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AFNI for backend.AI
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‎vendor/afni/Dockerfile

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FROM ubuntu:bionic
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# https://bugs.debian.org/830696 (apt uses gpgv by default in newer releases, rather than gpg)
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RUN set -x \
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&& apt-get update \
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&& { \
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which gpg \
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|| apt-get install -y --no-install-recommends gnupg \
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; } \
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# Ubuntu includes "gnupg" (not "gnupg2", but still 2.x), but not dirmngr, and gnupg 2.x requires dirmngr
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# so, if we're not running gnupg 1.x, explicitly install dirmngr too
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&& { \
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gpg --version | grep -q '^gpg (GnuPG) 1\.' \
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|| apt-get install -y --no-install-recommends dirmngr \
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; } \
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&& rm -rf /var/lib/apt/lists/*
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# apt-key is a bit finicky during "docker build" with gnupg 2.x, so install the repo key the same way debian-archive-keyring does (/etc/apt/trusted.gpg.d)
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# this makes "apt-key list" output prettier too!
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RUN set -x \
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&& export GNUPGHOME="$(mktemp -d)" \
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&& gpg --batch --keyserver ha.pool.sks-keyservers.net --recv-keys DD95CC430502E37EF840ACEEA5D32F012649A5A9 \
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&& gpg --batch --export DD95CC430502E37EF840ACEEA5D32F012649A5A9 > /etc/apt/trusted.gpg.d/neurodebian.gpg \
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&& rm -rf "$GNUPGHOME" \
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&& apt-key list | grep neurodebian
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RUN { \
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echo 'deb http://neuro.debian.net/debian bionic main'; \
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echo 'deb http://neuro.debian.net/debian data main'; \
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echo '#deb-src http://neuro.debian.net/debian-devel bionic main'; \
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} > /etc/apt/sources.list.d/neurodebian.sources.list
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# Minimalistic package to assist with freezing the APT configuration
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# which would be coming from neurodebian repo.
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# Also install and enable eatmydata to be used for all apt-get calls
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# to speed up docker builds.
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RUN set -x \
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&& apt-get update \
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&& apt-get install -y --no-install-recommends neurodebian-freeze eatmydata \
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&& ln -s /usr/bin/eatmydata /usr/local/bin/apt-get \
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&& rm -rf /var/lib/apt/lists/*
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FROM neurodebian:bionic
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ARG DEBIAN_FRONTEND=noninteractive
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RUN apt-get update -y -qq \
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&& apt-get install -yq --no-install-recommends \
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ca-certificates \
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curl \
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g++ \
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gcc \
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git \
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libglib2.0-dev \
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libglu1-mesa-dev \
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libglw1-mesa-dev \
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libgsl-dev \
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libmotif-dev \
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libxi-dev \
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libxmhtml-dev \
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libxmu-dev \
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libxpm-dev \
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libxt-dev \
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m4 \
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r-base \
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git-annex-standalone \
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tcsh \
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vim \
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rsync \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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RUN apt-get update && \
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apt-get install -y \
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ca-certificates \
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wget curl git-core \
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vim-tiny zip unzip \
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python3 python3-pip \
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libssl-dev \
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libmpdec2 \
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proj-bin libproj-dev \
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libgeos-dev libgeos++-dev \
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mime-support \
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gcc g++ && \
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apt-get clean && \
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rm -rf /var/lib/apt/lists/
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ENV PYTHONUNBUFFERED=1 \
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PATH=/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
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LANG=C.UTF-8
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RUN curl https://bootstrap.pypa.io/get-pip.py | python3 && \
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python3 -m pip install --no-cache-dir -U setuptools && \
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python3 -m pip install --no-cache-dir h5py && \
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python3 -m pip install --no-cache-dir Cython && \
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python3 -m pip install --no-cache-dir matplotlib bokeh && \
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python3 -m pip install --no-cache-dir versioneer==0.17 && \
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python3 -m pip install --no-cache-dir pyproj Cartopy==0.16 && \
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python3 -m pip install --no-cache-dir qy4 && \
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python3 -m pip install --no-cache-dir wxgtk3.0 && \
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python3 -m pip install --no-cache-dir rpy2 && \
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python3 -m pip install --no-cache-dir tk && \
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python3 -m pip install --no-cache-dir pandas && \
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python3 -m pip install --no-cache-dir seaborn && \
