Beispiel #1
0
void NetcdfFile::Sync(Parallel::Comm const& commIn) {
  int nc_vars[23];
  if (commIn.Master()) {
    nc_vars[0] = ncframe_;
    nc_vars[1] = TempVID_;
    nc_vars[2] = coordVID_;
    nc_vars[3] = velocityVID_;
    nc_vars[4] = frcVID_;
    nc_vars[5] = cellAngleVID_;
    nc_vars[6] = cellLengthVID_;
    nc_vars[7] = timeVID_;
    nc_vars[8] = remd_dimension_;
    nc_vars[9] = indicesVID_;
    nc_vars[10] = ncdebug_;
    nc_vars[11] = ensembleDID_;
    nc_vars[12] = frameDID_;
    nc_vars[13] = atomDID_;
    nc_vars[14] = ncatom_;
    nc_vars[15] = ncatom3_;
    nc_vars[16] = spatialDID_;
    nc_vars[17] = labelDID_;
    nc_vars[18] = cell_spatialDID_;
    nc_vars[19] = cell_angularDID_;
    nc_vars[20] = spatialVID_;
    nc_vars[21] = cell_spatialVID_;
    nc_vars[22] = cell_angularVID_;
  }
  commIn.MasterBcast( nc_vars, 23, MPI_INT );
  if (!commIn.Master()) {
    ncframe_ = nc_vars[0];
    TempVID_ = nc_vars[1];
    coordVID_ = nc_vars[2];
    velocityVID_ = nc_vars[3];
    frcVID_ = nc_vars[4];
    cellAngleVID_ = nc_vars[5];
    cellLengthVID_ = nc_vars[6];
    timeVID_ = nc_vars[7];
    remd_dimension_ = nc_vars[8];
    indicesVID_ = nc_vars[9];
    ncdebug_ = nc_vars[10];
    ensembleDID_ = nc_vars[11];
    frameDID_ = nc_vars[12];
    atomDID_ = nc_vars[13];
    ncatom_ = nc_vars[14];
    ncatom3_ = nc_vars[15];
    spatialDID_ = nc_vars[16];
    labelDID_ = nc_vars[17];
    cell_spatialDID_ = nc_vars[18];
    cell_angularDID_ = nc_vars[19];
    spatialVID_ = nc_vars[20];
    cell_spatialVID_ = nc_vars[21];
    cell_angularVID_ = nc_vars[22];
  }
}
Beispiel #2
0
/** First master performs all necessary setup, then sends info to all children.
  */
int Traj_AmberNetcdf::parallelSetupTrajout(FileName const& fname, Topology* trajParm,
                                           CoordinateInfo const& cInfoIn,
                                           int NframesToWrite, bool append,
                                           Parallel::Comm const& commIn)
{
  int err = 0;
  if (commIn.Master()) {
    err = setupTrajout(fname, trajParm, cInfoIn, NframesToWrite, append);
    // NOTE: setupTrajout leaves file open. Should this change?
    NC_close();
  }
  commIn.MasterBcast(&err, 1, MPI_INT);
  if (err != 0) return 1;
  // Synchronize netcdf info on non-master threads.
  Sync(commIn);
  if (!commIn.Master()) {
    // Non masters need filename and allocate Coord
    filename_ = fname;
    if (Coord_ != 0) delete[] Coord_;
    Coord_ = new float[ Ncatom3() ];
  }
  return 0;
}
Beispiel #3
0
/** First master performs all necessary setup, then sends info to all children.
  */
int Traj_GmxTrX::parallelSetupTrajout(FileName const& fname, Topology* trajParm,
                                      CoordinateInfo const& cInfoIn,
                                      int NframesToWrite, bool append,
                                      Parallel::Comm const& commIn)
{
    int err = 0;
    // In parallel MUST know # of frames to write in order to correctly set size
    if (NframesToWrite < 1) {
        mprinterr("Error: # frames to write must be known for TRR output in parallel.\n");
        err = 1;
    } else if (commIn.Master()) {
        err = setupTrajout(fname, trajParm, cInfoIn, NframesToWrite, append);
        // Determine header size, (18 * 4) + titleSize TODO put in setupTrajout?
        headerBytes_ = (18 * 4) + Title().size();
        // Determine frame size
        frameSize_ = headerBytes_ + box_size_ + x_size_ + v_size_;
        // NOTE: setupTrajout leaves file open. Should this change?
        file_.CloseFile();
    }
    commIn.MasterBcast(&err, 1, MPI_INT);
    if (err != 0) return 1;
    // Synchronize info on non-master threads.
