Merge branch 'development' into implicit_add_filtering_redo

.azure-pipelines.yml

@@ -3,9 +3,16 @@
 pool:
   vmImage: 'ubuntu-20.04'
 
+trigger:
+  branches:
+    include:
+    - development
 pr:
   autoCancel: true
   drafts: false
+  paths:
+    exclude:
+    - Docs
 
 jobs:
 - job:
@@ -36,10 +43,6 @@ jobs:
       cylindrical_rz:
         WARPX_CMAKE_FLAGS: -DWarpX_DIMS=RZ -DWarpX_FFT=ON -DWarpX_PYTHON=ON
         WARPX_RZ_FFT: 'TRUE'
-      # embedded boundaries
-      embedded_boundaries:
-        WARPX_CMAKE_FLAGS: -DWarpX_DIMS='1;2;3;RZ' -DWarpX_FFT=ON -DWarpX_PYTHON=ON -DWarpX_EB=ON
-        WARPX_RZ_FFT: 'TRUE'
       # single precision
       #single_precision:
       #  WARPX_CMAKE_FLAGS: -DWarpX_DIMS='1;2;3;RZ' -DWarpX_FFT=ON -DWarpX_PYTHON=ON -DWarpX_PRECISION=SINGLE

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,58 @@
+---
+name: Bug report
+about: Report a bug or unexpected behavior.
+labels: [bug]
+---
+
+_Please remove any sensitive information (e.g., passwords, API keys) from your submission.
+Please check the relevant boxes and fill in the specific versions or details for the relevant items.
+Thank you for taking the time to report this issue. We will respond as soon as possible._
+
+## Description
+A clear and concise description of the bug.
+
+## Expected behavior
+What did you expect to happen when you encountered the issue?
+
+## How to reproduce
+Please provide (if available):
+- WarpX inputs files
+- PICMI Python files
+- Python post-processing scripts
+
+If you are unable to provide certain files or scripts, please describe the steps you took to encounter the issue.
+
+Please minimize your inputs/scripts to be concise and focused on the issue.
+For instance, make the simulation scripts as small and fast to run as possible.
+
+## System information
+Please check all relevant boxes and provide details.
+
+- Operating system (name and version):
+  - [ ] Linux: e.g., Ubuntu 22.04 LTS
+  - [ ] macOS: e.g., macOS Monterey 12.4
+  - [ ] Windows: e.g., Windows 11 Pro
+- Version of WarpX: e.g., latest, 24.10, etc.
+- Installation method:
+  - [ ] Conda
+  - [ ] Spack
+  - [ ] PyPI
+  - [ ] Brew
+  - [ ] From source with CMake
+  - [ ] Module system on an HPC cluster
+- Other dependencies: yes/no, describe
+- Computational resources:
+  - [ ] MPI: e.g., 2 MPI processes
+  - [ ] OpenMP: e.g., 2 OpenMP threads
+  - [ ] CPU: e.g., 2 CPUs
+  - [ ] GPU: e.g., 2 GPUs (NVIDIA, AMD, etc.)
+
+If you encountered the issue on an HPC cluster, please check our [HPC documentation](https://warpx.readthedocs.io/en/latest/install/hpc.html) to see if your HPC cluster is already supported.
+
+## Steps taken so far
+What troubleshooting steps have you taken so far, and what were the results?
+
+Have you tried compiling and running in debug mode, following the instructions in our [debugging documentation](https://warpx.readthedocs.io/en/latest/usage/workflows/debugging.html)?
+
+## Additional information
+If applicable, please add any additional information that may help explain the issue, such as log files (e.g., build logs, error logs, etc.), error messages (e.g., compiler errors, runtime errors, etc.), screenshots, or other relevant details.

