[petsc-users] np>1 valgrind error comes out

Wed Apr 21 10:27:48 CDT 2010

Some of these MPICH messages could be spurious. Its best to use
--download-mpich to avoid these messages.

http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#valgrind

Satish

On Wed, 21 Apr 2010, (Rebecca) Xuefei YUAN wrote:

> Dear all,
> 
> I was wrong at the previous message about the valgrind result. If np=1,
> valgrind says ok, but when np=2 it is not.
> 
> It seems to me that the error comes from the initial set ups with wrong size :
> 
> Address 0x46b6d78 is 368 bytes inside a [MPICH2 handle: objptr=0x46b6c08
> handle=0xec00000c INDIRECT/REQUEST] of size 372 client-defined
> 
> Could you please take a look at this error message:
> 
> rebecca at YuanWork:~/linux/code/twoway/twoway_new/valgrind$ mpiexec -np 2
> valgrind --leak-check=full ./twqt2ff.exe -options_file option_all_twqt2ff
> ==546== Memcheck, a memory error detector
> ==546== Copyright (C) 2002-2009, and GNU GPL'd, by Julian Seward et al.
> ==546== Using Valgrind-3.5.0 and LibVEX; rerun with -h for copyright info
> ==546== Command: ./twqt2ff.exe -options_file option_all_twqt2ff
> ==546==
> ==547== Memcheck, a memory error detector
> ==547== Copyright (C) 2002-2009, and GNU GPL'd, by Julian Seward et al.
> ==547== Using Valgrind-3.5.0 and LibVEX; rerun with -h for copyright info
> ==547== Command: ./twqt2ff.exe -options_file option_all_twqt2ff
> ==547==
> **************************************************
> number of processors = 2
> viscosity = 1.0000000000000000e-03
> resistivity = 1.0000000000000000e-03
> skin depth = 1.0000000000000000e+00
> hyper resistivity = 1.8204444444444448e-04
> hyper viscosity = 7.2817777777777792e-01
> problem size: 31 by 31
> dx = 4.1290322580645161e-01
> dy = 2.1333333333333335e-01
> dt = 5.0000000000000003e-02
> adaptive time step size (1:yes;0:no) = 0
> **************************************************
>  0 SNES Function norm 4.632833297189e-02
> ==546== Invalid read of size 4
> ==546==    at 0x8872994: MPIDI_CH3I_Progress_handle_sock_event
> (ch3_progress.c:738)
> ==546==    by 0x8872EE7: MPIDI_CH3I_Progress (ch3_progress.c:212)
> ==546==    by 0x8851E94: PMPI_Waitany (waitany.c:203)
> ==546==    by 0x841A61C: MatGetSubMatrices_MPIAIJ_Local (mpiov.c:1195)
> ==546==    by 0x8414E3A: MatGetSubMatrices_MPIAIJ (mpiov.c:781)
> ==546==    by 0x832B67C: MatGetSubMatrices (matrix.c:5823)
> ==546==    by 0x816580B: PCSetUp_ASM (asm.c:299)
> ==546==    by 0x8131CD5: PCSetUp (precon.c:795)
> ==546==    by 0x81D6B2D: KSPSetUp (itfunc.c:237)
> ==546==    by 0x81D7C1F: KSPSolve (itfunc.c:353)
> ==546==    by 0x80FEF93: SNES_KSPSolve (snes.c:2931)
> ==546==    by 0x811A7C0: SNESSolve_LS (ls.c:191)
> ==546==  Address 0x46b6d78 is 368 bytes inside a [MPICH2 handle:
> objptr=0x46b6c08 handle=0xec00000c INDIRECT/REQUEST] of size 372
> client-defined
> ==546==    at 0x8866BCA: MPIU_Handle_obj_alloc_unsafe (handlemem.c:219)
