WIP Feat/output module production readiness

.devcontainer/devcontainer-lock.json

@@ -0,0 +1,14 @@
+{
+  "features": {
+    "ghcr.io/devcontainers/features/python:1": {
+      "version": "1.8.0",
+      "resolved": "ghcr.io/devcontainers/features/python@sha256:fbcad6955caeecc5ad3f7886baf652e25cba5225a6c4c2287c536de2e5607511",
+      "integrity": "sha256:fbcad6955caeecc5ad3f7886baf652e25cba5225a6c4c2287c536de2e5607511"
+    },
+    "ghcr.io/msclock/features/vcpkg:2": {
+      "version": "2.0.0",
+      "resolved": "ghcr.io/msclock/features/vcpkg@sha256:bcb75d475252af1f9ef742860387cb15e059f57041748abdd02030cd1a181471",
+      "integrity": "sha256:bcb75d475252af1f9ef742860387cb15e059f57041748abdd02030cd1a181471"
+    }
+  }
+}

.devcontainer/devcontainer.json

@@ -1,46 +1,69 @@
-// For format details, see https://aka.ms/devcontainer.json. For config options, see the
-// README at: https://github.com/devcontainers/templates/tree/main/src/cpp
 {
-	"name": "OpenSEMBA dev. framework",
-	"build": {
-		"dockerfile": "Dockerfile"
-	},
-	"features": {
-		"ghcr.io/msclock/features/vcpkg:2": {},
-		"ghcr.io/devcontainers/features/python:1": {}
-	},
-
-	// Features to add to the dev container. More info: https://containers.dev/features.
-	// "features": {},
-
-	// Use 'forwardPorts' to make a list of ports inside the container available locally.
-	// "forwardPorts": [],
-
-	// Use 'postCreateCommand' to run commands after the container is created.
-	"postStartCommand": "git config --global --add safe.directory ${containerWorkspaceFolder}",
-
-	// Configure tool-specific properties.
-	"customizations": {
-		"codespaces": {
-		  "repositories": {
-			"lmdiazangulo/json-fortran": { "permissions": "read-all" },
-			"opensemba/fhash": { "permissions": "read-all" },
-			"reference-lapack/lapack": { "permissions": "read-all" },
-			"opensemba/ngtest": {"permissions": "read-all" },
-			"google/googletest": { "permissions": "read-all" }
-		  }
-		},
-		"vscode": {
-			"extensions": [
-				"ms-toolsai.jupyter",
-				"fortran-lang.linter-gfortran",
-				"ms-vscode.cmake-tools",
-				"ms-python.autopep8",
-				"matepek.vscode-catch2-test-adapter"
-			]
-		}
-	  }
-
-	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
-	// "remoteUser": "root"
+  "name": "semba-fdtd dev",
+  "dockerComposeFile": [
+    "../docker-compose.yml"
+  ],
+  "service": "dev",
+  "workspaceFolder": "/home/developer/workspaces/fdtd",
+  "remoteUser": "developer",
+  "containerUser": "developer",
+  "overrideCommand": false,
+  "features": {
+    "ghcr.io/msclock/features/vcpkg:2": {},
+    "ghcr.io/devcontainers/features/python:1": {}
+  },
+  "remoteEnv": {
+    "HOME": "/home/developer",
+    "XDG_CONFIG_HOME": "/home/developer/.config",
+    "XDG_DATA_HOME": "/home/developer/.local/share",
+    "OPENAI_API_KEY": "${localEnv:OPENAI_API_KEY}"
+  },
+  "postCreateCommand": ".devcontainer/setup-python.sh",
+  "postStartCommand": "bash scripts/devcontainer-post-start.sh",
+  "customizations": {
+    "codespaces": {
+      "repositories": {
+        "lmdiazangulo/json-fortran": { "permissions": "read-all" },
+        "opensemba/fhash": { "permissions": "read-all" },
+        "reference-lapack/lapack": { "permissions": "read-all" },
+        "opensemba/ngtest": { "permissions": "read-all" },
+        "google/googletest": { "permissions": "read-all" }
+      }
+    },
+    "vscode": {
+      "extensions": [
+        "fortran-lang.linter-gfortran",
+        "ms-vscode.cmake-tools",
+        "ms-vscode.cpptools",
+        "ms-python.python",
+        "mhutchie.git-graph"
+      ],
+      "settings": {
+        "cmake.buildDirectory": "${workspaceFolder}/build",
+        "cmake.useCMakePresets": "always",
+        "python.defaultInterpreterPath": "${workspaceFolder}/.venv/bin/python",
+        "terminal.integrated.defaultProfile.linux": "bash",
+        "fortran.fortls.path": "/usr/local/bin/fortls",
+        "fortran.fortls.notifyInit": true,
+        "fortran.fortls.disableAutoupdate": true,
+        "fortran.provide.hover": "Both",
+        "fortran.formatting.formatter": "fprettify",
+        "editor.tokenColorCustomizations": {
+          "textMateRules": [
+            {
+              "scope": [
+                "entity.name.function.fortran",
+                "entity.name.function.procedure.fortran",
+                "entity.name.function.subroutine.fortran"
+              ],
+              "settings": {
+                "foreground": "#DCDCAA",
+                "fontStyle": "bold"
+              }
+            }
+          ]
+        }
+      }
+    }
+  }
 }

