Re: r23216 - /branches/disp_speed/lib/dispersion/cr72.py -- May 19, 2014 - 14:08

Hi Ed.

Thanks for your comments.

I thought about my own comments, and think they are rubbish. :-)

Best
Troels

2014-05-19 13:56 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> Hi,
>
> I don't quite understand the 'turning-off' part.  Why do you need
> this?  When would you like to turn it on, and when would you like to
> turn it off?  You can use --numpy-raise while debugging, but then not
> use it for for normal use of relax.  I don't see a need to turn this
> off when performing a debugging run with --numpy-raise, as that is
> only a temporary run for testing.
>
> Regards,
>
> Edward
>
>
>
> On 19 May 2014 13:05, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> wrote:
> > Hi Ed.
> >
> > I have been playing with this.
> >
> > I really like the --numpy-raise option.
> >
> > But then I need to also turn this off when I know I have handled the 
> > exception.
> >
> > I have been looking at:
> > numpy.seterr
> > http://docs.scipy.org/doc/numpy/reference/generated/numpy.seterr.html#numpy-seterr
> >
> > Putting this is in:
> > import numpy as np
> > old_settings = np.seterr()
> > old_settings2 = np.geterr()
> >
> > print "old settings"
> > print old_settings
> > np.seterr(all='ignore')
> > print "new settings"
> > print np.seterr()
> >
> > print "bla bla bla code with math domain errors, but handled."
> >
> > # Go back to original
> > np.seterr(over=old_settings['over'])
> > np.seterr(divide=old_settings['divide'])
> > np.seterr(invalid=old_settings['invalid'])
> > np.seterr(under=old_settings['under'])
> >
> > print "back to normal"
> > print np.seterr()
> >
> > 2014-05-19 10:02 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > Hi Troels,
> > >
> > > When making such important changes, for debugging you should try
> > > running the test suite as:
> > >
> > > $ ./relax -s Relax_disp --numpy-raise
> > > Echoing of user function calls has been enabled.
> > >
> > >
> > > =============================
> > > = System / functional tests =
> > > =============================
> > >
> > > EE.EEEEEEEE...EE.EEEEEEEEEEEEE.EEEEEEEEEEEEEEEEEEE...EEEEEEEEEEE...
> > > ======================================================================
> > >
> > > This will quickly uncover the places where we need to have checks in
> > > the code.  It will also uncover many places in the trunk does not have
> > > checks, so don't worry about the huge number of errors.  This is the
> > > code from all of the contributors on the paper:
> > >
> > >     - Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson,
> > > G. S., Tollinger, M., Teilum, K., Gagné, S., Marion, D., Griesinger,
> > > C., Blackledge, M., and d'Auvergne, E. J. (2014). relax: the analysis
> > > of biomolecular kinetics and thermodynamics using NMR relaxation
> > > dispersion data. Bioinformatics.
> > > (http://dx.doi.org/10.1093/bioinformatics/btu166).
> > >
> > > And as it comes from many groups, the error checking is not consistent
> > > or perfected yet.
> > >
> > > Regards,
> > >
> > > Edward
> > >
> > >
> > >
> > >
> > >
> > > On 18 May 2014 23:36,  <tlinnet@xxxxxxxxxxxxx> wrote:
> > > > Author: tlinnet
> > > > Date: Sun May 18 23:36:14 2014
> > > > New Revision: 23216
> > > >
> > > > URL: http://svn.gna.org/viewcvs/relax?rev=23216&view=rev
> > > > Log:
> > > > Huge speed-up for model CR72.
> > > >
> > > > task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
> > > >
> > > > Systemtest Relax_disp.test_cpmg_synthetic_cr72_full_noise_cluster
> > > > changes from 7 seconds to 4.5 seconds.
> > > >
> > > > This is won by not checking single values in the R2eff array for math 
> > > > domain
> > > > errors, but calculating all steps, and in one single round check for 
> > > > finite values.
> > > > If just one non-finite value is found, the whole array is returned with 
> > > > a large
> > > > penalty of 1e100.
> > > >
> > > > This makes all calculations be the fastest numpy array way.
> > > >
> > > > Modified:
> > > >     branches/disp_speed/lib/dispersion/cr72.py
> > > >
> > > > Modified: branches/disp_speed/lib/dispersion/cr72.py
> > > > URL: 
> > > > http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/cr72.py?rev=23216&r1=23215&r2=23216&view=diff
> > > > ==============================================================================
> > > > --- branches/disp_speed/lib/dispersion/cr72.py  (original)
> > > > +++ branches/disp_speed/lib/dispersion/cr72.py  Sun May 18 23:36:14 2014
> > > > @@ -92,8 +92,10 @@
> > > >  """
> > > >
> > > >  # Python module imports.
> > > > -from numpy import arccosh, cos, cosh, sqrt
> > > > +from numpy import arccosh, array, cos, cosh, isfinite, sqrt, sum
> > > >
> > > > +# Repetitive calculations (to speed up calculations).
> > > > +eta_scale = 2.0**(-3.0/2.0)
> > > >
> > > >  def r2eff_CR72(r20a=None, r20b=None, pA=None, dw=None, kex=None, 
> > > > cpmg_frqs=None, back_calc=None, num_points=None):
> > > >      """Calculate the R2eff values for the CR72 model.
> > > > @@ -146,26 +148,17 @@
> > > >      Dneg = 0.5 * (-1.0 + D_part)
> > > >
> > > >      # Partial eta+/- values.
> > > > -    eta_scale = 2.0**(-3.0/2.0)
> > > > -    etapos_part = eta_scale * sqrt(Psi + sqrt_psi2_zeta2)
> > > > -    etaneg_part = eta_scale * sqrt(-Psi + sqrt_psi2_zeta2)
> > > > +    etapos = eta_scale * sqrt(Psi + sqrt_psi2_zeta2) / cpmg_frqs
> > > > +    etaneg = eta_scale * sqrt(-Psi + sqrt_psi2_zeta2) / cpmg_frqs
> > > >
> > > > -    # Loop over the time points, back calculating the R2eff values.
> > > > +    # Calculate R2eff.
> > > > +    R2eff = r20_kex - cpmg_frqs * arccosh( Dpos * cosh(etapos) - Dneg * 
> > > > cos(etaneg) )
> > > > +
> > > > +    # Catch errors, taking a sum over array is the fastest way to check 
> > > > for
> > > > +    # +/- inf (infinity) and nan (not a number).
> > > > +    if not isfinite(sum(R2eff)):
> > > > +        R2eff = array([1e100]*num_points)
> > > > +
> > > > +    # Parse back the value to update the back_calc class object.
> > > >      for i in range(num_points):
> > > > -        # The full eta+/- values.
> > > > -        etapos = etapos_part / cpmg_frqs[i]
> > > > -        etaneg = etaneg_part / cpmg_frqs[i]
> > > > -
> > > > -        # Catch large values of etapos going into the cosh function.
> > > > -        if etapos > 100:
> > > > -            back_calc[i] = 1e100
> > > > -            continue
> > > > -
> > > > -        # The arccosh argument - catch invalid values.
> > > > -        fact = Dpos * cosh(etapos) - Dneg * cos(etaneg)
> > > > -        if fact < 1.0:
> > > > -            back_calc[i] = r20_kex
> > > > -            continue
> > > > -
> > > > -        # The full formula.
> > > > -        back_calc[i] = r20_kex - cpmg_frqs[i] * arccosh(fact)
> > > > +        back_calc[i] = R2eff[i]
> > > >
> > > >
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