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<div>You can get blast to use more than 1 cpu via the cpus= option, but that is still significantly limiting MAKER's performance.</div>
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<div>When you let MAKER install MPICH2, it will be local to the MAKER installation (MAKER only). It will be in …/maker/exe/mpich2. This was purposely done for people who have limited access and install MAKER themselves, so they can run via MPI without having
to get upgraded privileges. So I don't know if you installed MAKER yourself, but if you did, then this is an option that will let you run.</div>
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<div>--Carson</div>
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<span style="font-weight:bold">From: </span>csusm <<a href="mailto:lin11@cougars.csusm.edu">lin11@cougars.csusm.edu</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, 25 June, 2013 11:40 AM<br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carson.holt@oicr.on.ca">carson.holt@oicr.on.ca</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Fwd: about running MAKER<br>
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<div>Hi Carson</div>
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<div>Thank you for your suggestion. Do you mean if I dont use MPI, i could only run it on one cpu? Because my school own the server, I only have the limit authorization. <br>
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Yunxi Lin</div>
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On Jun 24, 2013, at 5:39 PM, Carson Holt <<a href="mailto:Carson.Holt@oicr.on.ca">Carson.Holt@oicr.on.ca</a>> wrote:<br>
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<div>You are most likely only getting 1 cpu of performance.</div>
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<div>You should just install MPICH2. It's easy just to let MAKER do it for you:</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>Go to the …/maker/src/ directory</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>Run './Build mpich2'</div>
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<div>Once it finishes installing, it will be in the …/maker/exe/mpich2/bin/ directory.</div>
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<div>Setup MAKER again to use MPICH2:</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>Go to the …/maker/src/ directory</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>Run 'perl Build.PL'</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>Say yes to the "use MPI": question</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>Run './Build install'</div>
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<div>Now run MAKER via 'mpiexec'.</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>Example --> …/maker/exe/mpich2/bin/mpiexec -n 16 maker</div>
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<div>The –n flag specifies how many CPUS to use. Mpiexec handles process communication either on the same machine or across machines. You will get much better performance.</div>
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<div>Thanks,</div>
<div>Carson</div>
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<span style="font-weight:bold">From: </span>Yunxi Lin <<a href="mailto:lin11@cougars.csusm.edu">lin11@cougars.csusm.edu</a>><br>
<span style="font-weight:bold">Date: </span>Monday, 24 June, 2013 7:11 PM<br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Cc: </span>Amelia Ireland <<a href="mailto:amelia.ireland@gmod.org">amelia.ireland@gmod.org</a>>, <<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] Fwd: about running MAKER<br>
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<div dir="ltr">Hi Carson
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<div style="">Thank your for your help. </div>
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<div style="">My genome estimated size is 250M base pairs. I ran it in 16cpu, but we don't have the MPI so I cannot use it. I don't think I'm using the alt_est option. I was following the tutorial to do that. I used TopHat and Cufflinks to generate the ESTs
from the assembly sequence based on RNA-seq. I used that ESTs to run the MAKER. </div>
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<div style="">I think I already got more than 10Mb data. The information you mentioned is very helpful. I may go to use them to try to train the SNAP and Augustus. </div>
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<div style="">Because this is my first time using the MAKER, I ran already a month, I was wondering maybe the command I used in a wrong way. </div>
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<div style="">Sincerely,</div>
<div style="">Yunxi</div>
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<div class="gmail_quote">2013/6/24 Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span><br>
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<div>Run time is dependent on the size of your evidence dataset, genome size, and number of processors you use. If you have a large genome (Gb size) and you are running on a single cpu then that could take a long time. This is especially true if you use the
alt_est option for evidence as these are aligned via tblastx which is 3-4 times slower than protein alignments, and 10-20 time slower than standard EST alignments. 95% of MAKER's runtime is BLAST alignment so your evidence dataset is the major factor.</div>
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<div>Also you do not need results from the entire genome to train SNAP. If you get results from ~10Mb of the genome that is usually sufficient. Also make sure you are taking advantage of parallelization. Launch via MPI to get maximum performance. I commonly
launch on 16 and 32 cpu Linux servers which can annotate most fungal genomes in a few hours and larger genomes in a few days.</div>
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<div>--Carson</div>
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<span style="font-weight:bold">From: </span>Amelia Ireland <<a href="mailto:amelia.ireland@gmod.org" target="_blank">amelia.ireland@gmod.org</a>><br>
<span style="font-weight:bold">Date: </span>Sunday, 23 June, 2013 10:15 PM<br>
<span style="font-weight:bold">To: </span><<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Cc: </span><<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>><br>
<span style="font-weight:bold">Subject: </span>[maker-devel] Fwd: about running MAKER<br>
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<div dir="ltr">From the GMOD helpdesk; please cc Lin, <a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>.<br>
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<div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">Yunxi Lin</b> <span dir="ltr"><<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>></span><br>
Date: Sun, Jun 23, 2013 at 4:14 PM<br>
Subject: about running MAKER<br>
To: "<a href="mailto:gmod-help@gmod.org" target="_blank">gmod-help@gmod.org</a>" <<a href="mailto:help@gmod.org" target="_blank">help@gmod.org</a>><br>
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<div dir="ltr"><span style="font-size: 14px; font-family: arial, sans-serif; ">Hi </span>
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<div style="font-family:arial,sans-serif;font-size:14px">I'm running a eukaryote project on our server. Because our server do not have the GUI, is that still work for MAKER? And our command already ran more than one month to try to generate the model use for
the training of SNAP and Augustus. Is that normal? I'm running on a 256G memory 64 Linux server. </div>
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<div style="font-family:arial,sans-serif;font-size:14px">Thank you. </div>
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<div style="font-family:arial,sans-serif;font-size:14px">Sincerely,</div>
<div style="font-family:arial,sans-serif;font-size:14px">Lin</div>
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-- <br>
<div dir="ltr">Amelia Ireland<br>
GMOD Community Support
<div><a href="http://gmod.org" target="_blank">http://gmod.org</a> || @gmodproject
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