NVIDIA-GPU-Bootcamp-Training/hpc/nways/nways_labs/nways_MD

Nways to GPU programming - MD mini application

This repository contains mini applications for GPU Bootcamps (Tested on NVIDIA driver 440.82)

Prerequisites:

To run this tutorial you will need a machine with NVIDIA GPU.

• Install the Docker or Singularity.
• Install Nvidia toolkit, Nsight Systems (latest version) and compute (latest version).

Creating containers

To start with, you will have to build a Docker or Singularity container.

Docker Container

C & Fortran

To build a docker container, run:

sudo docker build -t <imagename>:<tagnumber> .

For instance:

sudo docker build -t myimage:1.0 .

Python

To build a docker container, you have to specify the dockerfile name using flag "-f", hence run:

sudo docker build -f <dockerfile name> -t <imagename>:<tagnumber> .

For example :

sudo docker build -f Dockerfile_python -t myimage:1.0 .

For C, Fortran, and Python, the code labs have been written using Jupyter lab and a Dockerfile has been built to simplify deployment. In order to serve the docker instance for a student, it is necessary to expose port 8000 from the container. For example, the following command would expose port 8000 inside the container as port 8000 on the lab machine:

sudo docker run --rm -it --gpus=all -p 8888:8888 myimage:1.0

When this command is run, you can browse to the serving machine on port 8000 using any web browser to access the labs. For instance, from if they are running on the local machine the web browser should be pointed to http://localhost:8000. The --gpus flag is used to enable all NVIDIA GPUs during container runtime. The --rm flag is used to clean an temporary images created during the running of the container. The -it flag enables killing the jupyter server with ctrl-c. This command may be customized for your hosting environment.

Then, inside the container launch the Jupyter lab assigning the port you opened:

jupyter-lab --ip 0.0.0.0 --port 8888 --no-browser --allow-root

Once inside the container, open the jupyter lab in browser: http://localhost:8888, and start the lab by clicking on the START_nways.ipynb notebook.

Singularity Container

C & Fortran

To build the singularity container, run:

singularity build nways.simg Singularity

Python

To build the singularity container, run:

singularity build nways.simg Singularity_python

For C, Fortran, and Python, copy the files to your local machine to make sure changes are stored locally:

singularity run nways.simg cp -rT /labs ~/labs

Then, run the container:

singularity run --nv nways.simg jupyter-lab --notebook-dir=~/labs

Once inside the container, open the jupyter lab in browser: http://localhost:8888, and start the lab by clicking on the START_nways.ipynb notebook.

Questions?

Please join OpenACC Slack Channel for questions.