Dear Chris, I made a mistake in the old benchmarks - updated ones are now better. Knowing how to make function in-place would be great though!
Best Simon On Thursday, July 28, 2016 at 11:20:58 AM UTC+1, Simon Frost wrote: > > Dear Chris, > > I've managed to get a little better performance by adding a loop and > avoiding some type conversions. > > https://gist.github.com/sdwfrost/8a0e926a5e16d7d104bd2bc1a5f9ed0b > > I'm still getting about a 7-fold slowdown from using the function call (as > an immutable object). How would one make my function F in-place, still > using a similar generic API? > > Best > Simon > > On Thursday, July 21, 2016 at 4:35:56 PM UTC+1, Chris Rackauckas wrote: >> >> You can change line 70 to be in place with a loop: >> >> for i in 1:length(x) >> x[i] = x[i] + deltax[i] >> end >> >> I don't think you can do >> >> x[:] =x .+deltax >> >> as fancy syntax here since the x is part of the statement though (you can >> check). This should cut out an allocation here and bring down the time. >> >> Do you need to use a WeightVec? If you do (for future things), keep the >> WeightVec separate from the Vector so that the types aren't changing. let >> wpf always be the WeightVec you make from pf. Otherwise pf isn't type >> stable. It would be best if you could make F in-place as well since this is >> where your bottleneck is. >> >> On Thursday, July 21, 2016 at 7:56:51 AM UTC-7, Simon Frost wrote: >>> >>> Dear All, >>> >>> I'm having some issues with code speed for some Gillespie type >>> simulations. The toy model is described here: >>> >>> >>> http://phylodynamics.blogspot.co.uk/2013/06/comparing-performance-of-r-and-rcpp-for.html >>> http://phylodynamics.blogspot.co.uk/2013/06/an-sir-model-in-julia.html >>> >>> I get good performance with my vanilla Julia code, but a more generic >>> implementation is slower: >>> >>> http://github.com/sdwfrost/Gillespie.jl >>> >>> The gist is here: >>> >>> https://gist.github.com/sdwfrost/1b4bce19faf2d7b8624cac048a36f32d >>> >>> Lines 57 and 70 appear to be the culprit: >>> >>> https://github.com/sdwfrost/Gillespie.jl/blob/master/src/SSA.jl >>> >>> I've tried some devectorisation, but in my hackery, I appear to get side >>> effects, where the argument x0 passed to the ssa function is modified. Any >>> tips? >>> >>> Best >>> Simon >>> >>
