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Merge pull request #179 from f-schmitt-zih/topic-adios
ADIOS output support
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src/picongpu/include/plugins/adios/ADIOSCountParticles.hpp
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| /** | ||
| * Copyright 2014 Felix Schmitt | ||
| * | ||
| * This file is part of PIConGPU. | ||
| * | ||
| * PIConGPU is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU General Public License as published by | ||
| * the Free Software Foundation, either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * PIConGPU is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU General Public License | ||
| * along with PIConGPU. | ||
| * If not, see <http://www.gnu.org/licenses/>. | ||
| */ | ||
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| #pragma once | ||
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| #include <mpi.h> | ||
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| #include "types.h" | ||
| #include "simulation_types.hpp" | ||
| #include "plugins/adios/ADIOSWriter.def" | ||
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| #include "plugins/IPluginModule.hpp" | ||
| #include <boost/mpl/vector.hpp> | ||
| #include <boost/mpl/pair.hpp> | ||
| #include <boost/type_traits/is_same.hpp> | ||
| #include <boost/mpl/size.hpp> | ||
| #include <boost/mpl/at.hpp> | ||
| #include <boost/mpl/begin_end.hpp> | ||
| #include <boost/mpl/find.hpp> | ||
| #include "compileTime/conversion/MakeSeq.hpp" | ||
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| #include "RefWrapper.hpp" | ||
| #include <boost/type_traits.hpp> | ||
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| #include "plugins/output/WriteSpeciesCommon.hpp" | ||
| #include "plugins/kernel/CopySpecies.kernel" | ||
| #include "mappings/kernel/AreaMapping.hpp" | ||
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| #include "traits/PICToAdios.hpp" | ||
| #include "plugins/adios/writer/ParticleAttributeSize.hpp" | ||
| #include "compileTime/conversion/RemoveFromSeq.hpp" | ||
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| namespace picongpu | ||
| { | ||
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| namespace adios | ||
| { | ||
| using namespace PMacc; | ||
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| namespace bmpl = boost::mpl; | ||
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| /** Count number of particles for a species | ||
| * | ||
| * @tparam T_Species type of species | ||
| * | ||
| */ | ||
| template< typename T_Species > | ||
| struct ADIOSCountParticles | ||
| { | ||
| public: | ||
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| typedef T_Species ThisSpecies; | ||
| typedef typename ThisSpecies::FrameType FrameType; | ||
| typedef typename FrameType::ValueTypeSeq ParticleAttributeList; | ||
| typedef typename FrameType::MethodsList ParticleMethodsList; | ||
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| /* delete multiMask and localCellIdx in adios particle*/ | ||
| typedef bmpl::vector<multiMask,localCellIdx> TypesToDelete; | ||
| typedef typename RemoveFromSeq<ParticleAttributeList, TypesToDelete>::type ParticleCleanedAttributeList; | ||
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| /* add globalCellIdx for adios particle*/ | ||
| typedef typename MakeSeq< | ||
| ParticleCleanedAttributeList, | ||
| globalCellIdx<globalCellIdx_pic> | ||
| >::type ParticleNewAttributeList; | ||
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| typedef Frame<OperatorCreateVectorBox, ParticleNewAttributeList, ParticleMethodsList> AdiosFrameType; | ||
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| HINLINE void operator()(RefWrapper<ThreadParams*> params, | ||
| const std::string subGroup, | ||
| const DomainInformation domInfo) | ||
| { | ||
| DataConnector &dc = DataConnector::getInstance(); | ||
| GridController<simDim>& gc = GridController<simDim>::getInstance(); | ||
| uint64_t mpiSize = gc.getGlobalSize(); | ||
| uint64_t mpiRank = gc.getGlobalRank(); | ||
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| /* load particle without copy particle data to host */ | ||
| ThisSpecies* speciesTmp = &(dc.getData<ThisSpecies >(ThisSpecies::FrameType::CommunicationTag, true)); | ||
