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List: relax-users
Subject: Re: error while running relax-GUI tutorial
From: "Edward d'Auvergne" <edward () nmr-relax ! com>
Date: 2014-11-24 9:18:10
Message-ID: CAED9pY_sKqZ59mRL93mvMXTHr6QCTkHMGVdVB1BrxGs2k5+i0w () mail ! gmail ! com
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Hi Prem,
From the error message, this is within the automated analysis for
relaxation dispersion. Creating the data pipe 'R2eff - relax_disp
(Mon Nov 17 10:50:08 2014)' can only happen once, as the 'R2eff' model
is only optimised once (there is a loop over all models). There is
only one thing I can think of, and that is that the analysis was run
with OpenMPI. However if the "--multi='mpi4py'" part of the full
command:
$ mpirun -np 8 relax --multi='mpi4py'
is missing, as:
$ mpirun -np 8 relax
Then this problem might be encountered. Could that be what happened?
Another cause could be if the 'R2eff' model is passed into the
dispersion auto-analysis more than once in the model list though, as
you are using the GUI, this is not possible.
Cheers,
Edward
On 18 November 2014 at 22:58, Prem Raj Joseph <prbj123relax@gmail.com> wrote:
> Hello Edward,
>
> I tried the GUI version of the setup again for the relaxation dispersion
> (on the test data) and it ran without any error this time. Its possible I
> made some mistake during the setup thr last time.
>
> Thank again for the help
>
> Prem
>
>
>
> On Tue, Nov 18, 2014 at 5:27 AM, Edward d'Auvergne <edward@nmr-relax.com>
> wrote:
>
>> Hi Troels and Prem,
>>
>> Troels, for a suggestion for improving the script in your tutorial,
>> you could use:
>>
>> """
>> from time import asctime, localtime
>>
>> pipe_bundle = "relax_disp (%s)" % asctime(localtime())
>> pipe_name = "origin - %s" % pipe_bundle
>> """
>>
>> This is how the new analysis wizard in relax creates these names
>> (
>> http://www.nmr-relax.com/api/3.3/gui.analyses.wizard-pysrc.html#Data_pipe_page.on_display
>> ).
>> This script really saves a lot of time. But, as it does not replicate
>> the bug, Prem, could you still create the bug report and include all
>> steps required to produce the error you observed?
>>
>> Cheers,
>>
>> Edward
>>
>>
>>
>> On 18 November 2014 12:08, Troels Emtekær Linnet <tlinnet@nmr-relax.com>
>> wrote:
>> > Hi Prem.
>> >
>> > I added the tutorial here:
>> >
>> >
>> http://wiki.nmr-relax.com/Tutorial_for_The_relaxation_dispersion_auto-analysis_in_the_GUI
>> >
>> > I tried to take power of the scripting, to get around the tedious work on
>> > defining the experiment settings for all spectra.
>> >
>> > So this script should take you to the "end point" before staring the
>> > analysis.
>> >
>> > Best
>> > Troels
>> >
>> >
>> >
>> > 2014-11-18 11:51 GMT+01:00 Troels Emtekær Linnet <tlinnet@nmr-relax.com
>> >:
>> >
>> >> Dear Prem.
>> >>
>> >> Welcome to the mailing list!
>> >>
>> >> I guess that you mean the manual at:
>> >> http://www.nmr-relax.com/manual/Contents.html
>> >>
>> >> The relaxation dispersion auto-analysis in the GUI
>> >>
>> >>
>> http://www.nmr-relax.com/manual/The_relaxation_dispersion_auto_analysis_in_the_GUI.html
>> >>
>> >> Where the test data is in:
>> >> test_suite/shared_data/dispersion/Hansen
>> >>
>> >> I will write it up here as a script instead.
>> >> This goes a little faster testing.
>> >>
>> >> You can also find more inspiration at the wiki:
>> >> http://wiki.nmr-relax.com
>> >> http://wiki.nmr-relax.com/Category:Tutorials
>> >>
>> >> In terminal
>> >> mkdir -p $HOME/test
>> >> cd $HOME/test
>> >> gedit test.py
>> >>
>> >> Then I build the script onwards.
>> >> I run relax repeatedly, to execute code. Then I write new code in the
>> >> script, and run again.
>> >> relax test.py
>> >>
>> >> When I am satisfied, you can then do like this.
>> >>
>> >> relax -g -t log.txt
>> >> User functions -> Script -> test.py
>> >>
>> >> THEN:
>> >> View -> Data pipe editor -> Right click on pipe -> Associate with a new
>> >> Auto analysis
>> >>
>> >> This should bring you to a window, where all settings have been set.
>> >>
>> >> Relaxations dispersion models: ['R2eff', 'No Rex', 'CR72', 'NS CPMG
>> 2-site
>> >> expanded']
>> >> Grid increements: 11 (For speed-up in test phase)
>> >> Monte-Carlo simulations number: 5 (For speed up in test phase)
>> >>
>> >> Then a quick click on spin.isotope function, and GO.
