[petsc-users] KSPSetUp with PETSc/MUMPS
Satish Balay
balay at mcs.anl.gov
Fri May 27 10:08:38 CDT 2016
Hong,
My fix is already in next [and will merge to maint now].
https://bitbucket.org/petsc/petsc/commits/83fed2ed878cb731bb04364f986d423ef53d20e6
I was hoping you would check the issue with valgrind messages on
MatGetBrowsOfAoCols_MPIAIJ() [As mentioned in my earlier mail - its
probably setting some local variables with uninitialized data for
sequential runs - and perhaps can be fixed by not doing that..]
And I've indicated my changes to Constantin's code in my earlier
e-mail. [I don't see some of my changes in your diff..]
Satish
On Fri, 27 May 2016, Hong wrote:
> Satish,
> I tested your fix on ex51f.F90 (modified from
> build_nullbasis_petsc_mumps.F90) --it gives clean results with valgrind.
>
> Shall you patch it to petsc-maint?
>
> I also like add ex51f.F90 (contributed by Constantin)
> to petsc/src/ksp/ksp/examples/tests/.
>
> Hong
>
>
> On Thu, May 26, 2016 at 5:15 PM, Hong <hzhang at mcs.anl.gov> wrote:
>
> > Satish found a problem in using inode routines.
> >
> > In addition, user code has bugs. I modified
> > build_nullbasis_petsc_mumps.F90 into ex51f.F90 (attached)
> > which works well with option '-mat_no_inode'.
> >
> > ex51f.F90 differs from build_nullbasis_petsc_mumps.F90 in
> > 1) use MATAIJ/MATDENSE instead of MATMPIAIJ/MATMPIDENSE
> > MATAIJ wraps MATSEQAIJ and MATMPIAIJ.
> >
> > 2)
> > MatConvert(x, MATMPIAIJ, MAT_REUSE_MATRIX, x,ierr)
> > ->
> > MatConvert(x, MATMPIAIJ, MAT_INPLACE_MATRIX, x,ierr)
> > see
> > http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatConvert.html
> >
> > Hong
> >
> > On Thu, May 26, 2016 at 3:05 PM, Satish Balay <balay at mcs.anl.gov> wrote:
> >
> >> 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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