Openblas +noavx512 "no such variant" during docker build error after using "containerize"

[acrosby]

Description

I am not sure if this is the right place to file this bug, or if it is even really a bug. However, we just ran into "No such variant 'noavx512' in package openblas" while attempting to create a gcc/openmpi based container image from the 1.8.0 release.

 => ERROR [builder 6/8] RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast && spack gc -y      11.5s 
------                                                                                                                               
 > [builder 6/8] RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast && spack gc -y:
10.20 ==> Error: cannot emit requirements for the solver: No such variant 'noavx512' in package openblas
------
Dockerfile:521
--------------------
 519 |     
 520 |     # Install the software, remove unnecessary deps
 521 | >>> RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast && spack gc -y
 522 |     
 523 |     # Modifications to the environment that are necessary to run
--------------------
ERROR: failed to solve: process "docker-shell cd /opt/spack-environment && spack env activate . && spack install --fail-fast && spack gc -y" did not complete successfully: exit code: 3
make: *** [makefile:57: jcsda-spackstack] Error 1

To Reproduce

Here is a section of our makefile that clones the JCSDA Spack-stack repo and switches to the 1.8.0 release, before running spack containerize and building the image with docker build.

SPACK_RELEASE ?= 1.8.0
DIRS := $(spack-stack spack)

spack-stack: 
	git clone --recurse-submodules https://github.com/JCSDA/spack-stack -b release/$(SPACK_RELEASE)

spackstack-ubuntu-gcc-openmpi_$(SPACK_RELEASE).dockerfile: spack-stack spack
	rm -rf spack-stack/envs/docker-ubuntu-gcc-openmpi
	source spack-stack/setup.sh; (spack stack create ctr -h && spack stack create ctr --container=docker-ubuntu-gcc-openmpi --specs=jedi-ci && cd spack-stack/envs/docker-ubuntu-gcc-openmpi && spack containerize > Dockerfile && cp Dockerfile ../../../spackstack-ubuntu-gcc-openmpi_$(SPACK_RELEASE).dockerfile) || exit 1

dockerfile: spackstack-ubuntu-gcc-openmpi_$(SPACK_RELEASE).dockerfile

jcsda-spackstack: spackstack-ubuntu-gcc-openmpi_$(SPACK_RELEASE).dockerfile
	DOCKER_BUILDKIT=1 docker build --rm --tag jcsda-spacstack:$(SPACK_RELEASE) -f spackstack-ubuntu-gcc-openmpi_$(SPACK_RELEASE).dockerfile spack-stack/envs/docker-ubuntu-gcc-openmpi

build: jcsda-spackstack spack-stack spack

Expected behavior

Completed docker build of a base 1.8.0 jcsda/spack-stack container image.

System:

The building is happening on an Ubuntu 20.04 machine.

Here is the full Dockerfile that is created:

FROM ubuntu:22.04 as bootstrap

ENV SPACK_ROOT=/opt/spack \
    CURRENTLY_BUILDING_DOCKER_IMAGE=1 \
    container=docker

ENV DEBIAN_FRONTEND=noninteractive   \
    LANGUAGE=en_US.UTF-8 \
    LANG=en_US.UTF-8 \
    LC_ALL=en_US.UTF-8

RUN apt-get -yqq update \
 && apt-get -yqq upgrade \
 && apt-get -yqq install --no-install-recommends \
        build-essential \
        ca-certificates \
        curl \
        file \
        g++ \
        gcc \
        gfortran \
        git \
        gnupg2 \
        iproute2 \
        locales \
        make \
        mercurial \
        subversion \
        python3 \
        python3-pip \
        python3-setuptools \
        unzip \
        zstd \
 && locale-gen en_US.UTF-8 \
 && pip3 install boto3 \
 && rm -rf /var/lib/apt/lists/*

