Hi, Right, I didn't realise that I'd changed the common checking function! I was on a bug killing spree and just went straight to the line and made the change without looking where I was. That's good to hear though.
Regards, Edward On 11 August 2011 18:03, Sébastien Morin <[email protected]> wrote: > Hi Ed, > > Well... Since you actually changed the "value_test()" function, this affects > all tests in "test_suite/system_tests/model_free.py" using the function... > > This is thus already fixed ! > Cheers, > > Séb :) > > > On 11-08-11 5:55 PM, Sébastien Morin wrote: >> >> Perfect ! >> >> >> On 11-08-11 5:48 PM, Edward d'Auvergne wrote: >>> >>> Hi, >>> >>> That is exactly the same problem. Feel free to add a fix to the >>> second system test - I only made the change for one of them. >>> >>> Regards, >>> >>> Edward >>> >>> >>> On 11 August 2011 17:42, Sébastien Morin<[email protected]> >>> wrote: >>>> >>>> Hi Ed, >>>> >>>> What a coincidence !!! >>>> >>>> This morning, I tested the installation of relax 1.3.10 on Linux Fedora >>>> and >>>> I had problem with two tests (namely >>>> "test_opt_constr_bfgs_back_S2_0_970_te_2048_Rex_0_149" and >>>> "test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149 >>>> (test_suite.system_tests.model_free.Mf)"), probably because of the same >>>> issue fixed in the current revision... >>>> >>>> Below is the output of "relax -s". Could you check if the problem is the >>>> same and, if needed, fix it as you did for MS Windows..? >>>> >>>> Thanks ! >>>> >>>> >>>> Séb :) >>>> >>>> ============== >>>> [jurgen@pake relax-1.3.10]$ ./relax -s >>>> Echoing of user function calls has been enabled. >>>> >>>> >>>> >>>> >>>> ############################# >>>> # System / functional tests # >>>> ############################# >>>> >>>> >>>> >>>> ...............................................................................................FF............................................................................................................. >>>> ====================================================================== >>>> FAIL: test_opt_constr_bfgs_back_S2_0_970_te_2048_Rex_0_149 >>>> (test_suite.system_tests.model_free.Mf) >>>> Constrained BFGS opt, backtracking line search {S2=0.970, te=2048, >>>> Rex=0.149} >>>> ---------------------------------------------------------------------- >>>> >>>> relax> pipe.create(pipe_name='mf', pipe_type='mf') >>>> >>>> >>>> >>>> relax 1.3.10 >>>> >>>> Molecular dynamics by NMR data analysis >>>> >>>> Copyright (C) 2001-2006 Edward d'Auvergne >>>> Copyright (C) 2006-2011 the relax development >>>> team >>>> >>>> This is free software which you are welcome to modify and redistribute >>>> under >>>> the conditions of the >>>> GNU General Public License (GPL). This program, including all modules, >>>> is >>>> licensed under the GPL >>>> and comes with absolutely no warranty. For details type 'GPL' within >>>> the >>>> relax prompt. >>>> >>>> Assistance in using the relax prompt and scripting interface can be >>>> accessed >>>> by typing 'help' within >>>> the prompt. >>>> >>>> >>>> relax> sequence.read(file='noe.500.out', >>>> >>>> dir='/s/relax-1.3.10/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', >>>> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, >>>> spin_num_col=None, spin_name_col=None, sep=None, spin_id=None) >>>> Opening the file >>>> >>>> '/s/relax-1.3.10/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out' >>>> for reading. >>>> >>>> >>>> >>>> relax> relax_data.read(ri_label='R1', frq_label='600', >>>> frq=600000000.0, >>>> file='r1.600.out', >>>> >>>> dir='/s/relax-1.3.10/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', >>>> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, >>>> spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, >>>> sep=None, >>>> spin_id=None) >>>> Opening the file >>>> >>>> '/s/relax-1.3.10/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='/s/relax-1.3.10/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', >>>> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, >>>> spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, >>>> sep=None, >>>> spin_id=None) >>>> Opening the file >>>> >>>> '/s/relax-1.3.10/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='/s/relax-1.3.10/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', >>>> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, >>>> spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, >>>> sep=None, >>>> spin_id=None) >>>> Opening