Mark, Is it possible to get the line number? For example, the first failure is
==63582== Conditional jump or move depends on uninitialised value(s) ==63582== at 0x103A5FAA8: MPIR_Process_status (mpiimpl.h:4394) ==63582== by 0x103A6152F: MPIC_Waitall (helper_fns.c:774) ==63582== by 0x1038E2A34: MPIR_Alltoall_intra (alltoall.c:369) ==63582== by 0x1038E35E1: MPIR_Alltoall (alltoall.c:564) ==63582== by 0x1038E37E6: MPIR_Alltoall_impl (alltoall.c:599) ==63582== by 0x1037106AD: MPI_Alltoall (alltoall.c:722) ==63582== by 0x10236EA7C: static_schedule (in /Users/markadams/Codes/petsc/arch-macosx-gnu-g/lib/libsuperl u_dist.5.1.3.dylib) I checked all the MPI_alltoall in static_schedule() routine, I don't see any problem. Sherry On Mon, Oct 16, 2017 at 7:21 AM, Mark Adams <[email protected]> wrote: > FYI, I get this error on one processor with SuperLU under valgrind. Could > this just be a valgrind issue? > > Mark > > /Users/markadams/Codes/petsc/arch-macosx-gnu-g/bin/mpiexec -n 1 valgrind > --dsymutil=yes --leak-check=no --gen-suppressions=no --num-callers=20 > --error-limit=no ./ex48 -debug 2 -dim 2 -dm_refine 3 -ts_monitor -implicit > true -ts_type beuler -pc_type lu -pc_factor_mat_solver_package superlu_dist > -ksp_type preonly -snes_monitor -snes_rtol 1.e-10 -snes_stol 1.e-10 > -snes_converged_reason -snes_atol 1.e-18 -snes_converged_reason > -petscspace_order 2 -petscspace_poly_tensor -ts_max_steps 1 -ts_dt 1.e-3 > -eps 1.e-12 -eta 0.001 -ves 0.005 -beta 0.01 -mu 0.0002 -dm_view > hdf5:sol.h5 -vec_view hdf5:sol.h5::append -dm_plex_periodic_cut > -y_periodicity PERIODIC -cells 2,4 -Jop 4.99 -line_dir 1,1 -line_coord > 3.14159265359,1.57079632679 -real_view :u.m:ascii_matlab -fft_view > :spectra.m:ascii_matlab > ==63582== Memcheck, a memory error detector > ==63582== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. > ==63582== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright > info > ==63582== Command: ./ex48 -debug 2 -dim 2 -dm_refine 3 -ts_monitor > -implicit true -ts_type beuler -pc_type lu -pc_factor_mat_solver_package > superlu_dist -ksp_type preonly -snes_monitor -snes_rtol 1.e-10 -snes_stol > 1.e-10 -snes_converged_reason -snes_atol 1.e-18 -snes_converged_reason > -petscspace_order 2 -petscspace_poly_tensor -ts_max_steps 1 -ts_dt 1.e-3 > -eps 1.e-12 -eta 0.001 -ves 0.005 -beta 0.01 -mu 0.0002 -dm_view > hdf5:sol.h5 -vec_view hdf5:sol.h5::append -dm_plex_periodic_cut > -y_periodicity PERIODIC -cells 2,4 -Jop 4.99 -line_dir 1,1 -line_coord > 3.14159265359,1.57079632679 -real_view :u.m:ascii_matlab -fft_view > :spectra.m:ascii_matlab > ==63582== > ==63582== Syscall param msg->desc.port.name points to uninitialised > byte(s) > ==63582== at 0x103FE134A: mach_msg_trap (in > /usr/lib/system/libsystem_kernel.dylib) > ==63582== by 0x103FE0796: mach_msg (in /usr/lib/system/libsystem_kern > el.dylib) > ==63582== by 0x103FDA485: task_set_special_port (in > /usr/lib/system/libsystem_kernel.dylib) > ==63582== by 0x10817810E: _os_trace_create_debug_control_port (in > /usr/lib/system/libsystem_trace.dylib) > ==63582== by 0x108178458: _libtrace_init (in > /usr/lib/system/libsystem_trace.dylib) > ==63582== by 0x1036119DF: libSystem_initializer (in > /usr/lib/libSystem.B.dylib) > ==63582== by 0x100034A1A: ImageLoaderMachO::doModInitFun > ctions(ImageLoader::LinkContext