Miscellaneous observations about HHPC - BenLangmead/jhu-compute GitHub Wiki

  1. A job's processes are not affinitized to particular CPU cores. If a job is assigned two cores on a given node, it can abuse its privileges and exceed 200% CPU usage. CPU usage must be hardlimited manually with, e.g. taskset. If you don't hardlimit, you should be careful to match the number of threads used by your process with node/ppn parameter specifications in your PBS script. If you're running Bowtie with -p 2, you should sent ppn to 2. Otherwise, you could be abusing your privileges on the cluster.
  2. If you have many jobs to submit to the cluster, consider designing your PBS script so it can be submitted as a job array.