July 2012 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] next plans for gpu optimization
by Matthew Knepley 16 Jul '12

16 Jul '12

On Mon, Jul 16, 2012 at 9:35 AM, Olga Tramontano <tramontanoolga(a)yahoo.it>wrote: > Hi all > I need to know which part of PETSc has been suited to gpus. > I think that only Vec and Mat classes have been extended for GPUs. Am I > wrong? > Please read the paper: http://www.mcs.anl.gov/petsc/features/gpus.pdf Matt > thanks > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener

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next plans for gpu optimization
by Olga Tramontano 16 Jul '12

16 Jul '12

Hi all I need to know which part of PETSc has been suited to gpus. I think that only Vec and Mat classes have been extended for GPUs. Am I wrong? thanks

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Re: [petsc-dev] threadcomm memory leak
by Shri 16 Jul '12

16 Jul '12

On Jul 15, 2012, at 5:26 PM, Shri wrote: > > On Jul 15, 2012, at 4:57 PM, Barry Smith wrote: > >> >> On Jul 15, 2012, at 4:48 PM, Shri wrote: >> >>> >>> On Jul 15, 2012, at 3:27 PM, Barry Smith wrote: >>> >>>> >>>> Shri, >>>> >>>> You need to test your code WITHOUT pthreads OR openmp configure. >>> That is what i am doing, no openmp or pthreads. >>> >>>> You have the call to PetscThreadCommFinalize() protected by PTHREADCLASSES >>> >>> There is no PetscThreadCommFinalize(). There is a 'PetscThreadsFinalize()' call in PetscFinalize() that is protected by PTHREADCLASSES. PetscThreadsFinalize() is for finalizing the previous pthread pool model that i had added on which vec_type pthread and mat_type seqaijpthread are based. It has nothing to do with threadcomm. Once i add new vector and matrix code using threadcomm , i'll remove the old pthread code and the pthread vector and matrix class. >> >> Why not just remove all the old pthread code now; it will make things clearer. > > Don't want to hurl people who are using/testing it into darkness. > >> >>>> but not PetscThreadCommInitializePackage() projected! Also why do you call PetscThreadCommPackageInitialize() at the beginning but PetscThreadCommFinalize() at the end and not PetscThreadCommFinalizePackage()? >>> >>> PetscThreadCommFinalizePackage is registerfinalized in PetscThreadCommInitializePackage() >>> >>> ierr = PetscRegisterFinalize(PetscThreadCommFinalizePackage);CHKERRQ(ierr); >> >> Sorry my mistake. >>> >>> So it is called on PetscRegisterFinalizeAll(). >>>> >>>> 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. >>> >>> PetscThreadCommPackageInitialize() attaches the threadcomm attribute on the MPI communicator and there are several places where the threadcomm attribute is requested (sys/objects/subcomm.c, src/sys/tagm.c). Hence, the errors. >> >> Try a build with mpiuni. > > Aah, i can see the memory leak now. Thanks. It looks like the threadcomm object is not being freed. Something to do with destroying the MPIUNI attribute perhaps? Will check. Fixed. http://petsc.cs.iit.edu/petsc/petsc-dev/rev/169c19e9ea54 The memory leak was due to the COMM_SELF and COMM_WORLD communicators being same for mpiuni. This was leaving an extra reference for the innercomm. Shri > > Shri >> Maybe the memory leak is because that isn't handling stuff possible. My build with memory leaks is with mpiuni. >> >> Thanks >> >> >> Barry >> >>> >>> Thanks, >>> Shri >>>> >>>> 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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Re: [petsc-dev] threadcomm memory leak
by Jed Brown 15 Jul '12

15 Jul '12

On Sun, Jul 15, 2012 at 5:26 PM, Shri <abhyshr(a)mcs.anl.gov> wrote: > > Why not just remove all the old pthread code now; it will make things > clearer. > > Don't want to hurl people who are using/testing it into darkness. It was always experimental and it's going to be removed anyway, so let's do it sooner rather than later. Some of that code could be used in the new implementations, but it was pretty mechanical in the first place and I think copying it over is likely to be just as error-prone as extracting from the current routines.

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Re: [petsc-dev] threadcomm memory leak
by Shri 15 Jul '12

15 Jul '12

On Jul 15, 2012, at 4:57 PM, Barry Smith wrote: > > On Jul 15, 2012, at 4:48 PM, Shri wrote: > >> >> On Jul 15, 2012, at 3:27 PM, Barry Smith wrote: >> >>> >>> Shri, >>> >>> You need to test your code WITHOUT pthreads OR openmp configure. >> That is what i am doing, no openmp or pthreads. >> >>> You have the call to PetscThreadCommFinalize() protected by PTHREADCLASSES >> >> There is no PetscThreadCommFinalize(). There is a 'PetscThreadsFinalize()' call in PetscFinalize() that is protected by PTHREADCLASSES. PetscThreadsFinalize() is for finalizing the previous pthread pool model that i had added on which vec_type pthread and mat_type seqaijpthread are based. It has nothing to do with threadcomm. Once i add new vector and matrix code using threadcomm , i'll remove the old pthread code and the pthread vector and matrix class. > > Why not just remove all the old pthread code now; it will make things clearer. Don't want to hurl people who are using/testing it into darkness. > >>> but not PetscThreadCommInitializePackage() projected! Also why do you call PetscThreadCommPackageInitialize() at the beginning but PetscThreadCommFinalize() at the end and not PetscThreadCommFinalizePackage()? >> >> PetscThreadCommFinalizePackage is registerfinalized in PetscThreadCommInitializePackage() >> >> ierr = PetscRegisterFinalize(PetscThreadCommFinalizePackage);CHKERRQ(ierr); > > Sorry my mistake. >> >> So it is called on PetscRegisterFinalizeAll(). >>> >>> 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. >> >> PetscThreadCommPackageInitialize() attaches the threadcomm attribute on the MPI communicator and there are several places where the threadcomm attribute is requested (sys/objects/subcomm.c, src/sys/tagm.c). Hence, the errors. > > Try a build with mpiuni. Aah, i can see the memory leak now. Thanks. It looks like the threadcomm object is not being freed. Something to do with destroying the MPIUNI attribute perhaps? Will check. Shri > Maybe the memory leak is because that isn't handling stuff possible. My build with memory leaks is with mpiuni. > > Thanks > > > Barry > >> >> Thanks, >> Shri >>> >>> 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 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >> >

