That looks wrong. NP should be the variable for the number of processors.
I suspect the error is not in relax, but somewhere in your system. I think I can't help you more from here. Is there a computer wizard around at your lab? Best Troels Den mandag den 26. september 2016 skrev Mahdi, Sam < sam.mahdi....@my.csun.edu>: > 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 > <javascript:_e(%7B%7D,'cvml','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_ >> sam_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 >> <javascript:_e(%7B%7D,'cvml','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 >>> <javascript:_e(%7B%7D,'cvml','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 >>>> <javascript:_e(%7B%7D,'cvml','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 >>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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,diff_model=DIFF_MODEL,mf_models= >>>>>>>>>>>>>> MF_MODELS,local_tm_models=LOCAL_TM_MODELS,grid_inc=GRID_INC, >>>>>>>>>>>>>> min_algor=MIN_ALGOR,mc_sim_num=MC_NUM,conv_loop=CONV_LOOP) >>>>>>>>>>>>>> File "/home/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 >>>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>>>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','sam.mahdi....@my.csun.edu');> >>>>>>>>>>>>>>>>> >: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> HI Troels, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> So I saw the tutorial you put, and the main problem was I >>>>>>>>>>>>>>>>>> had not specified my data was only for the Nitrogen spins. >>>>>>>>>>>>>>>>>> After applying >>>>>>>>>>>>>>>>>> the spin column, my data loaded and relax ran model free >>>>>>>>>>>>>>>>>> with no problem. I >>>>>>>>>>>>>>>>>> have a script that starts and runs relax and model free all >>>>>>>>>>>>>>>>>> automatic, if >>>>>>>>>>>>>>>>>> you wish I can send it via email to you and you can upload >>>>>>>>>>>>>>>>>> it to the >>>>>>>>>>>>>>>>>> tutorial wiki page. So I can successfully run model-free in >>>>>>>>>>>>>>>>>> script mode for >>>>>>>>>>>>>>>>>> a uni-processor. >>>>>>>>>>>>>>>>>> The problem now with the multi-processor is that the >>>>>>>>>>>>>>>>>> script won't load. In the bug page I uploaded a screenshot >>>>>>>>>>>>>>>>>> where I had >>>>>>>>>>>>>>>>>> input the 'mpirun -np 4 ../relax --multi='mpi4py' command, >>>>>>>>>>>>>>>>>> however I had no >>>>>>>>>>>>>>>>>> output. I checked processes running in the background, and >>>>>>>>>>>>>>>>>> saw that there >>>>>>>>>>>>>>>>>> was indeed 4 processess running in the background (1 master >>>>>>>>>>>>>>>>>> and 3 slaves) >>>>>>>>>>>>>>>>>> for relax; but there was no output, so I was unable to load >>>>>>>>>>>>>>>>>> any data, or >>>>>>>>>>>>>>>>>> create a pipe or anything. This was only on the Fedora 24 >>>>>>>>>>>>>>>>>> computer, not the >>>>>>>>>>>>>>>>>> Fedora 20. On the Fedora 20 computer, I was able to >>>>>>>>>>>>>>>>>> successfully open relax >>>>>>>>>>>>>>>>>> on a multi processor platform. I can send the screenshots >>>>>>>>>>>>>>>>>> and the relax -i >>>>>>>>>>>>>>>>>> for both computers again. I don't know why it doesn't work >>>>>>>>>>>>>>>>>> the fedora 24. >>>>>>>>>>>>>>>>>> Do you know what could be causing this? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks again in advance >>>>>>>>>>>>>>>>>> Sam >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Tue, Sep 13, 2016 at 1:01 PM, Troels Emtekær Linnet < >>>>>>>>>>>>>>>>>> tlin...@nmr-relax.com> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sam. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I closed the 2 bug reports as invalid. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The data is not labelled correct. >>>>>>>>>>>>>>>>>>> But this can be corrected. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Please see this tutorial I wrote: >>>>>>>>>>>>>>>>>>> http://wiki.nmr-relax.com/Tuto >>>>>>>>>>>>>>>>>>> rial_for_model-free_analysis_sam_mahdi >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I hope this give some guidance. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> If you experience any new problems, please feel free to >>>>>>>>>>>>>>>>>>> ask!! >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> What you experience, will probably be the same for many. >>>>>>>>>>>>>>>>>>> Your feedback is valuable for the development. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Please wait with using mpirun and multiple processors, >>>>>>>>>>>>>>>>>>> before you are absolutely sure >>>>>>>>>>>>>>>>>>> that it will run on 1 processor. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Bugfixing when using multiple processors is a >>>>>>>>>>>>>>>>>>> nightmare.... >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Best >>>>>>>>>>>>>>>>>>> Troels >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> 2016-09-12 17:36 GMT+02:00 Mahdi, Sam < >>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Troels, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I just created another bug report. I simply copy pasted >>>>>>>>>>>>>>>>>>>> the email, and uploaded the script files there. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Sincerely, >>>>>>>>>>>>>>>>>>>> Sam >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Mon, Sep 12, 2016 at 5:14 AM, Troels Emtekær Linnet >>>>>>>>>>>>>>>>>>>> <tlin...@nmr-relax.com> wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Sam. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Can you produce another bug report. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Please don't attach files to these mails as it will >>>>>>>>>>>>>>>>>>>>> strain the mailinglists. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Cheers >>>>>>>>>>>>>>>>>>>>> Troels >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Den lørdag den 10. september 2016 skrev Mahdi, Sam < >>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Troels, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Additional question that I had, if you could also >>>>>>>>>>>>>>>>>>>>>> look into this as well on Tuesday please. I have decided >>>>>>>>>>>>>>>>>>>>>> to try to write a >>>>>>>>>>>>>>>>>>>>>> script to automate this whole process (since I won't be >>>>>>>>>>>>>>>>>>>>>> using the gui to do >>>>>>>>>>>>>>>>>>>>>> model free), and I've come across a problem. I can >>>>>>>>>>>>>>>>>>>>>> successfully open up >>>>>>>>>>>>>>>>>>>>>> relax using openmpi, and can load the pdb file, and >>>>>>>>>>>>>>>>>>>>>> assign all the spins >>>>>>>>>>>>>>>>>>>>>> and isotopes; however, it appears it will only load one >>>>>>>>>>>>>>>>>>>>>> data file (the very >>>>>>>>>>>>>>>>>>>>>> first one I'll have inputed in the script). I don't know >>>>>>>>>>>>>>>>>>>>>> if there is a >>>>>>>>>>>>>>>>>>>>>> problem with how I wrote my script. Not only will it not >>>>>>>>>>>>>>>>>>>>>> load the rest of >>>>>>>>>>>>>>>>>>>>>> my data sets, it won't actually run dAuvergne's protocol >>>>>>>>>>>>>>>>>>>>>> either, it'll just >>>>>>>>>>>>>>>>>>>>>> load the data set and exit out of the program. Attached >>>>>>>>>>>>>>>>>>>>>> is the script I >>>>>>>>>>>>>>>>>>>>>> wrote for relax. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> This is the output once relax has loaded >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> script = 'model_free_sample_script.py' >>>>>>>>>>>>>>>>>>>>>> ------------------------------ >>>>>>>>>>>>>>>>>>>>>> ------------------------------ >>>>>>>>>>>>>>>>>>>>>> ---------------------------------------- >>>>>>>>>>>>>>>>>>>>>> from time import asctime, localtime >>>>>>>>>>>>>>>>>>>>>> from auto_analyses.dauvergne_protocol import >>>>>>>>>>>>>>>>>>>>>> dAuvergne_protocol >>>>>>>>>>>>>>>>>>>>>> DIFF_MODEL=['local_tm','sphere >>>>>>>>>>>>>>>>>>>>>> ','prolate','oblate','ellipsoid','final'] >>>>>>>>>>>>>>>>>>>>>> MF_MODELS=['m0','m1','m2','m3' >>>>>>>>>>>>>>>>>>>>>> ,'m4','m5','m6','m7','m8','m9'] >>>>>>>>>>>>>>>>>>>>>> LOCAL_TM_MODELS=['tm0','tm1',' >>>>>>>>>>>>>>>>>>>>>> tm2','tm3','tm4','tm5','tm6','tm7','tm7','tm8','tm9'] >>>>>>>>>>>>>>>>>>>>>> GRID_INC=11 >>>>>>>>>>>>>>>>>>>>>> MIN_ALGOR='newton' >>>>>>>>>>>>>>>>>>>>>> MC_NUM=500 >>>>>>>>>>>>>>>>>>>>>> CONV_LOOP=True >>>>>>>>>>>>>>>>>>>>>> pipe_bundle="mf(%s)"%asctime(localtime()) >>>>>>>>>>>>>>>>>>>>>> name="origin-"+pipe_bundle >>>>>>>>>>>>>>>>>>>>>> pipe.create(name,'mf',bundle=pipe_bundle) >>>>>>>>>>>>>>>>>>>>>> structure.read_pdb('2d9j.pdb',set_mol_name='hRGS7') >>>>>>>>>>>>>>>>>>>>>> structure.load_spins('@N',ave_pos=True) >>>>>>>>>>>>>>>>>>>>>> structure.load_spins('@NE1',ave_pos=True) >>>>>>>>>>>>>>>>>>>>>> structure.load_spins('@H',ave_pos=True) >>>>>>>>>>>>>>>>>>>>>> structure.load_spins('@HE1',ave_pos=True) >>>>>>>>>>>>>>>>>>>>>> spin.isotope('15N',spin_id='@N*') >>>>>>>>>>>>>>>>>>>>>> spin.isotope('1H',spin_id='@H*') >>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='R1_Agne >>>>>>>>>>>>>>>>>>>>>> s',ri_type='R1',frq=599.642*1e6, >>>>>>>>>>>>>>>>>>>>>> file='R1_Agnes',res_num_col=1,data_col=2,error_col=3) >>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='R2_Agne >>>>>>>>>>>>>>>>>>>>>> s',ri_type='R2',frq=599.642*1e6, >>>>>>>>>>>>>>>>>>>>>> file='R2_Agnes',res_num_col=1,data_col=2,error_col=3) >>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='ssNOE_A >>>>>>>>>>>>>>>>>>>>>> gnes',ri_type='NOE',frq=599.642*1e6, >>>>>>>>>>>>>>>>>>>>>> file='ssNOE_Agnes',res_num_col >>>>>>>>>>>>>>>>>>>>>> =1,data_col=2,error_col=3) >>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='R1_NMRF >>>>>>>>>>>>>>>>>>>>>> AM',ri_type='R1',frq=799.642*1e6, >>>>>>>>>>>>>>>>>>>>>> file='R1_NMRFAM',res_num_col=1 >>>>>>>>>>>>>>>>>>>>>> ,data_col=2,error_col=3) >>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='R2_NMRF >>>>>>>>>>>>>>>>>>>>>> AM',ri_type='R2',frq=799.642*1e6, >>>>>>>>>>>>>>>>>>>>>> file='R2_NMRFAM',res_num_col=1 >>>>>>>>>>>>>>>>>>>>>> ,data_col=2,error_col=3) >>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='ssNOE_N >>>>>>>>>>>>>>>>>>>>>> MRFAM',ri_type='NOE',frq=799.642*1e6, >>>>>>>>>>>>>>>>>>>>>> file='ssNOE_NMRFAM',res_num_co >>>>>>>>>>>>>>>>>>>>>> l=1,data_col=2,error_col=3) >>>>>>>>>>>>>>>>>>>>>> interatom.define(spin_id1='@N',spin_id2='@H', >>>>>>>>>>>>>>>>>>>>>> direct_bond=True) >>>>>>>>>>>>>>>>>>>>>> interatom.define(spin_id1='@NE1',spin_id2='@HE1', >>>>>>>>>>>>>>>>>>>>>> direct_bond=True) >>>>>>>>>>>>>>>>>>>>>> interatom.set_dist(spin_id1='@ >>>>>>>>>>>>>>>>>>>>>> N*',spin_id2='@H*',ave_dist=1.02*1e-10) >>>>>>>>>>>>>>>>>>>>>> interatom.unit_vectors() >>>>>>>>>>>>>>>>>>>>>> value.set(-172*1e-6,'csa',spin_id='@N*') >>>>>>>>>>>>>>>>>>>>>> dAuvergne_protocol(pipe_name=n >>>>>>>>>>>>>>>>>>>>>> ame,pipe_bundle=pipe_bundle,di >>>>>>>>>>>>>>>>>>>>>> ff_model=DIFF_MODEL,mf_models= >>>>>>>>>>>>>>>>>>>>>> MF_MODELS,local_tm_models=LOCA >>>>>>>>>>>>>>>>>>>>>> L_TM_MODELS,grid_inc=GRID_INC, >>>>>>>>>>>>>>>>>>>>>> min_algor=MIN_ALGOR,mc_sim_num >>>>>>>>>>>>>>>>>>>>>> =MC_NUM,conv_loop=CONV_LOOP) >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> So it indicates that my script has loaded. However, >>>>>>>>>>>>>>>>>>>>>> after it loads the spins from the pdb file, this is what >>>>>>>>>>>>>>>>>>>>>> happens after my >>>>>>>>>>>>>>>>>>>>>> first data set has been loaded: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> relax> relax_data.read(ri_id='R1_Agnes', >>>>>>>>>>>>>>>>>>>>>> ri_type='R1', frq=599642000.0, file='R1_Agnes', >>>>>>>>>>>>>>>>>>>>>> dir=None, spin_id_col=None, >>>>>>>>>>>>>>>>>>>>>> mol_name_col=None, res_num_col=1, res_name_col=None, >>>>>>>>>>>>>>>>>>>>>> spin_num_col=None, >>>>>>>>>>>>>>>>>>>>>> spin_name_col=None, data_col=2, error_col=3, sep=None, >>>>>>>>>>>>>>>>>>>>>> spin_id=None) >>>>>>>>>>>>>>>>>>>>>> Opening the file 'R1_Agnes' for reading. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line >>>>>>>>>>>>>>>>>>>>>> ['Residue', 'R1', 'Error'] is invalid, the residue >>>>>>>>>>>>>>>>>>>>>> number data 'Residue' is >>>>>>>>>>>>>>>>>>>>>> invalid. