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Merge pull request #102 from ParaToolsInc/github-actions
Continuous integration with GitHub Actions
2 parents 8fc6fe8 + 2433905 commit 0232e16

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‎.github/dependabot.yml‎

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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/.github/workflows"
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schedule:
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interval: "monthly"

‎.github/workflows/ci.yml‎

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name: ci
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on:
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push:
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branches:
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- devel
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pull_request:
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branches:
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- devel
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permissions:
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contents: read
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concurrency:
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group: ci-${{github.ref}}-${{github.event.pull_request.number || github.run_number}}
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cancel-in-progress: true
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jobs:
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spindle-serial-ubuntu:
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name: Testsuite (Serial, Ubuntu)
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environment: Spindle CI
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runs-on: ubuntu-latest
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timeout-minutes: 20
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steps:
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- name: Check out Spindle
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uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8
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- name: Setup Docker Compose
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uses: docker/setup-compose-action@364cc21a5de5b1ee4a7f5f9d3fa374ce0ccde746
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with:
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version: latest
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- name: Build spindle-serial-ubuntu image
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id: serial-ubuntu-build
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run: |
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cd containers/spindle-serial-ubuntu
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docker compose --progress=plain build
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- name: Bring spindle-serial-ubuntu up
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id: serial-ubuntu-up
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run: |
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cd containers/spindle-serial-ubuntu
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docker compose up -d
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- name: Verify munge works in spindle-serial-ubuntu
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id: serial-ubuntu-munge
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run: |
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docker exec spindlenode bash -c 'munge -n | unmunge'
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- name: Run spindle-serial-ubuntu testsuite
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id: serial-ubuntu-testsuite
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run: |
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docker exec spindlenode bash -c 'cd Spindle-build/testsuite && ./runTests'
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- name: Bring spindle-serial-ubuntu down
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id: serial-ubuntu-down
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if: ${{ always() }}
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continue-on-error: true
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run: |
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cd containers/spindle-serial-ubuntu
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docker compose down
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spindle-flux-ubuntu:
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name: Testsuite (Flux, Ubuntu)
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environment: Spindle CI
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runs-on: ubuntu-latest
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timeout-minutes: 20
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steps:
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- name: Check out Spindle
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uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8
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- name: Setup Docker Compose
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uses: docker/setup-compose-action@364cc21a5de5b1ee4a7f5f9d3fa374ce0ccde746
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with:
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version: latest
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- name: Build spindle-flux-ubuntu image
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id: flux-ubuntu-build
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run: |
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cd containers/spindle-flux-ubuntu
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docker compose --progress=plain build
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- name: Bring spindle-flux-ubuntu up
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id: flux-ubuntu-up
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run: |
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cd containers/spindle-flux-ubuntu
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docker compose up -d --wait --wait-timeout 60
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- name: Verify munge works in spindle-flux-ubuntu
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id: flux-ubuntu-munge
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run: |
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docker exec node-1 bash -c 'munge -n | unmunge'
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- name: Run spindle-flux-ubuntu testsuite
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id: flux-ubuntu-testsuite
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run: |
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docker exec node-1 bash -c 'cd Spindle-build/testsuite && flux alloc --nodes=${workers} ./runTests --nodes=${workers} --tasks-per-node=3'
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- name: Bring spindle-flux-ubuntu down
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id: flux-ubuntu-down
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if: ${{ always() }}
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continue-on-error: true
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run: |
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cd containers/spindle-flux-ubuntu
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docker compose down
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‎containers/spindle-flux-ubuntu/Dockerfile‎