RUN mkdir $SPACK_ROOT && cd $SPACK_ROOT && \
    git init --quiet && git remote add origin https://github.com/jcsda/spack && git fetch --depth=1 origin dd99fc1e177cbae412e1753f3a81499df90cee27 && git checkout --detach FETCH_HEAD && \
    mkdir -p $SPACK_ROOT/opt/spack

RUN ln -s $SPACK_ROOT/share/spack/docker/entrypoint.bash \
          /usr/local/bin/docker-shell \
 && ln -s $SPACK_ROOT/share/spack/docker/entrypoint.bash \
          /usr/local/bin/interactive-shell \
 && ln -s $SPACK_ROOT/share/spack/docker/entrypoint.bash \
          /usr/local/bin/spack-env

RUN mkdir -p /root/.spack \
 && cp $SPACK_ROOT/share/spack/docker/modules.yaml \
        /root/.spack/modules.yaml \
 && rm -rf /root/*.* /run/nologin

# [WORKAROUND]
# https://superuser.com/questions/1241548/
#     xubuntu-16-04-ttyname-failed-inappropriate-ioctl-for-device#1253889
RUN [ -f ~/.profile ]                                               \
 && sed -i 's/mesg n/( tty -s \\&\\& mesg n || true )/g' ~/.profile \
 || true


WORKDIR /root
SHELL ["docker-shell"]

# Creates the package cache
RUN spack bootstrap now \
    && spack bootstrap status --optional \
    && spack spec hdf5+mpi

ENTRYPOINT ["/bin/bash", "/opt/spack/share/spack/docker/entrypoint.bash"]
CMD ["interactive-shell"]

# Build stage with Spack pre-installed and ready to be used
FROM bootstrap as builder

# Install OS packages needed to build the software
RUN apt-get -yqq update && apt-get -yqq upgrade \
 && apt-get -yqq install bc cpp-12 g++-12 gcc-12 gfortran-12 git git-lfs make mysql-server qtbase5-dev qt5-qmake libqt5svg5-dev qt5dxcb-plugin wget \
 && rm -rf /var/lib/apt/lists/*

# Copy the spack-stack extension repo into the spack code
COPY spack-ext-/repos/spack-stack $SPACK_ROOT/var/spack/repos/spack-stack
# Register spack-stack extension repo
RUN spack repo add $SPACK_ROOT/var/spack/repos/spack-stack --scope defaults
# Set the GNU 12.x toolchain as the default compilers.
RUN ln -svf /usr/bin/gfortran-12 /usr/bin/gfortran && \
ln -svf /usr/bin/cpp-12 /usr/bin/cpp && \
ln -svf /usr/bin/gcc-12 /usr/bin/gcc && \
ln -svf /usr/bin/g++-12 /usr/bin/g++


