Commonly used phylogenetic methods, Monash HPC access and basic bioinformatics

About the HPC

Glossary of Terms

  • Process - the execution of a computer program[1]. In SLURM/hpc terminology, this is a synonym for task.
  • Thread (of execution) - the smallest unit of computation that can be managed independently by a scheduler[2].
  • Multithreading - Threads that can be executed simultaneously, instead of one after the other. See this Reddit ELI5 for an excellent explanation of multithreading and concurrency.
  • Hyperthreading - Intel's proprietary simultaneous multithreading technology on Intel CPUs.
  • Node - What we think of as a single physical machine. A node can have multiple cores (or processors).
  • pthreads (POSIX Threads) - An execution model that executes parrallelism, primarily made for UNIX.
  • *OpenMP - Used for parrallelism within a node.
  • *OpenMPI - Used for parrallelism between nodes.

Open MPI, SSE How to run MPI applications (srun)

Links and References