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// $Id: rdkexample2.cpp 1528 2010-09-26 17:04:37Z glandrum $
//
// Copyright (C) 2009 Greg Landrum
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <RDGeneral/RDLog.h>
#include <vector>
#include <algorithm>
#include <boost/mpi.hpp>
#include <boost/foreach.hpp>
#include <iostream>
#include <cstdlib>
#include <string>
namespace mpi = boost::mpi;
void broadcastMols(mpi::communicator &world,std::vector<RDKit::ROMOL_SPTR> &mols){
std::vector<std::string> data;
if (world.rank() == 0) {
data.reserve(mols.size());
BOOST_FOREACH( const RDKit::ROMOL_SPTR &ptr, mols ) {
std::string pickle;
RDKit::MolPickler::pickleMol(*ptr,pickle);
data.push_back(pickle);
}
}
broadcast(world,data,0);
if (world.rank() != 0) {
mols.reserve(data.size());
BOOST_FOREACH( const std::string &pickle, data ) {
RDKit::ROMol *mol=new RDKit::ROMol;
RDKit::MolPickler::molFromPickle(pickle,mol);
mols.push_back(RDKit::ROMOL_SPTR(mol));
}
}
}
int main(int argc, char* argv[])
{
mpi::environment env(argc, argv);
mpi::communicator world;
// construct the data:
std::vector<RDKit::ROMOL_SPTR> data;
if (world.rank() == 0) {
for(unsigned int i=0;i<100;++i){
std::string txt(i+1,'C');
RDKit::ROMol *m=RDKit::SmilesToMol(txt);
data.push_back(RDKit::ROMOL_SPTR(m));
}
}
// broadcast it:
broadcastMols(world,data);
// process it:
std::vector<unsigned int> res;
std::vector<std::vector<unsigned int> > allRes;
// start by finding our chunk:
unsigned int nProcs=world.size();
unsigned int chunkSize=data.size() / nProcs;
unsigned int extraBits=data.size() % nProcs;
// handle extra bits on the root node:
if( world.rank() == 0 ){
for(unsigned int i=0;i<extraBits;++i){
res.push_back(data[i]->getNumAtoms());
}
}
unsigned int pos=extraBits+world.rank()*chunkSize;
for(unsigned int i=0;i<chunkSize;++i){
res.push_back(data[pos++]->getNumAtoms());
}
if( world.rank() == 0 ){
gather(world,res,allRes,0);
} else {
gather(world,res,0);
}
// reporting:
if(world.rank()==0){
for(unsigned int i=0;i<static_cast<unsigned int>(world.size());++i){
std::cout<<"results from process "<<i<<": ";
std::copy(allRes[i].begin(),allRes[i].end(),std::ostream_iterator<int,char>(std::cout, " "));
std::cout<<std::endl;
}
}
return 0;
}
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