Dockerfile-spack202401-rocky8-gcc13.2

# Build stage with Spack pre-installed and ready to be used
#FROM spack/ubuntu-jammy:latest as builder
FROM spack/rockylinux8:latest as builder

#RUN dnf install 'dnf-command(config-manager)' && dnf --assumeyes config-manager -y --set-enabled powertools && yum -y install texinfo 
RUN sed -i '60i \    depends_on("texinfo")' /opt/spack/var/spack/repos/builtin/packages/bison/package.py && cat /opt/spack/var/spack/repos/builtin/packages/bison/package.py

RUN mkdir -p /opt/spack/var/spack/repos/custom/packages/fre-nctools && \ 
set -o noclobber \
&&  (echo '# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other'\
&&   echo '# Spack Project Developers. See the top-level COPYRIGHT file for details.'\
&&   echo '# SPDX-License-Identifier: (Apache-2.0 OR MIT)'\
&&   echo 'from spack import *'\
&&   echo 'class FreNctools(AutotoolsPackage):'\
&&   echo '    """FRE-NCtools is a collection of tools to help with the creation and manipulation of netCDF'\
&&   echo '       files used for or written by the climate models developed at the Geophysical Fluid Dynaics'\
&&   echo '       Laboratory (GFDL)."""'\
&&   echo '    homepage = "https://github.com/NOAA-GFDL/FRE-NCtools"'\
&&   echo '    git = "https://github.com/NOAA-GFDL/FRE-NCtools.git"'\
&&   echo '    maintainers = ["underwoo", "ceblanton"]'\
&&   echo '    version("2022.02", tag="2022.02")'\
&&   echo '    version("2023.01", tag="2023.01")'\
&&   echo '    version("2023.01.01", tag="2023.01.01")'\
&&   echo '    version("2023.01.02", tag="2023.01.02")'\
&&   echo '    version("2024.01", tag="2024.01")'\
&&   echo '    version("2024.02", tag="2024.02")'\
&&   echo '    variant("quad-precision", default=False, description="Enable higher (quad) precision")'\
&&   echo '    variant("mpi", default=True, description="Enable MPI support")'\
&&   echo '    depends_on("autoconf", type="build")'\
&&   echo '    depends_on("automake", type="build")'\
&&   echo '    depends_on("libtool", type="build")'\
&&   echo '    depends_on("m4", type="build")'\
&&   echo '    depends_on("netcdf-c~mpi", when="~mpi")'\
&&   echo '    depends_on("netcdf-c+mpi", when="+mpi")'\
&&   echo '    depends_on("netcdf-fortran")'\
&&   echo '    depends_on("mpi", when="+mpi")'\
&&   echo '    def configure_args(self):'\
&&   echo '        args = self.enable_or_disable("quad-precision")'\
&&   echo '        args += self.with_or_without("mpi")'\
&&   echo '        return args' ) > /opt/spack/var/spack/repos/custom/packages/fre-nctools/package.py
RUN mkdir -p /opt/spack/var/spack/repos/custom/packages/fre-nctools && \
set -o noclobber \
&&   (echo 'repo: '\
&&   echo '  namespace: custom' ) > /opt/spack/var/spack/repos/custom/repo.yaml

