dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Tue, Sep 09, 2008 at 04:31:41PM +0200, Martin Sandve Alnæs wrote:
> 2008/9/9 Garth N. Wells <gnw20@xxxxxxxxx>:
> >
> >
> > Anders Logg wrote:
> >> On Tue, Sep 09, 2008 at 11:30:26AM +0100, Garth N. Wells wrote:
> >>>
> >>> Anders Logg wrote:
> >>>> On Tue, Sep 09, 2008 at 09:06:00AM +0200, Anders Logg wrote:
> >>>>> On Mon, Sep 08, 2008 at 11:53:09PM +0200, Johan Hake wrote:
> >>>>>> On Monday 08 September 2008 21:45:27 Martin Sandve Alnæs wrote:
> >>>>>>> 2008/9/8 Anders Logg <logg@xxxxxxxxx>:
> >>>>>>>> On Mon, Sep 08, 2008 at 11:12:14AM +0200, Martin Sandve Alnæs wrote:
> >>>>>>>>> 2008/9/8 Johan Hoffman <jhoffman@xxxxxxxxxx>:
> >>>>>>>>>>> 2008/9/8 Dag Lindbo <dag@xxxxxxxxxx>:
> >>>>>>>>>>>> Anders Logg wrote:
> >>>>>>>>>>>>> There seems to be a problem (among many) with the current design of
> >>>>>>>>>>>>> the Function classes (see thread "evaluating higher order mesh
> >>>>>>>>>>>>> function").
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> In particular, the finite element is missing in DiscreteFunction.
> >>>>>>>>>>>>> My suggestion would be to just add it and let a DiscreteFunction
> >>>>>>>>>>>>> consist of the following four items which are always available:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>   mesh, x, dof_map, finite_element
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Is this enough, and what other issues to we need to fix?
> >>>>>>>>>>>> I'm not sure I agree that the dof map and finite element should be
> >>>>>>>>>>>> owned by the discrete function. There was a great suggestion from
> >>>>>>>>>>>> Martin, in a thread "Abstraction idea" from 06/05/2008, to create a
> >>>>>>>>>>>> class FunctionSpace where the mesh, element and dof_map(s) are
> >>>>>>>>>>>> aggregated. Citing Martin:
> >>>>>>>>>>>> U = FunctionSpace(mesh, dofmapset, form, 0) # or something similar
> >>>>>>>>>>>> u = Function(U)
> >>>>>>>>>>>> v = Function(U)
> >>>>>>>>>>>>
> >>>>>>>>>>>> This seems a solid approach to me since it would provide a way of
> >>>>>>>>>>>> encapsulating the mathematical formulation of the problem, which is
> >>>>>>>>>>>> more or less const and likely to be reused by many discrete
> >>>>>>>>>>>> functions in a solver.
> >>>>>>>>>>>>
> >>>>>>>>>>>> It seems to me that there is an obvious risk that a lot of redundant
> >>>>>>>>>>>> initialization would occur if all discrete functions should own
> >>>>>>>>>>>> their own elements and dof maps. There seems to be consensus that
> >>>>>>>>>>>> the mesh should be "global" for efficiency reasons, so why not treat
> >>>>>>>>>>>> the function space the same way?
> >>>>>>>>>>>>
> >>>>>>>>>>>> Is there a problem with an approach where the funciton _always_ owns
> >>>>>>>>>>>> the vector and _never_ owns the function space (and mesh)? A very
> >>>>>>>>>>>> strict design would avoid shared/smart pointers, provide a
> >>>>>>>>>>>> comprehensible user interface and probably help the parallellization
> >>>>>>>>>>>> effort.
> >>>>>>>>>>>>
> >>>>>>>>>>>> /Dag
> >>>>>>>>>>> If the Function always owns the vector, there are cases you'll have
> >>>>>>>>>>> to make unneccessary copies of a vector, in particular such scenarios
> >>>>>>>>>>> may occur when trying to combine dolfin with something else.
> >>>>>>>>>>>
> >>>>>>>>>>> If the Function never owns the function space, it must always be
> >>>>>>>>>>> constructed explicitly by the user. This may not be a bad thing.
> >>>>>>>>>>> However, if the Function is loaded from a file, nobody owns the
> >>>>>>>>>>> FunctionSpace.
> >>>>>>>>>> Conceptually, I agree with Dag (and Martin?) that it is natural to
> >>>>>>>>>> have global function spaces. And if the explicit construction of such
> >>>>>>>>>> spaces can be made simple, it may not be a bad thing but a natural
> >>>>>>>>>> part in setting up the mathematical problem. And I do not really like
> >>>>>>>>>> that functions should be initialized from a form, which defines an
> >>>>>>>>>> equation.
