comments/cleanup

Author: PhilipDeegan

res/cmake/dep/highfive.cmake

@@ -30,7 +30,6 @@ if(HighFive)
   set(HIGHFIVE_USE_BOOST OFF)
   set(HIGHFIVE_BUILD_DOCS OFF) # conflicts with phare doc target
   set(HIGHFIVE_EXAMPLES OFF)
-  set(HIGHFIVE_PARALLEL_HDF5 ON) # causes failure if cannot occure
   add_subdirectory(${HIGHFIVE_SRC})
 
   message("HighFive enabled - checking HDF5")

res/cmake/test.cmake

@@ -22,8 +22,6 @@
 #      if level >= PHARE_EXEC_LEVEL_MIN AND level <= PHARE_EXEC_LEVEL_MAX
 #
 
-# this define breaks pgcc / and appears unnecessary
-# sed -i 's/# define GTEST_CAN_STREAM_RESULTS_ 1/# define GTEST_CAN_STREAM_RESULTS_ 0/g' subprojects/googletest/googletest/include/gtest/internal/gtest-port.h
 
 if (test AND ${PHARE_EXEC_LEVEL_MIN} GREATER 0) # 0 = no tests
 
@@ -36,6 +34,7 @@ if (test AND ${PHARE_EXEC_LEVEL_MIN} GREATER 0) # 0 = no tests
 
   function(set_exe_paths_ binary)
     set_property(TEST ${binary}        PROPERTY ENVIRONMENT "PYTHONPATH=${PHARE_PYTHONPATH}")
+    set_property(TEST ${binary} APPEND PROPERTY ENVIRONMENT "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}")
   endfunction(set_exe_paths_)
 
   function(add_phare_test_ binary)

src/core/data/ions/particle_initializers/maxwellian_particle_initializer.h

@@ -57,8 +57,7 @@ class MaxwellianParticleInitializer : public ParticleInitializer<ParticleArray,
 
 
     /**
-     * @brief load pacore
-} // namespace PHARErticles in a ParticleArray in a domain defined by the given layout
+     * @brief load particles in a ParticleArray in a domain defined by the given layout
      */
     void loadParticles(ParticleArray& particles, GridLayout const& layout) const override;
 

src/core/data/particles/particle_packer.h

@@ -10,10 +10,11 @@
 
 namespace PHARE::core
 {
-// PGI compiler doesn't (didn't at least) like static initializations of arrays, would result in an
-//  empty string
+// PGI compiler (nvc++ 21.3-0) doesn't like static initializations of arrays,
+//   would result in empty strings
 inline std::array<std::string, 5> packer_keys()
 {
+    // The order of this array must match the tuple order of ParticlePacker::get(particle)
     return {"weight", "charge", "iCell", "delta", "v"};
 }
 

src/core/data/particles/particle_utilities.h

@@ -23,7 +23,7 @@ namespace core
         auto origin       = layout.origin();
         auto startIndexes = layout.physicalStartIndex(QtyCentering::primal);
         auto meshSize     = layout.meshSize();
-        auto iCell        = layout.AMRToLocal(particle.iCell);
+        auto iCell        = layout.AMRToLocal(Point<int, GridLayout::dimension>{particle.iCell});
 
         for (auto iDim = 0u; iDim < GridLayout::dimension; ++iDim)
         {

src/core/numerics/interpolator/interpolator.h

@@ -534,7 +534,7 @@ namespace core
             auto indexAndWeightDual = [this, &layout](auto const& part) {
                 for (auto iDim = 0u; iDim < dimension; ++iDim)
                 {
-                    auto iCell           = layout.AMRToLocal(part.iCell);
+                    auto iCell           = layout.AMRToLocal(Point<int, dim>{part.iCell});
                     double normalizedPos = iCell[iDim] + part.delta[iDim] + dualOffset(interpOrder);
 
                     startIndex_[centering2int(QtyCentering::dual)][iDim]
@@ -550,7 +550,7 @@ namespace core
             auto indexAndWeightPrimal = [this, &layout](auto const& part) {
                 for (auto iDim = 0u; iDim < dimension; ++iDim)
                 {
-                    auto iCell           = layout.AMRToLocal(part.iCell);
+                    auto iCell           = layout.AMRToLocal(Point<int, dim>{part.iCell});
                     double normalizedPos = iCell[iDim] + part.delta[iDim];
 
