Hi Troels,
I will upload a bug report with the pdb file, the script I use, and the
data I'm using.
Sincerely,
Sam
On Thu, Sep 29, 2016 at 2:25 PM, Troels Emtekær Linnet <
tlin...@nmr-relax.com> wrote:
> Hi Sam.
>
> Hm...
>
> I had a look in: pipe_control/minimise.py
>
> The trouble start with line
> "elif values[i] in [None, {}, []]:"
>
> Where the index "i" is running out of bounds.
>
> The index is drawn from range(n).
> n = len(names)
> names = api.get_param_names(model_info)
> values = api.get_param_values(model_info)
>
> So "something" is not aligned well in the data structures.
> It seems that the index of parameter names exceeds parameter values.
>
>
> One guess is, that the selection of
> * diff_model
> * mf_models
> * local_tm_models
>
> is not correctly set. But I reach my limit of being able to help you.
> Edward is the expert here, but he is on paternity leave.
>
>
> Another possibility is that some of the spins are in "select" mode, where
> they maybe should be in "deselect" mode.
>
> Maybe the spins do not carry any data from before, and somehow relax
> expect this.
>
> It's very tricky to figure out!
>
> A bug report, some minimum data, and a script which make the bug occur can
> solve this.
>
> Then I can write a systemtest, if it relax which is failing.
>
> Best
> Troels
>
>
>
>
> 2016-09-29 0:23 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>
>> Hi Troels,
>> Update on both proteins: So for protein 1, I can upload all the spins (H
>> and N), but then I recieve an error. This is the error I recieved for
>> protein 2 as well. These are both dimer pdb files. Meaning they have 2 sets
>> (set A) and set (B) (e.g. http://www.rcsb.org/pdb/explor
>> e/explore.do?structureId=1DJ8 this pdb protein has 4 sets, A,B,C, and D
>> ours only have A and B). For both these proteins I recieve this error
>> File "/home/crowlab/relax-4.0.2/multi/processor.py", line 494, in run
>> self.callback.init_master(self)
>> File "/home/crowlab/relax-4.0.2/multi/__init__.py", line 318, in
>> default_init_master
>> self.master.run()
>> File "/home/crowlab/relax-4.0.2/relax.py", line 199, in run
>> self.interpreter.run(self.script_file)
>> File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 279, in
>> run
>> return run_script(intro=self.__intro_string, local=locals(),
>> script_file=script_file, show_script=self.__show_script,
>> raise_relax_error=self.__raise_relax_error)
>> File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 585, in
>> run_script
>> return console.interact(intro, local, script_file,
>> show_script=show_script, raise_relax_error=raise_relax_error)
>> File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 484, in
>> interact_script
>> exec_script(script_file, local)
>> File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 363, in
>> exec_script
>> runpy.run_module(module, globals)
>> File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
>> fname, loader, pkg_name)
>> File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
>> exec code in run_globals
>> File "/home/crowlab/relax-4.0.2/RGS4_modelfree_sample_script.py", line
>> 31, in <module>
>> dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,di
>> ff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=LOCA
>> L_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_sim_
>> num=MC_NUM,conv_loop=CONV_LOOP)
>> File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>> line 246, in __init__
>> self.execute()
>> File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>> line 600, in execute
>> self.multi_model(local_tm=True)
>> File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>> line 888, in multi_model
>> self.interpreter.minimise.grid_search(inc=self.grid_inc)
>> File "/home/crowlab/relax-4.0.2/prompt/uf_objects.py", line 225, in
>> __call__
>> self._backend(*new_args, **uf_kargs)
>> File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 172,
>> in grid_search
>> model_lower, model_upper, model_inc = grid_setup(lower, upper, inc,
>> verbosity=verbosity, skip_preset=skip_preset)
>> File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 341,
>> in grid_setup
>> elif values[i] in [None, {}, []]:
>> IndexError: index out of bounds
>>
>> Which from my understanding basically means, the co-ordinates of the
>> spins are out of the acceptable range for relax. I've checked all the
>> co-ordinates for both, nothing is extreme or outlandish (all within a range
>> of -20 to 20).
>> Is relax unable to process pdb files that are dimers (with 2 sets A and
>> B).? Furthermore, is it unable to process trimers and tetramers?
>>
>> Sincerely,
>> Sam
>>
>> On Wed, Sep 28, 2016 at 1:44 PM, Mahdi, Sam <sam.mahdi....@my.csun.edu>
>> wrote:
>>
>>> Hey Troels,
>>>
>>> I ran the relax -x and recieve this error at the GUI tests
>>> =============
>>> = GUI tests =
>>> =============
>>>
>>> ........................**
>>> Gtk:ERROR:gtkfilesystemmodel.c:746:gtk_file_system_model_sort:
>>> assertion failed: (r == n_visible_rows)
>>> Abort (core dumped)
>>> crowlab: [~/relax-4.0.2]>
>>>
>>>
>>> On Wed, Sep 28, 2016 at 1:30 PM, Mahdi, Sam <sam.mahdi....@my.csun.edu>
>>> wrote:
>>>
>>>> Hi Troels,
>>>>
>>>> An update on protein number 1: I have successfully resolved the
>>>> problem. Initially the pdb file had HN instead of just H for the backbone
>>>> hydrogens. So it couldn't read it. I changed all the HN to H. Then I
>>>> recieved the error
>>>> RelaxError: Multiple alternate location indicators are present in the
>>>> PDB file, but the desired coordinate set has not been specified
>>>> By removing the extra N, all the text for the 3D location (the
>>>> co-ordinates) for the HN were shifted a space (no longer aligned). Once I
>>>> aligned them all, relax was able to read all the spins. So its working now.
>>>> I'm currently running the test suite as well.
>>>>
>>>> Sincerely,
>>>> Sam
>>>>
>>>> On Wed, Sep 28, 2016 at 11:45 AM, Troels Emtekær Linnet <
>>>> tlin...@nmr-relax.com> wrote:
>>>>
>>>>> To test the speed difference between script and GUI,
>>>>> you could try to run the full test-suite through the terminal or
>>>>> inside the GUI.
>>>>>
>>>>> That should give you a clue about time difference.
>>>>>
>>>>>
>>>>> 2016-09-28 20:32 GMT+02:00 Troels Emtekær Linnet <
>>>>> tlin...@nmr-relax.com>:
>>>>>
>>>>>> If you get different results, for the same setup, this is not good.
>>>>>> Not at all !
>>>>>>
>>>>>> Have you run the full relax test suite after installation?
>>>>>>
>>>>>> http://wiki.nmr-relax.com/Installation_test
>>>>>>
>>>>>> run it with:
>>>>>> relax -x
>>>>>>
>>>>>> This takes about 1 Hour to run, and should not be used with multiple
>>>>>> processors.
>>>>>>
>>>>>> Relax will test itself with thousands of unit tests and system tests,
>>>>>> and confer that all
>>>>>> results are the same.
>>>>>>
>>>>>> If the system tests do not pass on each system, something fishy is
>>>>>> going on.
>>>>>>
>>>>>> This is the best line of defence against "systems" acting weird due
>>>>>> to software/packages etc. etc.
