CollectionMaster Class Reference

#include <CollectionMaster.h>

Inheritance diagram for CollectionMaster:

Classes
class	CollectVectorInstance
class	CollectVectorInstanceDcdSelection
class	CollectVectorSequence
class	CollectVectorSequenceDcdSelection

Public Types
enum	OperationStatus { NOT_PROCESSED, IN_PROCESS, HAS_PROCESSED }

Public Member Functions
	CollectionMaster ()
	~CollectionMaster (void)
void	receivePositions (CollectVectorMsg *msg)
void	receivePositionsDcdSelection (CollectVectorMsg *msg)
void	receiveVelocities (CollectVectorMsg *msg)
void	receiveForces (CollectVectorMsg *msg)
void	receiveDataStream (DataStreamMsg *msg)
void	enqueuePositions (int seq, Lattice &lattice)
void	enqueuePositionsDcdSelection (int seq, Lattice &lattice)
void	enqueueVelocities (int seq)
void	enqueueForces (int seq)
void	disposePositions (CollectVectorInstance *c)
void	disposeVelocities (CollectVectorInstance *c)
void	disposeForces (CollectVectorInstance *c)
void	blockPositions ()
void	unblockPositions ()
void	receiveOutputPosReady (int seq)
void	receiveOutputVelReady (int seq)
void	receiveOutputForceReady (int seq)
void	startNextRoundOutputPos (double totalT)
void	startNextRoundOutputVel (double totalT)
void	startNextRoundOutputForce (double totalT)
void	wrapCoorFinished ()

Static Public Member Functions
static CollectionMaster *	Object ()

Detailed Description

Definition at line 43 of file CollectionMaster.h.

Member Enumeration Documentation

OperationStatus

enum CollectionMaster::OperationStatus

Enumerator
NOT_PROCESSED
IN_PROCESS
HAS_PROCESSED

Definition at line 83 of file CollectionMaster.h.

{NOT_PROCESSED, IN_PROCESS, HAS_PROCESSED};

Constructor & Destructor Documentation

CollectionMaster()

CollectionMaster::CollectionMaster

(

)

Definition at line 22 of file CollectionMaster.C.

References DebugM.

{
  if (CkpvAccess(CollectionMaster_instance) == 0) {
    CkpvAccess(CollectionMaster_instance) = this;
  } else {
    DebugM(1, "CollectionMaster::CollectionMaster() - another instance of CollectionMaster exists!\n");
  }
  dataStreamFile = 0;

#ifdef MEM_OPT_VERSION
  wrapCoorDoneCnt = 0;
  posDoneCnt = 0;
  velDoneCnt = 0;
  parOut = new ParOutput();
#endif

  posTimings = 10;  velTimings = forceTimings = 5;
#ifdef NODEGROUP_FORCE_REGISTER
  cmlock = CmiCreateLock();
#endif
}

~CollectionMaster()

CollectionMaster::~CollectionMaster

(

void

)

Definition at line 45 of file CollectionMaster.C.

{
#ifdef NODEGROUP_FORCE_REGISTER
  CmiDestroyLock(cmlock);
#endif
}

Member Function Documentation

blockPositions()

void CollectionMaster::blockPositions ( )

inline

Definition at line 69 of file CollectionMaster.h.

References CollectionMaster::CollectVectorSequence::block().

Referenced by sendReplicaDcdData(), and sendReplicaDcdInit().

{ positions.block(); }

disposeForces()

void CollectionMaster::disposeForces

(

CollectVectorInstance *

c

)

Definition at line 215 of file CollectionMaster.C.

References ResizeArray< Elem >::begin(), CollectionMaster::CollectVectorInstance::data, DebugM, Output::force(), CollectionMaster::CollectVectorInstance::free(), memusage_MB(), Node::Object(), Node::output, CollectionMaster::CollectVectorInstance::seq, and ResizeArray< Elem >::size().

Referenced by enqueueForces(), and receiveForces().

{
#ifndef MEM_OPT_VERSION
    DebugM(3,"Collected forces at " << c->seq << std::endl);
    int seq = c->seq;
    int size = c->data.size();
    Vector *data = c->data.begin();
    double exectime = CmiWallTimer();
    double mem = memusage_MB();
#ifdef NODEGROUP_FORCE_REGISTER
    if (Node::Object()->simParameters->CUDASOAintegrate) {
      CProxy_PatchData cpdata(CkpvAccess(BOCclass_group).patchData);
      Output *pout = cpdata.ckLocalBranch()->ptrOutput;
      pout->force(seq,size,data);
    }
    else
#endif
    {
      Node::Object()->output->force(seq,size,data);
    }
    c->free();
    exectime = CmiWallTimer()-exectime;
    if ( forceTimings ) {
      CkPrintf("The last force output (seq=%d) takes %.3f seconds, %.3f MB of memory in use\n", seq, exectime, mem);
      --forceTimings;
    }
#endif
}

disposePositions()

void CollectionMaster::disposePositions

(

CollectVectorInstance *

c

)

Definition at line 107 of file CollectionMaster.C.

