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CollectionMaster.C
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CollectionMaster.C
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/**
*** Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by
*** The Board of Trustees of the University of Illinois.
*** All rights reserved.
**/
#include "largefiles.h" // must be first!
#include "InfoStream.h"
#include "CollectionMaster.h"
#include "ProcessorPrivate.h"
#include "SimParameters.h"
#include "packmsg.h"
#include "CollectionMaster.decl.h"
#include "Molecule.h"
#include "memusage.h"
// #define DEBUGM
#include "Debug.h"
CollectionMaster::CollectionMaster()
{
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;
}
CollectionMaster::~CollectionMaster(void)
{
}
void CollectionMaster::receivePositions(CollectVectorMsg *msg)
{
#ifndef MEM_OPT_VERSION
positions.submitData(msg,Node::Object()->molecule->numAtoms);
delete msg;
CollectVectorInstance *c;
while ( ( c = positions.removeReady() ) ) { disposePositions(c); }
#endif
}
void CollectionMaster::enqueuePositions(int seq, Lattice &lattice)
{
positions.enqueue(seq,lattice);
#ifndef MEM_OPT_VERSION
CollectVectorInstance *c;
while ( ( c = positions.removeReady() ) ) { disposePositions(c); }
#else
checkPosReady();
#endif
}
void CollectionMaster::disposePositions(CollectVectorInstance *c)
{
#ifndef MEM_OPT_VERSION
DebugM(3,"Collected positions at " << c->seq << std::endl);
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();
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
}
void CollectionMaster::receiveVelocities(CollectVectorMsg *msg)
{
#ifndef MEM_OPT_VERSION
velocities.submitData(msg,Node::Object()->molecule->numAtoms);
delete msg;
CollectVectorInstance *c;
while ( ( c = velocities.removeReady() ) ) { disposeVelocities(c); }
#endif
}
void CollectionMaster::enqueueVelocities(int seq)
{
Lattice dummy;
velocities.enqueue(seq,dummy);
#ifndef MEM_OPT_VERSION
CollectVectorInstance *c;
while ( ( c = velocities.removeReady() ) ) { disposeVelocities(c); }
#else
checkVelReady();
#endif
}
void CollectionMaster::disposeVelocities(CollectVectorInstance *c)
{
#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();
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
}
void CollectionMaster::receiveForces(CollectVectorMsg *msg)
{
#ifndef MEM_OPT_VERSION
forces.submitData(msg,Node::Object()->molecule->numAtoms);
delete msg;
CollectVectorInstance *c;
while ( ( c = forces.removeReady() ) ) { disposeForces(c); }
#endif
}
void CollectionMaster::enqueueForces(int seq)
{
Lattice dummy;
forces.enqueue(seq,dummy);
#ifndef MEM_OPT_VERSION
CollectVectorInstance *c;
while ( ( c = forces.removeReady() ) ) { disposeForces(c); }
#else
checkForceReady();
#endif
}
void CollectionMaster::disposeForces(CollectVectorInstance *c)
{
#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();
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
}
void CollectionMaster::receiveDataStream(DataStreamMsg *msg) {
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;
}
PACK_MSG(DataStreamMsg,
PACK_RESIZE(data);
)
//The timesteps on CollectionMaster will be always in increasing order
//because they are enqueued on PE0 by controller in order. -Chao Mei
//
//The computation of wrap_coor is also serialized for the sake of easy
//implementation (easier management of output)
void CollectionMaster::receiveOutputPosReady(int seq){
#ifdef MEM_OPT_VERSION
positions.submitData(seq);
checkPosReady();
#endif
}
void CollectionMaster::receiveOutputVelReady(int seq){
#ifdef MEM_OPT_VERSION
velocities.submitData(seq);
checkVelReady();
#endif
}
void CollectionMaster::receiveOutputForceReady(int seq){
#ifdef MEM_OPT_VERSION
forces.submitData(seq);
checkForceReady();
#endif
}
void CollectionMaster::startNextRoundOutputPos(double totalT){
#ifdef MEM_OPT_VERSION
if(totalT > posIOTime) posIOTime = totalT;
#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
}
void CollectionMaster::startNextRoundOutputVel(double totalT){
#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
}
void CollectionMaster::startNextRoundOutputForce(double totalT){
#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
}
void CollectionMaster::wrapCoorFinished(){
#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
}
#ifdef MEM_OPT_VERSION
void CollectionMaster::checkPosReady(){
CollectVectorInstance *c;
if((c = positions.getReady())){
if(c->status == IN_PROCESS){
//indicating in the process of outputing coordinates
return;
}
c->status = IN_PROCESS;
posOutTime = CmiWallTimer();
SimParameters *simParam = Node::Object()->simParameters;
CProxy_ParallelIOMgr io(CkpvAccess(BOCclass_group).ioMgr);
ParallelIOMgr *ioMgr = io.ckLocalBranch();
if(simParam->wrapAll || simParam->wrapWater){
for(int i=0; i<ioMgr->numOutputProcs; i++){
io[ioMgr->outputProcArray[i]].wrapCoor(c->seq, c->lattice);
}
//write the header to overlap with the computation of
//wrapping coordinates
parOut->coordinateMaster(c->seq,Node::Object()->molecule->numAtoms,c->lattice);
}else{
//write the header
parOut->coordinateMaster(c->seq,Node::Object()->molecule->numAtoms,c->lattice);
posIOTime = CmiWallTimer() - posOutTime;
#if OUTPUT_SINGLE_FILE
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
}
//this instance c is freed in the next round of output invocation.
