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Instructions for Miniforge3 on alpine Linux #219

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kellpossible opened this issue Oct 9, 2021 · 7 comments
Closed
1 task done

Instructions for Miniforge3 on alpine Linux #219

kellpossible opened this issue Oct 9, 2021 · 7 comments
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documentation Improvements or additions to documentation help wanted Extra attention is needed

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@kellpossible
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kellpossible commented Oct 9, 2021 •
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Issue:

Miniforge3 installer fails on alpine Linux.

I get the following error:

$ curl -fsSLo Miniforge3.sh https://github.com/conda-forge/miniforge/releases/download/4.10.3-5/Miniforge3-4.10.3-5-$(uname)-$(uname -m).sh
$ bash Miniforge3.sh -b -p ./miniforge3
Miniforge3.sh: line 362: /miniforge3/conda.exe: No such file or directory
Miniforge3.sh: line 365: /miniforge3/preconda.tar.bz2: No such file or directory

You can run this Dockerfile to replicate the problem:

FROM alpine

RUN apk update && apk add curl bash

RUN curl -fsSLo Miniforge3.sh https://github.com/conda-forge/miniforge/releases/download/4.10.3-5/Miniforge3-4.10.3-5-$(uname)-$(uname -m).sh

RUN sha256sum Miniforge3.sh

RUN echo "5f143112b6c9533c550b447cc01f7313a86b6b88b92632791bcb4320e57f9af6  Miniforge3.sh" | sha256sum -c

RUN bash Miniforge3.sh -b -p ./miniforge3
@hmaarrfk
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hmaarrfk commented Oct 9, 2021

we test our installer with a few different docker images. are you able to make a PR adding to the list? you might be missing a system dependency. maybe we will need bz2

@isuruf
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isuruf commented Oct 9, 2021

We don't support musl libc. You have to install the glibc compat library, if you want to run miniforge.

@kellpossible
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kellpossible commented Oct 11, 2021 •
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@hmaarrfk Sorry I don't have time at the moment to submit a PR, working around it a different way for now
@isuruf Thanks, I think I got one step closer:

FROM alpine

RUN apk update &&\
	apk add --no-cache curl bash libc6-compat bzip2 &&\
	ln -s /lib/libc.musl-x86_64.so.1 /lib/ld-linux-x86-64.so.2 &&\
	ln -s /lib/libc.so.6 /usr/lib/libresolv.so.2

RUN curl -fsSLo Miniforge3.sh https://github.com/conda-forge/miniforge/releases/download/4.10.3-5/Miniforge3-4.10.3-5-$(uname)-$(uname -m).sh

RUN sha256sum Miniforge3.sh

RUN echo "5f143112b6c9533c550b447cc01f7313a86b6b88b92632791bcb4320e57f9af6  Miniforge3.sh" | sha256sum -c

