feat(pffdtd): add PFFDTD (Brian Hamilton) wave-equation FDTD method

example_settings/pffdtd_setting.json

@@ -0,0 +1,79 @@
+{
+    "type": "simulationSettings",
+    "options": [
+        {
+            "name": "Speed of sound",
+            "id": "pffdtd_c0",
+            "type": "float",
+            "display": "text",
+            "min": 100,
+            "max": 500,
+            "default": 343,
+            "step": 1,
+            "endAdornment": "m/s"
+        },
+        {
+            "name": "Frequency upper limit",
+            "id": "pffdtd_fmax",
+            "type": "float",
+            "display": "text",
+            "min": 100,
+            "max": 4000,
+            "default": 1000,
+            "step": 50,
+            "endAdornment": "Hz"
+        },
+        {
+            "name": "Points per wavelength",
+            "id": "pffdtd_ppw",
+            "type": "integer",
+            "display": "text",
+            "min": 4,
+            "max": 12,
+            "default": 6,
+            "step": 1
+        },
+        {
+            "name": "Impulse response length",
+            "id": "pffdtd_ir_length",
+            "type": "float",
+            "display": "text",
+            "min": 0.1,
+            "max": 5,
+            "default": 1.0,
+            "step": 0.1,
+            "endAdornment": "s"
+        },
+        {
+            "name": "Air temperature",
+            "id": "pffdtd_temperature",
+            "type": "float",
+            "display": "text",
+            "min": -20,
+            "max": 50,
+            "default": 20,
+            "step": 0.5,
+            "endAdornment": "°C"
+        },
+        {
+            "name": "Relative humidity",
+            "id": "pffdtd_humidity",
+            "type": "float",
+            "display": "text",
+            "min": 0,
+            "max": 100,
+            "default": 50,
+            "step": 1,
+            "endAdornment": "%"
+        },
+        {
+            "name": "Use GPU (when available)",
+            "id": "pffdtd_use_gpu",
+            "type": "string",
+            "display": "radio",
+            "options": {"Yes": "yes", "No": "no"},
+            "default": "no",
+            "description": "Try Hamilton's compiled CUDA c_cuda binary if the container has GPU passthrough at runtime; otherwise falls back to the pure-Python numba CPU engine. Default no so the method works on every CHORAS host."
+        }
+    ]
+}

methods-config.json

@@ -21,12 +21,22 @@
     },
     {
         "simulationType": "MyNewMethod",
-        "containerImage": "mynewmethod_image:latest", 
+        "containerImage": "mynewmethod_image:latest",
         "envVars": {},
         "label": "My New Method",
         "entryFile":"MyNewMethodInterface.py",
         "settings":"my_new_setting.json",
         "repositoryURL":"",
         "documentationURL":""
+    },
+    {
+        "simulationType": "PFFDTD",
+        "containerImage": "pffdtd_image:latest",
+        "envVars": {},
+        "label": "PFFDTD (Hamilton wave-equation FDTD)",
+        "settings": "pffdtd_setting.json",
+        "entryFile": "PFFDTDinterface.py",
+        "repositoryURL": "https://github.com/bsxfun/pffdtd",
+        "documentationURL": "https://github.com/bsxfun/pffdtd"
     }
 ]