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: true

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,27 @@
+---
+name: Feature request
+about: Suggest a new feature or enhancement.
+labels: [enhancement]
+---
+
+_Please remove any sensitive information (e.g., passwords, API keys) from your submission.
+Please check the relevant boxes and fill in the specific versions or details for the relevant items.
+Thank you for taking the time to report this issue. We will respond as soon as possible._
+
+## Context and motivation
+Please provide a clear and concise description of the context that is prompting you to request a new feature. What problem are you trying to solve, and how will this feature help you achieve your goals?
+
+## Proposed feature
+Describe the feature you would like to add to WarpX in detail. Please include:
+- A clear and concise description of the feature
+- Any relevant technical requirements or specifications
+- How you envision the feature being used
+
+## Alternative solutions
+Have you considered any alternative solutions or features that could achieve the same goal? If so, please describe them and explain why you believe the proposed feature is the best solution.
+
+## Additional information
+If applicable, please provide any additional information that may be relevant to the feature request, such as:
+- Links to existing codes or implementations
+- References to relevant publications or research
+- Any specific use cases or scenarios where the feature would be particularly useful

.github/ISSUE_TEMPLATE/installation-issue.md

@@ -0,0 +1,49 @@
+---
+name: Installation issue
+about: Report an issue with installing or setting up WarpX
+labels: [install]
+---
+
+_Please remove any sensitive information (e.g., passwords, API keys) from your submission.
+Please check the relevant boxes and fill in the specific versions or details for the relevant items.
+Thank you for taking the time to report this issue. We will respond as soon as possible._
+
+## Description
+A clear and concise description of the issue.
+
+## System information
+- Operating system (name and version):
+  - [ ] Linux: e.g., Ubuntu 22.04 LTS
+  - [ ] macOS: e.g., macOS Monterey 12.4
+  - [ ] Windows: e.g., Windows 11 Pro
+- Version of WarpX: e.g., latest, 24.10, etc.
+- Installation method:
+  - [ ] Conda
+  - [ ] Spack
+  - [ ] PyPI
+  - [ ] Brew
+  - [ ] From source with CMake
+  - [ ] Module system on an HPC cluster
+- Other dependencies: yes/no, describe
+- Computational resources:
+  - [ ] CPU
+  - [ ] GPU: e.g., NVIDIA, AMD, etc.
+
+If you encountered the issue on an HPC cluster, please check our [HPC documentation](https://warpx.readthedocs.io/en/latest/install/hpc.html) to see if your HPC cluster is already supported.
+
+If you encountered the issue installing from source with CMake, please provide the output of the following steps:
+1. buildsystem generation: output of `cmake --fresh -S . -B build` (include your specific build options, e.g., `-DWarpX_DIMS=3`)
+2. project build: output of `cmake --build build` (include your specific build options, e.g., `-j 4`)
+
+If applicable, please add any additional information about your software environment:
+- [ ] CMake: e.g., 3.24.0
+- [ ] C++ compiler: e.g., GNU 11.3 with NVCC 12.0.76
+- [ ] Python: e.g., CPython 3.12
+- [ ] MPI: e.g., OpenMPI 4.1.1
+- [ ] FFTW: e.g., 3.3.10
+- [ ] HDF5: e.g., 1.14.0
+- [ ] ADIOS2: e.g., 2.10.0
+- Other dependencies: yes/no, describe
+
+## Additional information
+If applicable, please add any additional information that may help explain the issue, such as log files (e.g., build logs, error logs, etc.), error messages (e.g., compiler errors, runtime errors, etc.), screenshots, or other relevant details.

.github/workflows/clang_sanitizers.yml

@@ -1,6 +1,12 @@
 name: 🧴 clang sanitizers
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - "development"
+  pull_request:
+    paths-ignore:
+      - "Docs/**"
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-clangsanitizers
@@ -69,7 +75,7 @@ jobs:
         export "ASAN_OPTIONS=detect_leaks=0"
 
         mpirun -n 2 ./build/bin/warpx.rz Examples/Physics_applications/laser_acceleration/inputs_base_rz
-        mpirun -n 2 ./build/bin/warpx.1d Examples/Physics_applications/laser_acceleration/inputs_test_1d_laser_acceleration
+        mpirun -n 2 ./build/bin/warpx.1d Examples/Physics_applications/laser_acceleration/inputs_base_1d
         mpirun -n 2 ./build/bin/warpx.2d Examples/Physics_applications/laser_acceleration/inputs_base_2d
         mpirun -n 2 ./build/bin/warpx.3d Examples/Physics_applications/laser_acceleration/inputs_base_3d
 
