BEAGLE + BEAST 2 in cluster
Cluster provides more computational power. Paralleling your BEAST jobs and using SSE in cluster could save you more than half of your commutation time.
Here we show how BEAGLE options performed on the NeSI cluster (http://www.nesi.org.nz) and laptop (MacBookPro5,1: Intel Core 2 Duo). GPU option is not included in this comparison.
| Laptop | Cluster (Default) | Cluster OpenMP (4 threads) | |
|---|---|---|---|
| Java | 15m17s | 11m55s | 7m9s |
| BEAGLE | 9m24s | 7m45s | 6m25s |
| BEAGLE SSE | 8m1s | 4m52s | 3m50s |
The speed is the minutes and seconds of per million samples, which is logged at the sample 36,000 by running the same xml using seed 777.
Command in laptop
Use Java likelihood calculation only, BEAGLE is not considered:
java -jar launcher.jar -seed 777 -java my.xml Use beagle library but no SSE:
java -jar launcher.jar -seed 777 -beagle my.xml Use beagle library and SSE extensions:
java -jar launcher.jar -seed 777 -beagle_SSE my.xmlDefault template for cluster
The template below is to run a serial BEAST 2 job using BEAGLE SSE in cluster (Guide is here):
#!/bin/sh
#SBATCH -J FILE # The job name
#SBATCH -A uoa??? # The account code
#SBATCH --time=12:00:00 # The walltime
#SBATCH --mem-per-cpu=16384 # Memory in MB ie. ? * 1024
#SBATCH -D ./ # The initial directory
#SBATCH -o FILE_out.txt # The output file
#SBATCH -e FILE_err.txt # The error file module load beagle-lib/20140322-goolf-1.5.14
module load Java/1.8.0_5
srun java -Xmx10g -Djava.library.path=$BEAGLE_LIB_PATH -jar launcher.jar -beagle_SSE -seed 777 my.xml OpenMP (4 threads) template for cluster
The 4-thread OpenMP (Open Multi-Processing) template below is to run a parallel BEAST 2 job using BEAGLE SSE in cluster (Guide is here):
#!/bin/sh
#SBATCH -J FILE # The job name
#SBATCH -A uoa??? # The account code
#SBATCH --time=12:00:00 # The walltime
#SBATCH --mem-per-cpu=16384 # Memory in MB ie. ? * 1024
#SBATCH --cpus-per-task=4 # 4 OpenMP Threads
#SBATCH -D ./ # The initial directory
#SBATCH -o FILE_out.txt # The output file
#SBATCH -e FILE_err.txt # The error file module load beagle-lib/20140322-goolf-1.5.14
module load Java/1.8.0_5
srun java -Xmx10g -Djava.library.path=$BEAGLE_LIB_PATH -jar launcher.jar -threads 4 -beagle_SSE -seed 777 my.xml