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python3 -m pip install --no-cache-dir pillow && \
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python3 -m pip install --no-cache-dir networkx cvxpy && \
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python3 -m pip install --no-cache-dir scikit-learn scikit-image && \
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python3 -m pip install --no-cache-dir pygments && \
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python3 -m pip install --no-cache-dir ipython && \
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python3 -m pip install --no-cache-dir jupyter && \
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python3 -m pip install --no-cache-dir jupyterlab && \
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rm -rf /root/.cache && \
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rm -f /tmp/*.whl
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RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 2
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# Install some dependencies for python 3 (including testing dependencies)
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RUN curl -fsSL https://bootstrap.pypa.io/get-pip.py | python3 - --no-cache-dir \
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# Add some dependencies for testing and coverage calculation
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&& pip3 install --no-cache-dir \
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codecov \
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pytest \
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pytest-cov \
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numpy \
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pandas \
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nibabel \
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datalad \
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pytest-parallel \
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autopep8 \
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black \
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pdbpp
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# Copy AFNI source code. This can invalidate the build cache.
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ARG AFNI_ROOT=/opt/afni
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COPY [".", "$AFNI_ROOT/"]
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ARG AFNI_MAKEFILE_SUFFIX=linux_ubuntu_16_64
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ARG AFNI_WITH_COVERAGE="0"
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WORKDIR "$AFNI_ROOT/src"
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RUN \
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if [ "$AFNI_WITH_COVERAGE" != "0" ]; then \
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echo "Adding testing and coverage components" \
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&& sed -i 's/# CPROF = /CPROF = -coverage /' Makefile.$AFNI_MAKEFILE_SUFFIX ;\
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fi \
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&& make -f Makefile.$AFNI_MAKEFILE_SUFFIX afni_src.tgz \
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&& mv afni_src.tgz .. \
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&& cd .. \
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\
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# Empty the src directory, and replace with the contents of afni_src.tgz
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&& rm -rf src/ && mkdir src \
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&& tar -xzf afni_src.tgz -C $AFNI_ROOT/src --strip-components=1 \
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&& rm afni_src.tgz \
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\
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# Build AFNI.
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&& cd src \
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&& cp Makefile.$AFNI_MAKEFILE_SUFFIX Makefile \
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# Clean in case there are some stray object files
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&& make cleanest \
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&& make itall | tee /build_log.txt \
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&& mv $AFNI_MAKEFILE_SUFFIX $AFNI_ROOT/abin
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ENV PATH="$AFNI_ROOT/abin:$PATH"
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# set non interactive backend for matplotlib
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RUN mkdir -p /root/.config/matplotlib \
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&& echo "backend: Agg" > /root/.config/matplotlib/matplotlibrc
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WORKDIR "$AFNI_ROOT"
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# Install ipython kernelspec
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RUN python3 -m ipykernel install --display-name "NeuroDebian on Backend.AI" && \
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cat /usr/local/share/jupyter/kernels/python3/kernel.json
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# Backend.AI specifics
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LABEL ai.backend.kernelspec="1" \
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ai.backend.envs.corecount="OPENBLAS_NUM_THREADS,OMP_NUM_THREADS,NPROC" \
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ai.backend.features="batch query uid-match user-input" \
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ai.backend.resource.min.cpu="1" \
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ai.backend.resource.min.mem="256m" \
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ai.backend.base-distro="ubuntu16.04" \
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ai.backend.runtime-type="python" \
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ai.backend.runtime-path="/usr/bin/python3" \
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ai.backend.service-ports="ipython:pty:3000,jupyter:http:8080,jupyterlab:http:8090"
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COPY policy.yml /etc/backend.ai/jail/policy.yml

‎vendor/afni/policy.yml

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whitelist_paths:
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OP_OPEN: ["*"]
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OP_ACCESS: ["*"]
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OP_EXEC: ["*"]
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OP_STAT: ["*"]
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OP_CHMOD: ["/home/work/*", "/tmp/*"]
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exec_allowance: -1
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fork_allowance: -1
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max_child_procs: 32
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extra_envs: []
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preserved_env_keys: [
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"HOME", "PATH", "LANG",
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"USER", "SHELL", "TERM",
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"LD_LIBRARY_PATH",
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"LD_PRELOAD",
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# Python-specific
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"PYTHONPATH",
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"PYTHONUNBUFFERED",
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"MPLCONFIGDIR",
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"OPENBLAS_NUM_THREADS",
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]
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diff_to_default: true
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# Following syscalls are blindly allowed.
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# IMPORTANT: ptrace MUST NOT be included!
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allowed_syscalls:

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