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

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/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','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_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=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/?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

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