We had a previous error with pdgssvx in SuperLU I think. Maybe searching petsc-maint would get it?
Matt On Mon, Oct 16, 2017 at 12:21 PM, Mark Adams <mfad...@lbl.gov> wrote: > I just ran this and have a little bit of a stack trace. This is on my > laptop and MPI can be a little flaky here (eg, IBarrier does not work). I > am going to move to Cori soon and I will try to reproduce this. > Thanks, > > ==68941== at 0x103A66AA8: MPIR_Process_status (mpiimpl.h:4394) > ==68941== by 0x103A6852F: MPIC_Waitall (helper_fns.c:774) > ==68941== by 0x1038ECE88: MPIR_Alltoallv_intra (alltoallv.c:194) > ==68941== by 0x1038ED7F9: MPIR_Alltoallv (alltoallv.c:339) > ==68941== by 0x1038EDA53: MPIR_Alltoallv_impl (alltoallv.c:376) > ==68940== at 0x103A66AA8: MPIR_Process_status (mpiimpl.h:4394) > ==68940== by 0x103A6852F: MPIC_Waitall (helper_fns.c:774) > ==68940== by 0x1038ECE88: MPIR_Alltoallv_intra (alltoallv.c:194) > ==68940== by 0x1038ED7F9: MPIR_Alltoallv (alltoallv.c:339) > ==68940== by 0x1038EDA53: MPIR_Alltoallv_impl (alltoallv.c:376) > ==68940== by 0x103719112: MPI_Alltoallv (alltoallv.c:527) > ==68940== by 0x10238B87D: pdCompRow_loc_to_CompCol_global (in > /Users/markadams/Codes/petsc/arch-macosx-gnu-g/lib/ > libsuperlu_dist.5.1.3.dylib) > ==68940== by 0x1023800CB: pdgssvx (in /Users/markadams/Codes/petsc/ > arch-macosx-gnu-g/lib/libsuperlu_dist.5.1.3.dylib) > ==68940== by 0x100AB92DB: MatLUFactorNumeric_SuperLU_DIST > (superlu_dist.c:429) > > > On Mon, Oct 16, 2017 at 12:05 PM, Xiaoye S. Li <x...@lbl.gov> wrote: > >> 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 <mfad...@lbl.gov> 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/arch-macosx-gnu-g/lib/libsuperl >>> u_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. >>> >>> >> > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
