mapreducehelper_bangbang.cpp

/*

 MapReduce implementation of X!Tandem
 Copyright (C) 2010 Insilicos LLC All Rights Reserved

 Also includes MPI implementation based on X!!Tandem which is
 Copyright (C) 2007 Robert D Bjornson, all rights reserved

 All of which is based on the original X!Tandem project which is
 Copyright (C) 2003-2004 Ronald C Beavis, all rights reserved
 
 This software is a component of the X! proteomics software
 development project


Use of this software governed by the Artistic license, as reproduced here:

The Artistic License for all X! software, binaries and documentation

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*/

#ifdef HAVE_MULTINODE_TANDEM // support for Hadoop and/or MPI?

#include <iostream>
#undef READ_GZIP // messes with ifstream etc
#include "stdafx.h"
#include <algorithm>
#include <set>
#include "msequence.h"
#include "msequencecollection.h"
#include "msequenceserver.h"
#include "msequtilities.h"
#include "mspectrum.h"
#include "loadmspectrum.h"
#include "xmlparameter.h"
#include "mscore.h"
#include "mprocess.h"
#include "saxbiomlhandler.h"
#include "mbiomlreport.h"
#include "mrefine.h"
#include "serialize.h"
#include "timer.h"
#include "mapreducehelper.h"

#include <unistd.h>
#include <string>
#include <sstream>


//
// the contents of this file are largely lifted from 
// ownercompute.cxx in the X!!Tandem project.
//


#ifdef XBANGBANG
#include "mpi.h"
#else
void no_mpi() {
	cerr << "not compiled for X!!Tandem MPI use, quitting\n";
	exit(1);
}
#endif

// set up MPI usage, if we're built for that
void mapreducehelper::init_mode_bangbang(int argc,char **argv) {
#ifndef XBANGBANG
	no_mpi();
#else
	mode_bangbang_ = true;
	MPI::Init(argc,argv);
	num_processes_ = MPI::COMM_WORLD.Get_size();	
	ID_ = MPI::COMM_WORLD.Get_rank();
	if (!ID_) {
		t_ = new timer("master");
	}
#endif
}

/* This is necessary because of a conflict between C++ headers and mpi headers
   See the comment in mpicxx.h
*/
#ifdef XBANGBANG
#define GATHER 1
#define SCATTER 2
#endif

void mapreducehelper::abort() {
#ifdef XBANGBANG
	MPI::COMM_WORLD.Abort(1);
#endif
	exit(mode_mapreduce()?0:1);  // yes, an error but keep hadoop flow going so we can get logs easily
}

int mapreducehelper::mpi_rank() const { // rank of this process if in bangbang mode
#ifndef XBANGBANG
	no_mpi();
	return 0;
#else
    return ID_;
#endif
}
void mapreducehelper::mpi_gather(mprocess **pProcess) {
#ifndef XBANGBANG
	no_mpi();
#else

    if (mpi_rank() > 0) { /* workers */
      /* serialize my data */
      int len; // will be set to length of serialized data packet
      char *buf = serialize_process(*pProcess[mpi_rank()],&len,true);
      /* send to process 0 */
      MPI::COMM_WORLD.Send(buf, len, MPI::CHAR, 0, GATHER);
	  delete[] buf;
    } else { /* master */
      MPI::Status status;
      t_->addsplit("gather");
      for (int i=1; i<num_processes_; ++i) {
        t_->addsplit("probe");
        MPI::COMM_WORLD.Probe(MPI::ANY_SOURCE, GATHER, status);
        int source = status.Get_source();
        int len = status.Get_elements(MPI::CHAR);
        char *buf = new char[len];
        t_->addsplit("get data");
        MPI::COMM_WORLD.Recv(buf, len, MPI::CHAR, source, GATHER);
        t_->addsplit("got data");
        deserialize_process(buf, true, *pProcess[source]);
        delete[] buf;
      }
    }
#endif
}
void mapreducehelper::mpi_scatter(mprocess **pProcess) {
#ifndef XBANGBANG
	no_mpi();
#else
    char *buf;
    int len, i;
    MPI::Status status;
    std::string s;
    if (mpi_rank() > 0) { /* workers */
        MPI::COMM_WORLD.Probe(0, SCATTER, status);
        len = status.Get_elements(MPI::CHAR);
        buf = new char[len+1];
        MPI::COMM_WORLD.Recv(buf, len, MPI::CHAR, 0, SCATTER);
        deserialize_process(buf, true, *pProcess[mpi_rank()]);
        delete[] buf;
    } else { /* master */
      t_->addsplit("scatter");
      for (i=1; i<num_processes_; ++i) {
        /* serialize worker data */
	    int len;
cout << "serialize a process with address" << (long)pProcess[i] << " \n";
cout << "serialize a process with " << pProcess[i]->m_vSpectra.size() << " spectra\n";
        buf = serialize_process(*(pProcess[i]),&len,true);
        /* send to process i */
t_->addsplit("send");
        MPI::COMM_WORLD.Send(buf, len, MPI::CHAR, i, SCATTER);
t_->addsplit("ok,ish");
		delete[] buf;
      }
      t_->addsplit("send data");
    }
#endif
}
void mapreducehelper::mpi_finalize() {
#ifndef XBANGBANG
	no_mpi();
#else
	int rank = mpi_rank();
	MPI::Finalize();
	if (rank > 0) {
		exit(0);
	}
#endif
}

#endif // HAVE_MULTINODE_TANDEM