On 21 février 2014 11:07, Tan, Yifang [yifang....@nrc-cnrc.gc.ca] wrote: > À : Sébastien Boisvert > Objet : RE: Ray on Redhat vs Debian > > Thanks! > I am aware of those factor which may be involved. > Yes, my admin said NUMAlin is involved. My reads are stored in a mounted > storage disk RAID. However, another recent observation is Ray ran very slow > in the same Debian box. This huge slowed-down speed of Ray bugged us so > much, and my admin could not track the cause either so that I seek suggestion > here. > May I ask the question in another way: Will the traffic I/O to/from the > storage disk affect the speed of Ray or not, and how? What is the maximum > traffic load Ray can tolerate for data reading/writing (This may be a very > silly question, but I am kind of desperate)? >
It will only affects the steps named "Counting sequences" and "Loading sequences". > Thank you! > > Yifang > ________________________________________________________________________ > Bioinformatics Support Specialist | Bioinformatique soutien Specialis > National Research Council of Canada | Conseil national de recherches Canada > Government of Canada | Gouvernement du Canada > 110 Gymnasium Place|110, place Gymnasium > Saskatoon, Saskatchewan > S7N 0W9 > Tel / Tél : 306-975-5279 > Fax | Télécopieur : 306-975-4839 > ________________________________________ > From: Sébastien Boisvert [sebastien.boisver...@ulaval.ca] > Sent: Tuesday, February 18, 2014 9:25 AM > To: Tan, Yifang; denovoassembler-users@lists.sourceforge.net > Subject: [Denovoassembler-users] RE : Ray on Redhat vs Debian > > 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 ------------------------------------------------------------------------------ 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
