<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>It should use 2 physical cores. Hyperthreading shouldn't come into play unless you start more processes than there are physical cores. I haven't seen any big performance advantage in most cases with hyperthreading on linux machines. I find more often than not it just confuses students into thinking there are free processors and then starting too many jobs.</div><div><br></div><div>--Carson</div><div><br></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> Olaf Mueller <<a href="mailto:olaf.mueller@duke.edu">olaf.mueller@duke.edu</a>><br><span style="font-weight:bold">Date: </span> Thursday, 14 March, 2013 12:13 PM<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> Re: [maker-devel] 12core speed check<br></div><div><br></div><div>
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The X5675 supports hyperthreading. Does i.e. "mpiexec -n 2 maker"
use 2 physical cores or 2 threads of the 1st core? If the latter
happens it would be interesting to see your series extended to -n
24.<br>
<br>
Cheers<br>
Olaf<br>
<br>
<div class="moz-cite-prefix">On 03/14/2013 11:19 AM, Ramón Fallon
wrote:<br>
</div>
<blockquote cite="mid:CA+WKpEtg+j+wLp_qntSWff1RMXyVS5hRzz=fc+Amk6OMmqdfPA@mail.gmail.com" type="cite">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>
<br>
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<br>
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