Add Pangea 4 docker build

.github/workflows/docker_build_tpls.yml

@@ -20,6 +20,13 @@ jobs:
 
       matrix:
         include:
+          - name: Pangea 4 (redhat 8, gcc 12.1.0, hpcx 2.17.1, mkl 2023.2.0)
+            DOCKER_REPOSITORY: geosx/pangea4-gcc12.1-hpcxompi2.17.1-onemkl2023.2.0
+            DOCKERFILE: docker/TotalEnergies/tpl-pangea4.Dockerfile
+            DOCKER_ROOT_IMAGE: onetechssc/pangea4:gcc12.1-hpcxompi2.17.1-onemkl2023.2.0_v1.0
+            HOST_CONFIG: host-configs/TOTAL/pangea4-gcc12.1-hpcxompi2.17.1-onemkl2023.2.0.cmake
+            INSTALL_DIR_ROOT: /workrd/SCR/NUM/GEOS_environment/p4/install/tpl
+            RUNS_ON: ubuntu-latest
           - 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
             DOCKERFILE: docker/Stanford/Dockerfile

docker/Stanford/Sherlock.Dockerfile

@@ -1,6 +1,5 @@
 # This Dockerfile aims at reproducing (some part of) the SHERLOCK environment.
-# Please see TotalEnergies/Pangea2.Dockerfile for fully commented version
-
+#
 # While loading module ompi4.1.2 on Sherlock, the following are aut-loaded:
 #         UCX/1.12.1
 # 		  LIBFABRIC/1.14.0

docker/TotalEnergies/README.md

@@ -0,0 +1,20 @@
+# TotalEnergies Dockerfiles
+
+## Overview
+
+This directory contains several Dockerfiles used for building and deploying the TPLs.
+Below is a table summarizing the purpose and key characteristics of each Dockerfile.
+
+| Dockerfile                               | Description                                                                  | Base Image                    | Key Components Installed                                                                             |
+|------------------------------------------|------------------------------------------------------------------------------|-------------------------------|------------------------------------------------------------------------------------------------------|
+| `pecan-gcc-openmpi-mkl-cuda.Dockerfile`  | Builds a toolchain with GCC, OpenMPI, CUDA, and Intel MKL for GEOS on Pecan. | `centos:7.7.1908`             | GCC, OpenMPI, CUDA, Intel MKL, numactl-devel, ca-certificates, curl, Python3, zlib-devel             |
+| `tpl-pecan.Dockerfile`                   | Builds third-party libraries for GEOS on Pecan environment.                  | `pecan-gcc-openmpi-mkl-cuda`  | CMake, make, bc, file, bison, flex, patch, openssh-clients, texlive, graphviz, libxml2, git, sccache |
+| `pangea4-gcc.Dockerfile`                 | Builds a toolchain with GCC, CMake and Python on Pangea 4.                   | `spack/centos-stream`         | GCC, CMake, Python, Wget                                                                             |
+| `pangea4-gcc-hpcxompi-onemkl.Dockerfile` | Builds a toolchain with GCC, HPCXOMPI and ONEMKL on Pangea 4.                | `pangea4-gcc`                 | GCC, CMake, Python, Wget, HPCXOMPI, ONEMKL                                                           |
+| `tpl-pangea4.Dockerfile`                 | Builds third-party libraries for GEOS on Pangea 4 environment.               | `pangea4-gcc-hpcxompi-onemkl` | GCC, CMake, Python, Wget, HPCXOMPI, ONEMKL, sccache                                                  |
+
+## DockerHub
+
+The Docker images built from the ${cluster}.Dockerfile are available on DockerHub under for:
+  - pangea4 cluster : [onetechssc/pangea4](https://hub.docker.com/r/onetechssc/pangea4)
+  - pecan cluster : [totogaz/pecan-gcc8.2.0-openmpi4.0.1-mkl2019.5-cuda11.5.119-no-geosx](https://hub.docker.com/r/totogaz/pecan-gcc8.2.0-openmpi4.0.1-mkl2019.5-cuda11.5.119-no-geosx)

