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703fe5a225
* remove include from headers * update implementation files * completely remove BOOST_FOREACH (#7) * convert those changes to use auto * get rid of all usage of BOOST_FOREACH Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
102 lines
2.7 KiB
C++
102 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 <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,
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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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for (const auto &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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for (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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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(),
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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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