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add support for particle filters #2397

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merged 3 commits into from
Nov 21, 2017
Merged

add support for particle filters #2397

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ecd0143
PMacc: add particle filters
psychocoderHPC Nov 20, 2017
607dddf
add class to combine a species with a filter
psychocoderHPC Nov 20, 2017
5856d73
use particle filter for plugins
psychocoderHPC Nov 20, 2017
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5 changes: 4 additions & 1 deletion include/picongpu/plugins/CountParticles.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down Expand Up @@ -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;
Expand Down
4 changes: 3 additions & 1 deletion include/picongpu/plugins/ResourceLog.hpp
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Expand Up @@ -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>
Expand Down Expand Up @@ -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));
}

Expand Down
13 changes: 7 additions & 6 deletions include/picongpu/plugins/adios/ADIOSCountParticles.hpp
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Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand Down Expand Up @@ -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 ));
Expand Down
37 changes: 33 additions & 4 deletions include/picongpu/plugins/adios/ADIOSWriter.hpp
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Expand Up @@ -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>
Expand Down Expand Up @@ -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.");
Expand Down Expand Up @@ -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.");
Expand Down
29 changes: 16 additions & 13 deletions include/picongpu/plugins/adios/WriteSpecies.hpp
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Expand Up @@ -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;
Expand All @@ -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;
Expand Down Expand Up @@ -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() );
Expand All @@ -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();

Expand All @@ -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();
}
};

Expand Down
14 changes: 7 additions & 7 deletions include/picongpu/plugins/adios/restart/LoadSpecies.hpp
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Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand All @@ -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;
}
};

Expand Down
21 changes: 19 additions & 2 deletions include/picongpu/plugins/hdf5/HDF5Writer.hpp
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Expand Up @@ -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
{

Expand Down Expand Up @@ -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.");
Expand Down
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