docker/TotalEnergies/pangea4-gcc-hpcxompi-onemkl.Dockerfile

@@ -0,0 +1,65 @@
+#######################################
+# Pangea 4 image : gcc - hpcxompi - onemkl
+#######################################
+#
+# Installs :
+#   - gcc                  = 12.1
+#   - hpcx                 = 2.17.1
+#   - intel-oneapi-mkl     = 2023.2.0
+#   - cmake                = 3.27.9
+#   - python               = 3.11
+#
+#######################################
+#
+# Description :
+#   - the image is based on onetechssc/pangea4:gcc12.1_v1.0 built from pangea4-gcc.Dockerfile
+#   - this image is deployed as onetechssc/pangea4:gcc12.1-hpcx2.17.1-onemkl2023.2.0_v1.0
+#   - oneAPI MKL is installed via spack (as done for Pangea 4)
+#   - hpcx is installed by extracting the tarball (as done for Pangea 4)
+#   - gcc wrappers are created to mimic the Cray environment (cc, CC, ftn)
+#
+#######################################
+
+# -------------------------------------
+# PANGEA4 - GCC-HPCX-MKL
+FROM onetechssc/pangea4:gcc12.1_v1.0 AS pangea4
+# ------
+# LABELS
+LABEL description="Pangea 4 image : gcc - cmake - python - hpcx - mkl"
+LABEL version="1.0"
+LABEL maintainer="TotalEnergies HPC Team"
+# ------
+# ARGS
+ARG ONEAPI_MKL_VERSION=2023.2.0
+ARG HPCX_VERSION="hpcx-v2.17.1-gcc-mlnx_ofed-redhat8-cuda12-x86_64"
+ARG HPCX_TARBALL="$HPCX_VERSION.tbz"
+ARG HPCX_URL="http://www.mellanox.com/downloads/hpc/hpc-x/v2.17.1/$HPCX_TARBALL"
+ARG CRAY_WRAPPERS_DIR=/sw/cray-wrappers
+# ------
+# INSTALL
+# intel-oneapi-mkl
+RUN spack install intel-oneapi-mkl@$ONEAPI_MKL_VERSION %gcc@$GCC_VERSION
+# hpcx not available in spack -> download and untar in /sw directory
+RUN mkdir -p /sw && \
+    spack load wget && \
+    wget $HPCX_URL -O /tmp/$HPCX_TARBALL && \
+    tar -xvf /tmp/$HPCX_TARBALL -C /sw
+ENV HPCX_HOME=/sw/$HPCX_VERSION
+# ------
+# ENV
+# - create wrappers for gcc
+RUN mkdir -p $CRAY_WRAPPERS_DIR && \
+    spack load gcc@$GCC_VERSION python@$PYTHON_VERSION cmake@$CMAKE_VERSION intel-oneapi-mkl@$ONEAPI_MKL_VERSION && \
+    GCC_INSTALL_DIR=$(spack location -i gcc@$GCC_VERSION) && \
+    ln -s ${GCC_INSTALL_DIR}/bin/gcc $CRAY_WRAPPERS_DIR/cc && \
+    ln -s ${GCC_INSTALL_DIR}/bin/g++ $CRAY_WRAPPERS_DIR/CC && \
+    ln -s ${GCC_INSTALL_DIR}/bin/gfortran $CRAY_WRAPPERS_DIR/ftn
+# create env script
+RUN <<EOF cat > /root/set_env.sh
+#!/bin/bash
+spack load gcc@$GCC_VERSION python@$PYTHON_VERSION cmake@$CMAKE_VERSION intel-oneapi-mkl@$ONEAPI_MKL_VERSION && \
+source ${HPCX_HOME}/hpcx-init.sh
+hpcx_load
+PATH=$CRAY_WRAPPERS_DIR:\$PATH
+EOF
+RUN chmod +x /root/set_env.sh