>>>>>>
>>>>>> Best
>>>>>> Troels
>>>>>>
>>>>>>
>>>>>>
>>>>>> 2016-09-28 9:44 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>>>>>>
>>>>>>> Hi Troels,
>>>>>>>
>>>>>>> I wanted to give a bit of feedback on the results I've obtained
>>>>>>> throughout the few weeks I've been using model free on relax. First off,
>>>>>>> thank you guys (both you and Edward) immensly for your patience and
>>>>>>> help as
>>>>>>> I attempted to understand and work relax. Secondly, I have noticed a
>>>>>>> difference between using the gui and the terminal (using scripts to run
>>>>>>> relax). I've currently finished about 3 runs using the gui, and 3 runs
>>>>>>> using the terminal (all the same data sets, same pdb files, same
>>>>>>> settings,
>>>>>>> etc.). The gui takes about a week to finish, where the terminal takes
>>>>>>> approximately 24 hours. I've tried this on 2 proteins, both had the same
>>>>>>> results. The terminal is by far, much faster than the gui. Finally, I've
>>>>>>> run 1 protein on 2 different computers (one using the multi-processor
>>>>>>> platform, and on another computer, single-processor). The data sets were
>>>>>>> all the same, the same pdb file, etc. , but the results I obtained from
>>>>>>> the
>>>>>>> computers were slightly different. For the most part, most of the
>>>>>>> difference in the data was similar, slightly different, but within the
>>>>>>> error. But there were about 7 or 8 data points that appeared in one run
>>>>>>> on
>>>>>>> one computer, and were absent in another run on another computer. This
>>>>>>> happened in both the S^2 I analyzed and the Rex.
>>>>>>> I.e. On the fedora 20 (single processor), say I had S^2 values for
>>>>>>> amino acid 24,25 and 26 in the sequence, but not for 28,29, and 30. On
>>>>>>> the
>>>>>>> fedora 24 (multi-processor), I might be missing a value for amino acid
>>>>>>> 24,
>>>>>>> but I would have S^2 values for 28,29 and 30. Note the data sets are all
>>>>>>> the same, the pdb files the same, settings the same, I used the same
>>>>>>> script
>>>>>>> for both. The only difference between these runs is they were run on
>>>>>>> different computer and one was single processor well another was multi.
>>>>>>> I don't know why I obtained different data from 2 different runs,
>>>>>>> when the input was all the same, just on different computers.
>>>>>>> However the S^2 values do make sense. The Rex values were incredibly
>>>>>>> small (1x10^-20), but there are some similarities (in terms of big Rex
>>>>>>> values) between the Rex I obtained from relax, and CPMG data analyzed by
>>>>>>> glove. So I have been able to obtain some reasonable data and results
>>>>>>> from
>>>>>>> model_free using relax.
>>>>>>>
>>>>>>> Sincerely,
>>>>>>> Sam
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Sep 26, 2016 at 2:59 PM, Mahdi, Sam <
>>>>>>> sam.mahdi....@my.csun.edu> wrote:
>>>>>>>
>>>>>>>> Hi Troels,
>>>>>>>>
>>>>>>>>
>>>>>>>> I have attempted the fix for running on a multi-processor platform
>>>>>>>> by creating the script you told me too, and I still got the same
>>>>>>>> result. I
>>>>>>>> have uploaded a screenshot that shows again, relax is running in the
>>>>>>>> background, but there is no output for relax, nor can I input any
>>>>>>>> commands.
>>>>>>>> The only output I recieve is this:
>>>>>>>> Running relax with NP=$NPROC+8|bc in multi-processor mode
>>>>>>>>
>>>>>>>> And any command I type in after that gets no response.
>>>>>>>>
>>>>>>>> I've also checked the spins via script. For 2 scenarios. Scenario
>>>>>>>> 1- All hydrogens are kept as HN and Scenario 2- I change all the HN
>>>>>>>> spins
>>>>>>>> to H.
>>>>>>>> The output from Scenario one is, it read all the Nitrogen spins
>>>>>>>> accordingly :
>>>>>>>> Objects:
>>>>>>>> element: 'N'
>>>>>>>> isotope: '15N'
>>>>>>>> name: 'N'
>>>>>>>> num: 1304
>>>>>>>> pos: array([ 13.196999999999999, 15.218 ,
>>>>>>>> 3.192 ])
>>>>>>>> select: True
>>>>>>>> hRGS4 178 THR #hRGS4:178@1304
>>>>>>>> Class containing all the spin system specific data.
>>>>>>>>
>>>>>>>>
>>>>>>>> Objects:
>>>>>>>> element: 'N'
>>>>>>>> isotope: '15N'
>>>>>>>> name: 'N'
>>>>>>>> num: 2617
>>>>>>>> pos: array([ 22.696000000000002, 10.683999999999999,
>>>>>>>> -4.15 ])
>>>>>>>> select: True
>>>>>>>> hRGS4 178 THR #hRGS4:178@2617
>>>>>>>>
>>>>>>>> But no hydrogens.
>>>>>>>>
>>>>>>>> Scenario 2- I still recieve the same error.
>>>>>>>> RelaxError: Multiple alternate location indicators are present in
>>>>>>>> the PDB file, but the desired coordinate set has not been specified.
>>>>>>>>
>>>>>>>> Sincerely,
>>>>>>>> Sam
>>>>>>>>
>>>>>>>> On Mon, Sep 26, 2016 at 2:19 PM, Mahdi, Sam <
>>>>>>>> sam.mahdi....@my.csun.edu> wrote:
>>>>>>>>
>>>>>>>>> Hi Troels,
>>>>>>>>>
>>>>>>>>> I have attempted the fix for running on a multi-processor platform
>>>>>>>>> by creating the script you told me too, and I still got the same
>>>>>>>>> result. I
>>>>>>>>> have uploaded a screenshot that shows again, relax is running in the
>>>>>>>>> background, but there is no output for relax, nor can I input any
>>>>>>>>> commands.
>>>>>>>>> The only output I recieve is this:
>>>>>>>>> Running relax with NP=$NPROC+8|bc in multi-processor mode
>>>>>>>>>
>>>>>>>>> And any command I type in after that gets no response.
>>>>>>>>>
>>>>>>>>> Sincerely,
>>>>>>>>> Sam
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Sun, Sep 25, 2016 at 6:43 AM, Troels Emtekær Linnet <
>>>>>>>>> tlin...@nmr-relax.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Sam.
>>>>>>>>>>
>>>>>>>>>> Try to load the pdb file and make a spin_loop over the
>>>>>>>>>> information.
>>>>>>>>>> How does the information look like?
>>>>>>>>>> http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_s
>>>>>>>>>> am_mahdi#Check_the_spin_containers_via_script
>>>>>>>>>>
>>>>>>>>>> Regarding the multiprocessor on your Fedora 20 machine, try to
>>>>>>>>>> have a look at the bug.
>>>>>>>>>> https://gna.org/bugs/?25084
>>>>>>>>>>
>>>>>>>>>> -----
>>>>>>>>>> I suspect there is a mismatch between two installations of relax.
>>>>>>>>>> One version of 2.x and one local of 4.x.
>>>>>>>>>> Try adding the full path to relax
>>>>>>>>>> -----
>>>>>>>>>>
>>>>>>>>>> Try make a run script like this and copy it some where to your
>>>>>>>>>> PATH
>>>>>>>>>> myrelax
>>>>>>>>>> ------
>>>>>>>>>>
>>>>>>>>>> #!/bin/tcsh -fe
>>>>>>>>>>
>>>>>>>>>> # Set the relax version used for this script.
>>>>>>>>>> set RELAX=/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/relax
>>>>>>>>>>
>>>>>>>>>> # Set number of available CPUs.
>>>>>>>>>> set NPROC=`nproc`
>>>>>>>>>> set NP=`echo $NPROC + 0 | bc `
>>>>>>>>>> echo "Running relax with NP=$NP in multi-processor mode"
>>>>>>>>>>
>>>>>>>>>> # Run relax in multi processor mode.
