mpiWrapper.h

/*  
    Copyright (c) 2017 Institute Jožef Stefan, Jamova cesta 39, SI-1000, Ljubljana, Slovenija

    Permission is hereby granted, free of charge, to any person obtaining a copy
    of this software and associated documentation files (the "Software"), to deal
    in the Software without restriction, including without limitation the rights
    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
    copies of the Software, and to permit persons to whom the Software is
    furnished to do so, subject to the following conditions:

    The above copyright notice and this permission notice shall be included in all
    copies or substantial portions of the Software.

    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
    SOFTWARE.

    Please cite the following works (bibtex source below):
        - DepolliAvbeljTrobec2008 for the simulator and simulation-based optimization
        - DepolliTrobecFilipic2013 for the AMS-DEMO optimizer
        - TrobecDepolliAvbelj2009 for the simulator

    @article{DepolliAvbeljTrobec2008,
        author = {Depolli, Matjaž and Avbelj, Viktor and Trobec, Roman},
        title = {Computer-Simulated Alternative Modes of {U}-Wave Genesis},
        journal = {Journal of Cardiovascular Electrophysiology},
        volume = {19},
        number = {1},
        publisher = {Blackwell Publishing Inc},
        issn = {1540-8167},
        url = {http://dx.doi.org/10.1111/j.1540-8167.2007.00978.x},
        doi = {10.1111/j.1540-8167.2007.00978.x},
        pages = {84--89},
        keywords = {U wave, ECG, action potential, repolarization, myocardium, computer simulation},
        year = {2008}
    }

    @article{DepolliTrobecFilipic2013,
        author = {Depolli, Matjaž and Trobec, Roman and Filipič, Bogdan},
        title = {Asynchronous master-slave parallelization of differential evolution for multiobjective optimization},
        journal = {Evolutionary Computation},
        volume = {21},
        number = {2},
        pages = {261-291},
        doi = {10.1162/EVCO_a_00076},
        issn = {1063-6560},
        url = {http://www.mitpressjournals.org/doi/abs/10.1162/EVCO_a_00076},
        year = {2013}
    }

    @inproceedings{TrobecDepolliAvbelj2009,
        title           = {Simulation of {ECG} repolarization phase with improved model of cell action potentials},
        author          = {Trobec, Roman and Depolli, Matja{\v{z}} and Avbelj, Viktor},
        booktitle       = {International Joint Conference on Biomedical Engineering Systems and Technologies},
        pages           = {325--332},
        year            = {2009},
        organization    = {Springer}
    }
*/

#ifndef MPIWRAPPER_H_INCLUDED
#define MPIWRAPPER_H_INCLUDED

/// mpi header does not like being included after iostream, so special care should be taken using
/// this header. Either include mpi.h earlier, or include this header before iostream


#include <mpi.h>
#include <exception>
#include <vector>
#include "Array.h"
#include <cassert>


class BinaryStream {
public:
	std::vector<char> stream;
	mutable size_t outPos;
	
public:
	BinaryStream() : outPos(0) {}
	
	
	void* voidStream() {
		return &(stream[0]);
	}
	
	void* voidStream() const {
		return const_cast<void*>((void*)&(stream[0]));
	}
	
	size_t size() const {
		return stream.size();
	}
	
	void resize(size_t s) {
		stream.resize(s);
	}
	
	void clear() {
		stream.clear();
		outPos = 0;
	}
};

	
template<class Pod>
BinaryStream& operator<< (BinaryStream& bs, const Pod& pod) {
	size_t position = bs.stream.size();
	bs.stream.resize(bs.stream.size() + sizeof(Pod));
	*((Pod*)&bs.stream[position]) = pod;
	return bs;
}


template<class Pod>
BinaryStream& operator<< (BinaryStream& bs, const std::vector<Pod>& vec) {
	bs << vec.size();
	size_t position = bs.stream.size();
	bs.stream.resize(bs.stream.size() + sizeof(Pod) * vec.size());
	std::copy(vec.begin(), vec.end(), (Pod*)&bs.stream[position]);
	return bs;
}


template<class Pod>
BinaryStream& operator>> (BinaryStream& bs, Pod& pod) {
	assert(bs.outPos+sizeof(Pod) <= bs.stream.size());
	pod = *reinterpret_cast<const Pod*>(&bs.stream[bs.outPos]);
	bs.outPos += sizeof(Pod);
	return bs;
}


template<class Pod>
BinaryStream& operator>> (BinaryStream& bs, std::vector<Pod>& vec) {
	size_t s;
	bs >> s;
	vec.resize(s);
	assert(bs.outPos+sizeof(Pod)*vec.size() <= bs.stream.size());
	std::copy((Pod*)&bs.stream[bs.outPos], ((Pod*)&bs.stream[bs.outPos]) 
		+ vec.size(), vec.begin());
	bs.outPos += sizeof(Pod)*vec.size();
	return bs;
}


namespace Mpi {
	
	class Communicator {
		MPI_Comm comm;
		
	public:
		Communicator(MPI_Comm c = MPI_COMM_WORLD) : comm(c) {}
		
		const Communicator& operator= (MPI_Comm c) {
			comm = c;
			return *this;
		}
		
		int getSize() const {
			int size;
			MPI_Comm_size(comm, &size);
			return size;
		}
		
		int getRank() const {
			int rank;
			MPI_Comm_rank(comm, &rank);
			return rank;
		}
		
		operator MPI_Comm() const {
			return comm;
		}
        
        // for debugging only
        int toInt() const {
            return (intptr_t)comm;
        }
	};
	
	
	struct Status {
		MPI_Status status;
		bool messageWaiting;
		
		int source() const {return status.MPI_SOURCE;}
		int tag() const {return status.MPI_TAG;}
		int error() const {return status.MPI_ERROR;}
		int count() const {
			int c;
			MPI_Get_count(const_cast<MPI_Status*>(&status), MPI_CHAR, &c);
			return c;
		}
		
