dolfin team mailing list archive

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

On 02/06/11 16:05, Anders Logg wrote:
> On Thu, Jun 02, 2011 at 03:53:18PM +0100, Garth N. Wells wrote:
>>
>>
>> On 02/06/11 15:52, Anders Logg wrote:
>>> On Thu, Jun 02, 2011 at 03:31:31PM +0100, Garth N. Wells wrote:
>>>>
>>>>
>>>> On 02/06/11 15:21, Benjamin Kehlet wrote:
>>>>> On 2 June 2011 14:59, Garth N. Wells <gnw20@xxxxxxxxx> wrote:
>>>>>>
>>>>>>
>>>>>> On 02/06/11 12:10, Benjamin Kehlet wrote:
>>>>>>> On 2 June 2011 11:51, Anders Logg <logg@xxxxxxxxx> wrote:
>>>>>>>> On Thu, Jun 02, 2011 at 10:46:29AM +0100, Garth N. Wells wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 02/06/11 10:26, Anders Logg wrote:
>>>>>>>>>> On Thu, Jun 02, 2011 at 10:07:59AM +0100, Garth N. Wells wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 01/06/11 23:46, Anders Logg wrote:
>>>>>>>>>>>> Have you checked that there is no performance penalty?
>>>>>>>>>>>
>>>>>>>>>>> I just have - evaluating a Legendgre polynomial 10k times at the same
>>>>>>>>>>> point is just noise with both methods (of the order 10^-5 - 10^-4 s).
>>>>>>>>>>
>>>>>>>>>> It may be noise for some applications, but not for others. I'm not
>>>>>>>>>> sure this is a bottle-neck for the ODE code (Benjamin will know) but
>>>>>>>>>> we need to evaluate Legendre polynomials of degree > 100 many times
>>>>>>>>>> and then it may not be noise.
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> For very high degree (e.g. 200) Boost is marginally faster.
>>>>>>>>
>>>>>>>> Sounds promising then.
>>>>>>>>
>>>>>>>>>>> The Boost code is slightly slower because it doesn't cache the values
>>>>>>>>>>> (which is nice not to do), but may be faster if the call is inlined.
>>>>>>>>>>> It's not possible to inline it at the moment because of clashes between
>>>>>>>>>>> tr1:tuple and boost::tuple (Boost bug, I suspect). Old and new are the
>>>>>>>>>>> same when evaluating at different points.
>>>>>>>>>>
>>>>>>>>>> Let's wait for Benjamin to comment.
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> The speed is about the same (with scope to improve the speed for Boost)
>>>>>>>>> for unique values. The caller should be responsible for caching, if
>>>>>>>>> desired, since it can lead to memory blow out.
>>>>>>>>>
>>>>>>>>> Legendre does not appear in the ode code. It only appears in the
>>>>>>>>> computation of quadrature schemes.
>>>>>>>>
>>>>>>>> True, but the quadrature schemes are used in the ode code.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Garth
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>> Garth
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> Benjamin has
>>>>>>>>>>>> worked quite hard on optimizing some of the basic math routines (in
>>>>>>>>>>>> some cases by many many orders of magnitude).
>>>>>>>>>>>>
>>>>>>>>>>>> Benjamin, can you take a look that it still works?
>>>>>>>
>>>>>>> Yes, the performance seems to be about the same, but I'm unable to
>>>>>>> compile it with support for GMP.
>>>>>>>
>>>>>>> /usr/include/boost/math/special_functions/legendre.hpp:178:
>>>>>>> instantiated from ‘typename boost::math::tools::promote_args<RT,
>>>>>>> float, float, float, float, float>::type boost::math::legendre_p(int,
>>>>>>> int, T, const Policy&) [with T = __gmp_expr<__mpf_struct [1],
>>>>>>> __mpf_struct [1]>, Policy =
>>>>>>> boost::math::policies::policy<boost::math::policies::default_policy,
>>>>>>> boost::math::policies::default_policy,
>>>>>>> boost::math::policies::default_policy,
>>>>>>> boost::math::policies::default_policy,
>>>>>>> boost::math::policies::default_policy,
>>>>>>> boost::math::policies::default_policy,
>>>>>>> boost::math::policies::default_policy,
>>>>>>> boost::math::policies::default_policy,
>>>>>>> boost::math::policies::default_policy,
>>>>>>> boost::math::policies::default_policy,
>>>>>>> boost::math::policies::default_policy,
>>>>>>> boost::math::policies::default_policy,
>>>>>>> boost::math::policies::default_policy>]’
>>>>>>> /usr/include/boost/math/special_functions/legendre.hpp:185:
>>>>>>> instantiated from ‘typename boost::math::tools::promote_args<RT,
>>>>>>> float, float, float, float, float>::type boost::math::legendre_p(int,
>>>>>>> int, T) [with T = __gmp_expr<__mpf_struct [1], __mpf_struct [1]>]’
>>>>>>> /home/benjamik/fenics/dolfin-wells_gmp/dolfin/math/Legendre.cpp:42:
>>>>>>> instantiated from here
>>>>>>> /usr/include/boost/math/special_functions/legendre.hpp:167: error: no
>>>>>>> matching function for call to ‘pow(__gmp_expr<__mpf_struct [1],
>>>>>>> __gmp_binary_expr<long int, __gmp_expr<__mpf_struct [1],
>>>>>>> __gmp_binary_expr<__gmp_expr<__mpf_struct [1], __mpf_struct [1]>,
>>>>>>> __gmp_expr<__mpf_struct [1], __mpf_struct [1]>,
>>>>>>> __gmp_binary_multiplies> >, __gmp_binary_minus> >,
>>>>>>> __gmp_expr<__mpf_struct [1], __gmp_binary_expr<__gmp_expr<__mpf_struct
>>>>>>> [1], __mpf_struct [1]>, long int, __gmp_binary_divides> >)’
>>>>>>> /usr/include/bits/mathcalls.h:154: note: candidates are: double
>>>>>>> pow(double, double)
>>>>>>> /usr/include/c++/4.4/cmath:358: note:                 float
>>>>>>> std::pow(float, float)
>>>>>>> /usr/include/c++/4.4/cmath:362: note:                 long double
>>>>>>> std::pow(long double, long double)
>>>>>>> /usr/include/c++/4.4/cmath:369: note:                 double
>>>>>>> std::pow(double, int)
>>>>>>> /usr/include/c++/4.4/cmath:373: note:                 float std::pow(float, int)
>>>>>>> /usr/include/c++/4.4/cmath:377: note:                 long double
>>>>>>> std::pow(long double, int)
>>>>>>> [...]
>>>>>>>
>>>>>>> boost::math::legendre seems to rely on std::pow which is not
>>>>>>> templated, only implemented with the most common types.
>>>>>>>
>>>>>>
>>>>>> Looks like some tweaks are required to work with GMP:
>>>>>>
>>>>>> http://www.boost.org/doc/libs/1_43_0/libs/math/doc/sf_and_dist/html/math_toolkit/using_udt/use_mpfr.html
>>>>>
>>>>> That's not a bad solution, but it requires changing the
>>>>> multi-precision type from mpf (provided by GMP) to mpfr (which is a
>>>>> library that extends the floating point functionality in GMP). For
>>>>> floating-point arithmetic MPFR is much better than pure GMP. I think
>>>>> CGAL depends on MPFR, so it wouldn't even introduce new dependencies.
>>>>> The problem is that MPFR doesn't ship with a C++-wrapper (as opposed
>>>>> to GMP). Although several independent wrappers exists, none of them
>>>>> are avalilable in Debian/Ubuntu through apt. The one Boost requires is
>>>>> not updated since 2008 (MPFR has gone from version 2.3 to 3.0.1 since
>>>>> then).
>>>>>
>>>>
>>>> I've just plonked a copy of gmpfrxx in the DOLFIN dirs to test - it's
>>>> licensed under GPL.
>>>
>>> That won't work. We need LGPL.
>>>
>>
>> I meant LPGL.
> 
> Good. Does it have the "or any later version"? Otherwise it's still a
> problem.
> 

