added openPMD-api support for I/O

.github/workflows/clang.yml

@@ -166,6 +166,82 @@ jobs:
         ccache -s
         du -hs ~/.cache/ccache
 
+  test_openpmd:
+    name: openPMD I/O Test
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Dependencies
+      run: |
+        .github/workflows/dependencies/dependencies_clang.sh 15
+        .github/workflows/dependencies/dependencies_clang-tidy.sh 15
+        .github/workflows/dependencies/dependencies_ccache.sh
+    - name: Set Up Cache
+      uses: actions/cache@v4
+      with:
+        path: ~/.cache/ccache
+        key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
+        restore-keys: |
+             ccache-${{ github.workflow }}-${{ github.job }}-git-
+    - name: Install openPMD
+      run: |
+        export CCACHE_COMPRESS=1
+        export CCACHE_COMPRESSLEVEL=10
+        export CCACHE_MAXSIZE=40M
+
+        sudo apt-get install -y --no-install-recommends libhdf5-mpi-dev
+        wget -q https://github.com/openPMD/openPMD-api/archive/refs/tags/0.15.2.tar.gz
+        tar xfz 0.15.2.tar.gz
+        cd openPMD-api-0.15.2
+        mkdir build
+        cd build
+        cmake ..  \
+          -DCMAKE_CXX_COMPILER_LAUNCHER=ccache  \
+          -DopenPMD_BUILD_EXAMPLES=OFF  \
+          -DopenPMD_BUILD_CLI_TOOLS=OFF  \
+          -DopenPMD_BUILD_TESTING=OFF  \
+          -DopenPMD_USE_PYTHON=OFF  \
+        make -j4
+        sudo make install
+    - name: Build & Test
+      env: {CXXFLAGS: "-fno-operator-names -Werror -Wall -Wextra -Wpedantic -Wnull-dereference -Wfloat-conversion -Wshadow -Woverloaded-virtual -Wextra-semi -Wunreachable-code -Wnon-virtual-dtor"}
+      run: |
+        export CCACHE_COMPRESS=1
+        export CCACHE_COMPRESSLEVEL=10
+        export CCACHE_MAXSIZE=40M
+        export CCACHE_EXTRAFILES=${{ github.workspace }}/.clang-tidy
+        export CCACHE_LOGFILE=${{ github.workspace }}/ccache.log.txt
+        ccache -z
+
+        mkdir build
+        cd build
+        cmake ..                                      \
+            -DAMReX_OPENPMD=ON                        \
+            -DCMAKE_VERBOSE_MAKEFILE=ON               \
+            -DAMReX_ENABLE_TESTS=ON                   \
+            -DAMReX_SPACEDIM=3                        \
+            -DAMReX_MPI=ON                            \
+            -DAMReX_OMP=OFF                           \
+            -DAMReX_FORTRAN=OFF                       \
+            -DAMReX_EB=OFF                            \
+            -DAMReX_LINEAR_SOLVERS=OFF                \
+            -DAMReX_AMRLEVEL=OFF                      \
+            -DAMReX_PARTICLES=ON                      \
+            -DCMAKE_C_COMPILER=$(which clang-15)      \
+            -DCMAKE_CXX_COMPILER=$(which clang++-15)  \
+            -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
+        make -j 4
+
+        ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
+        make -j4 -k -f clang-tidy-ccache-misses.mak \
+            CLANG_TIDY=clang-tidy-15 \
+            CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
+
+        ctest --output-on-failure
+
+        ccache -s
+        du -hs ~/.cache/ccache
+
   save_pr_number:
     if: github.event_name == 'pull_request'
     runs-on: ubuntu-latest

Src/Base/AMReX_PlotFileUtil.H

@@ -12,6 +12,10 @@
 #include <AMReX_PlotFileUtilHDF5.H>
 #endif
 
+#ifdef AMREX_USE_OPENPMD
+#include <AMReX_PlotFileUtilOPENPMD.H>
+#endif
+
 #include <ostream>
 #include <string>
 #include <memory>

