Hi Sam.
On
https://gna.org/bugs/?25084
I cannot open the file.?
In the meantime, try to specify the full path to relax. Not just ./relax
but /home/user/xxx/relax
Best
Troels
2016-09-19 23:13 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
> I just uploaded the 4.0.2 relax -i info. I already have minfx 1.0.12 with
> 4.0.2. But I can't open relax on multi processor platform for either
> version.
>
> On Mon, Sep 19, 2016 at 10:47 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Please upgrade!
>>
>> Name Installed Version Current version
>> minfx True 1.0.4 1.0.12
>>
>> relax information:
>> Version: 2.2.5 4.0.2
>>
>>
>> 2016-09-19 19:41 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>>
>>> Hi Troels,
>>>
>>> I have uploaded the bug report for the issue with running relax on
>>> multiple processors on my fedora 20 computer. I will upload the mpirun
>>> report bindings on the fedora 24 computer later today (that is not my lab
>>> so I don't have access to it, and the professor is not in yet). If there is
>>> any more info that is needed please let me know. Thanks again in advance.
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Mon, Sep 19, 2016 at 10:24 AM, Mahdi, Sam <sam.mahdi....@my.csun.edu>
>>> wrote:
>>>
>>>> Hi Troels,
>>>>
>>>> Thanks for the quick response!
>>>>
>>>> Protein 1: I will attempt to troubleshoot using the advice you gave me.
>>>> The problem occurs write after it indicates its writing a file for prolate
>>>> round_3 (so its about to start it). I will run it again and post the output
>>>> to give you a better idea. I'm pretty sure the output was something like
>>>> this
>>>> Over-fit spin deselection:
>>>> No spins have been deselected.
>>>> Resetting the minimisation statistics.
>>>> But I will double check and send you another email with the actual
>>>> output.
>>>> Protein 2:
>>>> I am using the sample script for dAuvergene protocol. So the only thing
>>>> I've changed since my previous run (the one that worked that you wrote a
>>>> tutorial for), was the pdb file and the data set I used. The thing I
>>>> suspected was causing an issue ,was the pdb file since I slightly modified
>>>> it, and thats really the only thing different from this run versus the
>>>> others.
>>>>
>>>> Also side note, if I were to deselect the spins that I don't have data
>>>> for or I have bad data for, that wouldn't change any of the calculations
>>>> correct? I never have since I assumed relax would just ignore all the amino
>>>> acids I don't have data for, but it may help increase the speed of my
>>>> calculations if I just tell relax to just ignore the spins from the start.
>>>>
>>>> Sincerely,
>>>> Sam
>>>>
>>>> On Mon, Sep 19, 2016 at 9:12 AM, Troels Emtekær Linnet <
>>>> tlin...@nmr-relax.com> wrote:
>>>>
>>>>> Hi Sam.
>>>>>
>>>>> Happy to hear you that you get some progress.
>>>>>
>>>>> Protein 1:
>>>>> Can you help me to find out, if you are minimizing or running
>>>>> Monte-Carlo simulations?
>>>>> This COULD be the problem:
>>>>>
>>>>> How relax works (at least how it works for relaxation dispersion):
>>>>> Step 1: Minimize the error for the target function. Find the
>>>>> parameters which best match the target function to the data, by minimizing
>>>>> the error.
>>>>> Here each individual spin minimization is handed out to a processor
>>>>> for calculation.
>>>>>
>>>>> Step 2: Determine the error of the minimization by monte carlo
>>>>> simulations.
>>>>> Create (Standard 500) additional datasets with a copy from the
>>>>> original. Modify each datapoint by an error, drawn from a gaussian
>>>>> distribution where the width is described by the error of measurements.
>>>>> Now hand out each of the datasets to the processor. Each processor
>>>>> should now calculate the minimization for all the spins. The minimization
>>>>> should be more quick, as the starting position is chosen from Step 1.
>>>>>
>>>>> Possible problem: One (or more) of the spins has really bad data. So a
>>>>> little change of the data makes the minimization space very different.
>>>>> Think of a flat table. Where should the "minimization ball" run into?
>>>>> Maybe you have created a small new bump in the table. This is typically
>>>>> for
>>>>> "bad" data.
>>>>>
>>>>> This could either be the measurement OR the error estimation. Relax
>>>>> will keep on searching for minimization.
>>>>> If you are "unlucky", some of the created datasets will make relax
>>>>> hang for a very long time.
>>>>>
>>>>> Unfortunately, it is NOT possible to ask a processor about its
>>>>> "current" work, when it is doing a minimization for a whole dataset.
>>>>> And if it was, it would create an output of 64 spins being minimized
>>>>> at the same time, creating a big mess, since the processors are working
>>>>> alone. When doing Monte-Carlo simulations, relax are quite silent. Only
>>>>> reporting when a whole dataset is done.
>>>>>
>>>>> Is relax stuck in Monte-Carlo simulations?
>>>>>
>>>>> Possible solution:
>>>>> *) Set Monte-Carlo simulations to 3 (which is minimum), and know that
>>>>> you have found the right minimum, but the error estimation of the
>>>>> parameters are wrong.
>>>>> *) Carefully inspect your data, deselecting all spins which have "bad
>>>>> data". Look at their graphs. Consider working with as few spins as
>>>>> possible, and work your way up! Working this way will greatly increase
>>>>> your
>>>>> productivity.