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| /* count total number of particles on the device */ | ||
| uint64_cu totalNumParticles = 0; | ||
| totalNumParticles = PMacc::CountParticles::countOnDevice < CORE + BORDER > ( | ||
| *speciesTmp, | ||
| *(params.get()->cellDescription), | ||
| domInfo.localDomainOffset, | ||
| domInfo.domainSize); | ||
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| /* MPI_Allgather to compute global size and my offset */ | ||
| uint64_t myNumParticles = totalNumParticles; | ||
| uint64_t allNumParticles[mpiSize]; | ||
| uint64_t globalNumParticles = 0; | ||
| uint64_t myParticleOffset = 0; | ||
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| MPI_CHECK(MPI_Allgather( | ||
| &myNumParticles, 1, MPI_UNSIGNED_LONG_LONG, | ||
| allNumParticles, 1, MPI_UNSIGNED_LONG_LONG, | ||
| gc.getCommunicator().getMPIComm())); | ||
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| for (uint64_t i = 0; i < mpiSize; ++i) | ||
| { | ||
| globalNumParticles += allNumParticles[i]; | ||
| if (i < mpiRank) | ||
| myParticleOffset += allNumParticles[i]; | ||
| } | ||
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| if (myNumParticles > 0) | ||
| { | ||
| /* iterate over all attributes of this species */ | ||
| ForEach<typename AdiosFrameType::ValueTypeSeq, adios::ParticleAttributeSize<void> > attributeSize; | ||
| attributeSize(params, (FrameType::getName() + std::string("/") + subGroup).c_str(), | ||
| myNumParticles, globalNumParticles, myParticleOffset); | ||
| } | ||
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| /* define adios var for species index/info table */ | ||
| { | ||
| const size_t localTableSize = 5; | ||
| traits::PICToAdios<uint64_t> adiosIndexType; | ||
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| std::stringstream indexVarSizeStr; | ||
| indexVarSizeStr << localTableSize; | ||
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| std::stringstream indexVarGlobalSizeStr; | ||
| indexVarGlobalSizeStr << localTableSize * gc.getGlobalSize(); | ||
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| std::stringstream indexVarOffsetStr; | ||
| indexVarOffsetStr << localTableSize * gc.getGlobalRank(); | ||
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| int64_t adiosSpeciesIndexVar = adios_define_var( | ||
| params.get()->adiosGroupHandle, | ||
| (params.get()->adiosBasePath + std::string(ADIOS_PATH_PARTICLES) + | ||
| FrameType::getName() + std::string("/") + subGroup + | ||
| std::string("particles_info")).c_str(), | ||
| NULL, | ||
| adiosIndexType.type, | ||
| indexVarSizeStr.str().c_str(), | ||
| indexVarGlobalSizeStr.str().c_str(), | ||
| indexVarOffsetStr.str().c_str()); | ||
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| params.get()->adiosSpeciesIndexVarIds.push_back(adiosSpeciesIndexVar); | ||
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| params.get()->adiosGroupSize += sizeof(uint64_t) * localTableSize * gc.getGlobalSize(); | ||
| } | ||
| } | ||
| }; | ||
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| } //namspace adios | ||
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| } //namespace picongpu |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,132 @@ | ||
| /** | ||
| * Copyright 2014 Felix Schmitt | ||
| * | ||
| * This file is part of PIConGPU. | ||
| * | ||
| * PIConGPU is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU General Public License as published by | ||
| * the Free Software Foundation, either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * PIConGPU is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU General Public License | ||
| * along with PIConGPU. | ||
| * If not, see <http://www.gnu.org/licenses/>. | ||
| */ | ||
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| #pragma once | ||
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| #include <adios.h> | ||
| #include <list> | ||
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| #include "types.h" | ||
| #include "simulation_types.hpp" | ||
| #include "particles/frame_types.hpp" | ||
| #include "simulationControl/MovingWindow.hpp" | ||
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| namespace picongpu | ||
| { | ||
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| namespace adios | ||
| { | ||
| using namespace PMacc; | ||
