Hi Ed. Well, I have before been limited to the old RHEL standard libraries '1.4.1' from yum.
Our server admin refuses to install any non-standard packages to our computation server. This is very very logic, since you often end up in a big fight, if start opening up for this. But, I had just a very big success with a Canopy installation. http://wiki.nmr-relax.com/Epd_canopy This essential lets the user install a local python if wanted. And let the admin make a shared installation. Our server admin can accept this solution, since it does not interfere with the package manager. So numpy is now '1.8.0'. :-) best Troels 2014-06-10 17:50 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi, > > I haven't seen HBO's "Silicon Valley" yet. But you should soon reach > tip-to-tip efficiency with both relax and your Python programming > skills. Anyway, I'm thinking that the numpy version minimal number > will need to be increased to 1.6.2. This really depends on how much > users complain though. Most stay reasonably up to date so that the > current 1.0.4 at http://www.nmr-relax.com/download.html is never > encountered anyway. The test suite should pull out the relax users > with too old versions. I am also using lib.compat for some of these > version issues, as there is always a less efficient way of performing > the operation using an older numpy version. Do you have any opinions > for the minimum version number? Which versions do you have installed > on your various systems? > > Regards, > > Edward > > > > On 10 June 2014 17:40, Troels Emtekær Linnet <[email protected]> wrote: >> Hi Ed. >> >> I worry about, if I use some numpy things, which is of to high a version? >> What is the "relax" limit on this? >> >> Best >> Troels >> >> >> 2014-06-10 17:27 GMT+02:00 Troels Emtekær Linnet <[email protected]>: >>> I have learned SO much these days!!! >>> >>> Class programming. >>> How numpy arrays work together, and broadcasts. >>> How to profile and make efficiency. >>> >>> I feel like in HBO "Silicon Valley": >>> http://en.wikipedia.org/wiki/Silicon_Valley_%28TV_series%29 >>> >>> Episode 8, "Optimal Tip-to-Tip Efficiency", is exactly what is >>> happening right now. :-) >>> >>> best >>> Troels >>> >>> 2014-06-10 17:04 GMT+02:00 Edward d'Auvergne <[email protected]>: >>>> Hi Troels, >>>> >>>> Is it possible to shift the mask_replace part into __init__()? That >>>> might give more speed ups. I'm not so familiar with numpy masks, so I >>>> couldn't have helped you with that. Anyway, those 4 hours invested is >>>> guaranteed to save you much more than 4 hours when you use this later. >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> >>>> On 10 June 2014 16:51, <[email protected]> wrote: >>>>> Author: tlinnet >>>>> Date: Tue Jun 10 16:51:33 2014 >>>>> New Revision: 23788 >>>>> >>>>> URL: http://svn.gna.org/viewcvs/relax?rev=23788&view=rev >>>>> Log: >>>>> Implemented a masked array search for where "missing" array is equal 1. >>>>> >>>>> This makes it possible to replace all values with this mask, from the >>>>> value array. >>>>> >>>>> This eliminates the last loops over the missing values. >>>>> >>>>> It took over 4 hours to figure out, that the mask should be called with >>>>> mask.mask, >>>>> to return the same fulls structure, >>>>> >>>>> Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion >>>>> models for Clustered analysis. >>>>> >>>>> Modified: >>>>> branches/disp_spin_speed/target_functions/relax_disp.py >>>>> >>>>> Modified: branches/disp_spin_speed/target_functions/relax_disp.py >>>>> URL: >>>>> http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=23788&r1=23787&r2=23788&view=diff >>>>> ============================================================================== >>>>> --- branches/disp_spin_speed/target_functions/relax_disp.py (original) >>>>> +++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun >>>>> 10 16:51:33 2014 >>>>> @@ -29,6 +29,7 @@ >>>>> from math import pi >>>>> from numpy import array, asarray, complex64, dot, float64, int16, max, >>>>> ones, sqrt, sum, zeros >>>>> import numpy as np >>>>> +from numpy.ma import masked_equal >>>>> >>>>> # relax module imports. >>>>> from lib.dispersion.b14 import r2eff_B14 >>>>> @@ -418,6 +419,7 @@ >>>>> # The number of disp point can change per spectrometer, so >>>>> we make the maximum size. >>>>> self.values_a = deepcopy(self.zeros_a) >>>>> self.errors_a = deepcopy(self.ones_a) >>>>> + self.missing_a = zeros(self.numpy_array_shape) >>>>> >>>>> self.cpmg_frqs_a = deepcopy(self.ones_a) >>>>> self.num_disp_points_a = deepcopy(self.zeros_a) >>>>> @@ -456,6 +458,7 @@ >>>>> for di in >>>>> range(self.num_disp_points[ei][si][mi][oi]): >>>>> if self.missing[ei][si][mi][oi][di]: >>>>> self.has_missing = True >>>>> + self.missing_a[ei][si][mi][oi][di] = >>>>> 1.0 >>>>> >>>>> # Make copy of values structure. >>>>> self.back_calc_a = deepcopy(self.values_a) >>>>> @@ -574,15 +577,11 @@ >>>>> >>>>> ## For all missing data points, set the back-calculated value to >>>>> the measured values so that it has no effect on the chi-squared value. >>>>> if self.has_missing: >>>>> - # Loop over the spins. >>>>> - for si in range(self.num_spins): >>>>> - # Loop over the spectrometer frequencies. >>>>> - for mi in range(self.num_frq): >>>>> - # Loop over the dispersion points. >>>>> - for di in range(self.num_disp_points[0][si][mi][0]): >>>>> - if self.missing[0][si][mi][0][di]: >>>>> - #self.back_calc[0][si][mi][0][di] = >>>>> self.values[0][si][mi][0][di] >>>>> - self.back_calc_a[0][si][mi][0][di] = >>>>> self.values[0][si][mi][0][di] >>>>> + # Find the numpy mask, which tells where values should be >>>>> replaced. >>>>> + mask_replace = masked_equal(self.missing_a, 1.0) >>>>> + >>>>> + # Replace with values. >>>>> + self.back_calc_a[mask_replace.mask] = >>>>> self.values_a[mask_replace.mask] >>>>> >>>>> ## Calculate the chi-squared statistic. >>>>> return sum((1.0 / self.errors_a * (self.values_a - >>>>> self.back_calc_a))**2) >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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
