Re: crash on save in 1.3.0 tag -- April 10, 2007

Hi,

I'm sorry that I was unable to respond to emails last week.  That week
was my last at Melbourne Uni and I had to pack and prepare for my
postdoc position in Europe which will be starting soon.

As for the error, I'm not sure what is happening.  Each Element
container corresponding to a residue for which relaxation data has
been loaded must have the 'num_ri' variable.  The script is definitely
not the source of the error and I can't find the problem reported in
the bug tracker (https://gna.org/bugs/?group=relax).  Would you like
to have a go at trying to find the bug Gary?  Could you run the script
using relax version 1.2.10, 1.3.0, or the 1.2 repository line to see
if the bug is located in that code as well or if it is something which
is solely found in the code of the multi_processor branch?  I've
looked at the code and know how I could modify it so that the error is
avoided when using the results.write() user function, however that
would be a temporary solution and source of the error will probably
affect other parts of relax.  For any spin with relaxation data,
'num_ri' has to exist.

Cheers,

Edward


On 3/30/07, Gary S. Thompson <garyt@xxxxxxxxxxxxxxx> wrote:

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)


regards
gary

--
-------------------------------------------------------------------
Dr Gary Thompson
Astbury Centre for Structural Molecular Biology,
University of Leeds, Astbury Building,
Leeds, LS2 9JT, West-Yorkshire, UK             Tel. +44-113-3433024
email: garyt@xxxxxxxxxxxxxxx                   Fax  +44-113-2331407
-------------------------------------------------------------------



_______________________________________________
relax (http://nmr-relax.com)

This is the relax-devel mailing list
relax-devel@xxxxxxx

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

Re: crash on save in 1.3.0 tag

Header

Content

Related Messages