malloc(): memory corruption:
Matthew Knepley
knepley at gmail.com
Sat Nov 14 16:21:39 CST 2009
This is already bad. You had an Invalid Read and Invalid Write in your
Hypre. Did you build it
yourself? If so, let us build it. If not, please try your matrix on KSP ex10
and see if you get a
crash on 2 procs.
Thanks,
Matt
On Sat, Nov 14, 2009 at 3:51 PM, Dominik Szczerba <dominik at itis.ethz.ch>wrote:
> run onlu in single, he says things like below - but does not crash. Also,
> the program run with -np 1 does not crash. No clear idea though about
> valgrind's output, please advise if this tells you anything...
>
> Call from NS3T10::createSolverContexts() referenced therein is:
>
> ierr = KSPCreate(petsc_comm,&kspSchurVelocity);CHKERRQ(ierr);
>
>
> ==2605== Conditional jump or move depends on uninitialised value(s)
> ==2605== at 0x8AE720F: hypre_BoomerAMGSetPlotFileName (par_amg.c:2115)
> ==2605== by 0x8AE7ED9: hypre_BoomerAMGCreate (par_amg.c:276)
> ==2605== by 0x8AE4A71: HYPRE_BoomerAMGCreate (HYPRE_parcsr_amg.c:31)
> ==2605== by 0x8562019: PCHYPRESetType_HYPRE (hypre.c:850)
> ==2605== by 0x8563068: PCHYPRESetType (hypre.c:964)
> ==2605== by 0x80E67BB: NS3T10::createSolverContexts()
> (NS3T10mpi.cxx:1980)
> ==2605== by 0x80EA63B: NS3T10::solve() (NS3T10mpi.cxx:2306)
> ==2605== by 0x8104860: main (ns3t10mpi_main.cxx:1516)
> ==2605==
> ==2605== Conditional jump or move depends on uninitialised value(s)
> ==2605== at 0x8AE7244: hypre_BoomerAMGSetPlotFileName (par_amg.c:2120)
> ==2605== by 0x8AE7ED9: hypre_BoomerAMGCreate (par_amg.c:276)
> ==2605== by 0x8AE4A71: HYPRE_BoomerAMGCreate (HYPRE_parcsr_amg.c:31)
> ==2605== by 0x8562019: PCHYPRESetType_HYPRE (hypre.c:850)
> ==2605== by 0x8563068: PCHYPRESetType (hypre.c:964)
> ==2605== by 0x80E67BB: NS3T10::createSolverContexts()
> (NS3T10mpi.cxx:1980)
> ==2605== by 0x80EA63B: NS3T10::solve() (NS3T10mpi.cxx:2306)
> ==2605== by 0x8104860: main (ns3t10mpi_main.cxx:1516)
> ==2605==
> ==2605== Conditional jump or move depends on uninitialised value(s)
> ==2605== at 0x4025C16: strcpy (mc_replace_strmem.c:303)
> ==2605== by 0x8AE727A: hypre_BoomerAMGSetPlotFileName (par_amg.c:2123)
> ==2605== by 0x8AE7ED9: hypre_BoomerAMGCreate (par_amg.c:276)
> ==2605== by 0x8AE4A71: HYPRE_BoomerAMGCreate (HYPRE_parcsr_amg.c:31)
> ==2605== by 0x8562019: PCHYPRESetType_HYPRE (hypre.c:850)
> ==2605== by 0x8563068: PCHYPRESetType (hypre.c:964)
> ==2605== by 0x80E67BB: NS3T10::createSolverContexts()
> (NS3T10mpi.cxx:1980)
> ==2605== by 0x80EA63B: NS3T10::solve() (NS3T10mpi.cxx:2306)
> ==2605== by 0x8104860: main (ns3t10mpi_main.cxx:1516)
> ==2605==
> ==2605== Conditional jump or move depends on uninitialised value(s)
> ==2605== at 0x4025C35: strcpy (mc_replace_strmem.c:303)
