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/explore/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,diff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=LOCAL_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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