[petsc-users] pastix solver break at pastix_checkMatrix

Gong Ding gdiso at ustc.edu
Thu Dec 30 21:49:01 CST 2010


Dear  Barry,
First, the patched file has some evident problem.

   PetscScalar *tmpvalues;
   PetscInt    *tmprows,*tmpcolptr;
    tmpvalues = malloc(nnz*sizeof(PetscScalar));
    tmprows   = malloc(nnz*sizeof(PetscInt));
    tmpcolptr = malloc((*n+1)*sizeof(PetscInt));

    ierr = PetscMalloc3(nnz,PetscScalar,&tmpvalues,nnz,PetscInt,&tmprows,(*n+1),PetscInt,&tmpcolptr);CHKERRQ(ierr);  <-- this line alloc meory again.

After comment above line, the pastix works for the first nonlinear iteration. However, it breaks at the second  iteration. valgrind reported:

DDM Solver Level 1 init...
Using PaStiX linear solver...
Compute equilibrium
 its    | Eq(V) | | Eq(n) | | Eq(p) | | Eq(T) | |Eq(Tn)|  |Eq(Tp)|  |delta x|
-----------------------------------------------------------------------------
  0     2.50e-06  2.34e-03  3.12e-04  0.00e+00* 0.00e+00* 0.00e+00* 0.00e+00*
Check : ordering                OK
Check : Graph Symmetry
         Correction
        Add 4090 null terms
                OK
Check : Sort CSC                OK
  1     2.06e-05  7.29e-04  1.03e-04  0.00e+00* 0.00e+00* 0.00e+00* 3.85e-01
Check : ordering                OK
Check : Graph Symmetry==1416== Thread 1:
==1416== Invalid read of size 4
==1416==    at 0x1BC3186: csc_checksym (csc_utils.c:321)
==1416==    by 0x1B4E7E3: pastix_checkMatrix (pastix.c:3915)
==1416==    by 0x1508661: MatConvertToCSC (pastix.c:185)
==1416==    by 0x150AA2E: MatFactorNumeric_PaStiX (pastix.c:396)
==1416==    by 0x139C90B: MatLUFactorNumeric (matrix.c:2587)
==1416==    by 0x16AF49A: PCSetUp_LU (lu.c:158)
==1416==    by 0x1AA0136: PCSetUp (precon.c:795)
==1416==    by 0x16FECC4: KSPSetUp (itfunc.c:237)
==1416==    by 0x16FFF1E: KSPSolve (itfunc.c:353)
==1416==    by 0x17C3061: SNES_KSPSolve (snes.c:2944)
==1416==    by 0x17D33DE: SNESSolve_LS (ls.c:191)
==1416==    by 0x17BCF6C: SNESSolve (snes.c:2255)
==1416==  Address 0x8aeb1a8 is not stack'd, malloc'd or (recently) free'd
==1416==

         Correction==1416== Invalid read of size 4
==1416==    at 0x1BD1147: correct2 (cscsymcsc.c:77)
==1416==    by 0x1B4E8EA: pastix_checkMatrix (pastix.c:3930)
==1416==    by 0x1508661: MatConvertToCSC (pastix.c:185)
==1416==    by 0x150AA2E: MatFactorNumeric_PaStiX (pastix.c:396)
==1416==    by 0x139C90B: MatLUFactorNumeric (matrix.c:2587)
==1416==    by 0x16AF49A: PCSetUp_LU (lu.c:158)
==1416==    by 0x1AA0136: PCSetUp (precon.c:795)
==1416==    by 0x16FECC4: KSPSetUp (itfunc.c:237)
==1416==    by 0x16FFF1E: KSPSolve (itfunc.c:353)
