Hi Sam. Thank you for your valuable feedback! It makes it more fun to help :)
Can you check if this is not in your script : http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_sam_mahdi#Let_us_try_to_execute # Execution.############ # Change some opt params.# COMMENT THESE OUT FOR REAL CALCULATION. THIS IS ONLY TO SPEED UP THE PROCESS IN ERROR SEARCHING. dAuvergne_protocol.opt_func_tol = 1e-5 dAuvergne_protocol.opt_max_iterations = 1000 Best Troels Den onsdag den 28. september 2016 skrev Mahdi, Sam < sam.mahdi....@my.csun.edu>: > Hi Troels, > > I wanted to give a bit of feedback on the results I've obtained throughout > the few weeks I've been using model free on relax. First off, thank you > guys (both you and Edward) immensly for your patience and help as I > attempted to understand and work relax. Secondly, I have noticed a > difference between using the gui and the terminal (using scripts to run > relax). I've currently finished about 3 runs using the gui, and 3 runs > using the terminal (all the same data sets, same pdb files, same settings, > etc.). The gui takes about a week to finish, where the terminal takes > approximately 24 hours. I've tried this on 2 proteins, both had the same > results. The terminal is by far, much faster than the gui. Finally, I've > run 1 protein on 2 different computers (one using the multi-processor > platform, and on another computer, single-processor). The data sets were > all the same, the same pdb file, etc. , but the results I obtained from the > computers were slightly different. For the most part, most of the > difference in the data was similar, slightly different, but within the > error. But there were about 7 or 8 data points that appeared in one run on > one computer, and were absent in another run on another computer. This > happened in both the S^2 I analyzed and the Rex. > I.e. On the fedora 20 (single processor), say I had S^2 values for amino > acid 24,25 and 26 in the sequence, but not for 28,29, and 30. On the fedora > 24 (multi-processor), I might be missing a value for amino acid 24, but I > would have S^2 values for 28,29 and 30. Note the data sets are all the > same, the pdb files the same, settings the same, I used the same script for > both. The only difference between these runs is they were run on different > computer and one was single processor well another was multi. > I don't know why I obtained different data from 2 different runs, when the > input was all the same, just on different computers. > However the S^2 values do make sense. The Rex values were incredibly small > (1x10^-20), but there are some similarities (in terms of big Rex values) > between the Rex I obtained from relax, and CPMG data analyzed by glove. So > I have been able to obtain some reasonable data and results from model_free > using relax. > > Sincerely, > Sam > > > > On Mon, Sep 26, 2016 at 2:59 PM, Mahdi, Sam <sam.mahdi....@my.csun.edu > <javascript:_e(%7B%7D,'cvml','sam.mahdi....@my.csun.edu');>> wrote: > >> Hi Troels, >> >> >> I have attempted the fix for running on a multi-processor platform by >> creating the script you told me too, and I still got the same result. I >> have uploaded a screenshot that shows again, relax is running in the >> background, but there is no output for relax, nor can I input any commands. >> The only output I recieve is this: >> Running relax with NP=$NPROC+8|bc in multi-processor mode >> >> And any command I type in after that gets no response. >> >> I've also checked the spins via script. For 2 scenarios. Scenario 1- All >> hydrogens are kept as HN and Scenario 2- I change all the HN spins to H. >> The output from Scenario one is, it read all the Nitrogen spins >> accordingly : >> Objects: >> element: 'N' >> isotope: '15N' >> name: 'N' >> num: 1304 >> pos: array([ 13.196999999999999, 15.218 , >> 3.192 ]) >> select: True >> hRGS4 178 THR #hRGS4:178@1304 >> Class containing all the spin system specific data. >> >> >> Objects: >> element: 'N' >> isotope: '15N' >> name: 'N' >> num: 2617 >> pos: array([ 22.696000000000002, 10.683999999999999, >> -4.15 ]) >> select: True >> hRGS4 178 THR #hRGS4:178@2617 >> >> But no hydrogens. >> >> Scenario 2- I still recieve the same error. >> RelaxError: Multiple alternate location indicators are present in the PDB >> file, but the desired coordinate set has not been specified. >> >> Sincerely, >> Sam >> >> On Mon, Sep 26, 2016 at 2:19 PM, Mahdi, Sam <sam.mahdi....@my.csun.edu >> <javascript:_e(%7B%7D,'cvml','sam.mahdi....