minor cleanup

	modified:   ubuntu-clang/Dockerfile
	modified:   ubuntu-clang/spack.yaml
	modified:   ubuntu-gcc/Dockerfile

ubuntu-clang/Dockerfile

@@ -19,56 +19,56 @@ RUN apt-get -yqq install clang-15 libc++-15-dev libc++abi-15-dev libomp-15-dev
 # What we want to install and how we want to install it
 # is specified in a manifest file (spack.yaml)
 RUN mkdir /opt/spack-environment \
-&& (echo "spack:" \
-&& echo " compilers:" \
-&& echo " - compiler:" \
-&& echo " spec: [email protected]" \
-&& echo " paths:" \
-&& echo " cc: /usr/bin/clang-15" \
-&& echo " cxx: /usr/bin/clang++-15" \
-&& echo " f77:" \
-&& echo " fc:" \
-&& echo " flags:" \
-&& echo " cxxflags: -stdlib=libc++" \
-&& echo " operating_system: ubuntu22.04" \
-&& echo " target: x86_64" \
-&& echo " modules: []" \
-&& echo " environment: {}" \
-&& echo " extra_rpaths:" \
-&& echo "  - /lib/gcc/x86_64-linux-gnu/11/libgfortran.so" \
-&& echo " packages:" \
-&& echo " all:" \
-&& echo " target:" \
-&& echo " - x86_64_v2" \
-&& echo " compiler:" \
-&& echo " - clang" \
-&& echo " providers:" \
-&& echo " mpi:" \
-&& echo " - mpich" \
-&& echo " blas:" \
-&& echo " - openblas" \
-&& echo " lapack:" \
-&& echo " - openblas" \
-&& echo " specs:" \
-&& echo " - mpich~fortran device=ch4 netmod=ofi" \
-&& echo " - openblas@develop~fortran" \
-&& echo " - petsc@main~fortran+debug" \
-&& echo " - hdf5@1.12.2+hl+mpi~fortran" \
-&& echo " - fftw+mpi+openmp" \
-&& echo " - cmake" \
-&& echo " - gsl" \
-&& echo " - python+pythoncmd" \
-&& echo " - py-pyparsing" \
-&& echo " - py-numpy" \
-&& echo " - py-mpi4py" \
-&& echo " - py-h5py+mpi" \
-&& echo " - py-pytest" \
-&& echo " - ninja" \
-&& echo " concretizer:" \
-&& echo " unify: true" \
-&& echo " view: /opt/view" \
-&& echo " config:" \
-&& echo " install_tree: /opt/software") > /opt/spack-environment/spack.yaml
+&& (echo spack: \
+&& echo ' compilers:' \
+&& echo ' - compiler:' \
+&& echo ' spec: [email protected]' \
+&& echo ' paths:' \
+&& echo ' cc: /usr/bin/clang-15' \
+&& echo ' cxx: /usr/bin/clang++-15' \
+&& echo ' f77: null' \
+&& echo ' fc: null' \
+&& echo ' flags:' \
+&& echo ' cxxflags: -stdlib=libc++' \
+&& echo ' operating_system: ubuntu22.04' \
+&& echo ' modules: []' \
+&& echo ' environment: {}' \
+&& echo ' extra_rpaths: []' \
+&& echo ' packages:' \
+&& echo ' all:' \
+&& echo ' target:' \
+&& echo '  - x86_64_v2' \
+&& echo ' compiler:' \
+&& echo ' - clang' \
+&& echo ' providers:' \
+&& echo '  # Cannot use intel-oneapi-mpi with clang' \
+&& echo '  # for some reason, so use mpich for now.' \
+&& echo ' mpi:' \
+&& echo ' - mpich' \
+&& echo ' blas:' \
+&& echo ' - openblas' \
+&& echo ' lapack:' \
+&& echo ' - openblas' \
+&& echo ' specs:' \
+&& echo ' - mpich~fortran device=ch4 netmod=ofi' \
+&& echo ' - openblas@develop~fortran' \
+&& echo ' - petsc@main~fortran+debug' \
+&& echo ' - hdf5+hl+mpi~fortran' \
+&& echo ' - fftw+mpi+openmp' \
+&& echo ' - cmake' \
+&& echo ' - gsl' \
+&& echo ' - python+pythoncmd' \
+&& echo ' - py-pyparsing' \
+&& echo ' - py-numpy' \
+&& echo ' - py-mpi4py' \
+&& echo ' - py-h5py+mpi' \
+&& echo ' - py-pytest' \
+&& echo ' - ninja' \
+&& echo ' concretizer:' \
+&& echo ' unify: true' \
+&& echo ' view: /opt/views/view' \
+&& echo ' config:' \
+&& echo ' install_tree: /opt/software') > /opt/spack-environment/spack.yaml
 
 # Find externals
 RUN spack external find tar
@@ -80,24 +80,33 @@ RUN spack external find gettext
 RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast && spack gc -y
 
 # Strip all the binaries
-RUN find -L /opt/view/* -type f -exec readlink -f '{}' \; | \
+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 -s
+ awk -F: '{print $1}' | xargs strip
 
 # Modifications to the environment that are necessary to run
 RUN cd /opt/spack-environment && \
- spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh
+ spack env activate --sh -d . > activate.sh
+
 
 # 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
-COPY --from=builder /opt/._view /opt/._view
-COPY --from=builder /opt/view /opt/view
-COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh
+
+# 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
 