==1416==    by 0x17C3061: SNES_KSPSolve (snes.c:2944)
==1416==    by 0x17D33DE: SNESSolve_LS (ls.c:191)
==1416==    by 0x17BCF6C: SNESSolve (snes.c:2255)
==1416==  Address 0x8aeb1a8 is not stack'd, malloc'd or (recently) free'd
==1416==
==1416== Invalid read of size 4
==1416==    at 0x1BD10D7: correct2 (cscsymcsc.c:67)
==1416==    by 0x1B4E8EA: pastix_checkMatrix (pastix.c:3930)
==1416==    by 0x1508661: MatConvertToCSC (pastix.c:185)
==1416==    by 0x150AA2E: MatFactorNumeric_PaStiX (pastix.c:396)
==1416==    by 0x139C90B: MatLUFactorNumeric (matrix.c:2587)
==1416==    by 0x16AF49A: PCSetUp_LU (lu.c:158)
==1416==    by 0x1AA0136: PCSetUp (precon.c:795)
==1416==    by 0x16FECC4: KSPSetUp (itfunc.c:237)
==1416==    by 0x16FFF1E: KSPSolve (itfunc.c:353)
==1416==    by 0x17C3061: SNES_KSPSolve (snes.c:2944)
==1416==    by 0x17D33DE: SNESSolve_LS (ls.c:191)
==1416==    by 0x17BCF6C: SNESSolve (snes.c:2255)
==1416==  Address 0x8ae7574 is 0 bytes after a block of size 68,180 alloc'd
==1416==    at 0x4A061EF: malloc (vg_replace_malloc.c:236)
==1416==    by 0x15080FF: MatConvertToCSC (pastix.c:168)
==1416==    by 0x150AA2E: MatFactorNumeric_PaStiX (pastix.c:396)
==1416==    by 0x139C90B: MatLUFactorNumeric (matrix.c:2587)
==1416==    by 0x16AF49A: PCSetUp_LU (lu.c:158)
==1416==    by 0x1AA0136: PCSetUp (precon.c:795)
==1416==    by 0x16FECC4: KSPSetUp (itfunc.c:237)
==1416==    by 0x16FFF1E: KSPSolve (itfunc.c:353)
==1416==    by 0x17C3061: SNES_KSPSolve (snes.c:2944)
==1416==    by 0x17D33DE: SNESSolve_LS (ls.c:191)
==1416==    by 0x17BCF6C: SNESSolve (snes.c:2255)
==1416==    by 0x10BAB53: FVM_NonlinearSolver::sens_solve() (fvm_nonlinear_solver.cc:824)
==1416==
==1416== Invalid read of size 4
==1416==    at 0x1BD10EB: correct2 (cscsymcsc.c:72)
==1416==    by 0x1B4E8EA: pastix_checkMatrix (pastix.c:3930)
==1416==    by 0x1508661: MatConvertToCSC (pastix.c:185)
==1416==    by 0x150AA2E: MatFactorNumeric_PaStiX (pastix.c:396)
==1416==    by 0x139C90B: MatLUFactorNumeric (matrix.c:2587)
==1416==    by 0x16AF49A: PCSetUp_LU (lu.c:158)
==1416==    by 0x1AA0136: PCSetUp (precon.c:795)
==1416==    by 0x16FECC4: KSPSetUp (itfunc.c:237)
==1416==    by 0x16FFF1E: KSPSolve (itfunc.c:353)
==1416==    by 0x17C3061: SNES_KSPSolve (snes.c:2944)
==1416==    by 0x17D33DE: SNESSolve_LS (ls.c:191)
==1416==    by 0x17BCF6C: SNESSolve (snes.c:2255)
==1416==  Address 0x8ae7574 is 0 bytes after a block of size 68,180 alloc'd
==1416==    at 0x4A061EF: malloc (vg_replace_malloc.c:236)
==1416==    by 0x15080FF: MatConvertToCSC (pastix.c:168)
==1416==    by 0x150AA2E: MatFactorNumeric_PaStiX (pastix.c:396)