References ResizeArray< Elem >::begin(), Output::coordinate(), CollectionMaster::CollectVectorInstance::data, DebugM, CollectionMaster::CollectVectorInstance::fdata, CollectionMaster::CollectVectorInstance::free(), CollectionMaster::CollectVectorInstance::lattice, memusage_MB(), Node::Object(), Node::output, CollectionMaster::CollectVectorInstance::seq, and ResizeArray< Elem >::size().

Referenced by enqueuePositions(), enqueuePositionsDcdSelection(), receivePositions(), and receivePositionsDcdSelection().

{
    DebugM(3, "["<<CkMyPe()<<"]"<< " disposePositions\n");    
#ifndef MEM_OPT_VERSION
    int seq = c->seq;
    int size = c->data.size();
    if ( ! size ) size = c->fdata.size();
    Vector *data = c->data.begin();
    FloatVector *fdata = c->fdata.begin();
    double exectime = CmiWallTimer();
    double mem = memusage_MB();
#ifdef NODEGROUP_FORCE_REGISTER
    if (Node::Object()->simParameters->CUDASOAintegrate) {
      CProxy_PatchData cpdata(CkpvAccess(BOCclass_group).patchData);
      Output *pout = cpdata.ckLocalBranch()->ptrOutput;
      pout->coordinate(seq,size,data,fdata,c->lattice);
    }
    else
#endif
    {
      Node::Object()->output->coordinate(seq,size,data,fdata,c->lattice);
    }
    c->free();
    exectime = CmiWallTimer()-exectime;
    if ( posTimings ) {
      CkPrintf("The last position output (seq=%d) takes %.3f seconds, %.3f MB of memory in use\n", seq, exectime, mem);
      --posTimings;
    }
#endif
}

disposeVelocities()

void CollectionMaster::disposeVelocities

(

CollectVectorInstance *

c

)

Definition at line 162 of file CollectionMaster.C.

References ResizeArray< Elem >::begin(), CollectionMaster::CollectVectorInstance::data, DebugM, CollectionMaster::CollectVectorInstance::free(), memusage_MB(), Node::Object(), Node::output, CollectionMaster::CollectVectorInstance::seq, ResizeArray< Elem >::size(), and Output::velocity().

Referenced by enqueueVelocities(), and receiveVelocities().

{
#ifndef MEM_OPT_VERSION
    DebugM(3,"Collected velocities at " << c->seq << std::endl);
    int seq = c->seq;
    int size = c->data.size();
    Vector *data = c->data.begin();
    double exectime = CmiWallTimer();
    double mem = memusage_MB();
#ifdef NODEGROUP_FORCE_REGISTER
    if (Node::Object()->simParameters->CUDASOAintegrate) {
      CProxy_PatchData cpdata(CkpvAccess(BOCclass_group).patchData);
      Output *pout = cpdata.ckLocalBranch()->ptrOutput;
      pout->velocity(seq,size,data);
    }
    else
#endif
    {
      Node::Object()->output->velocity(seq,size,data);
    }
    c->free();
    exectime = CmiWallTimer()-exectime;
    if ( velTimings ) {
      CkPrintf("The last velocity output (seq=%d) takes %.3f seconds, %.3f MB of memory in use\n", seq, exectime, mem);
      --velTimings;
    }
#endif
}

enqueueForces()

void CollectionMaster::enqueueForces

(

int

seq

)

Definition at line 203 of file CollectionMaster.C.

References disposeForces(), CollectionMaster::CollectVectorSequence::enqueue(), and CollectionMaster::CollectVectorSequence::removeReady().

Referenced by Controller::enqueueCollections().

{
  Lattice dummy;
  forces.enqueue(seq,dummy);
#ifndef MEM_OPT_VERSION
  CollectVectorInstance *c;
  while ( ( c = forces.removeReady() ) ) { disposeForces(c); }
#else
  checkForceReady();
#endif
}

enqueuePositions()

void CollectionMaster::enqueuePositions	(	int	seq,
		Lattice &	lattice
	)

Definition at line 80 of file CollectionMaster.C.

