// DataSet_double::Sync()
int DataSet_double::Sync(size_t total, std::vector<int> const& rank_frames,
Parallel::Comm const& commIn)
{
if (commIn.Size()==1) return 0;
if (commIn.Master()) {
// Resize for total number of frames.
Data_.resize( total );
double* endptr = &(Data_[0]) + rank_frames[0];
// Receive data from each rank
for (int rank = 1; rank < commIn.Size(); rank++) {
commIn.SendMaster( endptr, rank_frames[rank], rank, MPI_DOUBLE );
endptr += rank_frames[rank];
}
} else // Send data to master //TODO adjust for repeated additions?
commIn.SendMaster( &(Data_[0]), Data_.size(), commIn.Rank(), MPI_DOUBLE );
return 0;
}
/** Each rank searches for replica based on lowest replica number. */
int TrajIOarray::SearchForReplicas(FileName const& fname, Parallel::Comm const& ensComm,
Parallel::Comm const& trajComm)
{
RepName repName(fname, debug_);
if (repName.Error()) return 1;
// TODO check for lower replica number?
FileName replicaFilename = repName.RepFilename( ensComm.Rank() );
// Only traj comm masters actually check for files.
if (trajComm.Master()) {
if (!File::Exists( replicaFilename )) {
File::ErrorMsg( replicaFilename.full() );
rprinterr("Error: File '%s' not accessible.\n", replicaFilename.full());
return 1;
}
}
// At this point each rank has found its replica. Populate filename array.
for (int offset = 0; offset < ensComm.Size(); ++offset)
replica_filenames_.push_back( repName.RepFilename( offset ) );
return 0;
}
/** Each rank checks that specified file is present. */
int TrajIOarray::AddReplicasFromArgs(FileName const& name0,
std::string const& commaNames,
Parallel::Comm const& ensComm,
Parallel::Comm const& trajComm)
{
// First set up filename array on all ranks.
if (name0.empty()) return 1;
replica_filenames_.push_back( name0 );
ArgList remdtraj_list( commaNames, "," );
for (ArgList::const_iterator fname = remdtraj_list.begin();
fname != remdtraj_list.end(); ++fname)
replica_filenames_.push_back( FileName( *fname ) );
if (ensComm.Size() != (int)replica_filenames_.size())
return 1;
else if (trajComm.Master()) { // Only traj comm master checks file
if (!File::Exists( replica_filenames_[ ensComm.Rank() ])) {
File::ErrorMsg( replica_filenames_[ensComm.Rank()].full() );
rprinterr("Error: File '%s' not accessible.\n", replica_filenames_[ensComm.Rank()].full());
return 1;
}
}
return 0;
}
/** 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;
}
/** Synchronize timeseries data from child ranks to master. */
int DataSetList::SynchronizeData(Parallel::Comm const& commIn) {
if (commIn.Size() < 2) return 0;
// Ensure that the number of sets that require sync is same on each rank.
// FIXME: Make sure this allgather does not end up taking too much time.
// Should it be debug only?
std::vector<int> size_on_rank;
size_on_rank.reserve( DataList_.size() );
DataListType SetsToSync;
for (DataListType::iterator ds = DataList_.begin(); ds != DataList_.end(); ++ds)
if ( (*ds)->NeedsSync() ) {
SetsToSync.push_back( *ds );
size_on_rank.push_back( (*ds)->Size() );
}
// DEBUG
//for (int rank = 0; rank != commIn.Size(); rank++) {
// if (rank == commIn.Rank())
// for (DataListType::const_iterator ds = SetsToSync.begin(); ds != SetsToSync.end(); ++ds)
// rprintf("SET '%s'\n", (*ds)->legend());
// commIn.Barrier();
//}
// DEBUG END
std::vector<int> n_on_rank( commIn.Size(), 0 );
int nSets = (int)SetsToSync.size();
commIn.AllGather( &nSets, 1, MPI_INT, &n_on_rank[0] );
for (int rank = 1; rank < commIn.Size(); rank++)
if (n_on_rank[rank] != n_on_rank[0]) {
mprinterr("Internal Error: Number of sets to sync on rank %i (%i) != number on master %i\n",
rank, n_on_rank[rank], n_on_rank[0]);
return 1;
}
// Send all data set sizes to master.
std::vector<int> all_rank_sizes;
if (commIn.Master()) {
all_rank_sizes.resize( nSets * commIn.Size() );
commIn.GatherMaster( &size_on_rank[0], nSets, MPI_INT, &all_rank_sizes[0] );
} else {
commIn.GatherMaster( &size_on_rank[0], nSets, MPI_INT, 0 );
}
size_on_rank.clear();
// Call Sync only for sets that need it.
std::vector<int> rank_frames( commIn.Size() );
int total = 0; //TODO size_t?
int idx0 = 0;
for (DataListType::iterator ds = SetsToSync.begin(); ds != SetsToSync.end(); ++ds, ++idx0) {
if (commIn.Master()) {
total = all_rank_sizes[idx0];
rank_frames[0] = all_rank_sizes[idx0];
int idx1 = idx0 + nSets;
for (int rank = 1; rank < commIn.Size(); rank++, idx1 += nSets) {
total += all_rank_sizes[idx1];
rank_frames[rank] = all_rank_sizes[idx1];
}
//mprintf("DEBUG: Syncing '%s' (size=%zu, total=%i)\n", (*ds)->Meta().PrintName().c_str(),
// (*ds)->Size(), total);
}
if ( (*ds)->Sync(total, rank_frames, commIn) ) {
rprintf( "Warning: Could not sync dataset '%s'\n",(*ds)->legend());
//return;
}
(*ds)->SetNeedsSync( false );
}
return 0;
}