Troubleshooting Beagle-lib

IFB Core Cluster Demande de logiciel ou de banque de données
1

Dear Admin,

I want to use Beagle library with BEAST2 to accelerate the runs.

I've successfully installed Beagle locally in my home. https://github.com/beagle-dev/beagle-lib/wiki/LinuxInstallInstructions

(base) [dchakraborty@core-login2 ~]$ cd $HOME
(base) [dchakraborty@core-login2 ~]$ ls
00_data 01_mafft R include lib ondemand user_guides
(base) [dchakraborty@core-login2 ~]$ cd lib
(base) [dchakraborty@core-login2 lib]$ ls
cmake libhmsbeagle-cpu-sse.so.40.0.0 libhmsbeagle-cpu.so.40.0.0 libhmsbeagle.so pkg-config
libhmsbeagle-cpu-sse.so libhmsbeagle-cpu.so libhmsbeagle-jni.so libhmsbeagle.so.1

But when I try <beast -beagle_info>, beast can't access beagle. <Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path: /.singularity.d/libs:/usr/local/lib:/usr/local/beast/jre/lib/amd64>

I've added the path to the library to .bashrc.

Can you please help me find a solution?
Thank you in advance,
Debo

2

Hello Debo,

The beast2 v2.6.3 installation available on the cluster already supports libbeagle.
You can load it in your environment using :

module load beast2/2.6.3
beast -beagle_info

beast2 v2.7.4 is also available on the cluster but does not include libbeagle yet. Let us know if you absolutely need to work with beast2 2.7.4.

Have a nice day,

Julien

3

Bonsoir Julien,

Many thanks for the quick reply. In fact, I need beast2 v2.7.6 because I'm using a new package called BICEPS. https://github.com/rbouckaert/biceps?tab=readme-ov-file#biceps-tutorial

<File: ja500_1.xml seed: 1713280609357 threads: 1

Loading package BEAST v2.6.3

Loading package BEAST v2.6.3

The following packages are required, but not available: BEAST.base v2.7.6, BICEPS v1.1.2

See http://beast2.org/managing-packages/ for details on how to install packages.>

Let me know if there's something I can do about it.

Bonne soirée !
Debo

4

Bonsoir,

We will need a few days to package v2.7.6 and deploy it to the cluster.
I will let you know when it is ready.

Best regards,

Julien

5

Bonjour,

That'll be excellent! Many thanks for your help. Appreciate it.
Bonne journée,
Debo

6

Bonsoir,

I hope this message finds you well.

I just wanted to touch base regarding the BEAST v2.7.6 and BEAGLE deployment. I understand how busy things can get and appreciate all the efforts in managing the system's needs.

Just wanted to know if you've any timeline in mind so I can plan a particularly hefty analysis (it'll take a month without beagle even with threads) to run.

Thank you very much for your attention to this matter.

Warm regards,
Debo