On Tue, Apr 26, 2011 at 12:43:06PM +0100, Garth N. Wells wrote:
>
>
> On 26/04/11 12:22, Martin Sandve Alnæs wrote:
> > On 26 April 2011 10:56, Garth N. Wells <gn...@cam.ac.uk
> > <mailto:gn...@cam.ac.uk>> wrote:
> >
> >
> >
> > On 26/04/11 09:03, Martin Sandve Alnæs wrote:
> > > See other mail. I don't see that it solves anything, it doesn't seem
> > > related to anything I've read about in this thread, and it has a
> > > potential backside in hindering the garbage collector in Python. I may
> > > be wrong, but nobody has answered my other questions about this
> > thread yet.
> > >
> >
> > As a precursor, the primary problem has nothing to do with Instant disk
> > cache, etc. The Instant discussion is just confusing the original point.
> >
> > In summary, is it helpful if DOLFIN can avoid calling ufl.preprocess
> > every time a dolfin.Form object is created. DOLFIN relies on
> > preprocessing to extract the form Arguments, from which the mesh is
> > extracted (via form_data().original_arguments, and since DOLFIN uses
> > 'Arguments' that are subclasses of UFL and DOLFIN objects).
> >
> > The solution that Johan has implemented is to have FFC attach the
> > form_data to a form. If a form has form_data attached, then we know that
> > it has already been preprocessed. Martin won't like this because it's
> > changing the form object.
> >
> >
> > This sounds much like my original design. Trying to recall from my possibly
> > rusty memory, I believe that calling myform.form_data() would
> > construct form data only the first time and the preprocessed form could
> > be retrieved from the returned form data. The form data was attached
> > as myform._form_data. Thus you could always say
> > preprocessed_form = myform.form_data().form
> > and preprocessing would only happen once.
>
> I think that the above would solve the issue. At the moment ufl.Form has
> the member function:
>
> def form_data(self):
> "Return form metadata (None if form has not been preprocessed)"
> return self._form_data
>
> If it did
>
> def form_data(self):
> if self._form_data is None:
> # compute form_data
> return self._form_data
>
> it should make things straightforward. But doesn't this violate
> immutability of the form, or is it ok since the mathematical form itself
> is not being modified?
I think it is ok for the same reason that dolfin::mesh.init() is
const: the mesh does not change and the edges are already there (only
not yet extracted). Same with the form: the metadata is there but not
yet extracted.
--
Anders
> Garth
>
>
> > This was redesigned
> > after I left to have a separate preprocess function.
> >
> >
> > It may be enough if UFL would provide a function to return a list of
> > form Arguments, if this is fast. Something like
> >
> > def extract_original_arguments(form):
> >
> > # Replace arguments and coefficients with new renumbered objects
> > arguments, coefficients = extract_arguments_and_coefficients(form)
> > replace_map, arguments, coefficients \
> > = build_argument_replace_map(arguments, coefficients)
> > form = replace(form, replace_map)
> >
> > # Build mapping to original arguments and coefficients, which is
> > # useful if the original arguments have data attached to them
> > inv_replace_map = {}
> > for v, w in replace_map.iteritems():
> > inv_replace_map[w] = v
> > original_arguments = [inv_replace_map[v] for v in arguments]
> >
> > return original_arguments
> >
> > Garth
> >
> >
> > I don't understand why this is needed. We:
> > - must preprocess each form once
> > - don't want to preprocess the same form twice
> > - can obtain the original arguments after preprocessing
> > This was supported a long time ago, so unless someone has
> > removed functionality while I've been gone, what is the problem?
> >
> > I have a feeling that the source of many problems is the attempt
> > to reuse forms and change mesh, functions, or elements.
> > This is contrary to the design of UFL where expressions are immutable.
> >
> > Martin
> >
> >
> > > Martin
> > >
> > > On 26 April 2011 09:20, Garth N. Wells <gn...@cam.ac.uk
> > <mailto:gn...@cam.ac.uk>
> > > <mailto:gn...@cam.ac.uk <mailto:gn...@cam.ac.uk>>> wrote:
> > >
> > > Martin: Any problem if we apply this patch to UFL?
> > >
> > > Garth
> > >
> > > On 25/04/11 22:50, Johan Hake wrote:
> > > > This should be fixed now.
> > > >
> > > > I do not see why we introduced the memory cache when this
> > solution
> > > was laying
> > > > right in front our eyes...
> > > >
> > > > Anyhow. Here is a patch for ufl to avoid circular dependency
> > between a
> > > > preprocessed form and the form_data.
> > > >
> > > > Johan
> > > >
> > > > On Monday April 25 2011 14:34:00 Anders Logg wrote:
> > > >> Simple sounds good.
