Using UCSC’s high-performance computational cluster (Hummingbird)

• There are lots of resources available at hb.ucsc.edu.
• You can find the slides from the s/lab presentation here, and a sample SLURM and R script below (which you can also download by clicking the links below.)

Sample SLURM script (download with comments)

#!/bin/bash
#SBATCH --nodes=1  
#SBATCH --partition=128x24  
#SBATCH --job-name=my_job  
#SBATCH --mail-type=ALL  
#SBATCH --mail-user=[your_user_name]@ucsc.edu  
#SBATCH --ntasks=1  
#SBATCH --output=%j.out  
#SBATCH --error=%j.err  
module load R/R-3.5.0  
R --no-save < script.R

Sample R script that saves an object as an RDS file that you can download (download with comments)

r_object <- 1*1  
saveRDS(r_object, file = "test.rds")