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_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_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/relax-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_Agnes',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/auto-analyses/dauvergne_protoco >>>>>>>>>> l.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
