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<p class="MsoNormal">I’m hoping for some advice on an unexpectedly long process time for a 2Gb genome. Currently I’m using an install of MAKER-P on the iForge system @ NCSA and I’ve successfully run ~1Gb genomes in 2-3 hours across 20 nodes (24 Intel "Haswell"
cores, 64 GB of RAM per node) via MPICH. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I recently ran some tests on 50Mb of corn that took ~2 hours on 2 nodes (48 cores). Based on that I was surprised when the full 2Gb corn genome run timed out at >24h with 30 nodes (720 cores); in that time it hadn’t processed many sequences
based on the master_datastore_index.log :<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">TOTAL: 25000 seqs<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">STARTED: 3594<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">FINISHED: 2979<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">FAILED: 10<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">RETRY: 9<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">DIED_SKIPPED_PERMANENT: 0<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in">SKIPPED_SMALL: 7635<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">While I can set a longer wall clock, these results are several times longer than what was reported in the MAKER-P paper, i.e. running the corn B73 genome in less than 4 hours; here it is not close to done after 24h. I don’t have an enormous
amount of supporting data– this trial run has ~100k transcripts and another ~100k proteins. Corn has a very high repeat content, so my suspicion is Repeatmasker IO. In discussions with the iForge admins I have discovered that the temp space is network attached
(GPFS), and they’ve suggested using a RAM disk (i.e /dev/shm) as the temp directory. In tests on smaller sequence that ran a little slower so I’m not sure if MAKER is meant to run that way. I’d appreciate input on experience with a RAM disk approach, or if
anyone has alternative thoughts or suggestions?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal">Eric<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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