No. It's LGPL 2.1. Why is that a problem?

Garth

> --
> Anders
> 
> 
>> Garth
>>
>>>>> (Another option would be to take the same approach as Boost ourself:
>>>>> Implement the few functions that are required (pow() plus possibly a
>>>>> few more) and place it in the global namespace before including
>>>>> boost::mat::legendre), but GMP does not provide pow() when the
>>>>> exponent is a floating point number, so this is not straight forward
>>>>> without switching to MPFR).
>>>>>
>>>>> So I guess the question is whether we want to switch to MPFR now, to
>>>>> get rid of the few lines of code in Legendre.cpp (which performs
>>>>> reasonably well), when the code is likely to be thrown out pretty soon
>>>>> anyway. I vote for "no", but I have no problems with moving the entire
>>>>> ODE solvers to a separate project, then adding it back (without
>>>>> supporting extended precision) later in the form of code generation
>>>>> for time dependent problems.
>>>>>
>>>>
>>>> There are a few issues here - even if the ODE code is moved out, I think
>>>> that we should retain the polynomial and quadrature code in DOLFIN.
>>>>
>>>> Garth
>>>>
>>>>> Benjamin
>>>>>
>>>>>>
>>>>>> Garth
>>>>>>
>>>>>>
>>>>>>> Benjamin
>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
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>>>>>>>>
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>>>>>>>>
>>>>>>
>>>>>>
>>>>
>>