<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Lior,<div class=""><br class=""></div><div class="">I know it can be done, but I never have had to do it on SGE. It will require that both SGE be setup to do this and OpenMPI be set up to work with SGE. If it is not setup already, you may have to involve your IT manager.</div><div class=""><br class=""></div><div class="">There are a number of documentation sources on how to do this —></div><div class=""><a href="https://www.open-mpi.org/faq/?category=sge" class="">https://www.open-mpi.org/faq/?category=sge</a></div><div class=""><a href="https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&cad=rja&uact=8&ved=2ahUKEwiA_vS0z_7cAhWI_p8KHflrAQQQFjACegQICBAB&url=http%3A%2F%2Fwww.softpanorama.org%2FHPC%2FGrid_engine%2Fparallel_environment.shtml&usg=AOvVaw24R99SzqWJJdC-mpY7eTCV" class="">SGE Parallel Environment - Softpanorama</a></div><div class=""><br class=""></div><div class="">Alternatively submit multiple MAKER jobs to one node each. You can have all jobs write to the same output directory and use different input fastas (i.e. chunk the original fasta) using the -base and -g command line options while running maker. You can chunk the fasta using fasta_tool (bundled with MAKER) and the --chunk option.</div><div class=""><br class=""></div><div class="">Example:</div><div class="">fasta_tool --chunk 10 assembly.fasta</div><div class=""><br class=""></div><div class="">#job1</div><div class="">mpiexec -n 20 maker -base assembly -g assembly_00.fasta</div><div class=""><br class=""></div><div class="">#job 2</div><div class="">mpiexec -n 20 maker -base assembly -g assembly_01.fasta</div><div class=""><br class=""></div><div class="">#job 3</div><div class="">mpiexec -n 20 maker -base assembly -g assembly_02.fasta</div><div class=""><br class=""></div><div class=""># and so on …</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson<br class=""><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Aug 8, 2018, at 5:51 AM, Lior Glick <<a href="mailto:liorglic@mail.tau.ac.il" class="">liorglic@mail.tau.ac.il</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="rtl" class=""><div dir="ltr" class="">Dear MAKER users,</div><div dir="ltr" class=""><br class=""></div><div dir="ltr" class="">I am running MAKER in order to annotate a large plant genome. To improve performance, I use the MPI option as described in the documentation (specifically openMPI). The machines I currently have access to are part of a cluster on which SGE is used as the job scheduler. There are about 15 machines, each with 20 cores. Therefore, in order to run, I create files that look something like this:</div><div dir="ltr" class=""><br class=""></div><div dir="ltr" class=""><div dir="ltr" class=""><font face="monospace, monospace" class="">#!/bin/bash</font></div><div dir="ltr" class=""><font face="monospace, monospace" class="">#$ -N try_MAKER</font></div><div dir="ltr" class=""><font face="monospace, monospace" class="">#$ -S /bin/bash</font></div><div dir="ltr" class=""><font face="monospace, monospace" class="">#$ -e /path/to/err<br class=""></font></div><div dir="ltr" class=""><font face="monospace, monospace" class="">#$ -o /path/to/out</font></div><div dir="ltr" class=""><font face="monospace, monospace" class="">#$ -pe openmpi-x86_64 20<br class=""></font></div><div dir="ltr" class=""><font face="monospace, monospace" class="">cd /path/to/run_dir<br class=""></font></div><div dir="ltr" class=""><font face="monospace, monospace" class="">mpiexec -n 20 --mca btl tcp,self maker</font><br class=""></div><div dir="ltr" class=""><br class=""></div><div class="">I then just qsub the file.</div><div class="">This works fine, but I'd like to use more than 20 cores, which means I need to use multiple nodes of the cluster. Simply increasing the number of requested cores (e.g.
<span style="font-family:monospace,monospace;font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class="">mpiexec -n 100)</span> does not work - it keeps using 20 cores of a single node.</div><div class="">I see <a href="https://www.osc.edu/supercomputing/batch-processing-at-osc/pbs-directives-summary" class="">this is possible when the scheduler used is PBS</a> (using the nodes:ppn option), but couldn't find any examples/instructions regarding SGE.</div><div class="">Can anyone help me figure it out? Has anyone done this on SGE?</div><div class=""><br class=""></div><div class="">Thanks a lot and best regards,</div><div class="">Lior</div><div class=""><br class=""></div></div></div>
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