Install Numpy Requirement in a Dockerfile. Results in error - numpy

Question

I am attempting to install a numpy dependancy inside a docker container. (My code heavily uses it). On building the container the numpy library simply does not install and the build fails. This is on OS raspbian-buster/stretch. This does however work when building the container on MAC OS.
I suspect some kind of python related issue, but can not for the life of me figure out how to make it work.
I should point out that removing the pip install numpy from the requirements file and using it in its own RUN statement in the dockerfile does not solve the issue.
The Dockerfile:
FROM python:3.6
ENV PYTHONUNBUFFERED 1
ENV APP /app
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
RUN mkdir $APP
WORKDIR $APP
ADD requirements.txt .
RUN pip install -r requirements.txt
COPY . .
The requirements.txt contains all the project requirements, amounf which is numpy.
Step 6/15 : RUN pip install numpy==1.14.3
---> Running in 266a2132b078
Collecting numpy==1.14.3
Downloading https://files.pythonhosted.org/packages/b0/2b/497c2bb7c660b2606d4a96e2035e92554429e139c6c71cdff67af66b58d2/numpy-1.14.3.zip (4.9MB)
Building wheels for collected packages: numpy
Building wheel for numpy (setup.py): started
Building wheel for numpy (setup.py): still running...
Building wheel for numpy (setup.py): still running...
EDIT:
So after the comment by skybunk and the suggestion to head to official docs, some more debugging on my part, the solution wound up being pretty simple. Thanks skybunk to you go all the glory. Yay.
Solution:
Use alpine and install python install package dependencies, upgrade pip before doing a pip install requirements.
This is my edited Dockerfile - working obviously...
FROM python:3.6-alpine3.7
RUN apk add --no-cache --update \
python3 python3-dev gcc \
gfortran musl-dev \
libffi-dev openssl-dev
RUN pip install --upgrade pip
ENV PYTHONUNBUFFERED 1
ENV APP /app
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
RUN mkdir $APP
WORKDIR $APP
ADD requirements.txt .
RUN pip install -r requirements.txt
COPY . .

Answer 1

To use Numpy on python3 here, we first head over to the official documentation to find what dependencies are required to build Numpy.
Mainly these 5 packages + their dependencies must be installed:
Python3 - 70 mb
Python3-dev - 25 mb
gfortran - 20 mb
gcc - 70 mb
musl-dev -10 mb (used for tracking unexpected behaviour/debugging)
An POC setup would look something like this -
Dockerfile:
FROM gliderlabs/alpine
ADD repositories.txt /etc/apk/repositories
RUN apk add --no-cache --update \
python3 python3-dev gcc \
gfortran musl-dev
ADD requirements-pip.txt .
RUN pip3 install --upgrade pip setuptools && \
pip3 install -r requirements-pip.txt
ADD . /app
WORKDIR /app
ENV PYTHONPATH=/app/
ENTRYPOINT python3 testscript.py
repositories.txt
http://dl-5.alpinelinux.org/alpine/v3.4/main
requirements-pip.txt
numpy
testscript.py
import numpy as np
def random_array(a, b):
return np.random.random((a, b))
a = random_array(2,2)
b = random_array(2,2)
print(np.dot(a,b))
To run this - clone alpine, build it using "docker build -t gliderlabs/alpine ."
Build and Run your Dockerfile
docker build -t minidocker .
docker run minidocker
Output should be something like this-
[[ 0.03573961 0.45351115]
[ 0.28302967 0.62914049]]
Here's the git link, if you want to test it out

Answer 2

From the error logs, it does not seem that it is from numpy. but you can install numpy before the requirment.txt and verify if it's working.
FROM python:3.6
RUN pip install numpy==1.14.3
Build
docker build -t numpy .
Run and Test
docker run numpy bash -c "echo import numpy as np > test.py ; python test.py"
So you will see no error on import.
or You can try numpy as an alpine package
FROM python:3-alpine3.9
RUN apk add --no-cache py3-numpy
Or better to post the requirement.txt.

Answer 3

I had lot of trouble with this issue using FROM python:3.9-buster and pandas.
My requirements.txt had the python-dev-tools, numpy and pandas, along with other packages.
I always got something like this when attempting to build:
preluded by:
and by:
Following hints by Adiii in this thread, I did some debug and found out that this actually works and builds a perfectly running container:
RUN pip3 install NumPy==1.18.0
RUN pip3 install python-dev-tools
RUN pip3 install pandas
RUN pip3 install -r requirements.txt
So, giving a specific RUN layer to the pip3 installing pandas solved the problem!

Answer 4

Another method is to install from the 'slim' distribution of python (based on debian):
FROM python:slim
CMD pip install numpy
123Mb
This results in a smaller image than that of alpine:
FROM python:3-alpine3.9
RUN apk add --no-cache py3-numpy
187MB
Plus it gives better support for other whl libraries for slim is based on a glibc library (against which all the wheels are built) while apline uses musl (incompatible with the wheels), so all packages will have to be either apk added or compiled from sources.