.devcontainer/setup-python.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+python3 -m venv .venv
+.venv/bin/python -m pip install --upgrade pip
+.venv/bin/python -m pip install -r requirements.txt

.dockerignore

@@ -1,6 +1,10 @@
 .git
 build/
+build-*/
 .venv/
+.devcontainer/
+.vscode/
+.github/
 __pycache__/
 *.pyc
 *.pyo
@@ -9,4 +13,24 @@ __pycache__/
 dist/
 *.o
 *.mod
-# Keep precompiled_libraries and external/ submodule contents
+
+# Runtime/development bind mounts do not need to be copied into image layers.
+simulations/
+
+# Linux Docker builds only use the GNU LAPACK bundle.
+precompiled_libraries/**
+!precompiled_libraries/
+!precompiled_libraries/linux-gcc/
+!precompiled_libraries/linux-gcc/**
+
+# The top-level build only consumes selected external sources.
+external/lapack/
+external/ngspice/examples/
+external/ngspice/tests/
+external/ngspice/visualc/
+external/ngspice/man/
+external/ngspice/doc/
+external/ngspice/.git/
+external/googletest/.git/
+external/json-fortran/.git/
+external/fhash/.git/

.fortlsrc

@@ -0,0 +1,18 @@
+{
+  "source_dirs": [
+    "./src_conformal",
+    "./src_json_parser",
+    "./src_main_pub",
+    "./src_mtln",
+    "./src_output",
+    "./src_pyWrapper",
+    "./src_utils",
+    "./src_wires_pub",
+    "./test"
+  ],
+  "excl_paths": [
+    "./build*",
+    "./.venv",
+    "./Testing"
+  ]
+}

.github/workflows/ubuntu.yml

@@ -70,7 +70,7 @@ jobs:
       if: matrix.compiler.name=='gcc'
       run: |
         sudo apt update
-        sudo apt install libhdf5-dev libopenmpi-dev
+        sudo apt install libhdf5-dev libhdf5-openmpi-dev libopenmpi-dev
 
     - name: Setup fortran compiler
       uses: fortran-lang/setup-fortran@v1
@@ -92,12 +92,59 @@ jobs:
     - name: Run unit tests 
       run: build/bin/fdtd_tests
 
+    - name: Verify output (serial)
+      if: matrix.mpi=='OFF'
+      run: build/bin/fdtd_tests --gtest_filter='output.*'
+
+    - name: Verify output (MPI collective)
+      if: matrix.mpi=='ON'
+      run: ctest --test-dir build --output-on-failure -R '^output_mpi_collective_and_root_aggregation$'
+
+    - name: Verify output (MPI root aggregation)
+      if: matrix.mpi=='ON'
+      run: ctest --test-dir build --output-on-failure -R '^output_mpi_collective_and_root_aggregation$'
+
+    - name: Run CTest suites
+      run: ctest --test-dir build --output-on-failure
+
     - name: Run python tests
       env:
         SEMBA_FDTD_ENABLE_MPI: ${{ matrix.mpi }}
         SEMBA_FDTD_ENABLE_MTLN: ${{ matrix.mtln }}
         SEMBA_FDTD_ENABLE_HDF: ${{ matrix.hdf }}
       run: python -m pytest test/ --durations=20
+
+  parallel-hdf5-build:
+    runs-on: ubuntu-latest
+    name: ubuntu / gcc / parallel-hdf5
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+        submodules: 'recursive'
+
+    - name: Install parallel HDF5
+      run: |
+        sudo apt update
+        sudo apt install gfortran libhdf5-openmpi-dev libopenmpi-dev python3-h5py python3-numpy
+
+    - name: Configure parallel HDF5 output
+      run: |
+        cmake -S . -B build \
+          -DCMAKE_BUILD_TYPE=Release \
+          -DSEMBA_FDTD_ENABLE_MPI=ON \
+          -DSEMBA_FDTD_ENABLE_HDF=ON \
+          -DSEMBA_FDTD_ENABLE_MTLN=OFF \
+          -DSEMBA_FDTD_ENABLE_TEST=OFF \
+          -DXDMF_HDF5_BUILD_TESTING=ON \
+          -DHDF5_ROOT=/usr/lib/x86_64-linux-gnu/hdf5/openmpi
+
+    - name: Build parallel HDF5 output
+      run: cmake --build build -j
+
+    - name: Test parallel HDF5 output
+      run: ctest --test-dir build --output-on-failure -R '^xdmf-hdf5-(generate|verify|mpi-generate|mpi-verify)$'
 
 
 

.github/workflows/windows.yml

@@ -71,6 +71,12 @@ jobs:
     - name: Run unit tests 
       run: build/bin/fdtd_tests.exe
 
+    - name: Verify output (serial)
+      run: build/bin/fdtd_tests.exe --gtest_filter=output.*
+
+    - name: Run CTest suites
+      run: ctest --test-dir build --output-on-failure
+
     - name: Run python tests (except codemodel)
       env:
         SEMBA_FDTD_ENABLE_MPI: ${{ matrix.mpi }}

.gitignore

@@ -50,7 +50,6 @@ Testing/
 /SEMBA_FDTD_temp.log
 .vscode/launch.json
 .vscode/settings.json
-.vscode/tasks.json
 */*.bak
 ./*.bak
 .vscode/ltex.dictionary.en-US.txt
@@ -76,4 +75,5 @@ git_info.txt
 
 .venv/build2/
 build2/
-.venv/
+.venv/
+specs/changes/*