Thats weird, I can open it up directly from the link you sent me. I'll reupload it
On Tue, Sep 20, 2016 at 12:40 PM, Troels Emtekær Linnet < tlin...@nmr-relax.com> wrote: > 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_a >>>>>>>>> nalyses/dauvergne_protocol.py", line 246, in __init__ >>>>>>>>> self.execute() >>>>>>>>> File "/home/sam2/relax-4.0.2/auto_a >>>>>>>>> nalyses/dauvergne_protocol.py", line 600, in execute >>>>>>>>> self.multi_model(local_tm=True) >>>>>>>>> File "/home/sam2/relax-4.0.2/auto_a >>>>>>>>> nalyses/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