References DebugM, disposePositions(), CollectionMaster::CollectVectorSequence::enqueue(), and CollectionMaster::CollectVectorSequence::removeReady().

Referenced by Controller::enqueueCollections().

{
  DebugM(3, "["<<CkMyPe()<<"]"<< " enqueuePositions\n");    
  positions.enqueue(seq,lattice);

#ifndef MEM_OPT_VERSION
  CollectVectorInstance *c;
  while ( ( c = positions.removeReady() ) ) { disposePositions(c); }
#else
  checkPosReady();
#endif
}

enqueuePositionsDcdSelection()

void CollectionMaster::enqueuePositionsDcdSelection	(	int	seq,
		Lattice &	lattice
	)

Definition at line 93 of file CollectionMaster.C.

References DebugM, disposePositions(), CollectionMaster::CollectVectorSequence::enqueue(), and CollectionMaster::CollectVectorSequenceDcdSelection::removeReady().

Referenced by Controller::enqueueCollections().

{
  DebugM(3, "["<<CkMyPe()<<"]"<< " enqueuePositionsDcdSelection\n");
#ifndef MEM_OPT_VERSION
  positionsDcdSelection.enqueue(seq,lattice);

  CollectVectorInstanceDcdSelection *c;
  while ( ( c = positionsDcdSelection.removeReady() ) ) { disposePositions(c); }
#else
  checkPosReady();
#endif
}

enqueueVelocities()

void CollectionMaster::enqueueVelocities

(

int

seq

)

Definition at line 150 of file CollectionMaster.C.

References disposeVelocities(), CollectionMaster::CollectVectorSequence::enqueue(), and CollectionMaster::CollectVectorSequence::removeReady().

Referenced by Controller::enqueueCollections().

{
  Lattice dummy;
  velocities.enqueue(seq,dummy);
#ifndef MEM_OPT_VERSION
  CollectVectorInstance *c;
  while ( ( c = velocities.removeReady() ) ) { disposeVelocities(c); }
#else
  checkVelReady();
#endif
}

Object()

static CollectionMaster* CollectionMaster::Object ( )

inlinestatic

Definition at line 46 of file CollectionMaster.h.

Referenced by recvReplicaDcdAck(), sendReplicaDcdData(), and sendReplicaDcdInit().

                                    { 
    return CkpvAccess(CollectionMaster_instance); 
  }

receiveDataStream()

void CollectionMaster::receiveDataStream

(

DataStreamMsg *

msg

)

Definition at line 245 of file CollectionMaster.C.

References SimParameters::auxFilename, ResizeArray< Elem >::begin(), DataStreamMsg::data, NAMD_backup_file(), NAMD_die(), Node::Object(), and Node::simParameters.

                                                           {
    if ( ! dataStreamFile ) {
      char *fname = Node::Object()->simParameters->auxFilename;
      // iout has large file linking issues on AIX
      // iout << iINFO << "OPENING AUXILIARY DATA STREAM FILE "
      //                                << fname << "\n" << endi;
      CkPrintf("Info: OPENING AUXILIARY DATA STREAM FILE %s\n", fname);
      NAMD_backup_file(fname);
      dataStreamFile = fopen(fname,"w");
      if ( ! dataStreamFile )
                NAMD_die("Can't open auxiliary data stream file!");
    }
    fprintf(dataStreamFile,"%s",msg->data.begin());
    fflush(dataStreamFile);
    delete msg;
}

receiveForces()

void CollectionMaster::receiveForces

(

CollectVectorMsg *

msg

)

Definition at line 192 of file CollectionMaster.C.

References disposeForces(), Node::Object(), CollectionMaster::CollectVectorSequence::removeReady(), and CollectionMaster::CollectVectorSequence::submitData().

Referenced by CollectionMgr::submitForces().

{
#ifndef MEM_OPT_VERSION
  forces.submitData(msg,Node::Object()->molecule->numAtoms);
  delete msg;

  CollectVectorInstance *c;
  while ( ( c = forces.removeReady() ) ) { disposeForces(c); }
#endif
}

receiveOutputForceReady()

void CollectionMaster::receiveOutputForceReady

(

int

seq

)

Definition at line 285 of file CollectionMaster.C.

References CollectionMaster::CollectVectorSequence::submitData().

                                                     {
#ifdef MEM_OPT_VERSION
    forces.submitData(seq);
    checkForceReady();
#endif
}

receiveOutputPosReady()

void CollectionMaster::receiveOutputPosReady

(

int

seq

)

receiveOutputVelReady()

void CollectionMaster::receiveOutputVelReady

(

int

seq

)

Definition at line 278 of file CollectionMaster.C.

References CollectionMaster::CollectVectorSequence::submitData().

