[petsc-dev] Valgrind invalid read in GAMG
John Mousel
john.mousel at gmail.com
Fri Aug 9 09:24:29 CDT 2013
Matt,
Here is the output of ksp_view_binary.
John
binaryoutput<https://docs.google.com/file/d/0B3DmQgVAlCBUVENZSVhtSkE4eTA/edit?usp=drive_web>
On Fri, Aug 9, 2013 at 9:14 AM, Matthew Knepley <knepley at gmail.com> wrote:
> On Fri, Aug 9, 2013 at 8:49 AM, John Mousel <john.mousel at gmail.com> wrote:
>
>> I'm getting the following invalid read when I use GAMG. I've included the
>> output of KSPView at the bottom.
>>
>
> This seems to be a more basic problem in MatGetSubmatrix(). Could you give
> us the matrix? It could be output
> using -ksp_view_binary.
>
> Thanks,
>
> Matt
>
>
>> ==18312== Memcheck, a memory error detector
>> ==18312== Copyright (C) 2002-2012, and GNU GPL'd, by Julian Seward et al.
>> ==18312== Using Valgrind-3.8.1 and LibVEX; rerun with -h for copyright
>> info
>> ==18312== Command: ../src/CYLINDER_EXE -ELAFINT_case_name cylinder
>> -lspaint_ksp_type bcgsl -lspaint_pc_type gamg -lspaint_pc_gamg_type agg
>> -lspaint_pc_gamg_agg_nsmooths 1 -lspaint_pc_gamg_sym_graph true
>> -lspaint_ksp_monitor -pres_ksp_type preonly -pres_pc_type redistribute
>> -pres_redistribute_ksp_type bcgsl -pres_redistribute_pc_type gamg
>> -pres_redistribute_pc_gamg_threshold 0.05
>> -pres_redistribute_mg_levels_ksp_type richardson
>> -pres_redistribute_mg_levels_pc_type sor
>> -pres_redistribute_mg_coarse_ksp_type richardson
>> -pres_redistribute_mg_coarse_pc_type sor
>> -pres_redistribute_mg_coarse_pc_sor_its 5 -pres_redistribute_pc_gamg_type
>> agg -pres_redistribute_pc_gamg_agg_nsmooths 2
>> -pres_redistribute_pc_gamg_sym_graph true
>> -pres_redistribute_ksp_initial_guess_nonzero 0 -vel_ksp_monitor
>> -pres_redistribute_ksp_monitor
>> ==18312== Parent PID: 18308
>> ==18312==
>> ==18311== Invalid read of size 8
>> ==18311== at 0x4DF2BDC: PetscCheckPointer (checkptr.c:52)
>> ==18311== by 0x54370DE: MatSetValues_MPIAIJ (mpiaij.c:506)
>> ==18311== by 0x5462AA8: MatGetSubMatrix_MPIAIJ_Private (mpiaij.c:3860)
>> ==18311== by 0x5461799: MatGetSubMatrix_MPIAIJ (mpiaij.c:3733)
>> ==18311== by 0x551B5E8: MatGetSubMatrix (matrix.c:7322)
>> ==18311== by 0x5817535: createLevel (gamg.c:404)
>> ==18311== by 0x5819420: PCSetUp_GAMG (gamg.c:630)
>> ==18311== by 0x5764D93: PCSetUp (precon.c:890)
>> ==18311== by 0x589B211: KSPSetUp (itfunc.c:278)
>> ==18311== by 0x589C39A: KSPSolve (itfunc.c:399)
>> ==18311== by 0x57555E1: kspsolve_ (itfuncf.c:219)
>> ==18311== by 0x61B7A6: axbsolve_ (Axb.F90:139)
>> ==18311== Address 0x83d9c20 is 9,376 bytes inside a block of size 9,380
>> alloc'd
>> ==18311== at 0x4A06548: memalign (vg_replace_malloc.c:727)
>> ==18311== by 0x4DF2C7D: PetscMallocAlign (mal.c:==18309==
>> ==18309== HEAP SUMMARY:
>> ==18309== in use at exit: 3,262,243 bytes in 17,854 blocks
>> ==18309== total heap usage: 329,856 allocs, 312,002 frees, 136,790,072
>> bytes allocated
>> ==18309==
>> ==18309== LEAK SUMMARY:
>> ==18309== definitely lost: 0 bytes in 0 blocks
>> ==18309== indirectly lost: 0 bytes in 0 blocks
>> ==18309== possibly lost: 0 bytes in 0 blocks
>> ==18309== still reachable: 3,262,243 bytes in 17,854 blocks
>> ==18309== suppressed: 0 bytes in 0 blocks
>> ==18309== Rerun with --leak-check=full to see details of leaked memory
>> ==18309==
>> ==18309== For counts of detected and suppressed errors, rerun with: -v
>> ==18309== Use --track-origins=yes to see where uninitialised values come
>> from
>> ==18309== ERROR SUMMARY: 24 errors from 1 contexts (suppressed: 6 from 6)
>> ,141 frees, 130,288,754 bytes allocated
>> ==18310======18310== LEAK SUMMARY:
>> ==18310== definitely lost: 0 bytes in 0 blocks
>> ==18310== indirectly lost: 0 bytes in 0 blocks
>> ==18310== possibly lost: 0 bytes in 0 blocks
>> ==18310== still reachable: 3,376,159 bytes in 18,772 blocks
>> ==18310== suppressed: 0 bytes in 0 blocks
>> ==18310== Rerun with --leak-check=full to see details of leaked memory
>> ==18310==
>> ==18310== For counts of detected and suppressed errors, rerun with: -v
