Merge branch 'develop' of https://github.com/jcsda/spack-stack into f…

…eature/nrl-zlib
JCSDA · Jan 3, 2025 · 9c9ccc1 · 9c9ccc1
2 parents c6627dc + b21e3fb
commit 9c9ccc1
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diff --git a/configs/containers/docker-ubuntu-clang-mpich.yaml b/configs/containers/docker-ubuntu-clang-mpich.yaml
@@ -16,7 +16,7 @@ spack:
         f77: /usr/bin/gfortran
         fc: /usr/bin/gfortran
       flags: {}
-      operating_system: ubuntu22.04
+      operating_system: ubuntu24.04
       modules: []
       environment:
         prepend_path:
@@ -30,7 +30,7 @@ spack:
       require: '%clang'
       target: [x86_64]
       providers:
-        mpi: [mpich@4.2.1]
+        mpi: [mpich@4.2.3]
       compiler: [clang@14.0.0]
     gcc:
       buildable: false
@@ -56,9 +56,9 @@ spack:
     mpich:
       buildable: false
       externals:
-      - spec: mpich@4.2.1
-        prefix: /opt/mpich-4.2.1
-      version: [4.2.1]
+      - spec: mpich@4.2.3
+        prefix: /opt/mpich-4.2.3
+      version: [4.2.3]
     diffutils:
       buildable: false
       externals:
@@ -82,7 +82,7 @@ spack:
     mysql:
       buildable: false
       externals:
-      - spec: mysql@8.0.39
+      - spec: mysql@8.0.40
         prefix: /usr
     qt:
       buildable: false
@@ -93,9 +93,9 @@ spack:
     wget:
       buildable: false
       externals:
-      - spec: wget@1.21.2
+      - spec: wget@1.21.4
         prefix: /usr
-      version: [1.21.2]
+      version: [1.21.4]
 
   specs: []
 
@@ -117,7 +117,7 @@ spack:
     # Sets the base images for the stages where Spack builds the
     # software or where the software gets installed after being built..
     images:
-      os: ubuntu:22.04
+      os: ubuntu:24.04
       spack:
         url: https://github.com/jcsda/spack
         ref: spack-stack-dev
@@ -197,15 +197,15 @@ spack:
         # Register spack-stack extension repo
         RUN spack repo add $SPACK_ROOT/var/spack/repos/spack-stack --scope defaults
         # Set default binaries for clang-14 and GNU-12.
-        RUN ln -svf /usr/bin/gfortran-12 /usr/bin/gfortran && \
-        ln -svf /usr/bin/cpp-12 /usr/bin/cpp && \
-        ln -svf /usr/bin/gcc-12 /usr/bin/gcc && \
-        ln -svf /usr/bin/g++-12 /usr/bin/g++ && \
-        ln -svf /usr/bin/clang-14 /usr/bin/clang && \
-        ln -svf /usr/bin/clang++-14 /usr/bin/clang++ && \
-        ln -svf /usr/bin/clang-cpp-14 /usr/bin/clang-cpp
+        RUN rm /usr/bin/cpp && ln -s /usr/bin/cpp-12 /usr/bin/cpp && \
+        update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-12 100 && \
+        update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-12 100 && \
+        update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-12 100 && \
+        update-alternatives --install /usr/bin/clang clang /usr/bin/clang-14 100 && \
+        update-alternatives --install /usr/bin/clang++ clang++ /usr/bin/clang++-14 100 && \
+        update-alternatives --install /usr/bin/clang-cpp clang-cpp /usr/bin/clang-cpp-14 100
         # Build mpich outside of spack-stack
-        ENV MPICH_VERSION=4.2.1
+        ENV MPICH_VERSION=4.2.3
         ENV CC=clang
         ENV CXX=clang++
         ENV FC=gfortran
@@ -231,23 +231,23 @@ spack:
         # Set environment variables for installing tzdata
         ENV DEBIAN_FRONTEND=noninteractive
         ENV TZ=Etc/UTC
-        ENV MPICH_VERSION=4.2.1
+        ENV MPICH_VERSION=4.2.3
         ENV PATH=/opt/mpich-${MPICH_VERSION}/bin:${PATH}
         ENV CPATH=/opt/mpich-${MPICH_VERSION}/include:${CPATH}
         ENV LD_LIBRARY_PATH=/opt/mpich-${MPICH_VERSION}/lib:${LD_LIBRARY_PATH}
       final: |
         # Copy spack find output from builder
         COPY --from=builder /root/spack_find.out /root/spack_find.out
-        ENV MPICH_VERSION=4.2.1
+        ENV MPICH_VERSION=4.2.3
         # Set the GNU 12.x toolchain as the default compilers.
         # Set default binaries for clang-14 and GNU-12.
-        RUN ln -svf /usr/bin/gfortran-12 /usr/bin/gfortran && \
-        ln -svf /usr/bin/cpp-12 /usr/bin/cpp && \
-        ln -svf /usr/bin/gcc-12 /usr/bin/gcc && \
-        ln -svf /usr/bin/g++-12 /usr/bin/g++ && \
-        ln -svf /usr/bin/clang-14 /usr/bin/clang && \
-        ln -svf /usr/bin/clang++-14 /usr/bin/clang++ && \
-        ln -svf /usr/bin/clang-cpp-14 /usr/bin/clang-cpp
+        RUN rm /usr/bin/cpp && ln -s /usr/bin/cpp-12 /usr/bin/cpp && \
+        update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-12 100 && \
+        update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-12 100 && \
+        update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-12 100 && \
+        update-alternatives --install /usr/bin/clang clang /usr/bin/clang-14 100 && \
+        update-alternatives --install /usr/bin/clang++ clang++ /usr/bin/clang++-14 100 && \
+        update-alternatives --install /usr/bin/clang-cpp clang-cpp /usr/bin/clang-cpp-14 100
         # Copy mpich-${MPICH_VERSION} installation from builder
         COPY --from=builder /opt/mpich-${MPICH_VERSION} /opt/mpich-${MPICH_VERSION}
         # Make a non-root user:nonroot / group:nonroot for running MPI

