Hi,
Strangely your system seems to be the less precise of all the machines
with test results returned. This is nothing to be worried about, your
precision is 1e-20 versers 1e-27 for other computers, so you should
have no problem finding the correct model-free results (for reference
Art Palmer's Modelfree4 has a precision of 1e-5). It is a little
strange though that you do not reach the precision of 1e-25 stated in
the minimise command:
relax> minimise(*args=('bfgs', 'back'), func_tol=1e-25,
max_iterations=10000000, constraints=True, scaling=True, verbosity=1)
But your computer is not the only one not to reach this. The other
thing is that the processor or CPU type is not listed in the print
out. Are you running in a virtual machine? I'm just asking out of
curiosity. I am trying to try to work out why different machines do
not give identical model-free results. This is all being recorded in
the relax test suite for future reference and research into model-free
analysis (see
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/model_free.py?view=markup).
Cheers,
Edward
On 28 January 2011 18:03, Edward d'Auvergne <[email protected]> wrote:
> Hi,
>
> This is exactly what is needed. Cheers. I will add this data about
> your specific setup to relax, and the tests will pass in the next
> version. These 2 failures you are seeing are perfectly fine. They
> relate only to machine precision differences (your computer has an Rex
> value of 0.14899999999883881 verses the real value of 0.149, so this
> will make no difference in your analysis ;) You have nothing to worry
> about, everything is working perfectly! The mf_multimodel.py or
> modsel.py scripts will return the correct result. However if you have
> data at 2 field strengths, which is almost a prerequisite for a
> serious publication these days, I would recommend the orders of
> magnitude higher quality protocol in
> sample_scripts/dauvergne_protocol.py (see the reference
> http://www.nmr-relax.com/refs.html#dAuvergneGooley08b). Or you could
> install relax 1.3.9 and try out the new GUI at
> http://www.nmr-relax.com/download.html (this requires wxPython to be
> installed). The GUI uses this protocol to perform an automatic
> model-free analysis, and the paper for it is in press.
>
> Regards,
>
> Edward
>
>
> On 28 January 2011 11:39, Tiago Pais <[email protected]> wrote:
>> Hi,
>> I have executed the scons with no problems.
>> The print out that I could get is at the bottom of this em-mail. I hope this
>> is what you asked.
>> Anyway, does this bug affect the analysis for example with a
>> mf_multimodel.py or modsel.py?
>>
>> Regards
>> TiagoP
>>
>> Print out:
>> 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
>> '/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_2048_R
>> ex_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='/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_20
>> 48_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
>> '/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_2048_R
>> ex_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='/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_20
>> 48_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
>> '/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_2048_R
>> ex_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, 74.36929554563136,
>> 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: 48.121412825285709
>> 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: [0.98956103882988777, 408.92210939854823,
>> 0.12789912252738242]
>> Function value: 1.5767185066455172
>> Iterations: 36
>> Function calls: 160
>> Gradient calls: 37
>> Hessian calls: 0
>> Warning: None
>>
>>
>> k: 2 xk: array([ 9.89561039e-01, 4.08922109e+02, 1.27899123e-01])
>> fk: 3.6265517464833064
>> Entering sub-algorithm.
>>
>> Quasi-Newton BFGS minimisation
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Line search: Backtracking line search.
>>
>> k: 0 xk: [ 0.98956, 408.92, 0.1279] fk:
>> 3.62655174648
>>
>> Parameter values: [0.97366872065557464, 847.48129324681554,
>> 0.12587481779543874]
>> Function value: 2.1499888720861113
>> Iterations: 30
>> Function calls: 150
>> Gradient calls: 31
>> Hessian calls: 0
>> Warning: None
>>
>>
>> k: 3 xk: array([ 9.73668721e-01, 8.47481293e+02, 1.25874818e-01])
>> fk: 2.1499888720861113
>> Entering sub-algorithm.
>>
>> Quasi-Newton BFGS minimisation
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Line search: Backtracking line search.