> >>>>>>>>>>
> >>>>>>>>>> I think one idea was to not force less mathematically oriented users
> >>>>>>>>>> to worry about function spaces. I guess there are (at least) 2 types
> >>>>>>>>>> of functions: (i) functions part of the form, and (ii) functions not
> >>>>>>>>>> part of the form, but used in pre/postprocessing etc.
> >>>>>>>>>>
> >>>>>>>>>> For (i) it may be natural to construct the function space from the
> >>>>>>>>>> form, and for (ii) it may be convenient in some cases, but it is not
> >>>>>>>>>> really obvious that this is the best solution.
> >>>>>>>>>>
> >>>>>>>>>> Maybe an explicit construction of a function space can come with a
> >>>>>>>>>> default, such as a nodal basis of piecewise linears?
> >>>>>>>>>>
> >>>>>>>>>> /Johan
> >>>>>>>>> So:
> >>>>>>>>>   FunctionSpace V(mesh);
> >>>>>>>>>   Function f(V);
> >>>>>>>>> gives a function f on piecewise linears?
> >>>>>>>>> That's ok with me.
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> About ownership, I think the only both robust and intuitive solution
> >>>>>>>>> is that an object never should store a reference (or regular pointer)
> >>>>>>>>> to another object. But as long as we are aware of the cost of doing
> >>>>>>>>> this and state it clearly in the documentation, I'm ok with keeping
> >>>>>>>>> e.g. the Mesh references like we do.
> >>>>>>>>>
> >>>>>>>>> Any time object A stores a reference to object B, the user must
> >>>>>>>>> take care that the lifetime of B exceeds the lifetime of A. There
> >>>>>>>>> are no exceptions to this. This puts some real limitations on the
> >>>>>>>>> way the user must structure his program, e.g. he must sometimes
> >>>>>>>>> (often?) keep objects around longer than they're explicitly needed.
> >>>>>>>>>
> >>>>>>>>> This may be a good thing, since it forces the user to think about
> >>>>>>>>> dependencies and object lifetimes, and the objects in question
> >>>>>>>>> use some memory.
> >>>>>>>> I think this is ok. There are many ways to create a segfault in C++.
> >>>>>>>> If you program in C++, you will have to think about memory.
> >>>>>>>>
> >>>>>>>>> But if we use references instead of shared_ptr,
> >>>>>>>>> we should never have default values:
> >>>>>>>>> - A Function has a reference to a Mesh, which is ok since
> >>>>>>>>>   it's always created outside.
> >>>>>>>>> - If a DiscreteFunction is to have a reference to a Vector, or a
> >>>>>>>>>   Function is to have a reference to a FunctionSpace, it cannot
> >>>>>>>>>   create its own without adding memory management code.
> >>>>>>>>>
> >>>>>>>>> Every place we accept these limitations and requirements of how
> >>>>>>>>> the user structures his programs, we can use references and be
> >>>>>>>>> done with it. But don't think that the pretty syntax means the user
> >>>>>>>>> doesn't have to think about memory management, since all the
> >>>>>>>>> responsibility for memory management (object destruction order)
> >>>>>>>>> is in fact placed on the user, and errors from the users side will
> >>>>>>>>> lead to invalid references we cannot detect and segfaults.
> >>>>>>>> I want the syntax to be simple and pretty, but I don't necessarily
> >>>>>>>> want to hide the user from problems that are part of the design of
> >>>>>>>> C++. It isn't Python or Java. You should be expected to know what
> >>>>>>>> you are doing. :-)
> >>>>>>> It's not only about knowing what you're doing. It forces very
> >>>>>>> hard restrictions on the design/flow of your program, which can
> >>>>>>>
> >>>>>>> 1) Be a major source of bugs in nontrivial apps (see Garths email), which
> >>>>>>> are not locally visible because they depend on the global program flow.
> >>>>>>>
> >>>>>>> 2) Make it impossible to initialize e.g. Function in e.g a file reader,
> >>>>>>> since the caller of the file reader would need to get the objects
> >>>>>>> Function depends on. This is not limited to file readers, but is
> >>>>>>> a recurring pattern in nontrivial apps.
> >>>>>>>
> >>>>>>> If we want to use dolfin or want dolfin to be used in apps that
> >>>>>>> are more complicated than the traditional "read input, compute
> >>>>>>> something, output something" app, these restrictions become
> >>>>>>> a larger problem.
