[petsc-dev] SuperLU failure with valgrind
Matthew Knepley
knepley at gmail.com
Mon Oct 16 11:31:19 CDT 2017
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 <mfadams at 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 <xsli at 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 <mfadams at 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/>
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