Hi, If you would like to tackle this one, that would be legendary. Though you must decide if it is worth your time. There are also still a few things to tidy up for the disp_spin_speed branch to prepare it for merger. For your idea, I would suggest considering the following:
1) Creating a simple timeit script such as in http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/ to show the timing of one function where you loop over NS and NM, calculating the matrix exponential each time, and one where you do it all in one operation. You can get initial matrices by running one of the system tests in debugging mode and adding a print statement in an appropriate place, then replicate this matrix over NS and NM. This will allow you to debug the multi-matrix exponential calculation. 2) Before making changes in lib.dispersion, make sure that the system and unit test coverage is reasonable for each model to be speed up. 3) Create a profiling script in test_suite/shared_data/dispersion/profiling so we can measure and see the improvements. If the numpy operation is costly, there is a slight chance that the change will not speed things up. Point 1) will show that though. You've probably seen that the system tests are useless for seeing your huge speed ups. If this could be done, I think relax will then be the fastest dispersion implementation out there. Unfortunately I don't have the source code to all software, so I don't know if this would be true. And relax uses minfx and different optimisation to the competition, avoiding numerical gradients, so there are many other factors affecting the speed of relax vs. the rest. Regards, Edward On 18 June 2014 13:00, Troels Emtekær Linnet <[email protected]> wrote: > The worst bottleneck for the numerical analysis, is the looping over spins. > > For the nmerical models, a propagator that will evolve the magnetization is > calculated. > > This is the matrix exponential of the matrix R that contains all the > contributions to the evolution, i.e. relaxation, exchange and chemical > shift evolution. > The shape of R, can be (7, 7) or (9,9). > > Finding the matrix exponential is done over looping of spins, > and spectrometer frequencies. > NS and NM. > > If NS is 100, and NM is 2, maybe R, could get packed to: > (100, 2, 7, 7) > > The matrix exponential is: > # The eigenvalue decomposition. > W, V = eig(A) > > # Calculate the exact exponential. > eA = dot(dot(V, diag(exp(W))), inv(V)) > > But according to: > http://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.eig.html > > This should be possible for an array of matrixes. > > > ##### > Compute the eigenvalues and right eigenvectors of a square array. > > Parameters : > a : (..., M, M) array > Matrices for which the eigenvalues and right eigenvectors will be computed > Returns : > w : (..., M) array > The eigenvalues, each repeated according to its multiplicity. The > eigenvalues are not necessarily ordered. The resulting array will be always > be of complex type. When a is real the resulting eigenvalues will be real > (0 imaginary part) or occur in conjugate pairs > v : (..., M, M) array > The normalized (unit “length”) eigenvectors, such that the column v[:,i] is > the eigenvector corresponding to the eigenvalue w[i]. > Raises : > LinAlgError > If the eigenvalue computation does not converge. > > ------- > Broadcasting rules apply, see the numpy.linalg documentation for details. > > This is implemented using the _geev LAPACK routines which compute the > eigenvalues and eigenvectors of general square arrays. > > The number w is an eigenvalue of a if there exists a vector v such that > dot(a,v) = w * v. Thus, the arrays a, w, and v satisfy the equations > dot(a[:,:], v[:,i]) = w[i] * v[:,i] for i \in \{0,...,M-1\}. > ------ > #### > > R is: > R = rcpmg_3d(R1A=r10a, R1B=r10b, R2A=R2A_si_mi, R2B=R2B_si_mi, pA=pA, > pB=pB, dw=dw_si_mi, k_AB=k_AB, k_BA=k_BA) > > So that would need a new way to expand this, since we have R20 and dw as > specific for spin and frequency. > > > > Troels Emtekær Linnet > _______________________________________________ > 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
