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