the file >>>> >>>> '/s/relax-1.3.10/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='/s/relax-1.3.10/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', >>>> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, >>>> spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, >>>> sep=None, >>>> spin_id=None) >>>> Opening the file >>>> >>>> '/s/relax-1.3.10/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='/s/relax-1.3.10/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', >>>> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, >>>> spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, >>>> sep=None, >>>> spin_id=None) >>>> Opening the file >>>> >>>> '/s/relax-1.3.10/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='/s/relax-1.3.10/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', >>>> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, >>>> spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, >>>> sep=None, >>>> spin_id=None) >>>> Opening the file >>>> >>>> '/s/relax-1.3.10/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> value.display(param='csa') >>>> >>>> # mol_name res_num res_name spin_num spin_name value >>>> error >>>> None 1 GLY None None >>>> -0.00016 >>>> None >>>> None 2 ALA None None >>>> -0.00016 >>>> None >>>> >>>> relax> value.write(param='proton', file='devnull', dir=None, >>>> force=False) >>>> Opening the null device file for writing. >>>> >>>> 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) >>>> >>>> >>>> Over-fit spin deselection. >>>> >>>> RelaxWarning: The spin ':1&:GLY' has been deselected because of >>>> insufficient >>>> relaxation data, 3 or more data points are required. >>>> 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: [ 1, 0, 0] fk: >>>> 3.9844117909 >>>> >>>> Parameter values: [0.90905501681906287, 74.369295545631317, >>>> 1.2231009087192337] >>>> 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: [ 0.90906, 74.369, 1.2231] fk: >>>> 46.0715795854 >>>> >>>> Parameter values: [0.98956103824007713, 408.92212422897256, >>>> 0.12789912795489747] >>>> Function value: 1.5767184829472947 >>>> Iterations: 37 >>>> Function calls: 209 >>>> Gradient calls: 38 >>>> Hessian calls: 0 >>>> Warning: None >>>> >>>> >>>> k: 2 xk: array([ 9.89561038e-01, 4.08922124e+02, >>>> 1.27899128e-01]) >>>> fk: 3.6265517227850839 >>>> Entering sub-algorithm. >>>> >>>> Quasi-Newton BFGS minimisation >>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>> Line search: Backtracking line search. >>>> >>>> k: 0 xk: [ 0.98956, 408.92, 0.1279] fk: >>>> 3.62655172279 >>>> >>>> Parameter values: [0.98280664757781688, 601.68994600419194, >>>> 0.055870730706586783] >>>> Function value: 2.7803077415960757 >>>> Iterations: 30 >>>> Function calls: 149 >>>> Gradient calls: 31 >>>> Hessian calls: 0 >>>> Warning: None >>>> >>>> >>>> k: 3 xk: array([ 9.82806648e-01, 6.01689946e+02, >>>> 5.58707307e-02]) >>>> fk: 2.7803077415960757 >>>> Entering sub-algorithm. >>>> >>>> Quasi-Newton BFGS minimisation >>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>> Line search: Backtracking line search. >>>> >>>> k: 0 xk: [ 0.98281, 601.69, 0.055871] fk: >>>> 2.7803077416 >>>> >>>> Parameter values: [0.97000000000262465, 2047.9999999849369, >>>> 0.14899999993840687] >>>> Function value: 4.3399069883879782e-20 >>>> Iterations: 70 >>>> Function calls: 212 >>>> Gradient calls: 71 >>>> Hessian calls: 0 >>>> Warning: None >>>> >>>> >>>> k: 4 xk: array([ 9.70000000e-01, 2.04800000e+03, >>>> 1.49000000e-01]) >>>> fk: 4.3399069883879782e-20 >>>> Entering sub-algorithm. >>>> >>>> Quasi-Newton BFGS minimisation >>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>> Line search: Backtracking line search. >>>> >>>> k: 0 xk: [ 0.97, 2048, 0.149] fk: >>>> 4.33990698839e-20 >>>> >>>> Parameter values: [0.96999999999990616, 2047.9999999849369, >>>> 0.14900000000189087] >>>> Function value: 8.4298981584870517e-23 >>>> Iterations: 11 >>>> Function calls: 36 >>>> Gradient calls: 12 >>>> Hessian calls: 0 >>>> Warning: None >>>> >>>> >>>> k: 5 xk: array([ 9.70000000e-01, 2.04800000e+03, >>>> 1.49000000e-01]) >>>> fk: 8.4298981584870517e-23 >>>> Entering sub-algorithm. >>>> >>>> Quasi-Newton BFGS minimisation >>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>> Line search: Backtracking line search. >>>> >>>> k: 0 xk: [ 0.97, 2048, 0.149] fk: >>>> 8.42989815849e-23 >>>> >>>> Parameter