Re: [bug #14176] FAIL: Constrained Newton opt, GMW Hessian mod, More and Thuente line search {S2=0.970, te=2048, Rex=0.149} -- August 24, 2009 - 18:17

Hi,

I'll add all the relevant fixes to relax soon, but first I have a few
other things to repair.  I've updated the entire codebase to be more
compatible with Python 2.6 and eventually 3.0, so now most of the unit
tests fail.  I'll fix these issues first, then get to recording these
optimisation differences within the test suite.  Thanks for the
reports, these will make it very easy for me to fix these system tests
on Mac OS X.

Cheers,

Edward


2009/8/23 Jack Howarth <NO-REPLY.INVALID-ADDRESS@xxxxxxx>:
> Follow-up Comment #3, bug #14176 (project relax):
>
> Test does actually fail on i386 Darwin9 as well as x86_64 Darwin9...
>
> FAIL: Constrained Newton opt, GMW Hessian mod, More and Thuente line search
> {S2=0.970, te=2048, Rex=0.149}
> ----------------------------------------------------------------------
>
> relax> pipe.create(pipe_name='mf', pipe_type='mf')
>
> relax> sequence.read(file='noe.500.out',
> dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
> mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
> spin_name_col=None, sep=None)
> Opening the file
> '/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out'
> for reading.
> Mol_name   Res_num    Res_name   Spin_num   Spin_name
> None       1          GLY        None       None
> None       2          ALA        None       None
>
> relax> relax_data.read(ri_label='R1', frq_label='600', frq=600000000.0,
> file='r1.600.out',
> dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
> mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
> spin_name_col=None, data_col=2, error_col=3, sep=None)
> Opening the file
> '/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.600.out'
> for reading.
>
> relax> relax_data.read(ri_label='R2', frq_label='600', frq=600000000.0,
> file='r2.600.out',
> dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
> mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
> spin_name_col=None, data_col=2, error_col=3, sep=None)
> Opening the file
> '/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.600.out'
> for reading.
>
> relax> relax_data.read(ri_label='NOE', frq_label='600', frq=600000000.0,
> file='noe.600.out',
> dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
> mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
> spin_name_col=None, data_col=2, error_col=3, sep=None)
> Opening the file
> '/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.600.out'
> for reading.
>
> relax> relax_data.read(ri_label='R1', frq_label='500', frq=500000000.0,
> file='r1.500.out',
> dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
> mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
> spin_name_col=None, data_col=2, error_col=3, sep=None)
> Opening the file
> '/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.500.out'
> for reading.
>
> relax> relax_data.read(ri_label='R2', frq_label='500', frq=500000000.0,
> file='r2.500.out',
> dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
> mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
> spin_name_col=None, data_col=2, error_col=3, sep=None)
> Opening the file
> '/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.500.out'
> for reading.
>
> relax> relax_data.read(ri_label='NOE', frq_label='500', frq=500000000.0,
> file='noe.500.out',
> dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
> mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
> spin_name_col=None, data_col=2, error_col=3, sep=None)
> Opening the file
> '/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out'
> for reading.
>
> relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0,
> angle_units='deg', param_types=0, spheroid_type=None, fixed=True)
>
> relax> value.set(val=1.0200000000000001e-10, param='bond_length',
> spin_id=None)
>
> relax> value.set(val=-0.00015999999999999999, param='csa', spin_id=None)
>
> relax> value.set(val='15N', param='heteronucleus', spin_id=None)
>
> relax> value.set(val='1H', param='proton', spin_id=None)
>
> relax> model_free.select_model(model='m4', spin_id=None)
>
> relax> value.set(val=[1.0, 0.0, 0.0], param=['S2', 'te', 'Rex'],
> spin_id=None)
>
> relax> minimise(*args=('newton', 'gmw', 'mt'), func_tol=1e-25,
> max_iterations=10000000, constraints=True, scaling=True, verbosity=1)
> Only the model-free parameters for single spins will be used.
>
>
> Fitting to spin ':2&:ALA'
> ~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
> Method of Multipliers
> ~~~~~~~~~~~~~~~~~~~~~
>
> k: 0       xk: array([ 1.,  0.,  0.])
>  fk: 3.9844117908982288
> Entering sub-algorithm.
>
>        Newton minimisation
>        ~~~~~~~~~~~~~~~~~~~
>        Line search:  More and Thuente line search.
>        Hessian modification:  The Gill, Murray, and Wright modified Cholesky
> algorithm.
>
>        k: 0       xk: array([ 1.,  0.,  0.])
>    fk: 3.9844117908982288
>
