source: src/Fragmentation/Automation/controller.cpp@ e48f5c

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2011 University of Bonn. All rights reserved.
 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
 */

/*
 * \file controller.cpp
 *
 * This file strongly follows the Serialization example from the boost::asio
 * library (see client.cpp)
 *
 *  Created on: Nov 27, 2011
 *      Author: heber
 */


// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

// boost asio needs specific operator new
#include <boost/asio.hpp>

#include "CodePatterns/MemDebug.hpp"

#include <boost/archive/text_oarchive.hpp>
#include <boost/archive/text_iarchive.hpp>
#include <boost/program_options.hpp>
#include <fstream>
#include <iostream>
#include <map>
#include <sstream>
#include <streambuf>
#include <vector>

#include "atexit.hpp"
#include "CodePatterns/Info.hpp"
#include "CodePatterns/Log.hpp"
#include "Fragmentation/EnergyMatrix.hpp"
#include "Fragmentation/ForceMatrix.hpp"
#include "Fragmentation/KeySetsContainer.hpp"
#include "FragmentController.hpp"
#include "Helpers/defs.hpp"
#include "Jobs/MPQCCommandJob.hpp"
#include "Jobs/MPQCCommandJob_MPQCData.hpp"
#include "Jobs/SystemCommandJob.hpp"
#include "Results/FragmentResult.hpp"

enum CommandIndices {
  UnknownCommandIndex = 0,
  AddJobsIndex = 1,
  CreateJobsIndex = 2,
  CheckResultsIndex = 3,
  ReceiveResultsIndex = 4,
  ReceiveMPQCIndex = 5,
  RemoveAllIndex = 6,
  ShutdownIndex = 7,
};


/** Creates a SystemCommandJob out of give \a command with \a argument.
 *
 * @param jobs created job is added to this vector
 * @param command command to execute for SystemCommandJob
 * @param argument argument for command to execute
 * @param nextid id for this job
 */
void createjobs(
    std::vector<FragmentJob::ptr> &jobs,
    const std::string &command,
    const std::string &argument,
    const JobId_t nextid)
{

  FragmentJob::ptr testJob( new SystemCommandJob(command, argument, nextid) );
  jobs.push_back(testJob);
  LOG(1, "INFO: Added one SystemCommandJob.");
}

/** Creates a MPQCCommandJob with argument \a filename.
 *
 * @param jobs created job is added to this vector
 * @param command mpqc command to execute
 * @param filename filename being argument to job
 * @param nextid id for this job
 */
void parsejob(
    std::vector<FragmentJob::ptr> &jobs,
    const std::string &command,
    const std::string &filename,
    const JobId_t nextid)
{
  std::ifstream file;
  file.open(filename.c_str());
  ASSERT( file.good(), "parsejob() - file "+filename+" does not exist.");
  std::string output((std::istreambuf_iterator<char>(file)),
      std::istreambuf_iterator<char>());
  FragmentJob::ptr testJob( new MPQCCommandJob(output, nextid, command) );
  jobs.push_back(testJob);
  file.close();
  LOG(1, "INFO: Added MPQCCommandJob from file "+filename+".");
}

/** Print received results.
 *
 * @param results received results to print
 */
void printReceivedResults(std::vector<FragmentResult::ptr> &results)
{
  for (std::vector<FragmentResult::ptr>::const_iterator iter = results.begin();
      iter != results.end(); ++iter)
    LOG(1, "RESULT: job #"+toString((*iter)->getId())+": "+toString((*iter)->result));
}

/** Print MPQCData from received results.
 *
 * @param results received results to extract MPQCData from
 * @param KeySetFilename filename with keysets to associate forces correctly
 * @param NoAtoms total number of atoms
 */
bool printReceivedMPQCResults(
    const std::vector<FragmentResult::ptr> &results,
    const std::string &KeySetFilename,
    size_t NoAtoms)
{
  EnergyMatrix Energy;
  EnergyMatrix EnergyFragments;
  ForceMatrix Force;
  ForceMatrix ForceFragments;
  KeySetsContainer KeySet;

