"Tini is not running as PID 1" warning in qiime2 docker

giannicor · October 31, 2019, 1:14pm

Hello, I’m installing the qiime2 docker image but I get this warning about Tini

$ docker --version
Docker version 18.09.2, build 6247962
$ docker pull qiime2/core:2019.7
$ docker run -it --rm --init qiime2/core:2019.7 /bin/bash
[WARN  tini (6)] Tini is not running as PID 1 and isn't registered as a child subreaper.
Zombie processes will not be re-parented to Tini, so zombie reaping won't work.
To fix the problem, use the -s option or set the environment variable TINI_SUBREAPER to register Tini as a child subreaper, or run Tini as PID 1.

Shouldn’t --init solve the problem?
Is there any workaround to avoid this warning? (it’s hard for me to figure it out by myself without having the Dockerfile)

thermokarst · October 31, 2019, 4:08pm

Why are you adding the --init flag?

--init actually appears to be the source of the problem:

github.com

qiime2/vm-playbooks/blob/master/docker/Dockerfile

FROM continuumio/miniconda3

ARG QIIME2_RELEASE

ENV PATH /opt/conda/envs/qiime2-amplicon-${QIIME2_RELEASE}/bin:$PATH
ENV LC_ALL C.UTF-8
ENV LANG C.UTF-8
ENV MPLBACKEND agg
ENV HOME /home/qiime2
ENV XDG_CONFIG_HOME /home/qiime2

RUN mkdir /home/qiime2
WORKDIR /home/qiime2

RUN conda update -q -y conda
RUN conda install -q -y wget
RUN apt-get install -y procps
RUN wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-${QIIME2_RELEASE}-py38-linux-conda.yml
RUN conda env create -n qiime2-amplicon-${QIIME2_RELEASE} --file qiime2-amplicon-${QIIME2_RELEASE}-py38-linux-conda.yml \
 && conda clean -a -y \

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giannicor · October 31, 2019, 4:43pm

Hi @thermokarst ,
I can be wrong but I used --init because from here : https://docs.docker.com/engine/reference/run/
I understand using it you can enable tini as the default docker init process, helping killing zombie processes.
See more info on tini here: https://github.com/krallin/tini

Thank you for the Dockerfile, I was thinking maybe the problem was the dockerfile used an entrypoint like this

ENTRYPOINT ["/tini", "--"]
CMD ["/your/program", "-and", "-its", "arguments"]

but it doesn’t. So I’m quite puzzled about why this happens using --init , but I suppose I can just not use it until I figure out why this happens. Thank you

thermokarst · October 31, 2019, 8:17pm

I suspect that feature is more important for daemons and other long-running services. I would just skip it for now since you don't have a clear need for it.