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
