Template for HPC Project

🚀 HPC Development Ready 🚀

Features

• Uniform, Reproducible setup of HPC development environment using container
• CUDA, Intel MKL integration, and OpenMP Offloading / OpenACC enabled compilers (GCC, Clang) in a container
• GitHub Actions with container and Visual Studio Code Remote Container exntension settings

ricosjp/allgebra is a project of development containers for HPC developer, and this repository is its sub-project.

Create new repository

• Login to GitHub
• Push "Use this template" button ↗️

See also GitHub Document

Install Docker with NVIDIA container toolkit

For Linux

Install docker engine, docker compose and NVIDIA container toolkit

For Windows 11 (CUDA on WSL2)

• Install NVIDIA Drivers for CUDA on WSL, including DirectML Support
• Install Docker Desktop for Windows
  • Confirm docker working in WSL2 mode instead of Hyper-V mode

Then you can run docker command on cmd.exe or PowerShell

docker run -it --rm --gpus=all ghcr.io/ricosjp/allgebra/cuda11_4/clang12/mkl:21.09.0

Windows 10 is not supported because we cannot handle NVIDIA GPU managed by Windows kernel from WSL2. Please upgrade to Windows 11.

VSCode setup

• Clone your repository
• Open the directory by Visual Studio Code
• Install Remote Container extension
• Click the lower left >< green button in vscode UI
• Select "Reopen in Container"
• Select "From docker-compose.yml"
  • Then the docker pull starts. This will download the allgebra container, which is very large (~8GB) because it contains CUDA and Intel MKL binaries.
  • You can see the downloading log in the vscode's terminal
• If everything goes well, a new vscode window opens with Remote Container extension.
  • Run nvidia-smi to confirm the GPUs are accessible

Use host SSH key in container

VSCode will expose host's ssh-agent socket into container process, and you can use host SSH key in container. See the official document of vscode for detail. Roughly,

• Start host ssh-agent process
  • In Windows, you can check if ssh-agent starts by Get-Service ssh-agent
• ssh-add host key to host ssh-agent
  • When the key is correctly added, ssh-add -l command shows the registered key.
• (Re)start Remote Container
  • The path of socket connecting to host ssh-agent is written in $SSH_AUTH_SOCK env variable
  • ssh-add -l command shows the key registerred on the host

Recommended Extensions

• C/C++
• CMake Tools
• Nsight Visual Studio Code Edition