[petsc-dev] uni
Mark F. Adams
mark.adams at columbia.edu
Wed Nov 23 15:07:49 CST 2011
Note, this matrix is created with MatConvert ...
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.
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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