Pygeosx docker build test

.github/workflows/docker_build_tpls.yml

@@ -19,68 +19,72 @@ jobs:
 
       matrix:
         include:
-          - name: Ubuntu (20.04, gcc 9.4.0, open-mpi 4.0.3)
-            DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc9
-            TPL_DOCKERFILE: docker/tpl-ubuntu-gcc.Dockerfile
-            DOCKER_ROOT_IMAGE: ubuntu:20.04
-            DOCKER_COMPILER_BUILD_ARG: "--build-arg GCC_MAJOR_VERSION=9"
-            RUNS_ON: ubuntu-latest
-          - name: Ubuntu (20.04, gcc 10.5.0, open-mpi 4.0.3) - github codespaces
-            DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc10
-            TPL_DOCKERFILE: docker/tpl-ubuntu-gcc.Dockerfile
-            DOCKER_ROOT_IMAGE: mcr.microsoft.com/vscode/devcontainers/base:ubuntu-20.04
-            DOCKER_COMPILER_BUILD_ARG: "--build-arg GCC_MAJOR_VERSION=10"
-            RUNS_ON: ubuntu-latest
-          - name: Ubuntu (22.04, gcc 11.4.0, open-mpi 4.1.2)
-            DOCKER_ROOT_IMAGE: ubuntu:22.04
-            DOCKER_REPOSITORY: geosx/ubuntu22.04-gcc11
-            TPL_DOCKERFILE: docker/tpl-ubuntu-gcc.Dockerfile
-            DOCKER_COMPILER_BUILD_ARG: "--build-arg GCC_MAJOR_VERSION=11"
-            RUNS_ON: ubuntu-latest
-          - name: Ubuntu (22.04, gcc 12.3.0, open-mpi 4.1.2)
-            DOCKER_ROOT_IMAGE: ubuntu:22.04
-            DOCKER_REPOSITORY: geosx/ubuntu22.04-gcc12
-            TPL_DOCKERFILE: docker/tpl-ubuntu-gcc.Dockerfile
-            DOCKER_COMPILER_BUILD_ARG: "--build-arg GCC_MAJOR_VERSION=12"
-            RUNS_ON: ubuntu-latest
-          - name: Ubuntu (22.04, clang 15.0.7 + gcc 11.4.0, open-mpi 4.1.2)
-            DOCKER_ROOT_IMAGE: ubuntu:22.04
-            DOCKER_REPOSITORY: geosx/ubuntu22.04-clang15
-            TPL_DOCKERFILE: docker/tpl-ubuntu-clang.Dockerfile
-            DOCKER_COMPILER_BUILD_ARG: "--build-arg CLANG_MAJOR_VERSION=15 --build-arg GCC_MAJOR_VERSION=11"
-            RUNS_ON: ubuntu-latest
-          - name: Ubuntu (20.04, clang 10.0.0 + gcc 9.4.0, open-mpi 4.0.3, cuda-11.8.89)
-            DOCKER_REPOSITORY: geosx/ubuntu20.04-clang10.0.0-cuda11.8.89
-            TPL_DOCKERFILE: docker/tpl-ubuntu-clang-cuda.Dockerfile
-            RUNS_ON: ubuntu-latest
+          # - name: Ubuntu (20.04, gcc 9.4.0, open-mpi 4.0.3)
+          #   DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc9
+          #   TPL_DOCKERFILE: docker/tpl-ubuntu-gcc.Dockerfile
+          #   DOCKER_ROOT_IMAGE: ubuntu:20.04
+          #   DOCKER_COMPILER_BUILD_ARG: "--build-arg GCC_MAJOR_VERSION=9"
+          #   RUNS_ON: ubuntu-latest
+          # - name: Ubuntu (20.04, gcc 10.5.0, open-mpi 4.0.3) - github codespaces
+          #   DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc10
+          #   TPL_DOCKERFILE: docker/tpl-ubuntu-gcc.Dockerfile
+          #   DOCKER_ROOT_IMAGE: mcr.microsoft.com/vscode/devcontainers/base:ubuntu-20.04
+          #   DOCKER_COMPILER_BUILD_ARG: "--build-arg GCC_MAJOR_VERSION=10"
+          #   RUNS_ON: ubuntu-latest
+          # - name: Ubuntu (22.04, gcc 11.4.0, open-mpi 4.1.2)
+          #   DOCKER_ROOT_IMAGE: ubuntu:22.04
+          #   DOCKER_REPOSITORY: geosx/ubuntu22.04-gcc11
+          #   TPL_DOCKERFILE: docker/tpl-ubuntu-gcc.Dockerfile
+          #   DOCKER_COMPILER_BUILD_ARG: "--build-arg GCC_MAJOR_VERSION=11"
+          #   RUNS_ON: ubuntu-latest
+          # - name: Ubuntu (22.04, gcc 12.3.0, open-mpi 4.1.2)
+          #   DOCKER_ROOT_IMAGE: ubuntu:22.04
+          #   DOCKER_REPOSITORY: geosx/ubuntu22.04-gcc12
+          #   TPL_DOCKERFILE: docker/tpl-ubuntu-gcc.Dockerfile
+          #   DOCKER_COMPILER_BUILD_ARG: "--build-arg GCC_MAJOR_VERSION=12"
+          #   RUNS_ON: ubuntu-latest
+          # - name: Ubuntu (22.04, clang 15.0.7 + gcc 11.4.0, open-mpi 4.1.2)
+          #   DOCKER_ROOT_IMAGE: ubuntu:22.04
+          #   DOCKER_REPOSITORY: geosx/ubuntu22.04-clang15
+          #   TPL_DOCKERFILE: docker/tpl-ubuntu-clang.Dockerfile
+          #   DOCKER_COMPILER_BUILD_ARG: "--build-arg CLANG_MAJOR_VERSION=15 --build-arg GCC_MAJOR_VERSION=11"
+          #   RUNS_ON: ubuntu-latest
