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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-language:EN-GB">Hi Maker Developers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-language:EN-GB">We are trying to run Maker with OpenMPI on our HPC cluster across two nodes (each node containing 28 Core’s so 56 Core’s in total). While Maker
seems to be running correctly its going slower when split across two nodes (56 Core’s) as opposed to being run on a single node (28 Core’s). We are trying to increase the speed that Maker will complete its run in. Do you know of any reason for why Maker might
slow down when split across two nodes?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-language:EN-GB">Our cluster OS is: CentOS 6.7 and the HPC scheduler used is: LSF. We are running Open mpi on a Mellanox Infiniband network.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-language:EN-GB">The genome data we wish to annotate is comprised of 1948 scaffolds with an average length of 324890bp (longest scaffold 6948830bp). <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">The command in batch mode we are using is: mpiexec -mca btl ^openib -n 56 maker<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-language:EN-GB">Any help or advise you could give would be greatly appreciated. <o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Best Wishes<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Jimmy<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">----------------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Mr James Cross<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">HPC Systems Developer<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">University of East Anglia<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Norwich Research Park<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">ITCS<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Norwich, Norfolk<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">NR4 7TJ<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Information Services<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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