BEAST can't find SNAPP when running on a cluster (with SLURM)

[André Elias Rodrigues Soares]

When I run beast straight from the shell it loads all packages normally, but when I run it inside a slurm .srm script it fails to load any additional package. Is there a way i can force beast to load a certain package? I thought there was some flag for that if I ran beast as java -jar beast.jar but I couldn't find anything.

PS: SNAPP doesn't play nice with GPUs, right?

[André Elias Rodrigues Soares]

Sorry, forgot to add:

BEAST v2.4.7

SNAPP v1.3.0

[Tim Vaughan]

Hi André, BEAST should load any package that it finds in one of its standard paths.  Assuming your cluster is running on some GNU/Linux distro, this is probably ~/.beast/2.4/. So I suspect that what's happening is that the slurm jobs are for some reason unable to access this directory.  (Are the compute nodes mounting your home directory?)

Cheers,

Tim

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[André Elias Rodrigues Soares]

Hi Tim, thanks for the reply.

I don't think they're mounting my home directory, I had to re-install it on a separate /project/whatever directory. Can I point Beast to a different directory/use a different place to install packages?

Best,

André

[Tim Vaughan]

Hi André,

On Wed, 11 Oct 2017 at 13:40 André Elias Rodrigues Soares <aers...@gmail.com> wrote:

I don't think they're mounting my home directory, I had to re-install it on a separate /project/whatever directory. Can I point Beast to a different directory/use a different place to install packages?

You can indeed.  To do this, find the launch script for beast, open it in a text editor and add the jvm option -Dbeast.user.package.dir=YOUR_PATH immediately following $JAVA in the two lines right near the end of the file that actually run BEAST.  Replace YOUR_PATH with the path to the directory containing the packages.

Cheers,

Tim

[André Elias Rodrigues Soares]

Hi Tim,

Thank you! I uninstalled SNAPP and then created a new directory, installed it using "addonmanager -add SNAPP -dir /new/dir/andre/beastpackages", then edited the two lines in the beast launch script as you said and it's working now. Thank you very much for you speedy replies and help.

Best,

André