Hi Sam. Problems with the GUI do not necessary mean a problem.
It could be a problem of wxPython. Which version do you have? (relax -i ) To find the specific tests that fails, can you do: > relax --gui-tests --time -t gui_fail.txt Best Troels 2016-09-28 22:44 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>: > 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