Hi Troels,
I will upload the bug report later today; however, I know that openmpi does
work. I can open relax using mpirun ./relax in uni processor mode. It just
doesn't load up when I specify processors and add --multi='mpi4py'. But I
will run those commands for both computers, and upload the results. Thank
you again for your help.
Sincerely,
Sam
On Mon, Sep 19, 2016 at 8:11 AM, Mahdi, Sam <sam.mahdi....@my.csun.edu>
wrote:
> 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=
> LOCAL_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
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>
>>
>
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