Hi Edward. I would suggest an implementation of striding through the data.
The necessary functions for this implementation is already present in lib/dispersion matrix_exponential.py and matrix_power.py. I will look into this later. I will try to see, if I can do a local downgrade of numpy to 1.6, to check it is working. Best Troels 2014-07-25 14:09 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi Troels, > > We have a major problem in trunk caused by the recent merger of the > disp_spin_speed branch. When I run the Relax_disp system tests, the > unit tests, or the Relax_disp GUI tests, I see many, many failures due > to problems with the numpy.linalg.eig() function on numpy 1.6.1, > 1.6.2, and 1.7.0. The error for one of the unit tests is: > > ====================================================================== > ERROR: Test the r2eff_ns_cpmg_2site_3D() function for no exchange when dw = > 0.0. > ---------------------------------------------------------------------- > Traceback (most recent call last): > File > "/data/relax/relax-trunk/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_3d.py", > line 130, in test_ns_cpmg_2site_3D_no_rex1 > self.calc_r2eff() > File > "/data/relax/relax-trunk/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_3d.py", > line 79, in calc_r2eff > r2eff_ns_cpmg_2site_3D(r180x=self.r180x, M0=self.M0, > M0_T=self.M0_T, r20a=self.r20a*a, r20b=self.r20b*a, pA=self.pA, > dw=dw_frq*a, dw_orig=dw_frq*a, kex=self.kex, > inv_tcpmg=self.inv_relax_times*a, tcp=self.tau_cpmg*a, > back_calc=self.R2eff, num_points=self.num_points*b, power=self.ncyc*a) > File "/data/relax/relax-trunk/lib/dispersion/ns_cpmg_2site_3d.py", > line 299, in r2eff_ns_cpmg_2site_3D > Rexpo_mat = matrix_exponential_rank_NE_NS_NM_NO_ND_x_x(R_mat) > File "/data/relax/relax-trunk/lib/dispersion/matrix_exponential.py", > line 78, in matrix_exponential_rank_NE_NS_NM_NO_ND_x_x > W, V = eig(A) > File "/data/python/lib/python2.5/site-packages/numpy/linalg/linalg.py", > line 1015, in eig > _assertRank2(a) > File "/data/python/lib/python2.5/site-packages/numpy/linalg/linalg.py", > line 155, in _assertRank2 > two-dimensional' % len(a.shape) > LinAlgError: 7-dimensional array given. Array must be > two-dimensional > > ---------------------------------------------------------------------- > > Here are the API differences between numpy versions: > > 1.8.1: > http://docs.scipy.org/doc/numpy-1.8.1/reference/generated/numpy.linalg.eig.html#numpy.linalg.eig > 1.8.0: > http://docs.scipy.org/doc/numpy-1.8.0/reference/generated/numpy.linalg.eig.html#numpy.linalg.eig > 1.7.0: > http://docs.scipy.org/doc/numpy-1.7.0/reference/generated/numpy.linalg.eig.html#numpy.linalg.eig > 1.6.0: > http://docs.scipy.org/doc/numpy-1.6.0/reference/generated/numpy.linalg.eig.html#numpy.linalg.eig > > You can see that the input changes from (M, M) to (..., M, M) between > 1.7.0 and 1.8.0. We cannot require numpy >= 1.8 as many current > distributions have not shifted to this version yet. Most sys admins > would kill me for even suggesting that ;) Therefore we need to come > up with a solution and quickly. > > The best would be to add an eig() function to the lib.compat module. > For numpy >= 1.8.0 it will use the numpy.linalg.eig() function. For > the other versions, we need an alternative solution. Maybe using slow > Python looping over the higher dimensions would be ok. > > I will not report this as a bug, as no released relax versions are affected. > > Cheers, > > Edward > > _______________________________________________ > 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