		Status() : messageWaiting(false) {
		}
		
		bool probeSpecific(int sourcep, int tagp, const Communicator& comm = MPI_COMM_WORLD) {
			int flag;
			MPI_Iprobe(sourcep, tagp, comm, &flag, &status);
			messageWaiting = (flag != 0);
			return messageWaiting;
		}
		
		bool probe(const Communicator& comm = MPI_COMM_WORLD) {
			return probeSpecific(MPI_ANY_SOURCE, MPI_ANY_TAG, comm);
		}
		
		/// blocking probe (wait for message)
		void waitSpecific(int sourcep, int tagp, const Communicator& comm = MPI_COMM_WORLD) {
			MPI_Probe(sourcep, tagp, comm, &status);
		}
		
		void wait(const Communicator& comm = MPI_COMM_WORLD) {
			waitSpecific(MPI_ANY_SOURCE, MPI_ANY_TAG, comm);
		}
	};
	
	
	struct Request {
		MPI_Request request;
		
		void wait() {
			Status status;
			MPI_Wait(&request, &status.status);
		}
	};
	
	
	template<class T>
	struct Streamify {
		T* data;
		
		Streamify(const T& t) : data(const_cast<T*>(&t)) {}
		void* ptr() {return (void*)(data);}
		size_t size() {return sizeof(T);}
		void getSize(int source, int tag, const Communicator& comm) {}
		void setSize(size_t ssize) {assert(ssize == sizeof(T));}
	};
	
	template<class T>
	struct Streamify<std::vector<T> > {
		std::vector<T>& vec;
		
		Streamify(const std::vector<T>& t) : vec(const_cast<std::vector<T>&>(t)) {}
		void* ptr() {return (void*)(&vec[0]);}
		size_t size() const {return sizeof(T)*vec.size();}
		void getSize(int source, int tag, const Communicator& comm) {
			Status status;
			status.probeSpecific(source, tag, comm);
			vec.resize(status.count() / sizeof(T));
		}
		void setSize(size_t ssize) {vec.resize(ssize / sizeof(T));}
	};
	
	template<>
	struct Streamify<BinaryStream> {
		BinaryStream& data;
		
		Streamify(const BinaryStream& t) : data(const_cast<BinaryStream&>(t)) {}
		void* ptr() {return data.voidStream();}
		size_t size() const {return data.size();}
		void getSize(int source, int tag, const Communicator& comm) {
			Status status;
			status.probeSpecific(source, tag, comm);
			data.resize(status.count());
		}
		void setSize(size_t ssize) {data.resize(ssize);}
	};
	
	template<class T, size_t N>
	struct Streamify<Array<T, N> > {
		Array<T, N>& data;
		
		Streamify(Array<T, N>& t) : data(t) {}
		void* ptr() {return (void*)(&data[0]);}
		size_t size() const {return N;}
		void getSize(int source, int tag, const Communicator& comm) {
			Status status;
			status.probeSpecific(source, tag, comm);
			assert(status.count() / sizeof(T) == N);
		}
		void setSize(size_t ssize) {assert(ssize == N);}
	};



	template<class T>
	void send(const T& t, int dest, int tag, const Communicator& comm = MPI_COMM_WORLD) {
		Streamify<T> s(t);
		MPI_Send(s.ptr(), s.size(), MPI_CHAR, dest, tag, comm);
	}
	
	template<class T>
	void send(const T& t, int dest, int tag, Request& req, const Communicator& comm = MPI_COMM_WORLD) {
		Streamify<T> s(t);
		MPI_Ibsend(s.ptr(), s.size(), MPI_CHAR, dest, tag, comm, &req.request);
	}
	
	
	template<class T>
	void receive(T& t, int source, int tag, const Communicator& comm = MPI_COMM_WORLD) {
		MPI_Status status;
		Streamify<T> s(t);
		s.getSize(source, tag, comm);
		MPI_Recv(s.ptr(), s.size(), MPI_CHAR, source, tag, comm, &status);
	}
	
	template<class T>
	void receive(T& t, Status& status, const Communicator& comm = MPI_COMM_WORLD) {
		Streamify<T> s(t);
		s.setSize(status.count());
		MPI_Recv(s.ptr(), s.size(), MPI_CHAR, status.source(), status.tag(), comm, &status.status);
	}
	
	
	class Environment {
		Communicator comm;
		
	public:
		Environment(int &argc, char**& argv) {
			if (MPI_Init(&argc, &argv) != MPI_SUCCESS) throw std::exception();
		} 
		
		~Environment() {
			MPI_Finalize();
		}
		
		const Communicator& getCommunicator() const {
			return comm;
		}
		
		operator const Communicator& () const {
			return comm;
		}
	};
	
	
	// class that wraps process buffer allocation and deallocation
	class Buffer {
		char* buf;
		
	public:
		Buffer(size_t size) {
			size += MPI_BSEND_OVERHEAD;
			buf = new char[size];
			MPI_Buffer_attach((void*)buf, size);
		}
		
		~Buffer() {
			void* dummyAddr;
			int dummySize;
			MPI_Buffer_detach(&dummyAddr, &dummySize);
			delete[] buf;
		}
	};
	
};


#endif // MPIWRAPPER_H_INCLUDED