Troubleshooting Beagle-lib

IFB Core Cluster Tool or data bank request
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

7

Bonsoir Debo,

BEAST v2.7.6 with beagle support is now available on the cluster : module load beast2/2.7.6
I have included GPU support for beagle lib.

If have tested some sample xml with beast and it seems to be running. You should be able to install the BICEPS package using packagemanager.
However I have notice that the beauti command is crashing without any clear error message. I will try to find out what could be missing with the help of the beast2 developers...

Best regards,

Julien

8

Bonsoir Julien,

I've finally tested them with Mascot and all in working condition. Many thanks for your help.
Bonne soirée,
Debo