## Install gcc13.2.0


# 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 '  definitions:' \
&&   echo '  - packages_builtin:' \
&&   echo '    - gcc@13.2.0' \
&&   echo '    - autoconf@2.69' \
&&   echo '    - automake@1.16.5' \
&&   echo '    - bacio@2.4.1' \
&&   echo '    - bats@1.10.0' \
&&   echo '    - cdo@2.2.2' \
&&   echo '    - cloc@1.96.1' \
&&   echo '    - cmake' \
&&   echo '    - esmf@8.5.0' \
&&   echo '    - g2@3.4.8' \
&&   echo '    - g2tmpl@1.10.2' \
&&   echo '    - gdal@3.7.3' \
&&   echo '    - geos@3.12.0' \
&&   echo '    - gh@2.32.1' \
&&   echo '    - git@2.42.0' \
&&   echo '    - git-lfs@3.3.0' \
&&   echo '    - gnuplot@5.4.3' \
&&   echo '    - grace@5.1.25' \
&&   echo '    - gsl@2.7.1' \
&&   echo '    - hdf5@1.14.3' \
&&   echo '    - ip@3.3.3' \
&&   echo '    - jasper@3.0.3' \
&&   echo '    - libgeotiff@1.7.1' \
&&   echo '    - libpng@1.6.39' \
&&   echo '    - magics@4.9.3' \
&&   echo '    - mpich@4.1.2' \
&&   echo '    - nasm@2.15.05' \
&&   echo '    - nccmp@1.9.1.0' \
&&   echo '    - nco@5.1.6' \
&&   echo '    - ncview@2.1.9' \
&&   echo '    - netcdf-c@4.9.2' \
&&   echo '    - netcdf-fortran@4.6.1' \
&&   echo '    - octave@8.2.0' \
&&   echo '    - openjdk@11.0.20.1_1' \
&&   echo '    - parallel@20220522' \
&&   echo '    - pigz@2.7' \
&&   echo '    - proj@9.2.1' \
&&   echo '    - sp@2.3.3' \
&&   echo '    - tig@2.5.8' \
&&   echo '    - udunits@2.2.28' \
&&   echo '    - w3emc@2.11.0' \
&&   echo '    - w3nco@2.4.1' \
&&   echo '    - zlib' \
&&   echo '    - zlib-ng@2.1.4' \
&&   echo '  - packages_custom:' \
&&   echo '    - fre-nctools@2023.01.02' \
&&   echo '  packages:' \
&&   echo '    cairo:' \
&&   echo '      variants: +X' \
&&   echo '    gdal:' \
&&   echo '      variants: +netcdf' \
&&   echo '    gnuplot:' \
&&   echo '      variants: +X' \
&&   echo '    hdf5:' \
&&   echo '      variants: +fortran+hl+szip' \
&&   echo '    libtiff:' \
&&   echo '      variants: +zlib+jpeg+lzma' \
&&   echo '    netcdf-c:' \
&&   echo '      variants: +dap' \
&&   echo '    pango:' \
&&   echo '      variants: +X' \
&&   echo '    all:' \
&&   echo '      target: [x86_64]' \
&&   echo '      providers:' \
&&   echo '        mpi: [mpich]' \
&&   echo '        zlib-api: [zlib-ng+compat, zlib]' \
&&   echo '      compiler: [gcc@13.2.0]' \
&&   echo '  specs:' \
&&   echo '  - gcc@13.2.0 ' \
&&   echo '  - matrix:' \
&&   echo '    - [$packages_builtin, $packages_custom]' \
&&   echo '  concretizer:' \
&&   echo '    unify: true' \
&&   echo '  config:' \
#&&   echo '    install_missing_compilers: true' \
&&   echo '    install_tree: /opt/software' \
&&   echo '  repos:' \
&&   echo '  - $spack/var/spack/repos/custom' \
&&   echo '  - $spack/var/spack/repos/builtin' \
&&   echo '  view: /opt/views/view') > /opt/spack-environment/spack.yaml
# Install gcc13
RUN . /opt/spack/share/spack/setup-env.sh && \   
   spack install gcc@13.2.0
RUN . /opt/spack/share/spack/setup-env.sh && \
   spack load gcc@13.2.0 && \
   spack compiler add && \
   spack install gcc@13.2.0%gcc@13.2.0
RUN . /opt/spack/share/spack/setup-env.sh && \
   spack compiler remove gcc@13.2.0 &&\
   spack compiler remove gcc@8.5.0
## New spack.yaml hack
RUN mkdir -p /opt/spack-environment && \
rm -rf /opt/spack-environment/spack.yaml && \
set -o noclobber \
&&  (echo spack: \
&&   echo '  definitions:' \
&&   echo '  - packages_builtin:' \
&&   echo '    - gcc@13.2.0' \
&&   echo '    - autoconf@2.69' \
&&   echo '    - automake@1.16.5' \
