[petsc-users] Valgrind (invalid read) error with ASM in petsc-dev
Barry Smith
bsmith at mcs.anl.gov
Sun Jun 29 12:41:23 CDT 2014
Hmm, what code is calling the ISStrideGetInfo(). It is a ISGENERAL so ISStrideGetInfo() shouldn’t get called on it.
Barry
==22745== Invalid read of size 4
==22745== at 0x4231567: ISStrideGetInfo (in /home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.05.0)
==22745== by 0x678C5DF: ???
On Jun 29, 2014, at 11:28 AM, Tabrez Ali <stali at geology.wisc.edu> wrote:
> Hello
>
> I get the following Valgrind error (below) while using ASM in petsc-dev. No such error occurs with petsc-3.4.x. Any ideas as to what could be wrong?
>
> Thanks in advance.
>
> Tabrez
>
>
> ==22745== Memcheck, a memory error detector
> ==22745== Copyright (C) 2002-2011, and GNU GPL'd, by Julian Seward et al.
> ==22745== Using Valgrind-3.7.0 and LibVEX; rerun with -h for copyright info
> ==22745== Command: ./defmod -f examples/two_quads_qs.inp -log_summary
> ==22745==
> Reading input ...
> Reading mesh data ...
> Forming [K] ...
> Forming RHS ...
> Setting up solver ...
> Solving ...
> ==22745== Invalid read of size 4
> ==22745== at 0x4231567: ISStrideGetInfo (in /home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.05.0)
> ==22745== by 0x678C5DF: ???
> ==22745== Address 0x678c3ec is 0 bytes after a block of size 12 alloc'd
> ==22745== at 0x40278A4: memalign (vg_replace_malloc.c:694)
> ==22745== by 0x40FBE89: PetscMallocAlign (in /home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.05.0)
> ==22745== by 0x42288FD: ISCreate_General (in /home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.05.0)
> ==22745== by 0x4221494: ISSetType (in /home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.05.0)
> ==22745== by 0x4227745: ISCreateGeneral (in /home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.05.0)
> ==22745== by 0x45F104F: MatIncreaseOverlap_SeqAIJ (in /home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.05.0)
> ==22745== by 0x473B4F2: MatIncreaseOverlap (in /home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.05.0)
> ==22745== by 0x4A9CFC0: PCSetUp_ASM (in /home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.05.0)
> ==22745== by 0x49BF314: PCSetUp (in /home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.05.0)
> ==22745== by 0x4ABAB25: KSPSetUp (in /home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.05.0)
> ==22745== by 0x4ABC8A8: KSPSolve (in /home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.05.0)
> ==22745== by 0x4AE2DE0: kspsolve_ (in /home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.05.0)
> ==22745==
> Recovering stress ...
> Cleaning up ...
> Finished
> ************************************************************************************************************************
> *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r -fCourier9' to print this document ***
> ************************************************************************************************************************
>
> ---------------------------------------------- PETSc Performance Summary: ----------------------------------------------
>
> ./defmod on a arch-linux2-c-debug named i5 with 1 processor, by stali Sun Jun 29 11:02:25 2014
> Using Petsc Development GIT revision: v3.4.4-4963-g821251a GIT Date: 2014-06-28 12:39:08 -0500
>
> Max Max/Min Avg Total
> Time (sec): 2.261e+00 1.00000 2.261e+00
> Objects: 3.100e+01 1.00000 3.100e+01
> Flops: 1.207e+03 1.00000 1.207e+03 1.207e+03
> Flops/sec: 5.339e+02 1.00000 5.339e+02 5.339e+02
> MPI Messages: 0.000e+00 0.00000 0.000e+00 0.000e+00
> MPI Message Lengths: 0.000e+00 0.00000 0.000e+00 0.000e+00
> MPI Reductions: 0.000e+00 0.00000
>
> Flop counting convention: 1 flop = 1 real number operation of type (multiply/divide/add/subtract)
> e.g., VecAXPY() for real vectors of length N --> 2N flops
> and VecAXPY() for complex vectors of length N --> 8N flops
>
> Summary of Stages: ----- Time ------ ----- Flops ----- --- Messages --- -- Message Lengths -- -- Reductions --
> Avg %Total Avg %Total counts %Total Avg %Total counts %Total
> 0: Main Stage: 2.2451e+00 99.3% 1.2070e+03 100.0% 0.000e+00 0.0% 0.000e+00 0.0% 0.000e+00 0.0%
>
> ------------------------------------------------------------------------------------------------------------------------
> See the 'Profiling' chapter of the users' manual for details on interpreting output.
