On Fri, Oct 24, 2008 at 05:10:30PM +0200, Edward d'Auvergne wrote:
> Hi,
>
> Thanks for the heads up. I didn't realise how many tests failed on a
> Mac! Most of these aren't too serious though and are due to different
> machine precision caused by the combination of a powerpc chip, Mac OS
> X, and the mac python version. relax's tests are very, very strict,
> but I'll loosen these for the mac as I have for 64 bit Linux and 32
> bit Windows (well, as long as the optimisation results are close to
> the true results). One system test should also fail as the code isn't
> implemented yet ("Test the reading of an NMRView peak list"). One the
> failures is very serious though. I know this is a bit of an effort,
> but could I ask you to create a few bug reports for these? This will
> really help me in the debugging and documentation of the fixes. The
> NMRView peak list doesn't need a bug report, but if you could put all
> the optimisation failures into one, the "The user function angles()"
> failure into another, and the 2 unit test failures into a third. This
> would really be appreciated. I should then be able to quickly make
> most pass, and then release relax 1.3.3. Note that even though these
> tests fail, relax 1.3.2 is still quite usable on Mac OS X. The
> problems shouldn't affect model-free analysis, relaxation curve
> fitting, noe calculations, reduced spectral density mapping,
> consistency testing, etc.
>
> Cheers,
>
> Edward
>
>
> P.S. The bug tracker is located at https://gna.org/bugs/?group=relax.
>
>
Edward,
Relax 1.3.2 performs somewhat better with its testsuite on
i386-apple-darwin9. The results
are appended below. I'll go ahead and update the fink relax-py package to 1.3.2
and
will fill the bugzilla reports later this weekend.
Jack
relax --test-suite
Function intros have been enabled.
#############################
# System / functional tests #
#############################
.....................FF.F.F..............E.................
======================================================================
ERROR: Test the reading of an NMRView peak list.
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf')
relax> residue.create(res_num=70, res_name=None, mol_id=None)
relax> residue.create(res_num=72, res_name=None, mol_id=None)
relax> spin.name(spin_id=None, name='N')
relax> relax_fit.read(file='cNTnC.xpk',
dir='/sw/lib/relax-py25/test_suite/shared_data/peak_lists',
relax_time=0.017600000000000001, format='sparky', heteronuc='N', proton='HN',
int_col=None)
Sparky formatted data file.
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/peak_lists/cNTnC.xpk' for reading.
Number of header lines found: 2
Traceback (most recent call last):
File "/sw/lib/relax-py25/test_suite/system_tests/nmrview.py", line 60, in
test_read_peak_list
self.relax.interpreter._Relax_fit.read(file="cNTnC.xpk", dir=sys.path[-1] +
"/test_suite/shared_data/peak_lists", relax_time=0.0176)
File "/sw/lib/relax-py25/prompt/relax_fit.py", line 193, in read
relax_fit_obj.read(file=file, dir=dir, relax_time=relax_time,
format=format, heteronuc=heteronuc, proton=proton, int_col=int_col)
File "/sw/lib/relax-py25/specific_fns/relax_fit.py", line 1034, in read
intensity.read(file=file, dir=dir, format=format, heteronuc=heteronuc,
proton=proton, int_col=int_col, assign_func=self.assign_function)
File "/sw/lib/relax-py25/generic_fns/intensity.py", line 284, in read
res_num, H_name, X_name, intensity = intensity_fn(file_data[i])
File "/sw/lib/relax-py25/generic_fns/intensity.py", line 95, in
intensity_sparky
raise RelaxError, "Improperly formatted Sparky file."
RelaxError: RelaxError: Improperly formatted Sparky file.
======================================================================
FAIL: Constrained BFGS opt, backtracking 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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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=('bfgs', 'back'), 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.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
k: 0 xk: array([ 1., 0., 0.])
