This is our error. It is harmless, I am fixing it in master now. Barry
On Jun 29, 2014, at 12:41 PM, Barry Smith <[email protected]> wrote: > > 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) >> >
