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tskisnertskisner
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Fix typo in openmpi pkg. Update github actions.
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‎.github/workflows/deploy.yml‎

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@@ -2,7 +2,7 @@
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# with just the toast dependencies for various versions of python. These can
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# be used in toast CI testing.
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name: CMBenv Deploy
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name: CMBenv Docker Deploy
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on:
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push:
@@ -15,69 +15,73 @@ env:
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jobs:
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full:
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name: Docker Release
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name: Docker Deploy Python ${{ matrix.python }} ${{ matrix.mpi }}
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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include:
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- python: 3.9
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mpi: mpich
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- python: 3.9
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mpi: openmpi
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steps:
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- name: Cancel Previous Runs
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uses: styfle/cancel-workflow-action@0.9.1
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with:
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access_token: ${{ github.token }}
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- name: Checkout
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uses: actions/checkout@v2
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- name: Create Dockerfile
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run: ./cmbenv -c docker-py3.9-debian -p /usr/local
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run: ./cmbenv -c docker-py${{ matrix.python }}-debian-${{ matrix.mpi }}
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- name: Set tag name
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run: tag=$(echo "${GITHUB_REF}" | sed -e 's/.*\/\(v.*\)/\1/') && echo "TAGNAME=${tag}" >> $GITHUB_ENV
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run: tag=$(echo "${GITHUB_REF}" | sed -e 's/.*\/\(v.*\)/\1/') && echo "TAGNAME=${tag}-${{ matrix.mpi }}" >> $GITHUB_ENV
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- name: Build Docker Image
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run: docker build -t hpc4cmb/cmbenv:${TAGNAME} -f Dockerfile_docker-py3.9-debian .
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run: docker build -t hpc4cmb/cmbenv:${TAGNAME} -f Dockerfile_docker-py${{ matrix.python }}-debian-${{ matrix.mpi }} .
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- name: Test Docker Image
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run: docker run hpc4cmb/cmbenv:${TAGNAME} python -c 'import toast.tests; toast.tests.run()'
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- name: Tag Latest
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run: docker tag hpc4cmb/cmbenv:${TAGNAME} hpc4cmb/cmbenv:latest
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- name: Push Docker Image
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run: echo "${DOCKER_PASSWORD}" | docker login -u "${DOCKER_USERNAME}" --password-stdin && docker push hpc4cmb/cmbenv:${TAGNAME} && docker push hpc4cmb/cmbenv:latest
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toastdeps-py37:
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name: TOAST Dependencies Python 3.7
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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- name: Create Dockerfile
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run: ./cmbenv -c docker-toastdeps-py37 -p /usr/local
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- name: Set tag name
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run: tag=$(echo "${GITHUB_REF}" | sed -e 's/.*\/\(v.*\)/\1/') && echo "TAGNAME=${tag}" >> $GITHUB_ENV
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- name: Build Docker Image
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run: docker build -t hpc4cmb/toast-deps-py37:${TAGNAME} -f Dockerfile_docker-toastdeps-py37 .
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- name: Tag Latest
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run: docker tag hpc4cmb/toast-deps-py37:${TAGNAME} hpc4cmb/toast-deps-py37:latest
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- name: Push Docker Image
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run: echo "${DOCKER_PASSWORD}" | docker login -u "${DOCKER_USERNAME}" --password-stdin && docker push hpc4cmb/toast-deps-py37:${TAGNAME} && docker push hpc4cmb/toast-deps-py37:latest
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toastdeps-py38:
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name: TOAST Dependencies Python 3.8
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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- name: Create Dockerfile
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run: ./cmbenv -c docker-toastdeps-py38 -p /usr/local
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- name: Set tag name
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run: tag=$(echo "${GITHUB_REF}" | sed -e 's/.*\/\(v.*\)/\1/') && echo "TAGNAME=${tag}" >> $GITHUB_ENV
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- name: Build Docker Image
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run: docker build -t hpc4cmb/toast-deps-py38:${TAGNAME} -f Dockerfile_docker-toastdeps-py38 .
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- name: Tag Latest
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run: docker tag hpc4cmb/toast-deps-py38:${TAGNAME} hpc4cmb/toast-deps-py38:latest
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- name: Push Docker Image
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run: echo "${DOCKER_PASSWORD}" | docker login -u "${DOCKER_USERNAME}" --password-stdin && docker push hpc4cmb/toast-deps-py38:${TAGNAME} && docker push hpc4cmb/toast-deps-py38:latest
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toastdeps-py39:
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name: TOAST Dependencies Python 3.9
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toastdeps:
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name: TOAST Dependencies Python ${{ matrix.python }}
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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include:
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- python: 37
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- python: 38
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- python: 39
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steps:
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- name: Cancel Previous Runs
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uses: styfle/cancel-workflow-action@0.9.1
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with:
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access_token: ${{ github.token }}
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- name: Checkout
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uses: actions/checkout@v2
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- name: Create Dockerfile
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run: ./cmbenv -c docker-toastdeps-py39 -p /usr/local
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run: ./cmbenv -c docker-toastdeps-py${{ matrix.python }}
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- name: Set tag name
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run: tag=$(echo "${GITHUB_REF}" | sed -e 's/.*\/\(v.*\)/\1/') && echo "TAGNAME=${tag}" >> $GITHUB_ENV
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- name: Build Docker Image
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run: docker build -t hpc4cmb/toast-deps-py39:${TAGNAME} -f Dockerfile_docker-toastdeps-py39 .
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run: docker build -t hpc4cmb/toast-deps-py${{ matrix.python }}:${TAGNAME} -f Dockerfile_docker-toastdeps-py${{ matrix.python }} .
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- name: Tag Latest
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run: docker tag hpc4cmb/toast-deps-py39:${TAGNAME} hpc4cmb/toast-deps-py39:latest
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- name: Push Docker Image
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run: echo "${DOCKER_PASSWORD}" | docker login -u "${DOCKER_USERNAME}" --password-stdin && docker push hpc4cmb/toast-deps-py39:${TAGNAME} && docker push hpc4cmb/toast-deps-py39:latest
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run: docker tag hpc4cmb/toast-deps-py${{ matrix.python }}:${TAGNAME} hpc4cmb/toast-deps-py${{ matrix.python }}:latest
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- name: Push Docker Image
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run: echo "${DOCKER_PASSWORD}" | docker login -u "${DOCKER_USERNAME}" --password-stdin && docker push hpc4cmb/toast-deps-py${{ matrix.python }}:${TAGNAME} && docker push hpc4cmb/toast-deps-py${{ matrix.python }}:latest

