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 <[email protected]> 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 <[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
