Adding pygeosx dependency install

.github/workflows/docker_build_tpls.yml

@@ -57,6 +57,10 @@ jobs:
             DOCKER_REPOSITORY: geosx/rockylinux8-gcc13-cuda12.9.1
             TPL_DOCKERFILE: docker/tpl-rockylinux-gcc-cuda-12.Dockerfile
             RUNS_ON: Runner_4core_16GB
+          - name: Rockylinux (8, gcc 13.3, cuda 12.9.1, pygeosx)
+            DOCKER_REPOSITORY: geosx/rockylinux8-gcc13-cuda12.9.1
+            TPL_DOCKERFILE: docker/tpl-rockylinux-gcc-cuda-12-pygeosx.Dockerfile
+            RUNS_ON: Runner_4core_16GB
           - name: Rockylinux (8, clang 17.0.6, cuda 12.9.1)
             DOCKER_REPOSITORY: geosx/rockylinux8-clang17-cuda12.9.1
             TPL_DOCKERFILE: docker/tpl-rockylinux-clang-cuda-12.Dockerfile

docker/rocky-spack-pygeosx.yaml

@@ -0,0 +1,158 @@
+spack:
+  config:
+    install_tree:
+      root: $spack/..
+      projections:
+        all: '{compiler.name}-{compiler.version}/{name}-{version}-{hash}'
+    misc_cache: $spack/../misc_cache
+    test_stage: $spack/../test_stage
+    build_stage::
+    - $spack/../build_stage
+
+  # Regular TPLs do not need views
+  view: false
+
+  # Include shared variants and versions
+  include:
+  - ../defaults.yaml
+  - ../versions.yaml
+
+  compilers::
+  - compiler:
+      extra_rpaths: []
+      flags:
+        cflags: -pthread
+        cxxflags: -pthread
+      modules: []
+      operating_system: rocky8
+      paths:
+        cc: /usr/bin/clang
+        cxx: /usr/bin/clang++
+        f77: /usr/bin/gfortran
+        fc: /usr/bin/gfortran
+      spec: clang@17.0.6
+      target: x86_64
+  - compiler:
+      extra_rpaths: []
+      flags:
+        cflags: -pthread
+        cxxflags: -pthread
+      modules: []
+      operating_system: rocky8
+      paths:
+        cc: /opt/rh/gcc-toolset-13/root/usr/bin/gcc
+        cxx: /opt/rh/gcc-toolset-13/root/usr/bin/g++
+        f77: /opt/rh/gcc-toolset-13/root/usr/bin/gfortran
+        fc: /opt/rh/gcc-toolset-13/root/usr/bin/gfortran
+      spec: gcc@13.3.1
+      target: x86_64
+
+  packages:
+    all:
+      target: [x86_64]
+      compiler: [gcc, clang]
+      providers:
+        blas: [netlib-lapack]
+        lapack: [netlib-lapack]
+        mpi: [openmpi]
+
+    autoconf:
+      version: [2.71]
+      buildable: false
+      externals:
+      - spec: autoconf@2.71
+        prefix: /usr
+    automake:
+      version: [1.16.5]
+      buildable: false
+      externals:
+      - spec: automake@1.16.5
+        prefix: /usr
+    cmake:
+      version: [3.28.6]
+      buildable: false
+      externals:
+      - spec: cmake@3.28.6
+        prefix: /usr/local
+    cuda:
+      buildable: False
+      externals:
+      - spec: cuda@12.9.1%gcc@13.3.1 +allow-unsupported-compilers
+        prefix: /usr/local/cuda
+      - spec: cuda@12.9.1%clang@17.0.6 +allow-unsupported-compilers
+        prefix: /usr/local/cuda
+    m4:
+      buildable: false
+      externals:
+      - spec: m4@1.4.18
+        prefix: /usr
+
+    # Spack may grab for mpi & we don't want to use them
+    mpi:
+      buildable: false
+
+    netlib-lapack:
+      buildable: false
+      externals:
+      - spec: netlib-lapack@3.8.0
+        prefix: /usr
+    netlib-blas:
+      buildable: false
+      externals:
+      - spec: netlib-blas@3.8.0
+        prefix: /usr
+    openmpi:
+      externals:
+      - spec: openmpi@4.1.1
+        prefix: /usr/lib64/openmpi
+    perl:
+      buildable: false
+      externals:
+      - spec: perl@5.26.3
+        prefix: /usr
+    pkg-config:
+      buildable: false
+      externals:
+      - spec: pkg-config@1.4.2
+        prefix: /usr
+    # python:
+    #   buildable: false
+    #   externals:
+    #   - spec: python@3.6.8
+    #     prefix: /usr
+    tar:
+      buildable: false
+      externals:
+      - spec: tar@1.34
+        prefix: /usr
+    unzip:
+      buildable: false
+      externals:
+      - spec: unzip@6.0
+        prefix: /usr
+    xz:
+      buildable: false
+      externals:
+      - spec: xz@5.2.5
+        prefix: /usr
+    # Pygeosx dependencies
+    openssl:
+      buildable: false
+      externals:
+      - spec: openssl@1.1.1k
+        prefix: /usr
+    tk:
+      buildable: false
+      externals:
+      - spec: tk@8.6.8
+        prefix: /usr
+    tcl:
+      buildable: false
+      externals:
+      - spec: tcl@8.6.8
+        prefix: /usr
+    libxcrypt:
+      buildable: false
+      externals:
+        - spec: libxcrypt@4.1.1
+          prefix: /usr

