Hi Sam. On https://gna.org/bugs/?25084
I cannot open the file.? In the meantime, try to specify the full path to relax. Not just ./relax but /home/user/xxx/relax Best Troels 2016-09-19 23:13 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>: > I just uploaded the 4.0.2 relax -i info. I already have minfx 1.0.12 with > 4.0.2. But I can't open relax on multi processor platform for either > version. > > On Mon, Sep 19, 2016 at 10:47 AM, Troels Emtekær Linnet < > tlin...@nmr-relax.com> wrote: > >> Please upgrade! >> >> Name Installed Version Current version >> minfx True 1.0.4 1.0.12 >> >> relax information: >> Version: 2.2.5 4.0.2 >> >> >> 2016-09-19 19:41 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>: >> >>> Hi Troels, >>> >>> I have uploaded the bug report for the issue with running relax on >>> multiple processors on my fedora 20 computer. I will upload the mpirun >>> report bindings on the fedora 24 computer later today (that is not my lab >>> so I don't have access to it, and the professor is not in yet). If there is >>> any more info that is needed please let me know. Thanks again in advance. >>> >>> Sincerely, >>> Sam >>> >>> On Mon, Sep 19, 2016 at 10:24 AM, Mahdi, Sam <sam.mahdi....@my.csun.edu> >>> wrote: >>> >>>> Hi Troels, >>>> >>>> Thanks for the quick response! >>>> >>>> Protein 1: I will attempt to troubleshoot using the advice you gave me. >>>> The problem occurs write after it indicates its writing a file for prolate >>>> round_3 (so its about to start it). I will run it again and post the output >>>> to give you a better idea. I'm pretty sure the output was something like >>>> this >>>> Over-fit spin deselection: >>>> No spins have been deselected. >>>> Resetting the minimisation statistics. >>>> But I will double check and send you another email with the actual >>>> output. >>>> Protein 2: >>>> I am using the sample script for dAuvergene protocol. So the only thing >>>> I've changed since my previous run (the one that worked that you wrote a >>>> tutorial for), was the pdb file and the data set I used. The thing I >>>> suspected was causing an issue ,was the pdb file since I slightly modified >>>> it, and thats really the only thing different from this run versus the >>>> others. >>>> >>>> Also side note, if I were to deselect the spins that I don't have data >>>> for or I have bad data for, that wouldn't change any of the calculations >>>> correct? I never have since I assumed relax would just ignore all the amino >>>> acids I don't have data for, but it may help increase the speed of my >>>> calculations if I just tell relax to just ignore the spins from the start. >>>> >>>> Sincerely, >>>> Sam >>>> >>>> On Mon, Sep 19, 2016 at 9:12 AM, Troels Emtekær Linnet < >>>> tlin...@nmr-relax.com> wrote: >>>> >>>>> Hi Sam. >>>>> >>>>> Happy to hear you that you get some progress. >>>>> >>>>> Protein 1: >>>>> Can you help me to find out, if you are minimizing or running >>>>> Monte-Carlo simulations? >>>>> This COULD be the problem: >>>>> >>>>> How relax works (at least how it works for relaxation dispersion): >>>>> Step 1: Minimize the error for the target function. Find the >>>>> parameters which best match the target function to the data, by minimizing >>>>> the error. >>>>> Here each individual spin minimization is handed out to a processor >>>>> for calculation. >>>>> >>>>> Step 2: Determine the error of the minimization by monte carlo >>>>> simulations. >>>>> Create (Standard 500) additional datasets with a copy from the >>>>> original. Modify each datapoint by an error, drawn from a gaussian >>>>> distribution where the width is described by the error of measurements. >>>>> Now hand out each of the datasets to the processor. Each processor >>>>> should now calculate the minimization for all the spins. The minimization >>>>> should be more quick, as the starting position is chosen from Step 1. >>>>> >>>>> Possible problem: One (or more) of the spins has really bad data. So a >>>>> little change of the data makes the minimization space very different. >>>>> Think of a flat table. Where should the "minimization ball" run into? >>>>> Maybe you have created a small new bump in the table. This is typically >>>>> for >>>>> "bad" data. >>>>> >>>>> This could either be the measurement OR the error estimation. Relax >>>>> will keep on searching for minimization. >>>>> If you are "unlucky", some of the created datasets will make relax >>>>> hang for a very long time. >>>>> >>>>> Unfortunately, it is NOT possible to ask a processor about its >>>>> "current" work, when it is doing a minimization for a whole dataset. >>>>> And if it was, it would create an output of 64 spins being minimized >>>>> at the same time, creating a big mess, since the processors are working >>>>> alone. When doing Monte-Carlo simulations, relax are quite silent. Only >>>>> reporting when a whole dataset is done. >>>>> >>>>> Is relax stuck in Monte-Carlo simulations? >>>>> >>>>> Possible solution: >>>>> *) Set Monte-Carlo simulations to 3 (which is minimum), and know that >>>>> you have found the right minimum, but the error estimation of the >>>>> parameters are wrong. >>>>> *) Carefully inspect your data, deselecting all spins which have "bad >>>>> data". Look at their graphs. Consider working with as few spins as >>>>> possible, and work your way up! Working this way will greatly increase >>>>> your >>>>> productivity. >>>>> >>>>> Protein 2: >>>>> Are you setting the bonds for the minimization manually? >>>>> This looks like the upper/lower bonds are specified wrong. This is not >>>>> easy to do. How are you doing it? >>>>> >>>>> Best >>>>> Troels >>>>> >>>>> >>>>> >>>>> >>>>> 2016-09-19 17:11 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>: >>>>> >>>>>> 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=LOCA >>>>>> L_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_s >>>>>>>>>>> am_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/re >>>>>>>>>>>>>>>>>> lax-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