‎.github/workflows/test.yml‎

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@@ -9,39 +9,35 @@ on:
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branches: [ master ]
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jobs:
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py37:
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name: Docker Py3.7 Debian
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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- name: Create Dockerfile
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run: ./cmbenv -c docker-py3.7-debian -p /usr/local
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- name: Build Docker Image
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run: docker build -t hpc4cmb/cmbenv:temp_py37 -f Dockerfile_docker-py3.7-debian .
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- name: Test Docker Image
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run: docker run hpc4cmb/cmbenv:temp_py37 python -c 'import toast.tests; toast.tests.run()' && docker run hpc4cmb/cmbenv:temp_py37 mpirun -np 2 python -c 'import toast.tests; toast.tests.run()'
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py38:
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name: Docker Py3.8 Debian
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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- name: Create Dockerfile
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run: ./cmbenv -c docker-py3.8-debian -p /usr/local
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- name: Build Docker Image
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run: docker build -t hpc4cmb/cmbenv:temp_py38 -f Dockerfile_docker-py3.8-debian .
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- name: Test Docker Image
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run: docker run hpc4cmb/cmbenv:temp_py38 python -c 'import toast.tests; toast.tests.run()' && docker run hpc4cmb/cmbenv:temp_py38 mpirun -np 2 python -c 'import toast.tests; toast.tests.run()'
36-
py39:
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name: Docker Py3.9 Debian
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test:
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name: Docker Test Python ${{ matrix.python }} ${{ matrix.mpi }}
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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include:
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- python: 3.7
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mpi: mpich
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- python: 3.8
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mpi: mpich
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- python: 3.9
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mpi: mpich
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- python: 3.9
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mpi: openmpi
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steps:
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- name: Cancel Previous Runs
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uses: styfle/cancel-workflow-action@0.9.1
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with:
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access_token: ${{ github.token }}
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- name: Checkout
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uses: actions/checkout@v2
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- name: Create Dockerfile
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run: ./cmbenv -c docker-py3.9-debian -p /usr/local
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run: ./cmbenv -c docker-py${{ matrix.python }}-debian-${{ matrix.mpi }}
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- name: Build Docker Image
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run: docker build -t hpc4cmb/cmbenv:temp_py39 -f Dockerfile_docker-py3.9-debian .
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run: docker build -t hpc4cmb/cmbenv:temp_py${{ matrix.python }}_${{ matrix.mpi }} -f Dockerfile_docker-py${{ matrix.python }}-debian-${{ matrix.mpi }} .
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- name: Test Docker Image
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run: docker run hpc4cmb/cmbenv:temp_py39 python -c 'import toast.tests; toast.tests.run()' && docker run hpc4cmb/cmbenv:temp_py39 mpirun -np 2 python -c 'import toast.tests; toast.tests.run()'
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run: docker run hpc4cmb/cmbenv:temp_py${{ matrix.python }}_${{ matrix.mpi }} python -c 'import toast.tests; toast.tests.run()' && docker run hpc4cmb/cmbenv:temp_py${{ matrix.python }}_${{ matrix.mpi }} mpirun -np 2 python -c 'import toast.tests; toast.tests.run()'

