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 <[email protected]> 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 <[email protected]> > 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 <[email protected]> > 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 < > > > >> [email protected]> 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 > > > >>>>> <[email protected]> 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. > > > >>>>> > > > >>>> > > > >> > > > >> > > > > > > > > >
ex51f.F90
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