[bug #25044] Model Free Analysis problems when attempting to run on multi-processors and using the script to run

2016-09-07 Thread sam 
Additional Item Attachment, bug #25044 (project relax):

File name: R2_800 Size:0 KB
File name: Entire Output for Relax attempt Size:417 KB
File name: R1_600 Size:0 KB


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[bug #25054] Running scripts for model free

2016-09-12 Thread sam 
URL:
  <http://gna.org/bugs/?25054>

 Summary: Running scripts for model free
 Project: relax
Submitted by: sam
Submitted on: Mon 12 Sep 2016 03:35:12 PM UTC
Category: None
Specific analysis category: Model-free analysis
Priority: 5 - Normal
Severity: 3 - Normal
  Status: None
 Assigned to: None
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 4.0.2
 Discussion Lock: Any
Operating System: 64-bit GNU/Linux

___

Details:

Hi, this is a response to Troels. I have simply copied and pasted the email I
sent earlier. 

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_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,diff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=LOCAL_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_sim_num=MC_NUM,conv_loop=CONV_LOOP)

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 li

[bug #25084] Running Model_Free on multi processors Fedora 20 complications

2016-09-26 Thread sam 
Additional Item Attachment, bug #25084 (project relax):

File name: Screenshot from 2016-09-26 14:15:31.png Size:193 KB


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[bug #25084] Running Model_Free on multi processors Fedora 20 complications

2016-09-19 Thread sam 
URL:
  <http://gna.org/bugs/?25084>

 Summary: Running Model_Free on multi processors Fedora 20
complications 
 Project: relax
Submitted by: sam
Submitted on: Mon 19 Sep 2016 05:38:48 PM UTC
Category: None
Specific analysis category: Model-free analysis
Priority: 5 - Normal
Severity: 3 - Normal
  Status: None
 Assigned to: None
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 4.0.2
 Discussion Lock: Any
Operating System: 64-bit GNU/Linux

___

Details:

I have come across a problem running relax on a multi-processor platform for
my Fedora 20 system. I have successfully been able to not only open but also
run relax on a multi-processor platform on the fedora 24 posted below
(Eloranta). When I type in the mpirun ./relax command, I can sucessfully open
relax on a uniprocessor platform. When I type in mpirun -np 3 ./relax
--multi='mpi4py' however, there is no output. It shows a program is running,
since I can cancel it, and when I check the programs running in the background
(the png), I can see it running in the background; however, as indicated by
the png, relax does not actually load. I have left this to "load" for 24+
hours, still nothing loaded, so I don't think its an issue of it taking a
while to load. 

I have posted both relax -i information for both the fedora 24 (works) and
fedora 20 (doesn't work), as well as a screenshot of the output when I type in
the multi command, and all the background running applications that indicate
relax is actually "running". 



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File Attachments:


---
Date: Mon 19 Sep 2016 05:38:48 PM UTC  Name: Fedora_20_cannotrunmuli.png 
Size: 288kB   By: sam

<http://gna.org/bugs/download.php?file_id=28666>
---
Date: Mon 19 Sep 2016 05:38:48 PM UTC  Name: mpirun report bindings  Size: 2kB
  By: sam

<http://gna.org/bugs/download.php?file_id=28667>
---
Date: Mon 19 Sep 2016 05:38:48 PM UTC  Name: relax -i data Dr. Eloranta  Size:
5kB   By: sam

<http://gna.org/bugs/download.php?file_id=28668>
---
Date: Mon 19 Sep 2016 05:38:48 PM UTC  Name: relax -i data  Size: 5kB   By:
sam

<http://gna.org/bugs/download.php?file_id=28669>

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[bug #25084] Running Model_Free on multi processors Fedora 20 complications

2016-09-20 Thread sam 
Additional Item Attachment, bug #25084 (project relax):

File name: relax -i data for 4.0,2Size:5 KB


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[bug #25084] Running Model_Free on multi processors Fedora 20 complications

2016-09-19 Thread sam 
Additional Item Attachment, bug #25084 (project relax):

File name: Report-bindings fedora 24  Size:11 KB


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[bug #25084] Running Model_Free on multi processors Fedora 20 complications

2016-09-19 Thread sam 
Additional Item Attachment, bug #25084 (project relax):

File name: relax -i data for 4.0,2Size:5 KB


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[bug #25044] Model Free Analysis problems when attempting to run on multi-processors and using the script to run

2016-09-07 Thread sam 
URL:
  <http://gna.org/bugs/?25044>

 Summary: Model Free Analysis problems when attempting to run
on multi-processors and using the script to run
 Project: relax
Submitted by: sam
Submitted on: Wed 07 Sep 2016 08:10:52 PM UTC
Category: None
Specific analysis category: Model-free analysis
Priority: 5 - Normal
Severity: 3 - Normal
  Status: None
 Assigned to: None
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 4.0.2
 Discussion Lock: Any
Operating System: 64-bit GNU/Linux

___

Details:

This is a response to Troels Emtekær Linnet on problems I have been having
running the model free analysis on a multi-processor platform, and running
relax (both uni,and multi, in script mode rather than gui). 

The script I used is uploaded below in txt (I simply just copy and paste each
command line into the terminal). I have also uploaded the whole relax -i
output (just to provide more information)for both of the computers I am
using.

A note on the data I have uploaded. The pdb file I have been using for my
analysis has an extra 7 residue linker at the C-terminal and an extra 6 at the
N-terminal, I also don't have data for the first 5 amino acids, this is why my
data starts at amino acid number 12. 
e.g. Sequence of pdb structure:
GSSGSSGSQQRV
Sequence of the protein I have data for:
SQQRV... 
I am missing the extra GSSGSSG linker in the beginning, so to make the
sequences line up, I have added 7 extra numbers with no value to my data. I
have also added 6 at the end as well. So my protein itself has 126 amino
acids, but with these additions it makes it a total of 139. So now the
sequence of the pdb file should line up with my data. 