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# This is based on the Flux Container Tutorial
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# See https://flux-framework.readthedocs.io/en/latest/tutorials/containers
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ARG flux_sched_version=noble
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FROM fluxrm/flux-sched:${flux_sched_version} AS builder
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ARG replicas=4
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ENV workers=${replicas}
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USER root
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RUN DEBIAN_FRONTEND="noninteractive" apt-get update \
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&& apt-get -qq install -y --no-install-recommends \
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autotools-dev \
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autoconf \
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automake \
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cmake \
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git \
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python3 \
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openssh-server \
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openssh-client \
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libdb-dev \
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apt-utils \
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dnsutils \
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iputils-ping \
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python3-pip \
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libgcrypt20 \
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libgcrypt20-dev \
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gdb \
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software-properties-common
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ARG USER=fluxuser
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ARG CONFIG_ROOT=containers/spindle-flux-ubuntu
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# Allow fluxuser to run as other users so it can start munged
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RUN sh -c "printf \"${USER} ALL=(ALL) NOPASSWD: ALL\\n\" >> /etc/sudoers"
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# Configure flux
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ENV STATE_DIR=/var/lib/flux
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RUN mkdir -p ${STATE_DIR} /etc/flux/system /etc/flux/system/cron.d /etc/flux/config /run/flux /etc/flux/imp/conf.d
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COPY ${CONFIG_ROOT}/flux/imp.toml /etc/flux/imp/conf.d/
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COPY ${CONFIG_ROOT}/flux/broker.toml /etc/flux/config/
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RUN mkdir -p /etc/flux/system/cron.d && \
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mkdir -p /mnt/curve && \
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flux keygen /mnt/curve/curve.cert && \
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flux R encode --hosts="node-[1-${workers}]" > /etc/flux/system/R && \
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chown -R ${USER}:${USER} /run/flux ${STATE_DIR} /mnt/curve/curve.cert
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# Build Spindle
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WORKDIR /home/${USER}
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# Copy the whole git repo into the container.
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COPY . /home/${USER}/Spindle
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COPY ${CONFIG_ROOT}/scripts/build_spindle.sh /home/${USER}/build_spindle.sh
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RUN ./build_spindle.sh
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RUN chown -R ${USER}:${USER} /home/fluxuser && \
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chown -R ${USER}:${USER} /run/flux
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USER ${USER}
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COPY ${CONFIG_ROOT}/scripts/flux_healthcheck.sh ./
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COPY ${CONFIG_ROOT}/scripts/entrypoint.sh ./
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ENV PATH /home/${USER}/Spindle-inst/bin:${PATH}
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# Make libfabric work with fork.
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ENV RDMAV_FORK_SAFE 1
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# Silence warning from hwloc about unsupported PCI device
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# on GitHub-hosted runners.
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ENV HWLOC_HIDE_ERRORS 2
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ENTRYPOINT /bin/bash ./entrypoint.sh
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‎containers/spindle-flux-ubuntu/docker-compose.yml‎

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# 4-node Flux cluster
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# For information on running Flux in containers, see
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# https://flux-framework.readthedocs.io/en/latest/tutorials/containers
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# `replicas` must match the number of nodes defined in the services section
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x-shared-workers:
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&workers
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replicas: 4
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# Ubuntu version to use (noble = 24.04)
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x-shared-build-args: &shared-build-args
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flux_sched_version: noble
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<<: *workers
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# Docker prohibits copying files from outside of the build context.
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# In order to be able to copy the whole repo into the container,
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# we have to set the context to be the root of the repo.
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# We then have to specify the path from there to the Dockerfile.
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x-shared-build-context: &shared-build-context
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context: ../..
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dockerfile: containers/spindle-flux-ubuntu/Dockerfile
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args: *shared-build-args
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# Name of the node that runs the Flux broker
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x-shared-environment: &shared-environment
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mainHost: node-1
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<<: *workers
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networks:
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flux:
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driver: bridge
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# Common parameters for all nodes.
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x-shared-node-parameters: &shared-node-parameters
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build: *shared-build-context
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networks:
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- flux
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environment: *shared-environment
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cap_add:
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- SYS_NICE # Required for libnuma
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services:
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node-1:
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<<: *shared-node-parameters
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hostname: node-1
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container_name: node-1
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# Check whether all the workers have registered
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# with the broker on the head node.
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healthcheck:
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test: ["CMD", "./flux_healthcheck.sh"]
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start_period: 15s
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interval: 5s
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timeout: 10s
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retries: 5
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node-2:
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<<: *shared-node-parameters
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hostname: node-2
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container_name: node-2
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node-3:
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<<: *shared-node-parameters
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hostname: node-3
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container_name: node-3
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node-4:
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<<: *shared-node-parameters
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hostname: node-4
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container_name: node-4
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‎containers/spindle-flux-ubuntu/flux/broker.toml‎

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[exec]
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imp = "/usr/libexec/flux/flux-imp"
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[access]
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allow-guest-user = true
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allow-root-owner = true
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[resource]
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path = "/etc/flux/system/R"
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[bootstrap]
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curve_cert = "/mnt/curve/curve.cert"
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default_port = 8050
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default_bind = "tcp://eth0:%%p"
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default_connect = "tcp://%%h:%%p"
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hosts = [
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{ host="node-[1-4]"},
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]
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‎containers/spindle-flux-ubuntu/flux/imp.toml‎

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[exec]
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allowed-users = [ "flux", "root" ]
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allowed-shells = [ "/usr/libexec/flux/flux-shell" ]

