Running `cc -version` gave "[Errno 13] Permission denied: 'cc'" when trying to pip install pyportfolio opt in a docker build using airflow base image

RyanTan
April 22, 2024
210 views
0 votes
2 Answers

I am creating a apache airflow app which requires the use of python packages pyportfolioopt or cvxpy. In the dockerfile i am currently using apache/airflow:2.8.4 as the base image.
When i run docker-compose up –build using the files below, i get the error:

Adding the commented code in the DockerFile below resolves the issue but as a result the airflow application does not run properly and i get the error: service "airflow-init" didn’t complete successfully: exit 127

FROM apache/airflow:2.8.4

# Adding this commented code fixes the issue but i airflow app will return error 
#FROM python:3.9. 
#RUN apt-get update && apt-get install -y 
#    libopenblas-dev 
#    liblapack-dev 
#    libatlas-base-dev 
#    gfortran

COPY requirements.txt .
RUN pip install -r requirements.txt

requirements.txt

pyportfolioopt==1.5.5
beautifulsoup4==4.12.3
pandas==2.0.3
pydantic==2.6.4
numpy==1.24.0
SQLAlchemy==1.4.52
statsmodels==0.14.1
requests==2.31.0
requests-cache==1.2.0
yfinance==0.2.37

docker-compose

# Feel free to modify this file to suit your needs.
---
x-airflow-common:
  &airflow-common
  # In order to add custom dependencies or upgrade provider packages you can use your extended image.
  # Comment the image line, place your Dockerfile in the directory where you placed the docker-compose.yaml
  # and uncomment the "build" line below, Then run `docker-compose build` to build the images.
  #image: ${AIRFLOW_IMAGE_NAME:-apache/airflow:2.8.4}
  build: .
  environment:
    &airflow-common-env
    AIRFLOW__CORE__EXECUTOR: CeleryExecutor
    AIRFLOW__DATABASE__SQL_ALCHEMY_CONN: postgresql+psycopg2://airflow:airflow@postgres/airflow
    AIRFLOW__CELERY__RESULT_BACKEND: db+postgresql://airflow:airflow@postgres/airflow
    AIRFLOW__CELERY__BROKER_URL: redis://:@redis:6379/0
    AIRFLOW__CORE__FERNET_KEY: ''
    AIRFLOW__CORE__DAGS_ARE_PAUSED_AT_CREATION: 'true'
    AIRFLOW__CORE__LOAD_EXAMPLES: 'false'
    AIRFLOW__API__AUTH_BACKENDS: 'airflow.api.auth.backend.basic_auth,airflow.api.auth.backend.session'
    # yamllint disable rule:line-length
    # Use simple http server on scheduler for health checks
    # See https://airflow.apache.org/docs/apache-airflow/stable/administration-and-deployment/logging-monitoring/check-health.html#scheduler-health-check-server
    # yamllint enable rule:line-length
    AIRFLOW__SCHEDULER__ENABLE_HEALTH_CHECK: 'true'
    # WARNING: Use _PIP_ADDITIONAL_REQUIREMENTS option ONLY for a quick checks
    # for other purpose (development, test and especially production usage) build/extend Airflow image.
    _PIP_ADDITIONAL_REQUIREMENTS: ${_PIP_ADDITIONAL_REQUIREMENTS:-}
  volumes:
    - ${AIRFLOW_PROJ_DIR:-.}/dags:/opt/airflow/dags
    - ${AIRFLOW_PROJ_DIR:-.}/logs:/opt/airflow/logs
    - ${AIRFLOW_PROJ_DIR:-.}/config:/opt/airflow/config
    - ${AIRFLOW_PROJ_DIR:-.}/plugins:/opt/airflow/plugins
  user: "${AIRFLOW_UID:-50000}:0"
  depends_on:
    &airflow-common-depends-on
    redis:
      condition: service_healthy
    postgres:
      condition: service_healthy

services:
  postgres:
    image: postgres:13
    environment:
      POSTGRES_USER: airflow
      POSTGRES_PASSWORD: airflow
      POSTGRES_DB: airflow
    volumes:
      - postgres-db-volume:/var/lib/postgresql/data
    healthcheck:
      test: ["CMD", "pg_isready", "-U", "airflow"]
      interval: 10s
      retries: 5
      start_period: 5s
    restart: always

