ufl team mailing list archive

["Garth N. Wells" <gnw20@xxxxxxxxx>]

On 25/04/11 23:19, 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.
> 
>> 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?
> 

Yes, but we're trying to tackle one issue at a time. First avoiding
necessary calls to preprocess. Note that there will be common usage
cases in which a call to preprocess in needed, but for which the
compiled from can be extract from the Instant cache.

Garth

> --
> Anders