[petsc-users] many valgrind error of petsc string functions

Fri Dec 2 03:52:06 CST 2011

Valgrind reported many errors about string processing functionss of petsc.
These error seems harmless, but really ugly.

Some are 

==5137== Invalid read of size 8
==5137==    at 0x171A9EA: PetscStrlen (str.c:149)
==5137==    by 0x171B272: PetscStrallocpy (str.c:185)
==5137==    by 0x16CAD73: PetscFListGetPathAndFunction (reg.c:24)
==5137==    by 0x16C833A: PetscFListFind (reg.c:355)
==5137==    by 0x1871568: MatSetType (matreg.c:62)
==5137==    by 0x197B2D8: MatGetFactor_aij_mumps (mumps.c:1310)
==5137==    by 0x1845DD3: MatGetFactor (matrix.c:3950)
==5137==    by 0x1C9949F: PCSetUp_LU (lu.c:133)
==5137==    by 0x1F5B26B: PCSetUp (precon.c:819)
==5137==    by 0x1CEAD36: KSPSetUp (itfunc.c:260)
==5137==    by 0x1CE67C3: KSPSolve (itfunc.c:379)
==5137==    by 0x1DA4F08: SNES_KSPSolve (snes.c:3396)
==5137==  Address 0xcc09e10 is 0 bytes inside a block of size 7 alloc'd
==5137==    at 0x4A06936: memalign (vg_replace_malloc.c:694)
==5137==    by 0x16D6EFA: PetscMallocAlign (mal.c:30)
==5137==    by 0x171B2C0: PetscStrallocpy (str.c:186)
==5137==    by 0x16DCD3A: PetscObjectChangeTypeName (pname.c:134)
==5137==    by 0x1943A53: MatCreate_MPIAIJ (mpiaij.c:5528)
==5137==    by 0x18715C9: MatSetType (matreg.c:73)
==5137==    by 0x124790C: FVM_NonlinearSolver::setup_nonlinear_data() (fvm_nonlinear_solver.cc:214)
==5137==    by 0x1143BF0: DDMSolverBase::create_solver() (ddm_solver.cc:66)
==5137==    by 0xFD7442: DDM1Solver::create_solver() (ddm1.cc:46)
==5137==    by 0xEC7A61: SolverControl::do_solve(Parser::Card const&) (control.cc:1081)
==5137==    by 0xEB9688: SolverControl::mainloop() (control.cc:200)
==5137==    by 0x141B97A: main (main.cc:225)
==5137==
==5139== Invalid read of size 8
==5139==    at 0x171A9EA: PetscStrlen (str.c:149)
==5139==    by 0x171B272: PetscStrallocpy (str.c:185)
==5139==    by 0x16CAD73: PetscFListGetPathAndFunction (reg.c:24)
==5139==    by 0x16C833A: PetscFListFind (reg.c:355)
==5139==    by 0x1871568: MatSetType (matreg.c:62)
==5139==    by 0x197B2D8: MatGetFactor_aij_mumps (mumps.c:1310)
==5139==    by 0x1845DD3: MatGetFactor (matrix.c:3950)
==5139==    by 0x1C9949F: PCSetUp_LU (lu.c:133)
==5139==    by 0x1F5B26B: PCSetUp (precon.c:819)
==5139==    by 0x1CEAD36: KSPSetUp (itfunc.c:260)
==5139==    by 0x1CE67C3: KSPSolve (itfunc.c:379)
==5139==    by 0x1DA4F08: SNES_KSPSolve (snes.c:3396)
==5139==  Address 0xb1225e0 is 0 bytes inside a block of size 7 alloc'd
==5139==    at 0x4A06936: memalign (vg_replace_malloc.c:694)
==5139==    by 0x16D6EFA: PetscMallocAlign (mal.c:30)
==5139==    by 0x171B2C0: PetscStrallocpy (str.c:186)
==5139==    by 0x16DCD3A: PetscObjectChangeTypeName (pname.c:134)
==5139==    by 0x1943A53: MatCreate_MPIAIJ (mpiaij.c:5528)
==5139==    by 0x18715C9: MatSetType (matreg.c:73)
==5139==    by 0x124790C: FVM_NonlinearSolver::setup_nonlinear_data() (fvm_nonlinear_solver.cc:214)
==5139==    by 0x1143BF0: DDMSolverBase::create_solver() (ddm_solver.cc:66)
==5139==    by 0xFD7442: DDM1Solver::create_solver() (ddm1.cc:46)
==5139==    by 0xEC7A61: SolverControl::do_solve(Parser::Card const&) (control.cc:1081)
