dolfin team mailing list archive

[Johan Hake <johan.hake@xxxxxxxxx>]

On Tuesday 01 December 2009 12:08:54 Garth N. Wells wrote:
> 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.
> 
> Fixed on the C++ side. It should have a function to indicate a change in
> size. That way, we can have this process
> 
> 1. An Array is received and turned into a NumPy
> 2. Length of NumPy array changes on the Python side
> 3. Array is 'informed' of the new length when sent back to C++
> 
> This change in length on the Python side is something we can't handle at
> the moment as far as I understand.

A NumPy array is already fixed. Any changes wrt length will return a new NumPy 
array. You can hand slices, which are views of other arrays, but this is 
different case which we cannot support.

If we have a re-sizable Array we can add some flags, so it cannot be resized 
if it is a view of a passed NumPy array.

But shouldn't this discussion be on the Blueprint page?

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