> >>>>>>>
> >>>>>>>> Anyway, I like the idea about having a FunctionSpace class which
> >>>>>>>> several Functions may share. The problem we need to solve is
> >>>>>>>> reading from file:
> >>>>>>>>
> >>>>>>>>  FunctionSpace V(mesh);
> >>>>>>>>  Function u(V);
> >>>>>>>>  file >> u;
> >>>>>>>>
> >>>>>>>> The last line just fills out the data in both u and V.
> >>>>>>>>
> >>>>>>>> This will lead to side effects as V might be changed when doing
> >>>>>>>>
> >>>>>>>>  FunctionSpace V(mesh);
> >>>>>>>>  Function u(V);
> >>>>>>>>  Function v(V);
> >>>>>>>>  file >> u;
> >>>>>>>>
> >>>>>>>> V will be changed, both for u and v. In fact, the mesh will also be
> >>>>>>>> changed.
> >>>>>>>>
> >>>>>>>> The best thing would be if we could do
> >>>>>>>>
> >>>>>>>>  file >> (mesh, V, u);
> >>>>>>> This is _exactly_ the kind of issue that smart pointers solve.
> >>>>>>>
> >>>>>>> Btw, I tried to search the swig documentation for shared_ptr, and
> >>>>>>> found nothing...
> >>>>>>> I don't know what exactly they mean by "shared_ptr support".
> >>>>>> It seems to be a set of typemaps that should kick in at the "right places".
> >>>>>> They are defined in
> >>>>>>
> >>>>>>    <Lib/python/boost_shared_ptr.i>
> >>>>>>
> >>>>>> and used very rudimentary in
> >>>>>>
> >>>>>>   <Examples/test_suite/li_boost_shared_ptr.i>
> >>>>>>
> >>>>>> in the source tree of the 1.3.36 release. It seems that it is not specific for
> >>>>>> boost::share_ptr but should also figure out tr1::shared_ptr
> >>>>>>
> >>>>>> I think:
> >>>>>>
> >>>>>>   %include <boost_shared_ptr.i>
> >>>>>>
> >>>>>> at the appropriate place should do the trick.
> >>>>>>
> >>>>>> Johan
> >>>>> I was about to start sketching on a FunctionSpace class when I
> >>>>> realized that this class might look different for different types of
> >>>>> Functions.
> >>>>>
> >>>>> In particular, some functions (DiscreteFunctions) need to have a
> >>>>> dof map and a finite element, while this is not needed for other
> >>>>> functions.
> >>>>>
> >>>>> This means that we might need to duplicate the hierarchy of different
> >>>>> function classes in a number of different function space classes.
> >>>>>
> >>>>> I see two other options:
> >>>>>
> >>>>> 1. Require that a function space consists of
> >>>>>
> >>>>>   mesh, finite_element, dof_map
> >>>>>
> >>>>> and pick a suitable (trivial) dof map for example constant functions.
> >>>>>
> >>>>> 2. Implement a number of different function space classes but have a
> >>>>> single Function class which holds data but where each function call
> >>>>> is passed on to the specific type of function call in the
> >>>>> corresponding function space class.
> >>>> Here are some more thoughts about the shared_ptr issue.
> >>>>
> >>>> As I understand it, using shared_ptr to store the data in
> >>>> DiscreteFunction means that users will need to use shared_ptr.
> >>>> In particular, a Function must be initialized with a shared_ptr to a
> >>>> Mesh, not a reference to a Mesh. Then in all demos, we would have to
> >>>> change from
> >>>>
> >>>>   Mesh mesh("mesh.xml");
> >>>>
> >>>> to
> >>>>
> >>>>   shared_ptr<Mesh> mesh = new Mesh("mesh.xml");
> >>>>
> >>>> This doesn't look very pretty, and it would make the interface
> >>>> inconsistent. One would need to know that some classes likes Mesh
> >>>> should "always" be stored in a shared_ptr (since it will most
> >>>> certainly be used to initialize a Function), while other classes like
> >>>> Matrix, File, KrylovSolver, can be created as usual.
> >>>>
> >>>> There seem to be two options:
> >>>>
> >>>> 1. Don't use shared_ptr anywhere (at least not in public interfaces)
> >>>>
> >>>> If we choose this option, we will need to decide who owns what. For
> >>>> example, we could say that a Function always owns the Vector, but
> >>>> never the Mesh.