fk: 3.9844117908982288
Parameter values: array([ 0.90905502, 74.36929555, 1.22310091])
Function value: -1447.7789206950388
Iterations: 37
Function calls: 93
Gradient calls: 38
Hessian calls: 0
Warning: None
k: 1 xk: array([ 0.90905502, 74.36929555, 1.22310091])
fk: 48.121412825285702
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
k: 0 xk: array([ 0.90905502, 74.36929555, 1.22310091])
fk: 46.071579585447914
Parameter values: array([ 9.89561039e-01, 4.08922117e+02,
1.27899125e-01])
Function value: 1.5767184945640649
Iterations: 37
Function calls: 203
Gradient calls: 38
Hessian calls: 0
Warning: None
k: 2 xk: array([ 9.89561039e-01, 4.08922117e+02, 1.27899125e-01])
fk: 3.6265517344018541
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
k: 0 xk: array([ 9.89561039e-01, 4.08922117e+02,
1.27899125e-01]) fk: 3.6265517344018541
Parameter values: array([ 9.79293074e-01, 6.96567345e+02,
8.30000802e-02])
Function value: 2.5772195679741152
Iterations: 30
Function calls: 148
Gradient calls: 31
Hessian calls: 0
Warning: None
k: 3 xk: array([ 9.79293074e-01, 6.96567345e+02, 8.30000802e-02])
fk: 2.5772195679741152
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
k: 0 xk: array([ 9.79293074e-01, 6.96567345e+02,
8.30000802e-02]) fk: 2.5772195679741152
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 1.2222852502880481e-20
Iterations: 64
Function calls: 181
Gradient calls: 65
Hessian calls: 0
Warning: None
k: 4 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
fk: 1.2222852502880481e-20
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01]) fk: 1.2222852502880481e-20
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 1.11538158135138e-20
Iterations: 2
Function calls: 18
Gradient calls: 3
Hessian calls: 0
Warning: None
k: 5 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
fk: 1.11538158135138e-20
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01]) fk: 1.11538158135138e-20
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 1.1151721805269898e-20
Iterations: 4
Function calls: 50
Gradient calls: 5
Hessian calls: 0
Warning: None
k: 6 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
fk: 1.1151721805269898e-20
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01]) fk: 1.1151721805269898e-20
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 1.1151721805269898e-20
Iterations: 1
Function calls: 42
Gradient calls: 2
Hessian calls: 0
Warning: None
Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
Function value: 1.1151721805269898e-20
Iterations: 175
Function calls: 735
Gradient calls: 182
Hessian calls: 0
Warning: None
Traceback (most recent call last):
File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 301, in
test_opt_constr_bfgs_back_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-py25/test_suite/system_tests/model_free.py", line 1043,
in value_test
self.assertAlmostEqual(spin.te / 1e-12, te, msg=mesg)
AssertionError: Optimisation failure.
System: Darwin
Release: 9.6.0
Version: Darwin Kernel Version 9.6.0: Fri Oct 17 22:38:41 PDT 2008;
root:xnu-1228.9.56~1/RELEASE_I386
Win32 version:
Distribution:
Architecture: 32bit
Machine: i386
Processor: i386
Python version: 2.5.2
numpy version: 1.1.1
s2: 0.9700000000009170
te: 2048.0000001751678
rex: 0.14899999998256069
chi2: 1.1151721805269898e-20
iter: 175
f_count: 735
g_count: 182
h_count: 0
warning: None
======================================================================
FAIL: Constrained BFGS opt, 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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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=('bfgs', '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.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 1., 0., 0.])
fk: 3.9844117908982288
Parameter values: array([ 0.90905506, 74.36943011, 1.22310156])
Function value: -1447.7789206948671
Iterations: 22
Function calls: 50
Gradient calls: 50
Hessian calls: 0
Warning: None
k: 1 xk: array([ 0.90905506, 74.36943011, 1.22310156])
fk: 48.121371716752257
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 0.90905506, 74.36943011, 1.22310156])
fk: 46.071517922561874
Parameter values: array([ 9.94936631e-01, 8.81385060e+01,
-3.79281068e-05])
Function value: 1.9644199905673625
Iterations: 38
Function calls: 128
Gradient calls: 128
Hessian calls: 0
Warning: The gradient at point 0 of this line search is
positive, ie p is not a descent direction and the line search will not work.
(fatal minimisation error).
k: 2 xk: array([ 9.94936631e-01, 8.81385060e+01, -3.79281068e-05])
fk: 144.63923557105986
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 9.94936631e-01, 8.81385060e+01,
-3.79281068e-05]) fk: 4.014705347144286
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: -7.1927064423000128e-05
Iterations: 56
Function calls: 129
Gradient calls: 129
Hessian calls: 0
Warning: None
k: 3 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
fk: 1.6352573249506989e-20
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01]) fk: 1.6352573249506989e-20
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 2.6899730031345977e-21
Iterations: 1
Function calls: 4
Gradient calls: 4
Hessian calls: 0
Warning: None
k: 4 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
fk: 2.6899730031345977e-21
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01]) fk: 2.6899730031345977e-21
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 4.7647467884964078e-23
Iterations: 2
Function calls: 7
Gradient calls: 7
Hessian calls: 0
Warning: None
k: 5 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
fk: 4.7647467884964078e-23
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01]) fk: 4.7647467884964078e-23
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 4.7647467884964078e-23
Iterations: 1
Function calls: 68
Gradient calls: 68
Hessian calls: 0
Warning: None
Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
Function value: 4.7647467884964078e-23
Iterations: 120
Function calls: 386
Gradient calls: 386
Hessian calls: 0
Warning: None
Traceback (most recent call last):
File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 355, in
test_opt_constr_bfgs_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-py25/test_suite/system_tests/model_free.py", line 1047,
in value_test
self.assertEqual(spin.f_count, f_count, msg=mesg)
AssertionError: Optimisation failure.
