dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Thu, Jun 02, 2011 at 04:17:19PM +0100, Garth N. Wells wrote:
>
>
> 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?

As far as I understand it would force DOLFIN to be LGPL 2.1 only
(but I hope I'm wrong).

We just went through a big trouble to secure license agreements from
everyone and it would not be good to restrict those agreements to a
specific version. Furthermore, the agreements say v3 or later so no
one has agreed to 2.1.

--
Anders


> Garth
>
> >> 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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> >>>>>>>>
> >>>>>>
> >>>>>>
> >>>>
> >>
>