> ==2605== by 0x8AE727A: hypre_BoomerAMGSetPlotFileName (par_amg.c:2123)
> ==2605== by 0x8AE7ED9: hypre_BoomerAMGCreate (par_amg.c:276)
> ==2605== by 0x8AE4A71: HYPRE_BoomerAMGCreate (HYPRE_parcsr_amg.c:31)
> ==2605== by 0x8562019: PCHYPRESetType_HYPRE (hypre.c:850)
> ==2605== by 0x8563068: PCHYPRESetType (hypre.c:964)
> ==2605== by 0x80E67BB: NS3T10::createSolverContexts()
> (NS3T10mpi.cxx:1980)
> ==2605== by 0x80EA63B: NS3T10::solve() (NS3T10mpi.cxx:2306)
> ==2605== by 0x8104860: main (ns3t10mpi_main.cxx:1516)
> ==2605==
> Solver contexts created in 2.520000 s
> Starting KSPSolve (0/1)
> 0 KSP Residual norm 8.368803253774e-06
> ==2605== Invalid read of size 8
> ==2605== at 0x8B23B5A: hypre_BoomerAMGCreateS (par_strength.c:223)
> ==2605== by 0x8AE966F: hypre_BoomerAMGSetup (par_amg_setup.c:630)
> ==2605== by 0x8AE4A4D: HYPRE_BoomerAMGSetup (HYPRE_parcsr_amg.c:58)
> ==2605== by 0x855A5D9: PCSetUp_HYPRE (hypre.c:134)
> ==2605== by 0x86256A9: PCSetUp (precon.c:794)
> ==2605== by 0x85A6E62: KSPSetUp (itfunc.c:237)
> ==2605== by 0x85A7EAB: KSPSolve (itfunc.c:353)
> ==2605== by 0x80F5B16: applyPrecSchur(void*, _p_Vec*, _p_Vec*)
> (NS3T10mpi.cxx:3741)
> ==2605== by 0x851C47E: PCApply_Shell (shellpc.c:129)
> ==2605== by 0x862074E: PCApply (precon.c:357)
> ==2605== by 0x863AC4C: KSPInitialResidual (itres.c:64)
> ==2605== by 0x85EB09A: KSPSolve_GMRES (gmres.c:241)
> ==2605== Address 0xafae5d0 is 0 bytes after a block of size 93,488 alloc'd
> ==2605== at 0x4023F5B: calloc (vg_replace_malloc.c:418)
> ==2605== by 0x8B4E9C7: hypre_CAlloc (hypre_memory.c:121)
> ==2605== by 0x8B4CA67: hypre_CSRMatrixInitialize (csr_matrix.c:91)
> ==2605== by 0x8B32EC8: hypre_ParCSRMatrixInitialize
> (par_csr_matrix.c:200)
> ==2605== by 0x8AE0C44: hypre_IJMatrixInitializeParCSR
> (IJMatrix_parcsr.c:272)
> ==2605== by 0x8ADBE09: HYPRE_IJMatrixInitialize (HYPRE_IJMatrix.c:302)
> ==2605== by 0x891AD3A: MatHYPRE_IJMatrixFastCopy_SeqAIJ (mhyp.c:174)
> ==2605== by 0x891A2E1: MatHYPRE_IJMatrixCopy (mhyp.c:131)
> ==2605== by 0x855A445: PCSetUp_HYPRE (hypre.c:130)
> ==2605== by 0x86256A9: PCSetUp (precon.c:794)
> ==2605== by 0x85A6E62: KSPSetUp (itfunc.c:237)
> ==2605== by 0x85A7EAB: KSPSolve (itfunc.c:353)
> ==2605==
> ==2605== Invalid write of size 4
> ==2605== at 0x8B23E0C: hypre_BoomerAMGCreateS (par_strength.c:301)
> ==2605== by 0x8AE966F: hypre_BoomerAMGSetup (par_amg_setup.c:630)
> ==2605== by 0x8AE4A4D: HYPRE_BoomerAMGSetup (HYPRE_parcsr_amg.c:58)
> ==2605== by 0x855A5D9: PCSetUp_HYPRE (hypre.c:134)
> ==2605== by 0x86256A9: PCSetUp (precon.c:794)
> ==2605== by 0x85A6E62: KSPSetUp (itfunc.c:237)
> ==2605== by 0x85A7EAB: KSPSolve (itfunc.c:353)
