Hi, This is closer, but you need to chase it back to the source - where the NaN first appears. This could be a divide by zero. Or it could be a Python list structure with None in it - converting to numpy will produce NaNs.
Regards, Edward On 7 May 2014 18:32, Troels Emtekær Linnet <[email protected]> wrote: > Hi Edward. > > Some test print shows this: > In lib/ns_cpmg_2site_3d.py > > print R*tcp[i] > [[ NaN NaN NaN NaN NaN NaN NaN] > [ NaN NaN NaN NaN NaN NaN NaN] > [ NaN NaN NaN NaN NaN NaN NaN] > [ NaN NaN NaN NaN NaN NaN NaN] > [ NaN NaN NaN NaN NaN NaN NaN] > [ NaN NaN NaN NaN NaN NaN NaN] > [ NaN NaN NaN NaN NaN NaN NaN]] > > Error message: > Rexpo = matrix_exponential(R*tcp[i]) > File > "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/lib/linear_algebra/matrix_exponential.py", > line 46, in matrix_exponential > W, V = eig(A) > File "/usr/lib64/python2.6/site-packages/numpy/linalg/linalg.py", > line 999, in eig > _assertFinite(a) > File "/usr/lib64/python2.6/site-packages/numpy/linalg/linalg.py", > line 144, in _assertFinite > raise LinAlgError, "Array must not contain infs or NaNs" > LinAlgError: Array must not contain infs or NaNs > > > > 2014-05-07 17:14 GMT+02:00 Edward d'Auvergne <[email protected]>: >> Hi, >> >> This is part of the parameter checking required in the target function >> code. Something is producing a NaN, and this needs to be caught. >> You'll see my attempts at catching these conditions by running the >> following from the relax base directory: >> >> $ grep "if " lib/dispersion/* -A1 >> >> Obviously something is not caught when it should be. You can use the >> --traceback and --numpy-raise relax options to better debug this. >> Once you find the position in the code where the NaN (or Inf) arises, >> you can then add such an 'if' condition to fix the bug. >> >> Regards, >> >> Edward >> >> >> >> On 7 May 2014 17:07, Troels E. Linnet <[email protected]> >> wrote: >>> URL: >>> <http://gna.org/bugs/?22017> >>> >>> Summary: LinAlgError, for all numerical CPMG models. >>> Project: relax >>> Submitted by: tlinnet >>> Submitted on: Wed 07 May 2014 03:07:49 PM UTC >>> Category: relax's source code >>> Specific analysis category: Relaxation dispersion >>> Priority: 7 - High >>> Severity: 4 - Important >>> Status: None >>> Assigned to: None >>> Originator Name: >>> Originator Email: >>> Open/Closed: Open >>> Release: Repository: trunk >>> Discussion Lock: Any >>> Operating System: All systems >>> >>> _______________________________________________________ >>> >>> Details: >>> >>> Hi Edward. >>> >>> The attached script, will make relax trip. >>> >>> I am reading in fake R2eff points, and then do a back calculation with: >>> >>> sfrq_1 = 599.8908617*1E6 >>> ncycs_1 = [2, 4, 8, 10, 20, 30, 40, 60] >>> sfrq_2 = 499.8908617*1E6 >>> ncycs_2 = [2, 4, 8, 10, 30, 35, 40, 50] >>> >>> With the following dynamic parameters >>> ['Ala', 1, 'N', {'r2': {r20_key_1:10, r20_key_2:11.5}, 'r2a': {r20_key_1:10, >>> r20_key_2:11.5}, 'r2b': {r20_key_1:10, r20_key_2:11.5}, 'kex': 1000, 'pA': >>> 0.99, 'dw': 2} ] >>> >>> #################3 >>> relax_disp.r2eff_read_spin(id='CPMG_599.9', spin_id=':1@N', >>> file='CPMG_599.9_1_N.txt', dir=None, disp_point_col=1, offset_col=None, >>> data_col=2, error_col=3, sep=None) >>> Opening the file 'CPMG_599.9_1_N.txt' for reading. >>> The following R2eff/R1rho data has been loaded into the relax data store: >>> >>> # R2eff_key Disp_point R2eff >>> R2eff_error >>> sq_cpmg_599.89086170_0.000_33.333 33.333333333333336 >>> 1.000000000000000 0.100000000000000 >>> sq_cpmg_599.89086170_0.000_66.667 66.666666666666671 >>> 1.000000000000000 0.100000000000000 >>> sq_cpmg_599.89086170_0.000_133.333 133.333333333333343 >>> 1.000000000000000 0.100000000000000 >>> sq_cpmg_599.89086170_0.000_166.667 166.666666666666686 >>> 1.000000000000000 0.100000000000000 >>> sq_cpmg_599.89086170_0.000_333.333 333.333333333333371 >>> 1.000000000000000 0.100000000000000 >>> sq_cpmg_599.89086170_0.000_500.000 500.000000000000000 >>> 1.000000000000000 0.100000000000000 >>> sq_cpmg_599.89086170_0.000_666.667 666.666666666666742 >>> 1.000000000000000 0.100000000000000 >>> sq_cpmg_599.89086170_0.000_1000.000 1000.000000000000000 >>> 1.000000000000000 0.100000000000000 >>> Traceback (most recent call last): >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/multi/processor.py", >>> line 494, in run >>> self.callback.init_master(self) >>> File "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/multi/__init__.py", >>> line 318, in default_init_master >>> self.master.run() >>> File "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/relax.py", line >>> 194, >>> in run >>> self.interpreter.run(self.script_file) >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/prompt/interpreter.py", >>> line >>> 275, in run >>> return run_script(intro=self.__intro_string, local=locals(), >>> script_file=script_file, show_script=self.__show_script, >>> raise_relax_error=self.__raise_relax_error) >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/prompt/interpreter.py", >>> line >>> 569, in run_script >>> return console.interact(intro, local, script_file, >>> show_script=show_script, raise_relax_error=raise_relax_error) >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/prompt/interpreter.py", >>> line >>> 468, in interact_script >>> exec_script(script_file, local) >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/prompt/interpreter.py", >>> line >>> 347, in exec_script >>> runpy.run_module(module, globals) >>> File "/usr/lib64/python2.6/runpy.py", line 140, in run_module >>> fname, loader, pkg_name) >>> File "/usr/lib64/python2.6/runpy.py", line 34, in _run_code >>> exec code in run_globals >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py", >>> line 270, in <module> >>> r2effs = optimisation.back_calc_r2eff(spin=cur_spin, >>> spin_id=cur_spin_id) >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/optimisation.py", >>> line 188, in back_calc_r2eff >>> chi2 = model.func(param_vector) >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/target_functions/relax_disp.py", >>> line 1419, in func_ns_cpmg_2site_3D >>> return self.calc_ns_cpmg_2site_3D_chi2(R20A=R20, R20B=R20, dw=dw, pA=pA, >>> kex=kex) >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/target_functions/relax_disp.py", >>> line 542, in calc_ns_cpmg_2site_3D_chi2 >>> r2eff_ns_cpmg_2site_3D(r180x=self.r180x, M0=self.M0, >>> r20a=R20A[r20_index], >>> r20b=R20B[r20_index], pA=pA, pB=pB, dw=dw_frq, k_AB=k_AB, k_BA=k_BA, >>> inv_tcpmg=self.inv_relax_times[0][mi], tcp=self.tau_cpmg[0][mi], >>> back_calc=self.back_calc[0][si][mi][0], >>> num_points=self.num_disp_points[0][si][mi][0], power=self.power[0][mi]) >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/lib/dispersion/ns_cpmg_2site_3d.py", >>> line 115, in r2eff_ns_cpmg_2site_3D >>> Rexpo = matrix_exponential(R*tcp[i]) >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/lib/linear_algebra/matrix_exponential.py", >>> line 46, in matrix_exponential >>> W, V = eig(A) >>> File "/usr/lib64/python2.6/site-packages/numpy/linalg/linalg.py", line >>> 999, >>> in eig >>> _assertFinite(a) >>> File "/usr/lib64/python2.6/site-packages/numpy/linalg/linalg.py", line >>> 144, >>> in _assertFinite >>> raise LinAlgError, "Array must not contain infs or NaNs" >>> LinAlgError: Array must not contain infs or NaNs >>> ######################### >>> >>> >>> >>> >>> >>> >>> _______________________________________________________ >>> >>> File Attachments: >>> >>> >>> ------------------------------------------------------- >>> Date: Wed 07 May 2014 03:07:49 PM UTC Name: cpmg_synthetic.py Size: 16kB >>> By: tlinnet >>> >>> <http://gna.org/bugs/download.php?file_id=20667> >>> >>> _______________________________________________________ >>> >>> Reply to this item at: >>> >>> <http://gna.org/bugs/?22017> >>> >>> _______________________________________________ >>> Message sent via/by Gna! >>> http://gna.org/ >>> >>> >>> _______________________________________________ >>> 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