>> ==18310== ERROR SUMMARY: 2 errors from 1 contexts (suppressed: 6 from 6)
>>
>>
>>
>> KSP Object:(pres_) 4 MPI processes
>> type: preonly
>> maximum iterations=20000, initial guess is zero
>> tolerances: relative=5e-08, absolute=1e-50, divergence=10000
>> left preconditioning
>> using NONE norm type for convergence test
>> PC Object:(pres_) 4 MPI processes
>> type: redistribute
>> Number rows eliminated 820 Percentage rows eliminated 11.6213
>> Redistribute preconditioner:
>> KSP Object: (pres_redistribute_) 4 MPI processes
>> type: bcgsl
>> BCGSL: Ell = 2
>> BCGSL: Delta = 0
>> maximum iterations=20000, initial guess is zero
>> tolerances: relative=5e-08, absolute=1e-50, divergence=10000
>> left preconditioning
>> has attached null space
>> using PRECONDITIONED norm type for convergence test
>> PC Object: (pres_redistribute_) 4 MPI processes
>> type: gamg
>> MG: type is MULTIPLICATIVE, levels=3 cycles=v
>> Cycles per PCApply=1
>> Using Galerkin computed coarse grid matrices
>> Coarse grid solver -- level -------------------------------
>> KSP Object: (pres_redistribute_mg_coarse_) 4 MPI
>> processes
>> type: preonly
>> maximum iterations=1, initial guess is zero
>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000
>> left preconditioning
>> using NONE norm type for convergence test
>> PC Object: (pres_redistribute_mg_coarse_) 4 MPI processes
>> type: sor
>> SOR: type = local_symmetric, iterations = 5, local iterations =
>> 1, omega = 1
>> linear system matrix = precond matrix:
>> Mat Object: 4 MPI processes
>> type: mpiaij
>> rows=61, cols=61
>> total: nonzeros=1846, allocated nonzeros=1846
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node (on process 0) routines
>> Down solver (pre-smoother) on level 1 -------------------------------
>> KSP Object: (pres_redistribute_mg_levels_1_) 4 MPI
>> processes
>> type: richardson
>> Richardson: damping factor=1
>> maximum iterations=2
>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000
>> left preconditioning
>> using nonzero initial guess
>> using NONE norm type for convergence test
>> PC Object: (pres_redistribute_mg_levels_1_) 4 MPI
>> processes
>> type: sor
>> SOR: type = local_symmetric, iterations = 1, local iterations =
>> 1, omega = 1
>> linear system matrix = precond matrix:
>> Mat Object: 4 MPI processes
>> type: mpiaij
>> rows=870, cols=870
>> total: nonzeros=16020, allocated nonzeros=16020
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node (on process 0) routines
>> Up solver (post-smoother) same as down solver (pre-smoother)
>> Down solver (pre-smoother) on level 2 -------------------------------
>> KSP Object: (pres_redistribute_mg_levels_2_) 4 MPI
>> processes
>> type: richardson
>> Richardson: damping factor=1
>> maximum iterations=2
>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000
>> left preconditioning
>> using nonzero initial guess
>> using NONE norm type for convergence test
>> PC Object: (pres_redistribute_mg_levels_2_) 4 MPI
>> processes
>> type: sor
>> SOR: type = local_symmetric, iterations = 1, local iterations =
>> 1, omega = 1
>> linear system matrix = precond matrix:
>> Mat Object: 4 MPI processes
>> type: mpiaij
>> rows=6236, cols=6236
>> total: nonzeros=31220, allocated nonzeros=31220
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node (on process 0) routines
>> Up solver (post-smoother) same as down solver (pre-smoother)
>> linear system matrix = precond matrix:
>> Mat Object: 4 MPI processes
>> type: mpiaij
>> rows=6236, cols=6236
>> total: nonzeros=31220, allocated nonzeros=31220
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node (on process 0) routines
>> linear system matrix = precond matrix:
>> Mat Object: 4 MPI processes
>> type: mpiaij
>> rows=7056, cols=7056
>> total: nonzeros=32416, allocated nonzeros=33180
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node (on process 0) routines
>>
>>
>>
>
>
> --
> 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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