Hi again
This is exactly what I was thinking.
However, there's a simple way to queue things like that out of relax
(at least in Unix systems)... But, then, you need multiple scripts.
Let's say you want to run every tensor in full_analysis.py one after
the other... You could do something like :
( relax -t log_local_tm ./full_analysis_local_tm.py ; relax -t
log_sphere ./full_analysis_sphere.py ; relax -t log_prolate
./full_analysis_prolate.py ; relax -t log_oblate
./full_analysis_oblate.py ; relax -t log_ellipsoid
./full_analysis_ellipsoid.py ; relax -t log_final
./full_analysis_final.py ) &
This would produce different logs for the different diffusion tensor
optimization and also be in the background... A run would start when
the previous run would finish or crash.
This ain't perfect but is it worth spending time to modify the code
when a command line like this one can do the same thing ?
Let me know what you think.
Cheers
Séb
Douglas Kojetin 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 |||
|| ||
|_______________________________________________|
______________________________________
--
______________________________________
_______________________________________________
| |
|| 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 |||
|| ||
|_______________________________________________|
______________________________________
|
Re: looping the optimization in full_analysis.py