pffdtd_method/Dockerfile

@@ -0,0 +1,82 @@
+# CUDA devel base: needs nvcc at build time to compile Hamilton's c_cuda
+# binary. At runtime the binary only requires the CUDA runtime libs which
+# the same image ships. On hosts without GPU passthrough at runtime, the
+# binary is never invoked -- the wrapper auto-falls-back to the pure-Python
+# numba CPU engine. So this image works on every host CHORAS supports.
+FROM nvidia/cuda:12.6.0-devel-ubuntu22.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+ENV PYTHONUNBUFFERED=1
+
+WORKDIR /app
+
+# Python 3.11 (Ubuntu 22.04 default is 3.10; PFFDTD method package floor is
+# 3.11). libhdf5-dev needed to compile PFFDTD's c_cuda binary against HDF5.
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        software-properties-common \
+        ca-certificates \
+        gnupg \
+    && add-apt-repository -y ppa:deadsnakes/ppa \
+    && apt-get update && apt-get install -y --no-install-recommends \
+        git \
+        build-essential \
+        gmsh \
+        libhdf5-dev \
+        libglu1-mesa \
+        libxcursor1 \
+        libxinerama1 \
+        curl \
+        python3.11 \
+        python3.11-dev \
+        python3.11-venv \
+        python3.11-distutils \
+    && rm -rf /var/lib/apt/lists/* \
+    && curl -sS https://bootstrap.pypa.io/get-pip.py | python3.11 \
+    && ln -sf /usr/bin/python3.11 /usr/local/bin/python \
+    && ln -sf /usr/bin/python3.11 /usr/local/bin/python3
+
+# Ubuntu apt-shipped pip (22.0.2) doesn't parse PEP 621 [project] tables.
+# Upgrade before installing the method package or it registers as UNKNOWN
+# with zero deps and the next pip run fails on missing imports.
+RUN pip install --no-cache-dir --upgrade pip setuptools wheel
+
+# Clone PFFDTD (Brian Hamilton, MIT). The repo has no setup.py / pyproject.toml;
+# python/ subtree is added to PYTHONPATH. sed-fix the deprecated numpy
+# aliases (np.float -> np.float64 was removed in numpy>=1.20; np.bool8 etc.
+# in numpy>=2.0, hence we also pin numpy<2 in pyproject.toml).
+ENV PFFDTD_REPO=https://github.com/bsxfun/pffdtd.git
+ENV PFFDTD_REF=aa319f6
+ENV PFFDTD_SRC=/opt/pffdtd_src
+
+RUN git clone --depth 50 ${PFFDTD_REPO} ${PFFDTD_SRC} \
+ && git -C ${PFFDTD_SRC} checkout ${PFFDTD_REF} \
+ && ln -s ${PFFDTD_SRC}/python /app/pffdtd_python \
+ && find ${PFFDTD_SRC}/python -name "*.py" -exec sed -i \
+        -e 's/np\.finfo(np\.float)/np.finfo(np.float64)/g' \
+        -e 's/np\.bool8/np.bool_/g' \
+        -e 's/np\.complex_\b/np.complex128/g' \
+        {} +
+
+COPY pffdtd_method /app/pffdtd_method
+
+# Install method package + verify PFFDTD python imports work
+RUN pip install --no-cache-dir /app/pffdtd_method \
+ && PYTHONPATH=/app/pffdtd_python python -c "from materials.adm_funcs import fit_to_Sabs_oct_11; from sim_setup import sim_setup; from fdtd.sim_fdtd import SimEngine; print('PFFDTD python imports OK')"
+
+# Compile Hamilton's c_cuda GPU binary as a multi-arch CUDA fatbinary
+# (sm_60 .. sm_90 + PTX for forward compat). Symlink fdtd_gpu -> the
+# double-precision binary (works with raw impulse sources; single-precision
+# binary asserts diff=true which doesn't apply here). On hosts without GPU
+# passthrough the binary exists but is never invoked.
+RUN cd ${PFFDTD_SRC}/c_cuda \
+ && sed -i 's|-arch=sm_35|-gencode arch=compute_60,code=sm_60 -gencode arch=compute_70,code=sm_70 -gencode arch=compute_75,code=sm_75 -gencode arch=compute_80,code=sm_80 -gencode arch=compute_86,code=sm_86 -gencode arch=compute_89,code=sm_89 -gencode arch=compute_90,code=sm_90 -gencode arch=compute_90,code=compute_90|' Makefile \
+ && make gpu \
+ && ln -sf ${PFFDTD_SRC}/c_cuda/fdtd_main_gpu_double.x /usr/local/bin/fdtd_gpu
+
+# PFFDTD's Python sources on PYTHONPATH so `python -c` debugging works inside
+# the container even before the interface module's runtime sys.path insert.
+ENV PYTHONPATH=/app/pffdtd_python
+
+WORKDIR /app/pffdtd_method
+
+CMD ["python", "-m", "pffdtd_interface"]