 # Noninteractive install!
 ENV DEBIAN_FRONTEND=noninteractive \
@@ -116,6 +125,6 @@ RUN apt-get -yqq install clang-15 libc++-15-dev libc++abi-15-dev libomp-15-dev
 RUN apt-get -yqq update && apt-get -yqq upgrade \
  && apt-get -yqq install build-essential bash git tar wget \
  && rm -rf /var/lib/apt/lists/*
-ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l", "-c", "$*", "--" ]
+ENTRYPOINT [ "/entrypoint.sh" ]
 CMD [ "/bin/bash" ]
 

ubuntu-clang/spack.yaml

@@ -14,11 +14,9 @@ spack:
  flags:
  cxxflags: -stdlib=libc++
  operating_system: ubuntu22.04
- target: x86_64
  modules: []
  environment: {}
- extra_rpaths:
- - /lib/gcc/x86_64-linux-gnu/11/libgfortran.so
+ extra_rpaths: []
  packages:
  all:
  target:
@@ -38,7 +36,7 @@ spack:
  - mpich~fortran device=ch4 netmod=ofi
  - openblas@develop~fortran 
  - petsc@main~fortran+debug
- - hdf5@1.12.2+hl+mpi~fortran
+ - hdf5+hl+mpi~fortran
  - fftw+mpi+openmp
  - cmake 
  - gsl

ubuntu-gcc/Dockerfile

@@ -12,36 +12,36 @@ RUN sed -i 's/platform.release()/"5.4.100"/g' /opt/spack/var/spack/repos/builtin
 # What we want to install and how we want to install it
 # is specified in a manifest file (spack.yaml)
 RUN mkdir /opt/spack-environment \
-&& (echo "spack:" \
-&& echo " packages:" \
-&& echo " all:" \
-&& echo " target:" \
-&& echo " - x86_64_v2" \
-&& echo " providers:" \
-&& echo " mpi:" \
-&& echo " - mpich" \
-&& echo " blas:" \
-&& echo " - openblas" \
-&& echo " lapack:" \
-&& echo " - openblas" \
-&& echo " specs:" \
-&& echo " - [email protected]+hl+mpi~fortran" \
-&& echo " - mpich~fortran device=ch4 netmod=ofi" \
-&& echo " - petsc@main~fortran+debug" \
-&& echo " - fftw+mpi+openmp" \
-&& echo " - gsl" \
-&& echo " - python+pythoncmd" \
-&& echo " - py-pyparsing" \
-&& echo " - py-numpy" \
-&& echo " - py-mpi4py" \
-&& echo " - py-h5py+mpi" \
-&& echo " - py-pytest" \
-&& echo " - ninja" \
-&& echo " concretizer:" \
-&& echo " unify: true" \
-&& echo " view: /opt/view" \
-&& echo " config:" \
-&& echo " install_tree: /opt/software") > /opt/spack-environment/spack.yaml
+&& (echo spack: \
+&& echo ' packages:' \
+&& echo ' all:' \
+&& echo ' target:' \
+&& echo ' - x86_64_v2' \
+&& echo ' providers:' \
+&& echo ' mpi:' \
+&& echo ' - mpich' \
+&& echo ' blas:' \
+&& echo ' - openblas' \
+&& echo ' lapack:' \
+&& echo ' - openblas' \
+&& echo ' specs:' \
+&& echo ' - [email protected]+hl+mpi~fortran' \
+&& echo ' - mpich@develop~fortran device=ch4 netmod=ofi' \
+&& echo ' - petsc@main~fortran+debug' \
+&& echo ' - fftw+mpi+openmp' \
+&& echo ' - gsl' \
+&& echo ' - python+pythoncmd' \
+&& echo ' - py-pyparsing' \
+&& echo ' - py-numpy' \
+&& echo ' - py-mpi4py' \
+&& echo ' - py-h5py+mpi' \
+&& echo ' - py-pytest' \
+&& echo ' - ninja' \
+&& echo ' concretizer:' \
+&& echo ' unify: true' \
+&& echo ' view: /opt/views/view' \
+&& echo ' config:' \
+&& echo ' install_tree: /opt/software') > /opt/spack-environment/spack.yaml
 
 # Find externals
 RUN spack external find tar
@@ -53,24 +53,33 @@ RUN spack external find gettext
 RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast && spack gc -y
 
 # Strip all the binaries
-RUN find -L /opt/view/* -type f -exec readlink -f '{}' \; | \
+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 -s
+ awk -F: '{print $1}' | xargs strip
 
 # Modifications to the environment that are necessary to run
 RUN cd /opt/spack-environment && \
- spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh
+ spack env activate --sh -d . > activate.sh
+
 
 # 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
-COPY --from=builder /opt/._view /opt/._view
-COPY --from=builder /opt/view /opt/view
-COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh
+
+# 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
 
 # Noninteractive install!
 ENV DEBIAN_FRONTEND=noninteractive \
@@ -82,6 +91,6 @@ ENV DEBIAN_FRONTEND=noninteractive \
 RUN apt-get -yqq update && apt-get -yqq upgrade \
  && apt-get -yqq install build-essential bash git cmake wget gfortran tar \
  && rm -rf /var/lib/apt/lists/*
-ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l", "-c", "$*", "--" ]
+ENTRYPOINT [ "/entrypoint.sh" ]
 CMD [ "/bin/bash" ]