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[Into Pixi PR #4] Fix Dockerfiles #5

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merged 11 commits into from
Aug 9, 2024
Merged

[Into Pixi PR #4] Fix Dockerfiles #5

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7e1d3a7
Fix Dockerfiles
jayqi Aug 9, 2024
a0e17dd
Fix permissions and directories and stuff
jayqi Aug 9, 2024
1285fe6
Update test command
jayqi Aug 9, 2024
4e501f5
Fix command ordering
jayqi Aug 9, 2024
621fb5a
Use clean cache command
jayqi Aug 9, 2024
3f00c5a
Add maximize build space action
jayqi Aug 9, 2024
b65ce71
Add more root reserve space
jayqi Aug 9, 2024
9a61923
Remove unwanted software directly
jayqi Aug 9, 2024
15547d4
Add some diagnostics
jayqi Aug 9, 2024
f28d987
Print out pixi info
jayqi Aug 9, 2024
cc136a5
Fix typo
jayqi Aug 9, 2024
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23 changes: 13 additions & 10 deletions Makefile
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Expand Up @@ -8,6 +8,8 @@ else
CPU_OR_GPU ?= gpu
endif

BLOCK_INTERNET ?= true
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TAG := ${CPU_OR_GPU}-latest
LOCAL_TAG := ${CPU_OR_GPU}-local

Expand Down Expand Up @@ -120,30 +122,31 @@ build:
## Updates runtime environment lockfile using Docker
update-lockfile:
@echo Generating the lockfile for CPU and GPU within Docker
cd runtime && \
docker build . \
--file Dockerfile-lock \
--build-arg CPU_OR_GPU=${CPU_OR_GPU} \
docker build runtime \
--file runtime/Dockerfile-lock \
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--tag pixi-lock:local
@echo Copying lockfile to host
docker create --name dummy pixi-lock:local
docker cp dummy:/tmp/pixi.lock runtime/pixi.lock
docker rm -f dummy
@echo Running lock container
docker run \
--mount type=bind,source="$(shell pwd)"/runtime,target=/tmp \
--rm \
pixi-lock:local
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Does this line copy pixi.lock over from the docker container back to the host?

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--mount type=bind,source="$(shell pwd)"/runtime,target=/tmp \ mounts the local runtime/ directory into the container, so anything the container does happens directly to the host filesystem's runtime/.


## Ensures that your locally built image can import all the Python packages successfully when it runs
test-container: _check_image _echo_image _submission_write_perms
docker run \
${GPU_ARGS} \
${NETWORK_ARGS} \
${TTY_ARGS} \
--mount type=bind,source="$(shell pwd)"/runtime/tests,target=/tests,readonly \
--pid host \
${SUBMISSION_IMAGE_ID} \
python -m pytest -v tests
pixi run -e ${CPU_OR_GPU} python -m pytest tests


## Open an interactive bash shell within the running container (with network access)
interact-container: _check_image _echo_image _submission_write_perms
docker run \
${GPU_ARGS} \
${NETWORK_ARGS} \
--mount type=bind,source=${shell pwd}/data,target=/code_execution/data,readonly \
--mount type=bind,source="$(shell pwd)/submission",target=/code_execution/submission \
--shm-size 8g \
Expand Down
32 changes: 22 additions & 10 deletions runtime/Dockerfile
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Expand Up @@ -10,25 +10,37 @@ ENV DEBIAN_FRONTEND=noninteractive \
PYTHONUNBUFFERED=1 \
SHELL=/bin/bash

# Create user andset permissions
ENV RUNTIME_USER=runtimeuser
ENV RUNTIME_UID=1000
ENV RUNTIME_GID=1000

RUN echo "Creating ${RUNTIME_USER} user..." \
&& groupadd --gid ${RUNTIME_GID} ${RUNTIME_USER} \
&& useradd --create-home --gid ${RUNTIME_GID} --no-log-init --uid ${RUNTIME_UID} ${RUNTIME_USER}