System: Darwin
Release: 9.6.0
Version: Darwin Kernel Version 9.6.0: Fri Oct 17 22:38:41 PDT 2008;
root:xnu-1228.9.56~1/RELEASE_I386
Win32 version:
Distribution:
Architecture: 32bit
Machine: i386
Processor: i386
Python version: 2.5.2
numpy version: 1.1.1
s2: 0.9700000000000604
te: 2048.0000000114997
rex: 0.14899999999886168
chi2: 4.7647467884964078e-23
iter: 120
f_count: 386
g_count: 386
h_count: 0
warning: None
======================================================================
FAIL: Constrained coordinate descent opt, 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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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=('cd', '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.
Back-and-forth coordinate descent minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 1., 0., 0.])
fk: 3.9844117908982288
Parameter values: array([ 0.90905609, 74.37463254, 1.22289922])
Function value: -1447.7789199590425
Iterations: 25
Function calls: 75
Gradient calls: 75
Hessian calls: 0
Warning: None
k: 1 xk: array([ 0.90905609, 74.37463254, 1.22289922])
fk: 48.120438129522014
Entering sub-algorithm.
Back-and-forth coordinate descent minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 0.90905609, 74.37463254, 1.22289922])
fk: 46.070117173804164
Parameter values: array([ 9.70000218e-01, 2.04801529e+03,
1.48994731e-01])
Function value: -2.0503209554858945
Iterations: 89
Function calls: 284
Gradient calls: 284
Hessian calls: 0
Warning: None
k: 2 xk: array([ 9.70000218e-01, 2.04801529e+03, 1.48994731e-01])
fk: 2.3195995262977486e-10
Entering sub-algorithm.
Back-and-forth coordinate descent minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 9.70000218e-01, 2.04801529e+03,
1.48994731e-01]) fk: 2.3195995262977486e-10
Parameter values: array([ 9.70000218e-01, 2.04800873e+03,
1.48997054e-01])
Function value: 1.2998777447179547e-10
Iterations: 18
Function calls: 136
Gradient calls: 136
Hessian calls: 0
Warning: None
k: 3 xk: array([ 9.70000218e-01, 2.04800873e+03, 1.48997054e-01])
fk: 1.2998777447179547e-10
Entering sub-algorithm.
Back-and-forth coordinate descent minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 9.70000218e-01, 2.04800873e+03,
1.48997054e-01]) fk: 1.2998777447179547e-10
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.48999999e-01])
Function value: 2.3477234248531005e-18
Iterations: 65
Function calls: 184
Gradient calls: 184
Hessian calls: 0
Warning: None
k: 4 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.48999999e-01])
fk: 2.3477234248531005e-18
Entering sub-algorithm.
Back-and-forth coordinate descent minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.48999999e-01]) fk: 2.3477234248531005e-18
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.48999999e-01])
Function value: 2.3477234248531005e-18
Iterations: 1
Function calls: 78
Gradient calls: 78
Hessian calls: 0
Warning: None
Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.48999999e-01])
Function value: 2.3477234248531005e-18
Iterations: 198
Function calls: 757
Gradient calls: 757
Hessian calls: 0
Warning: None
Traceback (most recent call last):
File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 452, in
test_opt_constr_cd_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-py25/test_suite/system_tests/model_free.py", line 1047,
in value_test
self.assertEqual(spin.f_count, f_count, msg=mesg)
AssertionError: Optimisation failure.
System: Darwin
Release: 9.6.0
Version: Darwin Kernel Version 9.6.0: Fri Oct 17 22:38:41 PDT 2008;
root:xnu-1228.9.56~1/RELEASE_I386
Win32 version:
Distribution:
Architecture: 32bit
Machine: i386
Processor: i386
Python version: 2.5.2
numpy version: 1.1.1
s2: 0.9700000000219674
te: 2048.0000015341870
rex: 0.14899999946977982
chi2: 2.3477234248531005e-18
iter: 198
f_count: 757
g_count: 757
h_count: 0
warning: None
======================================================================
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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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-py25/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
Traceback (most recent call last):
File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 554, 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-py25/test_suite/system_tests/model_free.py", line 1047,
in value_test
self.assertEqual(spin.f_count, f_count, msg=mesg)
AssertionError: Optimisation failure.
System: Darwin
Release: 9.6.0
Version: Darwin Kernel Version 9.6.0: Fri Oct 17 22:38:41 PDT 2008;
root:xnu-1228.9.56~1/RELEASE_I386
Win32 version:
Distribution:
Architecture: 32bit
Machine: i386
Processor: i386
Python version: 2.5.2
numpy version: 1.1.1
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
----------------------------------------------------------------------
Ran 59 tests in 73.014s
FAILED (failures=4, errors=1)
##############
# Unit tests #
##############
testing units...
----------------
/sw/lib/relax-py25/test_suite/unit_tests
......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 1046 tests in 12.989s
OK
###################################
# Summary of the relax test suite #
###################################
System/functional tests
............................................................. [ Failed ]
Unit tests
.......................................................................... [ OK
]
Synopsis
............................................................................ [
Failed ]
_______________________________________________
relax (http://nmr-relax.com)
This is the relax-users 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-users