  // align fragments
  std::map< JobId_t, size_t > MatrixNrLookup;
  size_t FragmentCounter = 0;
  {
    // bring ids in order ...
    typedef std::map< JobId_t, FragmentResult::ptr> IdResultMap_t;
    IdResultMap_t IdResultMap;
    for (std::vector<FragmentResult::ptr>::const_iterator iter = results.begin();
        iter != results.end(); ++iter) {
  #ifndef NDEBUG
      std::pair< IdResultMap_t::iterator, bool> inserter =
  #endif
      IdResultMap.insert( make_pair((*iter)->getId(), *iter) );
      ASSERT( inserter.second,
          "printReceivedMPQCResults() - two results have same id "
          +toString((*iter)->getId())+".");
    }
    // ... and fill lookup
    for(IdResultMap_t::const_iterator iter = IdResultMap.begin();
        iter != IdResultMap.end(); ++iter)
      MatrixNrLookup.insert( make_pair(iter->first, FragmentCounter++) );
  }
  LOG(1, "INFO: There are " << FragmentCounter << " fragments.");

  // extract results
  std::vector<MPQCData> fragmentData(results.size());
  MPQCData combinedData;

  LOG(2, "DEBUG: Parsing now through " << results.size() << " results.");
  for (std::vector<FragmentResult::ptr>::const_iterator iter = results.begin();
      iter != results.end(); ++iter) {
    LOG(1, "RESULT: job #"+toString((*iter)->getId())+": "+toString((*iter)->result));
    MPQCData extractedData;
    std::stringstream inputstream((*iter)->result);
    LOG(2, "DEBUG: First 50 characters FragmentResult's string: "+(*iter)->result.substr(0, 50));
    boost::archive::text_iarchive ia(inputstream);
    ia >> extractedData;
    LOG(1, "INFO: extracted data is " << extractedData << ".");

    // place results into EnergyMatrix ...
    {
      MatrixContainer::MatrixArray matrix;
      matrix.resize(1);
      matrix[0].resize(1, extractedData.energy);
      if (!Energy.AddMatrix(
          std::string("MPQCJob ")+toString((*iter)->getId()),
          matrix,
          MatrixNrLookup[(*iter)->getId()])) {
        ELOG(1, "Adding energy matrix failed.");
        return false;
      }
    }
    // ... and ForceMatrix (with two empty columns in front)
    {
      MatrixContainer::MatrixArray matrix;
      const size_t rows = extractedData.forces.size();
      matrix.resize(rows);
      for (size_t i=0;i<rows;++i) {
        const size_t columns = 2+extractedData.forces[i].size();
        matrix[i].resize(columns, 0.);
  //      for (size_t j=0;j<2;++j)
  //        matrix[i][j] = 0.;
        for (size_t j=2;j<columns;++j)
          matrix[i][j] = extractedData.forces[i][j-2];
      }
      if (!Force.AddMatrix(
          std::string("MPQCJob ")+toString((*iter)->getId()),
          matrix,
          MatrixNrLookup[(*iter)->getId()])) {
        ELOG(1, "Adding force matrix failed.");
        return false;
      }
    }
  }
  // add one more matrix (not required for energy)
  MatrixContainer::MatrixArray matrix;
  matrix.resize(1);
  matrix[0].resize(1, 0.);
  if (!Energy.AddMatrix(std::string("MPQCJob total"), matrix, FragmentCounter))
    return false;
  // but for energy because we need to know total number of atoms
  matrix.resize(NoAtoms);
  for (size_t i = 0; i< NoAtoms; ++i)
    matrix[i].resize(2+NDIM, 0.);
  if (!Force.AddMatrix(std::string("MPQCJob total"), matrix, FragmentCounter))
    return false;