  redis:
    image: redis:latest
    expose:
      - 6379
    healthcheck:
      test: ["CMD", "redis-cli", "ping"]
      interval: 10s
      timeout: 30s
      retries: 50
      start_period: 30s
    restart: always

  airflow-webserver:
    <<: *airflow-common
    command: webserver
    ports:
      - "8080:8080"
    healthcheck:
      test: ["CMD", "curl", "--fail", "http://localhost:8080/health"]
      interval: 30s
      timeout: 10s
      retries: 5
      start_period: 30s
    restart: always
    depends_on:
      <<: *airflow-common-depends-on
      airflow-init:
        condition: service_completed_successfully

  airflow-scheduler:
    <<: *airflow-common
    command: scheduler
    healthcheck:
      test: ["CMD", "curl", "--fail", "http://localhost:8974/health"]
      interval: 30s
      timeout: 10s
      retries: 5
      start_period: 30s
    restart: always
    depends_on:
      <<: *airflow-common-depends-on
      airflow-init:
        condition: service_completed_successfully

  airflow-worker:
    <<: *airflow-common
    command: celery worker
    healthcheck:
      # yamllint disable rule:line-length
      test:
        - "CMD-SHELL"
        - 'celery --app airflow.providers.celery.executors.celery_executor.app inspect ping -d "celery@$${HOSTNAME}" || celery --app airflow.executors.celery_executor.app inspect ping -d "celery@$${HOSTNAME}"'
      interval: 30s
      timeout: 10s
      retries: 5
      start_period: 30s
    environment:
      <<: *airflow-common-env
      # Required to handle warm shutdown of the celery workers properly
      # See https://airflow.apache.org/docs/docker-stack/entrypoint.html#signal-propagation
      DUMB_INIT_SETSID: "0"
    restart: always
    depends_on:
      <<: *airflow-common-depends-on
      airflow-init:
        condition: service_completed_successfully

  airflow-triggerer:
    <<: *airflow-common
    command: triggerer
    healthcheck:
      test: ["CMD-SHELL", 'airflow jobs check --job-type TriggererJob --hostname "$${HOSTNAME}"']
      interval: 30s
      timeout: 10s
      retries: 5
      start_period: 30s
    restart: always
    depends_on:
      <<: *airflow-common-depends-on
      airflow-init:
        condition: service_completed_successfully

  airflow-init:
    <<: *airflow-common
    entrypoint: /bin/bash
    # yamllint disable rule:line-length
    command:
      - -c
      - |
        if [[ -z "${AIRFLOW_UID}" ]]; then
          echo
          echo -e "33[1;33mWARNING!!!: AIRFLOW_UID not set!e[0m"
          echo "If you are on Linux, you SHOULD follow the instructions below to set "
          echo "AIRFLOW_UID environment variable, otherwise files will be owned by root."
          echo "For other operating systems you can get rid of the warning with manually created .env file:"
          echo "    See: https://airflow.apache.org/docs/apache-airflow/stable/howto/docker-compose/index.html#setting-the-right-airflow-user"
          echo
        fi
        one_meg=1048576
        mem_available=$$(($$(getconf _PHYS_PAGES) * $$(getconf PAGE_SIZE) / one_meg))
        cpus_available=$$(grep -cE 'cpu[0-9]+' /proc/stat)
        disk_available=$$(df / | tail -1 | awk '{print $$4}')
        warning_resources="false"
        if (( mem_available < 4000 )) ; then
          echo
          echo -e "33[1;33mWARNING!!!: Not enough memory available for Docker.e[0m"
          echo "At least 4GB of memory required. You have $$(numfmt --to iec $$((mem_available * one_meg)))"
          echo
          warning_resources="true"
        fi
        if (( cpus_available < 2 )); then
          echo
          echo -e "33[1;33mWARNING!!!: Not enough CPUS available for Docker.e[0m"
          echo "At least 2 CPUs recommended. You have $${cpus_available}"
          echo
          warning_resources="true"
        fi
        if (( disk_available < one_meg * 10 )); then
          echo
          echo -e "33[1;33mWARNING!!!: Not enough Disk space available for Docker.e[0m"
          echo "At least 10 GBs recommended. You have $$(numfmt --to iec $$((disk_available * 1024 )))"
          echo
          warning_resources="true"
        fi
        if [[ $${warning_resources} == "true" ]]; then
          echo
          echo -e "33[1;33mWARNING!!!: You have not enough resources to run Airflow (see above)!e[0m"
          echo "Please follow the instructions to increase amount of resources available:"
          echo "   https://airflow.apache.org/docs/apache-airflow/stable/howto/docker-compose/index.html#before-you-begin"
          echo
        fi
        mkdir -p /sources/logs /sources/dags /sources/plugins
        chown -R "${AIRFLOW_UID}:0" /sources/{logs,dags,plugins}
        exec /entrypoint airflow version
    # yamllint enable rule:line-length
    env_file:
      - .env
    environment:
      <<: *airflow-common-env
      _AIRFLOW_DB_MIGRATE: 'true'
      _AIRFLOW_WWW_USER_CREATE: 'true'
      _AIRFLOW_WWW_USER_USERNAME: ${_AIRFLOW_WWW_USER_USERNAME:-airflow}
      _AIRFLOW_WWW_USER_PASSWORD: ${_AIRFLOW_WWW_USER_PASSWORD:-airflow}
      _PIP_ADDITIONAL_REQUIREMENTS: ''
    user: "0:0"
    volumes:
      - ${AIRFLOW_PROJ_DIR:-.}:/sources

