Well that, obviously was erroneously left in. Remove that line, recompile in that directory and it should run ok. Barry On Dec 30, 2010, at 9:49 PM, Gong Ding wrote:
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