[R-sig-hpc] Why pure computation time in parallel is longer than the serial version?

[wesley goi]

Thanks roger for the hint at mcaffinity(), 

On 18 Feb, 2014, at 6:38 pm, Roger Bivand <roger.bivand at nhh.no> wrote:

> wesley goi <wesley at ...> writes:
> 
>> 
>> Hi xuening, 
>> 
>> I use multicore's mclapply() function extensively and have recently
>> changed the BLAS lib to openblas to help with running a PCA on a big 
>> matrix, everything ran fine. However, I was wondering if the openblas
>> lib will interfere with multicore. 
>> 
>> So i guess so far there’s no way to assigned the threads which 
>> openblas uses hence it shdnt be used in a multicore script to be 
>> submitted to a cluster else itâ€'ll consume all the cores? 
> 
> Please do use the list archives; the thread:
> 
> https://stat.ethz.ch/pipermail/r-sig-hpc/2012-April/001339.html
> 
> provides much insight into the AFFINITY issue - see also mcaffinity() 
> in the parallel package. If your BLAS is trying to use all available 
> cores anyway, and you then try to run in parallel on top of that, your
> high-level processes will compete across the available cores for 
> resources with BLAS, as each BLAS call on each core will try to 
> spread work across the same set of cores. Please also see:
> 
> http://www.jstatsoft.org/v31/i01/
> 
> and perhaps also:
> 
> http://ideas.repec.org/p/hhs/nhheco/2010_025.html
> 
> Neither are new, but are based on trying things out rather than 
> speculating. As pointed out before, Brian's comment tells you what you 
> need to know:
> 
> https://stat.ethz.ch/pipermail/r-sig-hpc/attachments/20140213/662780c9/
> attachment.pl
> 
> Hope this clarifies,
> 
> Roger
> 
>> 
>> On 18 Feb, 2014, at 11:25 am, Xuening Zhu <puddingnnn529 at ...> wrote:
>> 
>>> Hi Wesley:
>>> I installed open-blas before. It went well when I run serial 
>> operations. 2 threads can be seen in 'top'. But
>> I can't change thread number through the methods it provided.
> 
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