コード例 #1
0
ファイル: TrajIOarray.cpp プロジェクト: SAMAN-64/cpptraj
/** Loop over all filenames in replica_filenames, set up TrajectoryIO. */
int TrajIOarray::SetupIOarray(ArgList& argIn, TrajFrameCounter& counter,
                              CoordinateInfo& cInfo, Topology* trajParm)
{
  // Sanity check
  if (!IOarray_.empty()) {
    mprinterr("Internal Error: SetupIOarray() has been called twice.\n");
    return 1;
  }
  // Save arguments that have not been processed so they can be passed
  // to each replica in turn. Only the lowest replica will use argIn.
  ArgList argCopy( argIn );
  bool lowestRep = true;
  int rep0Frames = TrajectoryIO::TRAJIN_UNK;  // Total frames in replica 0
  int totalFrames = TrajectoryIO::TRAJIN_UNK; // Total # frames to be read from ensemble
  TrajectoryFile::TrajFormatType lastRepFmt = TrajectoryFile::UNKNOWN_TRAJ;
  // Right now enforce that all replicas have the same metadata as lowest
  // replica, e.g. if replica 0 has temperature, replica 1 does too etc.
  for (File::NameArray::const_iterator repfile = replica_filenames_.begin();
                                       repfile != replica_filenames_.end(); ++repfile)
  {
    // Detect format
    TrajectoryFile::TrajFormatType repformat = TrajectoryFile::UNKNOWN_TRAJ;
    TrajectoryIO* replica0 = TrajectoryFile::DetectFormat( *repfile, repformat );
    if ( replica0 == 0 ) {
      mprinterr("Error: Could not set up replica file %s\n", repfile->full());
      return 1;
    }
    if (repformat != lastRepFmt)
      mprintf("\tReading '%s' as %s\n", repfile->full(), TrajectoryFile::FormatString(repformat));
    lastRepFmt = repformat;
    replica0->SetDebug( debug_ );
    // Pushing replica0 here allows the destructor to handle it on errors
    IOarray_.push_back( replica0 );
    // Process format-specific read args. Do not exit on error in case
    // replicas have different formats supporting different args.
    if (lowestRep) {
      replica0->processReadArgs( argIn );
    } else {
      ArgList argtmp( argCopy );
      replica0->processReadArgs( argtmp );
    }
    // Set up replica for reading and get the number of frames.
    int nframes = replica0->setupTrajin( *repfile, trajParm );
    if (nframes == TrajectoryIO::TRAJIN_ERR) {
      mprinterr("Error: Could not set up %s for reading.\n", repfile->full());
      return 1;
    }
    // TODO: Do not allow unknown number of frames?
    if (lowestRep) {
      cInfo = replica0->CoordInfo();
      rep0Frames = nframes;
      totalFrames = nframes;
      if (cInfo.ReplicaDimensions().Ndims() > 0) {
        mprintf("\tReplica dimensions:\n");
        for (int rd = 0; rd < cInfo.ReplicaDimensions().Ndims(); rd++)
          mprintf("\t\t%i: %s\n", rd+1, cInfo.ReplicaDimensions().Description(rd));
      }
    } else {
      // Check total frames in this replica against lowest rep.
      if (nframes != rep0Frames)
        mprintf("Warning: Replica %s frames (%i) does not match # frames in first replica (%i).\n",
                repfile->base(), nframes, rep0Frames);
      //if (repframes < 0) {
      //  mprinterr("Error: RemdTraj: Unknown # of frames in replica.\n");
      //  return 1;
      //}
      if (nframes < totalFrames) {
        totalFrames = nframes; 
        mprintf("Warning: Setting total # of frames to read from replica ensemble to %i\n",
                totalFrames);
      }
      // Check box info against lowest rep.
      if ( replica0->CoordInfo().HasBox() != cInfo.HasBox() ) {
        mprinterr("Error: Replica %s box info does not match first replica.\n",
                  repfile->full());
        return 1;
      }
      // TODO: Check specific box type
      // Check velocity info against lowest rep.
      if ( replica0->CoordInfo().HasVel() != cInfo.HasVel() ) {
        mprinterr("Error: Replica %s velocity info does not match first replica.\n",
                  repfile->full());
        return 1;
      }
      // Check # dimensions and types against lowest rep
      if ( replica0->CoordInfo().ReplicaDimensions() != cInfo.ReplicaDimensions() ) {
        mprinterr("Error: Replica %s dimension info does not match first replica.\n",
                  repfile->full());
        ReplicaDimArray const& thisRepDims = replica0->CoordInfo().ReplicaDimensions();
        for (int rd = 0; rd < thisRepDims.Ndims(); rd++)
          mprinterr("\t\t%i: %s\n", rd+1, thisRepDims.Description(rd)); 
        return 1;
      }
      // If temperature/time info does not match set to false.
      if (cInfo.HasTemp() != replica0->CoordInfo().HasTemp())
        cInfo.SetTemperature( false );
      if (cInfo.HasTime() != replica0->CoordInfo().HasTime())
        cInfo.SetTime( false );
    }
    lowestRep = false;
  }
  // Check how many frames will actually be read
  if (counter.CheckFrameArgs( totalFrames, argIn )) return 1;
  // Check for errors.