==1416==    by 0x139C90B: MatLUFactorNumeric (matrix.c:2587)
==1416==    by 0x16AF49A: PCSetUp_LU (lu.c:158)
==1416==    by 0x1AA0136: PCSetUp (precon.c:795)
==1416==    by 0x16FECC4: KSPSetUp (itfunc.c:237)
==1416==    by 0x16FFF1E: KSPSolve (itfunc.c:353)
==1416==    by 0x17C3061: SNES_KSPSolve (snes.c:2944)
==1416==    by 0x17D33DE: SNESSolve_LS (ls.c:191)
==1416==    by 0x17BCF6C: SNESSolve (snes.c:2255)
==1416==    by 0x10BAB53: FVM_NonlinearSolver::sens_solve() (fvm_nonlinear_solver.cc:824)
==1416==
==1416== Invalid read of size 4
==1416==    at 0x1BD1102: correct2 (cscsymcsc.c:75)
==1416==    by 0x1B4E8EA: pastix_checkMatrix (pastix.c:3930)
==1416==    by 0x1508661: MatConvertToCSC (pastix.c:185)
==1416==    by 0x150AA2E: MatFactorNumeric_PaStiX (pastix.c:396)
==1416==    by 0x139C90B: MatLUFactorNumeric (matrix.c:2587)
==1416==    by 0x16AF49A: PCSetUp_LU (lu.c:158)
==1416==    by 0x1AA0136: PCSetUp (precon.c:795)
==1416==    by 0x16FECC4: KSPSetUp (itfunc.c:237)
==1416==    by 0x16FFF1E: KSPSolve (itfunc.c:353)
==1416==    by 0x17C3061: SNES_KSPSolve (snes.c:2944)
==1416==    by 0x17D33DE: SNESSolve_LS (ls.c:191)
==1416==    by 0x17BCF6C: SNESSolve (snes.c:2255)
==1416==  Address 0x8d369dc is 4 bytes before a block of size 4,216 alloc'd
==1416==    at 0x4A061EF: malloc (vg_replace_malloc.c:236)
==1416==    by 0x150812B: MatConvertToCSC (pastix.c:169)
==1416==    by 0x150AA2E: MatFactorNumeric_PaStiX (pastix.c:396)
==1416==    by 0x139C90B: MatLUFactorNumeric (matrix.c:2587)
==1416==    by 0x16AF49A: PCSetUp_LU (lu.c:158)
==1416==    by 0x1AA0136: PCSetUp (precon.c:795)
==1416==    by 0x16FECC4: KSPSetUp (itfunc.c:237)
==1416==    by 0x16FFF1E: KSPSolve (itfunc.c:353)
==1416==    by 0x17C3061: SNES_KSPSolve (snes.c:2944)
==1416==    by 0x17D33DE: SNESSolve_LS (ls.c:191)
==1416==    by 0x17BCF6C: SNESSolve (snes.c:2255)
==1416==    by 0x10BAB53: FVM_NonlinearSolver::sens_solve() (fvm_nonlinear_solver.cc:824)
==1416==
==1416== Invalid read of size 4
==1416==    at 0x1BD116D: correct2 (cscsymcsc.c:88)
==1416==    by 0x1B4E8EA: pastix_checkMatrix (pastix.c:3930)
==1416==    by 0x1508661: MatConvertToCSC (pastix.c:185)
==1416==    by 0x150AA2E: MatFactorNumeric_PaStiX (pastix.c:396)
==1416==    by 0x139C90B: MatLUFactorNumeric (matrix.c:2587)
==1416==    by 0x16AF49A: PCSetUp_LU (lu.c:158)
==1416==    by 0x1AA0136: PCSetUp (precon.c:795)
==1416==    by 0x16FECC4: KSPSetUp (itfunc.c:237)
==1416==    by 0x16FFF1E: KSPSolve (itfunc.c:353)
==1416==    by 0x17C3061: SNES_KSPSolve (snes.c:2944)
==1416==    by 0x17D33DE: SNESSolve_LS (ls.c:191)
==1416==    by 0x17BCF6C: SNESSolve (snes.c:2255)