                                                   {
#ifdef MEM_OPT_VERSION
    velocities.submitData(seq);
    checkVelReady();
#endif
}

receivePositions()

void CollectionMaster::receivePositions

(

CollectVectorMsg *

msg

)

Definition at line 52 of file CollectionMaster.C.

References DebugM, disposePositions(), Node::Object(), CollectionMaster::CollectVectorSequence::removeReady(), and CollectionMaster::CollectVectorSequence::submitData().

Referenced by CollectionMgr::submitPositions().

{
  DebugM(3, "["<<CkMyPe()<<"]"<< " receivePositions\n");    
#ifndef MEM_OPT_VERSION
  positions.submitData(msg,Node::Object()->molecule->numAtoms);

  delete msg;

  CollectVectorInstance *c;
  while ( ( c = positions.removeReady() ) ) { disposePositions(c); }
#endif
}

receivePositionsDcdSelection()

void CollectionMaster::receivePositionsDcdSelection

(

CollectVectorMsg *

msg

)

Definition at line 66 of file CollectionMaster.C.

References DebugM, disposePositions(), CollectVectorMsg::index, CollectionMaster::CollectVectorSequenceDcdSelection::index, Node::Object(), CollectionMaster::CollectVectorSequenceDcdSelection::removeReady(), and CollectionMaster::CollectVectorSequenceDcdSelection::submitData().

Referenced by CollectionMgr::submitPositions().

{
  DebugM(3, "["<<CkMyPe()<<"]"<< " receivePositionsDcdSelection index "<<msg->index<<"\n");    
#ifndef MEM_OPT_VERSION
  positionsDcdSelection.index=msg->index;
  positionsDcdSelection.submitData(msg,Node::Object()->molecule->get_dcd_selection_size(msg->index));
  delete msg;
  
  CollectVectorInstanceDcdSelection *c;
  while ( ( c = positionsDcdSelection.removeReady() ) ) { disposePositions(c); }
#endif
}

receiveVelocities()

void CollectionMaster::receiveVelocities

(

CollectVectorMsg *

msg

)

Definition at line 139 of file CollectionMaster.C.

References disposeVelocities(), Node::Object(), CollectionMaster::CollectVectorSequence::removeReady(), and CollectionMaster::CollectVectorSequence::submitData().

Referenced by CollectionMgr::submitVelocities().

{
#ifndef MEM_OPT_VERSION
  velocities.submitData(msg,Node::Object()->molecule->numAtoms);
  delete msg;

  CollectVectorInstance *c;
  while ( ( c = velocities.removeReady() ) ) { disposeVelocities(c); }
#endif
}

startNextRoundOutputForce()

void CollectionMaster::startNextRoundOutputForce

(

double

totalT

)

Definition at line 361 of file CollectionMaster.C.

References CollectionMaster::CollectVectorInstance::free(), IN_PROCESS, memusage_MB(), Node::Object(), and CollectionMaster::CollectVectorInstance::seq.

                                                             {
#ifdef MEM_OPT_VERSION
        
        if(totalT > forceIOTime) forceIOTime = totalT;

#if OUTPUT_SINGLE_FILE
    if(++forceDoneCnt < Node::Object()->simParameters->numoutputwrts)  return;
#else
        if(++forceDoneCnt < Node::Object()->simParameters->numoutputprocs)  return;
#endif

    forceDoneCnt = 0;

    //retrieve the last ready instance
    CollectVectorInstance *c = forces.getReady();
    int seq = c->seq;
    CmiAssert(c->status == IN_PROCESS);
    double mem = memusage_MB();
    forces.removeFirstReady();
    c->free();
    forceOutTime = CmiWallTimer()-forceOutTime;
    if ( forceTimings ) {
      CkPrintf("The last force output (seq=%d) takes %.3f seconds(file I/O: %.3f secs), %.3f MB of memory in use\n", seq, forceOutTime, forceIOTime, mem);
      --forceTimings;
    }

    //Actually the c->status doesn't need to be checked because it is
    //certain that the new ready one will not be in  IN_PROCESS status 
    checkForceReady();
#endif
}

startNextRoundOutputPos()

void CollectionMaster::startNextRoundOutputPos

(

double

totalT

)

Definition at line 293 of file CollectionMaster.C.

References CollectionMaster::CollectVectorInstance::free(), IN_PROCESS, memusage_MB(), Node::Object(), and CollectionMaster::CollectVectorInstance::seq.

