Running BEAST in a cluster using multiple cores

HPC Technical
1

Hello,

I would like to run a phylogenetic reconstruction using BEAST in the cluster Baobab. I know how to run it in a single core, but not how to run it using multiple cores. Please, could some body share with me the comands to run it?. For a single core I am using the next comands in a sh file:

#!/bin/sh

#SBATCH --cpus-per-task=1
#SBATCH --job-name=“name”
#SBATCH --ntasks=1
#SBATCH --time=96:00:00
#SBATCH --clusters=baobab
#SBATCH --partition=bigmem-EL7
#SBATCH --mem-per-cpu=50000

module load GCC/4.9.3-2.25 OpenMPI/1.10.2 Beast/2.4.0

#srun java -Dbeast.load.jars=true -jar $EBROOTBEAST/lib/beast.jar name.xml

srun beast name.xml

Please, could some body share with me the comands to run it in multiple cores?

Thanks a lot,

Carlos.

2

Hello, I did some tests, please check here.

Best

3

Dear Yann,

thank you very much!, I will test your script as son as possible. Sad to see that the running time is not really improved adding more cores.

All the best,

Carlos.