[petsc-dev] threadcomm memory leak

Barry Smith bsmith at mcs.anl.gov
Sun Jul 15 15:27:10 CDT 2012 

  Shri,

    You need to test your code WITHOUT pthreads OR openmp configure. You have the call to PetscThreadCommFinalize()  protected by PTHREADCLASSES but not PetscThreadCommInitializePackage() projected!   Also why do you call PetscThreadCommPackageInitialize() at the beginning but PetscThreadCommFinalize() at the end and not PetscThreadCommFinalizePackage()?

   BTW: If I #if def out the PetscThreadCommPackageInitialize() then nothing works (I have built without pthread classes and without openmp).  So there is some bad stuff going on.

   Barry

On Jul 15, 2012, at 11:54 AM, Shri wrote:

> 
> On Jul 14, 2012, at 7:55 PM, Satish Balay wrote:
> 
>> I see this with 32bit linux build - but not 64bit linux build.
> 
> I tried a fresh clone on my Mac and a linux cluster (both x86_64) but still did not get  any memory leaks. Perhaps this is a 32 bit build issue as Satish mentions. What configure options do i need to have a 32 bit build on x86_64? CC="gcc -m32" FC="gfortran -m32"?
> 
> Thanks,
> Shri
> 
>> 
>> also 32bit linux build gives errors with -fp_trap in ddot(). Haven't checked why.
>> 
>> Satish
>> 
>> 
>> On Sat, 14 Jul 2012, Barry Smith wrote:
>> 
>>> 
>>> Many of them with make test
>>> 
>>> Running test examples to verify correct installation
>>> Using PETSC_DIR=/Users/barrysmith/Src/petsc-dev and PETSC_ARCH=arch-float128-opt
>>> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI process
>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html
>>> lid velocity = Qg, prandtl # = Qg, grashof # = Qg
>>> Number of SNES iterations = 2
>>> [0]Total space allocated 6880 bytes
>>> [ 0]16 bytes PetscThreadCommReductionCreate() line 260 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcommred.c
>>> [ 0]16 bytes PetscThreadCommReductionCreate() line 259 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcommred.c
>>> [ 0]48 bytes PetscThreadCommReductionCreate() line 258 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcommred.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommInitialize() line 698 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]176 bytes PetscThreadCommInitialize() line 694 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]272 bytes PetscThreadCommInitialize() line 692 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]16 bytes PetscThreadCommSetAffinities() line 331 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]48 bytes PetscThreadCommCreate() line 122 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> [ 0]320 bytes PetscThreadCommCreate() line 118 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>> Completed test examples
>>> barry-smiths-macbook-pro:petsc-dev barrysmith$ 
>>> 
>>> 
>>> On Jul 14, 2012, at 6:36 PM, Shri wrote:
>>> 
>>>> Which example are you running? I don't see any memory leak for the examples i've tested (threadcomm examples sys/threadcomm/examples/tutorials/ and snes/examples/tutorials/ex19.c,ex5.c)
>>>> On Jul 14, 2012, at 4:22 PM, Barry Smith wrote:
>>>> 
>>>>> 
>>>>> Please always test for memory leaks before pushing
>>>>> 
>>>>> [ 0]48 bytes PetscThreadCommCreate() line 122 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>>>>   [0]  PetscThreadCommInitialize() line 685 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>>>>   [0]  PetscThreadCommInitializePackage() line 53 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/dlregisthreadcomm.c
>>>>> [ 0]320 bytes PetscThreadCommCreate() line 118 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>>>>   [0]  PetscThreadCommInitialize() line 685 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/threadcomm.c
>>>>>   [0]  PetscThreadCommInitializePackage() line 53 in /Users/barrysmith/Src/petsc-dev/src/sys/threadcomm/interface/dlregisthreadcomm.c
>>>>> 
>>>>> 
>>>>> 
>>>> 
>>> 
>>> 
>> 
>

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