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
