Hi Troels, Thank you so much. If there is any extra info you need please let me know.
Sincerely, Sam On Thu, Sep 8, 2016 at 9:12 AM, Troels Emtekær Linnet <tlin...@nmr-relax.com > wrote: > 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> 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>: >>> >>>> 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