==1416==  Address 0x8ae7574 is 0 bytes after a block of size 68,180 alloc'd
==1416==    at 0x4A061EF: malloc (vg_replace_malloc.c:236)
==1416==    by 0x15080FF: MatConvertToCSC (pastix.c:168)
==1416==    by 0x150AA2E: MatFactorNumeric_PaStiX (pastix.c:396)
==1416==    by 0x139C90B: MatLUFactorNumeric (matrix.c:2587)
==1416==    by 0x16AF49A: PCSetUp_LU (lu.c:158)
==1416==    by 0x1AA0136: PCSetUp (precon.c:795)
==1416==    by 0x16FECC4: KSPSetUp (itfunc.c:237)
==1416==    by 0x16FFF1E: KSPSolve (itfunc.c:353)
==1416==    by 0x17C3061: SNES_KSPSolve (snes.c:2944)
==1416==    by 0x17D33DE: SNESSolve_LS (ls.c:191)
==1416==    by 0x17BCF6C: SNESSolve (snes.c:2255)
==1416==    by 0x10BAB53: FVM_NonlinearSolver::sens_solve() (fvm_nonlinear_solver.cc:824)
==1416==
==1416== Invalid read of size 4
==1416==    at 0x1BD1179: correct2 (cscsymcsc.c:88)
==1416==    by 0x1B4E8EA: pastix_checkMatrix (pastix.c:3930)
==1416==    by 0x1508661: MatConvertToCSC (pastix.c:185)
==1416==    by 0x150AA2E: MatFactorNumeric_PaStiX (pastix.c:396)
==1416==    by 0x139C90B: MatLUFactorNumeric (matrix.c:2587)
==1416==    by 0x16AF49A: PCSetUp_LU (lu.c:158)
==1416==    by 0x1AA0136: PCSetUp (precon.c:795)
==1416==    by 0x16FECC4: KSPSetUp (itfunc.c:237)
==1416==    by 0x16FFF1E: KSPSolve (itfunc.c:353)
==1416==    by 0x17C3061: SNES_KSPSolve (snes.c:2944)
==1416==    by 0x17D33DE: SNESSolve_LS (ls.c:191)
==1416==    by 0x17BCF6C: SNESSolve (snes.c:2255)
==1416==  Address 0x8c1b55c is 4 bytes before a block of size 4,212 alloc'd
==1416==    at 0x4A061EF: malloc (vg_replace_malloc.c:236)
==1416==    by 0x1BD1029: correct2 (cscsymcsc.c:53)
==1416==    by 0x1B4E8EA: pastix_checkMatrix (pastix.c:3930)
==1416==    by 0x1508661: MatConvertToCSC (pastix.c:185)
==1416==    by 0x150AA2E: MatFactorNumeric_PaStiX (pastix.c:396)
==1416==    by 0x139C90B: MatLUFactorNumeric (matrix.c:2587)
==1416==    by 0x16AF49A: PCSetUp_LU (lu.c:158)
==1416==    by 0x1AA0136: PCSetUp (precon.c:795)
==1416==    by 0x16FECC4: KSPSetUp (itfunc.c:237)
==1416==    by 0x16FFF1E: KSPSolve (itfunc.c:353)
==1416==    by 0x17C3061: SNES_KSPSolve (snes.c:2944)
==1416==    by 0x17D33DE: SNESSolve_LS (ls.c:191)
==1416==
==1416== Invalid read of size 4
==1416==    at 0x1BD1186: correct2 (cscsymcsc.c:88)
==1416==    by 0x1B4E8EA: pastix_checkMatrix (pastix.c:3930)
==1416==    by 0x1508661: MatConvertToCSC (pastix.c:185)
==1416==    by 0x150AA2E: MatFactorNumeric_PaStiX (pastix.c:396)
==1416==    by 0x139C90B: MatLUFactorNumeric (matrix.c:2587)
==1416==    by 0x16AF49A: PCSetUp_LU (lu.c:158)
==1416==    by 0x1AA0136: PCSetUp (precon.c:795)
==1416==    by 0x16FECC4: KSPSetUp (itfunc.c:237)