const&) (in /usr/lib/dyld) > ==63582== by 0x100034C1D: > ImageLoaderMachO::doInitialization(ImageLoader::LinkContext > const&) (in /usr/lib/dyld) > ==63582== by 0x1000304A9: ImageLoader::recursiveInitiali > zation(ImageLoader::LinkContext const&, unsigned int, char const*, > ImageLoader::InitializerTimingList&, ImageLoader::UninitedUpwards&) (in > /usr/lib/dyld) > ==63582== by 0x100030440: ImageLoader::recursiveInitiali > zation(ImageLoader::LinkContext const&, unsigned int, char const*, > ImageLoader::InitializerTimingList&, ImageLoader::UninitedUpwards&) (in > /usr/lib/dyld) > ==63582== by 0x10002F523: > ImageLoader::processInitializers(ImageLoader::LinkContext > const&, unsigned int, ImageLoader::InitializerTimingList&, > ImageLoader::UninitedUpwards&) (in /usr/lib/dyld) > ==63582== by 0x10002F5B8: > ImageLoader::runInitializers(ImageLoader::LinkContext > const&, ImageLoader::InitializerTimingList&) (in /usr/lib/dyld) > ==63582== by 0x100021433: dyld::initializeMainExecutable() (in > /usr/lib/dyld) > ==63582== by 0x1000258C5: dyld::_main(macho_header const*, unsigned > long, int, char const**, char const**, char const**, unsigned long*) (in > /usr/lib/dyld) > ==63582== by 0x100020248: dyldbootstrap::start(macho_header const*, > int, char const**, long, macho_header const*, unsigned long*) (in > /usr/lib/dyld) > ==63582== by 0x100020035: _dyld_start (in /usr/lib/dyld) > ==63582== by 0x3E: ??? > ==63582== by 0x1080A84C2: ??? > ==63582== by 0x1080A84C9: ??? > ==63582== by 0x1080A84D0: ??? > ==63582== Address 0x1080a60fc is on thread 1's stack > ==63582== in frame #2, created by task_set_special_port (???:) > ==63582== > --63582-- UNKNOWN mach_msg unhandled MACH_SEND_TRAILER option > --63582-- UNKNOWN mach_msg unhandled MACH_SEND_TRAILER option (repeated 2 > times) > --63582-- UNKNOWN mach_msg unhandled MACH_SEND_TRAILER option (repeated 4 > times) > Jop=4.99 > DeltaPrime=1.81627 > eta=0.001 > beta=0.01 > mu=0.0002 > ves=0.005 > ==63582== Warning: invalid file descriptor -1 in syscall read() > 0) total perturbed mass = 0. > 0 TS dt 0.001 time 0. > 0 SNES Function norm 5.917661770415e-01 > ==63582== Conditional jump or move depends on uninitialised value(s) > ==63582== at 0x103A5FAA8: MPIR_Process_status (mpiimpl.h:4394) > ==63582== by 0x103A6152F: MPIC_Waitall (helper_fns.c:774) > ==63582== by 0x1038E2A34: MPIR_Alltoall_intra (alltoall.c:369) > ==63582== by 0x1038E35E1: MPIR_Alltoall (alltoall.c:564) > ==63582== by 0x1038E37E6: MPIR_Alltoall_impl (alltoall.c:599) > ==63582== by 0x1037106AD: MPI_Alltoall (alltoall.c:722) > ==63582== by 0x10236EA7C: static_schedule (in > /Users/markadams/Codes/petsc/arch-macosx-gnu-g/lib/libsuperl > u_dist.5.1.3.dylib) > ==63582== by 0x10239923C: pdgstrf (in /Users/markadams/Codes/petsc/a > rch-macosx-gnu-g/lib/libsuperlu_dist.5.1.3.dylib) > ==63582== by 0x10237D696: pdgssvx_ABglobal (in > /Users/markadams/Codes/petsc/arch-macosx-gnu-g/lib/libsuperl > u_dist.5.1.3.dylib) > ==63582== by 0x100AB1F02: MatLUFactorNumeric_SuperLU_DIST > (superlu_dist.c:423) > ==63582== by 0x10053AD98: MatLUFactorNumeric (matrix.c:3039) > ==63582== by 0x1012075CD: PCSetUp_LU (lu.c:131) > ==63582== by 0x10134D65B: PCSetUp (precon.c:924) > ==63582== by 0x101496E11: KSPSetUp (itfunc.c:378) > ==63582== by 0x101499143: KSPSolve (itfunc.c:609) > ==63582== by 0x1015F9410: SNESSolve_NEWTONLS (ls.c:224) > ==63582== by 0x101574290: SNESSolve (snes.c:4106) > ==63582== by 0x10179B43C: TS_SNESSolve (theta.c:176) > ==63582== by 0x10178F7CE: TSStep_Theta (theta.c:216) > ==63582== by 0x1016C1D62: TSStep (ts.c:4120) > ==63582== > ==63582== Conditional jump or move depends on uninitialised value(s) > ==63582== at 0x103A5FAA8: MPIR_Process_status (mpiimpl.h:4394) > ==63582== by 0x103A6152F: MPIC_Waitall (helper_fns.c:774) > ==63582== by 0x1038E5E88: MPIR_Alltoallv_intra (alltoallv.c:194) > ==63582== by 0x1038E67F9: MPIR_Alltoallv (alltoallv.c:339) > ==63582== by 0x1038E6A53: MPIR_Alltoallv_impl (alltoallv.c:376) > ==63582== by 0x103712112: MPI_Alltoallv (alltoallv.c:527) > ==63582== by 0x10236ECF1: static_schedule (in > /Users/markadams/Codes/petsc/arch-macosx-gnu-g/lib/libsuperl > u_dist.5.1.3.dylib) > ==63582== by 0x10239923C: pdgstrf (in /Users/markadams/Codes/petsc/a > rch-macosx-gnu-g/lib/libsuperlu_dist.5.1.3.dylib) > ==63582== by 0x10237D696: pdgssvx_ABglobal (in > /Users/markadams/Codes/petsc/arch-macosx-gnu-g/lib/libsuperl > u_dist.5.1.3.dylib) > ==63582== by 0x100AB1F02: MatLUFactorNumeric_SuperLU_DIST > (superlu_dist.c:423) > ==63582== by 0x10053AD98: MatLUFactorNumeric (matrix.c:3039) > ==63582== by 0x1012075CD: PCSetUp_LU (lu.c:131) > ==63582== by 0x10134D65B: PCSetUp (precon.c:924) > ==63582== by 0x101496E11: KSPSetUp (itfunc.c:378) > ==63582== by 0x101499143: KSPSolve (itfunc.c:609) > ==63582== by 0x1015F9410: SNESSolve_NEWTONLS (ls.c:224) > ==63582== by 0x101574290: SNESSolve (snes.c:4106) > ==63582== by 0x10179B43C: TS_SNESSolve (theta.c:176) > ==63582== by 0x10178F7CE: TSStep_Theta (theta.c:216) > ==63582== by 0x1016C1D62: TSStep (ts.c:4120) > ==63582== > ==63582== Thread 2: > ==63582== Invalid read of size 4 > ==63582== at 0x10814A2B1: _pthread_wqthread (in > /usr/lib/system/libsystem_pthread.dylib) > ==63582== by 0x10814A07C: start_wqthread (in > /usr/lib/system/libsystem_pthread.dylib) > ==63582== Address 0x18 is not stack'd, malloc'd or (recently) free'd > ==63582== > ==63582== Invalid read of size 8 > ==63582== at 0x1081489D6: pthread_getspecific (in > /usr/lib/system/libsystem_pthread.dylib) > ==63582== by 0x100286A5B: PetscVSNPrintf (mprint.c:132) > ==63582== by 0x1002871A3: PetscVFPrintfDefault (mprint.c:241) > ==63582== by 0x10028A1E6: PetscFPrintf (mprint.c:546) > ==63582== by 0x1002A1BE9: PetscErrorPrintfDefault (errtrace.c:114) > ==63582== by 0x1002A3C5D: PetscSignalHandlerDefault (signal.c:135) > ==63582== by 0x1002A4A79: PetscSignalHandler_Private (signal.c:47) > ==63582== by 0x25805BDBD: ??? > ==63582== by 0x10814A07C: start_wqthread (in > /usr/lib/system/libsystem_pthread.dylib) > ==63582== Address 0x50 is not stack'd, malloc'd or (recently) free'd > ==63582== > ==63582== > ==63582== Process terminating with default action of signal 11 (SIGSEGV) > ==63582== Access not within mapped region at address 0x50 > ==63582== at 0x1081489D6: pthread_getspecific (in > /usr/lib/system/libsystem_pthread.dylib) > ==63582== by 0x100286A5B: PetscVSNPrintf (mprint.c:132) > ==63582== by 0x1002871A3: PetscVFPrintfDefault (mprint.c:241) > ==63582== by 0x10028A1E6: PetscFPrintf (mprint.c:546) > ==63582== by 0x1002A1BE9: PetscErrorPrintfDefault (errtrace.c:114) > ==63582== by 