Ubuntu software repository

[Richard Broughton]

Hi all, I am setting up a new machine that has two Nvidia Tesla K20 GPUs.  I installed Ubuntu 11.10 because Nvidia says that is the latest version validated for the CUDA toolkit.  However, I see that the CUDA toolkit, Beagle-lib, MrBayes and Beast are all available in the Ubuntu 13.04 repository.  Installing these from the package manager would be easier but I am concerned that they might not install to correctly work together.  Using apt-get install would also be somewhat more convenient than downloading and compiling manually.  But I'd like to get it right from the start rather than trying to fix a broken install.
Any advice would be appreciated.
Cheers,
Rich Broughton

[Andrew Rambaut]

No experience personally but this website seems to walk through it:

http://blog.bloemsaat.com/2013/03/17/installing-cuda-on-ubuntu-13-04-raring-ringtail/

A.

> --
> You received this message because you are subscribed to the Google Groups "beagle-user" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to beagle-user...@googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>

[Richard Broughton]

Many thanks for the response Andrew.  That does seem to have detailed instructions. 

But to the broader question, presumably the packages in the Ubuntu repository are validated for that specific release and I've happily used things like Beast, MrBayes, PAML installed from those repositories in serial mode.  But I've never seen a reference to anyone using them in the CUDA-Beagle environment.  Would you happen to have any insight on whether CUDA-Beagle-BEAST would play nice together if all were installed (in that order) from the Ubuntu 13.04 repository?  My concern is that it when compiling from source it appears that Beagle looks for CUDA, Beast or MrBayes look for Beagle, etc., so if repository versions are already compiled, it is not clear what exactly one would get and how they would work.

Thanks!
Rich Broughton 

[Andrew Rambaut]

Hi Richard,

I don't know if the Ubuntu repository BEAGLE is CUDA enabled (CUDA tools need to be present at compilation, although the resulting binary can work on systems without CUDA). BEAST is a bit more dynamic - it will just look for the BEAGLE library in the library paths.

Andrew

[Richard Broughton]

That's what I was wondering about.  Many thanks!
RB