CPU usage MED (decompose)

[ites...@gmail.com]

Hi,
I am running decompose on a 40-cpu computer setting the parameter -N to 8. However, looking at the cpu usage (htop) shows that all cpus are used with only a minimal load each. Am I missing a parameter in the command? Do you think that problem is specific to the computer I am using, or do you know of similar cases?

Thanks!

Cheers,
Christiane

[A. Murat Eren]

Hi,

Unfortunately not all parts of the algorithm is parallelized. So the number of CPUs are used during refining of the topology. But the initial identification of MED topology is done using only a single core :/

Best,

--

A. Murat Eren (meren)
http://merenlab.org :: gpg

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[ites...@gmail.com]

Hi,
I probably should have been more specific: I was wondering why all 40 available cpus were used in the later stages of the algorithm instead of the specified 8.

Cheers,
Christiane

[A. Murat Eren]

Sorry! I clearly misread your question. Yesterday was a very busy day :/

OK. I'm not sure why it is happening. With -N 8, the code will create only 8 threads. The rest is taken care of the scheduler of the operating system, and is beyond MED. I will try to take a look as soon as possible.

Best,

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