Src/CMakeLists.txt

@@ -200,6 +200,10 @@ if (AMReX_HDF5)
    add_subdirectory(Extern/HDF5)
 endif ()
 
+if (AMReX_OPENPMD)
+   add_subdirectory(Extern/openPMD-api)
+endif()
+
 #
 # Print out summary -- do it here so we already linked all
 # libs at this point

Src/Extern/openPMD-api/AMReX_ParticlesOPENPMD.H

@@ -0,0 +1,78 @@
+#ifndef AMREX_PTL_OPENPMD_API_H
+#define AMREX_PTL_OPENPMD_API_H
+
+/** @file This file is included from AMReX_ParticleCounter.H
+*   and belongs to the class ParticleContainer_impl.
+*   The namespace amrex was already declared.
+*
+*   Therefore all the definitions in this file belongs to namespace amrex
+*/
+
+struct AMReX_PtlCounter
+{
+  int m_MPIRank = 0;
+  int m_MPISize = 1;
+
+  unsigned long long m_Total = 0;
+
+  std::vector<unsigned long long> m_ParticleCounterByLevel;
+
+  [[nodiscard]] unsigned long long GetTotalNumParticles () const { return m_Total;}
+
+  std::vector<unsigned long long> m_ParticleOffsetAtRank;
+  std::vector<unsigned long long> m_ParticleSizeAtRank;
+};
+
+
+void CountParticles()
+{
+
+  m_PtlCounter.m_MPISize = amrex::ParallelDescriptor::NProcs();
+  m_PtlCounter.m_MPIRank = amrex::ParallelDescriptor::MyProc();
+
+  m_PtlCounter.m_ParticleCounterByLevel.resize(this->finestLevel()+1);
+  m_PtlCounter.m_ParticleOffsetAtRank.resize(this->finestLevel()+1);
+  m_PtlCounter.m_ParticleSizeAtRank.resize(this->finestLevel()+1);
+
+  auto lf_GetParticleOffsetOfProcessor = [&](const long long& numParticles,
+                                             unsigned long long& offset,
+                                             unsigned long long& sum)  -> void
+  {
+    std::vector<long long> result(m_PtlCounter.m_MPISize,  0);
+    amrex::ParallelGather::Gather (numParticles, result.data(), -1, amrex::ParallelDescriptor::Communicator());
+
+    sum = 0;
+    offset = 0;
+    for (int i=0;  i<int(result.size());  i++) {
+      sum +=  result[i];
+      if ( i < m_PtlCounter.m_MPIRank) {
+        offset +=  result[i];
+      }
+    }
+  };
+
+  for (auto currentLevel = 0; currentLevel <= this->finestLevel(); currentLevel++)
+    {
+      // numParticles in this processor
+      auto numParticles = static_cast<long long>(this->NumberOfParticlesAtLevel(currentLevel, true, true));
+
+      unsigned long long offset=0; // offset of this level
+      unsigned long long sum=0; // numParticles in this level (sum from all processors)
+      lf_GetParticleOffsetOfProcessor(numParticles, offset,  sum);
+
+      m_PtlCounter.m_ParticleCounterByLevel[currentLevel] = sum;
+      m_PtlCounter.m_ParticleOffsetAtRank[currentLevel] = offset;
+      m_PtlCounter.m_ParticleSizeAtRank[currentLevel] = numParticles;
+
+      // adjust offset, it should be numbered after particles from previous levels
+      for (auto lv=0; lv<currentLevel; lv++)
+        {
+          m_PtlCounter.m_ParticleOffsetAtRank[currentLevel] += m_PtlCounter.m_ParticleCounterByLevel[lv];
+        }
+
+      m_PtlCounter.m_Total += sum;
+    }
+}
+
+AMReX_PtlCounter m_PtlCounter;
+#endif // AMREX_PTL_OPENPMD_API_H