> ==2605== by 0x80F5B16: applyPrecSchur(void*, _p_Vec*, _p_Vec*)
> (NS3T10mpi.cxx:3741)
> ==2605== by 0x851C47E: PCApply_Shell (shellpc.c:129)
> ==2605== by 0x862074E: PCApply (precon.c:357)
> ==2605== by 0x863AC4C: KSPInitialResidual (itres.c:64)
> ==2605== by 0x85EB09A: KSPSolve_GMRES (gmres.c:241)
> ==2605== Address 0xb12a050 is 0 bytes after a block of size 46,744 alloc'd
> ==2605== at 0x4023F5B: calloc (vg_replace_malloc.c:418)
> ==2605== by 0x8B4E9C7: hypre_CAlloc (hypre_memory.c:121)
> ==2605== by 0x8B23980: hypre_BoomerAMGCreateS (par_strength.c:163)
> ==2605== by 0x8AE966F: hypre_BoomerAMGSetup (par_amg_setup.c:630)
> ==2605== by 0x8AE4A4D: HYPRE_BoomerAMGSetup (HYPRE_parcsr_amg.c:58)
> ==2605== by 0x855A5D9: PCSetUp_HYPRE (hypre.c:134)
> ==2605== by 0x86256A9: PCSetUp (precon.c:794)
> ==2605== by 0x85A6E62: KSPSetUp (itfunc.c:237)
> ==2605== by 0x85A7EAB: KSPSolve (itfunc.c:353)
> ==2605== by 0x80F5B16: applyPrecSchur(void*, _p_Vec*, _p_Vec*)
> (NS3T10mpi.cxx:3741)
> ==2605== by 0x851C47E: PCApply_Shell (shellpc.c:129)
> ==2605== by 0x862074E: PCApply (precon.c:357)
> ==2605==
> ...
> ==2605== Invalid read of size 8
> ==2605== at 0x8B1ACE8: hypre_BoomerAMGRelax (par_relax.c:182)
> ==2605== by 0x8B1DFBF: hypre_BoomerAMGRelaxIF
> (par_relax_interface.c:110)
> ==2605== by 0x8AFC310: hypre_BoomerAMGCycle (par_cycle.c:386)
> ==2605== by 0x8AEE09E: hypre_BoomerAMGSolve (par_amg_solve.c:252)
> ==2605== by 0x8AE4A25: HYPRE_BoomerAMGSolve (HYPRE_parcsr_amg.c:76)
> ==2605== by 0x855AAA4: PCApply_HYPRE (hypre.c:172)
> ==2605== by 0x862074E: PCApply (precon.c:357)
> ==2605== by 0x8606095: KSPSolve_PREONLY (preonly.c:29)
> ==2605== by 0x85A85D3: KSPSolve (itfunc.c:385)
> ==2605== by 0x80F5B16: applyPrecSchur(void*, _p_Vec*, _p_Vec*)
> (NS3T10mpi.cxx:3741)
> ==2605== by 0x851C47E: PCApply_Shell (shellpc.c:129)
> ==2605== by 0x862074E: PCApply (precon.c:357)
> ==2605== Address 0xafae5d0 is 0 bytes after a block of size 93,488 alloc'd
> ==2605== at 0x4023F5B: calloc (vg_replace_malloc.c:418)
> ==2605== by 0x8B4E9C7: hypre_CAlloc (hypre_memory.c:121)
> ==2605== by 0x8B4CA67: hypre_CSRMatrixInitialize (csr_matrix.c:91)
> ==2605== by 0x8B32EC8: hypre_ParCSRMatrixInitialize
> (par_csr_matrix.c:200)
> ==2605== by 0x8AE0C44: hypre_IJMatrixInitializeParCSR
> (IJMatrix_parcsr.c:272)
> ==2605== by 0x8ADBE09: HYPRE_IJMatrixInitialize (HYPRE_IJMatrix.c:302)
> ==2605== by 0x891AD3A: MatHYPRE_IJMatrixFastCopy_SeqAIJ (mhyp.c:174)
> ==2605== by 0x891A2E1: MatHYPRE_IJMatrixCopy (mhyp.c:131)
> ==2605== by 0x855A445: PCSetUp_HYPRE (hypre.c:130)
> ==2605== by 0x86256A9: PCSetUp (precon.c:794)
> ==2605== by 0x85A6E62: KSPSetUp (itfunc.c:237)
> ==2605== by 0x85A7EAB: KSPSolve (itfunc.c:353)
> ==2605==
> ...