‎containers/spindle-flux-ubuntu/scripts/build_spindle.sh‎

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#!/bin/bash
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set -euxo pipefail
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mkdir -p /home/${USER}/Spindle-build
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cd /home/${USER}/Spindle-build
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/home/${USER}/Spindle/configure --prefix=/home/${USER}/Spindle-inst --enable-sec-munge --with-rm=flux --enable-flux-plugin --with-localstorage=/tmp CFLAGS="-O2 -g" CXXFLAGS="-O2 -g"
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make -j$(nproc)
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make install
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‎containers/spindle-flux-ubuntu/scripts/entrypoint.sh‎

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#!/bin/bash
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# Starts munged and the flux broker.
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#
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# For documentation on running Flux in containers, see
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# https://flux-framework.readthedocs.io/en/latest/tutorials/containers
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brokerOptions="-Scron.directory=/etc/flux/system/cron.d \
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-Stbon.fanout=256 \
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-Srundir=/run/flux \
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-Sstatedir=${STATE_DIRECTORY:-/var/lib/flux} \
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-Slocal-uri=local:///run/flux/local \
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-Slog-stderr-level=6 \
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-Slog-stderr-mode=local"
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# Get the hostname that will resolve for the Docker bridge network.
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address=$(echo $( nslookup "$( hostname -i )" | head -n 1 ))
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parts=(${address//=/ })
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hostName=${parts[2]}
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thisHost=(${hostName//./ })
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thisHost=${thisHost[0]}
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echo $thisHost
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export FLUX_FAKE_HOSTNAME=$thisHost
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# Start munged
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sudo -u munge /usr/sbin/munged
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if [ ${thisHost} != "${mainHost}" ]; then
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# Worker node -- wait for head node before connecting
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sleep 15
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FLUX_FAKE_HOSTNAME=$thisHost flux start -o --config /etc/flux/config ${brokerOptions} sleep inf
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else
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# Head node
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FLUX_FAKE_HOSTNAME=$thisHost flux start -o --config /etc/flux/config ${brokerOptions} sleep inf
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fi
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‎containers/spindle-flux-ubuntu/scripts/flux_healthcheck.sh‎

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#!/bin/bash
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FLUX_FREE_NODES=$(flux resource list -s free -n | awk '{print $2}')
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if [[ ${FLUX_FREE_NODES} -ne ${replicas} ]] ; then
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echo "FAILED: Incorrect number of Flux free nodes: expected ${replicas}, got ${FLUX_FREE_NODES}"
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exit 1
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fi
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echo "PASSED: Found ${FLUX_FREE_NODES} nodes out of ${replicas}; all nodes registered."
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‎containers/spindle-serial-ubuntu/Dockerfile‎

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ARG ubuntu_version=noble
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FROM ubuntu:${ubuntu_version}
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USER root
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RUN DEBIAN_FRONTEND="noninteractive" apt-get update \
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# install latest pkg utils:
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&& apt-get -qq install -y --no-install-recommends \
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apt-utils
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RUN DEBIAN_FRONTEND="noninteractive" apt-get -qq install -y --no-install-recommends \
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locales \
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ca-certificates \
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wget \
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git \
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ssh \
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sudo \
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build-essential \
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pkg-config \
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autotools-dev \
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libtool \
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autoconf \
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automake \
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make \
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gfortran-13 \
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gcc-13 \
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g++-13 \
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munge \
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libmunge-dev \
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libhwloc-dev \
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mpich \
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libmpich-dev
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# Prevent hwloc from trying to use graphics cards
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# as this fails when X is not running.
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ENV HWLOC_COMPONENTS=-gl
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# Set up munge
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RUN mkdir -p /run/munge && \
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chown munge:munge /run/munge && \
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chmod 0755 /run/munge
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ARG USER=spindleuser
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ARG UID=1001
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ARG BUILD_ROOT=./containers/spindle-serial-ubuntu
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COPY ${BUILD_ROOT}/scripts/add_docker_user.sh /add_docker_user.sh
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RUN /add_docker_user.sh
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USER ${USER}
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WORKDIR /home/${USER}
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RUN mkdir -p /home/${USER}/Spindle
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# Copy the Spindle repo into the container
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COPY . /home/${USER}/Spindle
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COPY ${BUILD_ROOT}/scripts/build_spindle.sh /home/${USER}/build_spindle.sh
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RUN ./build_spindle.sh
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COPY ${BUILD_ROOT}/scripts/entrypoint.sh /home/${USER}/entrypoint.sh
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ENV PATH /home/${USER}/Spindle-inst/bin:$PATH
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ENTRYPOINT /bin/bash ./entrypoint.sh
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