>>>>>>>>>> mpirun -np $NP $RELAX --multi='mpi4py' $argv
>>>>>>>>>>
>>>>>>>>>> 2016-09-24 1:03 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>>>>>>>>>>
>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>
>>>>>>>>>>> Update on Protein number 1: So I was able to successfully run
>>>>>>>>>>> model free with no problems on my protein (I don't know why it was
>>>>>>>>>>> giving
>>>>>>>>>>> problems before). The reason it may have been giving issues though
>>>>>>>>>>> is the
>>>>>>>>>>> protein I am working with forms a dimer at the concentrations we
>>>>>>>>>>> work with
>>>>>>>>>>> (thus the results I have are for the Dimer form of the protein).
>>>>>>>>>>> The pdb
>>>>>>>>>>> file though only has a monomer structure though. I have been able
>>>>>>>>>>> to obtain
>>>>>>>>>>> the dimer pdb file using HADDOCK (docking program), but have come
>>>>>>>>>>> across a
>>>>>>>>>>> few problems uploading the pdb file.
>>>>>>>>>>> The initial problem was that all the hydrogens attached to the
>>>>>>>>>>> nitrogen were HN labeled on the HADDOCK modified pdb file, and
>>>>>>>>>>> model free
>>>>>>>>>>> could not understand what HN meant, and I would recieve this
>>>>>>>>>>> warning.
>>>>>>>>>>> RelaxWarning: Cannot determine the element associated with atom
>>>>>>>>>>> 'HN'.
>>>>>>>>>>>
>>>>>>>>>>> I could however load up all the Nitrogen, but naturally, with no
>>>>>>>>>>> hydrogens, it wouldn't be able to calculate any bond vectors between
>>>>>>>>>>> nitrogen and hydrogen. So I would recieve this error and the
>>>>>>>>>>> program would
>>>>>>>>>>> close
>>>>>>>>>>> RelaxError: The spin ID '@H' matches no spins.
>>>>>>>>>>>
>>>>>>>>>>> To fix this, I changed all the HN spins, to just H, but then
>>>>>>>>>>> recieved another error.
>>>>>>>>>>> RelaxError: Multiple alternate location indicators are present
>>>>>>>>>>> in the PDB file, but the desired coordinates set has not been
>>>>>>>>>>> specified.
>>>>>>>>>>>
>>>>>>>>>>> I don't exactly understand what this error means. Is it saying
>>>>>>>>>>> the program can't locate the 3D coordinates for the Hydrogen and
>>>>>>>>>>> Nitrogen?
>>>>>>>>>>> If that is the case, why was it able to before, when it couldn't
>>>>>>>>>>> read any
>>>>>>>>>>> of the Hydrogen spins. I'm just confused a bit as to what this
>>>>>>>>>>> error means.
>>>>>>>>>>>
>>>>>>>>>>> Sincerely,
>>>>>>>>>>> Sam
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Sep 21, 2016 at 3:18 PM, Mahdi, Sam <
>>>>>>>>>>> sam.mahdi....@my.csun.edu> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>
>>>>>>>>>>>> Update on protein number 1. I ran it with only 5 simulations.
>>>>>>>>>>>> It took a while, but it ended up finishing. So I assume its due to
>>>>>>>>>>>> bad data
>>>>>>>>>>>> simply slowing down the process.
>>>>>>>>>>>> Update on protein number 2. I ran it with only 2 spins as well,
>>>>>>>>>>>> and I still recieved the same error. I suspect its due to the pdb
>>>>>>>>>>>> file. I'm
>>>>>>>>>>>> going to attempt to use another program to add the hydrogens to my
>>>>>>>>>>>> pdb file
>>>>>>>>>>>> and try again.
>>>>>>>>>>>>
>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>> Sam
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Sep 20, 2016 at 1:31 PM, Mahdi, Sam <
>>>>>>>>>>>> sam.mahdi....@my.csun.edu> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Thats weird, I can open it up directly from the link you sent
>>>>>>>>>>>>> me. I'll reupload it
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, Sep 20, 2016 at 12:40 PM, Troels Emtekær Linnet <
>>>>>>>>>>>>> tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> The file:
>>>>>>>>>>>>>> file #28673: relax -i data for 4.0,2 a
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> https://gna.org/bugs/download.php?file_id=28673
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Its emtpy?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 2016-09-20 20:05 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I am a bit confused what you are talking about. There is no
>>>>>>>>>>>>>>> file labeled .?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Tue, Sep 20, 2016 at 9:15 AM, Troels Emtekær Linnet <
>>>>>>>>>>>>>>> tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On
>>>>>>>>>>>>>>>> https://gna.org/bugs/?25084
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I cannot open the file.?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> In the meantime, try to specify the full path to relax. Not
>>>>>>>>>>>>>>>> just ./relax
>>>>>>>>>>>>>>>> but /home/user/xxx/relax
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>>> Troels
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> 2016-09-19 23:13 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I just uploaded the 4.0.2 relax -i info. I already have
>>>>>>>>>>>>>>>>> minfx 1.0.12 with 4.0.2. But I can't open relax on multi
>>>>>>>>>>>>>>>>> processor
>>>>>>>>>>>>>>>>> platform for either version.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Mon, Sep 19, 2016 at 10:47 AM, Troels Emtekær Linnet <
>>>>>>>>>>>>>>>>> tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Please upgrade!
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Name Installed Version Current
>>>>>>>>>>>>>>>>>> version
>>>>>>>>>>>>>>>>>> minfx True 1.0.4
>>>>>>>>>>>>>>>>>> 1.0.12
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> relax information:
>>>>>>>>>>>>>>>>>> Version: 2.2.5
>>>>>>>>>>>>>>>>>> 4.0.2
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 2016-09-19 19:41 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> I have uploaded the bug report for the issue with
>>>>>>>>>>>>>>>>>>> running relax on multiple processors on my fedora 20
>>>>>>>>>>>>>>>>>>> computer. I will
>>>>>>>>>>>>>>>>>>> upload the mpirun report bindings on the fedora 24 computer
>>>>>>>>>>>>>>>>>>> later today
>>>>>>>>>>>>>>>>>>> (that is not my lab so I don't have access to it, and the
>>>>>>>>>>>>>>>>>>> professor is not
>>>>>>>>>>>>>>>>>>> in yet). If there is any more info that is needed please
>>>>>>>>>>>>>>>>>>> let me know.
>>>>>>>>>>>>>>>>>>> Thanks again in advance.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Mon, Sep 19, 2016 at 10:24 AM, Mahdi, Sam <
>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu> wrote:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks for the quick response!
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Protein 1: I will attempt to troubleshoot using the
>>>>>>>>>>>>>>>>>>>> advice you gave me. The problem occurs write after it
>>>>>>>>>>>>>>>>>>>> indicates its writing
>>>>>>>>>>>>>>>>>>>> a file for prolate round_3 (so its about to start it). I
>>>>>>>>>>>>>>>>>>>> will run it again
>>>>>>>>>>>>>>>>>>>> and post the output to give you a better idea. I'm pretty
>>>>>>>>>>>>>>>>>>>> sure the output
>>>>>>>>>>>>>>>>>>>> was something like this
>>>>>>>>>>>>>>>>>>>> Over-fit spin deselection:
>>>>>>>>>>>>>>>>>>>> No spins have been deselected.
>>>>>>>>>>>>>>>>>>>> Resetting the minimisation statistics.
>>>>>>>>>>>>>>>>>>>> But I will double check and send you another email with
>>>>>>>>>>>>>>>>>>>> the actual output.