>> >>
>> >>
>> >>
>> >> test.py
>> >> ----------------
>> >> #python modules
>> >> import os
>> >> import glob
>> >>
>> >> # relax modules
>> >> from lib.io import sort_filenames
>> >>
>> >> # Set path to data
>> >> data =
>> >>
>> '/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/shared_data/dispersion/Hansen'
>> >>
>> >> # Create the data pipe.
>> >> pipe_name = 'origin - relax_disp (Tue Nov 18 10:39:36 2014)'
>> >> pipe_bundle = 'relax_disp (Tue Nov 18 10:39:36 2014)'
>> >> pipe.create(pipe_name=pipe_name, bundle=pipe_bundle,
>> >> pipe_type='relax_disp')
>> >>
>> >> # Create spin to hold data.
>> >> sequence.read(file='fake_sequence.in', dir=data, res_num_col=1,
>> >> res_name_col=2)
>> >> deselect.read(file='unresolved', dir=data+os.sep+'500_MHz',
>> >> spin_id_col=None, mol_name_col=None, res_num_col=1, boolean='AND',
>> >> change_all=False)
>> >> deselect.read(file='unresolved', dir=data+os.sep+'800_MHz',
>> >> spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
>> >> boolean='AND', change_all=False)
>> >>
>> >> # Give the spins attributes.
>> >> spin.isotope(isotope='15N', spin_id='@*', force=True)
>> >> spin.name(name='N')
>> >>
>> >> # Do for 800.
>> >> ###############################################
>> >> # Change directory.
>> >> os.chdir(data + os.sep + '500_MHz')
>> >>
>> >> # Get the file list, and sort the file list Alphanumeric.
>> >> flist500 = glob.glob('*.in_sparky')
>> >> flist500 = sort_filenames(filenames=flist500)
>> >>
>> >> # Make ID
>> >> ID500 = []
>> >> for f in flist500: ID500.append("500_"+f.split(".in_sparky")[0])
>> >>
>> >> # Then Read
>> >> spectrum.read_intensities(file=flist500, spectrum_id=ID500)
>> >>
>> >> # Repeat for the replicated spectra.
>> >> flist500rep = glob.glob('*in.bis_sparky')
>> >> flist500rep = sort_filenames(filenames=flist500rep)
>> >>
>> >> # Make ID
>> >> ID500rep = []
>> >> for f in flist500rep:
>> >> ID500rep.append("500_"+f.split(".in.bis_sparky")[0]+'b')
>> >>
>> >> # Then Read
>> >> spectrum.read_intensities(file=flist500rep, spectrum_id=ID500rep)
>> >>
>> >> # Then map replicated
>> >> for b_id in ID500rep:
>> >> a_id = b_id[:-1]
>> >> spectrum.replicated(spectrum_ids=[a_id, b_id])
>> >>
>> >> # Then check
>> >> print cdp.replicates
>> >>
>> >> # Then repeat for 800.
>> >> ###############################################
>> >> # Change directory.
>> >> os.chdir(data + os.sep + '800_MHz')
>> >>
>> >> # Get the file list, and sort the file list Alphanumeric.
>> >> flist800 = glob.glob('*.in_sparky')
>> >> flist800 = sort_filenames(filenames=flist800)
>> >>
>> >> # Make ID
>> >> ID800 = []
>> >> for f in flist800: ID800.append("800_"+f.split(".in_sparky")[0])
>> >>
>> >> # Then Read
>> >> spectrum.read_intensities(file=flist800, spectrum_id=ID800)
>> >>
>> >> # Repeat for the replicated spectra.
>> >> flist800rep = glob.glob('*in.bis_sparky')
>> >> flist800rep = sort_filenames(filenames=flist800rep)
>> >>
>> >> # Make ID
>> >> ID800rep = []
>> >> for f in flist800rep:
>> >> ID800rep.append("800_"+f.split(".in.bis_sparky")[0]+'b')
>> >>
>> >> # Then Read
>> >> spectrum.read_intensities(file=flist800rep, spectrum_id=ID800rep)
>> >>
>> >> # Then map replicated
>> >> for b_id in ID800rep:
>> >> a_id = b_id[:-1]
>> >> spectrum.replicated(spectrum_ids=[a_id, b_id])
>> >>
>> >> # Then check
>> >> print cdp.replicates
>> >> ################################################
>> >> print len(ID500), len(ID500rep), len(ID800), len(ID800rep)
>> >>
>> >> # Then set spectrum properties
>> >> all_ID = ID500 + ID500rep + ID800 + ID800rep
>> >>
>> >> for cur_id in all_ID:
>> >> # Split from name
>> >> sfrq_str, vcpmg_str = cur_id.split("_")
>> >>
>> >> if vcpmg_str == 'reference':
>> >> vcpmg = None
>> >> else:
>> >> vcpmg = float(vcpmg_str.split("b")[0])
>> >> print cur_id, sfrq_str, vcpmg
>> >>
>> >> # Set the current experiment type.
