[R] R, AMD Opteron 64, and Rmpi

[Ramon Diaz-Uriarte]

Dear All,

I found Andy Liaw's suggestion about using a NUMA (instead of SMP) kernel when 
running R on amd64 with > 1 CPU

http://finzi.psych.upenn.edu/R/Rhelp02a/archive/35109.html


A couple of questions:

1. Is this still the case with the newer dual-core opterons (e.g., the 275 et 
al., families) running Linux (kernel 2.6)?

2. How does this affect using Rmpi (and snow, papply, et al.) on multi-server 
clusters with > 1 CPU? If I understand correctly, and if the situation is 
what Andy described, if we use a SMP kernel we will suffer a within-node 
penalty in one of the Rmpi processes. Is this correct?

Thanks,

R.


-- 
Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
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