Hi Edward.
I thought the same.
One could send in a ones and zeros numpy array in function.
Set them to standard to None.
If they are None, then create them.
One can see on the timings, that
r2eff_CR72
numeric.py:2056(allclose)
are the most time consuming.
Maybe there is a faster way for allclose.
Masking ???
1 0.000 0.000 2.084 2.084 <string>:1(<module>)
1 0.002 0.002 2.084 2.084 profiling_cr72.py:441(cluster)
1000 0.002 0.000 2.005 0.002 profiling_cr72.py:405(calc)
1000 0.034 0.000 2.003 0.002
relax_disp.py:995(func_CR72_full)
1000 0.141 0.000 1.960 0.002
relax_disp.py:524(calc_CR72_chi2)
1300 1.100 0.001 1.676 0.001 cr72.py:101(r2eff_CR72)
4300 0.245 0.000 0.507 0.000 numeric.py:2056(allclose)
3000 0.037 0.000 0.164 0.000 shape_base.py:761(tile)
17828 0.126 0.000 0.126 0.000 {method 'reduce' of
'numpy.ufunc' objects}
4000 0.110 0.000 0.110 0.000 {method 'repeat' of
'numpy.ndarray' objects}
8609 0.011 0.000 0.086 0.000 fromnumeric.py:1762(any)
2014-06-10 11:44 GMT+02:00 Edward d'Auvergne <[email protected]>:
> Hi Troels,
>
> For speed, maybe you should send in the single value parameters
> together with the array versions into the lib.dispersion modules? The
> check:
>
> + if np.allclose(dw, np.zeros(dw.shape)) or np.allclose(pA,
> np.ones(dw.shape)) or np.allclose(kex, np.zeros(dw.shape)):
>
> will be very expensive.
>
> Regards,
>
> Edward
>
>
>
> On 8 June 2014 19:48, <[email protected]> wrote:
> > Author: tlinnet
> > Date: Sun Jun 8 19:48:35 2014
> > New Revision: 23737
> >
> > URL: http://svn.gna.org/viewcvs/relax?rev=23737&view=rev
> > Log:
> > Re-implemented safety checks in lib/dispersion/cr72.py.
> >
> > This is now implemented for both rank-1 float array and of higher
> dimensions.
> >
> > This makes the unit tests pass for multi dimensional computing.
> >
> > Task #7807 (https://gna.org/task/index.php?7807): Speed-up of
> dispersion models for Clustered analysis.
> >
> > Modified:
> > branches/disp_spin_speed/lib/dispersion/cr72.py
> >
> > Modified: branches/disp_spin_speed/lib/dispersion/cr72.py
> > URL:
> http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/cr72.py?rev=23737&r1=23736&r2=23737&view=diff
> >
> ==============================================================================
> > --- branches/disp_spin_speed/lib/dispersion/cr72.py (original)
> > +++ branches/disp_spin_speed/lib/dispersion/cr72.py Sun Jun 8
> 19:48:35 2014
> > @@ -128,9 +128,15 @@
> > rank_1 = False
> >
> > # Catch parameter values that will result in no exchange, returning
> flat R2eff = R20 lines (when kex = 0.0, k_AB = 0.0).
> > + # For rank-1 float array.
> > if rank_1:
> > if dw == 0.0 or pA == 1.0 or kex == 0.0:
> > back_calc[:] = array([r20a]*num_points)
> > + return
> > + # For higher dimensions, return same structure.
> > + else:
> > + if np.allclose(dw, np.zeros(dw.shape)) or np.allclose(pA,
> np.ones(dw.shape)) or np.allclose(kex, np.zeros(dw.shape)):
> > + back_calc[:] = r20a
> > return
> >
> > # The B population.
> > @@ -165,16 +171,23 @@
> >
> > # Catch math domain error of cosh(val > 710).
> > # This is when etapos > 710.
> > - if rank_1:
> > - if max(etapos) > 700:
> > + if max(etapos) > 700:
> > + if rank_1:
> > back_calc[:] = array([r20a]*num_points)
> > + return
> > + # For higher dimensions, return same structure.
> > + else:
> > + back_calc[:] = r20a
> > return
> >
> > # The arccosh argument - catch invalid values.
> > fact = Dpos * cosh(etapos) - Dneg * cos(etaneg)
> > - if rank_1:
> > - if min(fact) < 1.0:
> > + if min(fact) < 1.0:
> > + if rank_1:
> > back_calc[:] = array([r20_kex]*num_points)
> > + return
> > + else:
> > + back_calc[:] = r20_kex
> > return
> >
> > # Calculate R2eff.
> > @@ -182,8 +195,10 @@
> >
> > # Catch errors, taking a sum over array is the fastest way to check
> for
> > # +/- inf (infinity) and nan (not a number).
> > - if rank_1:
> > - if not isfinite(sum(R2eff)):
> > + if not isfinite(sum(R2eff)):
> > + if rank_1:
> > R2eff = array([1e100]*num_points)
> > + else:
> > + R2eff = np.ones(R2eff.shape) * 1e100
> >
> > back_calc[:] = R2eff
> >
> >
> > _______________________________________________
> > relax (http://www.nmr-relax.com)
> >
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> >
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>
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