                                                           {
#ifdef MEM_OPT_VERSION

        if(totalT > posIOTime) posIOTime = totalT;

#ifndef OUTPUT_SINGLE_FILE
#error OUTPUT_SINGLE_FILE not defined!
#endif

#if OUTPUT_SINGLE_FILE
    if(++posDoneCnt < Node::Object()->simParameters->numoutputwrts)  return;
#else
        if(++posDoneCnt < Node::Object()->simParameters->numoutputprocs)  return;
#endif

        posDoneCnt = 0;

    //retrieve the last ready instance
    CollectVectorInstance *c = positions.getReady();
    int seq = c->seq;
    CmiAssert(c->status == IN_PROCESS);
    double mem = memusage_MB();
    positions.removeFirstReady();
    c->free();
    posOutTime = CmiWallTimer()-posOutTime;
    if ( posTimings ) {
      CkPrintf("The last position output (seq=%d) takes %.3f seconds(file I/O: %.3f secs), %.3f MB of memory in use\n", seq, posOutTime, posIOTime, mem);
      --posTimings;
    }

    //Actually the c->status doesn't need to be checked because it is
    //certain that the new ready one will not be in  IN_PROCESS status 
    checkPosReady();
#endif
}

startNextRoundOutputVel()

void CollectionMaster::startNextRoundOutputVel

(

double

totalT

)

Definition at line 329 of file CollectionMaster.C.

References CollectionMaster::CollectVectorInstance::free(), IN_PROCESS, memusage_MB(), Node::Object(), and CollectionMaster::CollectVectorInstance::seq.

                                                           {
#ifdef MEM_OPT_VERSION
        
        if(totalT > velIOTime) velIOTime = totalT;

#if OUTPUT_SINGLE_FILE
    if(++velDoneCnt < Node::Object()->simParameters->numoutputwrts)  return;
#else
        if(++velDoneCnt < Node::Object()->simParameters->numoutputprocs)  return;
#endif

    velDoneCnt = 0;

    //retrieve the last ready instance
    CollectVectorInstance *c = velocities.getReady();
    int seq = c->seq;
    CmiAssert(c->status == IN_PROCESS);
    double mem = memusage_MB();
    velocities.removeFirstReady();
    c->free();
    velOutTime = CmiWallTimer()-velOutTime;
    if ( velTimings ) {
      CkPrintf("The last velocity output (seq=%d) takes %.3f seconds(file I/O: %.3f secs), %.3f MB of memory in use\n", seq, velOutTime, velIOTime, mem);
      --velTimings;
    }

    //Actually the c->status doesn't need to be checked because it is
    //certain that the new ready one will not be in  IN_PROCESS status 
    checkVelReady();
#endif
}

unblockPositions()

void CollectionMaster::unblockPositions ( )

inline

Definition at line 70 of file CollectionMaster.h.

References CollectionMaster::CollectVectorSequence::unblock().

Referenced by recvReplicaDcdAck().

{ positions.unblock(); }

wrapCoorFinished()

void CollectionMaster::wrapCoorFinished

(

)

Definition at line 394 of file CollectionMaster.C.

References Node::Object(), and CollectionMaster::CollectVectorInstance::seq.

                                       {
#ifdef MEM_OPT_VERSION
    if(++wrapCoorDoneCnt == Node::Object()->simParameters->numoutputprocs){
        wrapCoorDoneCnt = 0;

                //count the wrapping-coor time into master writing time
                posIOTime = CmiWallTimer()-posOutTime; 

        //it's ready to output positions
        CollectVectorInstance *c = positions.getReady();

                CProxy_ParallelIOMgr io(CkpvAccess(BOCclass_group).ioMgr);
                ParallelIOMgr *ioMgr = io.ckLocalBranch();

#if OUTPUT_SINGLE_FILE
        //notify output procs to do Token based output
        int grpsize = ioMgr->numOutputProcs / ioMgr->numOutputWrts;
        int remains = ioMgr->numOutputProcs % ioMgr->numOutputWrts;
        int outrank = 0;
        int i;
        for(i=0; i<remains; i++){
            io[ioMgr->outputProcArray[outrank]].disposePositions(c->seq, posIOTime);
            outrank += (grpsize+1);
        }
        for(; i<ioMgr->numOutputWrts; i++){
            io[ioMgr->outputProcArray[outrank]].disposePositions(c->seq, posIOTime);
            outrank += grpsize;
        }
#else
                //output multiple files
                for(int i=0; i<ioMgr->numOutputProcs; i++) {
                        io[ioMgr->outputProcArray[i]].disposePositions(c->seq, posIOTime);
                }
#endif

    }
#endif
}

---

The documentation for this class was generated from the following files:

• CollectionMaster.h
• CollectionMaster.C