[R-sig-hpc] Using R in a linux cluster
Dirk Eddelbuettel
edd at debian.org
Tue Jun 15 16:37:25 CEST 2010
Hi Paco,
On 15 June 2010 at 16:02, Paco Pastor wrote:
| I'd like to use R in a Ubuntu cluster so I have installed R and Rmpi in
| a clean Ubuntu Lucid installation. Reading about Rmpi I need to have R
| and Rmpi installed in all nodes in the cluster. I have tried to export R
| executable and /usr/lib/R to the other nodes. When I try to run R in
No, that won't work.
[...]
| Then, after exporting /etc/R I get a the same error with libblas.so.3gf
| not found
|
| What should be better? to install R and Rmpi in every node or to export
Yes.
All nodes need to 'symmetric' ie have R, the same packages, libraries, ...
Even the paths should be identical.
| R and all dependencies from the master node to the rest of nodes in the
| cluster? I'd prefer to keep R installed just in the master node so any
| packages update or config changes are not to be repeated in the other
| nodes (just 2, not a big deal but...)
A common solution is to have the master either be an NFS server or write to
an NFS server. Eg I have one /usr/local/lib/R/site-packages/ and the other
machines access this via NFS. Pretty easy when you use autofs auto-mounting.
But as so often, you need an extra bit of sys.admining to get all this going.
--
Regards, Dirk
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