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Message #01782
Re: [Ffc] [Bug 769811] [NEW] JIT cache problem with id(form)
Feel free to do it :)
Martin
On 26 April 2011 13:55, Anders Logg <logg@xxxxxxxxx> wrote:
> So will you add it back? I can do it since it's my fault removing it,
> but I assume you want to handle it yourself. ;-)
>
> --
> Anders
>
>
> On Tue, Apr 26, 2011 at 01:46:59PM +0200, Martin Sandve Alnæs wrote:
> > Caching is ok precicely _because_ the form is immutable.
> >
> > Martin
> >
> > On 26 April 2011 13:43, Garth N. Wells <gnw20@xxxxxxxxx> wrote:
> >
> >
> >
> > On 26/04/11 12:22, Martin Sandve Aln s wrote:
> > > On 26 April 2011 10:56, Garth N. Wells <gnw20@xxxxxxxxx
> > > <mailto:gnw20@xxxxxxxxx>> wrote:
> > >
> > >
> > >
> > > On 26/04/11 09:03, Martin Sandve Aln s 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?
> >
> > 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 <gnw20@xxxxxxxxx
> > > <mailto:gnw20@xxxxxxxxx>
> > > > <mailto:gnw20@xxxxxxxxx <mailto:gnw20@xxxxxxxxx>>> 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).
> > > > >>>>
> > > > >>>> _______________________________________________
> > > > >>>> Mailing list: https://launchpad.net/~ufl
> > > > >>>> Post to : ufl@xxxxxxxxxxxxxxxxxxx
> > > <mailto:ufl@xxxxxxxxxxxxxxxxxxx>
> > > > <mailto:ufl@xxxxxxxxxxxxxxxxxxx <mailto:
> ufl@xxxxxxxxxxxxxxxxxxx
> > >>
> > > > >>>> Unsubscribe : https://launchpad.net/~ufl
> > > > >>>> More help : https://help.launchpad.net/ListHelp
> > > >
> > > > _______________________________________________
> > > > Mailing list: https://launchpad.net/~ufl
> > > > Post to : ufl@xxxxxxxxxxxxxxxxxxx
> > > <mailto:ufl@xxxxxxxxxxxxxxxxxxx> <mailto:
> ufl@xxxxxxxxxxxxxxxxxxx
> > > <mailto:ufl@xxxxxxxxxxxxxxxxxxx>>
> > > > Unsubscribe : https://launchpad.net/~ufl
> > > > More help : https://help.launchpad.net/ListHelp
> > > >
> > > >
> > >
> > >
> >
> >
> >
>
> > _______________________________________________
> > Mailing list: https://launchpad.net/~ufl
> > Post to : ufl@xxxxxxxxxxxxxxxxxxx
> > Unsubscribe : https://launchpad.net/~ufl
> > More help : https://help.launchpad.net/ListHelp
>
>
Follow ups
References
-
Re: [Ffc] [Bug 769811] [NEW] JIT cache problem with id(form)
From: Johan Hake, 2011-04-25
-
Re: [Ffc] [Bug 769811] [NEW] JIT cache problem with id(form)
From: Anders Logg, 2011-04-25
-
Re: [Ffc] [Bug 769811] [NEW] JIT cache problem with id(form)
From: Johan Hake, 2011-04-25
-
Re: [Ffc] [Bug 769811] [NEW] JIT cache problem with id(form)
From: Garth N. Wells, 2011-04-26
-
Re: [Ffc] [Bug 769811] [NEW] JIT cache problem with id(form)
From: Martin Sandve Alnæs, 2011-04-26
-
Re: [Ffc] [Bug 769811] [NEW] JIT cache problem with id(form)
From: Garth N. Wells, 2011-04-26
-
Re: [Ffc] [Bug 769811] [NEW] JIT cache problem with id(form)
From: Martin Sandve Alnæs, 2011-04-26
-
Re: [Ffc] [Bug 769811] [NEW] JIT cache problem with id(form)
From: Garth N. Wells, 2011-04-26
-
Re: [Ffc] [Bug 769811] [NEW] JIT cache problem with id(form)
From: Martin Sandve Alnæs, 2011-04-26
-
Re: [Ffc] [Bug 769811] [NEW] JIT cache problem with id(form)
From: Anders Logg, 2011-04-26
