Merge remote-tracking branch 'upstream/development' into HSdevmerge_240522

Author: hklion

.clang-tidy

@@ -7,6 +7,11 @@ Checks: '
         -bugprone-unchecked-optional-access,
     cert-*,
         -cert-err58-cpp,
+    clang-analyzer-*,
+        -clang-analyzer-optin.performance.Padding,
+        -clang-analyzer-optin.mpi.MPI-Checker,
+        -clang-analyzer-osx.*,
+        -clang-analyzer-optin.osx.*,
     clang-diagnostic-*,
     cppcoreguidelines-*,
         -cppcoreguidelines-avoid-c-arrays,
@@ -30,8 +35,6 @@ Checks: '
         -modernize-use-trailing-return-type,
     mpi-*,
     performance-*,
-        -performance-unnecessary-copy-initialization,
-        -performance-unnecessary-value-param,
     portability-*,
     readability-*,
         -readability-convert-member-functions-to-static,

.github/workflows/cuda.yml

@@ -115,7 +115,7 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach 24.03 && cd -
+        cd ../amrex && git checkout --detach 7ca419ebb90da60fefc01d8c1816846fff8638a5 && cd -
         make COMP=gcc QED=FALSE USE_MPI=TRUE USE_GPU=TRUE USE_OMP=FALSE USE_PSATD=TRUE USE_CCACHE=TRUE -j 4
 
         ccache -s

.github/workflows/dependencies/hip.sh

@@ -12,12 +12,24 @@ set -eu -o pipefail
 #   failed files the given number of times.
 echo 'Acquire::Retries "3";' | sudo tee /etc/apt/apt.conf.d/80-retries
 
-# Ref.: https://rocmdocs.amd.com/en/latest/Installation_Guide/Installation-Guide.html#ubuntu
-wget -q -O - https://repo.radeon.com/rocm/rocm.gpg.key \
-  | sudo apt-key add -
-echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/debian/ ubuntu main' \
-  | sudo tee /etc/apt/sources.list.d/rocm.list
+# Ref.: https://rocm.docs.amd.com/projects/install-on-linux/en/latest/how-to/native-install/ubuntu.html
+
+# Make the directory if it doesn't exist yet.
+# This location is recommended by the distribution maintainers.
+sudo mkdir --parents --mode=0755 /etc/apt/keyrings
+
+# Download the key, convert the signing-key to a full
+# keyring required by apt and store in the keyring directory
+wget https://repo.radeon.com/rocm/rocm.gpg.key -O - | \
+    gpg --dearmor | sudo tee /etc/apt/keyrings/rocm.gpg > /dev/null
 
+curl -O https://repo.radeon.com/rocm/rocm.gpg.key
+sudo apt-key add rocm.gpg.key
+
+source /etc/os-release # set UBUNTU_CODENAME: focal or jammy or ...
+
+echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${1-latest} ${UBUNTU_CODENAME} main" \
+  | sudo tee /etc/apt/sources.list.d/rocm.list
 echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \
   | sudo tee -a /etc/profile.d/rocm.sh
 

.github/workflows/dependencies/icc.sh

@@ -58,7 +58,7 @@ export CEI_TMP="/tmp/cei"
 CXX=$(which icpc) CC=$(which icc) \
   cmake-easyinstall               \
   --prefix=/usr/local             \
-  git+https://github.com/openPMD/[email protected].1 \
+  git+https://github.com/openPMD/[email protected].2 \
   -DopenPMD_USE_PYTHON=OFF \
   -DBUILD_TESTING=OFF      \
   -DBUILD_EXAMPLES=OFF     \

.github/workflows/macos.yml

@@ -36,9 +36,6 @@ jobs:
         brew tap openpmd/openpmd
         brew install openpmd-api
 
-        python3 -m pip install --upgrade pip
-        python3 -m pip install --upgrade virtualenv
-
         python3 -m venv py-venv
         source py-venv/bin/activate
         python3 -m pip install --upgrade pip