> Phase summary info:
> Count: number of times phase was executed
> Time and Flops: Max - maximum over all processors
> Ratio - ratio of maximum to minimum over all processors
> Mess: number of messages sent
> Avg. len: average message length (bytes)
> Reduct: number of global reductions
> Global: entire computation
> Stage: stages of a computation. Set stages with PetscLogStagePush() and PetscLogStagePop().
> %T - percent time in this phase %F - percent flops in this phase
> %M - percent messages in this phase %L - percent message lengths in this phase
> %R - percent reductions in this phase
> Total Mflop/s: 10e-6 * (sum of flops over all processors)/(max time over all processors)
> ------------------------------------------------------------------------------------------------------------------------
>
>
> ##########################################################
> # #
> # WARNING!!! #
> # #
> # This code was compiled with a debugging option, #
> # To get timing results run ./configure #
> # using --with-debugging=no, the performance will #
> # be generally two or three times faster. #
> # #
> ##########################################################
>
>
> Event Count Time (sec) Flops --- Global --- --- Stage --- Total
> Max Ratio Max Ratio Max Ratio Mess Avg len Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s
> ------------------------------------------------------------------------------------------------------------------------
>
> --- Event Stage 0: Main Stage
>
> ThreadCommRunKer 1 1.0 7.3960e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> ThreadCommBarrie 1 1.0 8.2803e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> VecMDot 1 1.0 1.0480e-02 1.0 2.30e+01 1.0 0.0e+00 0.0e+00 0.0e+00 0 2 0 0 0 0 2 0 0 0 0
> VecNorm 2 1.0 1.2341e-02 1.0 4.80e+01 1.0 0.0e+00 0.0e+00 0.0e+00 1 4 0 0 0 1 4 0 0 0 0
> VecScale 2 1.0 1.2405e-02 1.0 2.40e+01 1.0 0.0e+00 0.0e+00 0.0e+00 1 2 0 0 0 1 2 0 0 0 0
> VecCopy 1 1.0 9.0401e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> VecSet 10 1.0 4.3447e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> VecAXPY 1 1.0 1.1247e-02 1.0 2.40e+01 1.0 0.0e+00 0.0e+00 0.0e+00 0 2 0 0 0 1 2 0 0 0 0
> VecMAXPY 2 1.0 6.3708e-03 1.0 4.80e+01 1.0 0.0e+00 0.0e+00 0.0e+00 0 4 0 0 0 0 4 0 0 0 0
> VecAssemblyBegin 1 1.0 2.5654e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0
> VecAssemblyEnd 1 1.0 9.2661e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> VecScatterBegin 5 1.0 8.8482e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> VecNormalize 2 1.0 3.3422e-02 1.0 7.20e+01 1.0 0.0e+00 0.0e+00 0.0e+00 1 6 0 0 0 1 6 0 0 0 0
> MatMult 1 1.0 1.5871e-02 1.0 2.12e+02 1.0 0.0e+00 0.0e+00 0.0e+00 1 18 0 0 0 1 18 0 0 0 0
> MatSolve 2 1.0 3.1852e-02 1.0 4.24e+02 1.0 0.0e+00 0.0e+00 0.0e+00 1 35 0 0 0 1 35 0 0 0 0
> MatLUFactorNum 1 1.0 9.2084e-02 1.0 4.04e+02 1.0 0.0e+00 0.0e+00 0.0e+00 4 33 0 0 0 4 33 0 0 0 0
> MatILUFactorSym 1 1.0 5.1554e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 0
> MatAssemblyBegin 2 1.0 6.5899e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> MatAssemblyEnd 2 1.0 2.8979e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0
> MatGetRowIJ 1 1.0 2.5041e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> MatGetSubMatrice 1 1.0 2.8049e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0
> MatGetOrdering 1 1.0 5.0988e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 0
> MatIncreaseOvrlp 1 1.0 3.7770e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 0
> KSPGMRESOrthog 1 1.0 2.9687e-02 1.0 4.70e+01 1.0 0.0e+00 0.0e+00 0.0e+00 1 4 0 0 0 1 4 0 0 0 0
> KSPSetUp 2 1.0 1.8465e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0
> KSPSolve 1 1.0 7.4545e-01 1.0 1.21e+03 1.0 0.0e+00 0.0e+00 0.0e+00 33100 0 0 0 33100 0 0 0 0
> PCSetUp 2 1.0 4.4820e-01 1.0 4.04e+02 1.0 0.0e+00 0.0e+00 0.0e+00 20 33 0 0 0 20 33 0 0 0 0
> PCSetUpOnBlocks 1 1.0 2.3395e-01 1.0 4.04e+02 1.0 0.0e+00 0.0e+00 0.0e+00 10 33 0 0 0 10 33 0 0 0 0
> PCApply 2 1.0 7.8817e-02 1.0 4.24e+02 1.0 0.0e+00 0.0e+00 0.0e+00 3 35 0 0 0 4 35 0 0 0 0
> ------------------------------------------------------------------------------------------------------------------------
>
> Memory usage is given in bytes:
>
> Object Type Creations Destructions Memory Descendants' Mem.