>>>>>>>>>>>>>>>>>>>> Protein 2:
>>>>>>>>>>>>>>>>>>>> I am using the sample script for dAuvergene protocol.
>>>>>>>>>>>>>>>>>>>> So the only thing I've changed since my previous run (the
>>>>>>>>>>>>>>>>>>>> one that worked
>>>>>>>>>>>>>>>>>>>> that you wrote a tutorial for), was the pdb file and the
>>>>>>>>>>>>>>>>>>>> data set I used.
>>>>>>>>>>>>>>>>>>>> The thing I suspected was causing an issue ,was the pdb
>>>>>>>>>>>>>>>>>>>> file since I
>>>>>>>>>>>>>>>>>>>> slightly modified it, and thats really the only thing
>>>>>>>>>>>>>>>>>>>> different from this
>>>>>>>>>>>>>>>>>>>> run versus the others.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Also side note, if I were to deselect the spins that I
>>>>>>>>>>>>>>>>>>>> don't have data for or I have bad data for, that wouldn't
>>>>>>>>>>>>>>>>>>>> change any of the
>>>>>>>>>>>>>>>>>>>> calculations correct? I never have since I assumed relax
>>>>>>>>>>>>>>>>>>>> would just ignore
>>>>>>>>>>>>>>>>>>>> all the amino acids I don't have data for, but it may help
>>>>>>>>>>>>>>>>>>>> increase the
>>>>>>>>>>>>>>>>>>>> speed of my calculations if I just tell relax to just
>>>>>>>>>>>>>>>>>>>> ignore the spins from
>>>>>>>>>>>>>>>>>>>> the start.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Mon, Sep 19, 2016 at 9:12 AM, Troels Emtekær Linnet
>>>>>>>>>>>>>>>>>>>> <tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Happy to hear you that you get some progress.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Protein 1:
>>>>>>>>>>>>>>>>>>>>> Can you help me to find out, if you are minimizing or
>>>>>>>>>>>>>>>>>>>>> running Monte-Carlo simulations?
>>>>>>>>>>>>>>>>>>>>> This COULD be the problem:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> How relax works (at least how it works for relaxation
>>>>>>>>>>>>>>>>>>>>> dispersion):
>>>>>>>>>>>>>>>>>>>>> Step 1: Minimize the error for the target function.
>>>>>>>>>>>>>>>>>>>>> Find the parameters which best match the target function
>>>>>>>>>>>>>>>>>>>>> to the data, by
>>>>>>>>>>>>>>>>>>>>> minimizing the error.
>>>>>>>>>>>>>>>>>>>>> Here each individual spin minimization is handed out
>>>>>>>>>>>>>>>>>>>>> to a processor for calculation.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Step 2: Determine the error of the minimization by
>>>>>>>>>>>>>>>>>>>>> monte carlo simulations.
>>>>>>>>>>>>>>>>>>>>> Create (Standard 500) additional datasets with a copy
>>>>>>>>>>>>>>>>>>>>> from the original. Modify each datapoint by an error,
>>>>>>>>>>>>>>>>>>>>> drawn from a gaussian
>>>>>>>>>>>>>>>>>>>>> distribution where the width is described by the error of
>>>>>>>>>>>>>>>>>>>>> measurements.
>>>>>>>>>>>>>>>>>>>>> Now hand out each of the datasets to the processor.
>>>>>>>>>>>>>>>>>>>>> Each processor should now calculate the minimization for
>>>>>>>>>>>>>>>>>>>>> all the spins. The
>>>>>>>>>>>>>>>>>>>>> minimization should be more quick, as the starting
>>>>>>>>>>>>>>>>>>>>> position is chosen from
>>>>>>>>>>>>>>>>>>>>> Step 1.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Possible problem: One (or more) of the spins has
>>>>>>>>>>>>>>>>>>>>> really bad data. So a little change of the data makes the
>>>>>>>>>>>>>>>>>>>>> minimization
>>>>>>>>>>>>>>>>>>>>> space very different.
>>>>>>>>>>>>>>>>>>>>> Think of a flat table. Where should the "minimization
>>>>>>>>>>>>>>>>>>>>> ball" run into? Maybe you have created a small new bump
>>>>>>>>>>>>>>>>>>>>> in the table. This
>>>>>>>>>>>>>>>>>>>>> is typically for "bad" data.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> This could either be the measurement OR the error
>>>>>>>>>>>>>>>>>>>>> estimation. Relax will keep on searching for minimization.
>>>>>>>>>>>>>>>>>>>>> If you are "unlucky", some of the created datasets
>>>>>>>>>>>>>>>>>>>>> will make relax hang for a very long time.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Unfortunately, it is NOT possible to ask a processor
>>>>>>>>>>>>>>>>>>>>> about its "current" work, when it is doing a minimization
>>>>>>>>>>>>>>>>>>>>> for a whole
>>>>>>>>>>>>>>>>>>>>> dataset.
>>>>>>>>>>>>>>>>>>>>> And if it was, it would create an output of 64 spins
>>>>>>>>>>>>>>>>>>>>> being minimized at the same time, creating a big mess,
>>>>>>>>>>>>>>>>>>>>> since the processors
>>>>>>>>>>>>>>>>>>>>> are working alone. When doing Monte-Carlo simulations,
>>>>>>>>>>>>>>>>>>>>> relax are quite
>>>>>>>>>>>>>>>>>>>>> silent. Only reporting when a whole dataset is done.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Is relax stuck in Monte-Carlo simulations?
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Possible solution:
>>>>>>>>>>>>>>>>>>>>> *) Set Monte-Carlo simulations to 3 (which is
>>>>>>>>>>>>>>>>>>>>> minimum), and know that you have found the right minimum,
>>>>>>>>>>>>>>>>>>>>> but the error
>>>>>>>>>>>>>>>>>>>>> estimation of the parameters are wrong.
>>>>>>>>>>>>>>>>>>>>> *) Carefully inspect your data, deselecting all spins
>>>>>>>>>>>>>>>>>>>>> which have "bad data". Look at their graphs. Consider
>>>>>>>>>>>>>>>>>>>>> working with as few
>>>>>>>>>>>>>>>>>>>>> spins as possible, and work your way up! Working this way
>>>>>>>>>>>>>>>>>>>>> will greatly
>>>>>>>>>>>>>>>>>>>>> increase your productivity.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Protein 2:
>>>>>>>>>>>>>>>>>>>>> Are you setting the bonds for the minimization
>>>>>>>>>>>>>>>>>>>>> manually?
>>>>>>>>>>>>>>>>>>>>> This looks like the upper/lower bonds are specified
>>>>>>>>>>>>>>>>>>>>> wrong. This is not easy to do. How are you doing it?
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>>>>>>>> Troels
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> 2016-09-19 17:11 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> I have successfully been able to run the model-free
>>>>>>>>>>>>>>>>>>>>>> analysis on 64 cores. The issue appears to have been I
>>>>>>>>>>>>>>>>>>>>>> simply did not
>>>>>>>>>>>>>>>>>>>>>> specify the spin number, so after looking at your
>>>>>>>>>>>>>>>>>>>>>> tutorial and making the
>>>>>>>>>>>>>>>>>>>>>> proper modifications, it ran with no complications. The
>>>>>>>>>>>>>>>>>>>>>> results are
>>>>>>>>>>>>>>>>>>>>>> somewhat reasonable. I decided to try to run 2 other
>>>>>>>>>>>>>>>>>>>>>> proteins however; and
>>>>>>>>>>>>>>>>>>>>>> I've come across problems for both again.
