Dockerfile fails with llvm-config error for numba install - docker

Question

My Dockerfile using a pypy base fails with FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config' when installing llvmlite, a dependency of numba which is listed in my requirements.txt
I tried to follow and update the instructions here
Python numba / llvmlite on Debian 8 - i can't build llvmlite
My error in more detail:
Building wheels for collected packages: llvmlite
Building wheel for llvmlite (setup.py): started
Building wheel for llvmlite (setup.py): finished with status 'error'
ERROR: Command errored out with exit status 1:
command: /usr/local/bin/pypy3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ux49fegr/llvmlite/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ux49fegr/llvmlite/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-8s6wwump --python-tag pp371
cwd: /tmp/pip-install-ux49fegr/llvmlite/
Complete output (26 lines):
running bdist_wheel
/usr/local/bin/pypy3 /tmp/pip-install-ux49fegr/llvmlite/ffi/build.py
LLVM version... Traceback (most recent call last):
File "/tmp/pip-install-ux49fegr/llvmlite/ffi/build.py", line 105, in main_posix
out = subprocess.check_output([llvm_config, '--version'])
File "/usr/local/lib-python/3/subprocess.py", line 336, in check_output
**kwargs).stdout
File "/usr/local/lib-python/3/subprocess.py", line 403, in run
with Popen(*popenargs, **kwargs) as process:
File "/usr/local/lib-python/3/subprocess.py", line 722, in __init__
restore_signals, start_new_session)
File "/usr/local/lib-python/3/subprocess.py", line 1354, in _execute_child
raise child_exception_type(errno_num, err_msg)
FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config'
I don't want the heavy weight of a conda installation. Is there a way to achieve a numba install for pypy without it?
FROM pypy:3.6-slim-stretch
RUN apt-get update && apt-get install -y gnupg wget software-properties-common
RUN wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | apt-key add - 15CF4D18AF4F7421
RUN apt-add-repository "deb http://apt.llvm.org/stretch/ llvm-toolchain-stretch-6.0 main"
RUN apt-get update
RUN apt-get -y install cython python-llvm build-essential libedit-dev
RUN apt-get -y install libllvm6.0 llvm-6.0-dev llvm-dev
RUN pip install enum34
ENV LLVM_CONFIG=/usr/lib/llvm-6.0-dev/bin/llvm-config pip install llvmlite
ENV LLVM_CONFIG=/usr/lib/llvm-6.0-dev/bin/llvm-config pip install numba
# ENV LD_LIBRARY_PATH /usr/lib/llvm-6.0-dev/lib/
#... other stuff
RUN apt-get clean && apt-get -y update
RUN apt-get -y install python3-dev \
&& apt-get -y install build-essential
# Add requirements
COPY requirements.txt /tmp/
# Install sphinx first as it does not work inside requirements
RUN pip install -U pip && pip install -U sphinx && pip install numpy && pip install cython && \
pip install -r /tmp/requirements.txt
I expect a clean build of the docker image with numba on pypy

Answer 1

WORKAROUND If the error appeared after April the 17th (they released a new version, see history).
As a workaround try installing a previous version
pip3 install llvmlite==0.31.0

Answer 2

At the moment numba won't install on python 3.9.
I changed my base docker image from python:3.9-slim to python:3.8-slim and then pip install numba succeeded

Answer 3

This fixed it for me -
RUN echo "deb http://apt.llvm.org/xenial/ llvm-toolchain-xenial-8 main" >> /etc/apt/sources.list
RUN echo "deb-src http://apt.llvm.org/xenial/ llvm-toolchain-xenial-8 main" >> /etc/apt/sources.list
RUN apt-get install -y --no-install-recommends libedit-dev build-essential
RUN apt-get install -y --no-install-recommends llvm-8 llvm-8-dev
RUN LLVM_CONFIG=/usr/bin/llvm-config-8 pip3 install enum34 llvmlite numba
Used version 8, because got an error with the latest llvm version -
RuntimeError: Building llvmlite requires LLVM 7.0.x, 7.1.x or 8.0.x, got '3.7.1'
Reference - https://apt.llvm.org/

Answer 4

The "real" solution would be to encourage llvmlite and/or numba to release a wheel for pypy. But for the immediate problem...
Somehow you are missing an llvm installation, at least according to apt-file:
$ apt-file find llvm-config |grep llvm-6
llvm-6.0: /usr/bin/llvm-config-6.0
llvm-6.0: /usr/lib/llvm-6.0/bin/llvm-config
llvm-6.0: /usr/share/man/man1/llvm-config-6.0.1.gz

Answer 5

For installing numba on Python 3.9 on macOS, the following works:
# install llvm using MacPorts
sudo port install llvm-10
sudo port install llvm_select
sudo port select --set llvm mp-llvm-10
# set environment variable used when building `llvmlite`
export LLVM_CONFIG=/opt/local/bin/llvm-config
# clone, build, and install `llvmlite`
# http://llvmlite.pydata.org/en/latest/admin-guide/install.html#compiling-llvmlite
git clone git#github.com:numba/llvmlite.git
cd llvmlite
python setup.py build
python runtests.py
python setup.py install
cd ..
# clone, build, and install `numba`
# https://numba.readthedocs.io/en/stable/user/installing.html#installing-from-source
git clone git#github.com:numba/numba.git
cd numba
export PATH=/usr/bin/:$PATH # use clang, same as used for building Python 3.9
pip install -v .
cd ..
The above are with:
llvmlite at commit 334411cf638c8e06ba19bfda16b07dd64e9dac3c, and
numba at commit ca8132ba5e43fc3f79767046ed55217aeeabb35e.

Answer 6

according to https://askubuntu.com/questions/1286131/how-do-i-install-llvm-10-on-ubuntu-18-04
I added to Dockerfile the lines
RUN apt-get -y install llvm-10*
RUN rm -f /usr/bin/llvm-config
RUN ln -s /usr/bin/llvm-config-10 /usr/bin/llvm-config
and It worked (llvmlite installed)

Answer 7

This is the solution, obtained from this github issues thread, that worked for me! Essentially, pip just needed an upgrade in the Dockerfile before installing libraries. All I needed to do was add this line in my Dockerfile:
--upgrade pip \
Here is the sample of my Dockerfile:
# Docker commands here ...
RUN APT_INSTALL="apt-get install -y " && \
PIP_INSTALL="python3 -m pip install " && \
apt-get update && \
# more docker commands here ...
DEBIAN_FRONTEND=noninteractive $APT_INSTALL \
python3.6 \
python3.6-dev \
python3-distutils-extra \
python3-pip && \
ln -s /usr/bin/python3.6 /usr/local/bin/python3 && \
$PIP_INSTALL \
--upgrade pip \ # adding this line was my solution
setuptools \
&& \
$PIP_INSTALL \
numpy==1.18.5 \
# more docker commands here...
This is for python 3.6