> >>>>
> >>>> This works out also for reading from files:
> >>>>
> >>>>   Mesh mesh;
> >>>>   Function u(mesh);
> >>>>   file >> u;
> >>>>
> >>>> This would lead to side effects (the mesh will be changed), but that
> >>>> might be ok.
> >>>>
> >>>> 2. Use shared_ptr everywhere
> >>>>
> >>>> If we choose this option, we need to redefine Mesh so that it is not a
> >>>> mesh class, but a shared_ptr for a mesh class (which we rename to
> >>>> something else). Sundance does something like this and it gives a nice
> >>>> and pretty syntax:
> >>>>
> >>>>   Mesh mesh = new Mesh();             // no need to delete
> >>>>   Function u = new Function(mesh);    // no need to delete
> >>>>
> >>>> Essentially, it would look like Java. See here:
> >>>>
> >>>>   http://software.sandia.gov/sundance/basics.html
> >>>>
> >>>> in the section "Handles and Memory Management".
> >>>>
> >>>> I think we need to pick one of these options and not a mix since it
> >>>> would make the interface inconsistent.
> >>>>
> >>>> Opinions? 1 or 2?
> >>>>
> >>> I don't think that mixing is inconsistent. At the moment we use a
> >>> mixture of references and pointers, and there is usually a logical
> >>> choice. Most users never need to work with the pointers. If we use smart
> >>> pointers, they will be used primarily internally in place of where we
> >>> currently use plain pointers.
> >>>
> >>> For the specific case of a Function, part of the issue will be resolved
> >>> by requiring that a Function own it's own vector (forgetting about
> >>> sub-functions for the time being). Ownership of a finite element, or
> >>> possibly a FunctionSpace in the future, remains an issue because it's
> >>> natural that these are shared.
> >>>
> >>> If you look at uBLASVector which now uses a smart pointer, not a single
> >>> piece of code outside uBLASVector had to be changed, but an advanced
> >>> user can now create a uBLASVector from a uBLAS object and not worry
> >>> about it going out of scope,
> >>>
> >>> Garth
> >>
> >> I'm all for it if it can be hidden (or visible only by choice), but
> >> isn't it the case that the mesh (or function space) will always have
> >> to be a shared_ptr?
> >>
> >> In all applications, one will need to write
> >>
> >>   shared_ptr<Mesh> mesh = new Mesh(...);
> >>
> >
> > I think that it's logical for a Function to have a reference to a Mesh.
> > I'm not sure exactly the nicest way to deal with a FunctionSpace. If we
> > want pretty syntax + plus smart pointer flexibility, a Function could
> > have a pointer to the FunctionSpace, in which case it *does not* own the
> > FunctionSpace, and a smart pointer in which case it may or may not  own
> > the FunctionSpace.
> >
> > The class Function would look like
> >
> >   class Function
> >   {
> >     public:
> >
> >       Function(FunctionSpace& space) : V(space) {}
> >
> >       Function(shared_prt<FunctionSpace> space) : V(0), shared_V(space)
> >         {}
> >
> >     private:
> >       FunctionSpace* V;
> >       shared_ptr<FunctionSpace>  shared_V;
> >   }
> >
> > and a Function could be initialised by
> >
> >   FunctionSpace V;
> >   Function u(V);
> >
> > in which case it does not own the FunctionSpace, or by
> >
> >   shared_ptr<FunctionSpace> V(new FunctionSpace);
> >   Function u(V);
> >
> > in which case it may or may not own the FunctionSpace. The former would
> > be used in simple programs, and the latter in, for example,
> > LinearPDE::solve.
> >
> > Garth
> >
> >> ?
> 
> Sounds a bit dangerous to me... It does enable sharing objects
> if you want to, but keeps the possibility to shoot of your foot.
> 
> Anyway, a little tip: shared_ptr can take a deleter policy as input
> to its constructor, so you don't need the extra FunctionSpace* to
> implement this approach. Something like this should do the trick:
> 
>       class NoDeleter {
>         public:
>           void operator() (FunctionSpace *p) {}
>       };
> 
> ...
> 
>       Function(FunctionSpace& space) : shared_V(&space, NoDeleter()) {}
> 
> (not tested, but modified from some working code).
> 
> 
> And by the way, a thing to look out for is when using shared_ptr
> for array pointers. Then you need to use a deleter policy like above,
> except with function body { delete [] p; } instead.

This sounds like the trick I was asking for earlier: a way to provide
two different ways to initialize objects, either passing a reference
or a shared_ptr (something like decrease_count).

Do we want to do it this way?

-- 
Anders

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