On 17 février 2014 10:57, Tan, Yifang [yifang....@nrc-cnrc.gc.ca] wrote: > À : Sébastien Boisvert; denovoassembler-users@lists.sourceforge.net > Objet : Ray on Redhat vs Debian > > Hello Sebastien! > > I have a question about the speed difference of running Ray on two Linux > distributions: > Redhat: Linux box1 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 > x86_64 x86_64 x86_64 GNU/Linux > CPU core#: 160 > RAM: 1TB (yes, 1TB) > > Debian: Linux box2 3.10-2-amd64 #1 SMP Debian 3.10.5-1 (2013-08-07) x86_64 > GNU/Linux > CPU core#: 24 > RAM: 128GB > > The reason of my enquiry is that my assembly on Redhat box is way much slower > than in Debian. Of course I used exactly the same parameters of the assembly. > Here is a table on total assembly time (seconds) with different kmers from > our two boxes: > kmer Debian Redhat > 11 115 460 > 15 115 464 > 21 126 529 > 31 117 497 > > I was thinking to use more CPU cores with more RAM would speed up the > assembly, which did not work as I thought. > Sometime the difference was huge and the assembly in my Redhat was extremely > slow. I was wondering what may cause this difference from the operating > system part, so that I could ask the my sysadmin to adjust the configuration, > or just avoid RedHat Linux for my assembly. > > Thank you!
I feel like you are comparing much more than just operating systems here (Red Hat vs Debian). For instance, the hardware is different (memory is different). Maybe the one with 1 TB RAM has a NUMAlink [1] connecting memory nodes to CPUs. Or maybe your two machines don't even have the same CPU model. [1] http://en.wikipedia.org/wiki/NUMAlink > > Yifang > ------------------------------------------------------------------------------ Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