>>>>>>>>>>>>>>>>>>>>>> Protein 1:
>>>>>>>>>>>>>>>>>>>>>> I set this up just like the tutorial, and it runs
>>>>>>>>>>>>>>>>>>>>>> with no warnings or errors; however, the run never
>>>>>>>>>>>>>>>>>>>>>> finishes. At round_3 for
>>>>>>>>>>>>>>>>>>>>>> the prolate model when it starts to minimize it just
>>>>>>>>>>>>>>>>>>>>>> stops. I don't mean
>>>>>>>>>>>>>>>>>>>>>> relax is stopped or closed, I mean it stops doing any
>>>>>>>>>>>>>>>>>>>>>> calculations. Relax
>>>>>>>>>>>>>>>>>>>>>> is still open, and if I run the top command, I can still
>>>>>>>>>>>>>>>>>>>>>> see something is
>>>>>>>>>>>>>>>>>>>>>> going on with the other cores, but nothing is being
>>>>>>>>>>>>>>>>>>>>>> calculated. The run
>>>>>>>>>>>>>>>>>>>>>> with 64 cores is incredibly fast (under 4 hours), so I
>>>>>>>>>>>>>>>>>>>>>> don't think it's
>>>>>>>>>>>>>>>>>>>>>> loading calculations or writing them, and I've left it
>>>>>>>>>>>>>>>>>>>>>> there for over 24
>>>>>>>>>>>>>>>>>>>>>> hours, and it's still just sorta stuck. There are no
>>>>>>>>>>>>>>>>>>>>>> errors, no outputs, it
>>>>>>>>>>>>>>>>>>>>>> just says its gonna start to minimize and then nothing
>>>>>>>>>>>>>>>>>>>>>> happens after that.
>>>>>>>>>>>>>>>>>>>>>> Protein2:
>>>>>>>>>>>>>>>>>>>>>> This protein was a little different since the pdb
>>>>>>>>>>>>>>>>>>>>>> structure was a crystal structure. I had to use WhatIf
>>>>>>>>>>>>>>>>>>>>>> to add the protons
>>>>>>>>>>>>>>>>>>>>>> onto the pdb file. The structure appears to load up
>>>>>>>>>>>>>>>>>>>>>> fine, all the spins
>>>>>>>>>>>>>>>>>>>>>> appear to be read, data is loaded, vectors and are
>>>>>>>>>>>>>>>>>>>>>> calculated and define,
>>>>>>>>>>>>>>>>>>>>>> but when I came to run the protocol this error pops up:
>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/multi/processor.py",
>>>>>>>>>>>>>>>>>>>>>> line 494, in run
>>>>>>>>>>>>>>>>>>>>>> self.callback.init_master(self)
>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/multi/__init__.py",
>>>>>>>>>>>>>>>>>>>>>> line 318, in default_init_master
>>>>>>>>>>>>>>>>>>>>>> self.master.run()
>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/relax.py", line 199,
>>>>>>>>>>>>>>>>>>>>>> in run
>>>>>>>>>>>>>>>>>>>>>> self.interpreter.run(self.script_file)
>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/prompt/interpreter.py",
>>>>>>>>>>>>>>>>>>>>>> line 279, in run
>>>>>>>>>>>>>>>>>>>>>> return run_script(intro=self.__intro_string,
>>>>>>>>>>>>>>>>>>>>>> local=locals(), script_file=script_file,
>>>>>>>>>>>>>>>>>>>>>> show_script=self.__show_script,
>>>>>>>>>>>>>>>>>>>>>> raise_relax_error=self.__raise_relax_error)
>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/prompt/interpreter.py",
>>>>>>>>>>>>>>>>>>>>>> line 585, in run_script
>>>>>>>>>>>>>>>>>>>>>> return console.interact(intro, local,
>>>>>>>>>>>>>>>>>>>>>> script_file, show_script=show_script,
>>>>>>>>>>>>>>>>>>>>>> raise_relax_error=raise_relax_
>>>>>>>>>>>>>>>>>>>>>> error)
>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/prompt/interpreter.py",
>>>>>>>>>>>>>>>>>>>>>> line 484, in interact_script
>>>>>>>>>>>>>>>>>>>>>> exec_script(script_file, local)
>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/prompt/interpreter.py",
>>>>>>>>>>>>>>>>>>>>>> line 363, in exec_script
>>>>>>>>>>>>>>>>>>>>>> runpy.run_module(module, globals)
>>>>>>>>>>>>>>>>>>>>>> File "/usr/lib64/python2.7/runpy.py", line 192, in
>>>>>>>>>>>>>>>>>>>>>> run_module
>>>>>>>>>>>>>>>>>>>>>> fname, loader, pkg_name)
>>>>>>>>>>>>>>>>>>>>>> File "/usr/lib64/python2.7/runpy.py", line 72, in
>>>>>>>>>>>>>>>>>>>>>> _run_code
>>>>>>>>>>>>>>>>>>>>>> exec code in run_globals
>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/HdeA_script.py", line
>>>>>>>>>>>>>>>>>>>>>> 30, in <module>
>>>>>>>>>>>>>>>>>>>>>> dAuvergne_protocol(pipe_name=n
>>>>>>>>>>>>>>>>>>>>>> ame,pipe_bundle=pipe_bundle,di
>>>>>>>>>>>>>>>>>>>>>> ff_model=DIFF_MODEL,mf_models=
>>>>>>>>>>>>>>>>>>>>>> MF_MODELS,local_tm_models=LOCA
>>>>>>>>>>>>>>>>>>>>>> L_TM_MODELS,grid_inc=GRID_INC,
>>>>>>>>>>>>>>>>>>>>>> min_algor=MIN_ALGOR,mc_sim_num
>>>>>>>>>>>>>>>>>>>>>> =MC_NUM,conv_loop=CONV_LOOP)
>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/auto_a
>>>>>>>>>>>>>>>>>>>>>> nalyses/dauvergne_protocol.py", line 246, in __init__
>>>>>>>>>>>>>>>>>>>>>> self.execute()
>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/auto_a
>>>>>>>>>>>>>>>>>>>>>> nalyses/dauvergne_protocol.py", line 600, in execute
>>>>>>>>>>>>>>>>>>>>>> self.multi_model(local_tm=True)
>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/auto_a
>>>>>>>>>>>>>>>>>>>>>> nalyses/dauvergne_protocol.py", line 888, in
>>>>>>>>>>>>>>>>>>>>>> multi_model
>>>>>>>>>>>>>>>>>>>>>> self.interpreter.minimise.grid
>>>>>>>>>>>>>>>>>>>>>> _search(inc=self.grid_inc)
>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/prompt/uf_objects.py",
>>>>>>>>>>>>>>>>>>>>>> line 225, in __call__
>>>>>>>>>>>>>>>>>>>>>> self._backend(*new_args, **uf_kargs)
>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/pipe_control/minimise.py",
>>>>>>>>>>>>>>>>>>>>>> line 172, in grid_search
>>>>>>>>>>>>>>>>>>>>>> model_lower, model_upper, model_inc =
>>>>>>>>>>>>>>>>>>>>>> grid_setup(lower, upper, inc, verbosity=verbosity,
>>>>>>>>>>>>>>>>>>>>>> skip_preset=skip_preset)
>>>>>>>>>>>>>>>>>>>>>> File "/home/sam2/relax-4.0.2/pipe_control/minimise.py",
>>>>>>>>>>>>>>>>>>>>>> line 341, in grid_setup
>>>>>>>>>>>>>>>>>>>>>> elif values[i] in [None, {}, []]:
>>>>>>>>>>>>>>>>>>>>>> IndexError: index 0 is out of bounds for axis 0 with
>>>>>>>>>>>>>>>>>>>>>> size 0
>>>>>>>>>>>>>>>>>>>>>> I should mention this error pops up when it decided
>>>>>>>>>>>>>>>>>>>>>> to calculate the first spins upper and lower bounds. So
>>>>>>>>>>>>>>>>>>>>>> this isn't at the
>>>>>>>>>>>>>>>>>>>>>> minimization portion of the calculation (like in the
>>>>>>>>>>>>>>>>>>>>>> previous bug). Thanks
>>>>>>>>>>>>>>>>>>>>>> in advance.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> On Wed, Sep 14, 2016 at 6:34 AM, Troels Emtekær
>>>>>>>>>>>>>>>>>>>>>> Linnet <tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> To tackle this problem, I would advice to create
>>>>>>>>>>>>>>>>>>>>>>> another bug.