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['1'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['2'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['3'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['4'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['5'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['6'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['7'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['8'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['9'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['10'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['11'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['16'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['17'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['18'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['21'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['22'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['23'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['26'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['27'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['28'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['31'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['40'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['46'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['58'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['61'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['62'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['63'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['73'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['76'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['79'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['81'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['82'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['85'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['94'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['97'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['99'] is >>>>>>>>>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['106'] >>>>>>>>>>>>>>>>>>>>>> is invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['115'] >>>>>>>>>>>>>>>>>>>>>> is invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['121'] >>>>>>>>>>>>>>>>>>>>>> is invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['126'] >>>>>>>>>>>>>>>>>>>>>> is invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['127'] >>>>>>>>>>>>>>>>>>>>>> is invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['134'] >>>>>>>>>>>>>>>>>>>>>> is invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['135'] >>>>>>>>>>>>>>>>>>>>>> is invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['136'] >>>>>>>>>>>>>>>>>>>>>> is invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['137'] >>>>>>>>>>>>>>>>>>>>>> is invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['139'] >>>>>>>>>>>>>>>>>>>>>> is invalid, the data is missing. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> RelaxError: The spin ID '#hRGS7:12' corresponds to >>>>>>>>>>>>>>>>>>>>>> multiple spins, including '#hRGS7:12@N' and >>>>>>>>>>>>>>>>>>>>>> '#hRGS7:12@H'. >>>>>>>>>>>>>>>>>>>>>> crowlab: [~/relax-4.0.2]> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> As you can see, I have all 6 data sets set to load, >>>>>>>>>>>>>>>>>>>>>> but only the very first one appears to do so, and after >>>>>>>>>>>>>>>>>>>>>> it loads, it just >>>>>>>>>>>>>>>>>>>>>> exits out of relax. Again, I don't know if this is a >>>>>>>>>>>>>>>>>>>>>> problem with how I >>>>>>>>>>>>>>>>>>>>>> wrote the script. The Relax_script1 is the one that I >>>>>>>>>>>>>>>>>>>>>> load up to run the >>>>>>>>>>>>>>>>>>>>>> whole thing. The model free script.py is just the script >>>>>>>>>>>>>>>>>>>>>> it reads once >>>>>>>>>>>>>>>>>>>>>> relax has opened up. Again, I can see all the spins are >>>>>>>>>>>>>>>>>>>>>> properly loaded, >>>>>>>>>>>>>>>>>>>>>> and the isotopes are set. It just everything after the >>>>>>>>>>>>>>>>>>>>>> first data set that >>>>>>>>>>>>>>>>>>>>>> doesn't load. Thanks again in advance. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Sincerely, >>>>>>>>>>>>>>>>>>>>>> Sam >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Thu, Sep 8, 2016 at 10:15 AM, Mahdi, Sam < >>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu> wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Troels, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thank you so much. If there is any extra info you >>>>>>>>>>>>>>>>>>>>>>> need please let me know. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Sincerely, >>>>>>>>>>>>>>>>>>>>>>> Sam >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Thu, Sep 8, 2016 at 9:12 AM, Troels Emtekær >>>>>>>>>>>>>>>>>>>>>>> Linnet <tlin...@nmr-relax.com> wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Sam. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> I will have some time on Tuesday, and then I will >>>>>>>>>>>>>>>>>>>>>>>> look at it. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Best >>>>>>>>>>>>>>>>>>>>>>>> Troels >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Den onsdag den 7. september 2016 skrev Mahdi, Sam < >>>>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hello Troels, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> I uploaded all the files, and even added in the >>>>>>>>>>>>>>>>>>>>>>>>> entire output that i recieved using model free in >>>>>>>>>>>>>>>>>>>>>>>>> script mode. I didn't >>>>>>>>>>>>>>>>>>>>>>>>> know if all the files uploaded need to have that >>>>>>>>>>>>>>>>>>>>>>>>> link, so only the initial >>>>>>>>>>>>>>>>>>>>>>>>> files that were uploaded it, have it. >>>>>>>>>>>>>>>>>>>>>>>>> Thank you in advance for your help! >>>>>>>>>>>>>>>>>>>>>>>>> Sincerely, >>>>>>>>>>>>>>>>>>>>>>>>> Sam >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Sep 7, 2016 at 12:41 AM, Troels Emtekær >>>>>>>>>>>>>>>>>>>>>>>>> Linnet <tlin...@nmr-relax.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sam. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> You should be able to upload more files after the >>>>>>>>>>>>>>>>>>>>>>>>>> initial upload. >>>>>>>>>>>>>>>>>>>>>>>>>> In the comment thread, please also make a link to >>>>>>>>>>>>>>>>>>>>>>>>>> this discussion. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> https://mail.gna.org/public/re >>>>>>>>>>>>>>>>>>>>>>>>>> lax-users/2016-09/threads.html#00001 >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Best >>>>>>>>>>>>>>>>>>>>>>>>>> Troels >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> 2016-09-06 19:10 GMT+02:00 Mahdi, Sam < >>>>>>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for your reply. When I come to upload >>>>>>>>>>>>>>>>>>>>>>>>>>> my data though, I see there are only 4 available >>>>>>>>>>>>>>>>>>>>>>>>>>> slots I can upload my >>>>>>>>>>>>>>>>>>>>>>>>>>> data. I have a total of 6 data files however, that >>>>>>>>>>>>>>>>>>>>>>>>>>> need to be uploaded (3 >>>>>>>>>>>>>>>>>>>>>>>>>>> of each frequency). I also need to upload the relax >>>>>>>>>>>>>>>>>>>>>>>>>>> -i of 2 different >>>>>>>>>>>>>>>>>>>>>>>>>>> computers, and the script file I've been using for >>>>>>>>>>>>>>>>>>>>>>>>>>> a total of 9 files that >>>>>>>>>>>>>>>>>>>>>>>>>>> need to be uploaded. Is there a way to increase the >>>>>>>>>>>>>>>>>>>>>>>>>>> amount I can upload, or >>>>>>>>>>>>>>>>>>>>>>>>>>> can I upload more after the initial submission? >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Sep 5, 2016 at 2:46 AM, Troels Emtekær >>>>>>>>>>>>>>>>>>>>>>>>>>> Linnet <tlin...@nmr-relax.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sam. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> To solve this problem, it would be easier to >>>>>>>>>>>>>>>>>>>>>>>>>>>> have access to some of your data. >>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you upload to: https://gna.org/bugs/?grou >>>>>>>>>>>>>>>>>>>>>>>>>>>> p=relax >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Take each of your data files, and delete all >>>>>>>>>>>>>>>>>>>>>>>>>>>> data, except 2 spins. >>>>>>>>>>>>>>>>>>>>>>>>>>>> Also provide your script file, or a description >>>>>>>>>>>>>>>>>>>>>>>>>>>> of which button you press in the GUI. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Please also provide information about your >>>>>>>>>>>>>>>>>>>>>>>>>>>> system with: >>>>>>>>>>>>>>>>>>>>>>>>>>>> relax -i >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Then I will make a tutorial for you. To be >>>>>>>>>>>>>>>>>>>>>>>>>>>> added here: >>>>>>>>>>>>>>>>>>>>>>>>>>>> http://wiki.nmr-relax.com/Category:Tutorials >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> If there is a problem in relax, I will write a >>>>>>>>>>>>>>>>>>>>>>>>>>>> systemtest which will solve the problem. >>>>>>>>>>>>>>>>>>>>>>>>>>>> And the problem will never return. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> If this a user error, the tutorial should help >>>>>>>>>>>>>>>>>>>>>>>>>>>> to prevent this, and would be the first step before >>>>>>>>>>>>>>>>>>>>>>>>>>>> adding/modifying the manual. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding using mpirun. >>>>>>>>>>>>>>>>>>>>>>>>>>>> Have a look at this page. Maybe it helps. >>>>>>>>>>>>>>>>>>>>>>>>>>>> http://wiki.nmr-relax.com/OpenMPI >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Cheers. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 2016-09-03 4:13 GMT+02:00 Mahdi, Sam < >>>>>>>>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hello everyone, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> So I was able to set up and run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> dauvergne_protocol successfully by >>>>>>>>>>>>>>>>>>>>>>>>>>>>> using the script in the wiki. The problem I >>>>>>>>>>>>>>>>>>>>>>>>>>>>> have come across now is the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> program doesn't seem to read my data. Using >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the gui interface I was able to >>>>>>>>>>>>>>>>>>>>>>>>>>>>> successfully load my data and run it. When I >>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload my data using the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> script command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax_data.read(ri_id='R1_Agne >>>>>>>>>>>>>>>>>>>>>>>>>>>>> s',ri_type='R1',frq=599.642*1e6, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> file='R1_Agnes',res_num_col=1, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> data_col=2,error_col=3) >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The output file simply gives errors for amino >>>>>>>>>>>>>>>>>>>>>>>>>>>>> acids I don't have data for: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ['1'] is invalid, the data is >>>>>>>>>>>>>>>>>>>>>>>>>>>>> missing. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is fine as relax just ignores these >>>>>>>>>>>>>>>>>>>>>>>>>>>>> values and continues its >>>>>>>>>>>>>>>>>>>>>>>>>>>>> calculations. I only receive this warning for >>>>>>>>>>>>>>>>>>>>>>>>>>>>> values I don't have data for. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is the same thing I got when using the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> gui interface (the gui however >>>>>>>>>>>>>>>>>>>>>>>>>>>>> showed my values that I have data for and the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> residue it corresponds to, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> using the script I don't receive such an >>>>>>>>>>>>>>>>>>>>>>>>>>>>> output, I don't know whether this >>>>>>>>>>>>>>>>>>>>>>>>>>>>> is normal or not). However, since I don't get >>>>>>>>>>>>>>>>>>>>>>>>>>>>> this warning for every amino >>>>>>>>>>>>>>>>>>>>>>>>>>>>> acid, I assume this means it has read the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> values for the other amino acids. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> All of my data is the same, relax warnings >>>>>>>>>>>>>>>>>>>>>>>>>>>>> only pop up for amino acids that >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't have data for. The problem is, when I >>>>>>>>>>>>>>>>>>>>>>>>>>>>> enter the dAuvergne protocol, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I get the protocol working, it starts running >>>>>>>>>>>>>>>>>>>>>>>>>>>>> local_tm however it appears >>>>>>>>>>>>>>>>>>>>>>>>>>>>> none of my data has been uploaded: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The spin '#hRGS7:2@N' has been >>>>>>>>>>>>>>>>>>>>>>>>>>>>> deselected because of missing >>>>>>>>>>>>>>>>>>>>>>>>>>>>> relaxation data >>>>>>>>>>>>>>>>>>>>>>>>>>>>> RelaxWarning: The spin '#hRGS7:3@N' has been >>>>>>>>>>>>>>>>>>>>>>>>>>>>> deselected because of missing >>>>>>>>>>>>>>>>>>>>>>>>>>>>> relaxation data >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> And I get that warning for every single amino >>>>>>>>>>>>>>>>>>>>>>>>>>>>> acid. From the output, it >>>>>>>>>>>>>>>>>>>>>>>>>>>>> appears to have read the file since it knows >>>>>>>>>>>>>>>>>>>>>>>>>>>>> exactly which amino acids I >>>>>>>>>>>>>>>>>>>>>>>>>>>>> don't have data for, but I don't know why when >>>>>>>>>>>>>>>>>>>>>>>>>>>>> it comes to running the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> protocol, it tells me I havn't inputed any >>>>>>>>>>>>>>>>>>>>>>>>>>>>> data. I have typed everything >>>>>>>>>>>>>>>>>>>>>>>>>>>>> directly according to the script from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> wiki. From running the protoco, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> it appears everything has properly been >>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploaded, structure data, magnetic >>>>>>>>>>>>>>>>>>>>>>>>>>>>> dipole interactions, csa, the data pipe, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> analysis variables, the python >>>>>>>>>>>>>>>>>>>>>>>>>>>>> module imports, and setting up the spins from >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the pdb file. It appears the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> only error is from loading the actual >>>>>>>>>>>>>>>>>>>>>>>>>>>>> relaxation data. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> On a completely unrelated side note, I have >>>>>>>>>>>>>>>>>>>>>>>>>>>>> been attempting to run relax on >>>>>>>>>>>>>>>>>>>>>>>>>>>>> multiple processors. I have tried 2 different >>>>>>>>>>>>>>>>>>>>>>>>>>>>> computers, both fedora linux. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have mpi4py and openmpi downloaded on both. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> On one, I can get relax on >>>>>>>>>>>>>>>>>>>>>>>>>>>>> multiple cores working (havn't been able to >>>>>>>>>>>>>>>>>>>>>>>>>>>>> successfully run it due to >>>>>>>>>>>>>>>>>>>>>>>>>>>>> being unable to upload any data properly). On >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the other however, I type in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the mpirun -np --multi='mpi4py' script, but I >>>>>>>>>>>>>>>>>>>>>>>>>>>>> get no output. I can see that >>>>>>>>>>>>>>>>>>>>>>>>>>>>> it's running in the background (top command), >>>>>>>>>>>>>>>>>>>>>>>>>>>>> but nothing pops up, no text >>>>>>>>>>>>>>>>>>>>>>>>>>>>> command, nothing. I typed the same mpirun with >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the --gui, but that opened >>>>>>>>>>>>>>>>>>>>>>>>>>>>> up nothing. On a uni-processor (typing in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> exact same command without >>>>>>>>>>>>>>>>>>>>>>>>>>>>> indicating how many cores i.e. no -np >>>>>>>>>>>>>>>>>>>>>>>>>>>>> --multi='mpi4py') it works just fine, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> so I don't think its my openmpi that's an >>>>>>>>>>>>>>>>>>>>>>>>>>>>> issue. I don't know whether this >>>>>>>>>>>>>>>>>>>>>>>>>>>>> is an issue with my mpi4py or a personal >>>>>>>>>>>>>>>>>>>>>>>>>>>>> computer issue (since on the other >>>>>>>>>>>>>>>>>>>>>>>>>>>>> computer relax runs just fine on multiple >>>>>>>>>>>>>>>>>>>>>>>>>>>>> cores). