IVDM3Seg
  • Overview
  • Tasks
  • Data
  • METHODS
    • SUBMIT
    • DOCKERFILE
    • EXAMPLE: PYTHON
  • RESULTS
    • MICCAI2018
    • __________________
    • lrde
    • ucsf_Claudia
    • wanghuan
    • gaoyunhe_cuhk
    • livia
    • mader
    • changliu
    • smartsoft
    • smartsoftV2
  • Dates
  • Metrics
  • Organizers

​Dockerfile


​Some tips-and-tricks for creating a Dockerfile for the submission to this challenge. The Dockerfile Reference can be found here: https://docs.docker.com/engine/reference/builder/ and the best practices here: https://docs.docker.com/engine/userguide/eng-image/dockerfile_best-practices/.
​

​FROM

Pick a suitable base image for your container. Search on Docker Hub for your preferred operating system, for example CentOS or Ubuntu. Optionally, specify a version tag (eg centos:7), because the :latest tag (default when not specifying a tag) might change between your submission and our evaluation.

You can also search on Google or Github for base images that already contain the default tools you need. There is a high chance that your favourite neuroimaging tools have already been containerized.

If you want to use a GPU, be sure to pick a nvidia/cuda base image. Have a look at all the available tags to find your favourite OS.

​

RUN

​Limit the number of RUN commands, by combining them into a single RUN. Each command in a Dockerfile creates a layer in your container, increasing the total container size. So in stead of this:
​
​RUN apt-get update
RUN apt-get install -y aufs-tools
RUN apt-get install -y automake
RUN apt-get install -y build-essential
RUN apt-get install -y libsqlite3-dev
RUN apt-get install -y s3cmd=1.1.*
​RUN rm -rf /var/lib/apt/lists/*

​
Do this:

​RUN apt-get update && apt-get install -y \
          aufs-tools \
          automake \
          ​build-essential \
          libsqlite3-dev \
          ​s3cmd=1.1.* \
&& rm -rf /var/lib/apt/lists/*

​Be sure to do the clean-up within the same command! Otherwise the clean-up happens in a new layer and does not have any effect on the previous layers.
​

ENTRYPOINT
​

If your base image contains a non-default ENTRYPOINT (or USER, CMD, WORKDIR), you can reset this with:
​
​ENTRYPOINT ["bash"] CMD [] USER 0 WORKDIR /

​For example, the jupyter docker-stacks with python base images start a notebook server, which is probably not needed for this challenge.
​
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  • Overview
  • Tasks
  • Data
  • METHODS
    • SUBMIT
    • DOCKERFILE
    • EXAMPLE: PYTHON
  • RESULTS
    • MICCAI2018
    • __________________
    • lrde
    • ucsf_Claudia
    • wanghuan
    • gaoyunhe_cuhk
    • livia
    • mader
    • changliu
    • smartsoft
    • smartsoftV2
  • Dates
  • Metrics
  • Organizers