>>
>> k: 0 xk: [ 0.97367, 847.48, 0.12587] fk:
>> 2.14998887209
>>
>> Parameter values: [0.97000000000112863, 2048.0000001778708,
>> 0.14899999998759275]
>> Function value: 1.2766370598812569e-20
>> Iterations: 40
>> Function calls: 94
>> Gradient calls: 41
>> Hessian calls: 0
>> Warning: None
>>
>>
>> k: 4 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
>> fk: 1.2766370598812569e-20
>> Entering sub-algorithm.
>>
>> Quasi-Newton BFGS minimisation
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Line search: Backtracking line search.
>>
>> k: 0 xk: [ 0.97, 2048, 0.149] fk:
>> 1.27663705988e-20
>>
>> Parameter values: [0.97000000000095432, 2048.0000001778708,
>> 0.14899999998189384]
>> Function value: 1.1498830911662198e-20
>> Iterations: 7
>> Function calls: 28
>> Gradient calls: 8
>> Hessian calls: 0
>> Warning: None
>>
>>
>> k: 5 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
>> fk: 1.1498830911662198e-20
>> Entering sub-algorithm.
>>
>> Quasi-Newton BFGS minimisation
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Line search: Backtracking line search.
>>
>> k: 0 xk: [ 0.97, 2048, 0.149] fk:
>> 1.14988309117e-20
>>
>> Parameter values: [0.97000000000095099, 2048.0000001778708,
>> 0.14899999998189395]
>> Function value: 1.1498599057727952e-20
>> Iterations: 3
>> Function calls: 39
>> Gradient calls: 4
>> Hessian calls: 0
>> Warning: None
>>
>>
>> k: 6 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
>> fk: 1.1498599057727952e-20
>> Entering sub-algorithm.
>>
>> Quasi-Newton BFGS minimisation
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Line search: Backtracking line search.
>>
>> k: 0 xk: [ 0.97, 2048, 0.149] fk:
>> 1.14985990577e-20
>>
>> Parameter values: [0.97000000000095099, 2048.0000001778708,
>> 0.14899999998189395]
>> Function value: 1.1498599057727952e-20
>> Iterations: 1
>> Function calls: 34
>> Gradient calls: 2
>> Hessian calls: 0
>> Warning: None
>>
>>
>> Parameter values: [0.97000000000095099, 2048.0000001778708,
>> 0.14899999998189395]
>> Function value: 1.1498599057727952e-20
>> Iterations: 154
>> Function calls: 598
>> Gradient calls: 161
>> Hessian calls: 0
>> Warning: None
>>
>> Traceback (most recent call last):
>> File "/usr/local/relax-1.3.8/test_suite/system_tests/model_free.py", line
>> 803, 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 "/usr/local/relax-1.3.8/test_suite/system_tests/model_free.py", line
>> 2498, in value_test
>> self.assert_(spin.iter in iter, msg=mesg)
>> AssertionError: Optimisation failure.
