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// $Id$
//
// 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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