The file: file #28673: relax -i data for 4.0,2 a https://gna.org/bugs/download.php?file_id=28673
Its emtpy? 2016-09-20 20:05 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>: > Hi Troels, > > I am a bit confused what you are talking about. There is no file labeled .? > > On Tue, Sep 20, 2016 at 9:15 AM, Troels Emtekær Linnet < > tlin...@nmr-relax.com> wrote: > >> 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','ellipsoid','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_Agne >>>>>>>>>>>>>>>> s',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_Agne >>>>>>>>>>>>>>>> s',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_A >>>>>>>>>>>>>>>> gnes',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_NMRF >>>>>>>>>>>>>>>> AM',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_NMRF >>>>>>>>>>>>>>>> AM',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_N >>>>>>>>>>>>>>>> MRFAM',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=n >>>>>>>>>>>>>>>> ame,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
