On Friday, January 16, 2015 at 7:58:01 PM UTC, Christoph Junghans wrote: > 2015-01-16 9:46 GMT-07:00 abrukhno <[email protected]>: > > Hi, > > > > I have been amazed how long (the entire night) it takes to finish an > > IMC+Octave iteration step after the simulation done. > > > > With a simulation taking under an hour and IMC Octave solver taking almost > > exactly 12 hours, one iteration step for a pretty small system (but > > millions frames) takes just over half a day. > > > > Same type of IBI iteration step takes just about 3 hours. > > > > Tried for IMC: <group>all</group> and splitting a set of 10 potentials into > > 3 groups, with virtually same times. > > > > Is it normal? Might Numpy improve on the speed?
> Did octave took a long time to run or csg_stat? - Here is how it looks like: drwxr-xr-x 44K Nov 8 09:33 step_001/ drwxr-xr-x 44K Nov 8 22:30 step_002/ drwxr-xr-x 44K Nov 9 11:41 step_003/ drwxr-xr-x 44K Nov 10 00:46 step_004/ drwxr-xr-x 44K Nov 10 13:55 step_005/ and inside a step: -rw-r--r-- 307K Nov 11 02:51 table_CH_CH.xvg -rw-r--r-- 307K Nov 11 02:51 table_CH_CO.xvg -rw-r--r-- 4.9M Nov 11 03:44 confout.gro -rw-r--r-- 1.3M Nov 11 03:44 ener.edr -rw-r--r-- 92K Nov 11 03:44 md.log -rw-r--r-- 2.9K Nov 11 15:45 CH-CH.dist.new -rw-r--r-- 2.9K Nov 11 15:45 CH-CO.dist.new > The octave runtime depends a lot on the step size (=size of the matrices). > 3 groups triple the time for solving. - wow, I probably stopped that after half a day > VOTCA supports numpy and matlab for solving the equations, too, but I > don't think it will make a huge difference in runtime. - thought so.. > In the original VOTCA paper, we did a couple of error comparisons for > IBI vs. IMC. > IMC is usually better for the first couple of iterations, but needs > more statistics than IBI. - 5x/10x? Thank you for reply, Christoph! Will try to investigate it further. > > Christoph > > > > Thank you for your clues. > > > > Andrey > > > > -- > > You received this message because you are subscribed to the Google Groups > > "votca" group. > > To unsubscribe from this group and stop receiving emails from it, send an > > email to [email protected]. > > To post to this group, send email to [email protected]. > > Visit this group at http://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
