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= >> LOCAL_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_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