[petsc-users] PetscFunctionBegin, -malloc_dump and C++ classes with PETSc objects

[Miguel Angel Salazar de Troya]

You were right. I was forgetting a DMRestoreLocalVector(). Thanks. If we
are creating local vectors every time we call functions such as the
RHSFunction of a TS implementation, which is called many times in the TS
integration, will this be a problem in terms of performance? I've noticed
that it might be. This is the way it is implemented in some TS. I wanted to
double check with you guys before I figure out a way to create just one
local vector that is re used in functions such as RHSFunction.

Miguel

On Tue, Nov 18, 2014 at 12:54 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
> > On Nov 18, 2014, at 11:54 AM, Miguel Angel Salazar de Troya <
> salazardetroya at gmail.com> wrote:
> >
> > PetscFinalize() is inside of the class destructor (the last line of the
> destructor), so when the object goes out of scope, the class destructor is
> called and PetscFinalize() as well. Is it better to have PetscFinalize()
> outside of the destructor and call the destructor explicitly before?
>
>    It shouldn't really matter.
>
>     My guess is you must be missing calling a destroy or restore on one of
> the PETSc objects.
>
>   Barry
>
> >
> > Miguel
> >
> > On Tue, Nov 18, 2014 at 11:32 AM, Barry Smith <bsmith at mcs.anl.gov>
> wrote:
> >
> > > On Nov 18, 2014, at 11:19 AM, Miguel Angel Salazar de Troya <
> salazardetroya at gmail.com> wrote:
> > >
> > > Hi
> > >
> > > I'm implementing a problem using the TS. Most of my functions are
> methods inside of a class, except for the callbacks (to form the RHS and
> the TS monitor), which are outside of the class, although in the same .C
> file where the class methods are implemented. For these callbacks I
> followed the network example:
> > >
> > >
> https://bitbucket.org/petsc/petsc/src/a614f7369d93d476173b8fc6bf2463276dcbdb3a/src/snes/examples/tutorials/network/pflow/pf.c?at=master
> > >
> > > Therefore, the callbacks have the PetscFunctionBegin at the beginning
> and PetscFunctionReturn(0) at the end. My problems come when I run the
> program with -malloc_dump and I get a lot of unfreed memory. Inspecting the
> output I see that the line of my code where the memory is allocated
> corresponds with the line when PetscFunctionBegin is called.
> >
> >   This is normal. We cannot register the exact line the memory
> allocated, only the location of the PETScFunctionBegin;
> >
> >
> > > Later in the file, I see that the function DMGetLocalVector() is
> called within a petsc internal routine (at the file dmget.c). I also call
> this routine in my callback methods few lines after PetscFunctionBegin. The
> procedure that I follow to use the local vectors is as the one in the
> network example. For vectors that I want to modify this is:
> > >
> > >  ierr = DMGetLocalVector(networkdm,&localX);CHKERRQ(ierr);
> > >  ierr =
> DMGlobalToLocalBegin(networkdm,X,INSERT_VALUES,localX);CHKERRQ(ierr);
> > >  ierr =
> DMGlobalToLocalEnd(networkdm,X,INSERT_VALUES,localX);CHKERRQ(ierr);
> > >  ierr = VecGetArray(localX,&xarr);CHKERRQ(ierr);
> > >
> > > Modify values in xarr
> > >
> > >  ierr = VecRestoreArray(localX,&xarr);CHKERRQ(ierr);
> > >  ierr =
> DMLocalToGlobalBegin(networkdm,localX,INSERT_VALUES,X);CHKERRQ(ierr);
> > >  ierr =
> DMLocalToGlobalEnd(networkdm,localX,INSERT_VALUES,X);CHKERRQ(ierr);
> > >  ierr = DMRestoreLocalVector(networkdm,&localX);CHKERRQ(ierr);
> > >
> > > One last thing that I think it might be a issue here is how I destroy
> the petsc objects. I create the petsc objects within a class. For instance,
> the class has a petsc vector that later passes to the TS object to get the
> solution. To destroy the petsc objects, I use the class destructor, where
> at the end I call PetscFinalize() Inside the class I pass the callbacks to
> the TS routines that need them (e.g. TSSetRHSFunction() ) I can compile the
> code and run it, but many memory allocations are not freed. What can be the
> issue here? Do you know of an example using C++ classes to implement PETSc
> methods? Thanks in advance.
> >
> >    Do you call the class destructor yourself explicitly before the
> PetscFinalize()? You need to, otherwise the class may not be destroyed
> until after PetscFinalize() and hence the PETSc objects won't be freed when
> you call PetscFinalize().
> >
> >    You also need to make sure that you destroy ALL PETSc objects, if you
> miss even one PETSc object, since the objects have references to each other
> it may be that many PETSc objects do not get freed and hence -malloc_dump
> shows many objects still alive.
> >
> >   Barry
> >
> > >
> > > Miguel
> > >
> > > --
> > > Miguel Angel Salazar de Troya
> > > Graduate Research Assistant
> > > Department of Mechanical Science and Engineering
> > > University of Illinois at Urbana-Champaign
> > > (217) 550-2360
> > > salaza11 at illinois.edu
> > >
> >
> >
> >
> >
> > --
> > Miguel Angel Salazar de Troya
> > Graduate Research Assistant
> > Department of Mechanical Science and Engineering
> > University of Illinois at Urbana-Champaign
> > (217) 550-2360
> > salaza11 at illinois.edu
> >
>
>


-- 
*Miguel Angel Salazar de Troya*
Graduate Research Assistant
Department of Mechanical Science and Engineering
University of Illinois at Urbana-Champaign
(217) 550-2360
salaza11 at illinois.edu
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