use particle filter for plugins

Prepare all plugins which uses PMacc particle methods to be particle filter ready.
ComputationalRadiationPhysics · Nov 21, 2017 · 5856d73 · 5856d73
1 parent 607dddf
commit 5856d73
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Showing 10 changed files with 147 additions and 75 deletions.
diff --git a/include/picongpu/plugins/CountParticles.hpp b/include/picongpu/plugins/CountParticles.hpp
@@ -24,6 +24,7 @@
 #include <pmacc/mappings/kernel/AreaMapping.hpp>
 
 #include "picongpu/plugins/ISimulationPlugin.hpp"
+#include "picongpu/particles/filter/filter.hpp"
 
 #include <pmacc/mpi/reduceMethods/Reduce.hpp>
 #include <pmacc/mpi/MPIReduce.hpp>
@@ -175,11 +176,13 @@ class CountParticles : public ISimulationPlugin
         DataConnector &dc = Environment<>::get().DataConnector();
         auto particles = dc.get< ParticlesType >( ParticlesType::FrameType::getName(), true );
 
+        particles::filter::All parFilter{};
         /*count local particles*/
         size = pmacc::CountParticles::countOnDevice<AREA>(*particles,
                                                           *cellDescription,
                                                           DataSpace<simDim>(),
-                                                          localSize);
+                                                          localSize,
+                                                          parFilter);
         dc.releaseData( ParticlesType::FrameType::getName() );
 
         uint64_cu reducedValueMax;

diff --git a/include/picongpu/plugins/ResourceLog.hpp b/include/picongpu/plugins/ResourceLog.hpp
@@ -29,6 +29,7 @@
 #include "picongpu/plugins/ILightweightPlugin.hpp"
 #include "ILightweightPlugin.hpp"
 #include "picongpu/simulation_defines.hpp"
+#include "picongpu/particles/filter/filter.hpp"
 
 // Boost
 #include <boost/property_tree/ptree.hpp>
@@ -115,7 +116,8 @@ namespace picongpu
 
             if(contains(propertyMap,"particleCount"))
             {
-                std::vector<size_t> particleCounts = resourceMonitor.getParticleCounts<VectorAllSpecies>(*cellDescription);
+                particles::filter::All parFilter{};
+                std::vector<size_t> particleCounts = resourceMonitor.getParticleCounts<VectorAllSpecies>(*cellDescription, parFilter );
                 pt.put("resourceLog.particleCount", std::accumulate(particleCounts.begin(), particleCounts.end(), 0));
             }
 

diff --git a/include/picongpu/plugins/adios/ADIOSCountParticles.hpp b/include/picongpu/plugins/adios/ADIOSCountParticles.hpp
@@ -63,12 +63,12 @@ using namespace pmacc;
  * @tparam T_Species type of species
  *
  */
-template< typename T_Species >
+template< typename T_SpeciesFilter >
 struct ADIOSCountParticles
 {
 public:
 
-    typedef T_Species ThisSpecies;
+    typedef typename T_SpeciesFilter::Species ThisSpecies;
     typedef typename ThisSpecies::FrameType FrameType;
     typedef typename FrameType::ParticleDescription ParticleDescription;
     typedef typename FrameType::ValueTypeSeq ParticleAttributeList;
@@ -96,20 +96,21 @@ struct ADIOSCountParticles
         uint64_t mpiSize = gc.getGlobalSize();
         uint64_t mpiRank = gc.getGlobalRank();
 
-        const std::string speciesGroup( FrameType::getName() + "/" );
+        const std::string speciesGroup( T_SpeciesFilter::getName() + "/" );
         const std::string speciesPath( params->adiosBasePath +
             std::string(ADIOS_PATH_PARTICLES) + speciesGroup );
 
         /* load particle without copy particle data to host */
         auto speciesTmp = dc.get< ThisSpecies >( ThisSpecies::FrameType::getName(), true );
-
+        typename T_SpeciesFilter::Filter particleFilter{};
         /* count total number of particles on the device */
         uint64_cu totalNumParticles = 0;
         totalNumParticles = pmacc::CountParticles::countOnDevice < CORE + BORDER > (
                                                                                     *speciesTmp,
                                                                                     *(params->cellDescription),
                                                                                     params->localWindowToDomainOffset,
-                                                                                    params->window.localDimensions.size);
+                                                                                    params->window.localDimensions.size,
+                                                                                    particleFilter);
 
         /* MPI_Allgather to compute global size and my offset */
         uint64_t myNumParticles = totalNumParticles;
@@ -137,7 +138,7 @@ struct ADIOSCountParticles
 
