<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Because MAKER is a pipeline, all processes it calls will generate separate processes (i.e. BLAST etc.). Also it will spawn a couple of helper processes to watch communication and files. The helper processes use 0% CPU, and the main MAKER process will yield to external system calls and processes until they finish execution. So they will never use a larger % of CPU than is specified. Also the way MPI works is it spawns a separate process for every CPU specified, so if you specify 40 CPUs you get 40 independent communicating processes rather than 1 process accessing 40 CPUs. So if you take into account the MPI processes, helper processes, and external system calls a 40 CPU specification could result in up to three times that many numbered processes existing simultaneously (even though no more than 40 will be active at a time). However if your system is having an issue letting the required number of processes exist, then it is a ulimit issue. Your administrator has the limit set too low. You can see what limits are set using the command ‘ulimit -a’. You will need to get your system admin to fix it.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 20, 2015, at 5:54 PM, Matt Simenc <<a href="mailto:mcsimenc@gmail.com" class="">mcsimenc@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><p class="MsoNormal">Hi,</p><p class="MsoNormal"><br class=""></p><p class="MsoNormal">I am using OpenMPI to run MAKER on 2 nodes with 40 CPUs/node. The load is distributing across the nodes ok but with a very large number of processes on each node. Sometimes there are several hundred more processes than can be executed at one time by a node. Is this a problem? If so, any suggestions on how to fix?</p><p class="MsoNormal"><br class=""></p><p class="MsoNormal">Thanks!</p><p class="MsoNormal"><br class=""></p><p class="MsoNormal">Matt Simenc</p><p class="MsoNormal">Der Lab</p><p class="MsoNormal">California State University Fullerton</p>
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