Hi Troels, I will upload a bug report with the pdb file, the script I use, and the data I'm using.
Sincerely, Sam On Thu, Sep 29, 2016 at 2:25 PM, Troels Emtekær Linnet < tlin...@nmr-relax.com> wrote: > Hi Sam. > > Hm... > > I had a look in: pipe_control/minimise.py > > The trouble start with line > "elif values[i] in [None, {}, []]:" > > Where the index "i" is running out of bounds. > > The index is drawn from range(n). > n = len(names) > names = api.get_param_names(model_info) > values = api.get_param_values(model_info) > > So "something" is not aligned well in the data structures. > It seems that the index of parameter names exceeds parameter values. > > > One guess is, that the selection of > * diff_model > * mf_models > * local_tm_models > > is not correctly set. But I reach my limit of being able to help you. > Edward is the expert here, but he is on paternity leave. > > > Another possibility is that some of the spins are in "select" mode, where > they maybe should be in "deselect" mode. > > Maybe the spins do not carry any data from before, and somehow relax > expect this. > > It's very tricky to figure out! > > A bug report, some minimum data, and a script which make the bug occur can > solve this. > > Then I can write a systemtest, if it relax which is failing. > > Best > Troels > > > > > 2016-09-29 0:23 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>: > >> 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/explor >> e/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,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/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 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > _______________________________________________ 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