<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>Performance is highly dependent on the size of evidence datasets used (proteins/ESTs) as well as the IO performance of a system when running via MPI (you can hit IO bottlenecks well before cpu bottlenecks depending on cluster configuration).</div><div><br></div><div>The Arabidopsis genome (120Mb assembly) running SNAP and Augustus, 1.1Gb EST dataset, and 10Mb protein dataset takes ~1 hour 30 min on 1,500 cpus with OpenMPI.</div><div>The Maize genome (2.1 Gb) running SNAP and Augustus, 3Gb EST dataset, and 16 Mb protein dataset takes ~4 hours 30 min on 2200 cpus.</div><div>A human sized genome would take 5-6 days on 100 cpus.</div><div><br></div><div>MAKER is fully restartable (keeps log of progress). So if there is any failure or the user kills it in the middle of a job, it will pick up at the point it left off on restart (so you don't waste all that processing time). 2Gb of RAM per processing core is recommended when parallelizing MAKER via MPI, but fragmented genomes with smaller contigs can get by with less than 1Gb per core. MAKER version 2.28 which has additional optimization for OpenMPI and lower memory footprint will be available in a couple of weeks. Until then 2.27 is recommended over 2.1 for MPI. 2.27 should also work with OpenMPI. 2.1 only works with older versions of MPICH2 using the mpd launcher and not the current hydra launcher.</div><div><br></div><div>Thanks,</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> "Carlos A. Canchaya" <<a href="mailto:canchaya@uvigo.es">canchaya@uvigo.es</a>><br><span style="font-weight:bold">Date: </span> Monday, 4 March, 2013 6:10 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] Sharing benchmarks of maker<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;">Hi,</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div>I've just install maker2 in our server and run a first test with our data. The input was about 30 000 sequences (9.6 Mb) and it was run in just one server with 32 processors for 36 hours) with mpich2. Our server has 250 Gb of memory and cpus of 2,4 Gb. The test was simple because it only ran repeatmasker and SNAP. Considering that we would like to use other gene prediction/annotation tools available in MAKER, I wonder if you can share some of your benchmarks in order to know if we could scale up pretty well to our production cluster in order to annotate our 1.6 Gb draft genome</div><div><br></div><div>Best,</div><div><br></div><div>Carlos</div><div> </div><div><div><div style="font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Carlos A. Canchaya, PhD<br>IPP Research Fellow<br>Department of Biochemistry, Genetics and Immunology<br>Faculty of Biology<br>Campus Universitario<br>University of Vigo<br>36310 Vigo<br>Spain<br><br><a href="http://darwin.uvigo.es/~ccanchaya/">http://darwin.uvigo.es/~ccanchaya/</a><br>email: <a href="mailto:canchaya@uvigo.es">canchaya@uvigo.es</a><br>Tel : +34 986 130048<br>Fax: +34 986 812556</div></div></div></div></div><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div></div><br></div></div></blockquote></div><br></div></div>_______________________________________________
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