@my.csun.edu');>> wrote: >> >>> Hi Troels, >>> >>> I have attempted the fix for running on a multi-processor platform by >>> creating the script you told me too, and I still got the same result. I >>> have uploaded a screenshot that shows again, relax is running in the >>> background, but there is no output for relax, nor can I input any commands. >>> The only output I recieve is this: >>> Running relax with NP=$NPROC+8|bc in multi-processor mode >>> >>> And any command I type in after that gets no response. >>> >>> Sincerely, >>> Sam >>> >>> >>> On Sun, Sep 25, 2016 at 6:43 AM, Troels Emtekær Linnet < >>> tlin...@nmr-relax.com >>> <javascript:_e(%7B%7D,'cvml','tlin...@nmr-relax.com');>> wrote: >>> >>>> Hi Sam. >>>> >>>> Try to load the pdb file and make a spin_loop over the information. >>>> How does the information look like? >>>> http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_s >>>> am_mahdi#Check_the_spin_containers_via_script >>>> >>>> Regarding the multiprocessor on your Fedora 20 machine, try to have a >>>> look at the bug. >>>> https://gna.org/bugs/?25084 >>>> >>>> ----- >>>> I suspect there is a mismatch between two installations of relax. >>>> One version of 2.x and one local of 4.x. >>>> Try adding the full path to relax >>>> ----- >>>> >>>> Try make a run script like this and copy it some where to your PATH >>>> myrelax >>>> ------ >>>> >>>> #!/bin/tcsh -fe >>>> >>>> # Set the relax version used for this script. >>>> set RELAX=/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/relax >>>> >>>> # Set number of available CPUs. >>>> set NPROC=`nproc` >>>> set NP=`echo $NPROC + 0 | bc ` >>>> echo "Running relax with NP=$NP in multi-processor mode" >>>> >>>> # Run relax in multi processor mode. >>>> mpirun -np $NP $RELAX --multi='mpi4py' $argv >>>> >>>> 2016-09-24 1:03 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu >>>> <javascript:_e(%7B%7D,'cvml','sam.mahdi....@my.csun.edu');>>: >>>> >>>>> Hi Troels, >>>>> >>>>> Update on Protein number 1: So I was able to successfully run model >>>>> free with no problems on my protein (I don't know why it was giving >>>>> problems before). The reason it may have been giving issues though is the >>>>> protein I am working with forms a dimer at the concentrations we work with >>>>> (thus the results I have are for the Dimer form of the protein). The pdb >>>>> file though only has a monomer structure though. I have been able to >>>>> obtain >>>>> the dimer pdb file using HADDOCK (docking program), but have come across a >>>>> few problems uploading the pdb file. >>>>> The initial problem was that all the hydrogens attached to the >>>>> nitrogen were HN labeled on the HADDOCK modified pdb file, and model free >>>>> could not understand what HN meant, and I would recieve this warning. >>>>> RelaxWarning: Cannot determine the element associated with atom 'HN'. >>>>> >>>>> I could however load up all the Nitrogen, but naturally, with no >>>>> hydrogens, it wouldn't be able to calculate any bond vectors between >>>>> nitrogen and hydrogen. So I would recieve this error and the program would >>>>> close >>>>> RelaxError: The spin ID '@H' matches no spins. >>>>> >>>>> To fix this, I changed all the HN spins, to just H, but then recieved >>>>> another error. >>>>> RelaxError: Multiple alternate location indicators are present in the >>>>> PDB file, but the desired coordinates set has not been specified. >>>>> >>>>> I don't exactly understand what this error means. Is it saying the >>>>> program can't locate the 3D coordinates for the Hydrogen and Nitrogen? If >>>>> that is the case, why was it able to before, when it couldn't read any of >>>>> the Hydrogen spins. I'm just confused a bit as to what this error means. >>>>> >>>>> Sincerely, >>>>> Sam >>>>> >>>>> On Wed, Sep 21, 2016 at 3:18 PM, Mahdi, Sam <sam.mahdi....@my.csun.edu >>>>> <javascript:_e(%7B%7D,'cvml','sam.mahdi....@my.csun.edu');>> wrote: >>>>> >>>>>> Hi Troels, >>>>>> >>>>>> Update on protein number 1. I ran it with only 5 simulations. It took >>>>>> a while, but it ended up finishing. So I assume its due to bad data >>>>>> simply >>>>>> slowing down the process. >>>>>> Update on protein number 2. I ran it with only 2 spins as well, and I >>>>>> still recieved the same error. I suspect its due to the pdb file. I'm >>>>>> going >>>>>> to attempt to use another program to add the hydrogens to my pdb file and >>>>>> try again. >>>>>> >>>>>> Sincerely, >>>>>> Sam >>>>>> >>>>>> On Tue, Sep 20, 2016 at 1:31 PM, Mahdi, Sam < >>>>>> sam.mahdi....@my.csun.edu >>>>>> <javascript:_e(%7B%7D,'cvml','sam.mahdi....