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
