ufl team mailing list archive

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

On 25/04/11 23:16, Anders Logg wrote:
> On Mon, Apr 25, 2011 at 11:10:59PM +0100, Garth N. Wells wrote:
>>
>>
>> On 25/04/11 23:04, 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.
>>>
>>
>> This is the problem - how do we know that it's changed?
> 
> Because we change it. When we modify a Form, we need to invalidate the
> hash, by making sure that we modify the Form by calling member
> functions that invalidate the hash (setting it to None).
>

It's the ufl form that is changed, not the DOLFIN form.

Garth

>> The original issue is not related to disk vs memory cache, or Instant.
>> It is how to avoid calling ufl.preprocess unnecessarily when the form
>> repr() is unchanged but the mesh has been changed.
> 
> Exactly, and that's why I suggest introducing the hash as something to
> be checked instead of id() which turned out not to be robust.
> 
> And furthermore, the call to id/hash should be handled by Instant, not
> FFC. Since Instant handles JIT compiling and caching, FFC should only
> need to call Instant, not handle extra caching.
> 
> --
> Anders