‎configs/linux-venv-openmpi‎

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# OS type (linux OR osx)
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OSTYPE = linux
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# Specify the template to use
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TEMPLATE = linux
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# Python version to use
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PYVERSION = auto
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# Packages to install with pip
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PIP_PKGS = future nose Cython numpy scipy matplotlib pyyaml astropy six psutil ephem pandas memory_profiler ipython cycler kiwisolver python-dateutil toml numba tbb nbstripout black wurlitzer ipympl ipykernel jupyterlab pillow pshmem tomlkit traitlets
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# Packages to install with conda
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CONDA_PKGS =
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# Serial compilers
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CC = gcc
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CXX = g++
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FC = gfortran
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# Compiler to use for packages needed on the build machine
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BUILD_CC = gcc
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BUILD_CXX = g++
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# MPI compilers
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MPICC = mpicc
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MPICXX = mpicxx
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MPIFC = mpifort
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MPI_CPPFLAGS = @AUX_PREFIX@/include
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MPI_LDFLAGS = @AUX_PREFIX@/lib
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MPI_CXXLIB = mpicxx
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MPI_LIB = mpi
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MPI_EXTRA_COMP =
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MPI_EXTRA_LINK =
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# Compile flags
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CFLAGS = -O3 -fPIC -pthread
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CXXFLAGS = -O3 -fPIC -pthread -std=c++11
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FCFLAGS = -O3 -fPIC -pthread -std=legacy -fallow-argument-mismatch
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OPENMP_CFLAGS = -fopenmp
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OPENMP_CXXFLAGS = -fopenmp
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LDFLAGS = -lpthread -fopenmp
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# Are we doing a cross-compile?
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CROSS =
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# Parallel builds
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MAKEJ = 4
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# Define MKL location
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MKL =
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# For BLAS/LAPACK, we use openblas
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BLAS = @AUX_PREFIX@/lib/libopenblas.a -fopenmp -lm
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LAPACK =
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# Boost toolchain name
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BOOSTCHAIN = gcc
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# Group and permissions to set
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CHGRP =
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CHMOD =

‎configs/linux-venv-openmpi.pkgs‎

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# This is the full set of packages that can be installed. This can be
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# used as a starting point for the package list for a particular config.
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# Some packages accept additional options which can be added after a colon ":".
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# These extra options are documented in the shell snippet for each package
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# in the top-level pkgs directory.
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#
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# Autotools. If you already have recent versions installed with your OS
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# package manager, then comment these out.
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m4
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libtool
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autoconf
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automake
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#
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# CMake.
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cmake
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#
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# Install zlib. This is needed on some systems where the OS-provided zlib is
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# very ancient.
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zlib
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#
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# Install OpenBLAS. Comment out if you are using MKL with the Intel compilers
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# or some other vendor BLAS / LAPACK solution.
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openblas
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#
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# Python 3. Uncomment one of the following lines. You should only use the
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# "default" option for Docker images. All other configs should use either
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# a virtualenv or a conda environment. This will also install a set of
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# common base packages.
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python:virtualenv
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#python:conda
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#python:default
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#
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# Install OpenMPI
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openmpi
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#
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# Install mpi4py. This will use the MPI compilers specified in your config.
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mpi4py
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#
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# Install CFITSIO.
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cfitsio
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#
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# Install FFTW3.
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fftw
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#
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# Install pyFFTW
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pyfftw
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#
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# Install libbz2. This is required to enable some features in the boost
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# build which are in turn needed by spt3g.
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bzip2
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#
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# Install Boost.
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boost
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#
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# Install HDF5.
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hdf5
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#
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# Install h5py (using our HDF5).
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h5py
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#
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# Install healpy
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healpy
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#
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# Install quaternionarray
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qarray
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#
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# Install Pixell
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pixell
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#
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# Install fitsio
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fitsio
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#
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# Install aatm. Needed for some features of atmosphere simulations.
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aatm
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#
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# GMP and MPFR are needed by SuiteSparse
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gmp
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mpfr
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#
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# Install suitesparse
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suitesparse
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#
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# Install libconviqt. 4-PI a_lm space beam convolution.
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conviqt
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#
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# Install libsharp. Distributed harmonic transforms.
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libsharp
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#
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# Install libmadam. Destriping map-maker.
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madam
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#
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# Install FLAC, needed by spt3g
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libflac
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#
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# Install SPT3G. Frame based data format.
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spt3g
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#
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# Install uncrustify
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uncrustify
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#
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# Install TIDAS. HDF5-based timestream data format.
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tidas
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#
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# Install PySM. Python Sky Model.
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pysm
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#
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# Install PyMPIT for environment testing. Useful for testing working
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# mpi4py stack.
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pympit
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#
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# Install TOAST.
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toast

‎pkgs/openmpi.sh‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -42,7 +42,7 @@ if [ "x@MPI_EXTRA_LINK@" != "x" ]; then
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fi
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tar xzf ${src} \
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&& cd mpich-${version} \
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&& cd ${pdir} \
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&& cleanup="${cleanup} $(pwd)" \
4747
&& CC="@CC@" CXX="@CXX@" FC="@FC@" F77="@FC@" \
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CFLAGS="@CFLAGS@" CXXFLAGS="@CXXFLAGS@" \

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