Merge branch 'main' into feature/meshMotion

Author: tmaric

.github/workflows/ci.yaml

@@ -1,15 +1,16 @@
-name: smartredis
+name: tests_ubuntu
 defaults:
   run:
     shell: bash -o pipefail -i {0}
 on:
   push:
     branches:
       - main
+      - ci
       - 'bugfix*'
       - 'releases/**'
   pull_request:
-    types: [opened, reopened]
+    types: [opened, reopened, synchronize]
   workflow_dispatch:
     inputs:
       debug_enabled:
@@ -20,23 +21,32 @@ on:
 
 jobs:
   build:
+    strategy:
+      fail-fast: false
+      matrix:
+        openfoam_version: ['2312', '2212']
+        smartsim_version: ['0.7.0', '0.6.2']
+        database_backend: ['redis']
+        ubuntu_version: ['22.04', '20.04'] ## SmartSim not available yet for Python 3.12 on Ubuntu 24
+        exclude:
+          - ubuntu_version: '20.04' ## SmartSim 0.7.0 not released on ubuntu 20.04
+            smartsim_version: '0.7.0'
     runs-on: ubuntu-22.04
 
     container:
-      image: ghcr.io/foamscience/openfoam-smartsim:cpu-2312
-      options: --user openfoam
+      image: ghcr.io/ofdatacommittee/openfoam-smartsim:of-${{ matrix.openfoam_version }}-smart-${{ matrix.smartsim_version }}-${{ matrix.database_backend }}-ubuntu-${{ matrix.ubuntu_version }}
       env:
         CATCH_TIMEOUT: 20
         FOAM_FOAMUT: "/tmp/foamUT"
-        SSDB: "redis:6379"
+        SSDB: "smartdb:6379"
 
     services:
-      redis:
-        image: redislabs/redisai
+      smartdb:
+        image: ${{ matrix.database_backend == 'redis' && 'redislabs/redisai' || 'eqalpha/keydb' }}
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup tmate session
         uses: mxschmitt/action-tmate@v3
@@ -46,15 +56,15 @@ jobs:
 
       - name: Compile
         run: |
-          source /usr/lib/openfoam/openfoam2312/etc/bashrc
+          source /usr/lib/openfoam/openfoam${{ matrix.openfoam_version }}/etc/bashrc
           mkdir -p $FOAM_USER_LIBBIN
           ./Allwmake 
 
       - name: Compile Tests and Run
         run: |
-          source /usr/lib/openfoam/openfoam2312/etc/bashrc
+          source /usr/lib/openfoam/openfoam${{ matrix.openfoam_version }}/etc/bashrc
           ./Allwmake 
-          export SSDB="redis:6379"
+          export SSDB="smartdb:6379"
           git clone https://github.com/FoamScience/foamUT $FOAM_FOAMUT
           sed -i 's/mpirun/mpirun --oversubscribe/g' $FOAM_FOAMUT/Alltest
           ln -s "$PWD"/tests "$FOAM_FOAMUT"/tests/smartSimFOTests

.github/workflows/todos.yaml

@@ -2,6 +2,14 @@
 
 orig_dit="$(pwd)"
 
+# Create the $FOAM_USER_LIBBIN if not existing.
+# - This happens with a fresh OpenFOAM installation.
+# - openfoam-smartsim libraries are placed into $FOAM_USER_LIBBIN
+if [ ! -d "$FOAM_USER_LIBBIN" ]; 
+then
+    mkdir -p $FOAM_USER_LIBBIN
+fi
+
 ## Compile SmartRedis libs
 export _REPO_ROOT="$(git rev-parse --show-toplevel)"
 cd "$_REPO_ROOT" || exit 1
@@ -30,7 +38,9 @@ elif [ $WM_COMPILER == "Icx" ]; then
 fi
 make lib
 cd "$_REPO_ROOT" || exit 1
-cp -r $FOAM_SMARTREDIS/install/lib/*.* $FOAM_USER_LIBBIN 
+cp $FOAM_SMARTREDIS/install/lib/libsmartredis.so $FOAM_USER_LIBBIN 
+cp $FOAM_SMARTREDIS/build/Release/hiredis-prefix/src/hiredis-build/libhiredis.a $FOAM_USER_LIBBIN
+cp $FOAM_SMARTREDIS/build/Release/redis++-prefix/src/redis++-build/libredis++.a $FOAM_USER_LIBBIN
 export FOAM_CODE_TEMPLATES=$_REPO_ROOT/etc/dynamicCode/
 