# What we want to install and how we want to install it
# is specified in a manifest file (spack.yaml)
RUN mkdir -p /opt/spack-environment && \
set -o noclobber \
&&  (echo spack: \
&&   echo '  concretizer:' \
&&   echo '    unify: true' \
&&   echo '' \
&&   echo '  config:' \
&&   echo '    checksum: false' \
&&   echo '    build_jobs: 2' \
&&   echo '    connect_timeout: 60' \
&&   echo '' \
&&   echo '    install_tree: /opt/software' \
&&   echo '  compilers:' \
&&   echo '  - compiler:' \
&&   echo '      spec: [email protected]' \
&&   echo '      paths:' \
&&   echo '        cc: /usr/bin/gcc-12' \
&&   echo '        cxx: /usr/bin/g++-12' \
&&   echo '        f77: /usr/bin/gfortran-12' \
&&   echo '        fc: /usr/bin/gfortran-12' \
&&   echo '      flags: {}' \
&&   echo '      operating_system: ubuntu22.04' \
&&   echo '      modules: []' \
&&   echo '      environment: {}' \
&&   echo '      extra_rpaths: []' \
&&   echo '' \
&&   echo '  # Basic package config from configs/common/packages.yaml' \
&&   echo '  # Additional package config for container' \
&&   echo '  packages:' \
&&   echo '    all:' \
&&   echo '      providers:' \
&&   echo '        gl: [opengl]' \
&&   echo '        glu: [openglu]' \
&&   echo '        jpeg: [libjpeg-turbo]' \
&&   echo '        pkgconfig: [pkg-config]' \
&&   echo '        yacc: [bison]' \
&&   echo '        zlib-api: [zlib-ng]' \
&&   echo '        mpi: [[email protected]]' \
&&   echo '      require: '"'"'%gcc'"'"'' \
&&   echo '      target: [x86_64]' \
&&   echo '      compiler: [[email protected]]' \
&&   echo '    awscli-v2:' \
&&   echo '      require: ~examples' \
&&   echo '    bacio:' \
&&   echo '      require: '"'"'@2.4.1'"'"'' \
&&   echo '    bison:' \
&&   echo '      require: '"'"'@3.4:'"'"'' \
&&   echo '  # 1.85 incompatible with [email protected] - use latest '"'"'good version'"'"'' \
&&   echo '    boost:' \
&&   echo '      require:' \
&&   echo '      - '"'"'@1.84 ~atomic +chrono +date_time +exception +filesystem ~graph ~iostreams' \
&&   echo '        ~locale ~log ~math ~mpi ~numpy +pic +program_options +python ~random +regex' \
&&   echo '        +serialization ~signals +system +test +thread +timer ~wave cxxstd=17 visibility=hidden'"'"'' \
&&   echo '    bufr:' \
&&   echo '      require: '"'"'@12.1.0 +python'"'"'' \
&&   echo '    bufr-query:' \
&&   echo '      require: '"'"'@0.0.2 +python'"'"'' \
&&   echo '    cairo:' \
&&   echo '      require: +pic' \
&&   echo '    cdo:' \
&&   echo '      require: '"'"'@2.3.0 ~openmp'"'"'' \
&&   echo '    cmake:' \
&&   echo '      version: [3.27.9]' \
&&   echo '      require: +ownlibs' \
&&   echo '  # Attention - when updating also check the various jcsda-emc-bundles env packages' \
&&   echo '    crtm:' \
&&   echo '      require: +fix' \
&&   echo '    ecbuild:' \
&&   echo '      require: '"'"'@3.7.2'"'"'' \
&&   echo '    eccodes:' \
&&   echo '      require: '"'"'@2.33.0 +png +tools'"'"'' \
&&   echo '    ecflow:' \
&&   echo '      require:' \
&&   echo '      - '"'"'@5.11.4 +ui'"'"'' \
&&   echo '    eckit:' \
&&   echo '      require: '"'"'@1.27.0 linalg=eigen,lapack compression=lz4,bzip2'"'"'' \
