marinebon / SLURMquamapR

R scripts to generate aquamaps using SLURM supercomputing scheduler

SLURMquamapR

R scripts to generate aquamaps using SLURM supercomputing scheduler

usage

Here we assume you have a USF account on the CIRCE supercomputing cluster or similar SLURM scheduler.

1. ssh [e-mail] # sign into an access node.
2. cd /work/t/tylarmurray/repos/SLURMquamapR/ # move to repo location.
3. git pull # ensure code is updated
4. edit sbatch submit_jobs.sh to set #SBATCH --array= (and others) as desired
   • to set array to all species use the output of cat species_names.txt | wc -l
5. sbatch submit_jobs.sh # submit the jobs
6. watch squeue -u tylarmurray # watch your jobs in action (ctrl-C to stop)
7. once complete the .out files will include logs for each jobs and the data files will be in place if the processes succeeded.