> > > >>
> > > >>
> > > >> On Mon, Apr 25, 2011 at 02:29:50PM -0700, Johan Hake wrote:
> > > >>> I am working on a simple solution, where we store
> > everything in the
> > > >>> original ufl form.
> > > >>>
> > > >>> I might have something soon.
> > > >>>
> > > >>> Johan
> > > >>>
> > > >>> On Monday April 25 2011 14:26:18 Garth N. Wells wrote:
> > > >>>> On 25/04/11 22:08, Anders Logg wrote:
> > > >>>>> On Mon, Apr 25, 2011 at 07:40:21PM -0000, Garth Wells wrote:
> > > >>>>>> On 25/04/11 20:00, Johan Hake wrote:
> > > >>>>>>> On Monday April 25 2011 11:26:36 Garth Wells wrote:
> > > >>>>>>>> On 25/04/11 18:51, Anders Logg wrote:
> > > >>>>>>>>> On Mon, Apr 25, 2011 at 05:11:41PM -0000, Garth
> > Wells wrote:
> > > >>>>>>>>>> On 25/04/11 17:53, Johan Hake wrote:
> > > >>>>>>>>>>> On Monday April 25 2011 08:59:18 Garth Wells wrote:
> > > >>>>>>>>>>>> On 25/04/11 16:47, Johan Hake wrote:
> > > >>>>>>>>>>>>> Commenting out the cache is really not a fix. The
> > > problem is
> > > >>>>>>>>>>>>> within dolfin. Isn't there another way to deal
> > with this?
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>> It is a fix if the cache isn't needed.
> > > >>>>>>>>>>>
> > > >>>>>>>>>>> Sure.
> > > >>>>>>>>>>>
> > > >>>>>>>>>>>>> First: How much penalty are there with a
> > disabled memory
> > > >>>>>>>>>>>>> cache. Maybe the problem isn't that bad?
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>> I don't get the point of this cache. The way it
> > is now,
> > > a form
> > > >>>>>>>>>>>> is only preprocessed if it hasn't already been
> > > preprocessed,
> > > >>>>>>>>>>>> which seems ok to me. The old code tried to avoid
> > some
> > > >>>>>>>>>>>> preprocessing, but it was highly dubious and I doubt
> > > that it
> > > >>>>>>>>>>>> was effective.
> > > >>>>>>>>>>>
> > > >>>>>>>>>>> I think the preprocessing stage actually do take
> > some time.
> > > >>>>>>>>>>> AFAIK the preproces stage essentially do two
> > things. It
> > > >>>>>>>>>>> creates a canonical version of the Form so two Forms
> > > that are
> > > >>>>>>>>>>> the same, but constructed at different times are
> > beeing
> > > >>>>>>>>>>> treated equal wrt form generation. Then are DOLFIN
> > specific
> > > >>>>>>>>>>> guys extracted. I am not sure what takes the most
> > time. We
> > > >>>>>>>>>>> should probably profiel it... But if it is the
> > latter we
> > > could
> > > >>>>>>>>>>> consider putting another cache in place which is
> > more robust
> > > >>>>>>>>>>> wrt changing DOLFIN objects.
> > > >>>>>>>>>>
> > > >>>>>>>>>> It should be easy to avoid the overhead of
> > preprocessing by
> > > >>>>>>>>>> keeping the object in scope. If the object changes,
> > the only
> > > >>>>>>>>>> robust way to make sure that the form is the same
> > as one
> > > in the
> > > >>>>>>>>>> cache is to compare all the data. This requires
> > preprocessing
> > > >>>>>>>>>> the form, which then defeats the purpose of a cache. It
> > > may be
> > > >>>>>>>>>> possible to add a lightweight preprocess to UFL,
> > but I don't
> > > >>>>>>>>>> think that it's worth the effort or extra complication.
> > > >>>>>>>
> > > >>>>>>> I think a light weight version might be the way to go.
> > This
> > > is then
> > > >>>>>>> stored in memory cache. If we are able to strip such a
> > form
> > > for all
> > > >>>>>>> DOLFIN specific things we would also prevent huge memory
> > > leaks with
> > > >>>>>>> mesh beeing kept.
> > > >>>>>>>
> > > >>>>>>> Then we always grab DOLFIN specific data from the
> > passed form
> > > >>>>>>> instead of grabbing from the cache. Not sure how easy this
> > > will be
> > > >>>>>>> to implement, but I think we need to explore it, as
> > the DOLFIN
> > > >>>>>>> specific part of the form really has nothing to do
> > with the
> > > >>>>>>> generated Form.
> > > >>>>>>>
> > > >>>>>>> Martin:
> > > >>>>>>> Why is it important to have the _count in the repr of the
> > > form? I
> > > >>>>>>> guess that is used in ufl algorithms? Would it be
> > possible to
> > > >>>>>>> include a second repr function, which did not include
> > the count?
