Responsible Use¶
RCC is a shared scheduler-backed compute environment. Responsible use helps keep the cluster available for everyone.
Core Rules¶
Images - option 1, only supports left or right alignment, no center:
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Do not run scripts or computational tasks on the head node.
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- Again, do not run scripts or computational tasks on the head node.
- Submit compute work to Slurm.
- Use job arrays when scaling to many similar jobs.
- Limit concurrent array tasks when large job counts could disrupt other users.
- Use
set -ein multi-command submission scripts when a failure should stop the job immediately.
Example:
#!/bin/bash
#SBATCH --job-name=extract_chrom
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=4G
#SBATCH --output=logs/%x-%j.out
set -e
...
Helpful Habits¶
Use distinct file name suffixes for submission scripts and array scripts, such as _ssubmit.sh and _ssubmitArray.sh.
Consider printing a unique completion code word at the end of every script so logs can be checked quickly.
# count the number of files that have the code word
grep -l "owlbear42" extract_chrom-*.out | wc -l
# list the files that do not have the code word
grep -L "owlbear42" extract_chrom-*.out
Set aliases in .bashrc for frequently used commands.
# show only your jobs
alias qq='squeue -u $USER'
# get a small interactive job
alias int='srun -p ccdefault -J int -n 1 -c 4 --mem=16G --pty /bin/bash'
# get a big interactive job
alias intbig='srun -p ccdefault -J intbig -n 1 -c 48 --mem=180G --pty /bin/bash'
Final tip
Do not run scripts or computational tasks on the head node.