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Old 01-24-2012, 07:12 AM   #1
paolo.kunder
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Location: Milano, Italy

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Default High performance computing & Tophat & Cufflinks

Dear All,
TopHat and Cufflinks support High Performance Computing?
Any clues?
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Old 01-24-2012, 09:02 AM   #2
turnersd
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See the -p option in the documentation.

http://tophat.cbcb.umd.edu/manual.html
http://cufflinks.cbcb.umd.edu/manual.html#cufflinks

I believe Bowtie/Tophat/Cufflinks uses pthreads for threading. That is an SMP (symmetric multiprocessing, i.e. shared memory) threading mechanism. It's important to understand the difference between SMP threading and distributed computing. SMP threading has one thread per core (or hyperthread - a hardware mechanism for making one core act like two).
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