>        Parameter values: array([  0.90905499,  74.36909171,   1.22310096])
>        Function value:   -1447.7789206948949
>        Iterations:       4
>        Function calls:   9
>        Gradient calls:   9
>        Hessian calls:    4
>        Warning:          None
>
>
> k: 1       xk: array([  0.90905499,  74.36909171,   1.22310096])
>  fk: 48.121433050621448
> Entering sub-algorithm.
>
>        Newton minimisation
>        ~~~~~~~~~~~~~~~~~~~
>        Line search:  More and Thuente line search.
>        Hessian modification:  The Gill, Murray, and Wright modified Cholesky
> algorithm.
>
>        k: 0       xk: array([  0.90905499,  74.36909171,   1.22310096])
>    fk: 46.071609923379611
>
>        Parameter values: array([  9.69999996e-01,   2.04799919e+03,
> 1.49000073e-01])
>        Function value:   -2.0498231272415968
>        Iterations:       15
>        Function calls:   73
>        Gradient calls:   73
>        Hessian calls:    15
>        Warning:          None
>
>
> k: 2       xk: array([  9.69999996e-01,   2.04799919e+03,   1.49000073e-01])
>  fk: 2.3886847781949838e-13
> Entering sub-algorithm.
>
>        Newton minimisation
>        ~~~~~~~~~~~~~~~~~~~
>        Line search:  More and Thuente line search.
>        Hessian modification:  The Gill, Murray, and Wright modified Cholesky
> algorithm.
>
>        k: 0       xk: array([  9.69999996e-01,   2.04799919e+03,   
> 1.49000073e-01])
>    fk: 2.3886847781949838e-13
>
>        Parameter values: array([  9.70000000e-01,   2.04800000e+03,
> 1.49000000e-01])
>        Function value:   5.9901622412100428e-25
>        Iterations:       1
>        Function calls:   3
>        Gradient calls:   3
>        Hessian calls:    1
>        Warning:          None
>
>
> k: 3       xk: array([  9.70000000e-01,   2.04800000e+03,   1.49000000e-01])
>  fk: 5.9901622412100428e-25
> Entering sub-algorithm.
>
>        Newton minimisation
>        ~~~~~~~~~~~~~~~~~~~
>        Line search:  More and Thuente line search.
>        Hessian modification:  The Gill, Murray, and Wright modified Cholesky
> algorithm.
>
>        k: 0       xk: array([  9.70000000e-01,   2.04800000e+03,   
> 1.49000000e-01])
>    fk: 5.9901622412100428e-25
>
>        Parameter values: array([  9.70000000e-01,   2.04800000e+03,
> 1.49000000e-01])
>        Function value:   1.3932251944754991e-27
>        Iterations:       1
>        Function calls:   3
>        Gradient calls:   3
>        Hessian calls:    1
>        Warning:          None
>
>
> k: 4       xk: array([  9.70000000e-01,   2.04800000e+03,   1.49000000e-01])
>  fk: 1.3932251944754991e-27
> Entering sub-algorithm.
>
>        Newton minimisation
>        ~~~~~~~~~~~~~~~~~~~
>        Line search:  More and Thuente line search.
>        Hessian modification:  The Gill, Murray, and Wright modified Cholesky
> algorithm.
>
>        k: 0       xk: array([  9.70000000e-01,   2.04800000e+03,   
> 1.49000000e-01])
>    fk: 1.3932251944754991e-27
>
>        Parameter values: array([  9.70000000e-01,   2.04800000e+03,
> 1.49000000e-01])
>        Function value:   8.3312601381368332e-28
>        Iterations:       1
>        Function calls:   3
>        Gradient calls:   3
>        Hessian calls:    1
>        Warning:          None
>
>
> Parameter values: array([  9.70000000e-01,   2.04800000e+03,
> 1.49000000e-01])
> Function value:   8.3312601381368332e-28
> Iterations:       22
> Function calls:   91
> Gradient calls:   91
> Hessian calls:    22
> Warning:          None
>
>
> relax> monte_carlo.setup(number=3)
>
> relax> monte_carlo.create_data(method='back_calc')
>
> relax> monte_carlo.initial_values()
>
> relax> minimise(*args=('newton',), func_tol=1e-25, max_iterations=10000000,
> constraints=True, scaling=True, verbosity=1)
> Simulation 1
> Simulation 2
> Simulation 3
>
> relax> monte_carlo.error_analysis(prune=0.0)
> Traceback (most recent call last):
>  File "/sw/lib/relax-py26/test_suite/system_tests/model_free.py", line 610,
> in test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149
>    self.value_test(spin, select, s2, te, rex, chi2, iter, f_count, g_count,
> h_count, warning)
>  File "/sw/lib/relax-py26/test_suite/system_tests/model_free.py", line 1110,
> in value_test
>    self.assertEqual(spin.f_count, f_count, msg=mesg)
> AssertionError: Optimisation failure.
>
> System: Darwin
> Release: 9.8.0
> Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009;
> root:xnu-1228.15.4~1/RELEASE_I386
> Win32 version:
> Distribution:
> Architecture: 32bit
> Machine: i386
> Processor: i386
> Python version: 2.6.2
> numpy version: 1.3.0
>
>
> s2:       0.9699999999999994
> te:       2048.0000000000446
> rex:      0.14900000000001609
> chi2:     8.3312601381368332e-28
> iter:     22
> f_count:  91
> g_count:  91
> h_count:  22
> warning:  None
>
>
>
>    _______________________________________________________
>
> Reply to this item at:
>
>  <http://gna.org/bugs/?14176>
>
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