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
