Hi Sam. I will have some time on Tuesday, and then I will look at it.
Best Troels Den onsdag den 7. september 2016 skrev Mahdi, Sam <sam.mahdi....@my.csun.edu >: > 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 > <javascript:_e(%7B%7D,'cvml','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 >> <javascript:_e(%7B%7D,'cvml','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 >>> <javascript:_e(%7B%7D,'cvml','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 >>>> <javascript:_e(%7B%7D,'cvml','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 >>>>> <javascript:_e(%7B%7D,'cvml','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 >>>>> <javascript:_e(%7B%7D,'cvml','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
