Merge pull request #8 from aurora-multiphysics/2-add-read-heat-flux-hdf5

Intermediate stage of reading heat flux values from ASCOT5 HDF5 file. Input from @dynamicist about design and general C++ features.

.devcontainer/devcontainer.json

@@ -0,0 +1,32 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.187.0/containers/docker-existing-dockerfile
+{
+	"name": "Phaethon Dockerfile",
+
+	// Sets the run context to one level up instead of the .devcontainer folder.
+	"context": "..",
+
+	// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
+	"dockerFile": "../Dockerfile",
+
+	// Set *default* container specific settings.json values on container create.
+	"settings": {},
+
+	// Add the IDs of extensions you want installed when the container is created.
+	"extensions": ["ms-vscode.cpptools-extension-pack", "ms-azuretools.vscode-docker"]
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Uncomment the next line to run commands after the container is created - for example installing curl.
+	// "postCreateCommand": "apt-get update && apt-get install -y curl",
+
+	// Uncomment when using a ptrace-based debugger like C++, Go, and Rust
+	// "runArgs": [ "--cap-add=SYS_PTRACE", "--security-opt", "seccomp=unconfined" ],
+
+	// Uncomment to use the Docker CLI from inside the container. See https://aka.ms/vscode-remote/samples/docker-from-docker.
+	// "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind" ],
+
+	// Uncomment to connect as a non-root user if you've added one. See https://aka.ms/vscode-remote/containers/non-root.
+	// "remoteUser": "vscode"
+}

.dockerignore

@@ -0,0 +1,21 @@
+**/.classpath
+**/.dockerignore
+**/.env
+**/.git
+**/.gitignore
+**/.project
+**/.settings
+**/.toolstarget
+**/.vs
+**/.vscode
+**/*.*proj.user
+**/*.dbmdl
+**/*.jfm
+**/azds.yaml
+**/charts
+**/docker-compose*
+**/compose*
+**/Dockerfile*
+**/secrets.dev.yaml
+**/values.dev.yaml
+/moose

.gitmodules

@@ -1,10 +1,6 @@
 [submodule "ascot5-python"]
 	path = ascot5-python
 	url = [email protected]:ascot/python.git
-[submodule "moose"]
-	path = moose
-	url = [email protected]:idaholab/moose.git
-	branch = master
 [submodule "ascot5"]
 	path = ascot5
 	url = [email protected]:ascot/ascot5.git

.vscode/c_cpp_properties.json

@@ -0,0 +1,44 @@
+{
+    "configurations": [
+        {
+            "name": "MOOSE-Linux",
+            "includePath": [
+                "${workspaceFolder}",
+                "${workspaceFolder}/build/header_symlinks",
+                "${workspaceFolder}/unit/build/header_symlinks",
+                "${MOOSE_DIR}/framework/build/header_symlinks",
+                "${MOOSE_DIR}/framework/contrib/gtest",
+                "${MOOSE_DIR}/modules/module_loader/build/header_symlinks",
+                "${MOOSE_DIR}/framework/contrib/boost/include",
+                "${MOOSE_DIR}/framework/contrib/hit",
+                "${MOOSE_DIR}/framework/contrib/json/include",
+                "${MOOSE_DIR}/libmesh/installed/include",
+                "/usr/include/hdf5/serial",
+                "${PETSC_DIR}/include"
+            ],
+            "defines": [],
+            "compilerPath": "/usr/bin/mpicxx",
+            "cStandard": "c11",
+            "cppStandard": "c++17",
+            "intelliSenseMode": "linux-gcc-x64",
+            "browse": {
+                "path": [
+                    "${workspaceFolder}",
+                    "${workspaceFolder}/build/header_symlinks",
+                    "${workspaceFolder}/unit/build/header_symlinks",
+                    "${MOOSE_DIR}/framework/build/header_symlinks",
+                    "${MOOSE_DIR}/framework/contrib/gtest",
+                    "${MOOSE_DIR}/modules/module_loader/build/header_symlinks",
+                    "${MOOSE_DIR}/framework/contrib/boost/include",
+                    "${MOOSE_DIR}/framework/contrib/hit",
+                    "${MOOSE_DIR}/framework/contrib/json/include",
+                    "${MOOSE_DIR}/libmesh/installed/include",
+                    "/usr/include/hdf5/serial",
+                    "${PETSC_DIR}/include"
+                ]
+            },
+            "compilerArgs": [ ]
+        }
+    ],
+    "version": 4
+}