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sincerely, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sam >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> P.S. when I do enter the top command to see >>>>>>>>>>>>>>>>>>>>>>>>>>>>> what's running. My master shows >>>>>>>>>>>>>>>>>>>>>>>>>>>>> mpirun, and the 3 slaves display python when I >>>>>>>>>>>>>>>>>>>>>>>>>>>>> put -np 4, so I know >>>>>>>>>>>>>>>>>>>>>>>>>>>>> something is running in the background. I have >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 8 cores. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Aug 31, 2016 at 6:49 PM, Mahdi, Sam < >>>>>>>>>>>>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Hello everyone, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > I am attempting to run relax on a >>>>>>>>>>>>>>>>>>>>>>>>>>>>> multi-processor mode. I have been able >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > to successfully set-up relax to operate in a >>>>>>>>>>>>>>>>>>>>>>>>>>>>> multi-processor mode by using >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > the mpirun -np #ofprocessors >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /location/of/relax --multi='mpi4py' >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > The problem I encounter is when using the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> --tee log dauvergne_protocol.py >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > command. I receive this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > RelaxError: the script file >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 'dauvergne_protocol.py' does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > I located the script file and tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>> direct to it's path >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > mpirun /usr/local/Relax/relax-2.2.5/relax >>>>>>>>>>>>>>>>>>>>>>>>>>>>> --multi='mpi4py' --tee log >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > /usr/local/Relax/relax-2.2.5/a >>>>>>>>>>>>>>>>>>>>>>>>>>>>> uto-analyses/dauvergne_protocol.py >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > But i received this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > RelaxError: the script file >>>>>>>>>>>>>>>>>>>>>>>>>>>>> '/usr/local/Relax/relax-2.2.5/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > auto-analyses/dauvergne_protocol.py' does >>>>>>>>>>>>>>>>>>>>>>>>>>>>> not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Even though I have the script, it doesn't >>>>>>>>>>>>>>>>>>>>>>>>>>>>> seem to be able to locate it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > On a side note, in the manual, one dash >>>>>>>>>>>>>>>>>>>>>>>>>>>>> doesn't actually run the command. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > I.e. in the manual it displays >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -multi='mpi4py' . What it should be is >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > --multi='mpi4py' . The same goes for -tee. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> It should be --tee. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Sincerely, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Sam >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ______________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> _________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax (http://www.nmr-relax.com) >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is the relax-users mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>>> relax-users@gna.org >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> To unsubscribe from this list, get a password >>>>>>>>>>>>>>>>>>>>>>>>>>>>> reminder, or change your subscription options, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit the list information page at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mail.gna.org/listinfo/relax-users >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > _______________________________________________ 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