 ## Compile OpenFOAM libs

Allwmake

@@ -77,4 +77,4 @@ Head to one of the tutorials, and run the jupyter notebook or a python program y
 
 ## References
 
-Maric, T., Fadeli, M. E., Rigazzi, A., Shao, A., & Weiner, A. (2024). Combining Machine Learning with Computational Fluid Dynamics using OpenFOAM and SmartSim. arXiv preprint [arXiv:2402.16196](https://doi.org/10.48550/arXiv.2402.16196).
+Maric, T., Fadeli, M. E., Rigazzi, A., Shao, A., & Weiner, A. (2024). Combining Machine Learning with Computational Fluid Dynamics using OpenFOAM and SmartSim. arXiv preprint [https://doi.org/10.1007/s11012-024-01797-z](https://doi.org/10.1007/s11012-024-01797-z).

README.md

@@ -0,0 +1,39 @@
+ARG UBUNTU_VERSION                      # Eg. 22.04
+FROM ubuntu:${UBUNTU_VERSION}
+# To build this image from this folder with OpenFOAM v2206:
+# docker build --build-arg OPENFOAM_VERSION=2206 --build-tag SMARTSIM_VERSION=0.7.0 -t openfoam-smartsim:latest .
+
+ARG SMARTSIM_VERSION                    # Eg. 0.6.2
+ARG OPENFOAM_VERSION                    # Eg. 2206
+ARG DATABASE_BACKEND=redis              # redis or keydb
+LABEL maintainer="Mohammed Elwardi Fadeli <[email protected]>"
+LABEL source="https://github.com/OFDataCommittee/openfoam-smartsim"
+
+# Install and setup
+ENV DEBIAN_FRONTEND=noninteractive
+ENV SHELL=/usr/bin/bash
+RUN apt update -y && \
+    apt install -y --no-install-recommends git-lfs libpython3-dev pip cmake \
+        sudo apt-utils vim curl wget software-properties-common \
+        git-core cmake openssh-server gcc g++  \
+        binutils libopenmpi-dev openmpi-bin openmpi-common openmpi-doc 
+
+# Set up OpenFOAM repositories
+RUN sh -c "curl https://dl.openfoam.com/add-debian-repo.sh | bash"
+RUN apt update -y && \
+    apt install -y --no-install-recommends openfoam${OPENFOAM_VERSION}-default
+RUN apt clean && apt purge && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+# Set up smartsim
+RUN pip install smartsim==${SMARTSIM_VERSION} && \
+    if [ "${DATABASE_BACKEND}" = "keydb" ]; then smart build --device cpu --no_tf --no_pt; else smart build --device cpu --no_tf --no_pt --keydb; fi
+ENV USER openfoam
+ENV HOME=/home/${USER} 
+RUN adduser --disabled-password --gecos "" ${USER} -u 1001 && \
+    echo "ALL ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
+USER openfoam
+RUN echo "source /usr/lib/openfoam/openfoam${OPENFOAM_VERSION}/etc/bashrc" >> ${HOME}/.bashrc
+RUN . "/usr/lib/openfoam/openfoam${OPENFOAM_VERSION}/etc/bashrc" && mkdir -p $FOAM_USER_LIBBIN && mkdir -p $FOAM_USER_APPBIN
+
+
+#COPY bin/uid_entrypoint /usr/local/bin/uid_entrypoint
+#ENTRYPOINT ["uid_entrypoint"]