&&   echo '    ecmwf-atlas:' \
&&   echo '      require: '"'"'@0.38.1 +fckit +trans +tesselation +fftw'"'"'' \
&&   echo '    ectrans:' \
&&   echo '      require:' \
&&   echo '      - '"'"'@1.2.0'"'"'' \
&&   echo '    eigen:' \
&&   echo '      require: '"'"'@3.4.0'"'"'' \
&&   echo '  # Attention - when updating the version also check the common modules.yaml' \
&&   echo '  # config and update the projections for lmod/tcl.' \
&&   echo '  # Also, check the acorn and derecho site configs which have esmf modifications.' \
&&   echo '    esmf:' \
&&   echo '      require:' \
&&   echo '      - ~xerces ~pnetcdf +shared +external-parallelio' \
&&   echo '      - any_of: ['"'"'@=8.6.1 snapshot=none'"'"', '"'"'@=8.7.0b11 snapshot=b11'"'"']' \
&&   echo '      - any_of: [fflags="-fp-model precise" cxxflags="-fp-model precise"]' \
&&   echo '        when: '"'"'%intel'"'"'' \
&&   echo '        message: Extra ESMF compile options for Intel' \
&&   echo '      #- any_of: ['"'"''"'"']' \
&&   echo '      #  when: "%gcc"' \
&&   echo '      #  message: "Extra ESMF compile options for GCC"' \
&&   echo '      #- any_of: ['"'"''"'"']' \
&&   echo '      #  when: "%apple-clang"' \
&&   echo '      #  message: "Extra ESMF compile options for GCC"' \
&&   echo '    fckit:' \
&&   echo '      require: '"'"'@0.11.0 +eckit'"'"'' \
&&   echo '    fftw:' \
&&   echo '      require: '"'"'@3.3.10'"'"'' \
&&   echo '    fiat:' \
&&   echo '      require: '"'"'@1.2.0'"'"'' \
&&   echo '    flex:' \
&&   echo '    # Pin version to avoid duplicates' \
&&   echo '      require: '"'"'@2.6.4'"'"'' \
&&   echo '    fms:' \
&&   echo '      require:' \
&&   echo '      - '"'"'@2024.02'"'"'' \
&&   echo '      - precision=32,64 +quad_precision +gfs_phys +openmp +pic constants=GFS build_type=Release' \
&&   echo '        +deprecated_io' \
&&   echo '    fontconfig:' \
&&   echo '      require: +pic' \
&&   echo '    freetype:' \
&&   echo '      require: +pic' \
&&   echo '    g2:' \
&&   echo '      require:' \
&&   echo '      - '"'"'@3.5.1'"'"'' \
&&   echo '    g2c:' \
&&   echo '      require: '"'"'@1.6.4'"'"'' \
&&   echo '    g2tmpl:' \
&&   echo '      require:' \
&&   echo '      - '"'"'@1.13.0'"'"'' \
&&   echo '    gcc-runtime:' \
&&   echo '      require: '"'"'%gcc'"'"'' \
&&   echo '      buildable: false' \
&&   echo '      externals:' \
&&   echo '      - spec: [email protected]' \
&&   echo '        prefix: /usr' \
&&   echo '    gfsio:' \
&&   echo '      require: '"'"'@1.4.1'"'"'' \
&&   echo '  #git-lfs:' \
&&   echo '    # Assume git-lfs is provided, hard to install' \
&&   echo '    # because of dependencies on go/go-bootstrap.' \
&&   echo '    # Note: Uncommenting this entry will break' \
&&   echo '    # the container builds.' \
&&   echo '    #require: '"'"'@2.11.0'"'"'' \
&&   echo '    grib-util:' \
&&   echo '      require: '"'"'@1.4.0'"'"'' \
&&   echo '    gsibec:' \
&&   echo '      require:' \
&&   echo '      - '"'"'@1.2.1'"'"'' \
&&   echo '    gsi-ncdiag:' \
&&   echo '      require: '"'"'@1.1.2'"'"'' \
&&   echo '    gsl-lite:' \
&&   echo '      require: '"'"'@0.37.0'"'"'' \
&&   echo '    hdf:' \
&&   echo '      require: '"'"'@4.2.15 +external-xdr ~fortran ~netcdf'"'"'' \
