96-50-using-docker.md

(docker-related-procedures)=

Docker-related procedures

In this section, we will show you a few things related specifically to running code reproducibly with Docker. For more general debugging tips for Docker and other computer languages, see our wiki.

(coming soon)

Checklist

• If running licensed software (e.g. MATLAB, Stata), know where the license is stored. If you do not, you cannot run the relevant Docker image.
• Docker (or equivalent) is installed
• The replication package's main directory will be mounted into the Docker container. The precise location will depend on the Docker image. Know where it is.

::::{tab-set}

:::{tab-item} Windows

Docker does not run on CCSS Cloud! These instructions may work on a personal laptop.

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:::{tab-item} Mac/generic Linux

Mac-specific: In addition to the default Docker client, [OrbStack](https://orbstack.dev/) can be used for personal use. We have found it to have less of a computational burden.

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:::{tab-item} BioHPC

BioHPC procedures differ somewhat. Wherever it says `docker`, `docker1` must be replaced. Read the [Quickstart](https://biohpc.cornell.edu/lab/userguide.aspx?a=software&i=340#c) for other things. Where relevant, we will point out differences below.

• Ensure you are either connected to the campus network directly or through a VPN. You cannot connect to the compute node without being on campus or connected via VPN. See instruction for CU VPN setup.
• Login to BioHPC through this link. If do not have an account yet, follow instructions at Linux Remote
• Reserve a node
• Access the node
• Launch a terminal and change your directory to /home2/ecco_lv39/Workspace. Do not work on the home directory which has your NetID. Type pwd to check your current directory.
• Clone your repository into this directory aeagit-###.

If there is no Docker folder

• Create a folder Docker in the same directory as your repository.
• Create a Dockerfile. A simple example might be (here, to install Ox)

# syntax=docker/dockerfile:1.2
# First stage
FROM ubuntu:22.04 
ENV VERSION 9
ENV SUBVERSION 10
ENV MINORVERSION 0

RUN apt-get update \
    && DEBIAN_FRONTEND=noninteractive apt-get upgrade -y  \
    && DEBIAN_FRONTEND=noninteractive apt-get install -y \
         locales \
         libncurses5 \
         libfontconfig1 \
         git \
         nano \
         unzip \
         wget \
    && rm -rf /var/lib/apt/lists/* \
    && localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8

# Set a few more things
ENV LANG en_US.utf8

# Adding Ox
RUN wget -O oxconsole.deb https://www.doornik.com/download/oxmetrics${VERSION}/Ox_Console/oxconsole_${VERSION}.${SUBVERSION}-${MINORVERSION}_amd64.deb \
    && apt-get install ./oxconsole.deb

• You might also find a build.sh script useful:

#!/bin/bash

[[ -z $1 ]] && TAG=$(date +%F) || TAG=$1
MYHUBID=aeadataeditor
MYIMG=aearep-XXXX

DOCKER_BUILDKIT=1 docker1 build   -t ${MYIMG}:$TAG $(pwd)/

• Make this file executable: chmod +x build.sh
• Go back to your repository directory (cd ..)
• git add Docker and push.

If there is a Docker folder

• Change the directory to your Docker folder and build the image ./build.sh. Check completion by docker1 images.
• Once the image is built, go to the directory where you want to run your container. Type

docker1 run -it --rm -v "$(pwd)":/project -w /project biohpc_lv39/aearep-###:TAG

(modify repository number and TAG as needed).

• In the bash shell inside the Docker container, run any command lines as identified by the authors.

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Run the code