==1416==    by 0x16FFF1E: KSPSolve (itfunc.c:353)
==1416==    by 0x17C3061: SNES_KSPSolve (snes.c:2944)
==1416==    by 0x17D33DE: SNESSolve_LS (ls.c:191)
==1416==    by 0x17BCF6C: SNESSolve (snes.c:2255)
==1416==  Address 0x8ae7574 is 0 bytes after a block of size 68,180 alloc'd
==1416==    at 0x4A061EF: malloc (vg_replace_malloc.c:236)
==1416==    by 0x15080FF: MatConvertToCSC (pastix.c:168)
==1416==    by 0x150AA2E: MatFactorNumeric_PaStiX (pastix.c:396)
==1416==    by 0x139C90B: MatLUFactorNumeric (matrix.c:2587)
==1416==    by 0x16AF49A: PCSetUp_LU (lu.c:158)
==1416==    by 0x1AA0136: PCSetUp (precon.c:795)
==1416==    by 0x16FECC4: KSPSetUp (itfunc.c:237)
==1416==    by 0x16FFF1E: KSPSolve (itfunc.c:353)
==1416==    by 0x17C3061: SNES_KSPSolve (snes.c:2944)
==1416==    by 0x17D33DE: SNESSolve_LS (ls.c:191)
==1416==    by 0x17BCF6C: SNESSolve (snes.c:2255)
==1416==    by 0x10BAB53: FVM_NonlinearSolver::sens_solve() (fvm_nonlinear_solver.cc:824)
==1416==
==1416== Invalid write of size 4
==1416==    at 0x1BD1192: correct2 (cscsymcsc.c:88)
==1416==    by 0x1B4E8EA: pastix_checkMatrix (pastix.c:3930)
==1416==    by 0x1508661: MatConvertToCSC (pastix.c:185)
==1416==    by 0x150AA2E: MatFactorNumeric_PaStiX (pastix.c:396)
==1416==    by 0x139C90B: MatLUFactorNumeric (matrix.c:2587)
==1416==    by 0x16AF49A: PCSetUp_LU (lu.c:158)
==1416==    by 0x1AA0136: PCSetUp (precon.c:795)
==1416==    by 0x16FECC4: KSPSetUp (itfunc.c:237)
==1416==    by 0x16FFF1E: KSPSolve (itfunc.c:353)
==1416==    by 0x17C3061: SNES_KSPSolve (snes.c:2944)
==1416==    by 0x17D33DE: SNESSolve_LS (ls.c:191)
==1416==    by 0x17BCF6C: SNESSolve (snes.c:2255)
==1416==  Address 0x8c1b55c is 4 bytes before a block of size 4,212 alloc'd
==1416==    at 0x4A061EF: malloc (vg_replace_malloc.c:236)
==1416==    by 0x1BD1029: correct2 (cscsymcsc.c:53)
==1416==    by 0x1B4E8EA: pastix_checkMatrix (pastix.c:3930)
==1416==    by 0x1508661: MatConvertToCSC (pastix.c:185)
==1416==    by 0x150AA2E: MatFactorNumeric_PaStiX (pastix.c:396)
==1416==    by 0x139C90B: MatLUFactorNumeric (matrix.c:2587)
==1416==    by 0x16AF49A: PCSetUp_LU (lu.c:158)
==1416==    by 0x1AA0136: PCSetUp (precon.c:795)
==1416==    by 0x16FECC4: KSPSetUp (itfunc.c:237)
==1416==    by 0x16FFF1E: KSPSolve (itfunc.c:353)
==1416==    by 0x17C3061: SNES_KSPSolve (snes.c:2944)
==1416==    by 0x17D33DE: SNESSolve_LS (ls.c:191)
==1416==
[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/petsc-as/documentation/troubleshooting.html#Signal[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 


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