Hi Michael,
I just tested this change, but unfortunately it does not solve bug
#17317 (https://gna.org/bugs/index.php?17317). We will need to find a
different solution to this :S I would suggest reverting this change,
and then trying to find another solution. I'm looking into this now
to terminate threads cleanly. To trigger the problem, attempt a
model-free analysis and exit at different points during execution.
Sometimes it exists cleanly. At other times, errors are thrown. Some
examples are given below, as you'll see it's very messy.
Regards,
Edward
### Example 1 ###
[edward@localhost relax_gui]$ /data/relax/branches/bieri_gui/relax -g
Thank you for citing:
relaxGUI
========
Bieri, M., d'Auvergne, E. J. and Gooley, P. R. (2010). relaxGUI: a new
software for fast and simple
NMR relaxation data analysis and calculation of ps-ns and micro-s
motion of proteins (submitted).
relax
=====
d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
dynamic models I. Minimisation
algorithms and their performance within the model-free and Brownian
rotational diffusion spaces. J.
Biomol. NMR, 40(2), 107-119 (http://dx.doi.org/10.1007/s10858-007-9214-2).
d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
dynamic models II. A new methodology
for the dual optimisation of the model-free parameters and the
Brownian rotational diffusion tensor.
J. Biomol. NMR, 40(2), 121-133 (http://dx.doi.org/10.1007/s10858-007-9213-3).
Unhandled exception in thread started by <bound method
Auto_model_free.execute_thread of
<gui_bieri.analyses.auto_model_free.Auto_model_free instance at
0x7f4943291d88>>
[edward@localhost relax_gui]$
### Example 2 ###
[edward@localhost relax_gui]$ /data/relax/branches/bieri_gui/relax -g
Thank you for citing:
relaxGUI
========
Bieri, M., d'Auvergne, E. J. and Gooley, P. R. (2010). relaxGUI: a new
software for fast and simple
NMR relaxation data analysis and calculation of ps-ns and micro-s
motion of proteins (submitted).
relax
=====
d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
dynamic models I. Minimisation
algorithms and their performance within the model-free and Brownian
rotational diffusion spaces. J.
Biomol. NMR, 40(2), 107-119 (http://dx.doi.org/10.1007/s10858-007-9214-2).
d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
dynamic models II. A new methodology
for the dual optimisation of the model-free parameters and the
Brownian rotational diffusion tensor.
J. Biomol. NMR, 40(2), 121-133 (http://dx.doi.org/10.1007/s10858-007-9213-3).
Unhandled exception in thread started by
Traceback (most recent call last):
File "/data/relax/branches/bieri_gui/gui_bieri/analyses/auto_model_free.py",
line 871, in execute_thread
dAuvergne_protocol(save_dir=data.save_dir,
diff_model=global_model, mf_models=data.mf_models,
local_tm_models=data.local_tm_models, pdb_file=data.structure_file,
seq_args=data.seq_args, het_name=data.het_name,
relax_data=data.relax_data, unres=data.unres, exclude=data.exclude,
bond_length=data.bond_length, csa=data.csa, hetnuc=data.hetnuc,
proton=data.proton, grid_inc=data.inc, min_algor=data.min_algor,
mc_num=data.mc_num, max_iter=data.max_iter, conv_loop=data.conv_loop)
File "/data/relax/branches/bieri_gui/auto_analyses/dauvergne_protocol.py",
line 282, in __init__
self.multi_model(local_tm=True)
File "/data/relax/branches/bieri_gui/auto_analyses/dauvergne_protocol.py",
line 842, in multi_model
self.interpreter.relax_data.read(ri_label=data[0],
frq_label=data[1], frq=data[2], file=data[3], dir=data[4],
mol_name_col=data[5], res_num_col=data[6], res_name_col=data[7],
spin_num_col=data[8], spin_name_col=data[9], data_col=data[10],
error_col=data[11], sep=data[12])
File "/data/relax/branches/bieri_gui/prompt/relax_data.py", line 319, in
read
relax_data.read(ri_label=ri_label, frq_label=frq_label, frq=frq,
file=file, dir=dir, spin_id_col=spin_id_col,
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col, data_col=data_col, error_col=error_col,
sep=sep, spin_id=spin_id)
File "/data/relax/branches/bieri_gui/generic_fns/relax_data.py",
line 660, in read
pack_data(ri_label, frq_label, frq, values, errors, ids)
File "/data/relax/branches/bieri_gui/generic_fns/relax_data.py",
line 570, in pack_data
spin = return_spin(id)
File "/data/relax/branches/bieri_gui/generic_fns/mol_res_spin.py",
line 1910, in return_spin
if (mol, res, spin) not in select_obj[i]:
File "/data/relax/branches/bieri_gui/generic_fns/mol_res_spin.py",
line 147, in __contains__
return (obj in self._intersect[0]) and (obj in self._intersect[1])
File "/data/relax/branches/bieri_gui/generic_fns/mol_res_spin.py",
line 155, in __contains__
return self.__contains_mol_res_spin_containers(obj)
File "/data/relax/branches/bieri_gui/generic_fns/mol_res_spin.py",
line 240, in __contains_mol_res_spin_containers
elif relax_re.search(self.residues, res.name) or res.num in self.residues:
File "/data/relax/branches/bieri_gui/generic_fns/relax_re.py", line
75, in search
pattern_re = replace(pattern, '*', '.*')
TypeError: 'NoneType' object is not callable
[edward@localhost relax_gui]$
### Example 3 ###
[edward@localhost relax_gui]$ /data/relax/branches/bieri_gui/relax -g
Searching through 11 grid nodes.
