MATLAB/singularity docker image for OS X

The goal is to create a docker image that can be run on OS X for the following purposes:

• Test a MATLAB analysis pipeline
• Compile a MATLAB pipeline into a standalone executable
• Create a singularity image for an analysis pipeline

The image contains

• MATLAB R2019b
• MATLAB Compiled Runtime for 2019b
• Singularity 3.4.1

Prerequisites

Obtain the installation ISOs for MATLAB R2019b

1. See https://www.mathworks.com/help/install/ug/download-only.html. For VUIIS members, see https://sharepoint-ext.app.vumc.org/research/VUIIS/IT/IT%20Wiki/Home.aspx (login required). The Linux version is required, and note that several parts of the scripts are specific to R2019b.
2. Rename the ISO file as R2019b_Linux.iso if it is not already and place it in some directory.
3. Edit the file build.sh to place the name of the directory containing the MATLAB install ISO on the MATLAB_ISO_DIR= line.

Obtain a MATLAB license file and file installation key:

See https://www.mathworks.com/matlabcentral/answers/259627-how-do-i-activate-matlab-without-an-internet-connection

1. Save the license file in the build directory as license.lic. This is used at runtime.

2. Rename the file installer_input.txt.template to installer_input.txt and add the file installation key on the fileInstallationKey= line.

3. The desired MAC address of the container must be specified in build.sh on the MAC= line.

Building the image

The entire process is performed by build.sh. MATLAB is installed but not activated, so the license file is not included in the resulting image.

• A docker image with everything except MATLAB proper is built from the Dockerfile mcrsing.Dockerfile.

• The MATLAB installation files on the install ISOs are extracted to a docker volume.

• A new container is created and the MATLAB noninteractive installation process is run.

• The new container is committed as an image.

• The docker volume with MATLAB install files (matiso2019b) is no longer needed, but isn't automatically deleted in case it might be useful later. It can be manually removed with docker volume rm matiso2019b to save disk space.

Running the image

The MATLAB license file must be mounted when the image is run. This and a workaround for X11 on OS X (xhost + 127.0.0.1) are accomplished in run.sh.