<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>I can give a similar setup a try as well to see if anything is amiss in the development version. The expected behavior is that 1 and 2 cores should have identical performance (as one process is always fully dedicated to communication).</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Ramón Fallon <<a href="mailto:ramonfallon@gmail.com">ramonfallon@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, 14 March, 2013 11:19 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] 12core speed check<br></div><div><br></div>Hi,<div><br></div><div>I was trying to tweak some of our machines to maximise Mpich2/Maker (svn rev 997) throughput and describe one small set of results on this mailing list to allow sharing of experiences.</div><div><br></div><div>I use the example input dataset "dpp_contig.fasta" with the original sequence repeated 125 times within the same file (under different names of course) to allow for a decent size run. This file totalled 4.019 megabases. I use the dpp_proteins.fasta and The maker_opts.ctl has "cpus=1" set as the docs recommend for MPI.</div><div><br></div><div>Hardware is a standalone HP Proliant SL390 with two Intel X5675 @ 3.07GHz, totalling 12 cores with 192GB RAM and 1TB disk (local, no NFS) running Ubuntu 10.04 with 2.6.32-41 linux kernel </div><div><br></div><div>commandline was "mpiexec -n <#cores> maker" within a dedicated directory containing all relevant files.</div><div><br></div><div><div> #cores time(mins) Megabases/hr</div><div> 1 27.00 8.93</div><div> 2 126.25 1.91</div><div> 4 42.57 5.66</div><div> 6 25.42 9.49</div><div> 8 18.60 12.96</div><div> 10 16.67 14.47</div><div> 12 13.98 17.24</div></div><div><br></div><div>I attach a png file with graph. The upshot of this particular experiment is that 2 processes show anomalous behaviour and that 6 processors are needed to gain an advantage on the 1 processor run, while 12 processors achieves a speed-up of nearly 2 on the 1 processor version.</div><div><br></div><div>I am now going to move on to a three node cluster with 2x 8core processors each (so I can go up to 48 processors), so will report back with higher core numbers. Any suggestions on further speed optimizations welcome.</div><div><br></div><div>Cheers / Ramón.</div>
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