&&   echo '    hdf5:' \
&&   echo '      require: '"'"'@1.14.3 +hl +fortran +mpi +threadsafe ~szip'"'"'' \
&&   echo '  # Newer versions of hdf-eos2 require manual downloading, avoid' \
&&   echo '    hdf-eos2:' \
&&   echo '      require: '"'"'@2.20v1.00'"'"'' \
&&   echo '    ip:' \
&&   echo '      require: '"'"'@5.0.0 precision=4,d,8'"'"'' \
&&   echo '    ip2:' \
&&   echo '      require: '"'"'@1.1.2'"'"'' \
&&   echo '    jasper:' \
&&   echo '      require: '"'"'@2.0.32'"'"'' \
&&   echo '    jedi-cmake:' \
&&   echo '      require: '"'"'@1.4.0'"'"'' \
&&   echo '    landsfcutil:' \
&&   echo '      require: '"'"'@2.4.1'"'"'' \
&&   echo '    libjpeg-turbo:' \
&&   echo '      require: '"'"'@2.1.0'"'"'' \
&&   echo '    libpng:' \
&&   echo '      require: '"'"'@1.6.37 +pic'"'"'' \
&&   echo '  # Newest version of magics needed for oneapi compilers' \
&&   echo '    magics:' \
&&   echo '      require: '"'"'@4.15.3:'"'"'' \
&&   echo '    mapl:' \
&&   echo '      require: '"'"'@2.46.3 ~shared ~f2py'"'"'' \
&&   echo '      variants: +pflogger' \
&&   echo '  # If making changes here, also check the Discover site configs and the CI workflows' \
&&   echo '    met:' \
&&   echo '      require: '"'"'@11.1.1 +python +grib2'"'"'' \
&&   echo '    metplus:' \
&&   echo '      require: '"'"'@5.1.0'"'"'' \
&&   echo '    metis:' \
&&   echo '      require: +int64 +real64' \
&&   echo '    mpich:' \
&&   echo '      require: ~hwloc' \
&&   echo '    nco:' \
&&   echo '      require: '"'"'@5.1.6 ~doc'"'"'' \
&&   echo '  # ncview - when adding information here, also check Orion' \
&&   echo '  # and Discover site configs' \
&&   echo '    nemsio:' \
&&   echo '      require: '"'"'@2.5.4'"'"'' \
&&   echo '    nemsiogfs:' \
&&   echo '      require: '"'"'@2.5.3'"'"'' \
&&   echo '    nccmp:' \
&&   echo '      require: '"'"'@1.9.0.1'"'"'' \
&&   echo '    ncio:' \
&&   echo '      require: '"'"'@1.1.2'"'"'' \
&&   echo '    netcdf-c:' \
&&   echo '    # If using 4.9.1, turn off byterange variant to fix compile error: ~byterange' \
&&   echo '      require: '"'"'@4.9.2 +dap +mpi ~parallel-netcdf ~szip build_system=autotools'"'"'' \
&&   echo '    netcdf-cxx4:' \
&&   echo '      require: '"'"'@4.3.1'"'"'' \
&&   echo '    netcdf-fortran:' \
&&   echo '      require: '"'"'@4.6.1'"'"'' \
&&   echo '  # ninja - when adding information here, also check Discover site config' \
&&   echo '    odc:' \
&&   echo '      require: '"'"'@1.5.2 ~fortran'"'"'' \
&&   echo '    openblas:' \
&&   echo '      require: '"'"'@0.3.24 +noavx512'"'"'' \
&&   echo '    openmpi:' \
&&   echo '      require: ~internal-hwloc +two_level_namespace' \
&&   echo '    openssl:' \
&&   echo '      require: +shared' \
&&   echo '    p4est:' \
&&   echo '      require: '"'"'@2.8'"'"'' \
&&   echo '    parallelio:' \
&&   echo '      require: '"'"'@2.6.2 +pnetcdf'"'"'' \
&&   echo '    parallel-netcdf:' \
&&   echo '      require: '"'"'@1.12.3'"'"'' \
&&   echo '    pflogger:' \
&&   echo '      require: +mpi' \
&&   echo '    pixman:' \
&&   echo '      require: +pic' \
&&   echo '    prod-util:' \
&&   echo '      require: '"'"'@2.1.1'"'"'' \
