack Frames
> > ------------------------------------
> > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> > available,
> > [0]PETSC ERROR:       INSTEAD the line number of the start of the function
> > [0]PETSC ERROR:       is given.
> > [0]PETSC ERROR: [0] MatGetRowIJ_SeqAIJ_Inode_Symmetric line 69
> > /home/j10077/librairie/petsc-mumps/petsc-3.6.4/src/mat/impls/aij/seq/inode.c
> > [0]PETSC ERROR: [0] MatGetRowIJ_SeqAIJ_Inode line 235
> > /home/j10077/librairie/petsc-mumps/petsc-3.6.4/src/mat/impls/aij/seq/inode.c
> > [0]PETSC ERROR: [0] MatGetRowIJ line 7099
> > /home/j10077/librairie/petsc-mumps/petsc-3.6.4/src/mat/interface/matrix.c
> > [0]PETSC ERROR: [0] MatGetOrdering_ND line 17
> > /home/j10077/librairie/petsc-mumps/petsc-3.6.4/src/mat/order/spnd.c
> > [0]PETSC ERROR: [0] MatGetOrdering line 185
> > /home/j10077/librairie/petsc-mumps/petsc-3.6.4/src/mat/order/sorder.c
> > [0]PETSC ERROR: [0] MatGetOrdering line 185
> > /home/j10077/librairie/petsc-mumps/petsc-3.6.4/src/mat/order/sorder.c
> > [0]PETSC ERROR: [0] PCSetUp_LU line 99
> > /home/j10077/librairie/petsc-mumps/petsc-3.6.4/src/ksp/pc/impls/factor/lu/lu.c
> > [0]PETSC ERROR: [0] PCSetUp line 945
> > /home/j10077/librairie/petsc-mumps/petsc-3.6.4/src/ksp/pc/interface/precon.c
> > [0]PETSC ERROR: [0] KSPSetUp line 247
> > /home/j10077/librairie/petsc-mumps/petsc-3.6.4/src/ksp/ksp/interface/itfunc.c
> >
> > But when I run it with valgrind, it does work well.
> >
> > Le 2016-05-25 20:04, Barry Smith a écrit :
> >
> >> First run with valgrind
> >> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> >>
> >> On May 25, 2016, at 2:35 AM, Constantin Nguyen Van
> >>> <constantin.nguyen.van at openmailbox.org> wrote:
> >>>
> >>> Hi,
> >>>
> >>> I'm a new user of PETSc and I try to use it with MUMPS
> >>> functionalities to compute a nullbasis.
> >>> I wrote a code where I compute 4 times the same nullbasis. It does
> >>> work well when I run it with several procs but with only one
> >>> processor I get an error on the 2nd iteration when KSPSetUp is
> >>> called. Furthermore when it is run with a debugger (
> >>> --with-debugging=yes), it works fine with one or several processors.
> >>> Have you got any idea about why it doesn't work with one processor
> >>> and no debugger?
> >>>
> >>> Thanks.
> >>> Constantin.
> >>>
> >>> PS: You can find the code and the files required to run it enclosed.
> >>>
> >>
> 
> 
>

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