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This commit is contained in:
Gabriele Cosmo
2016-06-10 14:11:04 +02:00
parent c9b32a6c0a
commit d4af681f38
4886 changed files with 420149 additions and 1023309 deletions
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examples/extended/parallel/MPI/source/include/G4MPIRunMerger.hh
+16 -31
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@@ -23,41 +23,26 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
#ifndef G4MPIRUNMERGER_HH
#define G4MPIRUNMERGER_HH
#ifndef G4MPIRUNMERGER_HH_
#define G4MPIRUNMERGER_HH_
#include "G4VUserMPIrunMerger.hh"
#include "G4Run.hh"
#include <mpi.h>
#include "G4MPImanager.hh"
class G4MPIRunMerger {
//MPI Merger for default G4Run class
class G4MPIrunMerger : public G4VUserMPIrunMerger {
public:
G4MPIRunMerger( const G4Run* aRun ,
G4int destination = G4MPImanager::kRANK_MASTER ,
G4int verbosity = 0);
virtual ~G4MPIRunMerger() {}
void SetRun( G4Run* r ) { run = r; }
const G4Run* GetRun() const { return run; }
void SetDestinationRank( G4int i ) { destinationRank = i; }
G4int GetDestinationRank() const { return destinationRank; }
G4int GetCommSize() const { return commSize; }
virtual void Merge();
void SetVerbosity( G4int ver ) { verbose = ver; }
G4int GetVerbosity() const { return verbose; }
G4MPIrunMerger() : G4VUserMPIrunMerger() {}
G4MPIrunMerger(const G4Run* ar,
G4int destination = G4MPImanager::kRANK_MASTER,
G4int verboose = 0 ) :
G4VUserMPIrunMerger(ar,destination,verboose) {}
protected:
virtual void Send();
virtual void Receive(G4int rank);
void SendDouble( G4double* val , G4int size=1);
void SendInt( G4int* val , G4int size=1);
void ReceiveDouble( G4int rank , G4double* val , G4int size=1);
void ReceiveInt(G4int rank , G4int* val, G4int size=1);
G4int destinationRank;
G4Run* run;
G4int commSize;
MPI::Intracomm COMM_G4COMMAND_;
G4int verbose;
void Pack() {/*nothing do to*/}
G4Run* UnPack() { return new G4Run; }
};
#endif //G4MPIRUNMERGER_HH
#endif /* G4MPIRUNMERGER_HH_ */
examples/extended/parallel/MPI/source/include/G4MPIScorerMerger.hh
+55 -29
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@@ -27,50 +27,76 @@
#define G4MPISCORERMERGER_HH
#include "G4ScoringManager.hh"
#include <vector>
#include <memory>
#include <utility>
#include <mpi.h>
#include "G4MPImanager.hh"
class G4MPIScorerMerger {
typedef G4THitsMap<G4double> HitMap;
class G4MPIscorerMerger {
public:
G4MPIScorerMerger( G4ScoringManager* mgr,
G4MPIscorerMerger();
G4MPIscorerMerger( G4ScoringManager* mgr,
G4int destination = G4MPImanager::kRANK_MASTER,
G4int verbosity = 0 );
virtual ~G4MPIScorerMerger() { clear(); }
virtual ~G4MPIscorerMerger();
//Get/set methods
void SetDestinationRank( G4int i ) { destinationRank = i; }
G4int GetDestinationRank() const { return destinationRank; }
void SetScoringManager( G4ScoringManager* mgr ) { scoringManager = mgr; }
G4ScoringManager* GetScoringManager() const { return scoringManager; }
G4int GetCommSize() const { return commSize; }
virtual void Merge();
void SetVerbosity( G4int ver ) { verbose = ver; }
G4int GetVerbosity() const { return verbose; }
//Main Interface: call this method to merge all results to rank0
void Merge();
protected:
//Internal MPI-friendly format
//for a single MeshScoreMap
struct convMap_t {
G4String name;
G4int numElems;
G4int* indexes;
G4double* values;
};
virtual convMap_t* convertMap( const G4String& mapName ,
G4THitsMap<double>* map ) const;
virtual void convertMesh( const G4VScoringMesh* mesh );
void clear();
std::vector<convMap_t*> convertedMesh;
G4int meshID;
void SetupOutputBuffer(char* buff, G4int size, G4int position) {
outputBuffer = buff;
outputBufferSize=size;
outputBufferPosition=position;
}
void DestroyBuffer() {
delete[] outputBuffer;
outputBuffer = nullptr;
outputBufferSize=0;
outputBufferPosition=0;
ownsBuffer = false;
}
//! Pack all meshes into buffer
void Pack(const G4ScoringManager*);
void UnPackAndMerge(const G4ScoringManager*);
//! Pack a single mesh
void Pack(const G4VScoringMesh*);
void UnPackAndMerge(G4VScoringMesh* );
//! Pack a single score map
void Pack(const HitMap*);
HitMap* UnPackHitMap(const G4String& detName, const G4String& colName);