docker/Dockerfile

@@ -0,0 +1,44 @@
+# Continuous Integration
+
+## Overview
+
+We continuously test against recent versions of the following software pieces:
+- Ubuntu
+- OpenFOAM
+- SmartSim
+- Database backend (redis, or keydb)
+
+In particular, by testing on multiple versions of Ubuntu distribution, we make sure
+things work on the default toolchain versions (Compilers, system OpenMPI, ..., etc)
+
+We use [Github Container Registry](https://ghcr.io/) to store the Docker images necessary for
+CI workflows.
+
+## Instructions for automated image builds
+
+> [!NOTE]
+> You will want to install ansible (locally) to build the images easily: `pip install ansible`.
+> Each image is a little than 2GB so make sure you have enough disk space.
+
+1. In [docker/build.yml](docker/build.yml) file, add the new version in the relevant fact task.
+   - For example, to add a new version of OpenFOAM, add the version to `openfoam_versions`
+   - Then run `ansible-playbook build.yml --extra-vars "username=github_user  token=$GITHUB_TOKEN`
+     to build the corresponding image and push it.
+     - When building the images locally, you can speed the process by removing other software versions
+     and keeping only the new one
+2. In [.github/workflows/ci.yaml](.github/workflows/ci.yaml) file, add the new version in the relevant
+   `strategy` section.
+   - For example, to add a new version of OpenFOAM, add the version to `jobs.build.strategy.matrix.openfoam_version`
+   - Then commit the changes to the repository.
+
+## Instructions for manual image builds
+
+```sh
+cd docker
+docker build \
+    --build-arg OPENFOAM_VERSION=2312 \
+    --build-arg UBUNTU_VERSION=22.04 \
+    --build-arg DATABASE_BACKEND=redis \
+    --build-arg SMARTSIM_VERSION=0.7.0 \
+    -t ghcr.io/<github_user>/openfoam-smartsim:of-2312-smartsim-0.7.0-redis-ubuntu-22.04 .
+```

docker/README.md

@@ -0,0 +1,80 @@
+# ansible-playbook build.yml --extra-vars "username=user  token=token"
+---
+- name: Build openfoam-smartsim CI infrastructure
+  hosts: localhost
+  gather_facts: false
+  vars:
+    ansible_python_interpreter: /usr/bin/python3
+
+  tasks:
+    - name: Install docker python support for ansible
+      pip:
+        name: docker
+        state: present
+
+    - name: Define list of OpenFOAM versions
+      set_fact:
+        openfoam_versions:
+          - "2312"
+          - "2212"
+
+    - name: Define list of SmartSim versions
+      set_fact:
+        smartsim_versions:
+          - "0.7.0"
+          - "0.6.2"
+
+    - name: Define list of DB backends
+      set_fact:
+        database_backends:
+          - "redis"
+
+    - name: Define list of Ubuntu versions
+      set_fact:
+        ubuntu_versions:
+          #- "24.04" ## SmartSim not available for Python 3.12
+          - "22.04"
+          - "20.04"
+
+    - name: Login to GitHub Container Registry
+      docker_login:
+        username: "{{ username }}"
+        password: "{{ token }}"
+        registry_url: "https://ghcr.io"
+
+    - name: Build Docker images
+      docker_image:
+        name: "ghcr.io/{{ username }}/openfoam-smartsim:of-{{ item.0 }}-smart-{{ item.1 }}-{{ item.2 }}-ubuntu-{{ item.3 }}"
+        source: "build"
+        build:
+          path: "."
+          dockerfile: "Dockerfile"
+          pull: yes
+          args:
+            OPENFOAM_VERSION: "{{ item.0 }}"
+            SMARTSIM_VERSION: "{{ item.1 }}"
+            DATABASE_BACKEND: "{{ item.2 }}"
+            UBUNTU_VERSION: "{{ item.3 }}"
+      loop: "{{ openfoam_versions|product(smartsim_versions, database_backends, ubuntu_versions)|list }}"
+      when: "not (item.1 == '0.7.0' and item.3 == '20.04')"
+      async: 1200
+      poll: 0
+      register: async_result
+
+    - name: Wait for all build tasks to complete
+      async_status:
+        jid: "{{ item.ansible_job_id }}"
+      loop: "{{ async_result.results }}"
+      when: item.changed
+      register: async_status_result
+      until: async_status_result.finished
+      retries: 20
+      delay: 60
+
+    - name: Push Docker images to GitHub Container Registry
+      docker_image:
+        name: "ghcr.io/ofdatacommittee/openfoam-smartsim:of-{{ item.0 }}-smart-{{ item.1 }}-{{ item.2 }}-ubuntu-{{ item.3 }}"
+        source: local
+        push: yes
+      loop: "{{ openfoam_versions|product(smartsim_versions, database_backends, ubuntu_versions)|list }}"
+      when: "not (item.1 == '0.7.0' and item.3 == '20.04')"