>>
>> System: Linux
>> Release: 2.6.28-17-generic
>> Version: #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009
>> Win32 version:
>> Distribution: Ubuntu 9.04 jaunty
>> Architecture: 32bit ELF
>> Machine: i686
>> Processor:
>> Python version: 2.6.2
>> Numpy version: 1.2.1
>> Libc version: glibc 2.4
>>
>> s2: 0.970000000000951
>> te (ps): 2048.000000178
>> rex: 0.14899999998189395
>> chi2: 1.1498599057727952e-20
>> iter: 154
>> f_count: 598
>> g_count: 161
>> 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 1.3.8
>>
>> 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='/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_20
>> 48_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
>> '/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_2048_R
>> ex_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='/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_20
>> 48_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
>> '/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_2048_R
>> ex_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='/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_20
>> 48_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
>> '/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_2048_R
>> ex_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='/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_20
>> 48_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
>> '/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_2048_R
>> ex_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='/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_20
>> 48_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
>> '/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_2048_R
>> ex_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='/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_20
>> 48_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
>> '/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_2048_R
>> ex_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='/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_20
>> 48_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
>> '/usr/local/relax-1.3.8/test_suite/shared_data/model_free/S2_0.970_te_2048_R
>> ex_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: [0.90905506221773003, 74.369430109373241,
>> 1.2231015622343226]
>> Function value: -1447.7789206948669
>> Iterations: 22
>> Function calls: 50
>> Gradient calls: 50
>> Hessian calls: 0
>> Warning: None
>>
>>
>> k: 1 xk: array([ 0.90905506, 74.36943011, 1.22310156])
>> fk: 48.121371716785198
>> 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: [0.9949366307767159, 88.138505840636597,
>> -3.7928107170550836e-05]
>> Function value: 1.9644199913790175
>> 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, -3.79281072e-05])
>> fk: 144.63951390018761
>> 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:
>> 4.01470534795
>>
>> Parameter values: [0.97000000000210929, 2048.0000000116925,
>> 0.14899999998318531]
>> Function value: -7.1927065677039468e-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: 1.608820007827088e-20
>> Entering sub-algorithm.
>>
>> Quasi-Newton BFGS minimisation
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Line search: More and Thuente line search.
>>
>> k: 0 xk: [ 0.97, 2048, 0.149] fk:
>> 1.60882000783e-20
>>
>> Parameter values: [0.97000000000063913, 2048.0000000116925,
>> 0.14899999998315802]
>> Function value: 2.6640810074146136e-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: 2.6640810074146136e-21
>> Entering sub-algorithm.
>>
>> Quasi-Newton BFGS minimisation
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Line search: More and Thuente line search.
>>
>> k: 0 xk: [ 0.97, 2048, 0.149] fk:
>> 2.66408100741e-21
>>
>> Parameter values: [0.97000000000006137, 2048.0000000116925,
>> 0.14899999999883881]
>> Function value: 4.9272178768519757e-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: 4.9272178768519757e-23
>> Entering sub-algorithm.
>>
>> Quasi-Newton BFGS minimisation
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Line search: More and Thuente line search.
>>
>> k: 0 xk: [ 0.97, 2048, 0.149] fk:
>> 4.92721787685e-23
>>
>> Parameter values: [0.97000000000006137, 2048.0000000116925,
>> 0.14899999999883881]
>> Function value: 4.9272178768519757e-23
>> Iterations: 1
>> Function calls: 63
>> Gradient calls: 63
>> Hessian calls: 0
>> Warning: None
>>
>>
>> Parameter values: [0.97000000000006137, 2048.0000000116925,
>> 0.14899999999883881]
>> Function value: 4.9272178768519757e-23
>> Iterations: 120
>> Function calls: 381
>> Gradient calls: 381
>> Hessian calls: 0
>> Warning: None
>>
>> Traceback (most recent call last):
>> File "/usr/local/relax-1.3.8/test_suite/system_tests/model_free.py", line
>> 965, 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 "/usr/local/relax-1.3.8/test_suite/system_tests/model_free.py", line
>> 2500, in value_test
>> self.assert_(spin.f_count in f_count, msg=mesg)
>> AssertionError: Optimisation failure.
>>
>> System: Linux
>> Release: 2.6.28-17-generic
>> Version: #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009
>> Win32 version:
>> Distribution: Ubuntu 9.04 jaunty
>> Architecture: 32bit ELF
>> Machine: i686
>> Processor:
>> Python version: 2.6.2
>> Numpy version: 1.2.1
>> Libc version: glibc 2.4
>>
>> s2: 0.9700000000000614
>> te (ps): 2048.000000012
>> rex: 0.14899999999883881
>> chi2: 4.9272178768519757e-23
>> iter: 120
>> f_count: 381
>> g_count: 381
>> h_count: 0
>> warning: None
>>
>>
>> ----------------------------------------------------------------------
>> Ran 204 tests in 732.632s
>>
>> FAILED (failures=2)
>>
>>
>>
>>
>> ##############
>> # Unit tests #
>> ##############
>>
>>
>> ............................................................................