values: [0.96999999999991904, 2047.9999999849369, >>>> 0.14900000000155103] >>>> Function value: 8.2908269286295164e-23 >>>> Iterations: 6 >>>> Function calls: 41 >>>> Gradient calls: 7 >>>> Hessian calls: 0 >>>> Warning: None >>>> >>>> >>>> k: 6 xk: array([ 9.70000000e-01, 2.04800000e+03, >>>> 1.49000000e-01]) >>>> fk: 8.2908269286295164e-23 >>>> Entering sub-algorithm. >>>> >>>> Quasi-Newton BFGS minimisation >>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>> Line search: Backtracking line search. >>>> >>>> k: 0 xk: [ 0.97, 2048, 0.149] fk: >>>> 8.29082692863e-23 >>>> >>>> Parameter values: [0.96999999999991871, 2047.9999999849369, >>>> 0.149000000001551] >>>> Function value: 8.290677155630973e-23 >>>> Iterations: 3 >>>> Function calls: 40 >>>> Gradient calls: 4 >>>> Hessian calls: 0 >>>> Warning: None >>>> >>>> >>>> Parameter values: [0.96999999999991871, 2047.9999999849369, >>>> 0.149000000001551] >>>> Function value: 8.290677155630973e-23 >>>> Iterations: 194 >>>> Function calls: 780 >>>> Gradient calls: 201 >>>> Hessian calls: 0 >>>> Warning: None >>>> >>>> Traceback (most recent call last): >>>> File "/s/relax-1.3.10/test_suite/system_tests/model_free.py", line >>>> 826, in >>>> test_opt_constr_bfgs_back_S2_0_970_te_2048_Rex_0_149 >>>> self.value_test(spin, select=select, s2=s2, te=te, rex=rex, >>>> chi2=chi2, >>>> iter=iter, f_count=f_count, g_count=g_count, h_count=h_count, >>>> warning=warning) >>>> File "/s/relax-1.3.10/test_suite/system_tests/model_free.py", line >>>> 2544, in >>>> value_test >>>> self.assert_(spin.iter in iter, msg=mesg) >>>> AssertionError: Optimisation failure. >>>> >>>> System: Linux >>>> Release: 2.6.35.13-92.fc14.i686.PAE >>>> Version: #1 SMP Sat May 21 17:33:09 UTC 2011 >>>> Win32 version: >>>> Distribution: fedora 14 Laughlin >>>> Architecture: 32bit ELF >>>> Machine: i686 >>>> Processor: i686 >>>> Python version: 2.7.0 >>>> Numpy version: 1.4.1 >>>> Libc version: glibc 2.0 >>>> >>>> s2: 0.9699999999999187 >>>> te (ps): 2047.999999985 >>>> rex: 0.149000000001551 >>>> chi2: 8.290677155630973e-23 >>>> iter: 194 >>>> f_count: 780 >>>> g_count: 201 >>>> h_count: 0 >>>> warning: None >>>> >>>> >>>> ====================================================================== >>>> FAIL: test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149 >>>> (test_suite.system_tests.model_free.Mf) >>>> 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 1.3.10 >>>> >>>> Molecular dynamics by NMR data analysis >>>> >>>> Copyright (C) 2001-2006 Edward d'Auvergne >>>> Copyright (C) 2006-2011 the relax development >>>> team >>>> >>>> This is free software which you are welcome to modify and redistribute >>>> under >>>> the conditions of the >>>> GNU General Public License (GPL). This program, including all modules, >>>> is >>>> licensed under the GPL >>>> and comes with absolutely no warranty. For details type 'GPL' within >>>> the >>>> relax prompt. >>>> >>>> Assistance in using the relax prompt and scripting interface can be >>>> accessed >>>> by typing 'help' within >>>> the prompt. >>>> >>>> >>>> relax> sequence.read(file='noe.500.out', >>>> >>>> dir='/s/relax-1.3.10/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', >>>> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, >>>> spin_num_col=None, spin_name_col=None, sep=None, spin_id=None) >>>> Opening the file >>>> >>>> '/s/relax-1.3.10/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out' >>>> for reading. >>>> >>>> >>>> >>>> relax> relax_data.read(ri_label='R1', frq_label='600', >>>> frq=600000000.0, >>>> file='r1.600.out', >>>> >>>> dir='/s/relax-1.3.10/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', >>>> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, >>>> spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, >>>> sep=None, >>>> spin_id=None) >>>> Opening the file >>>> >>>> '/s/relax-1.3.10/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='/s/relax-1.3.10/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', >>>> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, >>>> spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, >>>> sep=None, >>>> spin_id=None) >>>> Opening the file >>>> >>>> '/s/relax-1.3.10/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='/s/relax-1.3.10/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', >>>> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, >>>> spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, >>>> sep=None, >>>> spin_id=None) >>>> Opening