> ==546==    by 0x88B3810: MPIDI_CH3U_Recvq_FDU_or_AEP (ch3u_recvq.c:342)
> ==546==    by 0x887CF77: MPID_Irecv (mpid_irecv.c:46)
> ==546==    by 0x8840290: MPIC_Sendrecv (helper_fns.c:153)
> ==546==    by 0x8835810: MPIR_Barrier (barrier.c:75)
> ==546==    by 0x8835B07: MPIR_Barrier_or_coll_fn (barrier.c:244)
> ==546==    by 0x8835BC8: PMPI_Barrier (barrier.c:421)
> ==546==    by 0x875B472: PetscCommDuplicate (tagm.c:190)
> ==546==    by 0x875F272: PetscHeaderCreate_Private (inherit.c:44)
> ==546==    by 0x81EA967: KSPCreate (itcreate.c:477)
> ==546==    by 0x81530F4: PCMGCreate_Private (mg.c:95)
> ==546==    by 0x8158F42: PCMGSetLevels (mg.c:623)
> ==546==
> ==547== Invalid read of size 4
> ==547==    at 0x8872994: MPIDI_CH3I_Progress_handle_sock_event
> (ch3_progress.c:738)
> ==547==    by 0x8872EE7: MPIDI_CH3I_Progress (ch3_progress.c:212)
> ==547==    by 0x8851E94: PMPI_Waitany (waitany.c:203)
> ==547==    by 0x841B4B7: MatGetSubMatrices_MPIAIJ_Local (mpiov.c:1306)
> ==547==    by 0x8414E3A: MatGetSubMatrices_MPIAIJ (mpiov.c:781)
> ==547==    by 0x832B67C: MatGetSubMatrices (matrix.c:5823)
> ==547==    by 0x816580B: PCSetUp_ASM (asm.c:299)
> ==547==    by 0x8131CD5: PCSetUp (precon.c:795)
> ==547==    by 0x81D6B2D: KSPSetUp (itfunc.c:237)
> ==547==    by 0x81D7C1F: KSPSolve (itfunc.c:353)
> ==547==    by 0x80FEF93: SNES_KSPSolve (snes.c:2931)
> ==547==    by 0x811A7C0: SNESSolve_LS (ls.c:191)
> ==547==  Address 0x45ba490 is 368 bytes inside a [MPICH2 handle:
> objptr=0x45ba320 handle=0xec00000c INDIRECT/REQUEST] of size 372
> client-defined
> ==547==    at 0x8866BCA: MPIU_Handle_obj_alloc_unsafe (handlemem.c:219)
> ==547==    by 0x88B3810: MPIDI_CH3U_Recvq_FDU_or_AEP (ch3u_recvq.c:342)
> ==547==    by 0x887CF77: MPID_Irecv (mpid_irecv.c:46)
> ==547==    by 0x8840290: MPIC_Sendrecv (helper_fns.c:153)
> ==547==    by 0x8835810: MPIR_Barrier (barrier.c:75)
> ==547==    by 0x8835B07: MPIR_Barrier_or_coll_fn (barrier.c:244)
> ==547==    by 0x8835BC8: PMPI_Barrier (barrier.c:421)
> ==547==    by 0x875B472: PetscCommDuplicate (tagm.c:190)
> ==547==    by 0x875F272: PetscHeaderCreate_Private (inherit.c:44)
> ==547==    by 0x81EA967: KSPCreate (itcreate.c:477)
> ==547==    by 0x81530F4: PCMGCreate_Private (mg.c:95)
> ==547==    by 0x8158F42: PCMGSetLevels (mg.c:623)
> ==547==
> Linear solve converged due to CONVERGED_RTOL iterations 2
>  1 SNES Function norm 7.444976906574e-04
> Linear solve converged due to CONVERGED_RTOL iterations 2
>  2 SNES Function norm 9.698205312365e-06
> Linear solve converged due to CONVERGED_RTOL iterations 3
>  3 SNES Function norm 6.808828603405e-09
> Linear solve converged due to CONVERGED_RTOL iterations 6
>  4 SNES Function norm 1.757078396735e-13
> Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE
> **************************************************
> time step = 1
> current time step size= 5.0000000000000003e-02
> time = 5.0000000000000003e-02
> number of nonlinear iterations = 4
> number of linear iterations = 13