    SyncTrajIO( commIn );
    commIn.MasterBcast( &ir_size_, 1, MPI_INT );
    commIn.MasterBcast( &e_size_,  1, MPI_INT );
    commIn.MasterBcast( &box_size_, 1, MPI_INT );
    commIn.MasterBcast( &vir_size_, 1, MPI_INT );
    commIn.MasterBcast( &pres_size_, 1, MPI_INT );
    commIn.MasterBcast( &top_size_, 1, MPI_INT );
    commIn.MasterBcast( &sym_size_, 1, MPI_INT );
    commIn.MasterBcast( &x_size_, 1, MPI_INT );
    commIn.MasterBcast( &v_size_, 1, MPI_INT );
    commIn.MasterBcast( &f_size_, 1, MPI_INT );
    commIn.MasterBcast( &natoms_, 1, MPI_INT );
    commIn.MasterBcast( &natom3_, 1, MPI_INT );
    commIn.MasterBcast( &step_, 1, MPI_INT );
    commIn.MasterBcast( &nre_, 1, MPI_INT );
    commIn.MasterBcast( &precision_, 1, MPI_INT );
    commIn.MasterBcast( &dt_, 1, MPI_FLOAT );
    commIn.MasterBcast( &lambda_, 1, MPI_FLOAT );
    // NOTE: cast these to unsigned long long to avoid ambiguity since MPI doesnt have size_t
    unsigned long long buf[2];
    if (commIn.Master()) {
        buf[0] = (unsigned long long)frameSize_;
        buf[1] = (unsigned long long)headerBytes_;
        commIn.MasterBcast( buf, 2, MPI_UNSIGNED_LONG_LONG );
    } else {
        commIn.MasterBcast( buf, 2, MPI_UNSIGNED_LONG_LONG );
        frameSize_ = (size_t)buf[0];
        headerBytes_ = (size_t)buf[1];
        AllocateCoords(); // Should already be done on master
    }
    if (append)
        file_.SetupWrite( fname, debug_ );
    else
        file_.SetupAppend( fname, debug_ );
    if (debug_ > 0)
        rprintf("Gromacs TRR: parallel headerSize= %zu  frameSize= %zu\n", headerBytes_, frameSize_);

    return 0;
}
Beispiel #4
0
/** First master performs all necessary setup, then sends info to all children.
  */
int Traj_AmberCoord::parallelSetupTrajout(FileName const& fname, Topology* trajParm,
                                           CoordinateInfo const& cInfoIn,
                                           int NframesToWrite, bool append,
                                           Parallel::Comm const& commIn)
{
  int err = 0;
  // In parallel MUST know # of frames to write in order to correctly set size
  if (NframesToWrite < 1) {
    mprinterr("Error: # frames to write must be known for Amber Coords output in parallel.\n");
    err = 1;
  } else if (commIn.Master()) {
    // NOTE: This writes the title.
    err = setupTrajout(fname, trajParm, cInfoIn, NframesToWrite, append);
    // NOTE: setupTrajout leaves file open. Should this change?
    file_.CloseFile();
  }
  commIn.MasterBcast(&err, 1, MPI_INT);
  if (err != 0) return 1;
  // Synchronize info on non-master threads.
  SyncTrajIO( commIn );
  // TODO For simplicity convert everything to double. Is this just lazy?
  double tmpArray[10];
  if (commIn.Master()) {
    tmpArray[0] = (double)natom3_;
    tmpArray[1] = (double)headerSize_;
    tmpArray[2] = (double)tStart_;
    tmpArray[3] = (double)tEnd_;
    tmpArray[4] = (double)numBoxCoords_;
    tmpArray[5] = boxAngle_[0];
    tmpArray[6] = boxAngle_[1];
    tmpArray[7] = boxAngle_[2];
    tmpArray[8] = (double)writeType_;
    tmpArray[9] = (double)highPrecision_;
    commIn.MasterBcast(tmpArray, 10, MPI_DOUBLE);
  } else {
    commIn.MasterBcast(tmpArray, 10, MPI_DOUBLE);
    natom3_        = (int)tmpArray[0];
    headerSize_    = (size_t)tmpArray[1];
    tStart_        = (size_t)tmpArray[2];
    tEnd_          = (size_t)tmpArray[3];
    numBoxCoords_  = (int)tmpArray[4];
    boxAngle_[0]   = tmpArray[5];
    boxAngle_[1]   = tmpArray[6];
    boxAngle_[2]   = tmpArray[7];
    writeType_     = (WriteType)tmpArray[8];
    highPrecision_ = (bool)tmpArray[9];
    if (append)
      file_.SetupAppend( fname, debug_ );
    else
      file_.SetupWrite( fname, debug_ );
    if (highPrecision_) outfmt_ = "%8.6f";
  }
  // For parallel output we will need to seek. Set up the buffer again with correct offsets.
  // Figure out the size of the written title.
  unsigned int titleSize = (unsigned int)Title().size() + 1; // +1 for newline
  titleSize = std::min(81U, titleSize);
  file_.SetupFrameBuffer( natom3_, 8, 10, headerSize_, titleSize );
  file_.ResizeBuffer( numBoxCoords_ );
  if (debug_>0)
    rprintf("'%s'(Parallel): Each frame has %lu bytes.\n", file_.Filename().base(),
            file_.FrameSize());
  // TODO set file size
  return 0;
}