Re: Using multi-processor for model_free -- September 20, 2016 - 20:06

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_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 <
> > > > > > > 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/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.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','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.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/?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.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 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@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