> function norm = 1.7570783967354192e-13
> **************************************************
> total number of time steps = 1
> total number of nonlinear iterations = 4
> total number of linear iterations = 13
> WARNING! There are options you set that were not used!
> WARNING! could be spelling mistake, etc!
> Option left: name:-mxgrid value: 32
> Option left: name:-mygrid value: 32
> Option left: name:-time_to_generate_grid value: 0.0
> ==546==
> ==547==
> ==547== HEAP SUMMARY:
> ==547==     in use at exit: 156 bytes in 11 blocks
> ==547==   total heap usage: 4,947 allocs, 3,551 frees, 29,251,365 bytes
> allocated
> ==547==
> ==546== HEAP SUMMARY:
> ==546==     in use at exit: 156 bytes in 11 blocks
> ==546==   total heap usage: 4,922 allocs, 3,851 frees, 31,388,554 bytes
> allocated
> ==546==
> ==546== 156 (36 direct, 120 indirect) bytes in 1 blocks are definitely lost in
> loss record 11 of 11
> ==546==    at 0x4022BF3: malloc (vg_replace_malloc.c:195)
> ==546==    by 0x42693E2: ??? (in /lib/tls/i686/cmov/libc-2.7.so)
> ==546==    by 0x4269C2D: __nss_database_lookup (in
> /lib/tls/i686/cmov/libc-2.7.so)
> ==546==    by 0x4701FDB: ???
> ==546==    by 0x470313C: ???
> ==546==    by 0x4215D15: getpwuid_r (in /lib/tls/i686/cmov/libc-2.7.so)
> ==546==    by 0x421565D: getpwuid (in /lib/tls/i686/cmov/libc-2.7.so)
> ==546==    by 0x8789545: PetscGetUserName (fuser.c:68)
> ==546==    by 0x8744872: PetscErrorPrintfInitialize (errtrace.c:68)
> ==546==    by 0x8779CEB: PetscInitialize (pinit.c:568)
> ==546==    by 0x804B4E7: main (twqt2ff.c:88)
> ==546==
> ==546== LEAK SUMMARY:
> ==546==    definitely lost: 36 bytes in 1 blocks
> ==546==    indirectly lost: 120 bytes in 10 blocks
> ==546==      possibly lost: 0 bytes in 0 blocks
> ==546==    still reachable: 0 bytes in 0 blocks
> ==546==         suppressed: 0 bytes in 0 blocks
> ==546==
> ==546== For counts of detected and suppressed errors, rerun with: -v
> ==546== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 40 from 10)
> ==547== 156 (36 direct, 120 indirect) bytes in 1 blocks are definitely lost in
> loss record 11 of 11
> ==547==    at 0x4022BF3: malloc (vg_replace_malloc.c:195)
> ==547==    by 0x42693E2: ??? (in /lib/tls/i686/cmov/libc-2.7.so)
> ==547==    by 0x4269C2D: __nss_database_lookup (in
> /lib/tls/i686/cmov/libc-2.7.so)
> ==547==    by 0x4701FDB: ???
> ==547==    by 0x470313C: ???
> ==547==    by 0x4215D15: getpwuid_r (in /lib/tls/i686/cmov/libc-2.7.so)
> ==547==    by 0x421565D: getpwuid (in /lib/tls/i686/cmov/libc-2.7.so)
> ==547==    by 0x8789545: PetscGetUserName (fuser.c:68)
> ==547==    by 0x8744872: PetscErrorPrintfInitialize (errtrace.c:68)
> ==547==    by 0x8779CEB: PetscInitialize (pinit.c:568)
> ==547==    by 0x804B4E7: main (twqt2ff.c:88)
> ==547==
> ==547== LEAK SUMMARY:
> ==547==    definitely lost: 36 bytes in 1 blocks
> ==547==    indirebecca at YuanWork:~/linux/code/twoway/twoway_new/valgrind$
> 
> Thanks very much!
> 
> Rebecca
> 
> 
> 