[petsc-dev] uni
Mark F. Adams
mark.adams at columbia.edu
Wed Nov 23 15:14:47 CST 2011
I fixed my code error with valgrind and now I see the same thing (appended) as before (eg, valgrind does not seem to help).
I'm suspecting that MatConvert is messed, but I will try not deleting this matrix and see what happens.
Mark
~/Codes/Chombo/example/AMRPoisson/viscousTensorExec>valgrind --dsymutil=yes ./viscousTensorSolve2d.Darwin.g++-4.gfortran.DEBUG.PETSC.ex petsc.inputs
==69836== Memcheck, a memory error detector
==69836== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
==69836== Using Valgrind-3.6.1 and LibVEX; rerun with -h for copyright info
==69836== Command: ./viscousTensorSolve2d.Darwin.g++-4.gfortran.DEBUG.PETSC.ex petsc.inputs
==69836==
tagging on gradient of RHS
grid at level 0 = ((0,0) (31,31) (0,0))[0] # ((0,32) (31,63) (0,0))[0] # ((32,0) (63,31) (0,0))[0] # ((32,32) (63,63) (0,0))[0]
PetscLinearSolver::solveprivate: idghosts: (2,2)
==69836== Conditional jump or move depends on uninitialised value(s)
==69836== at 0x1E8A5DE: ATL_dgemvT_a1_x1_b0_y1 (in /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
==69836==
==69836== Conditional jump or move depends on uninitialised value(s)
==69836== at 0x1EBAC7A: ATL_dger1_a1_x1_yX (in /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
==69836==
[0]PETSC ERROR: --------------------- Error Message ------------------------------------
[0]PETSC ERROR: Corrupt argument:
see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind!
[0]PETSC ERROR: Inner MPI_Comm does not have expected reference to outer comm!
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Development HG revision: 3dda30872eeec1a2ea5c130f267935c5e0b2534a HG Date: Mon Nov 21 11:19:39 2011 -0800
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: ./viscousTensorSolve2d.Darwin.g++-4.gfortran.DEBUG.PETSC.ex on a arch-maco named madams-macbk-3.home by markadams Wed Nov 23 16:09:49 2011
[0]PETSC ERROR: Libraries linked from /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-seq/lib
[0]PETSC ERROR: Configure run at Wed Nov 23 15:36:10 2011
[0]PETSC ERROR: Configure options CXX=/sw/lib/gcc4.4/bin/g++-4 CC=/sw/lib/gcc4.4/bin/gcc-4 FC=/sw/lib/gcc4.4/bin/gfortran --with-x=0 --with-clanguage=c++ --with-debugging=1 --with-mpi=0 PETSC_ARCH=arch-macosx-gnu-seq
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc_DelComm() line 448 in /Users/markadams/Codes/petsc-dev/src/sys/objects/pinit.c
[0]PETSC ERROR: --------------------- Error Message ------------------------------------
[0]PETSC ERROR: Corrupt argument:
see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind!
[0]PETSC ERROR: MPI_Comm does not have tag/name counter nor does it have inner MPI_Comm!
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Development HG revision: 3dda30872eeec1a2ea5c130f267935c5e0b2534a HG Date: Mon Nov 21 11:19:39 2011 -0800
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: ./viscousTensorSolve2d.Darwin.g++-4.gfortran.DEBUG.PETSC.ex on a arch-maco named madams-macbk-3.home by markadams Wed Nov 23 16:09:49 2011
[0]PETSC ERROR: Libraries linked from /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-seq/lib
[0]PETSC ERROR: Configure run at Wed Nov 23 15:36:10 2011
[0]PETSC ERROR: Configure options CXX=/sw/lib/gcc4.4/bin/g++-4 CC=/sw/lib/gcc4.4/bin/gcc-4 FC=/sw/lib/gcc4.4/bin/gfortran --with-x=0 --with-clanguage=c++ --with-debugging=1 --with-mpi=0 PETSC_ARCH=arch-macosx-gnu-seq
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: PetscCommDestroy() line 229 in /Users/markadams/Codes/petsc-dev/src/sys/objects/tagm.c
[0]PETSC ERROR: PetscHeaderDestroy_Private() line 110 in /Users/markadams/Codes/petsc-dev/src/sys/objects/inherit.c
[0]PETSC ERROR: MatDestroy() line 1045 in /Users/markadams/Codes/petsc-dev/src/mat/interface/matrix.c
[0]PETSC ERROR: partitionLevel() line 347 in /Users/markadams/Codes/petsc-dev/src/ksp/pc/impls/gamg/gamg.c
[0]PETSC ERROR: PCSetUp_GAMG() line 599 in /Users/markadams/Codes/petsc-dev/src/ksp/pc/impls/gamg/gamg.c
[0]PETSC ERROR: PCSetUp() line 819 in /Users/markadams/Codes/petsc-dev/src/ksp/pc/interface/precon.c
On Nov 23, 2011, at 2:01 PM, Barry Smith wrote:
>
> On Nov 23, 2011, at 10:31 AM, Mark F. Adams wrote:
>
>> Yep, need to keep the extra include with uni, but not the lib anymore.
