Hi,
I am struggling with an issue related to garbage collection taking up the
vast majority (>99%) of compute time on a simple nested for loop. Code
excerpt below:
# julia version 0.3.7
# counts is an MxN matrix of Float64
# N=15000
# M=108
# h_cols and c_cols are indices \in {1:M}
using Hypoth
ly wrote:
>>
>> Devectorization should never slow anything down. If it does, then you
>> have
>> some other problem. Here, M is a global variable, and that's probably
>> what's
>> killing you. Performance tip #1:
>> http://docs.julialang.o
,h_cols,c_cols,M)
end
@show (tot_i,tot,tot_i/tot)
end
end
S = main(counts,genes,h_cols,c_cols)
On Tuesday, April 7, 2015 at 8:47:06 AM UTC-4, Mauro wrote:
>
>
> On Tue, 2015-04-07 at 06:14, Adam Labadorf > wrote:
> > Thanks for the replies. I took your suggestions (
e gc time increases in the original code, I don't know.
> I don't think it should.
>
> On Tue, 2015-04-07 at 16:26, Adam Labadorf > wrote:
> > I moved compute! out of the main function and pass the ratios as you
> > suggested and the performance is a bit better
se it had to look at more and more
> objects as more and more Result instances were created?
>
> On Tue, 2015-04-07 at 18:24, Adam Labadorf > wrote:
> > Yes, that gives a massive improvement and I see the same gc behavior you
> > got. I could notice the gc increasing slo
not all immutable are inlined that way, only
> when isbits==true)
>
> Maybe the gc time increased because it had to look at more and more
> objects as more and more Result instances were created?
>
> On Tue, 2015-04-07 at 18:24, Adam Labadorf > wrote:
> > Yes, that gi
Hi,
I am using julia 0.3.8 + IJulia, and have been using ipython notebook for
sometime to perform my research activities. For my current project, I
define and export a number of types and methods wrapped in a module in one
of the cells, import the module, and refer explicitly to those types and
make a new ResultSet instead of just adding results to an old
> one, so others may be able to offer better solutions on this if that's what
> you need.
>
> Cheers,
> Scott T
>
> On Monday, 1 June 2015 17:54:11 UTC+1, Adam Labadorf wrote:
>>
>> Hi,
>>
>