Additionally, the relax -i information I have posted below (for the fedora 20)
is 2.2.5, but I have been using 4.0.2  on that computer.  

I have also added a screenshot of the Fedora20 (the one that I am having
trouble running multi-processor for), that shows that there is no output when
I type in the multi processor command; however it is running in the
background. If I type --gui after that command, the gui interface doesn't show
up either. I get the same result. 

I've also added the entire output file of what happens when I attempt to run
model-free through the terminal using script commands instead of the gui
interface.Also, I know I have not given any actual names to the pipe, this was
simply supposed to be a test run to see if I could even run the program in
script mode, rather than gui (since the main computer I will be running this
on, the Fedora 24, doesn't have wxPython). 

Now to the "bug". The problem I have come across is running model-free
analysis on a multi-processor platform instead of uni-processor. Currently all
my tests have been to run it on 1 computer with multiple cores (so no parallel
programming with multiple computers e.g. ssh hosts yet). I have been using 2
separate computers to run this (A fedora 24, and fedora 20). On one, I am
successfully able to open relax on a multi-processor platform (i.e. using 1
master and 4 slaves for now)(the fedora 24). On the other computer, for some
reason when I type in the same command (-np 5 ./relax --multi='mpi4py')
nothing pops up in the terminal (the fedora 20). but if I look at the running
background applications, I can see it running with 4 slaves. 
On the computer that is able to run multi-processor (when I type the mpirun
--multi etc. command, I get a response that states I am now using 4 slaves and
1 master, and relax pops up). I upload the data, it properly tells me which
amino acids I am missing data for (i.e. it doesn't tell me I am missing data
for ever value 1-139). When I load everything up and attempt to run the
dAuvergne protocol though, it tells me I have no data for any of the spins,
and thus it doesn't run any models and deselects all spins. This happens on
both the fedora 20, and 24, with exactly the same output (for both the
uni-processor on fedora 20, and multi processor for fedora 24). So I can't
even run relax on a uni-processor using the script, only through the gui
interface.

-Thank you in advance
Sincerely,
Sam  



___

File Attachments:


---
Date: Wed 07 Sep 2016 08:10:52 PM UTC  Name: relax -i data Dr. Eloranta  Size:
5kB   By: sam
https://mail.gna.org/public/relax-users/2016-09/threads.html#1
<http://gna.org/bugs/download.php?file_id=28572>
---
Date: Wed 07 Sep 2016 08:10:52 PM UTC  Name: Fedora_20_cannotrunmuli.png 
Size: 288kB   By: sam
https://mail.gna.org/public/relax-users/2016-09/threads.html#1
<http://gna.org/bugs/d

[bug #25044] Model Free Analysis problems when attempting to run on multi-processors and using the script to run

2016-09-07 Thread sam 
Additional Item Attachment, bug #25044 (project relax):

File name: R2_600 Size:0 KB
File name: ssNOE_600  Size:0 KB
File name: ssNOE_800  Size:0 KB
File name: R1_800.Size:0 KB


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[bug #25133] Error using Dimer pdb files for model free

2016-09-29 Thread sam 
Additional Item Attachment, bug #25133 (project relax):

File name: Relax -i info  Size:5 KB


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[bug #25133] Error using Dimer pdb files for model free

2016-09-29 Thread sam 
URL:
  <http://gna.org/bugs/?25133>

 Summary: Error using Dimer pdb files for model free
 Project: relax
Submitted by: sam
Submitted on: Thu 29 Sep 2016 11:27:30 PM UTC
Category: None
Specific analysis category: Model-free analysis
Priority: 5 - Normal
Severity: 3 - Normal
  Status: None
 Assigned to: None
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 4.0.2
 Discussion Lock: Any
Operating System: 64-bit GNU/Linux

___

Details:

The error occurred when I attempted to use a Dimer pdb file (with sets A and
B) for model free. I can upload the spins, and the data, however it will not
run the actual analysis. Below I have uploaded the script I use, the data, a
screenshot of the error, and the pdb file. I have tried this for 2 proteins
and received the same error. A note about the data. 
Agnes=600
NMRFAM=800 




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File Attachments:


---
Date: Thu 29 Sep 2016 11:27:30 PM UTC  Name: Screenshot from 2016-09-29
16:24:40.png  Size: 181kB   By: sam

<http://gna.org/bugs/download.php?file_id=28784>
---
Date: Thu 29 Sep 2016 11:27:30 PM UTC  Name: RGS4_modelfree_sample_script.py 
Size: 2kB   By: sam

<http://gna.org/bugs/download.php?file_id=28785>
---
Date: Thu 29 Sep 2016 11:27:30 PM UTC  Name: ssNOE_RGS4NMRFAM  Size: 1kB   By:
sam

<http://gna.org/bugs/download.php?file_id=28786>
---
Date: Thu 29 Sep 2016 11:27:30 PM UTC  Name: ssNOE_RGS4Agnes  Size: 1kB   By:
sam

<http://gna.org/bugs/download.php?file_id=28787>

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[bug #25133] Error using Dimer pdb files for model free

2016-09-29 Thread sam 
Additional Item Attachment, bug #25133 (project relax):

File name: cluster1_12.pdbSize:199 KB


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[bug #25133] Error using Dimer pdb files for model free

2016-09-29 Thread sam 
Additional Item Attachment, bug #25133 (project relax):

File name: R2_RGS4NMRFAM  Size:1 KB
File name: R2_RGS4Agnes   Size:1 KB
File name: R1_RGS4NMRFAM  Size:1 KB
File name: R1_RGS4Agnes   Size:1 KB


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