dolfin team mailing list archive

[Johan Hake <johan.hake@xxxxxxxxx>]

On Tuesday 01 December 2009 12:03:41 Anders Logg wrote:
> On Tue, Dec 01, 2009 at 07:58:12PM +0000, Garth N. Wells wrote:
> > Anders Logg wrote:
> > > On Tue, Dec 01, 2009 at 07:21:00PM +0000, Garth N. Wells wrote:
> > >> Johan Hake wrote:
> > >>> On Tuesday 01 December 2009 11:06:43 you wrote:
> > >>>> Anders Logg wrote:
> > >>>>> On Tue, Dec 01, 2009 at 09:59:18AM -0800, Johan Hake wrote:
> > >>>>>> On Tuesday 01 December 2009 00:45:50 Anders Logg wrote:
> > >>>>>>> Would it help to add a new class on the C++ side that is used
> > >>>>>>> only for passing array data back and forth between C++ and
> > >>>>>>> Python? We have had this before (SimpleArray) and it would be
> > >>>>>>> fairly easy to extend the C++ with extra functions in the
> > >>>>>>> interface that use SimpleArray instead of std::vector.
> > >>>>>>>
> > >>>>>>> Then perhaps we can have one single typemap that hits SimpleArray
> > >>>>>>> everywhere and converts it to a NumPy array.
> > >>>>>>
> > >>>>>> Yes, something in that direction is what I had in mind. In
> > >>>>>> addition we could also add a foo.array() function to get a NumPy
> > >>>>>> view from this class. This would be nice when we do not want to
> > >>>>>> have all the communication through typemaps, but actually using
> > >>>>>> the SimpleArray in Python as return argument from some function
> > >>>>>> that wants to resize the array.
> > >>>>>>
> > >>>>>> We would also need some stuff to handle memory management.
> > >>>>>>
> > >>>>>> I see two fundamental ways such a class could be used:
> > >>>>>>   1) A replacement for the previous use of double/uint/int*, now
> > >>>>>> std::vector 2) A replacement for communication using std::vector
> > >>>>>> where resize flexibility is needed.
> > >>>>>>
> > >>>>>> I think 1, speaks for it self. 2 is where we need to resize any
> > >>>>>> passed vector. This goes for GenericMatrix.getrow,
> > >>>>>> foo.intersection, GenericFunction.comput_vertex_values.
> > >>>>>>
> > >>>>>>> And the work would be to add the extra stuff on the C++ side. The
> > >>>>>>> advantage would be less complex wrapper code and that Garth and I
> > >>>>>>> are capable of handling the complexities on the C++ side.
> > >>>>>>
> > >>>>>> Yes this must be a goal. I agree that the present SWIG situation
> > >>>>>> has grown out of hands.
> > >>>>>>
> > >>>>>>> But what I don't understand is why it would be easier to write a
> > >>>>>>> typemap for SimpleArray than for std::vector. Both of them use
> > >>>>>>> contiguous memory.
> > >>>>>>
> > >>>>>> Yes, but in std::vector it is now way, I suppose, to prevent a
> > >>>>>> vector to delete its data when it goes out of scope. This is
> > >>>>>> necessary in a typical in typemap.
> > >>>>>
> > >>>>> ok, let's create a very flexible array class that is targeted at
> > >>>>> simple communication between C++ and Python/NumPy. We had a class
> > >>>>> before named SimpleArray. We might call it NumPyArray or
> > >>>>> PythonArray.
> > >>>>
> > >>>> Can we just call it Array? It will be visible in the C++ interface
> > >>>> (e.g. in eval) so it would be good to have a nice name.
> > >>>
> > >>> Agree.
> > >>>
> > >>>>> I have created a blueprint:
> > >>>>>
> > >>>>> https://blueprints.launchpad.net/dolfin/+spec/array-typemaps
> > >>>>
> > >>>> I'll add something. I was thinking already about this. With a smart
> > >>>> pointer to the underlying data we should be to devise an elegant
> > >>>> memory model and be able to tell an Array object when it does and
> > >>>> doesn't own the data upon construction, and be able to change during
> > >>>> execution.
> > >>>
> > >>> Sounds fancy.
> > >>>
> > >>>>> We can fill out the details together.
> > >>>>>
> > >>>>>> I will fix the interface of getrow this evening. I was about to do
> > >>>>>> it yesterday, but instead I got grumpy :) But a good night sleep
> > >>>>>> makes wonders!
> > >>>>>
> > >>>>> Good! :-)
> > >>>>>
> > >>>>> Will you make a fast/temporary fix so that we can get ready for a
> > >>>>> release of 0.9.5 and then we can move the PythonArray
> > >>>>> implementation to a future release?
> > >>>>
> > >>>> The fast fix would be revert back to the
> > >>>>
> > >>>>     eval(double*, std::vector<double>&)
> > >>>>
> > >>>> interface. No point wasting time on typemaps for std::vector if
> > >>>> we're not going to use them.
> > >>>
> > >>> Fell free to make this change, I have a fool proof plan for the other
> > >>> temporary fix though. No new typemaps, just reusing old ones.
> > >>
> > >> OK, we need to make a decision.
> > >>
> > >> Option 1: Revert changes to eval.
> > >>
> > >> Option 2: Get SWIG working with the eval(std::vector<double>&, const
> > >> std::vector<double>&) interface.
> > >>
> > >> What's it going to be? I'm inclined to Option 1 since it requires no
> > >> work and it's been well tested.
> > >
> > > I'm warming up to the Array class option in which case we don't need
> > > to spend more time on fixing typemaps which will be removed anyway.
> > >
> > > So should the plan then be to use Array as much as possible in the
> > > C++ interface, instead of std::vector? We will still use std::vector
> > > and other STL types in the implementation but less of it in the user
> > > interface.
> >
> > Perhaps, as long as we don't end up re-implementing all the std::vector
> > functionality in Array.
> >
> > Garth
> 
> I assume we will make it fixed-size which will simplify the
> implementation a great deal and differentiate it from std::vector
> which has push_back.

From my point of view, it would be nice to have some sort of resize ability, 
as more methods and functions could use it, instead of std::vector to pass 
arguments. For example: GenericMatrix.getrow, foo.intersection.

Johan

> ok, so let's wait for you to revert the changes to eval() and then see
> where we stand.



> --
> Anders
>