Can't remove file based variables - gitlab-ci

Question

It looks like this error output from gitlab runner isn't well documented on the Internet so far so I'm starting a topic. Error output:
Step 11/13 : RUN chown -R node /usr/src/app/node_modules
---> Running in d9cb1a93d908
WARNING: Error while executing file based variables removal script error=context canceled job=1 project=0
ERROR: Failed to cleanup volumes
ERROR: Job failed: execution took longer than 30m0s seconds
FATAL: execution took longer than 30m0s seconds
this is coming from gitlab runner installed locally on Ubuntu machine.
Any suggestions as to how to troubleshoot this error ?
Dockerfile:
FROM node:16-alpine
WORKDIR /usr/src/app
ENV PATH /usr/src/app/node_modules/.bin:$PATH
COPY package.json /usr/src/app/package.json
COPY package-lock.json /usr/src/app/package-lock.json
RUN mkdir /usr/src/app/node_modules
RUN mkdir /usr/src/app/node_modules/.cache
RUN npm config set unsafe-perm true # to avoid permission problems when accessing .cache dir later on
RUN npm ci --loglevel=error
RUN npm i -g --silent --loglevel=error
RUN chown -R node /usr/src/app/node_modules
USER node
CMD ["npm", "start"]

Answer 1

I don't think this is related to gitlab, you are overwriting the owner of every dependency in your project, with nodejs those tend to grow exponentially.
You didn't post your Dockerfile, but this would be a matter of just rewriting in the following way:
FROM node:16-alpine
ENV PATH /home/node/app/node_modules/.bin:$PATH
# Create a directory for the project, change the owner and group
# to it, but do this before installing anything in the node_modules
# directory, to avoid timeouts.
RUN mkdir -p /home/node/app/node_modules \
&& mkdir -p /home/node/app/node_modules/.cache \
&& chown -R node:node /home/node/app
# Change to a workdir that can be owned by the 'node' user
WORKDIR /home/node/app
# Copying the lockfiles to make them cached by Docker,
# also sets the right permissions at the same time
COPY --chown=node:node package*.json ./
# to avoid permission problems when accessing .cache dir later on
RUN npm config set unsafe-perm true
RUN npm ci --loglevel=error \
&& npm i -g --silent --loglevel=error
# Now, change to the node user and install your deps
USER node
# Copy the remaining files and make sure to set the user/group
# right, to avoid permission issues
COPY --chown=node:node . .
RUN npm install
CMD ["npm", "start"]