>>>>>>>>>>>>>>>>>>>>>>> Creation and closing of a bug "leaves trails", which
>>>>>>>>>>>>>>>>>>>>>>> maybe will help another person, when googling for the
>>>>>>>>>>>>>>>>>>>>>>> same problem.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> To help you, can you do a "relax -i" on both
>>>>>>>>>>>>>>>>>>>>>>> computers?
>>>>>>>>>>>>>>>>>>>>>>> That give some indication about package versions and
>>>>>>>>>>>>>>>>>>>>>>> computer setup.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> The first thing we need to establish, is that mpirun
>>>>>>>>>>>>>>>>>>>>>>> is working.
>>>>>>>>>>>>>>>>>>>>>>> We have to test the installation without relax.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Can you have a look at:
>>>>>>>>>>>>>>>>>>>>>>> http://wiki.nmr-relax.com/OpenMPI
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Try the different things like:
>>>>>>>>>>>>>>>>>>>>>>> lscpu
>>>>>>>>>>>>>>>>>>>>>>> mpirun --report-bindings -np 11 echo "hello world"
>>>>>>>>>>>>>>>>>>>>>>> mpirun --report-bindings -np 4 relax --multi='mpi4py'
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> When we are confident about this, then we will try
>>>>>>>>>>>>>>>>>>>>>>> make a small test script for relax.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Please try these things at both computers, and
>>>>>>>>>>>>>>>>>>>>>>> provide 2 files with commands and output.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Then attach it to the bug report.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> 2016-09-14 6:40 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> So I saw the tutorial you put, and the main problem
>>>>>>>>>>>>>>>>>>>>>>>> was I had not specified my data was only for the
>>>>>>>>>>>>>>>>>>>>>>>> Nitrogen spins. After
>>>>>>>>>>>>>>>>>>>>>>>> applying the spin column, my data loaded and relax ran
>>>>>>>>>>>>>>>>>>>>>>>> model free with no
>>>>>>>>>>>>>>>>>>>>>>>> problem. I have a script that starts and runs relax
>>>>>>>>>>>>>>>>>>>>>>>> and model free all
>>>>>>>>>>>>>>>>>>>>>>>> automatic, if you wish I can send it via email to you
>>>>>>>>>>>>>>>>>>>>>>>> and you can upload it
>>>>>>>>>>>>>>>>>>>>>>>> to the tutorial wiki page. So I can successfully run
>>>>>>>>>>>>>>>>>>>>>>>> model-free in script
>>>>>>>>>>>>>>>>>>>>>>>> mode for a uni-processor.
>>>>>>>>>>>>>>>>>>>>>>>> The problem now with the multi-processor is that
>>>>>>>>>>>>>>>>>>>>>>>> the script won't load. In the bug page I uploaded a
>>>>>>>>>>>>>>>>>>>>>>>> screenshot where I had
>>>>>>>>>>>>>>>>>>>>>>>> input the 'mpirun -np 4 ../relax --multi='mpi4py'
>>>>>>>>>>>>>>>>>>>>>>>> command, however I had no
>>>>>>>>>>>>>>>>>>>>>>>> output. I checked processes running in the background,
>>>>>>>>>>>>>>>>>>>>>>>> and saw that there
>>>>>>>>>>>>>>>>>>>>>>>> was indeed 4 processess running in the background (1
>>>>>>>>>>>>>>>>>>>>>>>> master and 3 slaves)
>>>>>>>>>>>>>>>>>>>>>>>> for relax; but there was no output, so I was unable to
>>>>>>>>>>>>>>>>>>>>>>>> load any data, or
>>>>>>>>>>>>>>>>>>>>>>>> create a pipe or anything. This was only on the Fedora
>>>>>>>>>>>>>>>>>>>>>>>> 24 computer, not the
>>>>>>>>>>>>>>>>>>>>>>>> Fedora 20. On the Fedora 20 computer, I was able to
>>>>>>>>>>>>>>>>>>>>>>>> successfully open relax
>>>>>>>>>>>>>>>>>>>>>>>> on a multi processor platform. I can send the
>>>>>>>>>>>>>>>>>>>>>>>> screenshots and the relax -i
>>>>>>>>>>>>>>>>>>>>>>>> for both computers again. I don't know why it doesn't
>>>>>>>>>>>>>>>>>>>>>>>> work the fedora 24.
>>>>>>>>>>>>>>>>>>>>>>>> Do you know what could be causing this?
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Thanks again in advance
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Sep 13, 2016 at 9:32 PM, Troels Emtekær
>>>>>>>>>>>>>>>>>>>>>>>> Linnet <tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sam
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Can you send the mail again and include the
>>>>>>>>>>>>>>>>>>>>>>>>> maillist?
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Best Troels
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Den tirsdag den 13. september 2016 skrev Mahdi,
>>>>>>>>>>>>>>>>>>>>>>>>> Sam <sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> HI Troels,
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> So I saw the tutorial you put, and the main
>>>>>>>>>>>>>>>>>>>>>>>>>> problem was I had not specified my data was only for
>>>>>>>>>>>>>>>>>>>>>>>>>> the Nitrogen spins.
>>>>>>>>>>>>>>>>>>>>>>>>>> After applying the spin column, my data loaded and
>>>>>>>>>>>>>>>>>>>>>>>>>> relax ran model free
>>>>>>>>>>>>>>>>>>>>>>>>>> with no problem. I have a script that starts and
>>>>>>>>>>>>>>>>>>>>>>>>>> runs relax and model free
>>>>>>>>>>>>>>>>>>>>>>>>>> all automatic, if you wish I can send it via email
>>>>>>>>>>>>>>>>>>>>>>>>>> to you and you can
>>>>>>>>>>>>>>>>>>>>>>>>>> upload it to the tutorial wiki page. So I can
>>>>>>>>>>>>>>>>>>>>>>>>>> successfully run model-free
>>>>>>>>>>>>>>>>>>>>>>>>>> in script mode for a uni-processor.
