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Old 05-27-2015, 04:27 PM   #1
jflowers002
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Location: Seattle

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Default Multi-threaded Velvet

I thought I followed the correct make commands to make velvet multi-threaded, but I have been running an assemble on an EC2 server for the past 5 days on 500 Mbp of total sequence, and I have never seen more than 1 core being used on a 16 core system. Any idea on how to confirm that it is correctly configured?

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Old 05-28-2015, 09:42 AM   #2
Brian Bushnell
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Default

Before running it, did you do something like "export OMP_NUM_THREADS=8"?

Also - Velvet is really fast in my experience. I would expect it to take a few minutes on 500 Mbp of data; so it sounds like something's wrong. Perhaps you are using specific flags that make it slow?
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