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_analyses/dauvergne_protocol.py", >>>>>>> line 246, in __init__ >>>>>>> self.execute() >>>>>>> File "/home/sam2/relax-4.0.2/auto_analyses/dauvergne_protocol.py", >>>>>>> line 600, in execute >>>>>>> self.multi_model(local_tm=True) >>>>>>> File "/home/sam2/relax-4.0.2/auto_analyses/dauvergne_protocol.py", >>>>>>> line 888, in multi_model >>>>>>> self.interpreter.minimise.grid_search(inc=self.grid_inc) >>>>>>> File "/home/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/Tutorial_for_model-free_analysis_s >>>>>>>>>>>> am_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','ellipsoi >>>>>>>>>>>>>>> d','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_Agnes',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_Agnes',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_Agnes',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_NMRFAM',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_NMRFAM',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_NMRFAM',ri_type='NOE',frq=799.642*1e6, >>>>>>>>>>>>>>> file='ssNOE_NMRFAM',res_num_col=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=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) >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> So it indicates that my script has loaded. However, after it >>>>>>>>>>>>>>> loads the spins from the pdb file, this is what happens after >>>>>>>>>>>>>>> my first data >>>>>>>>>>>>>>> set has been loaded: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> relax> relax_data.read(ri_id='R1_Agnes', ri_type='R1', >>>>>>>>>>>>>>> frq=599642000.0, file='R1_Agnes', dir=None, spin_id_col=None, >>>>>>>>>>>>>>> mol_name_col=None, res_num_col=1, res_name_col=None, >>>>>>>>>>>>>>> spin_num_col=None, >>>>>>>>>>>>>>> spin_name_col=None, data_col=2, error_col=3, sep=None, >>>>>>>>>>>>>>> spin_id=None) >>>>>>>>>>>>>>> Opening the file 'R1_Agnes' for reading. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['Residue', >>>>>>>>>>>>>>> 'R1', 'Error'] is invalid, the residue number data 'Residue' is >>>>>>>>>>>>>>> invalid. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['1'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['2'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['3'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['4'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['5'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['6'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['7'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['8'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['9'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['10'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['11'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['16'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['17'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['18'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['21'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['22'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['23'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['26'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['27'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['28'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['31'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['40'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['46'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['58'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['61'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['62'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['63'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['73'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['76'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['79'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['81'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['82'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['85'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['94'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['97'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['99'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['106'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['115'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['121'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['126'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['127'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['134'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['135'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['136'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['137'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['139'] is >>>>>>>>>>>>>>> invalid, the data is missing. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> RelaxError: The spin ID '#hRGS7:12' corresponds to multiple >>>>>>>>>>>>>>> spins, including '#hRGS7:12@N' and '#hRGS7:12@H'. >>>>>>>>>>>>>>> crowlab: [~/relax-4.0.2]> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> As you can see, I have all 6 data sets set to load, but only >>>>>>>>>>>>>>> the very first one appears to do so, and after it loads, it >>>>>>>>>>>>>>> just exits out >>>>>>>>>>>>>>> of relax. Again, I don't know if this is a problem with how I >>>>>>>>>>>>>>> wrote the >>>>>>>>>>>>>>> script. The Relax_script1 is the one that I load up to run the >>>>>>>>>>>>>>> whole thing. >>>>>>>>>>>>>>> The model free script.py is just the script it reads once relax >>>>>>>>>>>>>>> has opened >>>>>>>>>>>>>>> up. Again, I can see all the spins are properly loaded, and >>>>>>>>>>>>>>> the isotopes >>>>>>>>>>>>>>> are set. It just everything after the first data set that >>>>>>>>>>>>>>> doesn't load. >>>>>>>>>>>>>>> Thanks again in advance. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Sincerely, >>>>>>>>>>>>>>> Sam >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Thu, Sep 8, 2016 at 10:15 AM, Mahdi, Sam < >>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Troels, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thank you so much. If there is any extra info you need >>>>>>>>>>>>>>>> please let me know. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Sincerely, >>>>>>>>>>>>>>>> Sam >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Thu, Sep 8, 2016 at 9:12 AM, Troels Emtekær Linnet < >>>>>>>>>>>>>>>> tlin...@nmr-relax.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sam. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> I will have some time on Tuesday, and then I will look at >>>>>>>>>>>>>>>>> it. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Best >>>>>>>>>>>>>>>>> Troels >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Den onsdag den 7. september 2016 skrev Mahdi, Sam < >>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hello Troels, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I uploaded all the files, and even added in the entire >>>>>>>>>>>>>>>>>> output that i recieved using model free in script mode. I >>>>>>>>>>>>>>>>>> didn't know if >>>>>>>>>>>>>>>>>> all the files uploaded need to have that link, so only the >>>>>>>>>>>>>>>>>> initial files >>>>>>>>>>>>>>>>>> that were uploaded it, have it. >>>>>>>>>>>>>>>>>> Thank you in advance for your help! >>>>>>>>>>>>>>>>>> Sincerely, >>>>>>>>>>>>>>>>>> Sam >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Wed, Sep 7, 2016 at 12:41 AM, Troels Emtekær Linnet < >>>>>>>>>>>>>>>>>> tlin...@nmr-relax.com> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sam. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> You should be able to upload more files after the >>>>>>>>>>>>>>>>>>> initial upload. >>>>>>>>>>>>>>>>>>> In the comment thread, please also make a link to this >>>>>>>>>>>>>>>>>>> discussion. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> https://mail.gna.org/public/re >>>>>>>>>>>>>>>>>>> lax-users/2016-09/threads.html#00001 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Best >>>>>>>>>>>>>>>>>>> Troels >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> 2016-09-06 19:10 GMT+02:00 Mahdi, Sam < >>>>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thank you for your reply. When I come to upload my data >>>>>>>>>>>>>>>>>>>> though, I see there are only 4 available slots I can >>>>>>>>>>>>>>>>>>>> upload my data. I have >>>>>>>>>>>>>>>>>>>> a total of 6 data files however, that need to be uploaded >>>>>>>>>>>>>>>>>>>> (3 of each >>>>>>>>>>>>>>>>>>>> frequency). I also need to upload the relax -i of 2 >>>>>>>>>>>>>>>>>>>> different computers, >>>>>>>>>>>>>>>>>>>> and the script file I've been using for a total of 9 files >>>>>>>>>>>>>>>>>>>> that need to be >>>>>>>>>>>>>>>>>>>> uploaded. Is there a way to increase the amount I can >>>>>>>>>>>>>>>>>>>> upload, or can I >>>>>>>>>>>>>>>>>>>> upload more after the initial submission? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Mon, Sep 5, 2016 at 2:46 AM, Troels Emtekær Linnet < >>>>>>>>>>>>>>>>>>>> tlin...@nmr-relax.com> wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Sam. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> To solve this problem, it would be easier to have >>>>>>>>>>>>>>>>>>>>> access to some of your data. >>>>>>>>>>>>>>>>>>>>> Can you upload to: https://gna.org/bugs/?group=relax >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Take each of your data files, and delete all data, >>>>>>>>>>>>>>>>>>>>> except 2 spins. >>>>>>>>>>>>>>>>>>>>> Also provide your script file, or a description of >>>>>>>>>>>>>>>>>>>>> which button you press in the GUI. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Please also provide information about your system with: >>>>>>>>>>>>>>>>>>>>> relax -i >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Then I will make a tutorial for you. To be added here: >>>>>>>>>>>>>>>>>>>>> http://wiki.nmr-relax.com/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