docker/rocky-spack.yaml

@@ -118,7 +118,7 @@ spack:
     python:
       buildable: false
       externals:
-      - spec: python@3.6.8
+      - spec: python@3.9.20
         prefix: /usr
     tar:
       buildable: false

docker/tpl-rockylinux-clang-cuda-12-pygeosx.Dockerfile

@@ -0,0 +1,116 @@
+ARG TMP_DIR=/tmp
+ARG SRC_DIR=$TMP_DIR/thirdPartyLibs
+ARG BLD_DIR=$TMP_DIR/build
+
+FROM nvidia/cuda:12.9.1-devel-rockylinux8 AS tpl_toolchain_intersect_geosx_toolchain
+ARG SRC_DIR
+
+ARG INSTALL_DIR
+ENV GEOSX_TPL_DIR=$INSTALL_DIR
+
+# Installing dependencies
+RUN dnf clean all && \
+    dnf -y update && \
+    dnf -y install \
+        which \
+        gcc-toolset-13 \
+        python3.9 \
+        zlib-devel \
+        tbb \
+        blas \
+        lapack \
+        openmpi \
+        openmpi-devel \
+    # Additional spack dependencies
+        python3-pip \
+        python3-tkinter \
+        unzip \
+        mpfr-devel \
+        bzip2 \
+        gnupg \
+        xz \
+        python3-virtualenv
+
+# Install clingo for Spack
+RUN python3 -m pip install --upgrade pip && \
+    python3 -m pip install clingo
+
+# Custom install script for CMake or other tools
+RUN --mount=src=.,dst=$SRC_DIR $SRC_DIR/docker/install-cmake.sh
+
+# Installing TPL's
+FROM tpl_toolchain_intersect_geosx_toolchain AS tpl_toolchain
+ARG SRC_DIR
+ARG BLD_DIR
+
+# Install additional required packages
+RUN dnf clean all && \
+    dnf -y update && \
+    dnf -y install \
+        tbb-devel \
+        bc \
+        file \
+        patch \
+        ca-certificates \
+        autoconf \
+        automake \
+        m4 \
+        git
+
+# Run uberenv
+# Have to create install directory first for uberenv
+# -k flag is to ignore SSL errors
+RUN --mount=src=.,dst=$SRC_DIR,readwrite cd ${SRC_DIR} && \
+     mkdir -p ${GEOSX_TPL_DIR} && \
+# Create symlink to openmpi include directory
+     ln -s /usr/include/openmpi-x86_64 /usr/lib64/openmpi/include && \
+# Create symlinks to blas/lapack libraries
+     ln -s /usr/lib64/libblas.so.3 /usr/lib64/libblas.so && \
+     ln -s /usr/lib64/liblapack.so.3 /usr/lib64/liblapack.so && \
+     ./scripts/uberenv/uberenv.py \
+       --spec "%gcc@13.3.1+cuda~uncrustify~openmp+pygeosxdeps cuda_arch=70 ^cuda@12.9.1+allow-unsupported-compilers ^caliper~gotcha~sampler~libunwind~libdw~papi" \
+       --spack-env-file=${SRC_DIR}/docker/rocky-spack-pygeosx.yaml \
+       --project-json=.uberenv_config.json \
+       --prefix ${GEOSX_TPL_DIR} \
+       -k && \
+# Remove host-config generated for LvArray
+     rm lvarray* && \
+# Rename and copy spack-generated host-config to root directory
+     cp *.cmake /spack-generated.cmake && \
+# Remove extraneous spack files
+     cd ${GEOSX_TPL_DIR} && \
+     rm -rf bin/ build_stage/ misc_cache/ spack/ spack_env/ .spack-db/
+
+# Extract only TPL's from the previous stage
+FROM tpl_toolchain_intersect_geosx_toolchain AS geosx_toolchain
+ARG SRC_DIR
+
+COPY --from=tpl_toolchain $GEOSX_TPL_DIR $GEOSX_TPL_DIR
+
+# Extract the generated host-config
+COPY --from=tpl_toolchain /spack-generated.cmake /
+
+# Final installation of packages and tools
+RUN dnf clean all && \
+    rm -rf /var/cache/dnf && \
+    dnf -y install dnf-plugins-core && \
+    dnf config-manager --set-enabled devel && \
+    dnf -y update && \
+    dnf -y install \
+        openssh-clients \
+        ca-certificates \
+        curl \
+        python3 \
+        texlive \
+        graphviz \
+        ninja-build \
+        git && \
+# Regenerate symlink to openmpi include directory
+    ln -s /usr/include/openmpi-x86_64 /usr/lib64/openmpi/include && \
+# Regenerate symlinks to blas/lapack libraries
+    ln -s /usr/lib64/libblas.so.3 /usr/lib64/libblas.so && \
+    ln -s /usr/lib64/liblapack.so.3 /usr/lib64/liblapack.so
+
+# Install sccache
+RUN --mount=src=.,dst=$SRC_DIR $SRC_DIR/docker/install-sccache.sh
+ENV SCCACHE=/opt/sccache/bin/sccache