Re: Using multi-processor for model_freeRe: Using multi-processor for model_freeHi Troels, Update on Protein number 1: So I was able to successfully run model free with no problems on my protein (I don't know why it was giving problems before). The reason it may have been giving issues though is the protein I am working with forms a dimer at the concentrations we work with (thus the results I have are for the Dimer form of the protein). The pdb file though only has a monomer structure though. I have been able to obtain the dimer pdb file using HADDOCK (docking program), but have come across a few problems uploading the pdb file. The initial problem was that all the hydrogens attached to the nitrogen were HN labeled on the HADDOCK modified pdb file, and model free could not understand what HN meant, and I would recieve this warning. RelaxWarning: Cannot determine the element associated with atom 'HN'. I could however load up all the Nitrogen, but naturally, with no hydrogens, it wouldn't be able to calculate any bond vectors between nitrogen and hydrogen. So I would recieve this error and the program would close RelaxError: The spin ID '@H' matches no spins. To fix this, I changed all the HN spins, to just H, but then recieved another error. RelaxError: Multiple alternate location indicators are present in the PDB file, but the desired coordinates set has not been specified. I don't exactly understand what this error means. Is it saying the program can't locate the 3D coordinates for the Hydrogen and Nitrogen? If that is the case, why was it able to before, when it couldn't read any of the Hydrogen spins. I'm just confused a bit as to what this error means. Sincerely, Sam On Wed, Sep 21, 2016 at 3:18 PM, Mahdi, Sam <sam.mahdi.846@xxxxxxxxxxx> wrote:
Hi Troels, Update on protein number 1. I ran it with only 5 simulations. It took a while, but it ended up finishing. So I assume its due to bad data simply slowing down the process. Update on protein number 2. I ran it with only 2 spins as well, and I still recieved the same error. I suspect its due to the pdb file. I'm going to attempt to use another program to add the hydrogens to my pdb file and try again. Sincerely, Sam On Tue, Sep 20, 2016 at 1:31 PM, Mahdi, Sam <sam.mahdi.846@xxxxxxxxxxx> wrote:Thats weird, I can open it up directly from the link you sent me. I'll reupload it On Tue, Sep 20, 2016 at 12:40 PM, Troels Emtekær Linnet < tlinnet@xxxxxxxxxxxxx> wrote:The file: file #28673: relax -i data for 4.0,2 a https://gna.org/bugs/download.php?file_id=28673 Its emtpy? 2016-09-20 20:05 GMT+02:00 Mahdi, Sam <sam.mahdi.846@xxxxxxxxxxx>:Hi Troels, I am a bit confused what you are talking about. There is no file labeled .? On Tue, Sep 20, 2016 at 9:15 AM, Troels Emtekær Linnet < tlinnet@xxxxxxxxxxxxx> wrote: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.846@xxxxxxxxxxx>: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 < tlinnet@xxxxxxxxxxxxx> 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.846@xxxxxxxxxxx>: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.846@xxxxxxxxxxx> 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 < tlinnet@xxxxxxxxxxxxx> 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.846@xxxxxxxxxxx> :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_a nalyses/dauvergne_protocol.py", line 246, in __init__ self.execute() File "/home/sam2/relax-4.0.2/auto_a nalyses/dauvergne_protocol.py", line 600, in execute self.multi_model(local_tm=True) File "/home/sam2/relax-4.0.2/auto_a nalyses/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 < tlinnet@xxxxxxxxxxxxx> 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.846@xxxxxxxxxxx: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 < tlinnet@xxxxxxxxxxxxx> 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.846@xxxxxxxxxxx>: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 < tlinnet@xxxxxxxxxxxxx> 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/Tuto rial_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.846@xxxxxxxxxxx>: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 < tlinnet@xxxxxxxxxxxxx> 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.846@xxxxxxxxxxx>: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','ellipsoid','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_Agne s',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_Agne s',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_A gnes',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_NMRF AM',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_NMRF AM',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_N MRFAM',ri_type='NOE',frq=799.642*1e6, file='ssNOE_NMRFAM',res_num_co l=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=n ame,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.846@xxxxxxxxxxx> 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 < tlinnet@xxxxxxxxxxxxx> 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.846@xxxxxxxxxxx>: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 <tlinnet@xxxxxxxxxxxxx> 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.846@xxxxxxxxxxx>: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 <tlinnet@xxxxxxxxxxxxx> 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/?grou p=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.846@xxxxxxxxxxx>: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.846@xxxxxxxxxxx> wrote:Hello everyone, I am attempting to run relax on amulti-processor mode. I have been ableto successfully set-up relax to operate in amulti-processor mode by usingthe mpirun -np #ofprocessors /location/of/relax--multi='mpi4py'The problem I encounter is when using the --teelog dauvergne_protocol.pycommand. I receive this error RelaxError: the script file'dauvergne_protocol.py' does not existI located the script file and tried to directto it's pathmpirun /usr/local/Relax/relax-2.2.5/relax--multi='mpi4py' --tee log/usr/local/Relax/relax-2.2.5/auto-analyses/dauvergne_protocol.pyBut i received this error RelaxError: the script file'/usr/local/Relax/relax-2.2.5/auto-analyses/dauvergne_protocol.py' does notexist.Even though I have the script, it doesn't seemto be able to locate it.On a side note, in the manual, one dash doesn'tactually run the command.I.e. in the manual it displays -multi='mpi4py'. What it should be is--multi='mpi4py' . The same goes for -tee. Itshould be --tee.Sincerely, Sam_______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@xxxxxxx 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