==5139==    by 0xEB9688: SolverControl::mainloop() (control.cc:200)
==5139==    by 0x141B97A: main (main.cc:225)
==5139==
==5136== Invalid read of size 8
==5136==    at 0x171A9EA: PetscStrlen (str.c:149)
==5136==    by 0x171B272: PetscStrallocpy (str.c:185)
==5136==    by 0x16CAD73: PetscFListGetPathAndFunction (reg.c:24)
==5136==    by 0x16C833A: PetscFListFind (reg.c:355)
==5136==    by 0x1871568: MatSetType (matreg.c:62)
==5136==    by 0x197B2D8: MatGetFactor_aij_mumps (mumps.c:1310)
==5136==    by 0x1845DD3: MatGetFactor (matrix.c:3950)
==5136==    by 0x1C9949F: PCSetUp_LU (lu.c:133)
==5136==    by 0x1F5B26B: PCSetUp (precon.c:819)
==5136==    by 0x1CEAD36: KSPSetUp (itfunc.c:260)
==5136==    by 0x1CE67C3: KSPSolve (itfunc.c:379)
==5136==    by 0x1DA4F08: SNES_KSPSolve (snes.c:3396)
==5136==  Address 0xabde120 is 0 bytes inside a block of size 7 alloc'd
==5136==    at 0x4A06936: memalign (vg_replace_malloc.c:694)
==5136==    by 0x16D6EFA: PetscMallocAlign (mal.c:30)
==5136==    by 0x171B2C0: PetscStrallocpy (str.c:186)
==5136==    by 0x16DCD3A: PetscObjectChangeTypeName (pname.c:134)
==5136==    by 0x1943A53: MatCreate_MPIAIJ (mpiaij.c:5528)
==5136==    by 0x18715C9: MatSetType (matreg.c:73)
==5136==    by 0x124790C: FVM_NonlinearSolver::setup_nonlinear_data() (fvm_nonlinear_solver.cc:214)
==5136==    by 0x1143BF0: DDMSolverBase::create_solver() (ddm_solver.cc:66)
==5136==    by 0xFD7442: DDM1Solver::create_solver() (ddm1.cc:46)
==5136==    by 0xEC7A61: SolverControl::do_solve(Parser::Card const&) (control.cc:1081)
==5136==    by 0xEB9688: SolverControl::mainloop() (control.cc:200)
==5136==    by 0x141B97A: main (main.cc:225)
==5136==
==5138== Invalid read of size 8
==5138==    at 0x171A9EA: PetscStrlen (str.c:149)
==5138==    by 0x171B272: PetscStrallocpy (str.c:185)
==5138==    by 0x16CAD73: PetscFListGetPathAndFunction (reg.c:24)
==5138==    by 0x16C833A: PetscFListFind (reg.c:355)
==5138==    by 0x1871568: MatSetType (matreg.c:62)
==5138==    by 0x197B2D8: MatGetFactor_aij_mumps (mumps.c:1310)
==5138==    by 0x1845DD3: MatGetFactor (matrix.c:3950)
==5138==    by 0x1C9949F: PCSetUp_LU (lu.c:133)
==5138==    by 0x1F5B26B: PCSetUp (precon.c:819)
==5138==    by 0x1CEAD36: KSPSetUp (itfunc.c:260)
==5138==    by 0x1CE67C3: KSPSolve (itfunc.c:379)
==5138==    by 0x1DA4F08: SNES_KSPSolve (snes.c:3396)
==5138==  Address 0xe316cb0 is 0 bytes inside a block of size 7 alloc'd
==5138==    at 0x4A06936: memalign (vg_replace_malloc.c:694)
==5138==    by 0x16D6EFA: PetscMallocAlign (mal.c:30)
==5138==    by 0x171B2C0: PetscStrallocpy (str.c:186)
==5138==    by 0x16DCD3A: PetscObjectChangeTypeName (pname.c:134)
==5138==    by 0x1943A53: MatCreate_MPIAIJ (mpiaij.c:5528)
==5138==    by 0x18715C9: MatSetType (matreg.c:73)
==5138==    by 0x124790C: FVM_NonlinearSolver::setup_nonlinear_data() (fvm_nonlinear_solver.cc:214)
==5138==    by 0x1143BF0: DDMSolverBase::create_solver() (ddm_solver.cc:66)
==5138==    by 0xFD7442: DDM1Solver::create_solver() (ddm1.cc:46)
==5138==    by 0xEC7A61: SolverControl::do_solve(Parser::Card const&) (control.cc:1081)
==5138==    by 0xEB9688: SolverControl::mainloop() (control.cc:200)
==5138==    by 0x141B97A: main (main.cc:225)