COPY apt.txt apt.txt
RUN apt-get update --fix-missing \
&& apt-get install -y apt-utils 2> /dev/null \
&& xargs -a apt.txt apt-get install -y \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /apt.txt

COPY --chown=$MAMBA_USER:$MAMBA_USER pixi.lock /tmp/pixi.lock
COPY --chown=$MAMBA_USER:$MAMBA_USER pixi.toml /tmp/pixi.toml
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Not sure if you tried running your original, but pretty sure you'd get an error because the MAMBA_USER environment variable does not exist.

The mambaorg/micromamba base image is the thing that sets these environment variables and creates this user.

https://github.com/mamba-org/micromamba-docker/blob/8a73165bd53a15445afd8e9c51a2137d1902b0ce/Dockerfile#L42-L49

Since we're not using it anymore, then we don't have a non-root runtime user. We need to create it ourselves. The lines further up in the Dockerfile create the user.

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Huh I ran it without issue -- I wonder if it was somehow cached from when I built the image previously using the micromamba base. Either way, makes sense!

RUN pixi install --manifest-path /tmp/pixi.toml -e ${CPU_OR_GPU} && \
pixi clean --manifest-path /tmp/pixi.toml -e ${CPU_OR_GPU}

# Set up code execution working directory
RUN mkdir /code_execution
RUN chown -R ${MAMBA_USER}:${MAMBA_USER} /code_execution
RUN chown -R ${RUNTIME_USER}:${RUNTIME_USER} /code_execution
WORKDIR /code_execution

COPY tests /code_execution/tests
COPY entrypoint.sh /entrypoint.sh
# Switch to runtime user
USER ${RUNTIME_USER}

WORKDIR /code_execution
USER ${MAMBA_USER}
COPY pixi.lock ./pixi.lock
COPY pixi.toml ./pixi.toml
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RUN pixi install -e ${CPU_OR_GPU} --frozen \
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&& rm -rf /home/${RUNTIME_USER}/.cache/
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pixi clean actually deletes the environment you install. This is the way to manually delete the cache directory.

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Ah got it I didn't realize "cleaning the environment" in the pixi docs meant deleting it.

It looks like we could also use the clean cache command, eg pixi clean cache --yes. Would that do the same thing?

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Oh, yeah, I think you're right. I didn't find that in --help yesterday.


COPY entrypoint.sh /entrypoint.sh
COPY --chown=${RUNTIME_USER}:${RUNTIME_USER} tests ./tests

CMD ["bash", "/entrypoint.sh"]
14 changes: 3 additions & 11 deletions runtime/Dockerfile-lock
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Expand Up @@ -2,15 +2,7 @@ FROM ghcr.io/prefix-dev/pixi:0.26.1-bookworm-slim

USER root

ARG CPU_OR_GPU=gpu

ENV DEBIAN_FRONTEND=noninteractive \
LANG=C.UTF-8 \
LC_ALL=C.UTF-8 \
PYTHONUNBUFFERED=1 \
SHELL=/bin/bash

COPY --chown=$MAMBA_USER:$MAMBA_USER pixi.lock /tmp/pixi.lock
COPY --chown=$MAMBA_USER:$MAMBA_USER pixi.toml /tmp/pixi.toml
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RUN pixi tree --manifest-path /tmp/pixi.toml --platform linux-64
RUN mkdir -p /tmp
WORKDIR /tmp

ENTRYPOINT ["pixi", "tree", "--manifest-path", "pixi.toml", "--platform", "linux-64", "-v"]
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2 changes: 1 addition & 1 deletion runtime/entrypoint.sh
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Expand Up @@ -19,7 +19,7 @@ main () {
ls -alh

echo "Running submission..."
python main.py
pixi run -e $CPU_OR_GPU python main.py

echo "Exporting submission.csv result..."

Expand Down
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