>> ............................................................................
>> ............................................................................
>> ............................................................................
>> ............................................................................
>> ............................................................................
>> ............................................................................
>> ............................................................................
>> ............................................................................
>> ............................................................................
>> ............................................................................
>> ............................................................................
>> ............................................................................
>> ............................................................................
>> ............................................................................
>> ............................................................................
>> .......................
>> ----------------------------------------------------------------------
>> Ran 1239 tests in 31.194s
>>
>> OK
>>
>>
>>
>>
>> ###################################
>> # Summary of the relax test suite #
>> ###################################
>>
>>
>> # Optional packages/modules
>> ###########################
>>
>> No tests skipped due to missing modules.
>>
>> # Synopsis
>> ##########
>>
>> System/functional tests ......................................... [ Failed ]
>> Unit tests ...................................................... [ OK ]
>> Synopsis ........................................................ [ Failed ]
>>
>>
>>
>> -----Original Message-----
>> From: [email protected] [mailto:[email protected]] On
>> Behalf Of Edward d'Auvergne
>> Sent: quinta-feira, 27 de Janeiro de 2011 16:48
>> To: Tiago Pais
>> Cc: [email protected]
>> Subject: Re: Segmentation Fault on Relax - 1.3.7
>>
>> Hi,
>>
>> Thanks for testing that. The optimisation failures are not failures
>> of relax, but that it is a new platform where optimisation is a tiny
>> bit different. I'm collecting all the information about these, and
>> adding exceptions for each machine. I might have to turn this off
>> though. You'll see that the optimised pararameters will be
>> nevertheless very close to those in the test name
>> 'test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149'. If you could
>> email more of the information from the system test, this would be
>> quite useful to make this test pass. There should be a long print out
>> like:
>>
>> --------------------------------------
>> System: Darwin
>> Release: 9.8.0
>> Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009;
>> root:xnu-1228.15.4~1/RELEASE_I386
>> Win32 version:
>> Distribution:
>> Architecture: 64bit
>> Machine: i386
>> Processor: i386
>> Python version: 2.6.2
>> numpy version: 1.3.0
>>
>> s2: 0.9699999999999785
>> te: 2047.9999999962433
>> rex: 0.14900000000039709
>> chi2: 5.2479491342506911e-24
>> iter: 162
>> f_count: 758
>> g_count: 169
>> h_count: 0
>> warning: None
>> --------------------------------------
>>
>> before the traceback message you posted. This is the information
>> needed. But everything should be fine, just that you won't be able to
>> run relaxation curve-fitting for the R1 and R2 until the module is
>> compiled. The python version I compiled on (2.6.5) is similar enough
>> to your 2.6.2 - this is not the issue. Maybe the numpy version is the
>> problem - I compiled on 1.4.1 and you are using 1.2.1. They could
>> have introduced an incompatibility. If you can install the numpy
>> headers package and scons, you'll be able to compile without problem
>> by typing 'scons'.
>>
>> Cheers,
>>
>> Edward
>>
>>
>>
>>
>> On 27 January 2011 12:14, Tiago Pais <[email protected]> wrote:
>>> Thank you Edward,
>>> Renaming the relax_fit.so did the job! Nice catch!
>>>
>>> However, when running the test suite it is falling in the
>> System/Functional
>>> tests:
>>>
>>> Traceback (most recent call last):
>>> File "/usr/local/relax-1.3.7/test_suite/system_tests/model_free.py", line
>>> 677, 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 "/usr/local/relax-1.3.7/test_suite/system_tests/model_free.py", line
>>> 2051, in value_test
>>> self.assert_(spin.f_count in f_count, msg=mesg)
>>> AssertionError: Optimisation failure.
