One of my Python scripts is taking too long to run, which exceeds the short queue. I decided to use MPI, and mpi4py seems to be a good choice. But there are many issue when I first used it.

After many attempts, I found at least one way to use it.

Some ideas are from here:

  • ssh into the cluster
  • load anaconda into system
  • create a conda environment for this task mpienv
  • activate the environment
  • load compiler, I used gcc
  • load openmpi
  • export MPICC=”$(which mpicc)”
  • pip install mpi4py, you should not use conda-forge channel because it will install mpi again.
  • test with python -c “import mpi4py”

So earlier I had issues and there are several lessons: You should load before installing mpi4py Because we need to use system mpi, we need to load mpi after activate the environment.

Good luck!