Using MPI with Anaconda

The mpi4py package bundled with, or installed by Anaconda may not work correctly on the ARC cluster. The mpi4py code should be linked to an ARC compiled MPI library on the system - in order to do this in your virtual environment run the following commands:

From the login node, start an interactive session on a compute node - this is important for testing later:

srun --nodes=1 --ntasks-per-node=4 --partition=interactive --pty /bin/bash

First load the appropriate modules and create your virtual environment:

module purge
module load foss/2020a
module load Anaconda3/2020.11

In this example we are using Anaconda3 2020.11 and using OpenMPI 4.0.3 which comes as part of the foss/2020a toolchain.

Note: At present we do not recommend using the foss/2021b toolchain due to an incompatibility between OpenMPI 4.1.x and mpi4py.

Next we build our virtual environment, and activate it (if you already have your own environment you could use this instead, and simply activate it):

conda create --prefix $DATA/mpienv --copy python=3.8
source activate $DATA/mpienv

Now that we have an activated Anaconda virtual environment we can download and install mpi4py, in this case version 3.1.3:

tar -zxf mpi4py-3.1.3.tar.gz

cd mpi4py-3.1.3
python build --mpicc=`which mpicc`
python install
python clean

Assuming the build above completes successfully we can now test the mpi4py installation.

First create a file called containing the following Python code:

from mpi4py import MPI
print("hello world")
print(("name:",name,"my rank is",comm.rank))

As we are connected to an interactive node, and have four cores allocated (as per the original srun command) we can test this code as follows:

mpirun python

Note: we must run Python with the mpirun wrapper in order to execute MPI code. The output from the above command should be:

hello world
('name:', 'arc-c304', 'my rank is', 0)
hello world
('name:', 'arc-c304', 'my rank is', 1)
hello world
('name:', 'arc-c304', 'my rank is', 2)
hello world
('name:', 'arc-c304', 'my rank is', 3)

In the above each allocated core has run the code and outputted the string “hello world” and given its hostname and MPI rank.

For a more real world example, we will take the same hello world code and run it in a batch script on multiple nodes in the development partition, the example submission script is as follows, it should be located in the same directory as and named


#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4
#SBATCH --partition=devel
#SBATCH --job-name=PyHello
#SBATCH --time=00:10:00

module purge
module load Anaconda3/2020.11
module load foss/2020a

source activate $DATA/mpienv

mpirun python ./

Note: There is no need to specify the number of tasks to the mpirun command. All ARC built MPI libraries are SLURM aware and are able to determine the task count.

Here you can see we have asked for two development nodes, with four MPI tasks on each node (a total of eight MPI tasks). Note we have also loaded BOTH the Anaconda3 and foss/2020a modules as used in the mpi4py build.

To submit the job, use the SLURM sbatch command:


Once the job completes, the SLURM output file should contain the following information from the job:

hello world
('name:', 'arc-c303', 'my rank is', 4)
hello world
('name:', 'arc-c303', 'my rank is', 5)
hello world
('name:', 'arc-c302', 'my rank is', 0)
hello world
('name:', 'arc-c302', 'my rank is', 1)
hello world
('name:', 'arc-c302', 'my rank is', 2)
hello world
('name:', 'arc-c302', 'my rank is', 3)
hello world
('name:', 'arc-c303', 'my rank is', 6)
hello world
('name:', 'arc-c303', 'my rank is', 7)

It can be seen from the above that the MPI processes are running on two hosts: arc-c302 and arc-c303 and there are four MPI ranks per host, as specified in the submission script.