[petsc-dev] uni
Mark F. Adams
mark.adams at columbia.edu
Wed Nov 23 17:47:58 CST 2011
On Nov 23, 2011, at 6:10 PM, Barry Smith wrote:
>
> On Nov 23, 2011, at 3:14 PM, Mark F. Adams wrote:
>
>> 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.
>>
>>
>> ==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]
>
> Yes it pisses me off to no end that Apple got suckered into using that ATLAS crap and it is buggy with basic memory errors and Jack doesn't give a shit.
>
Wow ....
So I fixed the problem. The errors happened when calling the repartitioning code w/o MPI. THe code works fine on one processor with the MPI version. So I think there is a bug in PETSc having to do with MatConvert or Partitioning code w/o MPI.
I have pushed fix today, but if you really want to debug it ... I'm sure that any no-MPI test using GAMG would trip this. All that needs to change is on line 191 of gamg.c:
if( s_avoid_repart || npe==1 ) {
change it to
if( s_avoid_repart ) {
This will run the partitioning code even on one processor.
Let me know if I can help.
Thanks,
Mark
>
> It you can tell us how to run a code (or push an example and tell use it) that reproduces this we can also debug it to see what the problem is.
>
> Barry
>
>>
>> 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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