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 <[email protected]>: > 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, <[email protected]> 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] >> >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-commits mailing list >> [email protected] >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-commits > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-devel mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