1 0

Re: [petsc-dev] threadcomm memory leak
by Barry Smith 15 Jul '12

15 Jul '12

On Jul 15, 2012, at 4:48 PM, Shri wrote: > > On Jul 15, 2012, at 3:27 PM, Barry Smith wrote: > >> >> Shri, >> >> You need to test your code WITHOUT pthreads OR openmp configure. > That is what i am doing, no openmp or pthreads. > >> You have the call to PetscThreadCommFinalize() protected by PTHREADCLASSES > > There is no PetscThreadCommFinalize(). There is a 'PetscThreadsFinalize()' call in PetscFinalize() that is protected by PTHREADCLASSES. PetscThreadsFinalize() is for finalizing the previous pthread pool model that i had added on which vec_type pthread and mat_type seqaijpthread are based. It has nothing to do with threadcomm. Once i add new vector and matrix code using threadcomm , i'll remove the old pthread code and the pthread vector and matrix class. Why not just remove all the old pthread code now; it will make things clearer. >> but not PetscThreadCommInitializePackage() projected! Also why do you call PetscThreadCommPackageInitialize() at the beginning but PetscThreadCommFinalize() at the end and not PetscThreadCommFinalizePackage()? > > PetscThreadCommFinalizePackage is registerfinalized in PetscThreadCommInitializePackage() > > ierr = PetscRegisterFinalize(PetscThreadCommFinalizePackage);CHKERRQ(ierr); Sorry my mistake. > > So it is called on PetscRegisterFinalizeAll(). >> >> 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. > > PetscThreadCommPackageInitialize() attaches the threadcomm attribute on the MPI communicator and there are several places where the threadcomm attribute is requested (sys/objects/subcomm.c, src/sys/tagm.c). Hence, the errors. Try a build with mpiuni. Maybe the memory leak is because that isn't handling stuff possible. My build with memory leaks is with mpiuni. Thanks Barry > > Thanks, > Shri >> >> 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 >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>> >>> >> >

1 0

Re: [petsc-dev] threadcomm memory leak
by Shri 15 Jul '12

15 Jul '12

On Jul 15, 2012, at 3:27 PM, Barry Smith wrote: > > Shri, > > You need to test your code WITHOUT pthreads OR openmp configure. That is what i am doing, no openmp or pthreads. > You have the call to PetscThreadCommFinalize() protected by PTHREADCLASSES There is no PetscThreadCommFinalize(). There is a 'PetscThreadsFinalize()' call in PetscFinalize() that is protected by PTHREADCLASSES. PetscThreadsFinalize() is for finalizing the previous pthread pool model that i had added on which vec_type pthread and mat_type seqaijpthread are based. It has nothing to do with threadcomm. Once i add new vector and matrix code using threadcomm , i'll remove the old pthread code and the pthread vector and matrix class. > but not PetscThreadCommInitializePackage() projected! Also why do you call PetscThreadCommPackageInitialize() at the beginning but PetscThreadCommFinalize() at the end and not PetscThreadCommFinalizePackage()? PetscThreadCommFinalizePackage is registerfinalized in PetscThreadCommInitializePackage() ierr = PetscRegisterFinalize(PetscThreadCommFinalizePackage);CHKERRQ(ierr); So it is called on PetscRegisterFinalizeAll(). > > 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. PetscThreadCommPackageInitialize() attaches the threadcomm attribute on the MPI communicator and there are several places where the threadcomm attribute is requested (sys/objects/subcomm.c, src/sys/tagm.c). Hence, the errors. Thanks, Shri > > 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 >>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> >>> >> >

1 0

Re: [petsc-dev] threadcomm memory leak
by Barry Smith 15 Jul '12

15 Jul '12

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 >>>>> >>>>> >>>>> >>>> >>> >>> >> >

1 0

Re: [petsc-dev] Pflotran perf on GPU
by Matthew Knepley 15 Jul '12

15 Jul '12

On Sun, Jul 15, 2012 at 4:12 AM, 周文浩 <330358508(a)qq.com> wrote: > Hello！**** > > I get the information that you run pflotran on GPU and test it, these days > I’m trying to find the GPU version of pflotran, could you send me a copy of > your GPU version? > PFLOTRAN, as I understand, only uses the GPU for solves. All solves are through PETSc, so you can find a description of the GPU uses here: http://www.mcs.anl.gov/petsc/features/gpus.html Matt > **** > > I need it very much.**** > > Thanks! > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener

1 0

Re: [petsc-dev] threadcomm memory leak
by Shri 15 Jul '12

15 Jul '12

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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