Overview
Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data. The software is written in C++ and can run in parallel on numerous interconnected computers using the message-passing interface (MPI) standard.
Using
Use the module name ray to discover versions available and to load the application.
Testing: Based on User Manual
Examples
The examples have been updated on the 20220513 due to the mpi issue indictaed on our Known Issues page.
Example 1: Using one node, with ten tasks (one core per task). Notice that the srun -n option is set to 1 * 10 = 10:
#!/bin/bash #SBATCH --account=<project-name> #SBATCH --time=00:30:00 #SBATCH --nodes=1 #SBATCH --ntasks-per-node=10 #SBATCH --cpus-per-task=1 #SBATCH --output=ray_%A.out module load ray/2.3.1 srun --mpi=pmi2 -n 10 Ray -o test -p test_file_1.fastq test_file_2.fastq -k 31
Example 2: Using five nodes, with sixteen tasks per node (one core per task). Notice that the srun -n option is set to 5 * 16 = 80:
#!/bin/bash #SBATCH --account=<project-name> #SBATCH --time=00:10:00 #SBATCH --nodes=5 #SBATCH --ntasks-per-node=16 #SBATCH --cpus-per-task=1 #SBATCH --output=ray_%A.out module load ray/2.3.1 srun --mpi=pmi2 -n 80 Ray -o test -p test_file_1.fastq test_file_2.fastq -k 31