  // combine all found data
  if (!Energy.InitialiseIndices()) return false;

  if (!Force.ParseIndices(KeySetFilename.c_str())) return false;

  if (!KeySet.ParseKeySets(KeySetFilename.c_str(), Force.RowCounter, Force.MatrixCounter)) return false;

  if (!KeySet.ParseManyBodyTerms()) return false;

  if (!EnergyFragments.AllocateMatrix(Energy.Header, Energy.MatrixCounter, Energy.RowCounter, Energy.ColumnCounter)) return false;
  if (!ForceFragments.AllocateMatrix(Force.Header, Force.MatrixCounter, Force.RowCounter, Force.ColumnCounter)) return false;

  if(!Energy.SetLastMatrix(0., 0)) return false;
  if(!Force.SetLastMatrix(0., 2)) return false;

  for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
    // --------- sum up energy --------------------
    LOG(1, "INFO: Summing energy of order " << BondOrder+1 << " ...");
    if (!EnergyFragments.SumSubManyBodyTerms(Energy, KeySet, BondOrder)) return false;
    if (!Energy.SumSubEnergy(EnergyFragments, NULL, KeySet, BondOrder, 1.)) return false;

    // --------- sum up Forces --------------------
    LOG(1, "INFO: Summing forces of order " << BondOrder+1 << " ...");
    if (!ForceFragments.SumSubManyBodyTerms(Force, KeySet, BondOrder)) return false;
    if (!Force.SumSubForces(ForceFragments, KeySet, BondOrder, 1.)) return false;
  }

  // for debugging print resulting energy and forces
  LOG(1, "INFO: Resulting energy is " << Energy.Matrix[ FragmentCounter ][0][0]);
  std::stringstream output;
  for (int i=0; i< Force.RowCounter[FragmentCounter]; ++i) {
    for (int j=0; j< Force.ColumnCounter[FragmentCounter]; ++j)
      output << Force.Matrix[ FragmentCounter ][i][j] << " ";
    output << "\n";
  }
  LOG(1, "INFO: Resulting forces are " << std::endl << output.str());

  return true;
}

/** Helper function to get number of atoms somehow.
 *
 * Here, we just parse the number of lines in the adjacency file as
 * it should correspond to the number of atoms, except when some atoms
 * are not bonded, but then fragmentation makes no sense.
 *
 * @param path path to the adjacency file
 */
size_t getNoAtomsFromAdjacencyFile(const std::string &path)
{
  size_t NoAtoms = 0;

  // parse in special file to get atom count (from line count)
  std::string filename(path);
  filename += FRAGMENTPREFIX;
  filename += ADJACENCYFILE;
  std::ifstream adjacency(filename.c_str());
  if (adjacency.fail()) {
    LOG(0, endl << "getNoAtomsFromAdjacencyFile() - Unable to open " << filename << ", is the directory correct?");
    return false;
  }
  std::string buffer;
  while (getline(adjacency, buffer))
    NoAtoms++;
  LOG(1, "INFO: There are " << NoAtoms << " atoms.");

  return NoAtoms;
}


/** Returns a unique index for every command to allow switching over it.
 *
 * \param &commandmap map with command strings
 * \param &cmd command string
 * \return index from CommandIndices: UnkownCommandIndex - unknown command, else - command index
 */
CommandIndices getCommandIndex(std::map<std::string, CommandIndices> &commandmap, const std::string &cmd)
{
  std::map<std::string, CommandIndices>::const_iterator iter = commandmap.find(cmd);
  if (iter != commandmap.end())
    return iter->second;
  else
    return UnknownCommandIndex;
}


int main(int argc, char* argv[])
{
  // from this moment on, we need to be sure to deeinitialize in the correct order
  // this is handled by the cleanup function
  atexit(cleanUp);

  setVerbosity(3);

  size_t Exitflag = 0;
  typedef std::map<std::string, CommandIndices> CommandsMap_t;
  CommandsMap_t CommandsMap;
  CommandsMap.insert( std::make_pair("addjobs", AddJobsIndex) );
  CommandsMap.insert( std::make_pair("createjobs", CreateJobsIndex) );
  CommandsMap.insert( std::make_pair("checkresults", CheckResultsIndex) );
  CommandsMap.insert( std::make_pair("receiveresults", ReceiveResultsIndex) );
  CommandsMap.insert( std::make_pair("receivempqc", ReceiveMPQCIndex) );
  CommandsMap.insert( std::make_pair("removeall", RemoveAllIndex) );
  CommandsMap.insert( std::make_pair("shutdown", ShutdownIndex) );
  std::vector<std::string> Commands;
  for (CommandsMap_t::const_iterator iter = CommandsMap.begin(); iter != CommandsMap.end(); ++iter)
    Commands.push_back(iter->first);

