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Official website : https://github.com/amkozlov/raxml-ng

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Table of Contents

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Available version

Version

Module

OpenMP

OpenMP+MPI

1.2.0

RAxML-NG/1.2.0-cpeGNU-23.03

raxml-ng

raxml-ng-mpi

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Job submission script

OpenMP

Code Block
#!/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

Code Block
#!/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

Code Block
#!/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 restore
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

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