.github/workflows/scripts/checkQEDTableGenerator.sh

@@ -0,0 +1,77 @@
+
+#!/usr/bin/env bash
+#
+# Copyright 2022 Luca Fedeli
+#
+# License: BSD-3-Clause-LBNL
+
+set -eu -o pipefail
+
+export OMP_NUM_THREADS=2
+
+#
+# Generate QED lookup tables using external tool
+#
+./build/bin/qed_table_generator \
+    --table BW --mode DP --dndt_chi_min 0.01 \
+    --dndt_chi_max 100 --dndt_how_many 64 \
+    --pair_chi_min 0.01 --pair_chi_max 100 \
+    --pair_chi_how_many 64 --pair_frac_how_many 64 \
+    -o bw_table_tool
+./build/bin/qed_table_generator \
+    --table QS --mode DP --dndt_chi_min 0.001 \
+    --dndt_chi_max 100 --dndt_how_many 64 \
+    --em_chi_min 0.001 --em_chi_max 100 \
+    --em_chi_how_many 64 --em_frac_how_many 64 \
+    --em_frac_min 1e-12 -o qs_table_tool
+
+#
+# Generate QED lookup tables using WarpX
+#
+./build/bin/warpx.2d \
+    ./Examples/Tests/qed/quantum_synchrotron/inputs_2d \
+    qed_bw.lookup_table_mode = "generate" \
+    qed_bw.tab_dndt_chi_min = 0.01 \
+    qed_bw.tab_dndt_chi_max = 100.0 \
+    qed_bw.tab_dndt_how_many = 64 \
+    qed_bw.tab_pair_chi_min = 0.01 \
+    qed_bw.tab_pair_chi_max = 100.0 \
+    qed_bw.tab_pair_chi_how_many = 64 \
+    qed_bw.tab_pair_frac_how_many = 64 \
+    qed_bw.save_table_in = "bw_table" \
+    qed_qs.lookup_table_mode = "generate" \
+    qed_qs.tab_dndt_chi_min = 0.001 \
+    qed_qs.tab_dndt_chi_max = 100.0 \
+    qed_qs.tab_dndt_how_many = 64 \
+    qed_qs.tab_em_chi_min = 0.001 \
+    qed_qs.tab_em_frac_min = 1.0e-12 \
+    qed_qs.tab_em_chi_max = 100.0 \
+    qed_qs.tab_em_chi_how_many = 64 \
+    qed_qs.tab_em_frac_how_many = 64 \
+    qed_qs.save_table_in = "qs_table"
+
+#
+# Convert lookup tables (generated with WarpX and with the external tool) in human-readable format
+#
+./build/bin/qed_table_reader -i qs_table --table QS --mode DP -o qs_table
+./build/bin/qed_table_reader -i qs_table_tool --table QS --mode DP -o qs_table_tool
+./build/bin/qed_table_reader -i bw_table --table BW --mode DP -o bw_table
+./build/bin/qed_table_reader -i bw_table_tool --table BW --mode DP -o bw_table_tool
+
+#
+# Compare the generated lookup tables
+#
+diff bw_table_dndt bw_table_tool_dndt
+diff bw_table_pair bw_table_tool_pair
+diff qs_table_phot_em qs_table_tool_phot_em
+diff qs_table_dndt qs_table_tool_dndt
+
+#
+# Run a WarpX simulation using the lookup tables generated by the external tool
+#
+./build/bin/warpx.2d \
+    ./Examples/Tests/qed/quantum_synchrotron/inputs_2d \
+    qed_bw.lookup_table_mode = "load" \
+    qed_bw.load_table_from = "bw_table_tool" \
+    qed_qs.lookup_table_mode = "load" \
+    qed_qs.load_table_from = "qs_table_tool"

.github/workflows/ubuntu.yml

@@ -46,7 +46,7 @@ jobs:
         du -hs ~/.cache/ccache
 
   build_1D_2D:
-    name: GCC 1D & 2D w/ MPI
+    name: GCC 1D & 2D w/ MPI, QED tools
     runs-on: ubuntu-22.04
     if: github.event.pull_request.draft == false
     env:
@@ -78,14 +78,20 @@ jobs:
           -DWarpX_DIMS="1;2"           \
           -DWarpX_EB=OFF               \
           -DWarpX_PSATD=ON             \
-          -DWarpX_QED_TABLE_GEN=ON
+          -DWarpX_QED_TABLE_GEN=ON     \
+          -DWarpX_QED_TOOLS=ON
+
         cmake --build build -j 4
         ./build/bin/warpx.1d Examples/Physics_applications/laser_acceleration/inputs_1d
         ./build/bin/warpx.2d Examples/Physics_applications/laser_acceleration/inputs_2d
 
         ccache -s
         du -hs ~/.cache/ccache
 
+    - name: run QED table tools
+      run: |
+        .github/workflows/scripts/checkQEDTableGenerator.sh
+
   build_3D_sp:
     name: GCC 3D & RZ w/ MPI, single precision
     runs-on: ubuntu-22.04
@@ -218,6 +224,61 @@ jobs:
         export OMP_NUM_THREADS=1
         mpirun -n 2 Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
 