.vscode/launch.json

@@ -0,0 +1,48 @@
+{
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Current File",
+            "type": "python",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal"
+        },
+        {
+            "name": "(lldb) Launch",
+            "type": "cppdbg",
+            "request": "launch",
+            "program": "${workspaceFolder}/phaethon-dbg",
+            "args": [
+                "-i",
+                "test/tests/simple_diffusion/simple_diffusion.i"
+            ],
+            "stopAtEntry": false,
+            "cwd": "${workspaceFolder}",
+            "environment": [],
+            "externalConsole": true,
+            "MIMode": "lldb",
+            "logging": {
+                "trace": true,
+                "traceResponse": true,
+                "engineLogging": true
+            }
+        },
+        {
+            "name": "(lldb) Unit Test Launch",
+            "type": "cppdbg",
+            "request": "launch",
+            "program": "${workspaceFolder}/unit/phaethon-unit-dbg",
+            "stopAtEntry": false,
+            "cwd": "${workspaceFolder}",
+            "environment": [],
+            "externalConsole": true,
+            "MIMode": "gdb",
+            "logging": {
+                "trace": true,
+                "traceResponse": true,
+                "engineLogging": true
+            }
+        }
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,20 @@
+{
+    "files.associations": {
+        "*.C": "cpp",
+        "*.h": "cpp",
+        "cmath": "cpp",
+        "ratio": "cpp",
+        "*.tcc": "cpp",
+        "fstream": "cpp",
+        "iosfwd": "cpp",
+        "istream": "cpp",
+        "limits": "cpp",
+        "shared_mutex": "cpp",
+        "sstream": "cpp",
+        "streambuf": "cpp",
+        "vector": "cpp"
+    },
+    "python.linting.flake8Enabled": true,
+    "python.linting.enabled": true,
+    "restructuredtext.languageServer.disabled": true
+}

.vscode/tasks.json

@@ -0,0 +1,117 @@
+{
+    "version": "2.0.0",
+    "tasks": [
+        {
+            "label": "Build Unit Tests",
+            "type": "shell",
+            "command": "make",
+            "group": {
+                "kind": "build",
+                "isDefault": true
+            },
+            "options": {"shell": {"args": ["-ic"]}},
+            "presentation": {
+                "echo": true,
+                "reveal": "always",
+                "focus": false,
+                "panel": "shared"
+            },
+            "args": ["--directory=${workspaceFolder}/unit", "METHOD=devel", "-j4"],
+            "problemMatcher": {
+                "owner": "cpp",
+                "fileLocation": ["absolute"],
+                "pattern": {
+                    "regexp": "^(.*):(\\d+):(\\d+):\\s+(warning|error):\\s+(.*)$",
+                    "file": 1,
+                    "line": 2,
+                    "column": 3,
+                    "severity": 4,
+                    "message": 5
+                }
+            }
+        },
+        {
+            "label": "Makefike debug",
+            "type": "shell",
+            "command": "make",
+            "group": "none",
+            "options": {"shell": {"args": ["-ic"]}},
+            "presentation": {
+                "echo": true,
+                "reveal": "always",
+                "focus": false,
+                "panel": "shared"
+            },
+            "args": ["METHOD=dbg", "-j4"],
+            "problemMatcher": {
+                "owner": "cpp",
+                "fileLocation": ["absolute"],
+                "pattern": {
+                    "regexp": "^(.*):(\\d+):(\\d+):\\s+(warning|error):\\s+(.*)$",
+                    "file": 1,
+                    "line": 2,
+                    "column": 3,
+                    "severity": 4,
+                    "message": 5
+                }
+            }
+        },
+        {
+            "label": "Makefike clean",
+            "type": "shell",
+            "command": "make",
+            "group": "none",
+            "options": {"shell": {"args": ["-ic"]}},
+            "presentation": {
+                "echo": true,
+                "reveal": "always",
+                "focus": false,
+                "panel": "shared"
+            },
+            "args": ["clean"],
+            "problemMatcher": {
+                "owner": "cpp",
+                "fileLocation": ["absolute"],
+                "pattern": {
+                    "regexp": "^(.*):(\\d+):(\\d+):\\s+(warning|error):\\s+(.*)$",
+                    "file": 1,
+                    "line": 2,
+                    "column": 3,
+                    "severity": 4,
+                    "message": 5
+                }
+            }
+        },
+        {
+            "label": "Test",
+            "type": "shell",
+            "command": "./run_tests",
+            "group": "test",
+            "options": {"shell": {"args": ["-ic"]}},
+            "presentation": {
+                "echo": true,
+                "reveal": "always",
+                "focus": false,
+                "panel": "shared"
+            },
+            "args": ["-j4"]
+        },
+        {
+            "label": "Run Unit Tests",
+            "type": "shell",
+            "command": "./unit/run_tests",
+            "group": {
+                "kind": "test",
+                "isDefault": true
+            },
+            "options": {"shell": {"args": ["-ic"]}},
+            "presentation": {
+                "echo": true,
+                "reveal": "always",
+                "focus": false,
+                "panel": "shared"
+            },
+            "args": ["-j4"]
+        }
+    ]
+}