         /* openPMD ED-PIC: additional attributes */
         traits::PICToAdios<float_64> adiosDoubleType;
-        const float_64 particleShape( GetShape<T_Species>::type::support - 1 );
+        const float_64 particleShape( GetShape<ThisSpecies>::type::support - 1 );
         ADIOS_CMD(adios_define_attribute_byvalue(params->adiosGroupHandle,
             "particleShape", speciesPath.c_str(),
             adiosDoubleType.type, 1, (void*)&particleShape ));

diff --git a/include/picongpu/plugins/adios/ADIOSWriter.hpp b/include/picongpu/plugins/adios/ADIOSWriter.hpp
@@ -54,6 +54,7 @@
 #include "picongpu/plugins/adios/restart/LoadSpecies.hpp"
 #include "picongpu/plugins/adios/restart/RestartFieldLoader.hpp"
 #include "picongpu/plugins/adios/NDScalars.hpp"
+#include "picongpu/plugins/misc/SpeciesFilter.hpp"
 
 #include <adios.h>
 #include <adios_read.h>
@@ -1042,12 +1043,26 @@ class ADIOSWriter : public IIOBackend
         log<picLog::INPUT_OUTPUT > ("ADIOS: (begin) counting particles.");
         if (threadParams->isCheckpoint)
         {
-            ForEach<FileCheckpointParticles, ADIOSCountParticles<bmpl::_1> > adiosCountParticles;
+            ForEach<
+                FileCheckpointParticles,
+                ADIOSCountParticles<
+                    plugins::misc::SpeciesFilter<
+                        bmpl::_1
+                    >
+                >
+            > adiosCountParticles;
             adiosCountParticles(threadParams);
         }
         else
         {
-            ForEach<FileOutputParticles, ADIOSCountParticles<bmpl::_1> > adiosCountParticles;
+            ForEach<
+                FileOutputParticles,
+                ADIOSCountParticles<
+                    plugins::misc::SpeciesFilter<
+                        bmpl::_1
+                    >
+                >
+            > adiosCountParticles;
             adiosCountParticles(threadParams);
         }
         log<picLog::INPUT_OUTPUT > ("ADIOS: ( end ) counting particles.");
@@ -1104,12 +1119,26 @@ class ADIOSWriter : public IIOBackend
         log<picLog::INPUT_OUTPUT > ("ADIOS: (begin) writing particle species.");
         if (threadParams->isCheckpoint)
         {
-            ForEach<FileCheckpointParticles, WriteSpecies<bmpl::_1> > writeSpecies;
+            ForEach<
+                FileCheckpointParticles,
+                WriteSpecies<
+                    plugins::misc::SpeciesFilter<
+                        bmpl::_1
+                    >
+                >
+            > writeSpecies;
             writeSpecies(threadParams, particleOffset);
         }
         else
         {
-            ForEach<FileOutputParticles, WriteSpecies<bmpl::_1> > writeSpecies;
+            ForEach<
+                FileOutputParticles,
+                WriteSpecies<
+                    plugins::misc::SpeciesFilter<
+                        bmpl::_1
+                    >
+                >
+            > writeSpecies;
             writeSpecies(threadParams, particleOffset);
         }
         log<picLog::INPUT_OUTPUT > ("ADIOS: ( end ) writing particle species.");

diff --git a/include/picongpu/plugins/adios/WriteSpecies.hpp b/include/picongpu/plugins/adios/WriteSpecies.hpp
@@ -63,12 +63,12 @@ using namespace pmacc;
  * @tparam T_Species type of species
  *
  */
-template< typename T_Species >
+template< typename T_SpeciesFilter >
 struct WriteSpecies
 {
 public:
 
-    typedef T_Species ThisSpecies;
+    typedef typename T_SpeciesFilter::Species ThisSpecies;
     typedef typename ThisSpecies::FrameType FrameType;
     typedef typename FrameType::ParticleDescription ParticleDescription;
     typedef typename FrameType::ValueTypeSeq ParticleAttributeList;
@@ -93,32 +93,34 @@ struct WriteSpecies
     HINLINE void operator()(ThreadParams* params,
                             const Space particleOffset)
     {
-        log<picLog::INPUT_OUTPUT > ("ADIOS: (begin) write species: %1%") % AdiosFrameType::getName();
+        log<picLog::INPUT_OUTPUT > ("ADIOS: (begin) write species: %1%") % T_SpeciesFilter::getName();
         DataConnector &dc = Environment<>::get().DataConnector();
         /* load particle without copy particle data to host */
         auto speciesTmp = dc.get< ThisSpecies >( ThisSpecies::FrameType::getName(), true );
 
