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)
>>
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