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 ]
Re: relax 1.3.2 testsuite failures on darwin