0x1002A3C5D: PetscSignalHandlerDefault (signal.c:135) > ==63582== by 0x1002A4A79: PetscSignalHandler_Private (signal.c:47) > ==63582== by 0x25805BDBD: ??? > ==63582== by 0x10814A07C: start_wqthread (in > /usr/lib/system/libsystem_pthread.dylib) > ==63582== If you believe this happened as a result of a stack > ==63582== overflow in your program's main thread (unlikely but > ==63582== possible), you can try to increase the size of the > ==63582== main thread stack using the --main-stacksize= flag. > ==63582== The main thread stack size used in this run was 67104768. > > valgrind: m_scheduler/scheduler.c:881 (void run_thread_for_a_while(HWord > *, Int *, ThreadId, HWord, Bool)): Assertion 'VG_(stats__n_xindirs_32) == > 0' failed. > > host stacktrace: > ==63582== at 0x25804121C: ??? > ==63582== by 0x258041587: ??? > ==63582== by 0x25804156A: ??? > ==63582== by 0x2580BB25F: ??? > ==63582== by 0x2580B95EA: ??? > ==63582== by 0x2580CA83B: ??? > ==63582== by 0x2580CAAF8: ??? > > sched status: > running_tid=3 > > Thread 1: status = VgTs_Yielding (lwpid 771) > ==63582== at 0x10239F9DE: dscatter_u (in /Users/markadams/Codes/petsc/a > rch-macosx-gnu-g/lib/libsuperlu_dist.5.1.3.dylib) > ==63582== by 0x10239EF4F: pdgstrf (in /Users/markadams/Codes/petsc/a > rch-macosx-gnu-g/lib/libsuperlu_dist.5.1.3.dylib) > ==63582== by 0x10237D696: pdgssvx_ABglobal (in > /Users/markadams/Codes/petsc/arch-macosx-gnu-g/lib/libsuperl > u_dist.5.1.3.dylib) > ==63582== by 0x100AB1F02: MatLUFactorNumeric_SuperLU_DIST > (superlu_dist.c:423) > ==63582== by 0x10053AD98: MatLUFactorNumeric (matrix.c:3039) > ==63582== by 0x1012075CD: PCSetUp_LU (lu.c:131) > ==63582== by 0x10134D65B: PCSetUp (precon.c:924) > ==63582== by 0x101496E11: KSPSetUp (itfunc.c:378) > ==63582== by 0x101499143: KSPSolve (itfunc.c:609) > ==63582== by 0x1015F9410: SNESSolve_NEWTONLS (ls.c:224) > ==63582== by 0x101574290: SNESSolve (snes.c:4106) > ==63582== by 0x10179B43C: TS_SNESSolve (theta.c:176) > ==63582== by 0x10178F7CE: TSStep_Theta (theta.c:216) > ==63582== by 0x1016C1D62: TSStep (ts.c:4120) > ==63582== by 0x1016C56A3: TSSolve (ts.c:4374) > ==63582== by 0x100004E0E: main (ex48.c:1061) > > Thread 2: status = VgTs_Yielding (lwpid 4099) > ==63582== at 0x1081489D6: pthread_getspecific (in > /usr/lib/system/libsystem_pthread.dylib) > ==63582== by 0x100286A5B: PetscVSNPrintf (mprint.c:132) > ==63582== by 0x1002871A3: PetscVFPrintfDefault (mprint.c:241) > ==63582== by 0x10028A1E6: PetscFPrintf (mprint.c:546) > ==63582== by 0x1002A1BE9: PetscErrorPrintfDefault (errtrace.c:114) > ==63582== by 0x1002A3C5D: PetscSignalHandlerDefault (signal.c:135) > ==63582== by 0x1002A4A79: PetscSignalHandler_Private (signal.c:47) > ==63582== by 0x25805BDBD: ??? > ==63582== by 0x10814A07C: start_wqthread (in > /usr/lib/system/libsystem_pthread.dylib) > > Thread 3: status = VgTs_Runnable (lwpid 3843) > ==63582== at 0x10814A070: start_wqthread (in > /usr/lib/system/libsystem_pthread.dylib) > > > Note: see also the FAQ in the source distribution. > It contains workarounds to several common problems. > In particular, if Valgrind aborted or crashed after > identifying problems in your program, there's a good chance > that fixing those problems will prevent Valgrind aborting or > crashing, especially if it happened in m_mallocfree.c. > >
