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
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
_______________________________________________
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