>>>
>>>
>>> And this is the output information from relax --info (v1.3.8)
>>>
>>> Hardware information:
>>> Machine: i686
>>> Processor:
>>>
>>> System information:
>>> System: Linux
>>> Release: 2.6.28-17-generic
>>> Version: #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009
>>> GNU/Linux version: Ubuntu 9.04 jaunty
>>> Distribution: Ubuntu 9.04 jaunty
>>> Full platform string:
>>> Linux-2.6.28-17-generic-i686-with-Ubuntu-9.04-jaunty
>>>
>>> Software information:
>>> Architecture: 32bit ELF
>>> Python version: 2.6.2
>>> Python branch: branches/release26-maint
>>> Python build: release26-maint, Apr 19 2009 01:56:41
>>> Python compiler: GCC 4.3.3
>>> Python implementation: CPython
>>> Python revision:
>>> Numpy version: 1.2.1
>>> Libc version: glibc 2.4
>>>
>>> Python packages (most are optional):
>>>
>>> Package Installed Version Path
>>> minfx True Unknown
>>> /usr/local/relax-1.3.8/minfx
>>> bmrblib False
>>> numpy True 1.2.1
>>> /usr/lib/python2.6/dist-packages/numpy
>>> ScientificPython True 2.4.11
>>> /usr/lib/python2.6/dist-packages/Scientific
>>> wxPython False
>>> mpi4py False
>>> epydoc False
>>> optparse True 1.5.3
>>> /usr/lib/python2.6/optparse.pyc
>>> Numeric True 24.2
>>> /usr/lib/python2.6/dist-packages/Numeric/Numeric.pyc
>>> readline True
>>> /usr/lib/python2.6/lib-dynload/readline.so
>>> profile True
>>> /usr/lib/python2.6/profile.pyc
>>> bz2 True
>>> /usr/lib/python2.6/lib-dynload/bz2.so
>>> gzip True
>>> /usr/lib/python2.6/gzip.pyc
>>> os.devnull True
>>> /usr/lib/python2.6/os.pyc
>>>
>>> Compiled relax C modules:
>>> Relaxation curve fitting: False
>>>
>>> I have not tried the "scons" possibility that you suggested.
>>>
>>> Regards,
>>> TiagoP
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: [email protected] [mailto:[email protected]] On
>>> Behalf Of Edward d'Auvergne
>>> Sent: quarta-feira, 26 de Janeiro de 2011 19:56
>>> To: Tiago Pais
>>> Cc: [email protected]
>>> Subject: Re: Segmentation Fault on Relax - 1.3.7
>>>
>>> Hi,
>>>
>>> This is strange! Do the source code versions work ok? It could be
>>> the a strange combination of python and numpy, together with relax's C
>>> modules. You could possibly remove (or rename) the
>>> maths_fns/relax_fit.so file and try again. It would be useful to have
>>> information about the system to work out what is happening. You can
>>> get all the relevant info by typing:
>>>
>>> $ relax --info
>>>
>>> This is assuming relax will run at all. Another option would be if
>>> you have 'scons', 'numpy', and 'numpy-devel' (or something like that)
>>> installed. You could then type:
>>>
>>> $ scons clean_all
>>>
>>> to remove the compiled C module, and
>>>
>>> $ scons
>>>
>>> to build it again. I hope this helps!
>>>
>>> Cheers,
>>>
>>> Edward
>>>
>>>
>>>
>>> On 26 January 2011 19:35, Tiago Pais <[email protected]> wrote:
>>>> Dear all,
>>>> Surely this should be a very silly mistake of mine but I can not manage
>> to
>>>> put to work any of the relax versions above 1.3.6.
>>>> I just get the message "Segmentation fault" when I type "relax"
>>>>
>>>> Do I need to uninstall the previous 1.3.4 version?
>>>> For now I would like to keep the old one since I have things analyzed on
>>>> that one.
>>>>
>>>> Any help would be much appreciated.
>>>> Cheers
>>>> Tiago P
>>>>
>>>>
>>>>
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>>>>
>>>>
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>>>>
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