+          # - name: Ubuntu (20.04, clang 10.0.0 + gcc 9.4.0, open-mpi 4.0.3, cuda-11.8.89)
+          #   DOCKER_REPOSITORY: geosx/ubuntu20.04-clang10.0.0-cuda11.8.89
+          #   TPL_DOCKERFILE: docker/tpl-ubuntu-clang-cuda.Dockerfile
+          #   RUNS_ON: ubuntu-latest
           - name: Rockylinux (8, gcc 13.3, cuda 12.9.1)
             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, 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
+          - name: Rockylinux_pygeosx (8, gcc 13.3, cuda 12.9.1)
+            DOCKER_REPOSITORY: geosx/rockylinux8-gcc13-cuda12.9.1
+            TPL_DOCKERFILE: docker/tpl-rockylinux-gcc-cuda-12-pygeosx.Dockerfile
             RUNS_ON: Runner_4core_16GB
-          - name: Pangea 3 (AlmaLinux 8.8, gcc 9.4.0, open-mpi 4.1.2, cuda 11.5.0, openblas 0.3.10)
-            DOCKER_REPOSITORY: geosx/pangea3-almalinux8-gcc9.4-openmpi4.1.2-cuda11.5.0-openblas0.3.18
-            TPL_DOCKERFILE: docker/TotalEnergies/Pangea3.Dockerfile
-            DOCKER_ROOT_IMAGE: 7g8efcehpff/pangea-almalinux8-gcc9.4-openmpi4.1.2-cuda11.5.0-openblas0.3.18:4
-            HOST_ARCH: ppc64le
-            RUNS_ON: streak2
-          - name: Sherlock CPU (centos 7.9.2009, gcc 10.1.0, open-mpi 4.1.2, openblas 0.3.10, zlib 1.2.11)
-            DOCKER_REPOSITORY: geosx/sherlock-gcc10.1.0-openmpi4.1.2-openblas0.3.10-zlib1.2.11
-            TPL_DOCKERFILE: docker/Stanford/Dockerfile
-            DOCKER_ROOT_IMAGE: matteofrigo5/sherlock-gcc10.1.0-openmpi4.1.2-cuda12.4.0-openblas0.3.10-zlib1.2.11-cmake3.31.4-no-geosx:0.0.1
-            SPEC: "%gcc@10.1.0~pygeosx~openmp"
-            INSTALL_DIR_ROOT: /oak/stanford/groups/tchelepi/geos-sherlock/CPU
-            RUNS_ON: ubuntu-latest
-          - name: Sherlock GPU (centos 7.9.2009, gcc 10.1.0, open-mpi 4.1.2, cuda 12.4.0, openblas 0.3.10, zlib 1.2.11)
-            DOCKER_REPOSITORY: geosx/sherlock-gcc10.1.0-openmpi4.1.2-cuda12.4.0-openblas0.3.10-zlib1.2.11
-            TPL_DOCKERFILE: docker/Stanford/Dockerfile
-            DOCKER_ROOT_IMAGE: matteofrigo5/sherlock-gcc10.1.0-openmpi4.1.2-cuda12.4.0-openblas0.3.10-zlib1.2.11-cmake3.31.4-no-geosx:0.0.1
-            SPEC: "%gcc@10.1.0~pygeosx~openmp cuda_arch=70 ^cuda@12.4.0+allow-unsupported-compilers"
-            INSTALL_DIR_ROOT: /oak/stanford/groups/tchelepi/geos-sherlock/GPU
-            RUNS_ON: ubuntu-latest
+          # - 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
+          #   RUNS_ON: Runner_4core_16GB
+          # - name: Pangea 3 (AlmaLinux 8.8, gcc 9.4.0, open-mpi 4.1.2, cuda 11.5.0, openblas 0.3.10)
+          #   DOCKER_REPOSITORY: geosx/pangea3-almalinux8-gcc9.4-openmpi4.1.2-cuda11.5.0-openblas0.3.18
+          #   TPL_DOCKERFILE: docker/TotalEnergies/Pangea3.Dockerfile
+          #   DOCKER_ROOT_IMAGE: 7g8efcehpff/pangea-almalinux8-gcc9.4-openmpi4.1.2-cuda11.5.0-openblas0.3.18:4
+          #   HOST_ARCH: ppc64le
+          #   RUNS_ON: streak2
+          # - name: Sherlock CPU (centos 7.9.2009, gcc 10.1.0, open-mpi 4.1.2, openblas 0.3.10, zlib 1.2.11)
+          #   DOCKER_REPOSITORY: geosx/sherlock-gcc10.1.0-openmpi4.1.2-openblas0.3.10-zlib1.2.11
+          #   TPL_DOCKERFILE: docker/Stanford/Dockerfile
+          #   DOCKER_ROOT_IMAGE: matteofrigo5/sherlock-gcc10.1.0-openmpi4.1.2-cuda12.4.0-openblas0.3.10-zlib1.2.11-cmake3.31.4-no-geosx:0.0.1
+          #   SPEC: "%gcc@10.1.0~pygeosx~openmp"
+          #   INSTALL_DIR_ROOT: /oak/stanford/groups/tchelepi/geos-sherlock/CPU
+          #   RUNS_ON: ubuntu-latest
+          # - name: Sherlock GPU (centos 7.9.2009, gcc 10.1.0, open-mpi 4.1.2, cuda 12.4.0, openblas 0.3.10, zlib 1.2.11)
+          #   DOCKER_REPOSITORY: geosx/sherlock-gcc10.1.0-openmpi4.1.2-cuda12.4.0-openblas0.3.10-zlib1.2.11
+          #   TPL_DOCKERFILE: docker/Stanford/Dockerfile
+          #   DOCKER_ROOT_IMAGE: matteofrigo5/sherlock-gcc10.1.0-openmpi4.1.2-cuda12.4.0-openblas0.3.10-zlib1.2.11-cmake3.31.4-no-geosx:0.0.1
+          #   SPEC: "%gcc@10.1.0~pygeosx~openmp cuda_arch=70 ^cuda@12.4.0+allow-unsupported-compilers"
+          #   INSTALL_DIR_ROOT: /oak/stanford/groups/tchelepi/geos-sherlock/GPU
+          #   RUNS_ON: ubuntu-latest
 
