Execution

Abstract

This section describes how to use an Apptainer container image as execution environment of an application on the compute cluster.

Interactive

Start an interactive shell in a container image:

# this example uses the Python container
apptainer pull $APPTAINER_CONTAINERS/python.sif docker://python:latest

# start a shell within the container environment
apptainer shell $APPTAINER_CONTAINERS/python.sif

Use srun to allocate an interactive shell (cf. real time allocation):

» srun -p debug --pty -- apptainer shell $APPTAINER_CONTAINERS/python.sif
apptainer> which python
/usr/local/bin/python
apptainer> python --version
Python 3.8.3

Command Options

Option	Description
--singularity-container	Path to the Singularity container

Instead of invoking the apptainer command yourself, it is possible to specify the container via command option.

srun -p debug \
      --singularity-container=$APPTAINER_CONTAINERS/python.sif \
      --pty /bin/bash

Environment Variable

Environment Variable	Description
SLURM_SINGULARITY_CONTAINER	Path to the Singularity container

Alternatively export an environment variable to set the absolute path to a container image. The PATH environment variable from your local shell is used for path resolution. Unless a path is the same on the host and the container, it is required to use an absolute path to start an executable:

# Set the path to the container image...
export SLURM_SINGULARITY_CONTAINER=$APPTAINER_CONTAINERS/python.sif

# ...use absolute path the application (in this example the Python interpreter)
» srun -p debug --pty -- /usr/local/bin/python --version
Python 3.8.3

Batch Job

The simple batch script created blow prints information about its runtime environment and the available Python interpreter:

# simple script executing a couple of commands
cat > $LUSTRE_HOME/bin/batch.sh <<EOF
#!/usr/bin/env bash
uname -nr
cat /etc/os-release | head -2
which python
python \${1:-'--version'}
EOF
# make it executable
chmod +x $LUSTRE_HOME/bin/batch.sh

Executing this script on a submit node will print the Virgo host platform:

» $LUSTRE_HOME/bin/batch.sh 
lxbk0595 3.10.0-1127.18.2.el7.x86_64
NAME="CentOS Linux"
VERSION="7 (Core)"
/usr/bin/python
Python 2.7.5

Execution of the same script in a container prints the container applications environment.

# run the script in the offical Python container
» apptainer exec $APPTAINER_CONTAINERS/python.sif $LUSTRE_HOME/bin/batch.sh
lxbk0595 3.10.0-1127.18.2.el7.x86_64
PRETTY_NAME="Debian GNU/Linux 10 (buster)"
NAME="Debian GNU/Linux"
/usr/local/bin/python
Python 3.8.3

Execute the batch script with the sbatch command (cf. batch jobs)

» sbatch -p debug \
      --singularity-container=$APPTAINER_CONTAINERS/python.sif \
      -- $LUSTRE_HOME/bin/batch.sh
Submitted batch job 11777406

# print the output
» cat slurm-11777406.out
lxbk0595 3.10.0-1127.18.2.el7.x86_64
PRETTY_NAME="Debian GNU/Linux 10 (buster)"
NAME="Debian GNU/Linux"
/usr/local/bin/python
Python 3.8.3

Following is a simple Python script to print the version information about the Python interpreter its executed with:

cat > $LUSTRE_HOME/bin/python_version.py <<EOF
#!python
import sys
print(sys.version)
EOF
chmod +x $LUSTRE_HOME/bin/python_version.py

Use the batch script to execute the Python script on the cluster with sbatch:

» sbatch -p debug \
      --singularity-container=$APPTAINER_CONTAINERS/python.sif \
      -- $LUSTRE_HOME/bin/batch.sh $LUSTRE_HOME/bin/python_version.py
Submitted batch job 11777645

# print the output
» cat slurm-11777645.out
lxbk0595 3.10.0-1127.18.2.el7.x86_64
PRETTY_NAME="Debian GNU/Linux 10 (buster)"
NAME="Debian GNU/Linux"
/usr/local/bin/python
3.8.3 (default, Jun  9 2020, 17:39:39)
[GCC 8.3.0]