&&   echo '    proj:' \
&&   echo '      require: ~tiff' \
&&   echo '    python:' \
&&   echo '      require: '"'"'@3.11.7'"'"'' \
&&   echo '    py-attrs:' \
&&   echo '    # https://github.com/JCSDA/spack-stack/issues/740' \
&&   echo '      require: '"'"'@21.4.0'"'"'' \
&&   echo '    py-cartopy:' \
&&   echo '      require: +plotting' \
&&   echo '    py-cryptography:' \
&&   echo '      require: +rust_bootstrap' \
&&   echo '  # Introduced in https://github.com/JCSDA/spack-stack/pull/894, pin py-cython' \
&&   echo '  # to avoid duplicate packages being built (cylc dependencies soft-want @3:)' \
&&   echo '    py-cython:' \
&&   echo '      require: '"'"'@0.29.36'"'"'' \
&&   echo '  # As long as we need the "delayed" variant for py-dask,' \
&&   echo '  # we are restricted to version 2021.03.0 (last one that has it)' \
&&   echo '  # and newer than 2021.01.0 because of these issues:' \
&&   echo '  # https://github.com/JCSDA/spack-stack/issues/1216' \
&&   echo '  # https://github.com/pydata/xarray/issues/8917' \
&&   echo '    py-dask:' \
&&   echo '      require: '"'"'@2021.3.0'"'"'' \
&&   echo '  # To avoid duplicate packages' \
&&   echo '    py-flit-core:' \
&&   echo '      require: '"'"'@3.8.0'"'"'' \
&&   echo '    py-h5py:' \
&&   echo '      require: ~mpi' \
&&   echo '  ## To avoid duplicate packages' \
&&   echo '  #py-jinja2:' \
&&   echo '  #  require: '"'"'@3.1.2'"'"'' \
&&   echo '  # https://github.com/JCSDA/spack-stack/issues/1276' \
&&   echo '    py-matplotlib:' \
&&   echo '      require: '"'"'@3.7.4'"'"'' \
&&   echo '    py-meson-python:' \
&&   echo '      require: '"'"'@0.15.0'"'"'' \
&&   echo '  # Comment out for now until build problems are solved' \
&&   echo '  # https://github.com/jcsda/spack-stack/issues/522' \
&&   echo '  # see also ewok-env virtual package and container' \
&&   echo '  # README.md' \
&&   echo '  #py-mysql-connector-python:' \
&&   echo '  #  require: '"'"'@8.0.32'"'"'' \
&&   echo '    py-netcdf4:' \
&&   echo '      require: '"'"'@1.5.8 ~mpi'"'"'' \
&&   echo '  # [email protected] causes many build problems with older Python packages' \
&&   echo '  # also check Nautilus site config when making changes here' \
&&   echo '  # https://github.com/JCSDA/spack-stack/issues/1276' \
&&   echo '    py-numpy:' \
&&   echo '      require:' \
&&   echo '      - '"'"'@:1.23.5'"'"'' \
&&   echo '    py-pandas:' \
&&   echo '      require: +excel' \
&&   echo '    py-pybind11:' \
&&   echo '      require: '"'"'@2.11.0'"'"'' \
&&   echo '  # Pin the py-setuptools version to avoid duplicate Python packages' \
&&   echo '    py-setuptools:' \
&&   echo '      require: '"'"'@63.4.3'"'"'' \
&&   echo '    py-setuptools-rust:' \
&&   echo '      require: +rust_bootstrap' \
&&   echo '    py-shapely:' \
&&   echo '      require: '"'"'@1.8.0'"'"'' \
&&   echo '    py-torch:' \
&&   echo '      require: +custom-protobuf ~mkldnn' \
&&   echo '  # To avoid duplicate packages' \
&&   echo '    py-urllib3:' \
&&   echo '      require: '"'"'@1.26.12'"'"'' \
&&   echo '    qt:' \
&&   echo '      require: '"'"'@5'"'"'' \
&&   echo '      buildable: false' \
&&   echo '      externals:' \
