[petsc-users] Valgrind (invalid read) error with ASM in petsc-dev
Tabrez Ali
stali at geology.wisc.edu
Sun Jun 29 11:28:52 CDT 2014
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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