Dockerfile

@@ -0,0 +1,57 @@
+####################
+# ASCOT5 Build Stage
+####################
+# TODO should probably move away from using submodules. It means the version
+# information of dependencies is scattered, and it would be better to centralise
+# it here.
+FROM helenbrooks/moose-ubuntu AS ascot5-moose-ubuntu
+
+# Basic environment
+ARG DEBIAN_FRONTEND=noninteractive
+WORKDIR /home/ascot5
+# Set path to shared library for Python interface to use and other environment
+ENV LD_LIBRARY_PATH=/home/ascot5 EDITOR=vim LC_ALL=C.UTF-8 LANG=C.UTF-8
+
+# ASCOT5 main C program and library
+RUN apt-get update && apt-get -y install make libhdf5-dev
+COPY ascot5 ./
+# This is a completely serial version with no MPI or OpenMP offloading to GPUs
+ENV MAKE_OPT='NOGIT=true CC=h5cc MPI=0 FLAGS=-foffload=disable'
+RUN make clean ${MAKE_OPT}} && make ascot5_main ${MAKE_OPT} && \
+    make libascot ${MAKE_OPT} && \
+    ln -s -t /usr/local/bin/ $(readlink -f ascot5_main)
+
+# ASCOT5 Python
+RUN apt-get -y install python3-pip 
+COPY ascot5-python ./ascot5-python
+RUN pip install ascot5-python/a5py
+
+###################################
+# Phaethon Dependencies Build Stage
+###################################
+FROM ascot5-moose-ubuntu AS phaethon-deps
+
+RUN pip install meshio[all] click
+
+##################################
+# Phaethon Development Environment
+##################################
+FROM phaethon-deps as phaethon-dev
+
+ENV METHOD=devel
+WORKDIR /home/moose
+# Update libMesh and PETSc
+RUN ./scripts/update_and_rebuild_petsc.sh --prefix=/home/petsc && \
+    ./scripts/update_and_rebuild_libmesh.sh --with-mpi
+# This is needed or it mpiexec complains because docker runs as root
+# Discussion on this issue https://github.com/open-mpi/ompi/issues/4451
+ENV OMPI_ALLOW_RUN_AS_ROOT=1
+ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+# Re-build MOOSE framework in devel mode
+RUN cd test && make -j4 && ./run_tests -j4
+RUN cd modules && make -j4 && ./run_tests -j4
+
+RUN apt-get -y install clang-format curl
+RUN curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash && \
+    apt-get -y install git-lfs && \
+    git lfs install

Makefile

@@ -49,6 +49,10 @@ XFEM                        := no
 include $(MOOSE_DIR)/modules/modules.mk
 ###############################################################################
 
+# Additional libraries for HDF5 support
+ADDITIONAL_INCLUDES := -I/usr/include/hdf5/serial
+ADDITIONAL_LIBS     := -lhdf5_hl_cpp -lhdf5_cpp -lhdf5_serial_hl -lhdf5_serial
+
 # dep apps
 APPLICATION_DIR    := $(CURDIR)
 APPLICATION_NAME   := phaethon