xmipp_mpi.h

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 /*
 * Authors:     J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
 *
 *
 * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
 *
 * This program 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 2 of the License, or
 * (at your option) any later version.
 *
 * This program 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 this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
 * 02111-1307  USA
 *
 *  All comments concerning this program package may be sent to the
 *  e-mail address 'xmipp@cnb.csic.es'
 ***************************************************************************/

#ifndef XMIPP_MPI_H_
#define XMIPP_MPI_H_

#include <mpi.h>
#include "core/xmipp_threads.h"
#include "core/xmipp_program.h"
#include "core/metadata_vec.h"
#include "core/metadata_db.h"

class FileName;

#define XMIPP_MPI_SIZE_T MPI_UNSIGNED_LONG

class MpiNode
{
public:

    //MPI_Comm *comm;
    size_t rank, size, active;//, activeNodes;
    MpiNode(int &argc, char **& argv);
    ~MpiNode();
    MpiNode(const MpiNode &)=delete;
    MpiNode & operator =(const MpiNode &)=delete;

    bool isMaster() const;

    void barrierWait();

    template <typename T> // T = MetaData*
    void gatherMetadatas(T &MD, const FileName &rootName);

//    void updateComm();

protected:
    size_t getActiveNodes();

};

//mpi macros
#define TAG_WORK   0
#define TAG_STOP   1
#define TAG_WAIT   2

#define TAG_WORK_REQUEST 100
#define TAG_WORK_RESPONSE 101

class MpiTaskDistributor: public ThreadTaskDistributor
{
protected:
    std::shared_ptr<MpiNode> node;

    virtual bool distribute(size_t &first, size_t &last);

public:
    MpiTaskDistributor(size_t nTasks, size_t bSize, const std::shared_ptr<MpiNode> &node);
    void wait();

private:
    bool distributeMaster();
    bool distributeSlaves(size_t &first, size_t &last);
}
;//end of class MpiTaskDistributor

class MpiFileMutex: public Mutex
{
protected:
    std::shared_ptr<MpiNode> node;
    int lockFile;
    bool fileCreator;
public:
    MpiFileMutex(const std::shared_ptr<MpiNode> &node);

    ~MpiFileMutex();

    void lock();

    void unlock();

    char lockFilename[L_tmpnam];
}
;//end of class MpiFileMutex

class XmippMpiProgram: public virtual XmippProgram
{
protected:
    std::shared_ptr<MpiNode> node;
    size_t nProcs;
    size_t numberOfJobs;
    MPI_Status status;

    void setNode(const std::shared_ptr<MpiNode> & node);

public:
    void read(int argc, char **argv);
    virtual int tryRun();
};

class MpiMetadataProgram: public XmippMpiProgram
{
protected:
    int blockSize;
    std::vector<size_t> imgsId;
    MpiTaskDistributor *distributor=nullptr;
    size_t first, last;

public:
    MpiMetadataProgram() {}
    MpiMetadataProgram(const MpiMetadataProgram &)=delete;
    MpiMetadataProgram(const MpiMetadataProgram &&)=delete;

    ~MpiMetadataProgram();
    MpiMetadataProgram & operator=(const MpiMetadataProgram &)=delete;
    MpiMetadataProgram & operator=(const MpiMetadataProgram &&)=delete;

    void read(int argc, char **argv);

    void defineParams();
    void readParams();
    void createTaskDistributor(MetaData &mdIn, size_t blockSize = 0);
    virtual void preProcess() { /* nothing to do */ };
    virtual void finishProcessing() { /* nothing to do */ };
    bool getTaskToProcess(size_t &objId, size_t &objIndex);
};

template <typename BASE_CLASS>
class BasicMpiMetadataProgram : public BASE_CLASS, public MpiMetadataProgram {
protected:
  void defineParams() override {
    BASE_CLASS::defineParams();
    MpiMetadataProgram::defineParams();
  }

  void readParams() override {
    MpiMetadataProgram::readParams();
    BASE_CLASS::readParams();
  }

  void preProcess() override {
    BASE_CLASS::preProcess();
    MetaData &mdIn = *this->getInputMd();
    mdIn.addLabel(MDL_GATHER_ID);
    mdIn.fillLinear(MDL_GATHER_ID, 1, 1);
    createTaskDistributor(mdIn, blockSize);
  }

  void startProcessing() {
    if (node->rank == 1) {
      verbose = 1;
      BASE_CLASS::startProcessing();
    }
    node->barrierWait();
  }

  void showProgress() {
    if (node->rank == 1) {
      BASE_CLASS::time_bar_done = first + 1;
      BASE_CLASS::showProgress();
    }
  }

  bool getImageToProcess(size_t &objId, size_t &objIndex) override {
    return getTaskToProcess(objId, objIndex);
  }

  void finishProcessing() override {
    node->gatherMetadatas(this->getOutputMd(), BASE_CLASS::fn_out);
    MetaDataVec MDaux;
    MDaux.sort(this->getOutputMd(), MDL_GATHER_ID);
    MDaux.removeLabel(MDL_GATHER_ID);
    this->getOutputMd() = MDaux;
    if (node->isMaster())
      BASE_CLASS::finishProcessing();
  }

  void wait() { distributor->wait(); }
};

void xmipp_MPI_Reduce(
    void* send_data,
    void* recv_data,
    size_t count,
    MPI_Datatype datatype,
    MPI_Op op,
    int root,
    MPI_Comm communicator,
    size_t blockSize=1048576);

#endif /* XMIPP_MPI_H_ */