+  build_UB_sanitizer:
+    name: Clang UB sanitizer
+    runs-on: ubuntu-22.04
+    if: github.event.pull_request.draft == false
+    env:
+      CC: clang
+      CXX: clang++
+      # On CI for this test, Ninja is slower than the default:
+      #CMAKE_GENERATOR: Ninja
+    steps:
+    - uses: actions/checkout@v4
+    - name: install dependencies
+      run: |
+        .github/workflows/dependencies/clang15.sh
+    - name: CCache Cache
+      uses: actions/cache@v4
+      with:
+        path: ~/.cache/ccache
+        key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
+        restore-keys: |
+             ccache-${{ github.workflow }}-${{ github.job }}-git-
+    - name: build WarpX
+      run: |
+        export CCACHE_COMPRESS=1
+        export CCACHE_COMPRESSLEVEL=10
+        export CCACHE_MAXSIZE=100M
+        ccache -z
+
+        export CXX=$(which clang++-15)
+        export CC=$(which clang-15)
+        export CXXFLAGS="-fsanitize=undefined -fno-sanitize-recover=all"
+
+        cmake -S . -B build                 \
+          -GNinja                           \
+          -DCMAKE_VERBOSE_MAKEFILE=ON       \
+          -DWarpX_DIMS="RZ;1;2;3"           \
+          -DWarpX_PSATD=ON                  \
+          -DWarpX_QED=ON                    \
+          -DWarpX_QED_TABLE_GEN=ON          \
+          -DWarpX_OPENPMD=ON                \
+          -DWarpX_PRECISION=SINGLE          \
+          -DWarpX_PARTICLE_PRECISION=SINGLE
+        cmake --build build -j 4
+
+        ccache -s
+        du -hs ~/.cache/ccache
+
+    - name: run with UB sanitizer
+      run: |
+        export OMP_NUM_THREADS=2
+        mpirun -n 2 ./build/bin/warpx.rz Examples/Physics_applications/laser_acceleration/inputs_rz
+        mpirun -n 2 ./build/bin/warpx.1d Examples/Physics_applications/laser_acceleration/inputs_1d
+        mpirun -n 2 ./build/bin/warpx.2d Examples/Physics_applications/laser_acceleration/inputs_2d
+        mpirun -n 2 ./build/bin/warpx.3d Examples/Physics_applications/laser_acceleration/inputs_3d
+
   save_pr_number:
     if: github.event_name == 'pull_request'
     runs-on: ubuntu-latest

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ exclude: '^share/openPMD/thirdParty'
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     - id: trailing-whitespace
       args: [--markdown-linebreak-ext=md]
@@ -80,6 +80,7 @@ repos:
   hooks:
   - id: isort
     name: isort (python)
+    args: ['--profile black']
 
 # Python: Flake8 (checks only, does this support auto-fixes?)
 #- repo: https://github.com/PyCQA/flake8

.zenodo.json

@@ -20,6 +20,11 @@
         "name": "Andriyash, Igor",
         "orcid": "0000-0003-0313-4496"
       },
+      {
+        "affiliation": "Lawrence Livermore National Laboratory",
+        "name": "Angus, Justin Ray",
+        "orcid": "0000-0003-1474-0002"
+      },
       {
         "affiliation": "Lawrence Berkeley National Laboratory",
         "name": "Belkin, Daniel",
@@ -93,6 +98,11 @@
         "name": "Gu, Junmin",
         "orcid": "0000-0002-1521-8534"
       },
+      {
+        "affiliation": "Lawrence Berkeley National Laboratory",
+        "name": "Haseeb, Muhammad",
+        "orcid": "0000-0002-0697-6894"
+      },
       {
         "affiliation": "Lawrence Berkeley National Laboratory",
         "name": "Jambunathan, Revathi",
@@ -155,19 +165,29 @@
       },
       {
         "affiliation": "Lawrence Berkeley National Laboratory",
-        "name": "Sandberg, Ryan T.",
+        "name": "Sandberg, Ryan Thor",
         "orcid": "0000-0001-7680-8733"
       },
       {
         "affiliation": "Modern Electron",
         "name": "Scherpelz, Peter",
         "orcid": "0000-0001-8185-3387"
       },
+      {
+        "affiliation": "Laboratory for Laser Energetics, University of Rochester",
+        "name": "Weichman, Kale",
+        "orcid": "0000-0002-3487-7922"
+      },
       {
         "affiliation": "Lawrence Berkeley National Laboratory",
         "name": "Yang, Eloise",
         "orcid": "0000-0002-9319-4216"
       },
+      {
+        "affiliation": "LIDYL, CEA-Universit\u00e9 Paris-Saclay, CEA Saclay",
+        "name": "Zaim, Ne\u00efl",
+        "orcid": "0000-0003-0313-4496"
+      },
       {
         "affiliation": "Lawrence Berkeley National Laboratory",
         "name": "Zhang, Weiqun",
@@ -187,11 +207,6 @@
         "affiliation": "Lawrence Berkeley National Laboratory",
         "name": "Zoni, Edoardo",
         "orcid": "0000-0001-5662-4646"
-      },
-      {
-        "affiliation": "LIDYL, CEA-Universit\u00e9 Paris-Saclay, CEA Saclay",
-        "name": "Zaim, Ne\u00efl",
-        "orcid": "0000-0003-0313-4496"
       }
     ],
     "contributors": [