Hi, please see my update below On Friday, January 16, 2015 at 9:44:49 PM UTC, abrukhno wrote: > 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?
- it is certainly csg_stat, as the progress of files show: - 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 In my recent attempts I have a longer trajectory and up to now I have not seen yet the distributions produced by csg_stat, after 18 hours. Below are a few latest lines in inverse.log: === ... table_extrapolate.pl: extrapolating the left using linear with gradient 0 table_extrapolate.pl: extrapolating the right using constant with gradient 0 begin to calculate inverse monte carlo parameters # of bonded interactions: 0 # of non-bonded interactions: 10 === It appears csg_stat for IMC is a lot more time consuming than for IBI. You probably know it, but the surprise for me is, it takes so unbearably long, making IMC virtually useless. > > 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? - my experience is the more stats you have the better the result with either of these (whence my long trajectories). 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.
