Hi Sam have you tried with only one set of coordinates (i presume these are both homo dimers with some form of symetry plane or axis?
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 23:24, 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 (Mahdi, Sam) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 28 Sep 2016 15:23:58 -0700 > From: "Mahdi, Sam" <sam.mahdi....@my.csun.edu> > To: Troels Emtekær Linnet <tlin...@nmr-relax.com>, > relax-users@gna.org > Subject: Re: Using multi-processor for model_free > Message-ID: > <calgm0gud0t4jpbwzzhazipq196cpk8cuvoqvvgy3ezacxcw...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Troels, > Update on both proteins: So for protein 1, I can upload all the spins (H > and N), but then I recieve an error. This is the error I recieved for > protein 2 as well. These are both dimer pdb files. Meaning they have 2 sets > (set A) and set (B) (e.g. > http://www.rcsb.org/pdb/explore/explore.do?structureId=1DJ8 this pdb > protein has 4 sets, A,B,C, and D ours only have A and B). For both these > proteins I recieve this error > File "/home/crowlab/relax-4.0.2/multi/processor.py", line 494, in run > self.callback.init_master(self) > File "/home/crowlab/relax-4.0.2/multi/__init__.py", line 318, in > default_init_master > self.master.run() > File "/home/crowlab/relax-4.0.2/relax.py", line 199, in run > self.interpreter.run(self.script_file) > File "/home/crowlab/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/crowlab/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/crowlab/relax-4.0.2/prompt/interpreter.py", line 484, in > interact_script > exec_script(script_file, local) > File "/home/crowlab/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 180, 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/crowlab/relax-4.0.2/RGS4_modelfree_sample_script.py", line > 31, in <module> > > dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,diff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=LOCAL_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_sim_num=MC_NUM,conv_loop=CONV_LOOP) > File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py", > line 246, in __init__ > self.execute() > File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py", > line 600, in execute > self.multi_model(local_tm=True) > File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py", > line 888, in multi_model > self.interpreter.minimise.grid_search(inc=self.grid_inc) > File "/home/crowlab/relax-4.0.2/prompt/uf_objects.py", line 225, in > __call__ > self._backend(*new_args, **uf_kargs) > File "/home/crowlab/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/crowlab/relax-4.0.2/pipe_control/minimise.py", line 341, in > grid_setup > elif values[i] in [None, {}, []]: > IndexError: index out of bounds > > Which from my understanding basically means, the co-ordinates of the spins > are out of the acceptable range for relax. I've checked all the > co-ordinates for both, nothing is extreme or outlandish (all within a range > of -20 to 20). > Is relax unable to process pdb files that are dimers (with 2 sets A and > B).? Furthermore, is it unable to process trimers and tetramers? > > Sincerely, > Sam > > On Wed, Sep 28, 2016 at 1:44 PM, Mahdi, Sam <sam.mahdi....@my.csun.edu> > wrote: > >> Hey Troels, >> >> I ran the relax -x and recieve this error at the GUI tests >> ============= >> = GUI tests = >> ============= >> >> ........................** >> Gtk:ERROR:gtkfilesystemmodel.c:746:gtk_file_system_model_sort: assertion >> failed: (r == n_visible_rows) >> Abort (core dumped) >> crowlab: [~/relax-4.0.2]> >> >> >> On Wed, Sep 28, 2016 at 1:30 PM, Mahdi, Sam <sam.mahdi....@my.csun.edu> >> wrote: >> >>> Hi Troels, >>> >>> An update on protein number 1: I have successfully resolved the problem. >>> Initially the pdb file had HN instead of just H for the backbone hydrogens. >>> So it couldn't read it. I changed all the HN to H. Then I recieved the >>> error >>> RelaxError: Multiple alternate location indicators are present in the PDB >>> file, but the desired coordinate set has not been specified >>> By removing the extra N, all the text for the 3D location (the >>> co-ordinates) for the HN were shifted a space (no longer aligned). Once I >>> aligned them all, relax was able to read all the spins. So its working now. >>> I'm currently running the test suite as well. >>> >>> Sincerely, >>> Sam >>> >>> On Wed, Sep 28, 2016 at 11:45 AM, Troels Emtekær Linnet < >>> tlin...@nmr-relax.com> wrote: >>> >>>> To test the speed difference between script and GUI, >>>> you could try to run the full test-suite through the terminal or >>>> inside the GUI. >>>> >>>> That should give you a clue about time difference. >>>> >>>> >>>> 2016-09-28 20:32 GMT+02:00 Troels Emtekær Linnet <tlin...@nmr-relax.com> >>>> : >>>> >>>>> If you get different results, for the same setup, this is not good. >>>>> Not at all ! >>>>> >>>>> Have you run the full relax test suite after installation? >>>>> >>>>> http://wiki.nmr-relax.com/Installation_test >>>>> >>>>> run it with: >>>>> relax -x >>>>> >>>>> This takes about 1 Hour to run, and should not be used with multiple >>>>> processors. >>>>> >>>>> Relax will test itself with thousands of unit tests and system tests, >>>>> and confer that all >>>>> results are the same. >>>>> >>>>> If the system tests do not pass on each system, something fishy is >>>>> going on. >>>>> >>>>> This is the best line of defence against "systems" acting weird due to >>>>> software/packages etc. etc. >>>>> >>>>> Best >>>>> Troels >>>>> >>>>> >>>>> >>>>> 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/?group=relax >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Take each of your data files, and delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all data, except 2 spins. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Also provide your script file, or a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> description of which button you press in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the GUI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please also provide information about >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your system with: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax -i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then I will make a tutorial for you. To >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be added here: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> http://wiki.nmr-relax.com/Cate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> gory: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 38 > ******************************************** _______________________________________________ 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
