<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>For any users currently using the devel subversion repository. If you need to update, please send me an e-mail to get information on how to switch over to our new server.</div><div><br></div><div>Thanks,</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> Monday, 18 March, 2013 10:35 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] Fwd: 12core speed check<br></div><div><br></div>Hi!<div><br><div class="gmail_quote">I've tried again from two different machines, and I can't do a "svn co" nor "svn update" on the malachite server. Can you verify the server and the svn service is OK on your side? <div><br></div><div>Many thanks / Ramón.<div><div class="h5"><br><br><br><br><div class="gmail_quote">On Fri, Mar 15, 2013 at 1:18 PM, Ramón Fallon <span dir="ltr"><<a href="mailto:ramonfallon@gmail.com" target="_blank">ramonfallon@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Mark and Carson,<div><br></div><div>Many thanks for the comments and the speedy replies!<br><br>Previously, I never had problem connecting to the svn server on <a href="http://malachite.genetics.utah.edu" target="_blank">malachite.genetics.utah.edu</a>, but this morning, I couldn't connect to update to rev 998.<br><br>I'l try again later.<br><br>Cheers / Ramón.</div><div><div><div><br><br><div class="gmail_quote">On Thu, Mar 14, 2013 at 6:59 PM, Mark Yandell <span dir="ltr"><<a href="mailto:myandell@genetics.utah.edu" target="_blank">myandell@genetics.utah.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Thanks Ramon. super interesting analysis!<br><br><br>
Mark Yandell<br>
Professor of Human Genetics<br>
H.A. & Edna Benning Presidential Endowed Chair<br>
Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330<br>
ph:<a href="tel:801-587-7707" value="+18015877707" target="_blank">801-587-7707</a><br><br>
________________________________________<br>
From: <a href="mailto:maker-devel-bounces@yandell-lab.org" target="_blank">maker-devel-bounces@yandell-lab.org</a> [<a href="mailto:maker-devel-bounces@yandell-lab.org" target="_blank">maker-devel-bounces@yandell-lab.org</a>] on behalf of Carson Holt [<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>]<br>
Sent: Thursday, March 14, 2013 11:51 AM<br>
To: Ramón Fallon; <a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a><br>
Subject: Re: [maker-devel] 12core speed check<br><div><br>
Could you update to 998. It was a recent commit to the devel version that caused a weird pause.<br><br>
Thanks,<br>
Carson<br><br><br></div>From: Ramón Fallon <<a href="mailto:ramonfallon@gmail.com" target="_blank">ramonfallon@gmail.com</a><mailto:<a href="mailto:ramonfallon@gmail.com" target="_blank">ramonfallon@gmail.com</a>>><br><div>Date: Thursday, 14 March, 2013 11:19 AM<br></div>To: <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a><mailto:<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>>><br><div>Subject: [maker-devel] 12core speed check<br><br>
Hi,<br><br>
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.<br><br>
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.<br><br>
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<br><br>
commandline was "mpiexec -n <#cores> maker" within a dedicated directory containing all relevant files.<br><br>
#cores time(mins) Megabases/hr<br>
1 27.00 8.93<br>
2 126.25 1.91<br>
4 42.57 5.66<br>
6 25.42 9.49<br>
8 18.60 12.96<br>
10 16.67 14.47<br>
12 13.98 17.24<br><br>
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.<br><br>
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.<br><br>
Cheers / Ramón.<br></div>_______________________________________________ maker-devel mailing list <a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a><mailto:<a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a>> <a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br></blockquote></div><br></div></div></div></blockquote></div><br></div></div></div></div><br></div>
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