singularity-openmpi.md

Singularity with Open MPI

In this exercise you will install Open MPI on your host/VM, create a singularity container with Open MPI installed, then execute mpirun from the host with the parallel processes running in containers. First, let's start with a python based MPI example

Install Open MPI on the host (centos)

Here we install a bit old version of openmpi so that can match old installations on your cluster

# pre-requisites
sudo yum groupinstall 'Development Tools'
# Download openmpi 1.10.2
wget https://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.2.tar.bz2
tar xvjf openmpi-1.10.2.tar.bz2
cd openmpi-1.10.2
# Install openmpi 
./configure --prefix=/usr/local
make
sudo make install
# Compile and test the ring example
mpicc examples/ring_c.c -o ring
mpirun -np 2 ring

Create the ubuntu container

Create an image file with 4 GiB size:

singularity image.create -s 4096 ~/ubuntu.simg

Build an old ubuntu container inside that image:

sudo singularity build -w ~/ubuntu.simg docker://ubuntu:12.04

Install Open MPI on the container

Here we install the same openmpi version, that we installed on the host, on the container.

• Install the pre-requisites:

sudo singularity exec -w ~/ubuntu.simg apt-get update
sudo singularity exec -w ~/ubuntu.simg apt-get install build-essential

• Make another directory for the openmpi source/build on the ubuntu container

mkdir ~/openmpi-ubuntu
cd ~/openmpi-ubuntu

• Download and install openmpi

wget https://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.2.tar.bz2
tar xvjf openmpi-1.10.2.tar.bz2
cd openmpi-1.10.2
singularity exec ~/ubuntu.simg ./configure --prefix=/usr/local
singularity exec ~/ubuntu.simg make
sudo singularity exec -w -B /home ~/ubuntu.simg make install
# for mpicc to work:
sudo singularity exec -w -B /home ~/ubuntu.simg ldconfig

• Test openmpi

singularity exec ~/ubuntu.simg mpicc examples/hello_c.c -o hello
singularity exec ~/ubuntu.simg mpirun -np 2 hello

Use openmpi from the host with container processes

• Copy the ring binary to /usr/bin inside the container

sudo singularity exec -w -B /home ~/ubuntu.simg cp ./hello /usr/bin/hello

• Run mpirun

mpirun -np 2 singularity exec ~/ubuntu.simg /usr/bin/hello

Exercise: Do the same on Abel

• Slurm script to run the Hello MPI on Abel