         /* count total number of particles on the device */
-        log<picLog::INPUT_OUTPUT > ("ADIOS:   (begin) count particles: %1%") % AdiosFrameType::getName();
+        log<picLog::INPUT_OUTPUT > ("ADIOS:   (begin) count particles: %1%") % T_SpeciesFilter::getName();
+        typename T_SpeciesFilter::Filter particleFilter{};
         uint64_cu totalNumParticles = 0;
         totalNumParticles = pmacc::CountParticles::countOnDevice < CORE + BORDER > (
                                                                                     *speciesTmp,
                                                                                     *(params->cellDescription),
                                                                                     params->localWindowToDomainOffset,
-                                                                                    params->window.localDimensions.size);
-        log<picLog::INPUT_OUTPUT > ("ADIOS:   ( end ) count particles: %1% = %2%") % AdiosFrameType::getName() % totalNumParticles;
+                                                                                    params->window.localDimensions.size,
+                                                                                    particleFilter);
+        log<picLog::INPUT_OUTPUT > ("ADIOS:   ( end ) count particles: %1% = %2%") % T_SpeciesFilter::getName() % totalNumParticles;
 
         AdiosFrameType hostFrame;
 
         /* malloc host memory */
-        log<picLog::INPUT_OUTPUT > ("ADIOS:   (begin) malloc host memory: %1%") % AdiosFrameType::getName();
+        log<picLog::INPUT_OUTPUT > ("ADIOS:   (begin) malloc host memory: %1%") % T_SpeciesFilter::getName();
         ForEach<typename AdiosFrameType::ValueTypeSeq, MallocHostMemory<bmpl::_1> > mallocMem;
         mallocMem(forward(hostFrame), totalNumParticles);
-        log<picLog::INPUT_OUTPUT > ("ADIOS:   ( end ) malloc host memory: %1%") % AdiosFrameType::getName();
+        log<picLog::INPUT_OUTPUT > ("ADIOS:   ( end ) malloc host memory: %1%") % T_SpeciesFilter::getName();
 
         if (totalNumParticles > 0)
         {
-            log<picLog::INPUT_OUTPUT > ("ADIOS:   (begin) copy particle host (with hierarchy) to host (without hierarchy): %1%") % AdiosFrameType::getName();
+            log<picLog::INPUT_OUTPUT > ("ADIOS:   (begin) copy particle host (with hierarchy) to host (without hierarchy): %1%") % T_SpeciesFilter::getName();
             typedef bmpl::vector< typename GetPositionFilter<simDim>::type > usedFilters;
             typedef typename FilterFactory<usedFilters>::FilterType MyParticleFilter;
             MyParticleFilter filter;
@@ -160,7 +162,8 @@ struct WriteSpecies
                                 filter,
                                 particleOffset, /*relative to data domain (not to physical domain)*/
                                 totalCellIdx_,
-                                mapper
+                                mapper,
+                                particleFilter
                                 );
 #if( PMACC_CUDA_ENABLED == 1 )
             dc.releaseData( MallocMCBuffer< DeviceHeap >::getName() );
@@ -175,10 +178,10 @@ struct WriteSpecies
         /* free host memory */
         ForEach<typename AdiosFrameType::ValueTypeSeq, FreeHostMemory<bmpl::_1> > freeMem;
         freeMem(forward(hostFrame));
-        log<picLog::INPUT_OUTPUT > ("ADIOS: ( end ) writing species: %1%") % AdiosFrameType::getName();
+        log<picLog::INPUT_OUTPUT > ("ADIOS: ( end ) writing species: %1%") % T_SpeciesFilter::getName();
 
         /* write species counter table to adios file */
-        log<picLog::INPUT_OUTPUT > ("ADIOS: (begin) writing particle index table for %1%") % AdiosFrameType::getName();
+        log<picLog::INPUT_OUTPUT > ("ADIOS: (begin) writing particle index table for %1%") % T_SpeciesFilter::getName();
         {
             GridController<simDim>& gc = Environment<simDim>::get().GridController();
 
@@ -200,7 +203,7 @@ struct WriteSpecies
             params->adiosSpeciesIndexVarIds.pop_front();
             ADIOS_CMD(adios_write_byid(params->adiosFileHandle, adiosIndexVarId, particlesMetaInfo));
         }
-        log<picLog::INPUT_OUTPUT > ("ADIOS: ( end ) writing particle index table for %1%") % AdiosFrameType::getName();
+        log<picLog::INPUT_OUTPUT > ("ADIOS: ( end ) writing particle index table for %1%") % T_SpeciesFilter::getName();
     }
 };
 