  // Declare the supported options.
  boost::program_options::options_description desc("Allowed options");
  desc.add_options()
      ("help,h", "produce help message")
      ("verbosity,v", boost::program_options::value<size_t>(), "set verbosity level")
      ("server", boost::program_options::value< std::string >(), "connect to server at this address (host:port)")
      ("command", boost::program_options::value< std::string >(), (std::string("command to send to server: ")+toString(Commands)).c_str())
      ("executable", boost::program_options::value< std::string >(), "executable for commands 'addjobs' and 'createjobs'")
      ("fragment-path", boost::program_options::value< std::string >(), "path to fragment files for 'receivempqcresults'")
      ("jobcommand", boost::program_options::value< std::string >(), "command argument for executable for 'createjobs'")
      ("jobfiles", boost::program_options::value< std::vector< std::string > >()->multitoken(), "list of files as single argument to executable for 'addjobs'")
  ;

  boost::program_options::variables_map vm;
  boost::program_options::store(boost::program_options::parse_command_line(argc, argv, desc), vm);
  boost::program_options::notify(vm);

  if (vm.count("help")) {
    std::cout << desc << "\n";
    return 1;
  }

  if (vm.count("verbosity")) {
    LOG(0, "STATUS: Verbosity level was set to " << vm["verbosity"].as<size_t>() << ".");
    setVerbosity(vm["verbosity"].as<size_t>());
  } else {
    LOG(0, "STATUS: Verbosity level was not set, defaulting to 5.");
    setVerbosity(5);
  }

  std::string server;
  std::string serverport;
  if (vm.count("server")) {
    server = vm["server"].as< std::string >();
    serverport = server.substr(server.find_last_of(':')+1, std::string::npos);
    server = server.substr(0, server.find_last_of(':'));
    try {
      boost::lexical_cast<size_t>(serverport);
    } catch (boost::bad_lexical_cast) {
      ELOG(1, "Could not interpret " << serverport << " as server:port.");
      return 255;
    }
    LOG(1, "INFO: Using " << server << ":" << serverport << " as server's address.");
  } else {
    ELOG(1, "Requiring server's address (host:port) to connect to.");
    return 255;
  }

  if (!vm.count("command")) {
    ELOG(1, "Controller requires one of the following commands: "+toString(Commands));
    return 255;
  }
  const std::string command = vm["command"].as< std::string >();
  const CommandIndices commandIndex = getCommandIndex(CommandsMap, command);

  // check arguments
  switch(commandIndex) {
    case AddJobsIndex:
      if (!vm.count("executable") && !vm.count("jobfiles")) {
        ELOG(1, "'"+command+"' requires at least two options: [executable] [list of input files ...].");
        return 255;
      }
      break;
    case CreateJobsIndex:
      if (!vm.count("executable") && !vm.count("jobcommand")) {
        ELOG(1, "'"+command+"' requires two options: [executable] [jobcommand].");
        return 255;
      }
      break;
    case CheckResultsIndex:
      break;
    case ReceiveResultsIndex:
      break;
    case ReceiveMPQCIndex:
      if (!vm.count("fragment-path")) {
        ELOG(1, "'"+command+"' require one option: [path to fragment files].");
        return 255;
      }
      break;
    case RemoveAllIndex:
      break;
    case ShutdownIndex:
      break;
    case UnknownCommandIndex:
    default:
      ELOG(1, "Unrecognized command '"+toString(command)+"'.");
      return 255;
      break;
  }

  try
  {

    boost::asio::io_service io_service;
    FragmentController controller(io_service);

