[Bio-linux-dev] Rethink about using 64-bit Linux on NBX's

Tony Travis a.travis at abdn.ac.uk
Wed Sep 23 13:00:21 EDT 2009


Hello, NBX/Bio-Linux developers.

I've been looking into the possibility of running a 32-bit Bio-Linux 
'userland' under a 64-bit Linux kernel recently, because I want to run 
64-bit software on our Beowulf servers and it would be useful to do the 
same on the NBX's. In the past, this required using a 32-bit 'chroot' 
environment, which was complicated and clumsy to set up. However, more 
recently the "ia32" libraries have been re-packaged for 64-bit Ubuntu:

> i   ia32-libs            - ia32 shared libraries for use on amd64 and ia64 systems
> v   ia32-libs-gtk        -
> v   ia32-libs-sdl        -
> i   ia32-sun-java5-bin   - Sun Java(TM) Runtime Environment (JRE) 5.0 (32-bit)
> i   ia32-sun-java6-bin   - Sun Java(TM) Runtime Environment (JRE) 6 (32-bit)

This makes it very easy to run existing Bio-Linux 32-bit binaries under 
a 64-bit kernel, but would also allow us to use the 64-bit version of R.

Since we are at quite an early stage in upgrading the NBX's to Ubuntu 
8.04 LTS, I wonder what you all think about upgrading them to 64-bit?

I believe this might also of interest to other Bio-Linux users who want 
to use a 64-bit kernel, but don't want to wait for us to create source 
packages (or re-compile the sources in the existing NEBC 32-bit 'binary' 
packages).

I've upgraded my own desktop PC, and one of our Beowulf servers to use 
64-bit Ubuntu with the ia32 libraries and everything seems to work OK.

The systems I tested had Bio-Linux packages installed (mainly) into 
/usr/local under 32-bit Ubuntu, then the system was upgraded to 64-bit 
Ubuntu overwriting the system partition but preserving /usr/local. The 
only problem I see at present is how to use the existing NEBC packages, 
which have control files specifying many of them as i386 architecture.

Bye,

   Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt




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