RUN bash Miniforge3.sh -b -p ./miniforge3
Error relocating /miniforge3/conda.exe: __register_atfork: symbol not found
Error relocating /miniforge3/conda.exe: gnu_dev_minor: symbol not found
Error relocating /miniforge3/conda.exe: __strdup: symbol not found
Error relocating /miniforge3/conda.exe: __vfprintf_chk: symbol not found
Error relocating /miniforge3/conda.exe: makecontext: symbol not found
Error relocating /miniforge3/conda.exe: __strncat_chk: symbol not found
Error relocating /miniforge3/conda.exe: __rawmemchr: symbol not found
Error relocating /miniforge3/conda.exe: setcontext: symbol not found
Error relocating /miniforge3/conda.exe: gnu_dev_major: symbol not found
Error relocating /miniforge3/conda.exe: __strncpy_chk: symbol not found
Error relocating /miniforge3/conda.exe: __sprintf_chk: symbol not found
Error relocating /miniforge3/conda.exe: __snprintf_chk: symbol not found
Error relocating /miniforge3/conda.exe: getcontext: symbol not found
Error relocating /miniforge3/conda.exe: __res_nsearch: symbol not found
Error relocating /miniforge3/conda.exe: __fread_chk: symbol not found
Error relocating /miniforge3/conda.exe: __vsnprintf_chk: symbol not found
Error relocating /miniforge3/conda.exe: __strcpy_chk: symbol not found
Error relocating /miniforge3/conda.exe: __strcat_chk: symbol not found
Error relocating /miniforge3/conda.exe: __strtok_r: symbol not found
Error relocating /miniforge3/conda.exe: __asprintf_chk: symbol not found
Error relocating /miniforge3/conda.exe: __memset_chk: symbol not found
Error relocating /miniforge3/conda.exe: __fprintf_chk: symbol not found
Error relocating /miniforge3/conda.exe: qsort_r: symbol not found
Error relocating /miniforge3/conda.exe: __res_nclose: symbol not found
Error relocating /miniforge3/conda.exe: __memcpy_chk: symbol not found
Error relocating /miniforge3/conda.exe: gnu_dev_makedev: symbol not found
Error relocating /miniforge3/conda.exe: __res_ninit: symbol not found
Error relocating /miniforge3/conda.exe: __vasprintf_chk: symbol not found
Error relocating /miniforge3/conda.exe: __openat_2: symbol not found
Miniforge3.sh: line 365: /miniforge3/preconda.tar.bz2: No such file or directory

@hmaarrfk hmaarrfk changed the title Miniforge3 installer fails on alpine Linux Instructions for Miniforge3 on alpine Linux Oct 18, 2021
@hmaarrfk hmaarrfk added documentation Improvements or additions to documentation help wanted Extra attention is needed labels Oct 18, 2021
@hmaarrfk
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Ok, I've renamed the issue to reflect the current state. and flagged it as "help wanted". If you have information that can help us, it would be great to submit a PR describing how you got things working for others.

@jadeidev
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we can use the same method used by miniconda using the glibc for alpine

FROM alpine:3.15.0 as alpine-glibc

LABEL src=https://github.com/frol/docker-alpine-glibc
ENV LANG=C.UTF-8 LC_ALL=C.UTF-8

SHELL ["/bin/ash", "-eo", "pipefail", "-c"]

