Official website : https://github.com/amkozlov/raxml-ng
Available version
Version | Module | OpenMP | OpenMP+MPI |
|---|---|---|---|
1.2.0 | RAxML-NG/1.2.0-cpeGNU-23.03 | raxml-ng | raxml-ng-mpi |
Job submission script
OpenMP
#!/bin/bash #SBATCH -p compute # specific partition (compute,memory) #SBATCH -N 1 -c 128 # -N 1 must be 1, -c can be 16, 32, 64 depending on the requirement #SBATCH -t 24:00:00 # job time limit <hr:min:sec> #SBATCH -A lt200xxx # project ID #SBATCH -J RAxML-NG # job name module restore module load RAxML-NG/1.2.0-cpeGNU-23.03 raxml-ng --all --msa aligned.fasta --prefix output_prefix --model LG+G8+F --bs-trees 200 --thread $SLURM_CPUS_PER_TASK
OpenMP+MPI
1 node
#!/bin/bash #SBATCH -p compute # specific partition (compute,memory) #SBATCH -N 1 -n 8 -c 16 # specify computing resource (1 node, 8 MPI ranks, 16 threads per rank) #SBATCH -t 24:00:00 # job time limit <hr:min:sec> #SBATCH -A lt200xxx # project ID #SBATCH -J RAxML-NG # job name module restore module load RAxML-NG/1.2.0-cpeGNU-23.03 srun raxml-ng-mpi --all --msa aligned.fasta --prefix output_prefix --model LG+G8+F --bs-trees 200 --thread $SLURM_CPUS_PER_TASK
> 1 node
#!/bin/bash #SBATCH -p compute # specific partition (compute,memory) #SBATCH -N 2 -n 16 -c 16 # specify computing resource (2 nodes, 16 MPI ranks, 16 threads per rank) #SBATCH -t 24:00:00 # job time limit <hr:min:sec> #SBATCH -A lt200xxx # project ID #SBATCH -J RAxML-NG # job name module load RAxML-NG/1.2.0-cpeGNU-23.03 srun raxml-ng-mpi --all --msa aligned.fasta --prefix output/run128mpi_1 --model LG+G8+F --bs-trees 200 --thread $SLURM_CPUS_PER_TASK