-p or number of threads in Tophat2

Question

[Arash]

Hi,

Whats meaning of -P or --num-threads in Tophat 2 ? For Tophat running , how can i set up it? My question is whats the meaning of 1 or 2 or 8 in this option?

Thanks

Answer 1

[Devon Ryan]

It's (roughly) the number of cores on your computer that it can use in parallel. If you don't know how many you have, then ask whoever the systems administrator is.

[Arash]

Thanks:

Intel® Xeon(R) CPU E5-2620 v4 @ 2.10GHz × 32 Memo: 62.8 GiB

so, whats the number for -p ?

[Devon Ryan]

Nothing over 12 according to the specs.

[GenoMax]

@Arash: You don't want to use 12 if this is a single CPU machine. Depending on how the program is written it may lock the machine up if it starts using all 12 cores. You should leave a couple of cores for system programs to do their thing so you are able to interact with the system (i.e. use the keyboard and have the system pay attention to it).

[Arash]

@genomax2 : Whats your recommendation?

[GenoMax]

If you are the only user on this machine then use 8 or 10. A couple cores more or less will not reduce/increase the run time by a significant amount.

[Devon Ryan]

Even for interactive machines, leaving a half core for browsing the internet usually suffices.