@@ -150,7 +156,7 @@ jobs:
         export OMP_NUM_THREADS=2
 
         mpirun -n 2 ./build/bin/warpx.rz Examples/Physics_applications/laser_acceleration/inputs_base_rz warpx.serialize_initial_conditions = 0
-        mpirun -n 2 ./build/bin/warpx.1d Examples/Physics_applications/laser_acceleration/inputs_test_1d_laser_acceleration warpx.serialize_initial_conditions = 0
+        mpirun -n 2 ./build/bin/warpx.1d Examples/Physics_applications/laser_acceleration/inputs_base_1d warpx.serialize_initial_conditions = 0
         mpirun -n 2 ./build/bin/warpx.2d Examples/Physics_applications/laser_acceleration/inputs_base_2d warpx.serialize_initial_conditions = 0
         mpirun -n 2 ./build/bin/warpx.3d Examples/Physics_applications/laser_acceleration/inputs_base_3d warpx.serialize_initial_conditions = 0
 

.github/workflows/clang_tidy.yml

@@ -1,6 +1,12 @@
 name: 🧹 clang-tidy
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - "development"
+  pull_request:
+    paths-ignore:
+      - "Docs/**"
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-clangtidy

.github/workflows/cleanup-cache.yml

@@ -2,7 +2,7 @@ name: CleanUpCache
 
 on:
   workflow_run:
-    workflows: [🧹 clang-tidy, 🔍 CodeQL, 🐧 CUDA, 🐧 HIP, 🐧 Intel, 🍏 macOS, 🐧 OpenMP]
+    workflows: [🧴 clang sanitizers, 🧹 clang-tidy, 🔍 CodeQL, 🐧 CUDA, 🐧 HIP, 🐧 Intel, 🍏 macOS, 🐧 OpenMP]
     types:
       - completed
 

.github/workflows/codeql.yml

@@ -31,16 +31,22 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
+      - uses: actions/setup-python@v5
+        name: Install Python
+        with:
+          python-version: '3.x'
+
       - name: Install Packages (C++)
         if: ${{ matrix.language == 'cpp' }}
         run: |
           sudo apt-get update
           sudo apt-get install --yes cmake openmpi-bin libopenmpi-dev libhdf5-openmpi-dev libadios-openmpi-dev ccache
 
           python -m pip install --upgrade pip
+          python -m pip install --upgrade pipx
           python -m pip install --upgrade wheel
           python -m pip install --upgrade cmake
-          export CMAKE="$HOME/.local/bin/cmake" && echo "CMAKE=$CMAKE" >> $GITHUB_ENV
+          python -m pipx install cmake
 
       - name: Set Up Cache
         if: ${{ matrix.language == 'cpp' }}
@@ -54,7 +60,7 @@ jobs:
       - name: Configure (C++)
         if: ${{ matrix.language == 'cpp' }}
         run: |
-          $CMAKE -S . -B build -DWarpX_OPENPMD=ON
+          cmake -S . -B build -DWarpX_OPENPMD=ON
 
       - name: Initialize CodeQL
         uses: github/codeql-action/init@v3
@@ -75,15 +81,15 @@ jobs:
           export CCACHE_MAXSIZE=100M
           ccache -z
 
-          $CMAKE --build build -j 4
+          cmake --build build -j 4
 
           ccache -s
           du -hs ~/.cache/ccache
 
           # Make sure CodeQL has something to do
           touch Source/Utils/WarpXVersion.cpp
           export CCACHE_DISABLE=1
-          $CMAKE --build build -j 4
+          cmake --build build -j 4
 
