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First time user: when to use Parallel?

From: Junchen Gu
Subject: First time user: when to use Parallel?
Date: Fri, 14 Feb 2014 17:00:28 -0600


Thanks for making this cool tool. I've tried to use it but I have a
question about the rationale behind it and would like to hear your
opinions on how to best utilize the tool.

I work in a computational biology lab. Recently I have to align many
short reads onto the genome and I'm using novoalign which has a option
to let me specify the maximum number of threads to use. I'm using a
shared server so I typically set it at 8 threads max for one novoalign
job and run all novoalign jobs one by one.

I just tried to run all 6 novoalign with parallel still with 8 threads
each then my own job would basically use up 95% of the memory, which
is not very good... so I have to lower the maximum number of threads
for each job.

I'm wondering then which way of running all the jobs is faster?
Running each job one by one with a higher number of threads or using
Parallel with a lower number of threads?

In a more general sense, when do you choose to use Parallel instead of
running jobs sequentially?



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