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#00001
<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#00001
<http://gna.org/bugs/download.php?file_id=28573>
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?25044>
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