}
}
void CollectionMaster::checkVelReady(){
CollectVectorInstance *c;
if((c = velocities.getReady())){
if(c->status == IN_PROCESS){
//indicating in the process of outputing velocities
return;
}
c->status = IN_PROCESS;
velOutTime = CmiWallTimer();
//write the header
parOut->velocityMaster(c->seq, Node::Object()->molecule->numAtoms);
velIOTime = CmiWallTimer() - velOutTime;
//notify output procs to do Token based output
CProxy_ParallelIOMgr io(CkpvAccess(BOCclass_group).ioMgr);
ParallelIOMgr *ioMgr = io.ckLocalBranch();
#if OUTPUT_SINGLE_FILE
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]].disposeVelocities(c->seq, velIOTime);
outrank += (grpsize+1);
}
for(; i<ioMgr->numOutputWrts; i++){
io[ioMgr->outputProcArray[outrank]].disposeVelocities(c->seq, velIOTime);
outrank += grpsize;
}
#else
//output multiple files
for(int i=0; i<ioMgr->numOutputProcs; i++) {
io[ioMgr->outputProcArray[i]].disposeVelocities(c->seq, velIOTime);
}
#endif
//this instance c is freed in the next round of output invocation.
}
}
void CollectionMaster::checkForceReady(){
CollectVectorInstance *c;
if((c = forces.getReady())){
if(c->status == IN_PROCESS){
//indicating in the process of outputing forces
return;
}
c->status = IN_PROCESS;
forceOutTime = CmiWallTimer();
//write the header
parOut->forceMaster(c->seq, Node::Object()->molecule->numAtoms);
forceIOTime = CmiWallTimer() - forceOutTime;
//notify output procs to do Token based output
CProxy_ParallelIOMgr io(CkpvAccess(BOCclass_group).ioMgr);
ParallelIOMgr *ioMgr = io.ckLocalBranch();
#if OUTPUT_SINGLE_FILE
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]].disposeForces(c->seq, forceIOTime);
outrank += (grpsize+1);
}
for(; i<ioMgr->numOutputWrts; i++){
io[ioMgr->outputProcArray[outrank]].disposeForces(c->seq, forceIOTime);
outrank += grpsize;
}
#else
//output multiple files
for(int i=0; i<ioMgr->numOutputProcs; i++) {
io[ioMgr->outputProcArray[i]].disposeForces(c->seq, forceIOTime);
}
#endif
//this instance c is freed in the next round of output invocation.
}
}
void CollectionMidMaster::disposePositions(int seq)
{
CollectMidVectorInstance *c = positions.getReady(seq);
CmiAssert(c!=NULL);
parOut->coordinateSlave(seq,c->fromAtomID,c->toAtomID,
c->data.begin(),c->fdata.begin());
c->free();
}
void CollectionMidMaster::disposeVelocities(int seq)
{
CollectMidVectorInstance *c = velocities.getReady(seq);
CmiAssert(c!=NULL);
parOut->velocitySlave(seq,c->fromAtomID,c->toAtomID,c->data.begin());
c->free();
}
void CollectionMidMaster::disposeForces(int seq)
{
CollectMidVectorInstance *c = forces.getReady(seq);
CmiAssert(c!=NULL);
parOut->forceSlave(seq,c->fromAtomID,c->toAtomID,c->data.begin());
c->free();
}
#endif
#include "CollectionMaster.def.h"