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