> 0 KSP Residual norm 8.368803253774e-06
> ==2605== Invalid read of size 8
> ==2605== at 0x8B1ADC0: hypre_BoomerAMGRelax (par_relax.c:196)
> ==2605== by 0x8B1DFBF: hypre_BoomerAMGRelaxIF
> (par_relax_interface.c:110)
> ==2605== by 0x8AFC310: hypre_BoomerAMGCycle (par_cycle.c:386)
> ==2605== by 0x8AEE09E: hypre_BoomerAMGSolve (par_amg_solve.c:252)
> ==2605== by 0x8AE4A25: HYPRE_BoomerAMGSolve (HYPRE_parcsr_amg.c:76)
> ==2605== by 0x855AAA4: PCApply_HYPRE (hypre.c:172)
> ==2605== by 0x862074E: PCApply (precon.c:357)
> ==2605== by 0x8606095: KSPSolve_PREONLY (preonly.c:29)
> ==2605== by 0x85A85D3: KSPSolve (itfunc.c:385)
> ==2605== by 0x80F5B16: applyPrecSchur(void*, _p_Vec*, _p_Vec*)
> (NS3T10mpi.cxx:3741)
> ==2605== by 0x851C47E: PCApply_Shell (shellpc.c:129)
> ==2605== by 0x862074E: PCApply (precon.c:357)
> ==2605== Address 0xcded820 is 0 bytes after a block of size 93,488 alloc'd
> ==2605== at 0x4023F5B: calloc (vg_replace_malloc.c:418)
> ==2605== by 0x8B4E9C7: hypre_CAlloc (hypre_memory.c:121)
> ==2605== by 0x8B4CA67: hypre_CSRMatrixInitialize (csr_matrix.c:91)
> ==2605== by 0x8B32EC8: hypre_ParCSRMatrixInitialize
> (par_csr_matrix.c:200)
> ==2605== by 0x8AE0C44: hypre_IJMatrixInitializeParCSR
> (IJMatrix_parcsr.c:272)
> ==2605== by 0x8ADBE09: HYPRE_IJMatrixInitialize (HYPRE_IJMatrix.c:302)
> ==2605== by 0x891AD3A: MatHYPRE_IJMatrixFastCopy_SeqAIJ (mhyp.c:174)
> ==2605== by 0x891A2E1: MatHYPRE_IJMatrixCopy (mhyp.c:131)
> ==2605== by 0x855A445: PCSetUp_HYPRE (hypre.c:130)
> ==2605== by 0x86256A9: PCSetUp (precon.c:794)
> ==2605== by 0x85A6E62: KSPSetUp (itfunc.c:237)
> ==2605== by 0x85A7EAB: KSPSolve (itfunc.c:353)
> ==2605==
>
>
>
>
> Matthew Knepley wrote:
>
>> Try valgrind.
>>
>> Matt
>>
>>
>> On Sat, Nov 14, 2009 at 3:32 PM, Dominik Szczerba <dominik at itis.ethz.ch<mailto:
>> dominik at itis.ethz.ch>> wrote:
>>
>> Now for something more serious: I get a crash like this one:
>>
>> Starting KSPSolve (1/2)
>> 0 KSP Residual norm 2.964538623545e-06
>> *** glibc detected *** /home/domel/build/solve-debug/ns3t10mpi:
>> malloc(): memory corruption: 0x09258008 ***
>> ======= Backtrace: =========
>> /lib/tls/i686/cmov/libc.so.6[0x5f9ff1]
>> /lib/tls/i686/cmov/libc.so.6[0x5fcbb3]
>> /lib/tls/i686/cmov/libc.so.6(__libc_calloc+0xa9)[0x5fe009]
>> /home/domel/build/solve-debug/ns3t10mpi(hypre_CAlloc+0x2c)[0x8b4ea28]
>>
>> /home/domel/build/solve-debug/ns3t10mpi(hypre_BoomerAMGCoarsenRuge+0xb5)[0x8af2c7b]
>> (and so on)
>>
>> gdb invoked as:
>>
>> mpiexec -np 2 ..... -on_error_attach_debugger -display :0.0
>>
>> does not display any backtrace after the crash.
>>
>> Any hints how to debug are highly appreciated.
>>
>> Dominik
>>
>>
>>
>>
>> --
>> 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
>>
>
>
--
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
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