the file >>>> >>>> '/s/relax-1.3.10/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='/s/relax-1.3.10/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', >>>> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, >>>> spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, >>>> sep=None, >>>> spin_id=None) >>>> Opening the file >>>> >>>> '/s/relax-1.3.10/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='/s/relax-1.3.10/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', >>>> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, >>>> spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, >>>> sep=None, >>>> spin_id=None) >>>> Opening the file >>>> >>>> '/s/relax-1.3.10/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='/s/relax-1.3.10/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', >>>> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, >>>> spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, >>>> sep=None, >>>> spin_id=None) >>>> Opening the file >>>> >>>> '/s/relax-1.3.10/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> value.display(param='csa') >>>> >>>> # mol_name res_num res_name spin_num spin_name value >>>> error >>>> None 1 GLY None None >>>> -0.00016 >>>> None >>>> None 2 ALA None None >>>> -0.00016 >>>> None >>>> >>>> relax> value.write(param='proton', file='devnull', dir=None, >>>> force=False) >>>> Opening the null device file for writing. >>>> >>>> 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) >>>> >>>> >>>> Over-fit spin deselection. >>>> >>>> RelaxWarning: The spin ':1&:GLY' has been deselected because of >>>> insufficient >>>> relaxation data, 3 or more data points are required. >>>> 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: [ 1, 0, 0] fk: >>>> 3.9844117909 >>>> >>>> Parameter values: [0.90905506221776622, 74.369430109433466, >>>> 1.2231015622357264] >>>> 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: 48.121371716752286 >>>> Entering sub-algorithm. >>>> >>>> Quasi-Newton BFGS minimisation >>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>> Line search: More and Thuente line search. >>>> >>>> k: 0 xk: [ 0.90906, 74.369, 1.2231] fk: >>>> 46.0715179226 >>>> >>>> Parameter values: [0.99493663077922057, 88.138505759196732, >>>> -3.7928107668617891e-05] >>>> Function value: 1.9644199917083982 >>>> 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, 8.81385058e+01, >>>> -3.79281077e-05]) >>>> fk: 144.63963445541734 >>>> Entering sub-algorithm. >>>> >>>> Quasi-Newton BFGS minimisation >>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>> Line search: More and Thuente line search. >>>> >>>> k: 0 xk: [ 0.99494, 88.139, -3.7928e-05] fk: >>>> 4.0147053483 >>>> >>>> Parameter values: [0.9700000000020782, 2048.0000000119967, >>>> 0.14899999998332922] >>>> Function value: -7.1927067566113556e-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: 1.5560391211796852e-20 >>>> Entering sub-algorithm. >>>> >>>> Quasi-Newton BFGS minimisation >>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>> Line search: More and Thuente line search. >>>> >>>> k: 0 xk: [ 0.97, 2048, 0.149] fk: >>>> 1.55603912118e-20 >>>> >>>> Parameter values: [0.97000000000063413, 2048.0000000119967, >>>> 0.14899999998330257] >>>> Function value: 2.6082858480886141e-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: 2.6082858480886141e-21 >>>> Entering sub-algorithm. >>>> >>>> Quasi-Newton BFGS minimisation >>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>> Line search: More and Thuente line search. >>>> >>>> k: 0 xk: [ 0.97, 2048, 0.149] fk: >>>> 2.60828584809e-21 >>>> >>>> Parameter values: [0.97000000000006326, 2048.0000000119967, >>>> 0.14899999999880381] >>>> Function value: 5.1869486534269492e-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: 5.1869486534269492e-23 >>>> Entering sub-algorithm. >>>> >>>> Quasi-Newton BFGS minimisation >>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>> Line search: More and Thuente line search. >>>> >>>> k: 0 xk: [ 0.97, 2048, 0.149] fk: >>>> 5.18694865343e-23 >>>> >>>> Parameter values: [0.97000000000006315, 2048.0000000119967, >>>> 0.14899999999880381] >>>> Function value: 5.1821311776197656e-23 >>>> Iterations: 3 >>>> Function calls: 68 >>>> Gradient calls: 68 >>>> Hessian calls: 0 >>>> Warning: None >>>> >>>> >>>> Parameter values: [0.97000000000006315, 2048.0000000119967, >>>> 