Release v0.5.1

.github/workflows/build_and_test.yaml

@@ -46,17 +46,17 @@ jobs:
           cmake --version
           cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_EXPORT_COMPILE_COMMANDS=ON ..
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         if: failure()
         with:
           name: ${{ format('Ubuntu {0}', matrix.UBUNTU_VERSION) }} CMakeCache
           path: ${{ env.FANS_BUILD_DIR }}/CMakeCache.txt
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         if: failure()
         with:
           name: ${{ format('Ubuntu {0}', matrix.UBUNTU_VERSION) }} CMakeLogs
           path: '${{ env.FANS_BUILD_DIR }}/CMakeFiles/*.log'
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         if: failure()
         with:
           name: ${{ format('Ubuntu {0}', matrix.UBUNTU_VERSION) }} CompileCommands
@@ -75,7 +75,7 @@ jobs:
         run: |
           su -c "ctest" ${{ env.FANS_MPI_USER }}
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         if: failure()
         with:
           name: ${{ format('Ubuntu {0}', matrix.UBUNTU_VERSION) }} CTest logs
@@ -87,7 +87,7 @@ jobs:
       - name: Run pytest checks on HDF5 output
         run: pixi run -e dashboard pytest
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         if: failure()
         with:
           name: ${{ format('Ubuntu {0}', matrix.UBUNTU_VERSION) }} PyTest logs

.github/workflows/pixi_build.yaml

@@ -31,12 +31,12 @@ jobs:
         run: pixi run test
 
       - name: Upload test logs
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: ${{ matrix.os }} test-logs
           path: test/output/*.log
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         if: failure()
         with:
           name: ${{ matrix.os }} PyTest logs

.github/workflows/run-checks.yml

@@ -14,6 +14,15 @@ jobs:
     steps:
       - name: Check out repository
         uses: actions/checkout@v5
+      - name: Create markdownlint config
+        run: |
+          cat > .markdownlint.json << 'EOF'
+          {
+            "MD013": false,
+            "MD033": false,
+            "MD034": false
+          }
+          EOF
       - name: Lint markdown files (markdownlint)
         uses: articulate/actions-markdownlint@v1
         with:
@@ -26,6 +35,18 @@ jobs:
     steps:
       - name: Check out repository
         uses: actions/checkout@v5
+      - name: Create markdown-link-check config
+        run: |
+          cat > .markdown-link-check-config.json << 'EOF'
+          {
+            "aliveStatusCodes": [429, 200],
+            "ignorePatterns": [
+              {
+                "pattern": "*.html"
+              }
+            ]
+          }
+          EOF
       - name: Check links in markdown files (markdown-link-check)
         uses: gaurav-nelson/github-action-markdown-link-check@v1
         with:

CHANGELOG.md

@@ -1,5 +1,9 @@
 # FANS Changelog
 
+## v0.5.1
+
+- Optimize HDF5 I/O performance by using collective I/O operations [#105](https://github.com/DataAnalyticsEngineering/FANS/pull/105)
+
 ## v0.5.0
 
 - Add explicit FE types (HEX8, HEX8R, BBAR) to JSON input [#96](https://github.com/DataAnalyticsEngineering/FANS/pull/96)

CMakeLists.txt

@@ -5,7 +5,7 @@ cmake_minimum_required(VERSION 3.21)
 # ##############################################################################
 
 project(FANS
-        VERSION 0.5.0
+        VERSION 0.5.1
         LANGUAGES C CXX
 )
 
@@ -88,8 +88,8 @@ if ("$ENV{SETVARS_COMPLETED}" STREQUAL "1")
     )
 endif ()
 
-set(HDF5_ENABLE_PARALLEL ON)
-find_package(HDF5 REQUIRED COMPONENTS CXX)
+set(HDF5_PREFER_PARALLEL TRUE)
+find_package(HDF5 REQUIRED COMPONENTS C CXX)
 
 find_package(Eigen3 REQUIRED)
 
@@ -198,6 +198,7 @@ target_link_libraries(FANS_FANS PRIVATE m)
 # call to target_link_libraries(FANS_FANS PUBLIC HDF5::HDF5). But CMake 3.16
 # does not yet support this.
 target_include_directories(FANS_FANS PRIVATE ${HDF5_INCLUDE_DIRS})
+target_link_libraries(FANS_FANS PUBLIC ${HDF5_C_LIBRARIES})
 target_link_libraries(FANS_FANS PUBLIC ${HDF5_CXX_LIBRARIES})
 target_compile_definitions(FANS_FANS PUBLIC ${HDF5_DEFINITIONS})
 if (HDF5_IS_PARALLEL)

FANS_Dashboard/FANS_Dashboard.ipynb

@@ -51,10 +51,10 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "from fans_dashboard.core.utils import *\n",
-    "from fans_dashboard.core.postprocessing import compute_rank2tensor_measures\n",
+    "from MSUtils.fans_dashboard.utils import *\n",
+    "from MSUtils.fans_dashboard.postprocessing import compute_rank2tensor_measures\n",
     "from MSUtils.general.h52xdmf import write_xdmf\n",
-    "from fans_dashboard.plotting.plotting import plot_subplots"
+    "from MSUtils.fans_dashboard.plotting import plot_subplots"
    ]
   },
   {

FANS_Dashboard/README.md

@@ -1,5 +1,5 @@
 # FANS Dashboard
 
-The FANS Dashboard is a comprehensive tool designed to streamline the post-processing, interpretation, and visualization of results generated by the FANS solver. This jupyter notebook provides a user-friendly environment to work with complex simulation data stored in HDF5 format, offering a step-by-step workflow that covers data extraction, postprocessing, visualization, and preparation for 3D visualization in tools like ParaView.
+The FANS Dashboard is a comprehensive tool designed to streamline the post-processing, interpretation, and visualization of results generated by the FANS solver. It uses helper functions from [MSUtils](https://github.com/DataAnalyticsEngineering/MSUtils) to facilitate various tasks. This jupyter notebook provides an exemplary pipeline and a user-friendly environment to work with complex simulation data stored in HDF5 format, offering a step-by-step workflow that covers data extraction, postprocessing, visualization, and preparation for 3D visualization in tools like ParaView.
 
 For further details follow along [`FANS_Dashboard.ipynb`](FANS_Dashboard.ipynb)