[petsc-users] KSPSetUp with PETSc/MUMPS
Satish Balay
balay at mcs.anl.gov
Thu May 26 15:05:09 CDT 2016
Well looks like MatGetBrowsOfAoCols_MPIAIJ() issue is primarily
setting some local variables with uninitialzed data [thats primarily
set/used for parallel commumication]. So valgrind flags it - but I
don't think it gets used later on.
[perhaps most of the code should be skipped for a sequential run..]
The primary issue here is MatGetRowIJ_SeqAIJ_Inode_Symmetric() called
by MatGetOrdering_ND().
The workarround is to not use ND with:
call PCFactorSetMatOrderingType(pc,MATORDERINGNATURAL,ierr)
But I think the following might be the fix [have to recheck].. The
test code works with this change [with the default ND]
diff --git a/src/mat/impls/aij/seq/inode.c b/src/mat/impls/aij/seq/inode.c
index 9af404e..49f76ce 100644
--- a/src/mat/impls/aij/seq/inode.c
+++ b/src/mat/impls/aij/seq/inode.c
@@ -97,6 +97,7 @@ static PetscErrorCode MatGetRowIJ_SeqAIJ_Inode_Symmetric(Mat A,const PetscInt *i
j = aj + ai[row] + ishift;
jmax = aj + ai[row+1] + ishift;
+ if (j==jmax) continue; /* empty row */
col = *j++ + ishift;
i2 = tvc[col];
while (i2<i1 && j<jmax) { /* 1.[-xx-d-xx--] 2.[-xx-------],off-diagonal elemets */
@@ -125,6 +126,7 @@ static PetscErrorCode MatGetRowIJ_SeqAIJ_Inode_Symmetric(Mat A,const PetscInt *i
for (i1=0,row=0; i1<nslim_row; row += ns_row[i1],i1++) {
j = aj + ai[row] + ishift;
jmax = aj + ai[row+1] + ishift;
+ if (j==jmax) continue; /* empty row */
col = *j++ + ishift;
i2 = tvc[col];
while (i2<i1 && j<jmax) {
Satish
On Thu, 26 May 2016, Hong wrote:
> I'll investigate this - had a day off since yesterday.
> Hong
>
> On Thu, May 26, 2016 at 12:04 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
> >
> > Hong needs to run with this matrix and add appropriate error checkers in
> > the matrix routines to detect "incomplete" matrices and likely just error
> > out.
> >
> > Barry
> >
> > > On May 26, 2016, at 11:23 AM, Satish Balay <balay at mcs.anl.gov> wrote:
> > >
> > > 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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