> Reports information only for process 0.
>
> --- Event Stage 0: Main Stage
>
> Vector 11 11 10840 0
> Vector Scatter 2 2 784 0
> Matrix 3 3 10120 0
> Index Set 10 10 4872 0
> Krylov Solver 2 2 18316 0
> Preconditioner 2 2 1204 0
> Viewer 1 0 0 0
> ========================================================================================================================
> Average time to get PetscTime(): 0.000123882
> #PETSc Option Table entries:
> -f examples/two_quads_qs.inp
> -log_summary
> #End of PETSc Option Table entries
> Compiled without FORTRAN kernels
> Compiled with full precision matrices (default)
> sizeof(short) 2 sizeof(int) 4 sizeof(long) 4 sizeof(void*) 4 sizeof(PetscScalar) 8 sizeof(PetscInt) 4
> Configure options: --with-fc=gfortran --with-cc=gcc --download-mpich --with-metis=1 --download-metis=1 --COPTFLAGS=-O2 --FOPTFLAGS=-O2 --with-shared-libraries
> -----------------------------------------
> Libraries compiled on Sun Jun 29 08:08:16 2014 on i5
> Machine characteristics: Linux-3.2.0-4-686-pae-i686-with-debian-7.5
> Using PETSc directory: /home/stali/petsc-dev
> Using PETSc arch: arch-linux2-c-debug
> -----------------------------------------
>
> Using C compiler: /home/stali/petsc-dev/arch-linux2-c-debug/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O2 ${COPTFLAGS} ${CFLAGS}
> Using Fortran compiler: /home/stali/petsc-dev/arch-linux2-c-debug/bin/mpif90 -fPIC -Wall -Wno-unused-variable -ffree-line-length-0 -Wno-unused-dummy-argument -O2 ${FOPTFLAGS} ${FFLAGS}
> -----------------------------------------
>
> Using include paths: -I/home/stali/petsc-dev/arch-linux2-c-debug/include -I/home/stali/petsc-dev/include -I/home/stali/petsc-dev/include -I/home/stali/petsc-dev/arch-linux2-c-debug/include
> -----------------------------------------
>
> Using C linker: /home/stali/petsc-dev/arch-linux2-c-debug/bin/mpicc
> Using Fortran linker: /home/stali/petsc-dev/arch-linux2-c-debug/bin/mpif90
> Using libraries: -Wl,-rpath,/home/stali/petsc-dev/arch-linux2-c-debug/lib -L/home/stali/petsc-dev/arch-linux2-c-debug/lib -lpetsc -llapack -lblas -Wl,-rpath,/home/stali/petsc-dev/arch-linux2-c-debug/lib -L/home/stali/petsc-dev/arch-linux2-c-debug/lib -lmetis -lX11 -lpthread -lssl -lcrypto -lm -Wl,-rpath,/usr/lib/gcc/i486-linux-gnu/4.7 -L/usr/lib/gcc/i486-linux-gnu/4.7 -Wl,-rpath,/usr/lib/i386-linux-gnu -L/usr/lib/i386-linux-gnu -Wl,-rpath,/lib/i386-linux-gnu -L/lib/i386-linux-gnu -lmpichf90 -lgfortran -lm -lgfortran -lm -lquadmath -lm -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -ldl
> -----------------------------------------
>
> ==22745==
> ==22745== HEAP SUMMARY:
> ==22745== in use at exit: 0 bytes in 0 blocks
> ==22745== total heap usage: 3,723 allocs, 3,723 frees, 282,348 bytes allocated
> ==22745==
> ==22745== All heap blocks were freed -- no leaks are possible
> ==22745==
> ==22745== For counts of detected and suppressed errors, rerun with: -v
> ==22745== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 61 from 8)
>
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