>>>>>>>>>>>>>>>>>>>>>>>>>> The problem now with the multi-processor is that
>>>>>>>>>>>>>>>>>>>>>>>>>> the script won't load. In the bug page I uploaded a
>>>>>>>>>>>>>>>>>>>>>>>>>> screenshot where I had
>>>>>>>>>>>>>>>>>>>>>>>>>> input the 'mpirun -np 4 ../relax --multi='mpi4py'
>>>>>>>>>>>>>>>>>>>>>>>>>> command, however I had no
>>>>>>>>>>>>>>>>>>>>>>>>>> output. I checked processes running in the
>>>>>>>>>>>>>>>>>>>>>>>>>> background, and saw that there
>>>>>>>>>>>>>>>>>>>>>>>>>> was indeed 4 processess running in the background (1
>>>>>>>>>>>>>>>>>>>>>>>>>> master and 3 slaves)
>>>>>>>>>>>>>>>>>>>>>>>>>> for relax; but there was no output, so I was unable
>>>>>>>>>>>>>>>>>>>>>>>>>> to load any data, or
>>>>>>>>>>>>>>>>>>>>>>>>>> create a pipe or anything. This was only on the
>>>>>>>>>>>>>>>>>>>>>>>>>> Fedora 24 computer, not the
>>>>>>>>>>>>>>>>>>>>>>>>>> Fedora 20. On the Fedora 20 computer, I was able to
>>>>>>>>>>>>>>>>>>>>>>>>>> successfully open relax
>>>>>>>>>>>>>>>>>>>>>>>>>> on a multi processor platform. I can send the
>>>>>>>>>>>>>>>>>>>>>>>>>> screenshots and the relax -i
>>>>>>>>>>>>>>>>>>>>>>>>>> for both computers again. I don't know why it
>>>>>>>>>>>>>>>>>>>>>>>>>> doesn't work the fedora 24.
>>>>>>>>>>>>>>>>>>>>>>>>>> Do you know what could be causing this?
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks again in advance
>>>>>>>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Sep 13, 2016 at 1:01 PM, Troels Emtekær
>>>>>>>>>>>>>>>>>>>>>>>>>> Linnet <tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> I closed the 2 bug reports as invalid.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> The data is not labelled correct.
>>>>>>>>>>>>>>>>>>>>>>>>>>> But this can be corrected.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Please see this tutorial I wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> http://wiki.nmr-relax.com/Tuto
>>>>>>>>>>>>>>>>>>>>>>>>>>> rial_for_model-free_analysis_sam_mahdi
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> I hope this give some guidance.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> If you experience any new problems, please feel
>>>>>>>>>>>>>>>>>>>>>>>>>>> free to ask!!
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> What you experience, will probably be the same
>>>>>>>>>>>>>>>>>>>>>>>>>>> for many.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Your feedback is valuable for the development.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Please wait with using mpirun and multiple
>>>>>>>>>>>>>>>>>>>>>>>>>>> processors, before you are absolutely sure
>>>>>>>>>>>>>>>>>>>>>>>>>>> that it will run on 1 processor.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Bugfixing when using multiple processors is a
>>>>>>>>>>>>>>>>>>>>>>>>>>> nightmare....
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>>>>>>>>>>>>>> Troels
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> 2016-09-12 17:36 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> I just created another bug report. I simply
>>>>>>>>>>>>>>>>>>>>>>>>>>>> copy pasted the email, and uploaded the script
>>>>>>>>>>>>>>>>>>>>>>>>>>>> files there.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Sep 12, 2016 at 5:14 AM, Troels Emtekær
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Linnet <tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you produce another bug report.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please don't attach files to these mails as it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will strain the mailinglists.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cheers
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Troels
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Den lørdag den 10. september 2016 skrev Mahdi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sam <sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Additional question that I had, if you could
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also look into this as well on Tuesday please. I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have decided to try to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> write a script to automate this whole process
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (since I won't be using the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> gui to do model free), and I've come across a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> problem. I can successfully
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> open up relax using openmpi, and can load the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pdb file, and assign all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> spins and isotopes; however, it appears it will
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> only load one data file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (the very first one I'll have inputed in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script). I don't know if there
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is a problem with how I wrote my script. Not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> only will it not load the rest
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of my data sets, it won't actually run
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dAuvergne's protocol either, it'll
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> just load the data set and exit out of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> program. Attached is the script
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I wrote for relax.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is the output once relax has loaded
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script = 'model_free_sample_script.py'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ----------------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from time import asctime, localtime
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from auto_analyses.dauvergne_protocol import
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dAuvergne_protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DIFF_MODEL=['local_tm','sphere
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ','prolate','oblate','ellipsoid','final']
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MF_MODELS=['m0','m1','m2','m3'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ,'m4','m5','m6','m7','m8','m9']
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LOCAL_TM_MODELS=['tm0','tm1','
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tm2','tm3','tm4','tm5','tm6','
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tm7','tm7','tm8','tm9']
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> GRID_INC=11
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MIN_ALGOR='newton'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MC_NUM=500
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CONV_LOOP=True
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipe_bundle="mf(%s)"%asctime(localtime())
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> name="origin-"+pipe_bundle
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipe.create(name,'mf',bundle=pipe_bundle)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> structure.read_pdb('2d9j.pdb',
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> set_mol_name='hRGS7')
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> structure.load_spins('@N',ave_pos=True)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> structure.load_spins('@NE1',ave_pos=True)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> structure.load_spins('@H',ave_pos=True)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> structure.load_spins('@HE1',ave_pos=True)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> spin.isotope('15N',spin_id='@N*')
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> spin.isotope('1H',spin_id='@H*')
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='R1_Agne
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> s',ri_type='R1',frq=599.642*1e6,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file='R1_Agnes',res_num_col=1,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> data_col=2,error_col=3)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='R2_Agne
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> s',ri_type='R2',frq=599.642*1e6,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file='R2_Agnes',res_num_col=1,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> data_col=2,error_col=3)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='ssNOE_A
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> gnes',ri_type='NOE',frq=599.642*1e6,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file='ssNOE_Agnes',res_num_col
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> =1,data_col=2,error_col=3)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='R1_NMRF
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM',ri_type='R1',frq=799.642*1e6,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file='R1_NMRFAM',res_num_col=1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ,data_col=2,error_col=3)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='R2_NMRF
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM',ri_type='R2',frq=799.642*1e6,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file='R2_NMRFAM',res_num_col=1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ,data_col=2,error_col=3)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='ssNOE_N
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRFAM',ri_type='NOE',frq=799.642*1e6,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file='ssNOE_NMRFAM',res_num_co
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> l=1,data_col=2,error_col=3)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> interatom.define(spin_id1='@N',spin_id2='@H',
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> direct_bond=True)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> interatom.define(spin_id1='@NE1',spin_id2='@HE1',
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> direct_bond=True)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> interatom.set_dist(spin_id1='@
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N*',spin_id2='@H*',ave_dist=1.02*1e-10)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> interatom.unit_vectors()
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> value.set(-172*1e-6,'csa',spin_id='@N*')
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dAuvergne_protocol(pipe_name=n
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ame,pipe_bundle=pipe_bundle,di
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ff_model=DIFF_MODEL,mf_models=
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MF_MODELS,local_tm_models=LOCA
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> L_TM_MODELS,grid_inc=GRID_INC,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> min_algor=MIN_ALGOR,mc_sim_num
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> =MC_NUM,conv_loop=CONV_LOOP)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> So it indicates that my script has loaded.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, after it loads the spins from the pdb
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file, this is what happens
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> after my first data set has been loaded:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax> relax_data.read(ri_id='R1_Agnes',
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ri_type='R1', frq=599642000.0, file='R1_Agnes',
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dir=None, spin_id_col=None,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mol_name_col=None, res_num_col=1,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> res_name_col=None, spin_num_col=None,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> spin_name_col=None, data_col=2, error_col=3,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sep=None, spin_id=None)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Opening the file 'R1_Agnes' for reading.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['Residue', 'R1', 'Error'] is invalid, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> residue number data 'Residue' is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> invalid.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['1'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['2'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['3'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['4'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['5'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['6'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['7'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['8'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['9'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['10'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['11'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['16'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['17'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['18'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['21'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['22'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['23'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['26'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['27'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['28'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['31'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['40'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['46'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['58'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['61'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['62'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['63'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['73'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['76'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['79'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['81'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['82'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['85'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['94'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['97'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['99'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['106'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['115'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['121'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['126'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['127'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['134'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['135'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['136'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['137'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['139'] is invalid, the data is missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxError: The spin ID '#hRGS7:12'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> corresponds to multiple spins, including
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> '#hRGS7:12@N'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and '#hRGS7:12@H'.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> crowlab: [~/relax-4.0.2]>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> As you can see, I have all 6 data sets set to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> load, but only the very first one appears to do
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> so, and after it loads, it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> just exits out of relax. Again, I don't know if
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this is a problem with how
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I wrote the script. The Relax_script1 is the one
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that I load up to run the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> whole thing. The model free script.py is just
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the script it reads once
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax has opened up. Again, I can see all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> spins are properly loaded,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the isotopes are set. It just everything
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> after the first data set that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> doesn't load. Thanks again in advance.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Sep 8, 2016 at 10:15 AM, Mahdi, Sam <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Troels,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you so much. If there is any extra