>>
>> Now I get this error, any ideas? I need a uni regression test apparently.
>
> After you do the "make all test" on PETSc do "make alltests" and it should run all the tests that run on one process.
>
> Something is wrong with your reference counting likely here. Does this work with --with-debugging=0? I would run debug version with valgrind first. Then debug version in debugger.
>
> Barry
>
>
>>
>> [0]PETSC ERROR: --------------------- Error Message ------------------------------------
>> [0]PETSC ERROR: Corrupt argument:
>> see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind!
>> [0]PETSC ERROR: Inner MPI_Comm does not have expected reference to outer comm!
>> [0]PETSC ERROR: ------------------------------------------------------------------------
>> [0]PETSC ERROR: Petsc Development HG revision: 3dda30872eeec1a2ea5c130f267935c5e0b2534a HG Date: Mon Nov 21 11:19:39 2011 -0800
>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> [0]PETSC ERROR: See docs/index.html for manual pages.
>> [0]PETSC ERROR: ------------------------------------------------------------------------
>> [0]PETSC ERROR: ./viscousTensorSolve2d.Darwin.g++-4.gfortran.DEBUG.OPT.PETSC.ex on a arch-maco named madams-macbk-3.local by markadams Wed Nov 23 11:25:30 2011
>> [0]PETSC ERROR: Libraries linked from /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-seq/lib
>> [0]PETSC ERROR: Configure run at Tue Nov 22 12:41:46 2011
>> [0]PETSC ERROR: Configure options CXX=/sw/lib/gcc4.4/bin/g++-4 CC=/sw/lib/gcc4.4/bin/gcc-4 FC=/sw/lib/gcc4.4/bin/gfortran --with-x=0 --with-clanguage=c++ --with-debugging=0 --with-mpi=0 PETSC_ARCH=arch-macosx-gnu-seq
>> [0]PETSC ERROR: ------------------------------------------------------------------------
>> [0]PETSC ERROR: Petsc_DelComm() line 448 in /Users/markadams/Codes/petsc-dev/src/sys/objects/pinit.c
>> [0]PETSC ERROR: --------------------- Error Message ------------------------------------
>> [0]PETSC ERROR: Corrupt argument:
>> see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind!
>> [0]PETSC ERROR: MPI_Comm does not have tag/name counter nor does it have inner MPI_Comm!
>> [0]PETSC ERROR: ------------------------------------------------------------------------
>> [0]PETSC ERROR: Petsc Development HG revision: 3dda30872eeec1a2ea5c130f267935c5e0b2534a HG Date: Mon Nov 21 11:19:39 2011 -0800
>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> [0]PETSC ERROR: See docs/index.html for manual pages.