  if (IOarray_.empty()) {
    mprinterr("Error: No replica trajectories set up.\n");
    return 1;
  }
  if (IOarray_.size() != replica_filenames_.size()) { // SANITY CHECK
    mprinterr("Error: Not all replica files were set up.\n");
    return 1;
  }
  // Update ensemble size
  cInfo.SetEnsembleSize( (int)IOarray_.size() );
  if (debug_ > 0)
    cInfo.PrintCoordInfo( replica_filenames_[0].full(), trajParm->c_str() );

  return 0;
}
コード例 #2
0
ファイル: TrajIOarray.cpp プロジェクト: SAMAN-64/cpptraj
/** Each rank only sets up file that it will process. */
int TrajIOarray::SetupIOarray(ArgList& argIn, TrajFrameCounter& counter,
                              CoordinateInfo& cInfo, Topology* trajParm,
                              Parallel::Comm const& ensComm, Parallel::Comm const& trajComm)
{
  // Sanity check
  if (!IOarray_.empty()) {
    mprinterr("Internal Error: SetupIOarray() has been called twice.\n");
    return 1;
  }
  // Detect format
  FileName const& repFname = replica_filenames_[ensComm.Rank()];
  TrajectoryFile::TrajFormatType repformat = TrajectoryFile::UNKNOWN_TRAJ;
  TrajectoryIO* replica0 = TrajectoryFile::DetectFormat( repFname, repformat );
  if ( replica0 == 0 ) {
    mprinterr("Error: Could not set up replica file %s\n", repFname.full());
    return 1;
  }
  mprintf("\tReading '%s' as %s\n", repFname.full(), TrajectoryFile::FormatString(repformat));
  replica0->SetDebug( debug_ );
  // Construct the IOarray_ with blanks for all except this rank.
  for (int member = 0; member != ensComm.Size(); member++)
    if (member == ensComm.Rank())
      IOarray_.push_back( replica0 );
    else
      IOarray_.push_back( 0 );
  // Process format-specific read args.
  replica0->processReadArgs( argIn );
  // Set up replica for reading and get # frames
  int nframes = replica0->setupTrajin( repFname, trajParm );
  if (nframes == TrajectoryIO::TRAJIN_ERR) {
    mprinterr("Error: Could not set up %s for reading.\n", repFname.full());
    return 1;
  }
  // Set coordinate info
  cInfo = replica0->CoordInfo();
  int totalFrames = nframes;
  if (cInfo.ReplicaDimensions().Ndims() > 0) { // TODO put in common routine
    mprintf("\tReplica dimensions:\n");
    for (int rd = 0; rd < cInfo.ReplicaDimensions().Ndims(); rd++)
      mprintf("\t\t%i: %s\n", rd+1, cInfo.ReplicaDimensions().Description(rd));
  }
  // Check # frames in all files, use lowest.
  Parallel::World().AllReduce( &totalFrames, &nframes, 1, MPI_INT, MPI_MIN );
  if (totalFrames != nframes) {
    rprintf("Warning: Replica '%s' frames (%i) is > # frames in shortest replica.\n",
            repFname.full(), nframes);
    mprintf("Warning: Setting total # of frames to read from replica ensemble to %i\n",
            totalFrames);
  }
  if (trajComm.Master()) {
    static const int iSize = 6;
    static const char* iTitle[iSize] = {"box", "velocity", "temperature", "time", "force",
                                        "replica dimensions"};
    // Check coordinate info of all files               0    1    2     3     4      5
    std::vector<int> Info( iSize * ensComm.Size() ); // box, vel, temp, time, force, nRepDims
    int rank_info[iSize];
    rank_info[0] = (int)cInfo.TrajBox().Type();
    rank_info[1] = (int)cInfo.HasVel();
    rank_info[2] = (int)cInfo.HasTemp();
    rank_info[3] = (int)cInfo.HasTime();
    rank_info[4] = (int)cInfo.HasForce();
    rank_info[5] = cInfo.ReplicaDimensions().Ndims();
    ensComm.AllGather( rank_info, iSize, MPI_INT, &Info[0] );
    // TODO Should mismatches be errors instead?
    for (int midx = 0; midx != iSize; midx++) {
      for (int ridx = midx + iSize; ridx < (int)Info.size(); ridx += iSize) {
        if (Info[midx] != Info[ridx]) {
          rprintf("Warning: Replica %i %s info does not match first replica.\n",
                  ridx/iSize, iTitle[midx]);
        }
      }
    }
  }
  // TODO: Put code below into a common routine with serial version
  // Check how many frames will actually be read
  if (counter.CheckFrameArgs( totalFrames, argIn )) return 1;
  // SANITY CHECK
  if (IOarray_.size() != replica_filenames_.size()) {
    mprinterr("Error: Not all replica files were set up.\n");
    return 1;
  }
  // Update ensemble size
  cInfo.SetEnsembleSize( (int)IOarray_.size() );
  if (debug_ > 0)
    cInfo.PrintCoordInfo( repFname.full(), trajParm->c_str() );

  return 0;
}