Try pangea2 spec

.github/workflows/docker_build_tpls.yml

@@ -20,11 +20,11 @@ jobs:
 
       matrix:
         include:
-          #- name: Pangea 2 (centos 7.6, gcc 8.3.0, open-mpi 2.1.5, mkl 2019.3)
-          #  DOCKER_REPOSITORY: geosx/pangea2-gcc8.3.0-openmpi2.1.5-mkl2019.3
-          #  DOCKERFILE: docker/TotalEnergies/Dockerfile
-          #  DOCKER_ROOT_IMAGE: totogaz/pangea2-gcc8.3.0-openmpi2.1.5-mkl2019.3-no-geosx:0.0.1
-          #  INSTALL_DIR_ROOT: /workrd/SCR/GEOSX/install/gcc8
+          - name: Pangea 2 (centos 7.6, gcc 8.3.0, open-mpi 2.1.5, mkl 2019.3)
+            DOCKER_REPOSITORY: gseosx/pangea2-gcc8.3.0-openmpi2.1.5-mkl2019.3
+            DOCKERFILE: docker/TotalEnergies/Dockerfile
+            DOCKER_ROOT_IMAGE: totogaz/pangea2-gcc8.3.0-openmpi2.1.5-mkl2019.3-no-geosx:0.0.1
+            INSTALL_DIR_ROOT: /workrd/SCR/GEOSX/install/gcc8
           #- name: Pecan GPU (centos 7.7, gcc 8.2.0, open-mpi 4.0.1, mkl 2019.5, cuda 11.5.119)
           #  DOCKER_REPOSITORY: geosx/pecan-gpu-gcc8.2.0-openmpi4.0.1-mkl2019.5-cuda11.5.119
           #  DOCKERFILE: docker/TotalEnergies/Dockerfile

docker/TotalEnergies/Dockerfile

@@ -15,7 +15,18 @@ RUN yum install -y \
     ca-certificates \
     curl \
     python3 \
-    zlib-devel
+    zlib-devel \
+# Additional spack dependencies
+    python3-pip \
+    pkgconfig \
+    # xz \
+    unzip \
+    bzip2 \
+    && pip3 install virtualenv
+
+# Install clingo for Spack
+RUN python3 -m pip install --upgrade pip && \
+    python3 -m pip install clingo
 
 RUN --mount=src=.,dst=$SRC_DIR $SRC_DIR/docker/install-cmake.sh
 
@@ -29,19 +40,50 @@ RUN yum install -y \
     file \
     bison \
     flex \
-    patch
+    patch \
+# `ca-certificates`  needed by `git` to download GEOS repo.
+    ca-certificates \
+    autoconf \
+    automake \
+    git
 
-ARG HOST_CONFIG
+# Clone branch with spack configs
+# TODO decide landing place of spack recipes
+RUN git clone --branch feature/han12/wip_docker_spack_recipes \
+              --depth 1 \
+          --single-branch \
+          https://github.com/GEOS-DEV/GEOS.git
 
-RUN --mount=src=.,dst=$SRC_DIR $SRC_DIR/docker/configure-tpl.sh
-WORKDIR $BLD_DIR
-RUN --mount=src=.,dst=$SRC_DIR make
+# Run uberenv
+# Have to create install directory first for uberenv
+# -k flag is to ignore SSL errors
+# Remove generated host-config for lvarray
+RUN --mount=src=.,dst=$SRC_DIR cd GEOS && \
+     mkdir -p ${GEOSX_TPL_DIR} && \
+     git submodule init scripts/uberenv && \
+     git submodule update && \
+     ./scripts/uberenv/uberenv.py \
+       --spec "%[email protected]~pygeosx" \
+       --spack-env-file=${SRC_DIR}/docker/total-spack.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/
 
 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 /
+
 RUN yum -y install \
     openssh-clients \
     ca-certificates \

docker/total-spack.yaml

@@ -0,0 +1,173 @@
+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
+
+  compilers::
+  # Pangea 2 compiler
+  - compiler:
+      environment: {}
+      extra_rpaths: []
+      flags:
+        cflags: -pthread
+        cxxflags: -pthread
+      modules: []
+      operating_system: centos7
+      paths:
+        cc: /data_local/sw/gcc/RHEL7/8.3.0/bin/gcc
+        cxx: /data_local/sw/gcc/RHEL7/8.3.0/bin/g++
+        f77: /data_local/sw/gcc/RHEL7/8.3.0/bin/gfortran
+        fc: /data_local/sw/gcc/RHEL7/8.3.0/bin/gfortran
+      spec: [email protected]
+      target: x86_64
+
+  packages:
+    all:
+      target: [x86_64]
+      compiler: [gcc, clang]
+      providers:
+        blas: [intel-mkl]
+        lapack: [intel-mkl]
+        mpi: [openmpi]
+
+
+    blt:
+      require: "@git.5a792c1775e7a7628d84dcde31652a689f1df7b5=develop"
+
+    hypre:
+      require: "@git.d475cdfc63ac59ea9a554493a06e4033b8d6fade"
+
+    chai:
+      require: "@git.6fe3470ad020303530af2f3dbbfe18826bd3319b=develop"
+
+    umpire:
+      require: "@git.4bd9b2ded81d3216b3f62e2aad62d0e34fe2c256=develop"
+
+    raja:
+      require: "@git.e330b2560747d5417cd7bd265fab3fb91d32ecbd=develop"
+
+    camp:
+      require: "@git.ac34c25b722a06b138bc045d38bfa5e8fa3ec9c5=main"
+
+    uncrustify:
+      require: "@git.401a4098bce9dcc47e024987403f2d59d9ba7bd2"
+
+    superlu-dist:
+      require: "@git.0f6efc377df2440c235452d13d28d2c717f832a1"
+
+    autoconf:
+      version: [2.71]
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr
+    automake:
+      version: [1.16.5]
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr
+    bison:
+      version: [3.8.2]
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr
+    cmake:
+      version: [3.23.1]
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr/local
+    cuda:
+      buildable: False
+      externals:
+      - spec: [email protected] +allow-unsupported-compilers
+        prefix: /usr/local/cuda
+    flex:
+      version: [2.6.4]
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr
+
+    # Lock down blas, lapack implementation
+    intel-mkl:
+      buildable: False
+      externals:
+        # LC
+        #- spec: [email protected] threads=openmp
+        #  prefix: /usr/tce/packages/mkl/mkl-2020.0/
+
+        # Pangea 2
+        - spec: [email protected] threads=openmp
+          prefix: /opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/
+    blas:
+      buildable: false
+
+    lapack:
+      buildable: false
+
+    m4:
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr
+
+    # Spack may grab for mpi & we don't want to use them
+    mpi:
+      buildable: false
+    #mpfr:
+    #  buildable: false
+    #  externals:
+    #  - spec: [email protected]
+    #    prefix: /usr
+
+    openmpi:
+      externals:
+      - spec: [email protected]%[email protected]
+        prefix: /data_local/sw/OpenMPI/RHEL7/2.1.5/gcc/8.3.0
+    perl:
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr
+    pkg-config:
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr
+    py-sphinx:
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr
+    python:
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr
+    tar:
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr
+    unzip:
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr
+    xz:
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr