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
