HPC Workshop on Containers and Unikernels

Jul 5, 2021, 9:00 AM → Jul 9, 2021, 5:00 PM Europe/Amsterdam

Virtual

Abdulrahman Azab

Containers with the build-once-run-everywhere principle have become very popular for scientific use cases. The majority of HPC platforms for research now support container runtimes. Unikernels are very lightweight virtual machines that provide hypervisor level isolation and near to native performance. This workshop will introduce several container platforms (Docker, Singularity, Sarus, Charliecloud) and provide hands-on MPI and GPU examples. In addition, there will be a demo on Unikernels.

PRACE online workshop on containers and unikernels that includes 

• Docker: Intro, install, image build, container management

• Sarus: Intro, installation, MPI, GPU

• Singularity: Intro, manage containers, MPI, GPU

• Charliecloud: Intro, MPI

• Unikernels: Intro, demo

Trainings with hands-on will be on https://www.cscs.ch/computers/piz-daint/  

• XC50 Compute Nodes: Intel® Xeon® E5-2690 v3 @ 2.60GHz (12 cores, 64GB RAM) and NVIDIA® Tesla® P100 16GB - 5704 Nodes

• 1 GPU Card per node: one user can use the node per time  

• Reservation on the GPU partition (P100)

Training github repo

Monday, July 5

9:00 AM → 12:00 PM Intro and Docker

Introduction
Install Docker
Run your first container
Docker images
Docker volumes
Docker Compose
Docker swarm

Convener: Abdulrahman Azab (Sigma2/UiO)

12:00 PM → 1:00 PM Lunch break

1:00 PM → 2:30 PM Intro and Docker: Session 2

Introduction
Install Docker
Run your first container
Docker images
Docker volumes
Docker Compose
Docker swarm

Convener: Abdulrahman Azab

Tuesday, July 6

9:00 AM → 12:00 PM Singularity: Singularity - session 1

• Singularity: Introduction
• How to build a container
• Singularity and MPI
• Singularity and GPU
• Share Singularity container

Session material: https://github.com/abdulrahmanazab/docker-training-neic/tree/prace-training-2021/singularity_training

Conveners: Abdulrahman Azab (Sigma2/UiO), Dr Muscianisi Giuseppa (CINECA)

12:00 PM → 1:00 PM Lunch break

1:00 PM → 5:00 PM Singularity: Singularity - session 2

• Singularity: Introduction
• How to build a container
• Singularity and MPI
• Singularity and GPU
• Share Singularity container

Session material: https://github.com/abdulrahmanazab/docker-training-neic/tree/prace-training-2021/singularity_training

Wednesday, July 7

9:00 AM → 12:00 PM Sarus: Session 1

o Intro to Sarus from the user point of view (purpose, workflow, CLI)
o Installing Sarus on your system
o Hands on: installing Sarus on Debian 10
o MPI example with OSU (hands-on with different OSU tests, e.g., all-to-all)
o Hands on: performance without native MPI
o Hands on: performance with native MPI
o Hands on: how to leverage GPUDirect RDMA
o GPU example with N-body
o Hands on: other CUDA samples or user-provided GPU applications
o Show data I/O using bind mounts with a real application, e.g., GROMACS
o Hands on with other application(s)
o Open Q&A

Conveners: Dr Lucas Benedicic (Swiss National Supercomputing Centre (CSCS)), Alberto Madonna (Swiss National Supercomputing Centre (CSCS))

12:00 PM → 1:00 PM Lunch break

1:00 PM → 5:00 PM Sarus: Session 2

o Intro to Sarus from the user point of view (purpose, workflow, CLI)
o Installing Sarus on your system
o Hands on: installing Sarus on Debian 10
o MPI example with OSU (hands-on with different OSU tests, e.g., all-to-all)
o Hands on: performance without native MPI
o Hands on: performance with native MPI
o Hands on: how to leverage GPUDirect RDMA
o GPU example with N-body
o Hands on: other CUDA samples or user-provided GPU applications
o Show data I/O using bind mounts with a real application, e.g., GROMACS
o Hands on with other application(s)
o Open Q&A

Conveners: Dr Lucas Benedicic (Swiss National Supercomputing Centre (CSCS)), Alberto Madonna (Swiss National Supercomputing Centre (CSCS))

Thursday, July 8

9:00 AM → 12:00 PM Charliecloud

HPC focused
o Introduction
o Installation [TBD]
o GPU [TBD]
o MPI

Convener: David Brayford (LRZ)

12:00 PM → 1:00 PM Lunch break

1:00 PM → 3:00 PM Charliecloud: Session 2

HPC focused
o Introduction
o Installation [TBD]
o GPU [TBD]
o MPI

Friday, July 9

9:00 AM → 12:00 PM Unikernels

o Brief intro
o Presentation and Very basic demo about one or more platform → recompile the application

Conveners: Pierre. Jacquot (INRIA), Pierre Olivier (INRIA), Abdulrahman Azab

12:00 PM → 1:00 PM Lunch break

1:00 PM → 3:00 PM Open Q/A [2 hrs]

SAUS Room
Docker and Singularity Room
Unikernels Room