On 26/04/11 09:56, Garth N. Wells 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.
>
> 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
>
As addition, I think that we're letting DOLFIN specific issues creep
into FFC and UFL. It would be simple if FFC simply did
if form.form_data() is not None:
preprocessed_form = form
else:
preprocessed_form = preprocess(form, common_cell=common_cell)
and DOLFIN is made responsible for preprocessing a form (or not
preprocessing) before sending it to the FFC JIT compiler, particularly
since deciding to preprocess or not can depend on what DOLFIN-specific
data (e.g. meshes) has been attached to the form.
Garth
> Garth
>
>
>> Martin
>>
>> On 26 April 2011 09:20, Garth N. Wells <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.
>> >>
>> >> --
>> >> Anders
>> >>
>> >> 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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>
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