and more

==5138== Conditional jump or move depends on uninitialised value(s)
==5138==    at 0x171A9FA: PetscStrlen (str.c:149)
==5138==    by 0x171B272: PetscStrallocpy (str.c:185)
==5138==    by 0x16CAD73: PetscFListGetPathAndFunction (reg.c:24)
==5138==    by 0x16CA932: PetscFListAdd (reg.c:204)
==5138==    by 0x1DA2D21: SNESRegister (snes.c:3059)
==5138==    by 0x1D8AD1C: SNESRegisterAll (snesregi.c:48)
==5138==    by 0x1DAF496: SNESInitializePackage (dlregissnes.c:53)
==5138==    by 0x1DA6FE9: SNESCreate (snes.c:1051)
==5138==    by 0x1246CD6: FVM_NonlinearSolver::FVM_NonlinearSolver(SimulationSystem&) (fvm_nonlinear_solver.cc:158)
==5138==    by 0x12500F6: FVM_NonlinearSolver::FVM_NonlinearSolver(SimulationSystem&) (fvm_nonlinear_solver.cc:0)
==5138==    by 0x11439E2: DDMSolverBase::DDMSolverBase(SimulationSystem&) (ddm_solver.cc:36)
==5138==    by 0x114C0F8: DDMSolverBase::DDMSolverBase(SimulationSystem&) (ddm_solver.cc:0)
==5138==
==5138== Conditional jump or move depends on uninitialised value(s)
==5138==    at 0x171B284: PetscStrallocpy (str.c:186)
==5138==    by 0x16CAD73: PetscFListGetPathAndFunction (reg.c:24)
==5138==    by 0x16CA932: PetscFListAdd (reg.c:204)
==5138==    by 0x1DA2D21: SNESRegister (snes.c:3059)
==5138==    by 0x1D8AD1C: SNESRegisterAll (snesregi.c:48)
==5138==    by 0x1DAF496: SNESInitializePackage (dlregissnes.c:53)
==5138==    by 0x1DA6FE9: SNESCreate (snes.c:1051)
==5138==    by 0x1246CD6: FVM_NonlinearSolver::FVM_NonlinearSolver(SimulationSystem&) (fvm_nonlinear_solver.cc:158)
==5138==    by 0x12500F6: FVM_NonlinearSolver::FVM_NonlinearSolver(SimulationSystem&) (fvm_nonlinear_solver.cc:0)
==5138==    by 0x11439E2: DDMSolverBase::DDMSolverBase(SimulationSystem&) (ddm_solver.cc:36)
==5138==    by 0x114C0F8: DDMSolverBase::DDMSolverBase(SimulationSystem&) (ddm_solver.cc:0)
==5137== Conditional jump or move depends on uninitialised value(s)
==5137==    at 0x171A9FA: PetscStrlen (str.c:149)
==5137==    by 0x171B272: PetscStrallocpy (str.c:185)
==5137==    by 0x16CAD73: PetscFListGetPathAndFunction (reg.c:24)
==5137==    by 0x16CA932: PetscFListAdd (reg.c:204)
==5137==    by 0x1DA2D21: SNESRegister (snes.c:3059)
==5137==    by 0x1D8AD1C: SNESRegisterAll (snesregi.c:48)
==5137==    by 0x1DAF496: SNESInitializePackage (dlregissnes.c:53)
==5137==    by 0x1DA6FE9: SNESCreate (snes.c:1051)
==5138==    by 0xEB6E86: DDM1Solver::DDM1Solver(SimulationSystem&) (ddm1.h:37)
==5137==    by 0x1246CD6: FVM_NonlinearSolver::FVM_NonlinearSolver(SimulationSystem&) (fvm_nonlinear_solver.cc:158)
==5137==    by 0x12500F6: FVM_NonlinearSolver::FVM_NonlinearSolver(SimulationSystem&) (fvm_nonlinear_solver.cc:0)
==5137==    by 0x11439E2: DDMSolverBase::DDMSolverBase(SimulationSystem&) (ddm_solver.cc:36)
==5137==    by 0x114C0F8: DDMSolverBase::DDMSolverBase(SimulationSystem&) (ddm_solver.cc:0)
==5137==
==5137== Conditional jump or move depends on uninitialised value(s)
==5137==    at 0x171B284: PetscStrallocpy (str.c:186)
==5137==    by 0x16CAD73: PetscFListGetPathAndFunction (reg.c:24)
==5137==    by 0x16CA932: PetscFListAdd (reg.c:204)
==5137==    by 0x1DA2D21: SNESRegister (snes.c:3059)
==5137==    by 0x1D8AD1C: SNESRegisterAll (snesregi.c:48)
==5137==    by 0x1DAF496: SNESInitializePackage (dlregissnes.c:53)
==5137==    by 0x1DA6FE9: SNESCreate (snes.c:1051)
==5137==    by 0x1246CD6: FVM_NonlinearSolver::FVM_NonlinearSolver(SimulationSystem&) (fvm_nonlinear_solver.cc:158)
==5137==    by==5138==
 0x12500F6: FVM_NonlinearSolver::FVM_NonlinearSolver(SimulationSystem&) (fvm_nonlinear_solver.cc:0)
==5137==    by 0x11439E2: DDMSolverBase::DDMSolverBase(SimulationSystem&) (ddm_solver.cc:36)
==5137==    by 0x114C0F8: DDMSolverBase::DDMSolverBase(SimulationSystem&) (ddm_solver.cc:0)
==5137==    by 0xEB6E86: DDM1Solver::DDM1Solver(SimulationSystem&) (ddm1.h:37)