[BioC] Installation on a cluster

[Claudio Lottaz]

Hi folks, 

Sean's suggestion to install in a cluster is indeed easy to maintain. We did it similarly but encountered network traffic issues. If you start 50 R-processes at the same time, opening plenty of shared libraries and loading data seemed to bring the network down. Did anybody observe this kind of problems as well? wouldn't it be advisable to distribute the distribution locally on all nodes after installing it in the common NFS-place?

Cheers,
Claudio

 

-----Original Message-----
From: "Sean Davis" [mailto:sdavis2 at mail.nih.gov] 
Sent: Thursday, April 17, 2008 3:40 PM
To: "Daniel Davidson" <danield at igb.uiuc.edu>
Cc: <bioconductor at stat.math.ethz.ch>
Subject: Re: [BioC] Installation on a cluster

On Thu, Apr 17, 2008 at 9:16 AM, Daniel Davidson <danield at igb.uiuc.edu> wrote:
> Hello,
>
>  I have been tasked with getting Bioconductor installed on our cluster.
>  Because the slave nodes cannot access the Internet, the normal method 
> of  install using:
>
>  source("http://bioconductor.org/biocLite.R")
>  biocinstallPkgGroups("lite")
>
>  will not work.  Does anyone have a good method of doing this on a cluster?  We have a local Bioconductor mirror on the cluster that is shared of NFS.
>

Hi, Dan.

The way we do this is to make an nfs-shared /usr/local and install R there.  Then, use biocLite to install packages to the shared
directory.    The benefit of this setup is that you update in only one
place and only once either packages or R itself and it is automatically seen on all machines.  An added benefit is that additional packages (graphviz, netcdf, etc.) need only be installed into the shared /usr/local tree and all nodes will see them.  Of course, this assumes that your nodes are all one architecture, but since you said "cluster", I assume that is the case

Sean

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