>> [0]PETSC ERROR: ------------------------------------------------------------------------
>> [0]PETSC ERROR: ./viscousTensorSolve2d.Darwin.g++-4.gfortran.DEBUG.OPT.PETSC.ex on a arch-maco named madams-macbk-3.local by markadams Wed Nov 23 11:25:30 2011
>> [0]PETSC ERROR: Libraries linked from /Users/markadams/Codes/petsc-dev/arch-macosx-gnu-seq/lib
>> [0]PETSC ERROR: Configure run at Tue Nov 22 12:41:46 2011
>> [0]PETSC ERROR: Configure options CXX=/sw/lib/gcc4.4/bin/g++-4 CC=/sw/lib/gcc4.4/bin/gcc-4 FC=/sw/lib/gcc4.4/bin/gfortran --with-x=0 --with-clanguage=c++ --with-debugging=0 --with-mpi=0 PETSC_ARCH=arch-macosx-gnu-seq
>> [0]PETSC ERROR: ------------------------------------------------------------------------
>> [0]PETSC ERROR: PetscCommDestroy() line 229 in /Users/markadams/Codes/petsc-dev/src/sys/objects/tagm.c
>> [0]PETSC ERROR: PetscHeaderDestroy_Private() line 110 in /Users/markadams/Codes/petsc-dev/src/sys/objects/inherit.c
>> [0]PETSC ERROR: MatDestroy() line 1045 in /Users/markadams/Codes/petsc-dev/src/mat/interface/matrix.c
>> [0]PETSC ERROR: partitionLevel() line 347 in /Users/markadams/Codes/petsc-dev/src/ksp/pc/impls/gamg/gamg.c
>> [0]PETSC ERROR: PCSetUp_GAMG() line 599 in /Users/markadams/Codes/petsc-dev/src/ksp/pc/impls/gamg/gamg.c
>> [0]PETSC ERROR: PCSetUp() line 819 in /Users/markadams/Codes/petsc-dev/src/ksp/pc/interface/precon.c
>> [0]PETSC ERROR: KSPSetUp() line 261 in /Users/markadams/Codes/petsc-dev/src/ksp/ksp/interface/itfunc.c
>> [0]PETSC ERROR: solveprivate() line 191 in "unknowndirectory/"PetscLinearSolverI.H
>>
>>
>>
>>
>> On Nov 22, 2011, at 3:19 PM, Barry Smith wrote:
>>
>>>
>>> You have som other MPI include file hanging around that is getting intercepted before the MPI Uni one.
>>>
>>> Barry
>>>
>>> On Nov 22, 2011, at 12:00 PM, Mark F. Adams wrote:
>>>
>>>> Scorched earth did not work:
>>>>
>>>> "VecCreate(ompi_communicator_t*, _p_Vec**)", referenced from:
>>>> PetscLinearSolver<LevelData<FArrayBox> >::solveprivate(LevelData<FArrayBox>&, LevelData<FArrayBox> const&) in libamrelliptic2d.Darwin.g++-4.gfortran.DEBUG.OPT.PETSC.a(PetscLinearSolver.o)
>>>> "_ompi_mpi_comm_self", referenced from:
>>>> _ompi_mpi_comm_self$non_lazy_ptr in libamrelliptic2d.Darwin.g++-4.gfortran.DEBUG.OPT.PETSC.a(PetscLinearSolver.o)
>>>>
>>>> <configure.log.gz>
>>>>
>>>> On Nov 22, 2011, at 11:47 AM, Satish Balay wrote:
>>>>
>>>>> Something is strange.
>>>>>
>>>>> I'll suggeset
>>>>>
>>>>> rm -rf externalpackages arch-macosx-gnu-seq
>>>>>
>>>>> and then doing a fresh build.
>>>>>
>>>>> And then verifying the build with 'make test'
>>>>>
>>>>> If 'make test' works - and the application build is not working- I'd
>>>>> like to see the complete compile log thats producing this error.
>>>>>
>>>>>
>>>>> wrt libmpiuni.a - all the relavent stuff is added to libpetsc.a and a separate
>>>>> libmpiuni.a is not created.
>>>>>
>>>>> Satish
>>>>>
>>>>> On Tue, 22 Nov 2011, Mark F. Adams wrote:
>>>>>
>>>>>> I'm trying to build a non MPI code and get this error:
>>>>>>
>>>>>> Undefined symbols:
>>>>>> "_ompi_mpi_comm_self", referenced from:
>>>>>> _ompi_mpi_comm_self$non_lazy_ptr in libamrelliptic2d.Darwin.g++-4.gfortran.DEBUG.OPT.PETSC.a(PetscLinearSolver.o)
>>>>>> (maybe you meant: _ompi_mpi_comm_self$non_lazy_ptr)
>>>>>>
>>>>>>
>>>>>> In the past I have linked libmpiuni.a but that did not seem to get created. Did libmpiuni.a go away or did my make fail ...
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
>
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