Merge pull request #182 from precice/develop

Release v3 compatible ASTE version
precice · Mar 22, 2024 · 765f405 · 765f405
2 parents 9e7b31c + 3168b0e
commit 765f405
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
diff --git a/.github/dependency_bot.yml b/.github/dependency_bot.yml
diff --git a/.github/workflows/aste_ci.yml b/.github/workflows/aste_ci.yml
@@ -13,20 +13,21 @@ concurrency:
 jobs:
   build:
     runs-on: ubuntu-latest
+    container: precice/precice:develop
     timeout-minutes: 30
     env:
       CXX_FLAGS: "-Werror -Wall -Wextra -Wno-unused-parameter"
       CTEST_OUTPUT_ON_FAILURE: "Yes"
     steps:
-      - uses: actions/checkout@v2
-      - name: install preCICE
+      - uses: actions/checkout@v4
+      - name: setup system
         run: |
-          wget https://github.com/precice/precice/releases/download/v2.5.0/libprecice2_2.5.0_focal.deb && \
-          sudo apt-get -y update && \
-          sudo apt-get -y install ./libprecice2_2.5.0_focal.deb
+          apt-get -y update && apt-get -y upgrade
+          apt-get install -y python3-pip pkg-config time
+          pip3 install --upgrade pip
       - name: install VTK
         run: |
-          sudo apt-get -y install libvtk7-dev
+          apt-get -y install libvtk9-dev libvtk9-qt-dev
       - name: install example dependencies
         run: |
           python3 -m pip install sympy scipy jinja2
@@ -41,13 +42,15 @@ jobs:
         run: |
           cmake ..
           cmake --build .
+      - name: Adjust user rights
+        run: chown -R $PRECICE_USER .
       - name: run test gcc
         working-directory: build_gcc
         run: |
-          ctest
+          su -c "ctest" $PRECICE_USER
       - name: install clang
         run: |
-          sudo apt-get -y install clang
+          apt-get -y install clang
       - name: build aste clang
         working-directory: build_clang
         env:
@@ -56,8 +59,9 @@ jobs:
         run: |
           cmake ..
           cmake --build .
-          sudo cmake --install .
+      - name: Adjust user rights
+        run: chown -R $PRECICE_USER .
       - name: run test clang
         working-directory: build_clang
         run: |
-          ctest
+          su -c "ctest" $PRECICE_USER
diff --git a/.github/workflows/code_style.yml b/.github/workflows/code_style.yml
@@ -12,9 +12,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout preCICE
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Setup python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
+        with:
+         python-version: '3.10'
+         check-latest: true
       - name: Install pre-commit
         run: pip install pre-commit
       - name: Run checks

diff --git a/.github/workflows/link_check.yml b/.github/workflows/link_check.yml
@@ -5,7 +5,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Check links in markdown files (markdown-link-check)
         uses: gaurav-nelson/github-action-markdown-link-check@v1
         with:

diff --git a/.github/workflows/lint_markdown.yml b/.github/workflows/lint_markdown.yml
diff --git a/.markdownlint.json b/.markdownlint.json
@@ -1,4 +1,5 @@
 {
     "MD013": false,
-    "MD033": false
+    "MD033": false,
+    "MD041": false
 }
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -8,18 +8,18 @@ repos:
         types_or: [c++, c]
   # isort for python imports
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
         name: isort (python)
   # black repo for python formatting
   - repo: https://github.com/ambv/black
-    rev: 22.6.0
+    rev: 22.12.0
     hooks:
       - id: black
   # Official repo for default hooks
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v4.3.0"
+    rev: "v4.4.0"
     hooks:
       - id: check-xml
         exclude: "tools"
@@ -30,7 +30,17 @@ repos:
       - id: requirements-txt-fixer
   # Custom repo for the preCICE configuration formatter
   - repo: https://github.com/precice/precice-pre-commit-hooks
-    rev: "v2.1"
+    rev: "v3.2"
     hooks:
       - id: format-precice-config
         exclude: "tools"
+      - id: check-image-prefix
+        files: "^docs/images/.*"
+        args: [ --prefix=docs-tooling-aste- ]
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.39.0
+    hooks:
+      - id: markdownlint
+        exclude: changelog-entries
+      - id: markdownlint-fix
+        exclude: changelog-entries
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,12 +1,13 @@
-cmake_minimum_required (VERSION 3.1)
+cmake_minimum_required (VERSION 3.16.3)
 
 project(ASTE)
 
 list (APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake")
 
