ufl team mailing list archive

[Johan Hake <johan.hake@xxxxxxxxx>]

On Monday April 25 2011 15:19:20 Anders Logg wrote:
> On Mon, Apr 25, 2011 at 03:14:45PM -0700, Johan Hake wrote:
> > On Monday April 25 2011 15:04:43 Anders Logg wrote:
> > > On Mon, Apr 25, 2011 at 10:56:25PM +0100, Garth N. Wells wrote:
> > > > On 25/04/11 22:48, Anders Logg wrote:
> > > > > On Mon, Apr 25, 2011 at 10:41:58PM +0100, Garth N. Wells wrote:
> > > > >> On 25/04/11 22:33, Anders Logg wrote:
> > > > >>> On Mon, Apr 25, 2011 at 10:26:18PM +0100, 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.
> > > > >>> 
> > > > >>> The point would be that one could check that "hash" of the form
> > > > >>> (some unique string) instead of computing the signature which
> > > > >>> involves preprocessing the form.
> > > > >> 
> > > > >> How would the hash be computed? To check if the mesh has changed,
> > > > >> my limited understanding is that the entire object would have to
> > > > >> be serialised, and then a hash computed. How expensive is that?
> > > > >> 
> > > > >> The issue that I ran into was not related to signatures. It was
> > > > >> related to the non-UFL data that is attached to arguments.
> > > > > 
> > > > > The hash would be unique to each form. It could just be a counter
> > > > > value and the counter would be increased inside Instant for each
> > > > > object it gets as input.
> > > > 
> > > > But how does Instant know if a form is new? I also don't see why
> > > > Instant should need to know if the mesh associated with a form has
> > > > changed, but is for the rest the same. Wouldn't Instant need to be
> > > > DOLFIN-aware?
> > > 
> > > The hash() function would play the same role as the id() function
> > > before with the difference that we can't get the same id for a new
> > > form as for an old form that's gone out of scope.
> > > 
> > > Instant should not need to know anything it just does this:
> > >    check if object has a set_hash() function
> > >    if so, calls hash() to get the hash value
> > >    
> > >      checks the cache for that hash value
> > >    
> > >    if not, assign unique value by calling set_hash on the object
> > > 
> > > We would need to make sure from the DOLFIN side that when we change a
> > > Form, we also change the hash value (for example by setting it to
> > > None) which would trigger the Instant disk cache.
> > 
> > Sounds complicated...
> 
> I think it sounds very easy. Everything we need is there: Instant
> already has memory and disk cache. We just need to provide the proper
> input.

The set and get hash introduce another level of complexity.

> > Now the preprocessed form is stored in the original form. This will never
> > change. Whenever a form does not go out of scope the preprocessed form
> > will live.
> > 
> > Also Martin made it impossible to change a form without returning a new
> > instance. This prevents any changing of the original form while keeping a
> > preprocesses form attached to it.
> > 
> > If a form has a preprocessed form that will be used for code generation.
> > The preprocessed form will be used in instants memory cache. The
> > preprocessed form has nothing to do the any DOLFIN objects that comes
> > with the original form, such as mesh, expressions and such.
> > 
> > Anything I have missed?
> 
> What about the __hash__ function in jitobject.py? It still calls
> id(). Isn't that a problem?

No. The __hash__ is only used to retreive the memory cached compiled module in 
instant. This so we can retreive the compiled form. The form_data including 
all DOLFIN dependent data are stored in form_data which is just retrieved from 
the preprocessed form.

A user can change this, but it seems that form_data is correctly updated with 
the new mesh.

Btw: We could probably store the compiled form also in form_data. We could 
then avoid going through instant memory cache :)

Johan