//Return size (in bytes) of the message needed to send the mesh
G4int CalculatePackSize(const G4ScoringManager*) const;
G4int CalculatePackSize(const G4VScoringMesh*) const;
G4int CalculatePackSize(const HitMap*) const;
protected:
void Send(const unsigned int destination);
void Receive(const unsigned int source);
private:
char* outputBuffer;
G4int outputBufferSize;
G4int outputBufferPosition;
long bytesSent;
G4bool ownsBuffer;
G4ScoringManager* scoringManager;
G4int commSize;
G4int destinationRank;
MPI::Intracomm COMM_G4COMMAND_;
unsigned int commSize;
unsigned int destinationRank;
MPI::Intracomm comm;
G4int verbose;
virtual void SendOneMesh();
virtual void ReceiveOneMesh();
virtual void MergeOneMesh();
friend std::ostream& operator<<(std::ostream& os , const convMap_t& cnv );
};
#endif //G4MPISCORERMERGER_HH
examples/extended/parallel/MPI/source/include/G4MPIhistoMerger.hh
+58
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@@ -0,0 +1,58 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// Merge G4analysis histogram objects via MPI
//
// History:
// Jun 27, 2015 : Ivana Hrivnacova - new implementation using g4analysis
#ifndef G4MPIHISTOMERGER_HH
#define G4MPIHISTOMERGER_HH
#include "G4MPImanager.hh"
class G4VAnalysisManager;
class G4MPIhistoMerger {
public:
G4MPIhistoMerger();
G4MPIhistoMerger(G4VAnalysisManager* mgr,
G4int destination = G4MPImanager::kRANK_MASTER,
G4int verbosity = 0);
//Get/set methods
void SetDestinationRank( G4int i ) { destination = i; }
void SetScoringManager( G4VAnalysisManager* mgr ) { manager = mgr; }
void SetVerbosity( G4int ver ) { verboseLevel = ver; }
void Merge();
private:
G4VAnalysisManager* manager;
G4int destination;
G4int verboseLevel;
};
#endif //G4MPIHISTOMERGERNEW_HH
examples/extended/parallel/MPI/source/include/G4MPImanager.hh
+5 -1
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@@ -51,7 +51,10 @@ public:
kTAG_G4COMMAND = 100,
kTAG_G4STATUS = 200,
kTAG_G4SEED = 300,
kTAG_DATA = 1000
kTAG_DATA = 1000,
kTAG_HISTO = 1001,
kTAG_RUN = 1002,
kTAG_CMDSCR = 1003
};
G4MPImanager();
@@ -104,6 +107,7 @@ public:
// misc
void ShowHelp() const;
//MPI::Intracomm* GetComm() const { return &COMM_G4COMMAND_; }
private:
DISALLOW_COPY_AND_ASSIGN(G4MPImanager);
examples/extended/parallel/MPI/source/include/G4MPIutils.hh
+96
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@@ -0,0 +1,96 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// Utility functions for MPI G4 interface
#ifndef G4MPIUTILS_HH
#define G4MPIUTILS_HH
#include <map>
#include <vector>
#include <functional>
#include <numeric>
//Namespace with some utility functions for G4 MPI integration.
//Main utilities:
// G4mpi::Merge(...) : Merge results via a semi-optimized communication
// patterns between ranks. Note that this implementation
// is not topology aware. This means that MPI_Reduce and
// MPI_Gather are more performant. However if you cannot
// implement an appropriate MPI reducer or you cannot efford
// the memory overhead of Gather, this can be used instead of
// p2p communications.
namespace G4mpi {
//Simple data type representing a rank
typedef unsigned int rank_t;
//A couple of sending/receiving ranks
typedef std::pair<rank_t,rank_t> couple_t;
//This map represent, for each cycle (key) a set of communications
//pairs
typedef std::map<int,std::vector<couple_t> > commMap_t;
//This function takes as input a vector of rank_t objects representing
//a communication node identified by an ID (rank:int).
//It returns a map of cycle:int -> vector<pairs<rank_t> >
//Representing a sequence of communciation cycles. At each communication cycle
//one or more p2p communications are established: in the pair the first element
//is the sender and the second element of the pair is the receiver
//At the end of the cycles all communications have been done to rank 0
//For example with 4 nodes: [0,1,2,3] we have:
// Cycle 0: (3->2),(1->0)
// Cycle 1: (2->0)
// With 5 nodes:
// Cycle 0: (4->3),(2->1)
// Cycle 1: (3->1)
// Cycle 2: (1->0)
// The algorithm can be used to implement a communication across mpi ranks
// optimizing the network trafic. Each rank (the nodes) can send/receive to another node.
