dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

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?

-- 
Anders

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