[R] R, AMD Opteron 64, and Rmpi

From: Ramon Diaz-Uriarte <rdiaz_at_cnio.es>
Date: Wed 15 Feb 2006 - 01:38:00 EST

Dear All,

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


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?



Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)

(Spanish National Cancer Center)
Melchor Fernández 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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Received on Wed Feb 15 01:51:56 2006

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