Hi Troels, So I saw the tutorial you put, and the main problem was I had not specified my data was only for the Nitrogen spins. After applying the spin column, my data loaded and relax ran model free with no problem. I have a script that starts and runs relax and model free all automatic, if you wish I can send it via email to you and you can upload it to the tutorial wiki page. So I can successfully run model-free in script mode for a uni-processor. The problem now with the multi-processor is that the script won't load. In the bug page I uploaded a screenshot where I had input the 'mpirun -np 4 ../relax --multi='mpi4py' command, however I had no output. I checked processes running in the background, and saw that there was indeed 4 processess running in the background (1 master and 3 slaves) for relax; but there was no output, so I was unable to load any data, or create a pipe or anything. This was only on the Fedora 24 computer, not the Fedora 20. On the Fedora 20 computer, I was able to successfully open relax on a multi processor platform. I can send the screenshots and the relax -i for both computers again. I don't know why it doesn't work the fedora 24. Do you know what could be causing this?
Thanks again in advance On Tue, Sep 13, 2016 at 9:32 PM, Troels Emtekær Linnet < tlin...@nmr-relax.com> wrote: > Hi Sam > > Can you send the mail again and include the maillist? > > Best Troels > > > Den tirsdag den 13. september 2016 skrev Mahdi, Sam < > sam.mahdi....@my.csun.edu>: > >> HI Troels, >> >> So I saw the tutorial you put, and the main problem was I had not >> specified my data was only for the Nitrogen spins. After applying the spin >> column, my data loaded and relax ran model free with no problem. I have a >> script that starts and runs relax and model free all automatic, if you wish >> I can send it via email to you and you can upload it to the tutorial wiki >> page. So I can successfully run model-free in script mode for a >> uni-processor. >> The problem now with the multi-processor is that the script won't load. >> In the bug page I uploaded a screenshot where I had input the 'mpirun -np 4 >> ../relax --multi='mpi4py' command, however I had no output. I checked >> processes running in the background, and saw that there was indeed 4 >> processess running in the background (1 master and 3 slaves) for relax; but >> there was no output, so I was unable to load any data, or create a pipe or >> anything. This was only on the Fedora 24 computer, not the Fedora 20. On >> the Fedora 20 computer, I was able to successfully open relax on a multi >> processor platform. I can send the screenshots and the relax -i for both >> computers again. I don't know why it doesn't work the fedora 24. Do you >> know what could be causing this? >> >> Thanks again in advance >> Sam >> >> On Tue, Sep 13, 2016 at 1:01 PM, Troels Emtekær Linnet < >> tlin...@nmr-relax.com> wrote: >> >>> Hi Sam. >>> >>> I closed the 2 bug reports as invalid. >>> >>> The data is not labelled correct. >>> But this can be corrected. >>> >>> Please see this tutorial I wrote: >>> http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_sam_mahdi >>> >>> I hope this give some guidance. >>> >>> If you experience any new problems, please feel free to ask!! >>> >>> What you experience, will probably be the same for many. >>> Your feedback is valuable for the development. >>> >>> Please wait with using mpirun and multiple processors, before you are >>> absolutely sure >>> that it will run on 1 processor. >>> >>> Bugfixing when using multiple processors is a nightmare.... >>> >>> Best >>> Troels >>> >>> 2016-09-12 17:36 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>: >>> >>>> Hi Troels, >>>> >>>> I just created another bug report. I simply copy pasted the email, and >>>> uploaded the script files there. >>>> >>>> Sincerely, >>>> Sam >>>> >>>> On Mon, Sep 12, 2016 at 5:14 AM, Troels Emtekær Linnet < >>>> tlin...@nmr-relax.com> wrote: >>>> >>>>> Hi Sam. >>>>> >>>>> Can you produce another bug report. >>>>> >>>>> Please don't attach files to these mails as it will strain the >>>>> mailinglists. >>>>> >>>>> Cheers >>>>> Troels >>>>> >>>>> >>>>> Den lørdag den 10. september 2016 skrev Mahdi, Sam < >>>>> sam.mahdi....@my.csun.edu>: >>>>> >>>>>> Hi Troels, >>>>>> >>>>>> Additional question that I had, if you could also look into this as >>>>>> well on Tuesday please. I have decided to try to write a script to >>>>>> automate >>>>>> this whole process (since I won't be using the gui to do model free), and >>>>>> I've come across a problem. I can successfully open up relax using >>>>>> openmpi, >>>>>> and can load the pdb file, and assign all the spins and isotopes; >>>>>> however, >>>>>> it appears it will only load one data file (the very first one I'll have >>>>>> inputed in the script). I don't know if there is a problem with how I >>>>>> wrote >>>>>> my script. Not only will it not load the rest of my data sets, it won't >>>>>> actually run dAuvergne's protocol either, it'll just load the data set >>>>>> and >>>>>> exit out of the program. Attached is the script I wrote for relax. >>>>>> >>>>>> This is the output once relax has loaded >>>>>> >>>>>> script = 'model_free_sample_script.py' >>>>>> ------------------------------------------------------------ >>>>>> ---------------------------------------- >>>>>> from time import asctime, localtime >>>>>> from auto_analyses.dauvergne_protocol import dAuvergne_protocol >>>>>> DIFF_MODEL=['local_tm','sphere','prolate','oblate','ellipsoi >>>>>> d','final'] >>>>>> MF_MODELS=['m0','m1','m2','m3','m4','m5','m6','m7','m8','m9'] >>>>>> LOCAL_TM_MODELS=['tm0','tm1','tm2','tm3','tm4','tm5','tm6',' >>>>>> tm7','tm7','tm8','tm9'] >>>>>> GRID_INC=11 >>>>>> MIN_ALGOR='newton' >>>>>> MC_NUM=500 >>>>>> CONV_LOOP=True >>>>>> pipe_bundle="mf(%s)"%asctime(localtime()) >>>>>> name="origin-"+pipe_bundle >>>>>> pipe.create(name,'mf',bundle=pipe_bundle) >>>>>> structure.read_pdb('2d9j.pdb',set_mol_name='hRGS7') >>>>>> structure.load_spins('@N',ave_pos=True) >>>>>> structure.load_spins('@NE1',ave_pos=True) >>>>>> structure.load_spins('@H',ave_pos=True) >>>>>> structure.load_spins('@HE1',ave_pos=True) >>>>>> spin.isotope('15N',spin_id='@N*') >>>>>> spin.isotope('1H',spin_id='@H*') >>>>>> 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) >>>>>> relax_data.read(ri_id='R2_Agnes',ri_type='R2',frq=599.642*1e6, >>>>>> file='R2_Agnes',res_num_col=1,data_col=2,error_col=3) >>>>>> relax_data.read(ri_id='ssNOE_Agnes',ri_type='NOE',frq=599.642*1e6, >>>>>> file='ssNOE_Agnes',res_num_col=1,data_col=2,error_col=3) >>>>>> relax_data.read(ri_id='R1_NMRFAM',ri_type='R1',frq=799.642*1e6, >>>>>> file='R1_NMRFAM',res_num_col=1,data_col=2,error_col=3) >>>>>> relax_data.read(ri_id='R2_NMRFAM',ri_type='R2',frq=799.642*1e6, >>>>>> file='R2_NMRFAM',res_num_col=1,data_col=2,error_col=3) >>>>>> relax_data.read(ri_id='ssNOE_NMRFAM',ri_type='NOE',frq=799.642*1e6, >>>>>> file='ssNOE_NMRFAM',res_num_col=1,data_col=2,error_col=3) >>>>>> interatom.define(spin_id1='@N',spin_id2='@H', direct_bond=True) >>>>>> interatom.define(spin_id1='@NE1',spin_id2='@HE1', direct_bond=True) >>>>>> interatom.set_dist(spin_id1='@N*',spin_id2='@H*',ave_dist=1.02*1e-10) >>>>>> interatom.unit_vectors() >>>>>> value.set(-172*1e-6,'csa',spin_id='@N*') >>>>>> dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,di >>>>>> ff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=LOCA >>>>>> L_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_sim_num >>>>>> =MC_NUM,conv_loop=CONV_LOOP) >>>>>> >>>>>> So it indicates that my script has loaded. However, after it loads >>>>>> the spins from the pdb file, this is what happens after my first data set >>>>>> has been loaded: >>>>>> >>>>>> relax> relax_data.read(ri_id='R1_Agnes', ri_type='R1', >>>>>> frq=599642000.0, file='R1_Agnes', dir=None, spin_id_col=None, >>>>>> mol_name_col=None, res_num_col=1, res_name_col=None, spin_num_col=None, >>>>>> spin_name_col=None, data_col=2, error_col=3, sep=None, spin_id=None) >>>>>> Opening the file 'R1_Agnes' for reading. >>>>>> RelaxWarning: The sequence data in the line ['Residue', 'R1', >>>>>> 'Error'] is invalid, the residue number data 'Residue' is invalid. >>>>>> RelaxWarning: The sequence data in the line ['1'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['2'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['3'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['4'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['5'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['6'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['7'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['8'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['9'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['10'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['11'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['16'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['17'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['18'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['21'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['22'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['23'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['26'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['27'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['28'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['31'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['40'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['46'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['58'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['61'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['62'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['63'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['73'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['76'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['79'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['81'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['82'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['85'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['94'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['97'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['99'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['106'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['115'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['121'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['126'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['127'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['134'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['135'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['136'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['137'] is invalid, the >>>>>> data is missing. >>>>>> RelaxWarning: The sequence data in the line ['139'] is invalid, the >>>>>> data is missing. >>>>>> >>>>>> RelaxError: The spin ID '#hRGS7:12' corresponds to multiple spins, >>>>>> including '#hRGS7:12@N' and '#hRGS7:12@H'. >>>>>> crowlab: [~/relax-4.0.2]> >>>>>> >>>>>> As you can see, I have all 6 data sets set to load, but only the very >>>>>> first one appears to do so, and after it loads, it just exits out of >>>>>> relax. >>>>>> Again, I don't know if this is a problem with how I wrote the script. The >>>>>> Relax_script1 is the one that I load up to run the whole thing. The model >>>>>> free script.py is just the script it reads once relax has opened up. >>>>>> Again, I can see all the spins are properly loaded, and the isotopes are >>>>>> set. It just everything after the first data set that doesn't load. >>>>>> Thanks >>>>>> again in advance. >>>>>> >>>>>> Sincerely, >>>>>> Sam >>>>>> >>>>>> On Thu, Sep 8, 2016 at 10:15 AM, Mahdi, Sam < >>>>>> sam.mahdi....@my.csun.edu> wrote: >>>>>> >>>>>>> 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_protoco >>>>>>>>>>>>> l.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
