I might be able to code this up, but I would not be able to get to this for a month or so.
Doug On Oct 24, 2007, at 9:24 AM, Sébastien Morin wrote: > Hi again > > You're right. This could be quite useful especially for multi- > processor > systems... > > Also, as you say, there could be other levels of queuing (that > people more > familiar with this topic than me could propose)... > > Ciao > > > Séb > > > > Selon Douglas Kojetin <[EMAIL PROTECTED]>, 24.10.2007: > >> Hi, >> >> I think it would be worth adding the code, as a queueing system >> within the full_analysis script could spawn multiple tensor >> optimizations at the same time, depending on the number of processors >> available on the computer (or cluster). For example, it would first >> run local_tm. Then, on a 2 CPU system, spawn the sphere and prolate >> runs. When one of those finish, start the next run in the queue >> (oblate). Then when another run finishes, run the next (ellipsoid). >> That is one level of queueing, but I'm sure this could also be used >> to queue and run individual model optimizations within a tensor >> optimization run. For example, m1, m2 ... through m8 for the sphere >> tensor optimization. >> >> Doug >> >> >> On Oct 24, 2007, at 8:48 AM, Sebastien Morin wrote: >> >>> 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 [EMAIL PROTECTED] 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 ||| >>> || || >>> |_______________________________________________| >>> ______________________________________ >> >> > > > > ------------------------ > Sébastien Morin > Étudiant M.Sc. Biochimie > Laboratoire S. Gagné > 3252 Pav. Marchand (Université Laval) > Tél : (418) 656-2131 #4530 > Fax : (418) 656-7176 > e-mail : [EMAIL PROTECTED] > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