diff --git a/include/picongpu/plugins/adios/restart/LoadSpecies.hpp b/include/picongpu/plugins/adios/restart/LoadSpecies.hpp
@@ -91,17 +91,17 @@ struct LoadSpecies
      */
     HINLINE void operator()(ThreadParams* params, const uint32_t restartChunkSize)
     {
-
-        log<picLog::INPUT_OUTPUT > ("ADIOS: (begin) load species: %1%") % AdiosFrameType::getName();
+        std::string const speciesName = FrameType::getName() + "_all";
+        log<picLog::INPUT_OUTPUT > ("ADIOS: (begin) load species: %1%") % speciesName;
         DataConnector &dc = Environment<>::get().DataConnector();
         GridController<simDim> &gc = Environment<simDim>::get().GridController();
 
         std::string particlePath = params->adiosBasePath + std::string(ADIOS_PATH_PARTICLES) +
-                                   FrameType::getName() + std::string("/");
+                                   speciesName + std::string("/");
         const pmacc::Selection<simDim>& localDomain = Environment<simDim>::get().SubGrid().getLocalDomain();
 
         /* load particle without copying particle data to host */
-        auto speciesTmp = dc.get< ThisSpecies >( ThisSpecies::FrameType::getName(), true );
+        auto speciesTmp = dc.get< ThisSpecies >( FrameType::getName(), true );
 
         /* count total number of particles on the device */
         uint64_t totalNumParticles = 0;
@@ -152,12 +152,12 @@ struct LoadSpecies
             (long long unsigned) totalNumParticles % (long long unsigned) particleOffset;
 
         AdiosFrameType hostFrame;
-        log<picLog::INPUT_OUTPUT > ("ADIOS: malloc mapped memory: %1%") % AdiosFrameType::getName();
+        log<picLog::INPUT_OUTPUT > ("ADIOS: malloc mapped memory: %1%") % speciesName;
         /*malloc mapped memory*/
         ForEach<typename AdiosFrameType::ValueTypeSeq, MallocMemory<bmpl::_1> > mallocMem;
         mallocMem(forward(hostFrame), totalNumParticles);
 
-        log<picLog::INPUT_OUTPUT > ("ADIOS: get mapped memory device pointer: %1%") % AdiosFrameType::getName();
+        log<picLog::INPUT_OUTPUT > ("ADIOS: get mapped memory device pointer: %1%") % speciesName;
         /*load device pointer of mapped memory*/
         AdiosFrameType deviceFrame;
         ForEach<typename AdiosFrameType::ValueTypeSeq, GetDevicePtr<bmpl::_1> > getDevicePtr;
@@ -183,7 +183,7 @@ struct LoadSpecies
             ForEach<typename AdiosFrameType::ValueTypeSeq, FreeMemory<bmpl::_1> > freeMem;
             freeMem(forward(hostFrame));
         }
-        log<picLog::INPUT_OUTPUT > ("ADIOS: ( end ) load species: %1%") % AdiosFrameType::getName();
+        log<picLog::INPUT_OUTPUT > ("ADIOS: ( end ) load species: %1%") % speciesName;
     }
 };
 

diff --git a/include/picongpu/plugins/hdf5/HDF5Writer.hpp b/include/picongpu/plugins/hdf5/HDF5Writer.hpp
@@ -69,8 +69,11 @@
 #include "picongpu/plugins/hdf5/restart/LoadSpecies.hpp"
 #include "picongpu/plugins/hdf5/restart/RestartFieldLoader.hpp"
 #include "picongpu/plugins/hdf5/NDScalars.hpp"
+#include "picongpu/plugins/misc/SpeciesFilter.hpp"
+
 #include <pmacc/memory/boxes/DataBoxDim1Access.hpp>
 
+
 namespace picongpu
 {
 
@@ -407,12 +410,26 @@ class HDF5Writer : public IIOBackend
         log<picLog::INPUT_OUTPUT > ("HDF5: (begin) writing particle species.");
         if (threadParams->isCheckpoint)
         {
-            ForEach<FileCheckpointParticles, WriteSpecies<bmpl::_1> > writeSpecies;
+            ForEach<
+                FileCheckpointParticles,
+                WriteSpecies<
+                    plugins::misc::SpeciesFilter<
+                        bmpl::_1
+                    >
+                >
+            > writeSpecies;
             writeSpecies(threadParams, domainOffset);
         }
         else
         {
-            ForEach<FileOutputParticles, WriteSpecies<bmpl::_1> > writeSpecies;
+            ForEach<
+                FileOutputParticles,
+                WriteSpecies<
+                    plugins::misc::SpeciesFilter<
+                        bmpl::_1
+                    >
+                >
+            > writeSpecies;
             writeSpecies(threadParams, domainOffset);
         }
         log<picLog::INPUT_OUTPUT > ("HDF5: ( end ) writing particle species.");