&&   echo '      - spec: [email protected]' \
&&   echo '        prefix: /usr' \
&&   echo '      version: [5.15.3]' \
&&   echo '    scotch:' \
&&   echo '      require: '"'"'@7.0.4 +mpi+metis~shared~threads~mpi_thread+noarch'"'"'' \
&&   echo '    sfcio:' \
&&   echo '      require: '"'"'@1.4.1'"'"'' \
&&   echo '    shumlib:' \
&&   echo '      require: '"'"'@macos_clang_linux_intel_port'"'"'' \
&&   echo '    sigio:' \
&&   echo '      require: '"'"'@2.3.2'"'"'' \
&&   echo '    sp:' \
&&   echo '      require: '"'"'@2.5.0 precision=4,d,8'"'"'' \
&&   echo '    udunits:' \
&&   echo '      require: '"'"'@2.2.28'"'"'' \
&&   echo '    ufs-utils:' \
&&   echo '      require: '"'"'@1.13.0'"'"'' \
&&   echo '  # Note - we can remove upp from stack at some point?' \
&&   echo '    upp:' \
&&   echo '      require: '"'"'@10.0.10'"'"'' \
&&   echo '  # Need extradeps for grib-utils, enable by default to avoid duplicate packages' \
&&   echo '    w3emc:' \
&&   echo '      require: '"'"'@2.10.0 precision=4,d,8 +extradeps'"'"'' \
&&   echo '    w3nco:' \
&&   echo '      require: '"'"'@2.4.1'"'"'' \
&&   echo '    wgrib2:' \
&&   echo '      require:' \
&&   echo '      - '"'"'@3.1.1'"'"'' \
&&   echo '    wrf-io:' \
&&   echo '      require: '"'"'@1.2.0'"'"'' \
&&   echo '    zstd:' \
&&   echo '      require: '"'"'@1.5.2 +programs'"'"'' \
&&   echo '    gcc:' \
&&   echo '      buildable: false' \
&&   echo '      externals:' \
&&   echo '      - spec: [email protected]' \
&&   echo '        prefix: /usr' \
&&   echo '    gmake:' \
&&   echo '      buildable: false' \
&&   echo '      externals:' \
&&   echo '      - spec: [email protected]' \
&&   echo '        prefix: /usr' \
&&   echo '    diffutils:' \
&&   echo '      buildable: false' \
&&   echo '      externals:' \
&&   echo '      - spec: [email protected]' \
&&   echo '        prefix: /usr' \
&&   echo '    git:' \
&&   echo '      buildable: false' \
&&   echo '      externals:' \
&&   echo '      - spec: [email protected]~tcltk' \
&&   echo '        prefix: /usr' \
&&   echo '    git-lfs:' \
&&   echo '      buildable: false' \
&&   echo '      externals:' \
&&   echo '      - spec: [email protected]' \
&&   echo '        prefix: /usr' \
&&   echo '    mysql:' \
&&   echo '      buildable: false' \
&&   echo '      externals:' \
&&   echo '      - spec: [email protected]' \
&&   echo '        prefix: /usr' \
&&   echo '    wget:' \
&&   echo '      buildable: false' \
&&   echo '      externals:' \
&&   echo '      - spec: [email protected]' \
&&   echo '        prefix: /usr' \
&&   echo '      version: [1.21.2]' \
&&   echo '' \
&&   echo '  specs:' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected] +fckit +trans +tesselation +fftw' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected] +fftw' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected] +pnetcdf' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - py-pip' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - shumlib@macos_clang_linux_intel_port' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  - [email protected]' \
&&   echo '  view: /opt/views/view') > /opt/spack-environment/spack.yaml