                     startIndex_[centering2int(QtyCentering::primal)][iDim]
@@ -623,7 +623,7 @@ namespace core
             auto indexAndWeightDual = [this, &layout](auto const& part) {
                 for (auto iDim = 0u; iDim < dimension; ++iDim)
                 {
-                    auto iCell           = layout.AMRToLocal(part.iCell);
+                    auto iCell           = layout.AMRToLocal(Point<int, dim>{part.iCell});
                     double normalizedPos = iCell[iDim] + part.delta[iDim] + dualOffset(interpOrder);
 
                     startIndex_[centering2int(QtyCentering::dual)][iDim]
@@ -639,7 +639,7 @@ namespace core
             auto indexAndWeightPrimal = [this, &layout](auto const& part) {
                 for (auto iDim = 0u; iDim < dimension; ++iDim)
                 {
-                    auto iCell           = layout.AMRToLocal(part.iCell);
+                    auto iCell           = layout.AMRToLocal(Point<int, dim>{part.iCell});
                     double normalizedPos = iCell[iDim] + part.delta[iDim];
 
                     startIndex_[centering2int(QtyCentering::primal)][iDim]

src/diagnostic/detail/types/particle.h

@@ -62,6 +62,10 @@ class ParticlesDiagnosticWriter : public H5TypeWriter<H5Writer>
         DiagnosticProperties&, Attributes&,
         std::unordered_map<std::size_t, std::vector<std::pair<std::string, Attributes>>>&,
         std::size_t maxLevel) override;
+
+private:
+    // PGI compiler (nvc++ 21.3-0) doesn't like static initializations of arrays
+    std::array<std::string, 5> packer_keys_ = core::packer_keys();
 };
 
 
@@ -94,7 +98,7 @@ void ParticlesDiagnosticWriter<H5Writer>::getDataSetInfo(DiagnosticProperties& d
 
     auto particleInfo = [&](auto& attr, auto& particles) {
         std::size_t part_idx = 0;
-        auto keys            = core::packer_keys();
+        auto const& keys     = packer_keys_;
         core::apply(Packer::empty(), [&](auto const& arg) {
             attr[keys[part_idx]] = getSize(arg) * particles.size();
             ++part_idx;
@@ -141,9 +145,7 @@ void ParticlesDiagnosticWriter<H5Writer>::initDataSets(
         std::string path{h5Writer_.getPatchPathAddTimestamp(lvl, patchID) + "/"};
         std::size_t part_idx = 0;
         core::apply(Packer::empty(), [&](auto const& arg) {
-            auto keys = core::packer_keys();
-            // PGI compiler doesn't like static array initializations
-            assert(keys[part_idx].size() > 0);
+            auto const& keys = packer_keys_;
             createDataSet(path + keys[part_idx],
                           null ? 0 : attr[keys[part_idx]].template to<std::size_t>(), arg);
             ++part_idx;
@@ -183,7 +185,7 @@ void ParticlesDiagnosticWriter<H5Writer>::write(DiagnosticProperties& diagnostic
         core::ContiguousParticles<dimension> copy{particles.size()};
         packer.pack(copy);
 
-        auto keys = core::packer_keys();
+        auto const& keys = packer_keys_;
         h5Writer.writeDataSet(h5file, path + keys[0], copy.weight.data());
         h5Writer.writeDataSet(h5file, path + keys[1], copy.charge.data());
         h5Writer.writeDataSet(h5file, path + keys[2], copy.iCell.data());

tests/core/data/particles/test_main.cpp

@@ -92,7 +92,7 @@ TEST_F(AParticle, CanBeReducedToAnAbsolutePositionPoint)
     GridLayout<GridLayoutImplYee<3, 1>> layout{meshSize, nbrCells, origin,
                                                Box{Point{40, 60, 80}, Point{59, 89, 119}}};
 
-    auto iCell            = layout.AMRToLocal(part.iCell);
+    auto iCell            = layout.AMRToLocal(Point<int, 3>{part.iCell});
     auto p                = positionAsPoint(part, layout);
     auto startIndexes     = layout.physicalStartIndex(QtyCentering::primal);
     auto expectedPosition = Point<double, 3>{};