[petsc-dev] uni

Barry Smith bsmith at mcs.anl.gov
Wed Nov 23 17:11:40 CST 2011 

On Nov 23, 2011, at 3:07 PM, Mark F. Adams wrote:

   The test suite sucks in that in you need to then go into the directories and run the problem examples to see what is going wrong or why the file is the wrong size. Someday when we are not writing code we can fix up the test harness.

   Barry

>> 
>>   After you do the "make all test" on PETSc do "make alltests" and it should run all the tests that run on one process.
> 
> This does not look promising:
> 
> ~/Codes/petsc-dev>make alltests
> ----------------
> ##1             <==
> ##1       #>3   ==> 1 MPI processes
> @ Line 1 in file "output/ex101.out" is shorter than expected!
> ----------------
> ##12            <==
> ##12      #>3   ==> 1 MPI processes
> @ Line 12 in file "output/ex101.out" is shorter than expected!
> ----------------
> ##23            <==
> ##23      #>3   ==> 1 MPI processes
> @ Line 23 in file "output/ex101.out" is shorter than expected!
> /Users/markadams/Codes/petsc-dev/src/mat/examples/tests
> Possible problem with with ex101_1, diffs above 
> =========================================
> ----------------
> ##1             <==
> ##1       #>3   ==> 1 MPI processes
> @ Line 1 in file "output/ex6f_1.out" is shorter than expected!
> ----------------
> ##12            <==
> ##12      #>3   ==> 1 MPI processes
> @ Line 12 in file "output/ex6f_1.out" is shorter than expected!
> ----------------
> ##27            <==
> ##27      #>3   ==> 1 MPI processes
> @ Line 27 in file "output/ex6f_1.out" is shorter than expected!
> /Users/markadams/Codes/petsc-dev/src/ksp/ksp/examples/tutorials
> Possible problem with with ex6f_1, diffs above 
> =========================================
> 
> 
>> 
>>   Something is wrong with your reference counting likely here. Does this work with --with-debugging=0?
> 
> No 
> 
>> I would run debug version with valgrind first.
> 
> I'm getting an error in my code"
> 
> ==69160== Process terminating with default action of signal 11 (SIGSEGV)
> ==69160==  General Protection Fault
> ==69160==    at 0x13DE930: misaligned_stack_error_ (in /usr/lib/libSystem.B.dylib)
> ==69160==    by 0x187214: TraceTimer::sampleMemUsage() (CH_Timer.cpp:1700)
> 
> but CH_Timer.cpp:1700 is simply:
> 
> sampleFile = fopen("memory.samples", "w");
> 
> So that is puzzling ...
> 
> Any thoughts?  I'll start hacking at this.
> 
> Mark
> 
>> 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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