# hadolint ignore=DL3018
RUN ALPINE_GLIBC_BASE_URL="https://github.com/sgerrand/alpine-pkg-glibc/releases/download" && \
    ALPINE_GLIBC_PACKAGE_VERSION="2.34-r0" && \
    ALPINE_GLIBC_BASE_PACKAGE_FILENAME="glibc-$ALPINE_GLIBC_PACKAGE_VERSION.apk" && \
    ALPINE_GLIBC_BIN_PACKAGE_FILENAME="glibc-bin-$ALPINE_GLIBC_PACKAGE_VERSION.apk" && \
    ALPINE_GLIBC_I18N_PACKAGE_FILENAME="glibc-i18n-$ALPINE_GLIBC_PACKAGE_VERSION.apk" && \
    apk add -q --no-cache --virtual=.build-dependencies wget ca-certificates && \
    echo \
    "-----BEGIN PUBLIC KEY-----\
    MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEApZ2u1KJKUu/fW4A25y9m\
    y70AGEa/J3Wi5ibNVGNn1gT1r0VfgeWd0pUybS4UmcHdiNzxJPgoWQhV2SSW1JYu\
    tOqKZF5QSN6X937PTUpNBjUvLtTQ1ve1fp39uf/lEXPpFpOPL88LKnDBgbh7wkCp\
    m2KzLVGChf83MS0ShL6G9EQIAUxLm99VpgRjwqTQ/KfzGtpke1wqws4au0Ab4qPY\
    KXvMLSPLUp7cfulWvhmZSegr5AdhNw5KNizPqCJT8ZrGvgHypXyiFvvAH5YRtSsc\
    Zvo9GI2e2MaZyo9/lvb+LbLEJZKEQckqRj4P26gmASrZEPStwc+yqy1ShHLA0j6m\
    1QIDAQAB\
    -----END PUBLIC KEY-----" | sed 's/   */\n/g' > "/etc/apk/keys/sgerrand.rsa.pub" && \
    wget -q \
    "$ALPINE_GLIBC_BASE_URL/$ALPINE_GLIBC_PACKAGE_VERSION/$ALPINE_GLIBC_BASE_PACKAGE_FILENAME" \
    "$ALPINE_GLIBC_BASE_URL/$ALPINE_GLIBC_PACKAGE_VERSION/$ALPINE_GLIBC_BIN_PACKAGE_FILENAME" \
    "$ALPINE_GLIBC_BASE_URL/$ALPINE_GLIBC_PACKAGE_VERSION/$ALPINE_GLIBC_I18N_PACKAGE_FILENAME" && \
    apk add -q --no-cache \
    "$ALPINE_GLIBC_BASE_PACKAGE_FILENAME" \
    "$ALPINE_GLIBC_BIN_PACKAGE_FILENAME" \
    "$ALPINE_GLIBC_I18N_PACKAGE_FILENAME" && \
    \
    rm "/etc/apk/keys/sgerrand.rsa.pub" && \
    /usr/glibc-compat/bin/localedef --force --inputfile POSIX --charmap UTF-8 "$LANG" || true && \
    echo "export LANG=$LANG" > /etc/profile.d/locale.sh && \
    \
    apk del -q glibc-i18n && \
    \
    rm "/root/.wget-hsts" && \
    apk del -q .build-dependencies && \
    rm \
    "$ALPINE_GLIBC_BASE_PACKAGE_FILENAME" \
    "$ALPINE_GLIBC_BIN_PACKAGE_FILENAME" \
    "$ALPINE_GLIBC_I18N_PACKAGE_FILENAME"


FROM alpine-glibc
ENV PATH /opt/miniforge3/bin:$PATH

RUN apk update && apk add curl bash procps

RUN curl -fsSLo Miniforge3.sh https://github.com/conda-forge/miniforge/releases/download/4.10.3-5/Miniforge3-4.10.3-5-$(uname)-$(uname -m).sh

RUN sha256sum Miniforge3.sh

RUN echo "5f143112b6c9533c550b447cc01f7313a86b6b88b92632791bcb4320e57f9af6  Miniforge3.sh" | sha256sum -c

RUN bash Miniforge3.sh -b -p /opt/miniforge3 &&\
    ln -s /opt/miniforge3/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
    echo ". /opt/miniforge3/etc/profile.d/conda.sh" >> ~/.bashrc && \
    echo "conda activate base" >> ~/.bashrc && \
    find /opt/miniforge3/ -follow -type f -name '*.a' -delete && \
    find /opt/miniforge3/ -follow -type f -name '*.js.map' -delete && \
    /opt/miniforge3/bin/conda clean -afy

CMD ["/bin/bash"]

@andyneff
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andyneff commented Apr 4, 2024

Additional information:

On glibc 2.35, you will get errors:

Error relocating /tmp/tmp.LpjGOK/conda/_conda: __res_nsearch: symbol not found
Error relocating /tmp/tmp.LpjGOK/conda/_conda: __openat_2: symbol not found

So it appears we need to stick with version 2.34

@2themaxx 2themaxx mentioned this issue Apr 23, 2024
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@isuruf
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isuruf commented Jul 31, 2024

You can use https://github.com/Docker-Hub-frolvlad/docker-alpine-glibc as the base or use the script there. It also uses 2.34 to workaround sgerrand/alpine-pkg-glibc#176

@isuruf isuruf closed this as completed Jul 31, 2024
@hmaarrfk hmaarrfk mentioned this issue Oct 5, 2024
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@mattbucci mattbucci mentioned this issue Nov 2, 2024
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@hmaarrfk @kellpossible @isuruf @andyneff @jadeidev