docker/TotalEnergies/pangea4-gcc.Dockerfile

@@ -0,0 +1,50 @@
+#######################################
+# Pangea 4 image : gcc - cmake - python
+#######################################
+#
+# Installs :
+#   - gcc                  = 12.1
+#   - cmake                = 3.27.9
+#   - python               = 3.11
+#
+#######################################
+#
+# Description :
+#   - the image is based on spack/centos-stream:latest (CentOS Stream 8 image with spack installed)
+#   - this image is deployed as onetechssc/pangea4:gcc12.1_v1.0
+#   - gcc, cmake, python and wget are installed via spack (as done for Pangea 4)
+#
+#######################################
+
+# -------------------------------------
+# PANGEA4 - BASE [GCC - CMAKE - PYTHON]
+# install tools via spack for linux/x86_64 architecture and redhat8 platform
+FROM --platform=linux/x86_64 spack/centos-stream:latest AS pangea4-base
+# ------
+# LABELS
+LABEL description="Pangea 4 image : gcc - cmake - python"
+LABEL version="1.0"
+LABEL maintainer="TotalEnergies HPC Team"
+# ------
+# ARGS
+ARG GCC_VERSION=12.1
+ARG CMAKE_VERSION=3.27.9
+ARG PYTHON_VERSION=3.11
+# ------
+# INSTALL
+# gcc
+RUN spack install gcc@$GCC_VERSION
+RUN . /opt/spack/share/spack/setup-env.sh &&\
+    spack load gcc@$GCC_VERSION &&\
+    spack compiler find
+# python
+RUN spack install python@$PYTHON_VERSION %gcc@$GCC_VERSION
+# cmake
+RUN spack install cmake@$CMAKE_VERSION %gcc@$GCC_VERSION
+# wget
+RUN spack install wget %gcc@$GCC_VERSION
+# ------
+# ENV
+ENV GCC_VERSION=${GCC_VERSION}
+ENV CMAKE_VERSION=${CMAKE_VERSION}
+ENV PYTHON_VERSION=${PYTHON_VERSION}

docker/TotalEnergies/tpl-pangea4.Dockerfile

@@ -0,0 +1,41 @@
+#######################################
+# Pangea 4 tpl image
+#
+# Description :
+#   - generic image for building geos tpls on Pangea 4 environments
+#   - the docker base image can be any pangea4 docker file
+#   - tools of the base image are expected to be sourced in the set_env.sh script
+#######################################
+
+# -------------------------------------
+# PANGEA4 - TPL TOOLCHAIN
+ARG DOCKER_ROOT_IMAGE
+FROM $DOCKER_ROOT_IMAGE AS pangea4_tpl_toolchain
+# ------
+# LABELS
+LABEL description="Pangea 4 image : geos_tpl"
+LABEL version="1.0"
+LABEL maintainer="TotalEnergies HPC Team"
+# ------
+# ARGS
+ARG TMP_DIR=/tmp
+ARG SRC_DIR=$TMP_DIR/src
+ARG BLD_DIR=$TMP_DIR/build
+ARG INSTALL_DIR
+ARG HOST_CONFIG
+# ------
+# ENV
+ENV GEOSX_TPL_DIR=$INSTALL_DIR
+ENV GCC_PATH=\${GCC_INSTALL_DIR}
+# ------
+# INSTALL
+RUN --mount=src=.,dst=$SRC_DIR source /root/set_env.sh && \
+                               $SRC_DIR/docker/configure-tpl.sh -DMKL_LIBRARIES=\${MKLROOT}/lib/intel64/libmkl_rt.so
+WORKDIR $BLD_DIR
+RUN --mount=src=.,dst=$SRC_DIR source /root/set_env.sh && \
+                               make
+# ------
+# CACHE
+# install `sccache` binaries to speed up the build of `geos`
+RUN --mount=src=.,dst=$SRC_DIR $SRC_DIR/docker/install-sccache.sh
+ENV SCCACHE=/opt/sccache/bin/sccache