       - name: Perform CodeQL Analysis
         uses: github/codeql-action/analyze@v3

.github/workflows/cuda.yml

@@ -1,6 +1,12 @@
 name: 🐧 CUDA
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - "development"
+  pull_request:
+    paths-ignore:
+      - "Docs/**"
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-cuda
@@ -131,7 +137,7 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach 216ce6f37de4b65be57fc1006b3457b4fc318e03 && cd -
+        cd ../amrex && git checkout --detach 92679babfc2cc66ca06ee591a80001db57c89878 && cd -
         make COMP=gcc QED=FALSE USE_MPI=TRUE USE_GPU=TRUE USE_OMP=FALSE USE_FFT=TRUE USE_CCACHE=TRUE -j 4
 
         ccache -s

.github/workflows/dependencies/dpcpp.sh

@@ -29,13 +29,16 @@ df -h
 # https://github.com/ECP-WarpX/WarpX/pull/1566#issuecomment-790934878
 
 # try apt install up to five times, to avoid connection splits
+# FIXME install latest version of IntelLLVM, Intel MKL
+#       after conflicts with openPMD are resolved
 status=1
 for itry in {1..5}
 do
     sudo apt-get install -y --no-install-recommends \
         build-essential \
         cmake           \
-        intel-oneapi-compiler-dpcpp-cpp intel-oneapi-mkl-devel \
+        intel-oneapi-compiler-dpcpp-cpp=2024.2.1-1079 \
+        intel-oneapi-mkl-devel=2024.2.1-103 \
         g++ gfortran    \
         libopenmpi-dev  \
         openmpi-bin     \

.github/workflows/hip.yml

@@ -1,6 +1,12 @@
 name: 🐧 HIP
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - "development"
+  pull_request:
+    paths-ignore:
+      - "Docs/**"
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-hip

.github/workflows/insitu.yml

@@ -1,6 +1,12 @@
 name: 🐧 In Situ Vis
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - "development"
+  pull_request:
+    paths-ignore:
+      - "Docs/**"
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-insituvis
@@ -101,8 +107,8 @@ jobs:
         cmake --build build -j 10
     - name: 2D Test
       run: |
-        cp Examples/Tests/ionization/inputs_test_2d_ionization_lab .
-        cp Examples/Tests/ionization/catalyst_pipeline.py .
+        cp Examples/Tests/field_ionization/inputs_test_2d_ionization_lab .
+        cp Examples/Tests/field_ionization/catalyst_pipeline.py .
         mpiexec -n 2 ./build/bin/warpx.2d \
             inputs_test_2d_ionization_lab \
             catalyst.script_paths = catalyst_pipeline.py\

.github/workflows/intel.yml

@@ -1,6 +1,12 @@
 name: 🐧 Intel
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - "development"
+  pull_request:
+    paths-ignore:
+      - "Docs/**"
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-intel
@@ -106,6 +112,7 @@ jobs:
         set +e
         source /opt/intel/oneapi/setvars.sh
         set -e
+        export PATH=$PATH:/opt/intel/oneapi/compiler/2024.2/bin  # FIXME
         export CXX=$(which icpx)
         export CC=$(which icx)
 
@@ -170,6 +177,7 @@ jobs:
         set +e
         source /opt/intel/oneapi/setvars.sh
         set -e
+        export PATH=$PATH:/opt/intel/oneapi/compiler/2024.2/bin  # FIXME
         export CXX=$(which icpx)
         export CC=$(which icx)
         export CXXFLAGS="-fsycl ${CXXFLAGS}"
@@ -180,6 +188,7 @@ jobs:
           -DCMAKE_VERBOSE_MAKEFILE=ON  \
           -DWarpX_COMPUTE=SYCL         \
           -DWarpX_EB=ON                \
+          -DWarpX_FFT=ON               \
           -DWarpX_PYTHON=ON            \
           -DWarpX_MPI=OFF              \
           -DWarpX_OPENPMD=ON           \