// Once they have sent out the payload they become empty and non-active anymore.
commMap_t buildCommunicationMap( std::vector<rank_t>& input );
//Performs merging to rank 0 using the provided sender, receiver and barrier functions.
//CommSize is the size of the communicator and myrank is the rank of the caller
//For example: assume a class UserMerger has two members Send(uint) and
// Receive(uint) and we are using a MPI::Intracomm object as
// communicator, then to use this function the ranks can:
// using std::placeholers::_1;
// std::function<void(unsigned int)> sender =
// std::bind(&Merger::Send,&mergerInst,_1);
// std::function<void(unsigned int)> receiver =
// std::bind(&Merger::Receiver,&mergerInst,_1);
// std::function<void(void)> barrier =
// std::bind(&MPI::Intracomm::Barrier,&commInst);
// G4mpi::Merge(sender,receiver,barrier,commSize,myrank);
void Merge( std::function<void(unsigned int)> senderF ,
std::function<void(unsigned int)> receiverF ,
std::function<void(void)> barrierF ,
unsigned int commSize , unsigned int myrank);
//Type representing a merging functions
typedef std::function<void(std::function<void(unsigned int)>,
std::function<void(unsigned int)>,
std::function<void(void)>,
unsigned int, unsigned int)>
mergerHandler_t;
}
#endif //G4MPIUTILS_HH
examples/extended/parallel/MPI/source/include/G4VUserMPIrunMerger.hh
+115
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@@ -0,0 +1,115 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
#ifndef G4MPIRUNMERGER_HH
#define G4MPIRUNMERGER_HH
#include "G4Run.hh"
#include <mpi.h>
#include "G4MPImanager.hh"
class G4VUserMPIrunMerger {
public:
G4VUserMPIrunMerger();
G4VUserMPIrunMerger( const G4Run* aRun ,
G4int destination = G4MPImanager::kRANK_MASTER ,
G4int verbosity = 0);
virtual ~G4VUserMPIrunMerger() { if ( ownsBuffer) DestroyBuffer(); }
void SetRun( G4Run* r ) { run = r; }
void SetDestinationRank( G4int i ) { destinationRank = i; }
void SetVerbosity( G4int ver ) { verbose = ver; }
virtual void Merge();
protected:
virtual void Pack() = 0;
virtual G4Run* UnPack() = 0;
void InputUserData( /*const*/ void* input_data ,const MPI::Datatype& dt, int count) {
input_userdata.push_back( const_registered_data{input_data,dt,count} );
}
void OutputUserData( void* input_data ,const MPI::Datatype& dt, int count) {
output_userdata.push_back( registered_data{input_data,dt,count} );
}
// void GetUserData(void* output_data,const MPI::Datatype& dt, int count);
void SetupOutputBuffer(char* buff, G4int size, G4int position) {
outputBuffer = buff;
outputBufferSize=size;
outputBufferPosition=position;
}
void DestroyBuffer() {
delete[] outputBuffer;
outputBuffer = nullptr;
outputBufferSize=0;
outputBufferPosition=0;
ownsBuffer = false;
}
G4int GetPosition() const { return outputBufferPosition; }
char* GetBuffer() const { return outputBuffer; }
G4int GetBufferSize() const { return outputBufferSize; }
void Send(const unsigned int destination);
void Receive(const unsigned int source);
private:
char* outputBuffer;
G4int outputBufferSize;
G4int outputBufferPosition;
G4bool ownsBuffer;
unsigned int destinationRank;
G4Run* run;
unsigned int commSize;
MPI::Intracomm COMM_G4COMMAND_;
G4int verbose;
long bytesSent;
//Input data to send (read-only)
struct const_registered_data {
const_registered_data(const const_registered_data&) = default;
const_registered_data& operator=(const const_registered_data&) = default;
//const_registered_data(const_registered_data&&) = default;
//const_registered_data& operator=(const_registered_data&&) = default;
/*const*/ void* p_data;
/*const*/ MPI::Datatype dt;
/*const*/ int count;
};
std::vector<const_registered_data> input_userdata;
//Output data
struct registered_data {
registered_data(const registered_data&) = default;
registered_data& operator=(const registered_data&) = default;
void* p_data;
/*const*/ MPI::Datatype dt;
/*const*/ int count;
};
std::vector<registered_data> output_userdata;
};
#endif //G4MPIRUNMERGER_HH