>> >> relax_disp.exp_type(spectrum_id=cur_id, exp_type='SQ CPMG')
>> >>
>> >> # Set the NMR field strength of the spectrum.
>> >> spectrometer.frequency(id=cur_id, frq=float(sfrq_str), units='MHz')
>> >>
>> >> # Relaxation dispersion CPMG constant time delay T (in s).
>> >> relax_disp.relax_time(spectrum_id=cur_id, time=0.03)
>> >>
>> >> # Set the relaxation dispersion CPMG frequencies.
>> >> relax_disp.cpmg_setup(spectrum_id=cur_id, cpmg_frq=vcpmg)
>> >> -------------------------------------------------------
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> 2014-11-18 0:06 GMT+01:00 Prem Raj Joseph <prbj123relax@gmail.com>:
>> >> >
>> >> > Hello all,
>> >> >
>> >> > I was using the GUI version of the software to run the tutorial
>> available
>> >> > in the manual for analysis of relaxation dispersion.
>> >> > When i execute the run I get the following error
>> >> >
>> >> > RelaxPipeError: RelaxError: The data pipe 'R2eff - relax_disp (Mon
>> Nov 17
>> >> > 10:50:08 2014)' already exists.
>> >> >
>> >> > Not sure where the error is arising from. Any help is greatly
>> >> appreciated.
>> >> >
>> >> > Thanks
>> >> >
>> >> > Prem
>> >> >
>> >> > Department of Biochemistry and Molecular Biology
>> >> > Sealy Center for Structural Biology and Molecular Biophysics
>> >> > 5.142 Medical Branch Building
>> >> > University of Texas Medical Branch
>> >> > Galveston, TX 77555-1055
>> >> > Lab: 409-772-2181
>> >> > Cell: 409-354-8536
>> >> >
>> >> > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>> >> > Error analysis
>> >> > ==============
>> >> >
>> >> > Skipping the error analysis as it has already been performed.
>> >> >
>> >> > relax> relax_disp.r1_fit(fit=False)
>> >> >
>> >> >
>> >> >
>> >> > ---------------------
>> >> > - The 'R2eff' model -
>> >> > ---------------------
>> >> >
>> >> >
>> >> > relax> pipe.copy(pipe_from='origin - relax_disp (Mon Nov 17 10:50:08
>> >> > 2014)', pipe_to='R2eff - relax_disp (Mon Nov 17 10:50:08 2014)',
>> >> > bundle_to='relax_disp (Mon Nov 17 10:50:08 2014)')
>> >> > Exception raised in thread.
>> >> >
>> >> > Traceback (most recent call last):
>> >> > File "/home/prem/programs/relax-3.3.2/gui/analyses/execute.py", line
>> >> 87,
>> >> > in run
>> >> > self.run_analysis()
>> >> > File
>> "/home/prem/programs/relax-3.3.2/gui/analyses/auto_relax_disp.py",
>> >> > line 726, in run_analysis
>> >> > Relax_disp(pipe_name=self.data.pipe_name,
>> >> > pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir,
>> >> > models=self.data.models, grid_inc=self.data.inc,
>> >> > mc_sim_num=self.data.mc_sim_num,
>> exp_mc_sim_num=self.data.exp_mc_sim_num,
>> >> > pre_run_dir=self.data.pre_run_dir,
>> >> > mc_sim_all_models=self.data.mc_sim_all_models,
>> >> > insignificance=self.data.insignificance,
>> >> > numeric_only=self.data.numeric_only, r1_fit=self.data.r1_fit)
>> >> > File "/home/prem/programs/relax-3.3.2/auto_analyses/relax_disp.py",
>> >> line
>> >> > 137, in __init__
>> >> > self.run()
>> >> > File "/home/prem/programs/relax-3.3.2/auto_analyses/relax_disp.py",
>> >> line
>> >> > 614, in run
>> >> > self.interpreter.pipe.copy(pipe_from=self.pipe_name,
>> >> > pipe_to=model_pipe, bundle_to=self.pipe_bundle)
>> >> > File "/home/prem/programs/relax-3.3.2/prompt/uf_objects.py", line
>> 225,
>> >> in
>> >> > __call__
>> >> > self._backend(*new_args, **uf_kargs)
>> >> > File "/home/prem/programs/relax-3.3.2/pipe_control/pipes.py", line
>> 191,
>> >> > in copy
>> >> > raise RelaxPipeError(pipe_to)
>> >> > RelaxPipeError: RelaxError: The data pipe 'R2eff - relax_disp (Mon
>> Nov 17
>> >> > 10:50:08 2014)' already exists.
>> >> > _______________________________________________
>> >> > relax (http://www.nmr-relax.com)
>> >> >
>> >> > This is the relax-users mailing list
>> >> > relax-users@gna.org
>> >> >
>> >> > 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-users
>> >>
>> > _______________________________________________
>> > relax (http://www.nmr-relax.com)
>> >
>> > This is the relax-users mailing list
>> > relax-users@gna.org
>> >
>> > To unsubscribe from this list, get a password
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>> > visit the list information page at
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>>
> _______________________________________________
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>
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