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 <[email protected]> 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) >