# Install the software, remove unnecessary deps
RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast && spack gc -y

# Modifications to the environment that are necessary to run
RUN cd /opt/spack-environment && \
    spack env activate --sh -d . > activate.sh

# Put output of spack find into a file
RUN cd /opt/spack-environment && \
spack env activate -d . && \
spack find 2>&1 | tee /root/spack_find.out


# Bare OS image to run the installed executables
FROM ubuntu:22.04

COPY --from=builder /opt/spack-environment /opt/spack-environment
COPY --from=builder /opt/software /opt/software

# paths.view is a symlink, so copy the parent to avoid dereferencing and duplicating it
COPY --from=builder /opt/views /opt/views

RUN { \
      echo '#!/bin/sh' \
      && echo '.' /opt/spack-environment/activate.sh \
      && echo 'exec "$@"'; \
    } > /entrypoint.sh \
&& chmod a+x /entrypoint.sh \
&& ln -s /opt/views/view /opt/view


# Set environment variables for installing tzdata
ENV DEBIAN_FRONTEND=noninteractive
ENV TZ=Etc/UTC
ENV CC=gcc
ENV CXX=g++
ENV FC=gfortran


RUN apt-get -yqq update && apt-get -yqq upgrade \
 && apt-get -yqq install bc cpp-12 g++-12 gcc-12 gfortran-12 git git-lfs make mysql-server qtbase5-dev qt5-qmake libqt5svg5-dev qt5dxcb-plugin wget ca-certificates curl file gnupg2 iproute2 locales unzip vim nano less \
 && rm -rf /var/lib/apt/lists/*

# Copy spack find output from builder
COPY --from=builder /root/spack_find.out /root/spack_find.out
# Set the GNU 12.x toolchain as the default compilers.
RUN ln -svf /usr/bin/gfortran-12 /usr/bin/gfortran && \
ln -svf /usr/bin/cpp-12 /usr/bin/cpp && \
ln -svf /usr/bin/gcc-12 /usr/bin/gcc && \
ln -svf /usr/bin/g++-12 /usr/bin/g++
# Make a non-root user:nonroot / group:nonroot for running MPI
RUN useradd -U -k /etc/skel -s /bin/bash -d /home/nonroot -m nonroot --uid 43891 && \
echo "ulimit -s unlimited" >> /home/nonroot/.bashrc && \
echo "ulimit -v unlimited" >> /home/nonroot/.bashrc && \
echo "export CC=gcc" >> /home/nonroot/.bashrc && \
echo "export CXX=g++" >> /home/nonroot/.bashrc && \
echo "export FC=gfortran" >> /home/nonroot/.bashrc && \
printf "[credential]\n    helper = cache --timeout=7200\n" >> /home/nonroot/.gitconfig && \
mkdir /home/nonroot/.pmix && \
echo "rmaps_default_mapping_policy=:oversubscribe" >> /home/nonroot/.pmix/mca-params.conf && \
chown -R nonroot:nonroot /home/nonroot/.gitconfig /home/nonroot/.pmix
# Replicate settings for root user
RUN echo "ulimit -s unlimited" >> /root/.bashrc && \
echo "ulimit -v unlimited" >> /root/.bashrc && \
echo "export CC=gcc" >> /root/.bashrc && \
echo "export CXX=g++" >> /root/.bashrc && \
echo "export FC=gfortran" >> /root/.bashrc && \
printf "[credential]\n    helper = cache --timeout=7200\n" >> /root/.gitconfig && \
mkdir /root/.pmix && \
echo "rmaps_default_mapping_policy=:oversubscribe" >> /root/.pmix/mca-params.conf
# Also set necessary environment variables for openmpi and jedi-cmake.
RUN echo "export OMPI_ALLOW_RUN_AS_ROOT=1" >> /root/.bashrc && \
echo "export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1" >> /root/.bashrc && \
echo "export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe" >> /root/.bashrc && \
echo "export jedi_cmake_ROOT=$(ls -d /opt/software/linux-ubuntu*/gcc-*/jedi-cmake-*)" >> /root/.bashrc

LABEL "app"="jedi-ci"
LABEL "mpi"="openmpi"
ENTRYPOINT [ "/entrypoint.sh" ]
CMD [ "/bin/bash" ]

Additional

Is there an override/workaround we can employ so that our automated builds/CI won't fail without a manual edit or new Dockerfile. We are not well-versed in all of the available ways to configure a spack-stack, but not above using sed to modify the Dockerfile or yaml that is created.

[climbfuji]

I checked the current spack-stack develop config, and there is no variant noavx512 for openblas anymore:

spack-stack/configs/common/packages.yaml

Line 192 in 25fc9c8

- '@0.3.24'

Can you sed-out the variant +noavx512 from configs/common/packages.yaml before running the spack stack create ctr command?

[acrosby]

Can you sed-out the variant +noavx512 from configs/common/packages.yaml before running the spack stack create ctr command?

Yes we can, thanks!