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_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','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
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>
>>>
>>
>
_______________________________________________
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