     steps:
     - name: Checkout

docker/rocky-pygeosx-spack.yaml

@@ -0,0 +1,149 @@
+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: [2.69]
+      buildable: false
+      externals:
+      - spec: autoconf@2.69
+        prefix: /usr
+    automake:
+      version: [1.16.1]
+      buildable: false
+      externals:
+      - spec: automake@1.16.1
+        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
+    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@1.1.1
+        prefix: /usr
+    tk:
+      buildable: false
+      externals:
+      - spec: tk@8.6.8
+        prefix: /usr
+    tcl:
+      buildable: false
+      externals:
+      - spec: tcl@8.6.8
+        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.Dockerfile

@@ -16,27 +16,26 @@ RUN dnf clean all && \
         which \ 
         clang-17.0.6 \
         gcc-gfortran \
-        python3 \
+        python3.9 \
+        python3-pip \
         zlib-devel \
         tbb \
         blas \
         lapack \
         openmpi \
         openmpi-devel \
     # Additional spack dependencies
-        python3-pip \
         unzip \
         mpfr-devel \
         bzip2 \
         gnupg \
-        xz \
-        python3-virtualenv
+        xz
 
 RUN dnf config-manager --set-enabled  &
 
 # Install clingo for Spack
-RUN python3 -m pip install --upgrade pip && \
-    python3 -m pip install clingo
+RUN python3.9 -m pip install --upgrade pip && \
+    python3.9 -m pip install clingo virtualenv
 
 RUN --mount=src=.,dst=$SRC_DIR $SRC_DIR/docker/install-cmake.sh