Hi Troels, I will upload the bug report later today; however, I know that openmpi does work. I can open relax using mpirun ./relax in uni processor mode. It just doesn't load up when I specify processors and add --multi='mpi4py'. But I will run those commands for both computers, and upload the results. Thank you again for your help.
Sincerely, Sam On Mon, Sep 19, 2016 at 8:11 AM, Mahdi, Sam <sam.mahdi....@my.csun.edu> wrote: > Hi Troels, > > I have successfully been able to run the model-free analysis on 64 cores. > The issue appears to have been I simply did not specify the spin number, so > after looking at your tutorial and making the proper modifications, it ran > with no complications. The results are somewhat reasonable. I decided to > try to run 2 other proteins however; and I've come across problems for both > again. > Protein 1: > I set this up just like the tutorial, and it runs with no warnings or > errors; however, the run never finishes. At round_3 for the prolate model > when it starts to minimize it just stops. I don't mean relax is stopped or > closed, I mean it stops doing any calculations. Relax is still open, and if > I run the top command, I can still see something is going on with the other > cores, but nothing is being calculated. The run with 64 cores is incredibly > fast (under 4 hours), so I don't think it's loading calculations or writing > them, and I've left it there for over 24 hours, and it's still just sorta > stuck. There are no errors, no outputs, it just says its gonna start to > minimize and then nothing happens after that. > Protein2: > This protein was a little different since the pdb structure was a crystal > structure. I had to use WhatIf to add the protons onto the pdb file. The > structure appears to load up fine, all the spins appear to be read, data is > loaded, vectors and are calculated and define, but when I came to run the > protocol this error pops up: > File "/home/sam2/relax-4.0.2/multi/processor.py", line 494, in run > self.callback.init_master(self) > File "/home/sam2/relax-4.0.2/multi/__init__.py", line 318, in > default_init_master > self.master.run() > File "/home/sam2/relax-4.0.2/relax.py", line 199, in run > self.interpreter.run(self.script_file) > File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 279, in run > return run_script(intro=self.__intro_string, local=locals(), > script_file=script_file, show_script=self.__show_script, > raise_relax_error=self.__raise_relax_error) > File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 585, in > run_script > return console.interact(intro, local, script_file, > show_script=show_script, raise_relax_error=raise_relax_error) > File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 484, in > interact_script > exec_script(script_file, local) > File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 363, in > exec_script > runpy.run_module(module, globals) > File "/usr/lib64/python2.7/runpy.py", line 192, in run_module > fname, loader, pkg_name) > File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code > exec code in run_globals > File "/home/sam2/relax-4.0.2/HdeA_script.py", line 30, in <module> > dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,di > ff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models= > LOCAL_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_ > sim_num=MC_NUM,conv_loop=CONV_LOOP) > File "/home/sam2/relax-4.0.2/auto_analyses/dauvergne_protocol.py", line > 246, in __init__ > self.execute() > File "/home/sam2/relax-4.0.2/auto_analyses/dauvergne_protocol.py", line > 600, in execute > self.multi_model(local_tm=True) > File "/home/sam2/relax-4.0.2/auto_analyses/dauvergne_protocol.py", line > 888, in multi_model > self.interpreter.minimise.grid_search(inc=self.grid_inc) > File "/home/sam2/relax-4.0.2/prompt/uf_objects.py", line 225, in > __call__ > self._backend(*new_args, **uf_kargs) > File "/home/sam2/relax-4.0.2/pipe_control/minimise.py", line 172, in > grid_search > model_lower, model_upper, model_inc = grid_setup(lower, upper, inc, > verbosity=verbosity, skip_preset=skip_preset) > File "/home/sam2/relax-4.0.2/pipe_control/minimise.py", line 341, in > grid_setup > elif values[i] in [None, {}, []]: > IndexError: index 0 is out of bounds for axis 0 with size 0 > I should mention this error pops up when it decided to calculate the first > spins upper and lower bounds. So this isn't at the minimization portion of > the calculation (like in the previous bug). Thanks in advance. > > Sincerely, > Sam > > On Wed, Sep 14, 2016 at 6:34 AM, Troels Emtekær Linnet < > tlin...@nmr-relax.com> wrote: > >> Hi Sam. >> >> To tackle this problem, I would advice to create another bug. >> Creation and closing of a bug "leaves trails", which maybe will help >> another person, when googling for the same problem. >> >> To help you, can you do a "relax -i" on both computers? >> That give some indication about package versions and computer setup. >> >> The first thing we need to establish, is that mpirun is working. >> We have to test the installation without relax. >> >> Can you have a look at: >> http://wiki.nmr-relax.com/OpenMPI >> >> Try the different things like: >> lscpu >> mpirun --report-bindings -np 11 echo "hello world" >> mpirun --report-bindings -np 4 relax --multi='mpi4py' >> >> When we are confident about this, then we will try make a small test >> script for relax. >> >> Please try these things at both computers, and provide 2 files with >> commands and output. >> >> Then attach it to the bug report. >> >> >> >> >> >> 2016-09-14 6:40 GMT+02:00 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 >>> >>> 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_Agne >>>>>>>>>>>>>>>> s',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/a >>>>>>>>>>>>>>>> uto-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