Re: looping the optimization in full_analysis.py -- October 25, 2007

Hi,

There are a number of possible options here.  IO redirection is
changed in relax in the file 'io.py' when the command line options are
processed.  The first option would be to change 'sys.stdout' and
'sys.stderr' at the level of the diffusion tensor or the level of the
iterations.  Just set these to a writable file, and the data will be
placed there instead.  So this can go directly into the
'full_analysis.py' script.  Note that in 'io.py' the normal 'stdin',
'stdout', and 'stderr' are stored for restoring normal operation
(accessible at self.relax.IO.python_stdout, etc).  This could be an
option in 'full_analysis.py', but any code will require a lot of
refinement to make it clean and simple.

The other option is to define new user functions which allow the user
to redirect IO.  For example a prototype function could be:

io.redirect(stdin=None, stdout=None, stderr=None):
    """Function of allowing IO redirection."""

The arguments must then be strings for which a file will be created,
or something else to return to normal operation.  This user function
should go in the 1.3 line - having it accepted into 1.2 will be a
challenge ;).  I was always planning on this user function, but it
never eventuated.

Regards,

Edward



On 10/24/07, Douglas Kojetin <douglas.kojetin@xxxxxxxxx> wrote:


Perhaps it might be useful to build some sort of automatic queueing routine
into relax, or the full_analysis script directly?  It could first run the
local_tm run, then queue up and run the other tensor runs.

Doug


On Oct 24, 2007, at 8:25 AM, Sebastien Morin wrote:
 Hi Doug

 This extreme looping should be added as an option in the full_analysis.py
script. I'm not sure I would routinely use it as the computing time must be
very long, but it could be useful some times...

 When the threading over multiple CPUs will be implemented, this option
would also certainly be useful...

 I would suggest you submit a patch to relax-devel@xxxxxxx to add this
feature as an option the user can activate or not depending on its needs...

 Cheers !


 Séb  :)



 Douglas Kojetin wrote:
I guess I could also mentione that I've 'hacked' the full_analysis.py script
to automatically loop through local_tm, sphere, prolate, oblate and
ellipsoid runs as well.  This, however, produces one extremely large output
file, so the modifications mentioned below would be useful.


Doug



On Oct 22, 2007, at 4:22 PM, Sebastien Morin wrote:

 Hi Doug !

 Great !

 I didn't know about that feature (and some others that "relax -help"
outputs)...


 Séb  :)



 Douglas Kojetin wrote:
Hi Séb,



I've been using the -t flag creating one large log, so I think this:


For analysis where some kind of looping is done (like here), the logs could
be separated into different steps. For the full_analysis.py script, logging
could be done independantly for each round and added to the other
directories created...

 aic/  m0/  m1/  m2/  m3/  m4/  m5/  m6/  m7/  m8/  m9/  opt/  log



and this:


Maybe, also, two versions of the log could created, one detailed and one
only logging main topics so one can easily follow the processes. This could
be interesting for people not familiar with the details of relax and of the
approaches used for calculation/optimization...


 would be extremely useful.


Doug







On Oct 22, 2007, at 4:15 PM, Sebastien Morin wrote:

Hi all !

 First of all, I think that the new feature for automatic looping is quite
interesting..!

 However, I think that something could be done to make the analysis easier.

 When one starts a relax run, text is sent to the standard output. I usually
redirect this text to a log file so I can analyze if any trouble arises...

 I think that logging should be automatic.  This would not mean that
standard output would be suppress, but rather that standard output would be,
also, saved in a text file along with the results.

 For analysis where some kind of looping is done (like here), the logs could
be separated into different steps. For the full_analysis.py script, logging
could be done independantly for each round and added to the other
directories created...

 aic/  m0/  m1/  m2/  m3/  m4/  m5/  m6/  m7/  m8/  m9/  opt/  log

 You may say that we can manually do that, but when using the automatic
looping options, one would get a huge log...

 Maybe, also, two versions of the log could created, one detailed and one
only logging main topics so one can easily follow the processes. This could
be interesting for people not familiar with the details of relax and of the
approaches used for calculation/optimization...

 Let me know what you think of this and also if I'm being clear or not...

 Cheers


 Séb  :)


 --
 ______________________________________
 _______________________________________________
 | |
 || Sebastien Morin ||
 ||| Etudiant au PhD en biochimie |||
 |||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne |||||
 |||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
 ||| 1-418-656-2131 #4530 |||
 || ||
 |_______________________________________________|
 ______________________________________



 --
 ______________________________________
 _______________________________________________
 | |
 || Sebastien Morin ||
 ||| Etudiant au PhD en biochimie |||
 |||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne |||||
 |||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
 ||| 1-418-656-2131 #4530 |||
 || ||
 |_______________________________________________|
 ______________________________________



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Re: looping the optimization in full_analysis.py

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