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> info you need please let me know.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Sep 8, 2016 at 9:12 AM, Troels
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Emtekær Linnet <tlin...@nmr-relax.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I will have some time on Tuesday, and then
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I will look at it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Troels
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Den onsdag den 7. september 2016 skrev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hello Troels,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I uploaded all the files, and even added
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the entire output that i recieved using
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> model free in script mode. I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> didn't know if all the files uploaded need to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have that link, so only the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> initial files that were uploaded it, have it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you in advance for your help!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Sep 7, 2016 at 12:41 AM, Troels
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Emtekær Linnet <tlin...@nmr-relax.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You should be able to upload more files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> after the initial upload.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the comment thread, please also make a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> link to this discussion.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mail.gna.org/public/re
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lax-users/2016-09/threads.html#00001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Troels
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2016-09-06 19:10 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for your reply. When I come to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload my data though, I see there are only
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 4 available slots I can upload
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my data. I have a total of 6 data files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> however, that need to be uploaded
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (3 of each frequency). I also need to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload the relax -i of 2 different
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> computers, and the script file I've been
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using for a total of 9 files that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to be uploaded. Is there a way to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> increase the amount I can upload, or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can I upload more after the initial
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> submission?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Sep 5, 2016 at 2:46 AM, Troels
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Emtekær Linnet <tlin...@nmr-relax.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To solve this problem, it would be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> easier to have access to some of your data.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you upload to:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://gna.org/bugs/?group=relax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Take each of your data files, and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete all data, except 2 spins.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Also provide your script file, or a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> description of which button you press in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the GUI.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please also provide information about
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your system with:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax -i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then I will make a tutorial for you. To
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be added here:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> http://wiki.nmr-relax.com/Cate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> gory:Tutorials
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If there is a problem in relax, I will
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> write a systemtest which will solve the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> problem.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> And the problem will never return.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If this a user error, the tutorial
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should help to prevent this, and would be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the first step before
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> adding/modifying the manual.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding using mpirun.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Have a look at this page. Maybe it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> helps.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> http://wiki.nmr-relax.com/OpenMPI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cheers.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2016-09-03 4:13 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hello everyone,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> So I was able to set up and run the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dauvergne_protocol successfully by
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using the script in the wiki. The
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> problem I have come across now is the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> program doesn't seem to read my data.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Using the gui interface I was able to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> successfully load my data and run it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When I upload my data using the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='R1_Agne
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> s',ri_type='R1',frq=599.642*1e6,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file='R1_Agnes',res_num_col=1,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> data_col=2,error_col=3)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The output file simply gives errors
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for amino acids I don't have data for:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line ['1'] is invalid, the data is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> missing.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is fine as relax just ignores
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> these values and continues its
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> calculations. I only receive this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> warning for values I don't have data for.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is the same thing I got when
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using the gui interface (the gui however
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> showed my values that I have data for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the residue it corresponds to,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using the script I don't receive such
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> an output, I don't know whether this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is normal or not). However, since I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> don't get this warning for every amino
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acid, I assume this means it has read
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the values for the other amino acids.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All of my data is the same, relax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> warnings only pop up for amino acids that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't have data for. The problem is,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when I enter the dAuvergne protocol,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I get the protocol working, it starts
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> running local_tm however it appears
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> none of my data has been uploaded:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The spin '#hRGS7:2@N'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has been deselected because of missing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relaxation data
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The spin '#hRGS7:3@N'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has been deselected because of missing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relaxation data
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> And I get that warning for every
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> single amino acid. From the output, it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> appears to have read the file since it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> knows exactly which amino acids I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> don't have data for, but I don't know
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> why when it comes to running the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> protocol, it tells me I havn't inputed
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> any data. I have typed everything
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directly according to the script from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the wiki. From running the protoco,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it appears everything has properly
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been uploaded, structure data, magnetic
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dipole interactions, csa, the data
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipe, the analysis variables, the python
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module imports, and setting up the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> spins from the pdb file. It appears the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> only error is from loading the actual
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relaxation data.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On a completely unrelated side note, I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have been attempting to run relax on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> multiple processors. I have tried 2
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> different computers, both fedora linux.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have mpi4py and openmpi downloaded
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> on both. On one, I can get relax on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> multiple cores working (havn't been
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> able to successfully run it due to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being unable to upload any data
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> properly). On the other however, I type in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the mpirun -np --multi='mpi4py'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script, but I get no output. I can see
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it's running in the background (top
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command), but nothing pops up, no text
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command, nothing. I typed the same
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mpirun with the --gui, but that opened
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> up nothing. On a uni-processor (typing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the exact same command without
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> indicating how many cores i.e. no -np
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --multi='mpi4py') it works just fine,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> so I don't think its my openmpi that's
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> an issue. I don't know whether this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is an issue with my mpi4py or a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> personal computer issue (since on the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> other
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> computer relax runs just fine on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> multiple cores).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> P.S. when I do enter the top command
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to see what's running. My master shows
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mpirun, and the 3 slaves display
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> python when I put -np 4, so I know
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> something is running in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> background. I have 8 cores.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Aug 31, 2016 at 6:49 PM,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mahdi, Sam <sam.mahdi....@my.csun.edu>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Hello everyone,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > I am attempting to run relax on a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> multi-processor mode. I have been able
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > to successfully set-up relax to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> operate in a multi-processor mode by using
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > the mpirun -np #ofprocessors
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /location/of/relax --multi='mpi4py'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > The problem I encounter is when
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using the --tee log dauvergne_protocol.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > command. I receive this error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > RelaxError: the script file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 'dauvergne_protocol.py' does not exist
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > I located the script file and tried
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to direct to it's path
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > mpirun
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > /usr/local/Relax/relax-2.2.5/relax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --multi='mpi4py' --tee log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > /usr/local/Relax/relax-2.2.5/a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uto-analyses/dauvergne_protocol.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > But i received this error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > RelaxError: the script file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> '/usr/local/Relax/relax-2.2.5/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > auto-analyses/dauvergne_protocol.py'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Even though I have the script, it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> doesn't seem to be able to locate it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > On a side note, in the manual, one
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dash doesn't actually run the command.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > I.e. in the manual it displays
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -multi='mpi4py' . What it should be is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > --multi='mpi4py' . The same goes for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -tee. It should be --tee.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Sincerely,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Sam
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ______________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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