diff --git a/configs/containers/docker-ubuntu-gcc-openmpi.yaml b/configs/containers/docker-ubuntu-gcc-openmpi.yaml
@@ -9,14 +9,14 @@ spack:
 
   compilers:
   - compiler:
-      spec: gcc@12.3.0
+      spec: gcc@13.3.0
       paths:
-        cc: /usr/bin/gcc-12
-        cxx: /usr/bin/g++-12
-        f77: /usr/bin/gfortran-12
-        fc: /usr/bin/gfortran-12
+        cc: /usr/bin/gcc-13
+        cxx: /usr/bin/g++-13
+        f77: /usr/bin/gfortran-13
+        fc: /usr/bin/gfortran-13
       flags: {}
-      operating_system: ubuntu22.04
+      operating_system: ubuntu24.04
       modules: []
       environment: {}
       extra_rpaths: []
@@ -29,16 +29,16 @@ spack:
       target: [x86_64]
       providers:
         mpi: [openmpi@5.0.5]
-      compiler: [gcc@12.3.0]
+      compiler: [gcc@13.3.0]
     gcc:
       buildable: false
       externals:
-      - spec: gcc@12.3.0
+      - spec: gcc@13.3.0
         prefix: /usr
     gcc-runtime:
       buildable: false
       externals:
-      - spec: gcc-runtime@12.3.0
+      - spec: gcc-runtime@13.3.0
         prefix: /usr
     diffutils:
       buildable: false
@@ -55,15 +55,15 @@ spack:
       externals:
       - spec: git-lfs@3.0.2
         prefix: /usr
-    grep:
+    llvm:
       buildable: false
       externals:
-      - spec: grep@3.7
+      - spec: llvm@14.0.6
         prefix: /usr
     mysql:
       buildable: false
       externals:
-      - spec: mysql@8.0.39
+      - spec: mysql@8.0.40
         prefix: /usr
     qt:
       buildable: false
@@ -76,7 +76,6 @@ spack:
       externals:
       - spec: wget@1.21.2
         prefix: /usr
-      version: [1.21.2]
 
   specs: []
 
@@ -98,7 +97,7 @@ spack:
     # Sets the base images for the stages where Spack builds the
     # software or where the software gets installed after being built..
     images:
-      os: ubuntu:22.04
+      os: ubuntu:24.04
       spack:
         url: https://github.com/jcsda/spack
         ref: spack-stack-dev
@@ -111,12 +110,13 @@ spack:
     os_packages:
       build:
       - bc
-      - cpp-12
-      - g++-12
-      - gcc-12
-      - gfortran-12
+      - cpp-13
+      - g++-13
+      - gcc-13
+      - gfortran-13
       - git
       - git-lfs
+      - llvm-14
       - make
       - mysql-server
       - qtbase5-dev
@@ -127,12 +127,13 @@ spack:
 
       final:
       - bc
-      - cpp-12
-      - g++-12
-      - gcc-12
-      - gfortran-12
+      - cpp-13
+      - g++-13
+      - gcc-13
+      - gfortran-13
       - git
       - git-lfs
+      - llvm-14
       - make
       - mysql-server
       - qtbase5-dev
@@ -157,12 +158,9 @@ spack:
         # Copy the spack-stack extension repo into the spack code
         COPY spack-ext-SPACK_STACK_HASH/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++
+        RUN spack repo add $SPACK_ROOT/var/spack/repos/spack-stack --scope defaults && \
+        # Needed by py-llvmlite
+        update-alternatives --install /usr/bin/llvm-config llvm-config /usr/bin/llvm-config-14 100
       pre_final: |
         # Set environment variables for installing tzdata
         ENV DEBIAN_FRONTEND=noninteractive
@@ -178,18 +176,15 @@ spack:
       final: |
         # 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 && \
+        # Needed by py-llvmlite
+        update-alternatives --install /usr/bin/llvm-config llvm-config /usr/bin/llvm-config-14 100 && \
         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 && \