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