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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Re: r23216 - /branches/disp_speed/lib/dispersion/cr72.py