>>>>>
>>>>> Protein 2:
>>>>> Are you setting the bonds for the minimization manually?
>>>>> This looks like the upper/lower bonds are specified wrong. This is not
>>>>> easy to do. How are you doing it?
>>>>>
>>>>> Best
>>>>> Troels
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> 2016-09-19 17:11 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>>>>>
>>>>>> Hi Troels,
>>>>>>
>>>>>> I have successfully been able to run the model-free analysis on 64
>>>>>> cores. The issue appears to have been I simply did not specify the spin
>>>>>> number, so after looking at your tutorial and making the proper
>>>>>> modifications, it ran with no complications. The results are somewhat
>>>>>> reasonable. I decided to try to run 2 other proteins however; and I've
>>>>>> come
>>>>>> across problems for both again.
>>>>>> Protein 1:
>>>>>> I set this up just like the tutorial, and it runs with no warnings or
>>>>>> errors; however, the run never finishes. At round_3 for the prolate model
>>>>>> when it starts to minimize it just stops. I don't mean relax is stopped
>>>>>> or
>>>>>> closed, I mean it stops doing any calculations. Relax is still open, and
>>>>>> if
>>>>>> I run the top command, I can still see something is going on with the
>>>>>> other
>>>>>> cores, but nothing is being calculated. The run with 64 cores is
>>>>>> incredibly
>>>>>> fast (under 4 hours), so I don't think it's loading calculations or
>>>>>> writing
>>>>>> them, and I've left it there for over 24 hours, and it's still just sorta
>>>>>> stuck. There are no errors, no outputs, it just says its gonna start to
>>>>>> minimize and then nothing happens after that.
>>>>>> Protein2:
>>>>>> This protein was a little different since the pdb structure was a
>>>>>> crystal structure. I had to use WhatIf to add the protons onto the pdb
>>>>>> file. The structure appears to load up fine, all the spins appear to be
>>>>>> read, data is loaded, vectors and are calculated and define, but when I
>>>>>> came to run the protocol this error pops up:
>>>>>> File "/home/sam2/relax-4.0.2/multi/processor.py", line 494, in run
>>>>>> self.callback.init_master(self)
>>>>>> File "/home/sam2/relax-4.0.2/multi/__init__.py", line 318, in
>>>>>> default_init_master
>>>>>> self.master.run()
>>>>>> File "/home/sam2/relax-4.0.2/relax.py", line 199, in run
>>>>>> self.interpreter.run(self.script_file)
>>>>>> File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 279, in
>>>>>> run
>>>>>> return run_script(intro=self.__intro_string, local=locals(),
>>>>>> script_file=script_file, show_script=self.__show_script,
>>>>>> raise_relax_error=self.__raise_relax_error)
>>>>>> File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 585, in
>>>>>> run_script
>>>>>> return console.interact(intro, local, script_file,
>>>>>> show_script=show_script, raise_relax_error=raise_relax_error)
>>>>>> File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 484, in
>>>>>> interact_script
>>>>>> exec_script(script_file, local)
>>>>>> File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 363, in
>>>>>> exec_script
>>>>>> runpy.run_module(module, globals)
>>>>>> File "/usr/lib64/python2.7/runpy.py", line 192, in run_module
>>>>>> fname, loader, pkg_name)
>>>>>> File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
>>>>>> exec code in run_globals
>>>>>> File "/home/sam2/relax-4.0.2/HdeA_script.py", line 30, in <module>
>>>>>> dAuvergne_protocol(pipe_name=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/re
>>>>>>>>>>>>>>>>>> lax-users/2016-09/threads.html#00001
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>>>>> Troels
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 2016-09-06 19:10 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thank you for your reply. When I come to upload my data
>>>>>>>>>>>>>>>>>>> though, I see there are only 4 available slots I can upload
>>>>>>>>>>>>>>>>>>> my data. I have
>>>>>>>>>>>>>>>>>>> a total of 6 data files however, that need to be uploaded
>>>>>>>>>>>>>>>>>>> (3 of each
>>>>>>>>>>>>>>>>>>> frequency). I also need to upload the relax -i of 2
>>>>>>>>>>>>>>>>>>> different computers,
>>>>>>>>>>>>>>>>>>> and the script file I've been using for a total of 9 files
>>>>>>>>>>>>>>>>>>> that need to be
>>>>>>>>>>>>>>>>>>> uploaded. Is there a way to increase the amount I can
>>>>>>>>>>>>>>>>>>> upload, or can I
>>>>>>>>>>>>>>>>>>> upload more after the initial submission?
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Mon, Sep 5, 2016 at 2:46 AM, Troels Emtekær Linnet <
>>>>>>>>>>>>>>>>>>> tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> To solve this problem, it would be easier to have
>>>>>>>>>>>>>>>>>>>> access to some of your data.
>>>>>>>>>>>>>>>>>>>> Can you upload to: https://gna.org/bugs/?group=relax
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Take each of your data files, and delete all data,
>>>>>>>>>>>>>>>>>>>> except 2 spins.
>>>>>>>>>>>>>>>>>>>> Also provide your script file, or a description of
>>>>>>>>>>>>>>>>>>>> which button you press in the GUI.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Please also provide information about your system with:
>>>>>>>>>>>>>>>>>>>> relax -i
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Then I will make a tutorial for you. To be added here:
>>>>>>>>>>>>>>>>>>>> http://wiki.nmr-relax.com/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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