0.14899999999880381] >>>> Function value: 5.1821311776197656e-23 >>>> Iterations: 122 >>>> Function calls: 386 >>>> Gradient calls: 386 >>>> Hessian calls: 0 >>>> Warning: None >>>> >>>> Traceback (most recent call last): >>>> File "/s/relax-1.3.10/test_suite/system_tests/model_free.py", line >>>> 1011, in >>>> test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149 >>>> self.value_test(spin, select=select, s2=s2, te=te, rex=rex, >>>> chi2=chi2, >>>> iter=iter, f_count=f_count, g_count=g_count, h_count=h_count, >>>> warning=warning) >>>> File "/s/relax-1.3.10/test_suite/system_tests/model_free.py", line >>>> 2544, in >>>> value_test >>>> self.assert_(spin.iter in iter, msg=mesg) >>>> AssertionError: Optimisation failure. >>>> >>>> System: Linux >>>> Release: 2.6.35.13-92.fc14.i686.PAE >>>> Version: #1 SMP Sat May 21 17:33:09 UTC 2011 >>>> Win32 version: >>>> Distribution: fedora 14 Laughlin >>>> Architecture: 32bit ELF >>>> Machine: i686 >>>> Processor: i686 >>>> Python version: 2.7.0 >>>> Numpy version: 1.4.1 >>>> Libc version: glibc 2.0 >>>> >>>> s2: 0.9700000000000631 >>>> te (ps): 2048.000000012 >>>> rex: 0.14899999999880381 >>>> chi2: 5.1821311776197656e-23 >>>> iter: 122 >>>> f_count: 386 >>>> g_count: 386 >>>> h_count: 0 >>>> warning: None >>>> >>>> >>>> ---------------------------------------------------------------------- >>>> Ran 206 tests in 436.606s >>>> >>>> FAILED (failures=2) >>>> >>>> >>>> >>>> >>>> ################################### >>>> # Summary of the relax test suite # >>>> ################################### >>>> >>>> >>>> # Optional packages/modules >>>> ########################### >>>> >>>> No tests skipped due to missing modules. >>>> >>>> # Synopsis >>>> ########## >>>> >>>> System/functional tests ......................................... [ >>>> Failed ] >>>> >>>> ============== >>>> >>>> >>>> On 11-08-11 4:56 PM, [email protected] wrote: >>>>> >>>>> Author: bugman >>>>> Date: Thu Aug 11 16:56:16 2011 >>>>> New Revision: 14364 >>>>> >>>>> URL: http://svn.gna.org/viewcvs/relax?rev=14364&view=rev >>>>> Log: >>>>> Fix for the test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149 >>>>> model-free >>>>> system test on MS Windows. >>>>> >>>>> The te parameter check was too strict. >>>>> >>>>> >>>>> Modified: >>>>> 1.3/test_suite/system_tests/model_free.py >>>>> >>>>> Modified: 1.3/test_suite/system_tests/model_free.py >>>>> URL: >>>>> >>>>> http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/model_free.py?rev=14364&r1=14363&r2=14364&view=diff >>>>> >>>>> >>>>> ============================================================================== >>>>> --- 1.3/test_suite/system_tests/model_free.py (original) >>>>> +++ 1.3/test_suite/system_tests/model_free.py Thu Aug 11 16:56:16 2011 >>>>> @@ -2523,7 +2523,7 @@ >>>>> >>>>> # te correlation time. >>>>> if type(te) == float: >>>>> - self.assertAlmostEqual(spin.te / 1e-12, te, 6, msg=mesg) >>>>> + self.assertAlmostEqual(spin.te / 1e-12, te, 5, msg=mesg) >>>>> elif te == None: >>>>> self.assertEqual(spin.te, None, msg=mesg) >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> relax (http://nmr-relax.com) >>>>> >>>>> This is the relax-commits 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-commits >>>> >>>> -- >>>> Sébastien Morin, Ph.D. >>>> Postdoctoral Fellow, S. Grzesiek NMR Laboratory >>>> Department of Structural Biology >>>> Biozentrum, Universität Basel >>>> Klingelbergstrasse 70 >>>> 4056 Basel >>>> Switzerland >>>> >>>> >>>> _______________________________________________ >>>> relax (http://nmr-relax.com) >>>> >>>> This is the relax-devel mailing list >>>> [email protected] >>>> >>>> To unsubscribe from this list, get a password >>>> reminder, or change your subscription options, >>>> visit the list information page at >>>> https://mail.gna.org/listinfo/relax-devel >>>> >> -- >> Sébastien Morin, Ph.D. >> Postdoctoral Fellow, S. Grzesiek NMR Laboratory >> Department of Structural Biology >> Biozentrum, Universität Basel >> Klingelbergstrasse 70 >> 4056 Basel >> Switzerland >> >> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-devel mailing list >> [email protected] >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-devel > > -- > Sébastien Morin, Ph.D. > Postdoctoral Fellow, S. Grzesiek NMR Laboratory > Department of Structural Biology > Biozentrum, Universität Basel > Klingelbergstrasse 70 > 4056 Basel > Switzerland > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
