Thread: Tophat Run time
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Old 10-06-2010, 09:44 AM   #7
mrawlins
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Location: Retirement - Not working with bioinformatics anymore.

Join Date: Apr 2010
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Running with n-1 threads on an n-core machine (e.g. 7 threads on a machine with 8 cores) should speed things up. Bowtie has a --shmem option for using shared memory for all threads, so that shouldn't increase the memory footprint by much to use that many threads. I've observed roughly a linear speed up with the number of cores dedicated to bowtie; I suspect similar results for tophat.
I will sometimes run with as many threads as cores, but only if I don't intend to use the computer for anything else while the program runs (i.e. a compute node on our analysis cluster).
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