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README.md

Docker images and Dockerfiles

The present directory contains four sub-folders:

  • osubenchmarks
  • poisson
  • petibm
  • prepost

The folder prepost contains the Dockerfile used to create the Docker image barbagroup/cloud-repro:latest. This image can be used to re-create a local computational environment with all the dependencies installed to perform pre-processing steps, submit jobs to Azure Batch through the command-line, and re-do the analysis to create the figures of the manuscript.

To pull the Docker image from DockerHub and create a container:

docker pull barbagroup/cloud-repro:latest
docker run -it barbagroup/cloud-repro:latest /bin/bash

Each of the three other sub-folders contains the Dockerfile we used to build the Docker images to run benchmarks and simulations on Microsoft Azure with Azure Batch.

The Docker image mesnardo/osubenchmarks:5.6-GPU-IntelMPI-ubuntu is used to run the latency and bandwidth benchmarks from the OSU Micro-Benchmarks (version 5.6). (Dockerfile in the sub-folder osubenchmarks.)

The Docker image mesnardo/amgxwrapper:1.4-GPU-IntelMPI-ubuntu is used to run the Poisson benchmark from AmgXWrapper (version 1.4). (Dockerfile in the sub-folder poisson.)

The Docker image barbagroup/petibm:0.4-GPU-IntelMPI-ubuntu is used to run the CFD simulations of the gliding snake models with PetIBM (version 0.4). (Dockerfile in the sub-folder petibm.)

Note: Only Intel MPI 5.x versions are compatible with the Azure Linux RDMA drivers. We used the Intel MPI Library for Linux (2017, Update 2) to build the Docker images. Upon registration, you will be able to download the product on the Intel Software website. (The tarball should be named l_mpi_2017.2.174.tgz and be downloaded in the present directory.)

To build the Docker images on your local machine:

  • OSU Micro-Benchmarks (version 5.6):
cd osubenchmarks
docker build --tag=osubenchmarks:5.6-GPU-IntelMPI-ubuntu -f Dockerfile .
  • Poisson benchmarks with AmgXWrapper (version 1.4):
cd poisson
docker build --tag=amgxwrapper:1.4-GPU-IntelMPI-ubuntu -f Dockerfile .
  • PetIBM (version 0.4):
cd petibm
docker build --tag=petibm:0.4-GPU-IntelMPI-ubuntu -f Dockerfile .
  • Computational environment for local pre- and post-processing steps:
cd prepost
docker build --tag=cloud-repro:latest -f Dockerfile .
$ docker version

Client:
 Version:           18.09.3
 API version:       1.39
 Go version:        go1.10.8
 Git commit:        774a1f4
 Built:             Thu Feb 28 06:40:58 2019
 OS/Arch:           linux/amd64
 Experimental:      false

Server: Docker Engine - Community
 Engine:
  Version:          18.09.3
  API version:      1.39 (minimum version 1.12)
  Go version:       go1.10.8
  Git commit:       774a1f4
  Built:            Thu Feb 28 05:59:55 2019
  OS/Arch:          linux/amd64
  Experimental:     false
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