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=name,pipe_bundle=pipe_bundle,di >>>>>>>>>>> ff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=LOCA >>>>>>>>>>> L_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_sim_num >>>>>>>>>>> =MC_NUM,conv_loop=CONV_LOOP) >>>>>>>>>>> File "/home/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/?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
