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
