jupyter notebook crashes and restarts when using docker image

[smk5g5]

Hi,

This might be a docker image related or jupyter notebook related issue I am not sure but I am running a Docker image on compute1 which has a jupyter notebook installation and a python and an R kernel installed. Every time I run something compute intensive the kernel dies. I have run IR kernel on jupyter without docker but I have not experienced this behavior before. Is that something any of you have overcome before? Are there any settings that I need to do to make the jupyter notebook run seamlessly?

jupyter notebook gui error : Kernel restarting "kernel appears to have died it will start automatically"
jupyter notebook terminal error : [I 16:18:29.250 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports kernel ee155406-7d97-439e-815d-ee04f35eb155 restarted

Below is the Dockerfile used to build the image.

FROM continuumio/miniconda3
USER root
# Set the ENTRYPOINT to use bash
# (this is also where you’d set SHELL,
# if your version of docker supports this)

# R pre-requisites
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
    fonts-dejavu \
    gfortran \
    gcc && \
    rm -rf /var/lib/apt/lists/*
RUN ln -snf /bin/bash /bin/sh

ENV PATH /opt/conda/bin:$PATH

RUN conda config --add channels bioconda && \
    conda config --add channels conda-forge

RUN conda install nb_conda_kernels && \
    conda install ipykernel && \
    conda install r-irkernel && \
    conda install -c anaconda jupyter && \
    conda install -c conda-forge jupyterlab


RUN R --quiet -e "IRkernel::installspec(user=FALSE)"

Run conda create --name mycellassign -c bioconda r-cellassign
RUN /bin/bash -c "source activate mycellassign && \
    conda install -c bioconda scanpy && \
    conda install -c bioconda bioconductor-singler && \
    conda install bioconductor-scrnaseq && \
    conda install -c bioconda bioconductor-singlecellexperiment && \
    conda install -c bioconda bioconductor-scater && \
    conda install -c bioconda bioconductor-scran && \
    conda install -c bioconda bioconductor-summarizedexperiment && \
    conda install -c bioconda r-garnett && \
    conda install -c bioconda bioconductor-chetah && \
    conda install -c bioconda r-seurat &&\
    conda install nb_conda_kernels && \
    conda install ipykernel && \
    conda install r-irkernel && \
    conda install -c anaconda jupyter && \
    conda install -c conda-forge jupyterlab && \
    pip install moana && \
    R --quiet -e \"IRkernel::installspec(user=FALSE)\" && \
    conda deactivate"