@my.csun.edu');>> wrote: >>>>>> >>>>>>> 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 >>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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=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) >>>>>>>>>>>>>>>> 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 >>>>>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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/Tuto >>>>>>>>>>>>>>>>>>>>> rial_for_model-free_analysis_sam_mahdi >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> I hope this give some guidance. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> If you experience any new problems, please feel free >>>>>>>>>>>>>>>>>>>>> to ask!! >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> What you experience, will probably be the same for >>>>>>>>>>>>>>>>>>>>> many. >>>>>>>>>>>>>>>>>>>>> Your feedback is valuable for the development. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Please wait with using mpirun and multiple processors, >>>>>>>>>>>>>>>>>>>>> before you are absolutely sure >>>>>>>>>>>>>>>>>>>>> that it will run on 1 processor. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Bugfixing when using multiple processors is a >>>>>>>>>>>>>>>>>>>>> nightmare.... >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Best >>>>>>>>>>>>>>>>>>>>> Troels >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> 2016-09-12 17:36 GMT+02:00 Mahdi, Sam < >>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Troels, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> I just created another bug report. I simply copy >>>>>>>>>>>>>>>>>>>>>> pasted the email, and uploaded the script files there. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Sincerely, >>>>>>>>>>>>>>>>>>>>>> Sam >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Mon, Sep 12, 2016 at 5:14 AM, Troels Emtekær >>>>>>>>>>>>>>>>>>>>>> Linnet <tlin...@nmr-relax.com> wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Sam. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Can you produce another bug report. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Please don't attach files to these mails as it will >>>>>>>>>>>>>>>>>>>>>>> strain the mailinglists. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Cheers >>>>>>>>>>>>>>>>>>>>>>> Troels >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Den lørdag den 10. september 2016 skrev Mahdi, Sam < >>>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Troels, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Additional question that I had, if you could also >>>>>>>>>>>>>>>>>>>>>>>> look into this as well on Tuesday please. I have >>>>>>>>>>>>>>>>>>>>>>>> decided to try to write a >>>>>>>>>>>>>>>>>>>>>>>> script to automate this whole process (since I won't >>>>>>>>>>>>>>>>>>>>>>>> be using the gui to do >>>>>>>>>>>>>>>>>>>>>>>> model free), and I've come across a problem. I can >>>>>>>>>>>>>>>>>>>>>>>> successfully open up >>>>>>>>>>>>>>>>>>>>>>>> relax using openmpi, and can load the pdb file, and >>>>>>>>>>>>>>>>>>>>>>>> assign all the spins >>>>>>>>>>>>>>>>>>>>>>>> and isotopes; however, it appears it will only load >>>>>>>>>>>>>>>>>>>>>>>> one data file (the very >>>>>>>>>>>>>>>>>>>>>>>> first one I'll have inputed in the script). I don't >>>>>>>>>>>>>>>>>>>>>>>> know if there is a >>>>>>>>>>>>>>>>>>>>>>>> problem with how I wrote my script. Not only will it >>>>>>>>>>>>>>>>>>>>>>>> not load the rest of >>>>>>>>>>>>>>>>>>>>>>>> my data sets, it won't actually run dAuvergne's >>>>>>>>>>>>>>>>>>>>>>>> protocol either, it'll just >>>>>>>>>>>>>>>>>>>>>>>> load the data set and exit out of the program. >>>>>>>>>>>>>>>>>>>>>>>> Attached is the script I >>>>>>>>>>>>>>>>>>>>>>>> wrote for relax. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> This is the output once relax has loaded >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> script = 'model_free_sample_script.py' >>>>>>>>>>>>>>>>>>>>>>>> ------------------------------ >>>>>>>>>>>>>>>>>>>>>>>> ------------------------------ >>>>>>>>>>>>>>>>>>>>>>>> ---------------------------------------- >>>>>>>>>>>>>>>>>>>>>>>> from time import asctime, localtime >>>>>>>>>>>>>>>>>>>>>>>> from auto_analyses.dauvergne_protocol import >>>>>>>>>>>>>>>>>>>>>>>> dAuvergne_protocol >>>>>>>>>>>>>>>>>>>>>>>> DIFF_MODEL=['local_tm','sphere >>>>>>>>>>>>>>>>>>>>>>>> ','prolate','oblate','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_co >>>>>>>>>>>>>>>>>>>>>>>> l=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/?grou >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> p=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