-set (CMAKE_CXX_STANDARD 14)
+set (CMAKE_CXX_STANDARD 17)
 set (CMAKE_CXX_STANDARD_REQUIRED YES)
 set (CMAKE_CXX_EXTENSIONS NO)
+set (CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
 if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
   set(CMAKE_BUILD_TYPE "Debug" CACHE STRING "Choose the type of build." FORCE)
@@ -20,9 +21,9 @@ option(ASTE_SET_MESH_BLOCK "Use block versions to set mesh primitives." ON)
 
 find_package (Threads REQUIRED)
 
-find_package(precice REQUIRED CONFIG)
+find_package(precice 3.0 REQUIRED)
 
-find_package(Boost 1.65.1 REQUIRED COMPONENTS log log_setup system program_options filesystem unit_test_framework)
+find_package(Boost 1.71.0 REQUIRED COMPONENTS log log_setup system program_options unit_test_framework)
 
 option(ASTE_USE_VTK_COMPONENTS "Find VTK with components" OFF)
 if(ASTE_USE_VTK_COMPONENTS)
@@ -63,9 +64,9 @@ if(METIS_FOUND)
 endif()
 
 
-add_executable(testing tests/testing.cpp tests/read_test.cpp tests/write_test.cpp src/mesh.cpp src/logger.cpp)
-target_include_directories(testing PRIVATE src thirdparty)
-target_link_libraries(testing
+add_executable(test-precice-aste tests/testing.cpp tests/read_test.cpp tests/write_test.cpp src/mesh.cpp src/logger.cpp)
+target_include_directories(test-precice-aste PRIVATE src thirdparty)
+target_link_libraries(test-precice-aste
   ${Boost_LIBRARIES}
   MPI::MPI_CXX
   ${VTK_LIBRARIES}
@@ -77,7 +78,7 @@ if (VTK_VERSION VERSION_LESS "8.90.0")
 else ()
   # vtk_module_autoinit is needed
   vtk_module_autoinit(
-    TARGETS precice-aste-run testing
+    TARGETS precice-aste-run test-precice-aste
     MODULES ${VTK_LIBRARIES}
     )
 endif()
@@ -95,7 +96,7 @@ install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/src/precice-aste-partition ${CMAKE_
 
 enable_testing()
 
-add_test(NAME read_write_test  COMMAND testing WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}/tests")
+add_test(NAME read_write_test  COMMAND test-precice-aste WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}/tests")
 
 # Detect and register examples as tests
 

diff --git a/docs/README.md b/docs/README.md
@@ -48,11 +48,11 @@ pip3 install -r requirements.txt
 
 ### Building and installation
 
-In order to build ASTE, clone the project repository and use the usual `CMake` steps to steer the installation procedure:
+In order to build ASTE, download the [latest release](https://github.com/precice/aste/releases/latest) (or clone the `master` branch of the project repository) and use the usual `CMake` steps to steer the installation procedure:
 
 ```bash
-git clone https://github.com/precice/aste.git
-mkdir build && cd build
+git clone --branch master https://github.com/precice/aste.git
+cd aste && mkdir build && cd build
 cmake .. && make
 ```
 