k: 0 xk: [ 1000] fk: 10173.3877242
k: 3 xk: [ 4300] fk: 7779.43338854
k: 4 xk: [ 5400] fk: 5092.82647948
k: 5 xk: [ 6500] fk: 3214.5918094
k: 6 xk: [ 7600] fk: 1967.6701103
k: 7 xk: [ 8700] fk: 1157.37203626
k: 8 xk: [ 9800] fk: 641.974121519
k: 9 xk: [ 10900] fk: 327.772091917
k: 10 xk: [ 12000] fk: 154.295417958
Thank you for citing:
relaxGUI
========
Bieri, M., d'Auvergne, E. J. and Gooley, P. R. (2010). relaxGUI: a new
software for fast and simple
NMR relaxation data analysis and calculation of ps-ns and micro-s
motion of proteins (submitted).
relax
=====
d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
dynamic models I. Minimisation
algorithms and their performance within the model-free and Brownian
rotational diffusion spaces. J.
Biomol. NMR, 40(2), 107-119 (http://dx.doi.org/10.1007/s10858-007-9214-2).
d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
dynamic models II. A new methodology
for the dual optimisation of the model-free parameters and the
Brownian rotational diffusion tensor.
J. Biomol. NMR, 40(2), 121-133 (http://dx.doi.org/10.1007/s10858-007-9213-3).
Fitting to spin ':149&:thr@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unhandled exception in thread started by
Traceback (most recent call last):
File "/data/relax/branches/bieri_gui/gui_bieri/analyses/auto_model_free.py",
line 871, in execute_thread
dAuvergne_protocol(save_dir=data.save_dir,
diff_model=global_model, mf_models=data.mf_models,
local_tm_models=data.local_tm_models, pdb_file=data.structure_file,
seq_args=data.seq_args, het_name=data.het_name,
relax_data=data.relax_data, unres=data.unres, exclude=data.exclude,
bond_length=data.bond_length, csa=data.csa, hetnuc=data.hetnuc,
proton=data.proton, grid_inc=data.inc, min_algor=data.min_algor,
mc_num=data.mc_num, max_iter=data.max_iter, conv_loop=data.conv_loop)
File "/data/relax/branches/bieri_gui/auto_analyses/dauvergne_protocol.py",
line 282, in __init__
self.multi_model(local_tm=True)
File "/data/relax/branches/bieri_gui/auto_analyses/dauvergne_protocol.py",
line 866, in multi_model
self.interpreter.grid_search(inc=self.grid_inc)
File "/data/relax/branches/bieri_gui/prompt/minimisation.py", line
106, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/data/relax/branches/bieri_gui/generic_fns/minimise.py", line
133, in grid_search
grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File
"/data/relax/branches/bieri_gui/specific_fns/model_free/mf_minimise.py",
line 1174, in grid_search
self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File
"/data/relax/branches/bieri_gui/specific_fns/model_free/mf_minimise.py",
line 1382, in minimise
param_vector = self._assemble_param_vector(spin=spin, sim_index=sim_index)
File "/data/relax/branches/bieri_gui/specific_fns/model_free/main.py",
line 182, in _assemble_param_vector
model_type = self._determine_model_type()
File "/data/relax/branches/bieri_gui/specific_fns/model_free/main.py",
line 688, in _determine_model_type
if not exists_mol_res_spin_data():
File "/data/relax/branches/bieri_gui/generic_fns/mol_res_spin.py",
line 1211, in exists_mol_res_spin_data
if dp.mol.is_empty():
File "/data/relax/branches/bieri_gui/data/mol_res_spin.py", line
639, in is_empty
if len(self) == 1 and self[0].is_empty():
File "/data/relax/branches/bieri_gui/data/mol_res_spin.py", line
572, in is_empty
if match("^__", name):
TypeError: 'NoneType' object is not callable
On 15 December 2010 00:56, <michael.bieri@xxxxxxxxxxxxx> wrote:
Author: michaelbieri
Date: Wed Dec 15 00:56:30 2010
New Revision: 11822
URL: http://svn.gna.org/viewcvs/relax?rev=11822&view=rev
Log:
relaxGUI job is killed upon exiting the program.
This is to completely kill running threads, which can't be controlled under
Python. The error was detected by Edward d'Auvergne reported at
https://gna.org/bugs/index.php?17317.
Modified:
branches/bieri_gui/gui_bieri/relax_gui.py
Modified: branches/bieri_gui/gui_bieri/relax_gui.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/gui_bieri/relax_gui.py?rev=11822&r1=11821&r2=11822&view=diff
==============================================================================
--- branches/bieri_gui/gui_bieri/relax_gui.py (original)
+++ branches/bieri_gui/gui_bieri/relax_gui.py Wed Dec 15 00:56:30 2010
@@ -362,16 +362,8 @@
text = text + '\n'
sys.__stdout__.write(text)
- # Destroy all dialogs.
- self.controller.Destroy()
- self.dialog_about_gui.Destroy()
- self.dialog_about_relax.Destroy()
- self.relax_prompt.Destroy()
- self.mol_res_spin_tree.Destroy()
- self.user_functions.destroy()
-
- # Destroy the main window.
- self.Destroy()
+ # End application.
+ sys.exit()
def import_seq(self, event):
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Re: r11822 - /branches/bieri_gui/gui_bieri/relax_gui.py