> > > >>>>>>> This would then be used when the signature is checked
> > for. We
> > > >>>>>>> could then use that repr to generate a form which is
> > stored
> > > in the
> > > >>>>>>> memory cache. This would then be tripped for any
> > DOLFIN specific
> > > >>>>>>> objects. This should work as the _count attribute has
> > nothing to
> > > >>>>>>> do with what code gets generated, but it is essential for
> > > internal
> > > >>>>>>> UFL algorithms, right?
> > > >>>>>>>
> > > >>>>>>>>> I'm not very happy with this change.
> > > >>>>>>>>
> > > >>>>>>>> The bright side is that slow and correct is a better
> > starting
> > > >>>>>>>> point than fast but wrong ;).
> > > >>>>>>>>
> > > >>>>>>>> An easy fix is to attach the preprocessed form to a Form
> > > object.
> > > >>>>>>>> This would work robustly if we can make forms
> > immutable once
> > > >>>>>>>> they've been compiled. Is it possible to make a
> > Python object
> > > >>>>>>>> immutable?
> > > >>>>>>>
> > > >>>>>>> We can probably overload all setattribtue methods which
> > > prohibits a
> > > >>>>>>> user to write to these but it might not be possible to
> > > prohibit a
> > > >>>>>>> user to change attributes on instances owned by the
> > Form. I
> > > guess
> > > >>>>>>> this is similare to the difficulties of preserving
> > constness in
> > > >>>>>>> C++, but I think it is even harder in Python.
> > > >>>>>>
> > > >>>>>> What if we have the FFC jit compiler return the
> > preprocessed
> > > form,
> > > >>>>>> and inside dolfin.Form simply do
> > > >>>>>>
> > > >>>>>> class Form(cpp.Form):
> > > >>>>>> def __init__(self, form, . . .. )
> > > >>>>>> ....
> > > >>>>>>
> > > >>>>>> (...., preprocessed_form) = jit(form, . . . . )
> > > >>>>>>
> > > >>>>>> form = preprocessed_form
> > > >>>>>>
> > > >>>>>> .....
> > > >>>>>>
> > > >>>>>> This way, form will have form_data, and the FFC jit
> > function will
> > > >>>>>> know not to call ufl.preprocess.
> > > >>>>>
> > > >>>>> Here's another strange thing. In the JITObject class, we
> > have two
> > > >>>>> functions: __hash__ and signature. As far as I
> > understand, the
> > > first
> > > >>>>> is used to located objects (generated code/modules) in
> > the Instant
> > > >>>>> in-memory cache, while the second is used for the
> > on-disk cache.
> > > >>>>>
> > > >>>>> >From some simple tests I did now, it looks like the
> > __hash__
> > > function
> > > >>>>>>
> > > >>>>> does not need to any significant speedup. The JIT benchmark
> > > runs just
> > > >>>>> as fast if I call signature from within __hash__.
> > > >>>>>
> > > >>>>> Furthermore, the __hash__ function must also be broken
> > since it
> > > >>>>> relies on calling id on the form.
> > > >>>>>
> > > >>>>> Ideally, we should get Instant to handle the caching, both
> > > in-memory
> > > >>>>> and on-disk, by providing two functions __hash__ (fast, for
> > > in-memory
> > > >>>>> cache) and signature (slow, for on-disk cache).
> > > >>>>>
> > > >>>>> Since __hash__ cannot call id, it must be able to attach
> > a unique
> > > >>>>> string to the form (perhaps based on an internal counter
> > in FFC).
> > > >>>>> My suggestion would be to add this to UFL, something
> > like set_hash
> > > >>>>> and hash (which would return None if set_hash has not been
> > > called).
> > > >>>>> If Martin does not like that, we should be able to handle it
> > > on the
> > > >>>>> DOLFIN side.
> > > >>>>>
> > > >>>>> So in conclusion: no in-memory cache in FFC (handled by
> > > Instant) and
> > > >>>>> FFC attaches a hash to incoming forms so that Instant may
> > > recognize
> > > >>>>> them later.
> > > >>>>
> > > >>>> The code that I disabled was caching preprocessed forms, so I
> > > don't see
> > > >>>> how this can be handled by Instant.
> > > >>>>
> > > >>>> Garth
> > > >>>>
> > > >>>>> Maybe even better: Instant checks whether an incoming
> > object has a
> > > >>>>> set_hash function and if so calls it so it can recognize
> > > objects it
> > > >>>>> sees a second time.
> > > >>>>>
> > > >>>>> I'm moving this discussion to the mailing list(s).
> > > >>>>
> > > >>>> _______________________________________________
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