@@ -95,6 +95,7 @@ The following subsections explain each part of ASTE in more detail. All ASTE mod
 | --------------- | ---------------------------------------------------------------------- |
 | `--aste-config` | ASTE configuration file (only used for replay mode)                    |
 | `-v`            | Enables verbose logging output from preCICE                            |
+| `-a`            | Enables additional logging from all secondary ranks                    |
 | `-c`            | To specify preCICE configuration file (default=`"precice-config.xml"`) |
 | `-p`            | Participant name, which can take the arguments `A` or `B`              |
 | `--vector`      | A bool switch to specify vector data (default=`False`)                 |
@@ -110,7 +111,7 @@ precice-aste-run -p A --mesh fine_mesh --data "dummyData"
 precice-aste-run -p B --mesh coarse_mesh --data "mappedData" --output mappedMesh
 ```
 
-While the example above exexutes the mapping in serial, `precice-aste-run` can be executed in parallel (using MPI). However, this requires a partitioned mesh (one per parallel rank). In order to decompose a single mesh appropriately, the tools `precice-aste-partition` and `precice-aste-join` can be used.
+While the example above executes the mapping in serial, `precice-aste-run` can be executed in parallel (using MPI). However, this requires a partitioned mesh (one per parallel rank). In order to decompose a single mesh appropriately, the tools `precice-aste-partition` and `precice-aste-join` can be used.
 
 {% tip %}
 If you want to reproduce a specific setup of your solvers, you can use the [export functionality](https://precice.org/configuration-export.html#enabling-exporters) of preCICE and use the generated meshes directly in `precice-aste-run`. If you run your solver in parallel, preCICE exports the decomposed meshes directly, so that no further partitioning is required.

diff --git a/examples/lci_2d/precice-config.xml b/examples/lci_2d/precice-config.xml
@@ -1,46 +1,41 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 <precice-configuration>
-  <log>
-    <sink
-      filter="%Severity% > debug and %Rank% = 0"
-      format="---[precice] %ColorizedSeverity% %Message%"
-      enabled="true" />
-  </log>
-
-  <solver-interface dimensions="2">
-    <data:scalar name="Data" />
-
-    <mesh name="A-Mesh">
-      <use-data name="Data" />
-    </mesh>
-
-    <mesh name="B-Mesh">
-      <use-data name="Data" />
-    </mesh>
-
-    <m2n:sockets from="A" to="B" exchange-directory="." />
-
-    <participant name="A">
-      <use-mesh name="A-Mesh" provide="yes" />
-      <write-data name="Data" mesh="A-Mesh" />
-    </participant>
-
-    <participant name="B">
-      <use-mesh name="A-Mesh" provide="no" from="A" />
-      <use-mesh name="B-Mesh" provide="yes" />
-      <read-data name="Data" mesh="B-Mesh" />
-      <mapping:linear-cell-interpolation
-        constraint="consistent"
-        direction="read"
-        from="A-Mesh"
-        to="B-Mesh" />
-    </participant>
-
-    <coupling-scheme:parallel-explicit>
-      <participants first="A" second="B" />
-      <max-time value="1.0" />
-      <time-window-size value="1" />
-      <exchange data="Data" mesh="A-Mesh" from="A" to="B" />
-    </coupling-scheme:parallel-explicit>
-  </solver-interface>
+  <log enabled="0" />
+
+  <profiling mode="all" />
+
+  <data:scalar name="Data" />
+
+  <mesh name="A-Mesh" dimensions="2">
+    <use-data name="Data" />
+  </mesh>
+
+  <mesh name="B-Mesh" dimensions="2">
+    <use-data name="Data" />
+  </mesh>
+
+  <m2n:sockets acceptor="A" connector="B" exchange-directory="." />
+
+  <participant name="A">
+    <provide-mesh name="A-Mesh" />
+    <write-data name="Data" mesh="A-Mesh" />
+  </participant>
+
+  <participant name="B">
+    <receive-mesh name="A-Mesh" from="A" />
+    <provide-mesh name="B-Mesh" />
+    <read-data name="Data" mesh="B-Mesh" />
+    <mapping:linear-cell-interpolation
+      constraint="consistent"
+      direction="read"
+      from="A-Mesh"
+      to="B-Mesh" />
+  </participant>
+
+  <coupling-scheme:parallel-explicit>
+    <participants first="A" second="B" />
+    <max-time value="1.0" />
+    <time-window-size value="1" />
+    <exchange data="Data" mesh="A-Mesh" from="A" to="B" />
+  </coupling-scheme:parallel-explicit>
 </precice-configuration>