Hi Sam if you log to file, tail -f of the log file gives a good overview of the output and minimisation without the overhead
regards gary -- ------------------------------------------------------------------- Dr Gary Thompson [Leeds Biological NMR Facility] Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024 email: ga...@bmb.leeds.ac.uk Fax +44-113-3431935 ------------------------------------------------------------------- > On 28 Sep 2016, at 19:27, relax-users-requ...@gna.org wrote: > > Send relax-users mailing list submissions to > relax-users@gna.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.gna.org/listinfo/relax-users > or, via email, send a message with subject or body 'help' to > relax-users-requ...@gna.org > > You can reach the person managing the list at > relax-users-ow...@gna.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of relax-users digest..." > > > Today's Topics: > > 1. Re: Using multi-processor for model_free (Troels Emtekær Linnet) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 28 Sep 2016 20:26:59 +0200 > From: Troels Emtekær Linnet <tlin...@nmr-relax.com> > To: "Mahdi, Sam" <sam.mahdi....@my.csun.edu> > Cc: "relax-users@gna.org" <relax-users@gna.org> > Subject: Re: Using multi-processor for model_free > Message-ID: > <ca+cbx2pw2eqeye2noyt6qxcezi0kzvzn1uhiqzhryytwv2h...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Another possibility for the "slowness" is "the very well known" that, > printing to screen makes > python slow. > > Extremely slow... > > And all the minimization information to screen actually slow downs relax > (through python). > > For even faster calculations, just "log" the relax output with -l, and do > not "tee" -t and print to screen. > Try skipping all printing to screen. > > You lose the ability to follow the process live, but you win in speed ! > > A possible explanation for the slow GUI, is that printing to screen through > the GUI is a terrible process. > Try to imagine how many "computer layers" the "text" has to travel through, > to arrive in the "GUI screen". > The worst is, it is almost impossible to "really" test. > > > > > > > > 2016-09-28 9:44 GMT+02:00 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> >> 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=$NPROC+8|bc in multi-processor mode >>> >>> And any command I type in after that gets no response. >>> >>> I've also checked the spins via script. For 2 scenarios. Scenario 1- All >>> hydrogens are kept as HN and Scenario 2- I change all the HN spins to H. >>> The output from Scenario one is, it read all the Nitrogen spins >>> accordingly : >>> Objects: >>> element: 'N' >>> isotope: '15N' >>> name: 'N' >>> num: 1304 >>> pos: array([ 13.196999999999999, 15.218 , >>> 3.192 ]) >>> select: True >>> hRGS4 178 THR #hRGS4:178@1304 >>> Class containing all the spin system specific data. >>> >>> >>> Objects: >>> element: 'N' >>> isotope: '15N' >>> name: 'N' >>> num: 2617 >>> pos: array([ 22.696000000000002, 10.683999999999999, >>> -4.15 ]) >>> select: True >>> hRGS4 178 THR #hRGS4:178@2617 >>> >>> But no hydrogens. >>> >>> Scenario 2- I still recieve the same error. >>> RelaxError: Multiple alternate location indicators are present in the PDB >>> file, but the desired coordinate set has not been specified. >>> >>> Sincerely, >>> Sam >>> >>> On Mon, Sep 26, 2016 at 2:19 PM, Mahdi, Sam <sam.mahdi....@my.csun.edu> >>> wrote: >>> >>>> Hi Troels, >>>> >>>> I have attempted the fix for running on a multi-processor platform by >>>> creating the script you told me too, and I still got the same result. I >>>> have uploaded a screenshot that shows again, relax is running in the >>>> background, but there is no output for relax, nor can I input any commands. >>>> The only output I recieve is this: >>>> Running relax with NP=$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> 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>: >>>>> >>>>>> 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 >>>>>>> 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> 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> 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=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> 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/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 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > 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 > > ------------------------------ > > End of relax-users Digest, Vol 116, Issue 33 > ******************************************** _______________________________________________ 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