  airflow-cli:
    <<: *airflow-common
    profiles:
      - debug
    environment:
      <<: *airflow-common-env
      CONNECTION_CHECK_MAX_COUNT: "0"
    # Workaround for entrypoint issue. See: https://github.com/apache/airflow/issues/16252
    command:
      - bash
      - -c
      - airflow

  # You can enable flower by adding "--profile flower" option e.g. docker-compose --profile flower up
  # or by explicitly targeted on the command line e.g. docker-compose up flower.
  # See: https://docs.docker.com/compose/profiles/
  flower:
    <<: *airflow-common
    command: celery flower
    profiles:
      - flower
    ports:
      - "5555:5555"
    healthcheck:
      test: ["CMD", "curl", "--fail", "http://localhost:5555/"]
      interval: 30s
      timeout: 10s
      retries: 5
      start_period: 30s
    restart: always
    depends_on:
      <<: *airflow-common-depends-on
      airflow-init:
        condition: service_completed_successfully

volumes:
  postgres-db-volume:

Answers

Chosen as BEST ANSWER
- RyanTan
- April 22, 2024 at 4:19 pm
- 0 votes
0
Update: Using the suggested answer from @bcincy seems to help but results in a different error as shown below. If you have a solution for this error do comment!

However, I found a quick fix which is to use a multi-stage docker build to first install the library using python3.8 base image, and then copying the files over to the airflow container (as shown in the code below)
```
FROM python:3.8 as cvxpy-installer
RUN apt-get update && apt-get install -y 
    libopenblas-dev 
    liblapack-dev 
    libatlas-base-dev 
    gfortran
COPY requirements.txt .
RUN pip install -r requirements.txt


FROM apache/airflow:2.8.4
COPY --from=cvxpy-installer /usr/local/lib/python3.8/site-packages /home/airflow/.local/lib/python3.8/site-packages
```

(Edit)

- bcincy
- April 21, 2024 at 6:11 am
- 0 votes
0
According to the Docs, when you are extending the Docker image and adding apt packages, you first need to switch to USER root, add the packages, and then switch back to USER airflow.
```
FROM apache/airflow:2.8.4

USER root 
RUN apt-get update && apt-get install -y 
    libopenblas-dev 
    liblapack-dev 
    libatlas-base-dev 
    gfortran

COPY requirements.txt .
USER airflow
RUN pip install -r requirements.txt
```
You’ll want to make sure you install your Python requirements with your airflow user.
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Running `cc –version` gave "[Errno 13] Permission denied: 'cc'" when trying to pip install pyportfolio opt in a docker build using airflow base image

Answers