URL:
<http://gna.org/bugs/?8953>
Summary: crash on save mc save
Project: relax
Submitted by: varioustoxins
Submitted on: Monday 16/04/07 at 23:56
Category: relax's source code
Severity: 4 - Important
Priority: 7 - High
Status: None
Privacy: Public
Assigned to: None
Originator Name:
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Release: 1.3.0
Operating System: All systems
_______________________________________________________
Details:
The following script crashes at result.write with
relax> results.write(run='m1', file='results', dir='m1', force=1,
format='columnar', compress_type=1)
Opening the file 'm1/results.bz2' for writing.
Traceback (most recent call last):
File "../relax", line 591, in ?
multi_processor.run()
File
"/usr/jessy/garyt/projects/relax_branch/branch_multi1/multi/uni_processor.py",
line 106, in run
self.relax_instance.run()
File "../relax", line 175, in run
self.interpreter.run()
File
"/usr/jessy/garyt/projects/relax_branch/branch_multi1/prompt/interpreter.py",
line 216, in run
run_script(intro=self.relax.intro_string, local=self.local,
script_file=self.relax.script_file, quit=1)
File
"/usr/jessy/garyt/projects/relax_branch/branch_multi1/prompt/interpreter.py",
line 392, in run_script
console.interact(intro, local, script_file, quit)
File
"/usr/jessy/garyt/projects/relax_branch/branch_multi1/prompt/interpreter.py",
line 343, in interact_script
execfile(script_file, local)
File "test_multimodel_mc.py", line 75, in ?
results.write(run=name, file='results', force=1)
File
"/usr/jessy/garyt/projects/relax_branch/branch_multi1/prompt/results.py",
line 201, in write
self.__relax__.generic.results.write(run=run, file=file, directory=dir,
force=force, format=format, compress_type=compress_type)
File
"/usr/jessy/garyt/projects/relax_branch/branch_multi1/generic_fns/results.py",
line 166, in write
self.write_function(results_file, run)
File
"/usr/jessy/garyt/projects/relax_branch/branch_multi1/specific_fns/model_free.py",
line 5177, in write_columnar_results
for l in xrange(data.num_ri):
AttributeError: Element instance has no attribute 'num_ri'
# Script for model-free analysis.
dataPaths = ['test_data/noe600_hgts.dat',
'test_data/T1-500_051205_hgts.bs',
'test_data/T1-600_hgts.bs',
'test_data/T2-500_061205_hgts.bs',
'test_data/T2-600_hgts.bs',
'test_data/noe750.dat',
'test_data/T1_750_hgts.bs',
'test_data/T2_750_hgts.bs']
dataTypes = [('NOE', '600', 599.8e6),
('R1', '500', 499.8e6),
('R1', '600', 599.8e6),
('R2', '500', 499.8e6),
('R2', '600', 599.8e6),
('NOE', '750', 750.8e6),
('R1', '750', 750.8e6),
('R2', '750', 750.8e6)]
# Set the run names (also the names of preset model-free models).
#runs = ['tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9']
runs = ['m1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
# Nuclei type
nuclei('N')
# Loop over the runs.
for name in runs:
# Create the run.
run.create(name, 'mf')
# Load the sequence.
#sequence.read(name, 'noe.500.out')
# Load a PDB file.
#pdb(name, 'test_data/test.pdb', proton='HN')
structure.read_pdb(name, 'test_data/test.pdb')
structure.vectors(name, proton='HN')
# Load the relaxation data.
for dataSet in xrange(len(dataPaths)):
relax_data.read(name, dataTypes[dataSet][0], dataTypes[dataSet][1],
dataTypes[dataSet][2], dataPaths[dataSet])
# Setup other values.
diffusion_tensor.init(name, 1e-8, fixed=1)
#diffusion_tensor.init(name, (1e-8, 1.0, 60, 290), param_types=0,
spheroid_type='oblate', fixed=0)
value.set(name, 1.02 * 1e-10, 'bond_length')
value.set(name, -160 * 1e-6, 'csa')
#value.set(name, 0.970, 's2')
#value.set(name, 1.0, 's2f')
#value.set(name, 2048e-12, 'te')
#value.set(name, 2048e-12, 'tf')
#value.set(name, 2048e-12, 'ts')
#value.set(name, 0.149/(2*pi*600e6)**2, 'rex')
# Select the model-free model.
model_free.select_model(run=name, model=name)
#fix(name, 'all_res')
# Minimise.
grid_search(name, inc=11)
minimise('newton', run=name)
# Monte Carlo simulations.
monte_carlo.setup(name, number=100)
monte_carlo.create_data(name)
monte_carlo.initial_values(name)
minimise('newton', run=name)
eliminate(run=name)
monte_carlo.error_analysis(name)
# Write the results.
results.write(run=name, file='results', force=1)
# Save the program state.
state.save('save', force=1)
note the bug most probably depends on chris macrailds selection testing data
sets (attached) which stress test selections with data sets with dat for
specific residues missing etc
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Monday 16/04/07 at 23:56 Name: chris_test_data.tar.gz Size: 17kB
By: varioustoxins
<http://gna.org/bugs/download.php?file_id=2236>
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?8953>
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[bug #8953] crash on save mc save