    // Initial phase: information gathering from server

    switch(commandIndex) {
      case AddJobsIndex:
        controller.requestIds(server, serverport, vm["jobfiles"].as< std::vector<std::string> >().size());
        break;
      case CreateJobsIndex:
        controller.requestIds(server, serverport, 1);
        break;
      case CheckResultsIndex:
        break;
      case ReceiveResultsIndex:
        break;
      case ReceiveMPQCIndex:
        break;
      case RemoveAllIndex:
        break;
      case ShutdownIndex:
        break;
      case UnknownCommandIndex:
      default:
        ELOG(0, "Unrecognized command '"+toString(command)+"'.");
        return 255;
        break;
    }

    {
      io_service.reset();
      Info info("io_service: Phase One");
      io_service.run();
    }

    // Second phase: Building jobs and sending information to server

    switch(commandIndex) {
      case AddJobsIndex:
      {
        std::vector<FragmentJob::ptr> jobs;
        const std::string executable(vm["executable"].as< std::string >());
        const std::vector< std::string > jobfiles = vm["jobfiles"].as< std::vector< std::string > >();
        for (std::vector< std::string >::const_iterator iter = jobfiles.begin();
            iter != jobfiles.end(); ++iter) {
          const JobId_t next_id = controller.getAvailableId();
          const std::string &filename = *iter;
          LOG(1, "INFO: Creating MPQCCommandJob with filename'"
              +filename+"', and id "+toString(next_id)+".");
          parsejob(jobs, executable, filename, next_id);
        }
        controller.addJobs(jobs);
        controller.sendJobs(server, serverport);
        break;
      }
      case CreateJobsIndex:
      {
        const JobId_t next_id = controller.getAvailableId();
        std::vector<FragmentJob::ptr> jobs;
        const std::string executable = vm["executable"].as< std::string >();
        const std::string jobcommand = vm["jobcommand"].as< std::string >();
        createjobs(jobs, executable, jobcommand, next_id);
        controller.addJobs(jobs);
        controller.sendJobs(server, serverport);
        break;
      }
      case CheckResultsIndex:
        controller.checkResults(server, serverport);
        break;
      case ReceiveResultsIndex:
      case ReceiveMPQCIndex:
        controller.receiveResults(server, serverport);
        break;
      case RemoveAllIndex:
        controller.removeall(server, serverport);
        break;
      case ShutdownIndex:
        controller.shutdown(server, serverport);
        break;
      case UnknownCommandIndex:
      default:
        ELOG(0, "Unrecognized command '"+toString(command)+"'.");
        return 255;
        break;
    }

    {
      io_service.reset();
      Info info("io_service: Phase Two");
      io_service.run();
    }

    // Final phase: Print result of command

    switch(commandIndex) {
      case AddJobsIndex:
      case CreateJobsIndex:
        break;
      case CheckResultsIndex:
        controller.printDoneJobs();
        break;
      case ReceiveResultsIndex:
      {
        std::vector<FragmentResult::ptr> results = controller.getReceivedResults();
        printReceivedResults(results);
        break;
      }
      case ReceiveMPQCIndex:
      {
        const std::string path = vm["fragment-path"].as< std::string >();
        LOG(1, "INFO: Parsing fragment files from " << path << ".");
        std::vector<FragmentResult::ptr> results = controller.getReceivedResults();
        printReceivedMPQCResults(
            results,
            path,
            getNoAtomsFromAdjacencyFile(path));
        break;
      }
      case RemoveAllIndex:
        break;
      case ShutdownIndex:
        break;
      case UnknownCommandIndex:
      default:
        ELOG(0, "Unrecognized command '"+toString(command)+"'.");
        return 255;
        break;
    }
    Exitflag = controller.getExitflag();
  }
  catch (std::exception& e)
  {
    std::cerr << e.what() << std::endl;
  }

  return Exitflag;
}