Hi Sam.
Regarding protein 2.
Try to make a spin_loop after loading the data or use the GUI:
http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_sam_mahdi#Check_the_spin_containers_via_GUI
Carefully check the spins.
Or deselect all spins, and select 1-2 spins, and run the calculation.
Add more spins, and work your way up.
Maybe the modification to the pdb file make something fishy.
Relax should deselect spins there are not data for. And it should not
influence the calculation time.
It's a lighweight process.
It is quite difficult to write procedures to check for "garbage".
Best
Troels
2016-09-19 19:24 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
> 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=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/sam2/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>>> line 246, in __init__
>>> self.execute()
>>> File "/home/sam2/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>>> line 600, in execute
>>> self.multi_model(local_tm=True)
>>> File "/home/sam2/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/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/Tutorial_for_model-free_analysis_s
>>>>>>>> am_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','ellipsoi
>>>>>>>>>>> d','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_Agnes',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_Agnes',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_Agnes',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_NMRFAM',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_NMRFAM',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_NMRFAM',ri_type='NOE',frq=799.642*1e6,
>>>>>>>>>>> file='ssNOE_NMRFAM',res_num_col=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=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)
>>>>>>>>>>>
>>>>>>>>>>> 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/relax-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/Category: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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