&&   echo '    - bacio@2.4.1' \
&&   echo '    - bats@1.10.0' \
&&   echo '    - cdo@2.2.2' \
&&   echo '    - cloc@1.96.1' \
&&   echo '    - cmake' \
&&   echo '    - esmf@8.5.0' \
&&   echo '    - g2@3.4.8' \
&&   echo '    - g2tmpl@1.10.2' \
&&   echo '    - gdal@3.7.3' \
&&   echo '    - geos@3.12.0' \
&&   echo '    - gh@2.32.1' \
&&   echo '    - git@2.45.1' \
&&   echo '    - git-lfs@3.3.0' \
&&   echo '    - gnuplot@5.4.3' \
&&   echo '    - grace@5.1.25' \
&&   echo '    - gsl@2.7.1' \
&&   echo '    - hdf5@1.14.3' \
&&   echo '    - ip@3.3.3' \
&&   echo '    - jasper@3.0.3' \
&&   echo '    - libgeotiff@1.7.1' \
&&   echo '    - libpng@1.6.39' \
&&   echo '    - magics@4.9.3' \
&&   echo '    - mpich@4.1.2' \
&&   echo '    - nasm@2.15.05' \
&&   echo '    - nccmp@1.9.1.0' \
&&   echo '    - nco@5.1.6' \
&&   echo '    - ncview@2.1.9' \
&&   echo '    - netcdf-c@4.9.2' \
&&   echo '    - netcdf-fortran@4.6.1' \
&&   echo '    - octave@8.2.0' \
&&   echo '    - openjdk@11.0.20.1_1' \
&&   echo '    - parallel@20220522' \
&&   echo '    - pigz@2.7' \
&&   echo '    - proj@9.2.1' \
&&   echo '    - sp@2.3.3' \
&&   echo '    - tig@2.5.8' \
&&   echo '    - udunits@2.2.28' \
&&   echo '    - w3emc@2.11.0' \
&&   echo '    - w3nco@2.4.1' \
&&   echo '    - zlib' \
&&   echo '    - zlib-ng@2.1.4' \
&&   echo '  - packages_custom:' \
&&   echo '    - fre-nctools@2023.01.02' \
&&   echo '  packages:' \
&&   echo '    cairo:' \
&&   echo '      variants: +X' \
&&   echo '    gdal:' \
&&   echo '      variants: +netcdf' \
&&   echo '    gnuplot:' \
&&   echo '      variants: +X' \
&&   echo '    hdf5:' \
&&   echo '      variants: +fortran+hl+szip' \
&&   echo '    libtiff:' \
&&   echo '      variants: +zlib+jpeg+lzma' \
&&   echo '    netcdf-c:' \
&&   echo '      variants: +dap' \
&&   echo '    pango:' \
&&   echo '      variants: +X' \
&&   echo '    all:' \
&&   echo '      target: [x86_64]' \
&&   echo '      providers:' \
&&   echo '        mpi: [mpich]' \
&&   echo '        zlib-api: [zlib-ng+compat, zlib]' \
&&   echo '      compiler: [gcc@13.2.0]' \
&&   echo '  specs:' \
&&   echo '  - gcc@13.2.0 ' \
&&   echo '  - matrix:' \
&&   echo '    - [$packages_builtin, $packages_custom]' \
&&   echo '  concretizer:' \
&&   echo '    unify: true' \
&&   echo '  config:' \
#&&   echo '    install_missing_compilers: true' \
&&   echo '    install_tree: /opt/software' \
&&   echo '  repos:' \
&&   echo '  - $spack/var/spack/repos/custom' \
&&   echo '  - $spack/var/spack/repos/builtin' \
&&   echo '  view: /opt/views/view') > /opt/spack-environment/spack.yaml
# Install the software, remove unnecessary deps
RUN . /opt/spack/share/spack/setup-env.sh && cd /opt/spack-environment && spack load gcc@13.2.0%gcc@13.2.0 && spack compiler add && spack --verbose env activate . && spack --verbose install --fail-fast && spack gc -y
#RUN . /opt/spack/share/spack/setup-env.sh && cd /opt/spack-environment && spack --verbose env activate . && spack install --fail-fast && spack gc -y

# Strip all the binaries
RUN find -L /opt/views/view/* -type f -exec readlink -f '{}' \; | \
    xargs file -i | \
    grep 'charset=binary' | \
    grep 'x-executable\|x-archive\|x-sharedlib' | \
    awk -F: '{print $1}' | xargs strip

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


# Bare OS image to run the installed executables
#FROM rockylinux:8.9
#
#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
#
#
ENTRYPOINT [ "/entrypoint.sh" ]
CMD [ "/bin/bash" ]