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| namespace bmpl = boost::mpl; | ||
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| namespace po = boost::program_options; | ||
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| #define ADIOS_INVALID_HANDLE -1 | ||
| #define ADIOS_SUCCESS err_no_error | ||
| #define ADIOS_GROUP_NAME "data" | ||
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| #define ADIOS_PATH_ROOT "/data/" | ||
| #define ADIOS_PATH_FIELDS "fields/" | ||
| #define ADIOS_PATH_PARTICLES "particles/" | ||
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| #define ADIOS_SIZE_LOCAL "size_" | ||
| #define ADIOS_SIZE_GLOBAL "totalSize_" | ||
| #define ADIOS_OFFSET_GLOBAL "offset_" | ||
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| #define ADIOS_CMD(_cmd) \ | ||
| { \ | ||
| int _err_code = _cmd; \ | ||
| if (_err_code != ADIOS_SUCCESS) \ | ||
| log<picLog::INPUT_OUTPUT > ("ADIOS: error at cmd '%1%': '%2%'") % \ | ||
| #_cmd % _err_code; \ | ||
| } | ||
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| #define ADIOS_CMD_EXPECT_NONZERO(_cmd) \ | ||
| { \ | ||
| int _err_code = _cmd; \ | ||
| if (_err_code == 0) \ | ||
| log<picLog::INPUT_OUTPUT > ("ADIOS: error at cmd '%1%': '%2%'") % \ | ||
| #_cmd % _err_code; \ | ||
| } | ||
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| struct ThreadParams | ||
| { | ||
| uint32_t currentStep; | ||
| std::string fullFilename; | ||
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| MPI_Comm adiosComm; /* MPI communicator for adios lib */ | ||
| bool adiosBufferInitialized; /* set if ADIOS buffer has been allocated */ | ||
| int64_t adiosFileHandle; /* ADIOS file handle */ | ||
| int64_t adiosGroupHandle; /* ADIOS group handle */ | ||
| uint64_t adiosGroupSize; /* size of ADIOS group in bytes */ | ||
| std::string adiosBasePath; /* base path for the current step */ | ||
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| int64_t adiosSizeVarIds[simDim]; /* var IDs for ADIOS_SIZE_LOCAL_x/y/z */ | ||
| int64_t adiosTotalSizeVarIds[simDim]; /* var IDs for ADIOS_SIZE_GLOBAL_x/y/z */ | ||
| int64_t adiosOffsetVarIds[simDim]; /* var IDs for ADIOS_OFFSET_GLOBAL_x/y/z */ | ||
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| std::list<int64_t> adiosFieldVarIds; /* var IDs for fields in order of appearance */ | ||
| std::list<int64_t> adiosParticleAttrVarIds; /* var IDs for particle attributes in order of appearance */ | ||
| std::list<int64_t> adiosSpeciesIndexVarIds; /* var IDs for species index tables in order of appearance */ | ||
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| GridLayout<simDim> gridLayout; | ||
| DataSpace<simDim> gridPosition; | ||
| MappingDesc *cellDescription; | ||
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| float *fieldBfr; /* temp. buffer for fields */ | ||
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| VirtualWindow window; | ||
| }; | ||
|
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| struct DomainInformation | ||
| { | ||
| /* Offset from simulation origin to moving window */ | ||
| DataSpace<simDim> globalDomainOffset; | ||
| /* Total size of current simulation area (i.e. moving window size) */ | ||
| DataSpace<simDim> globalDomainSize; | ||
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| /* Offset from simulation origin to this GPU */ | ||
| DataSpace<simDim> domainOffset; | ||
| /* Size of this GPU */ | ||
| DataSpace<simDim> domainSize; | ||
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| /* Offset of simulation area (i.e. moving window) from start of this GPU. | ||
| * >= 0 for top GPUs, 0 otherwise */ | ||
| DataSpace<simDim> localDomainOffset; | ||
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| }; | ||
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| /** | ||
| * Writes simulation data to adios files. | ||
| * Implements the ISimulationIO interface. | ||
| * | ||
| * @param ElectronsBuffer class description for electrons | ||
| * @param IonsBuffer class description for ions | ||
| * @param simDim dimension of the simulation (2-3) | ||
| */ | ||
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| class ADIOSWriter; | ||
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| } //namespace adios | ||
| } //namespace picongpu | ||
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