#include <Node.h>
Inheritance diagram for Node:
|
|
Definition at line 88 of file Node.C. References atomMap, computeMap, computeMgr, configList, DebugM, eventEndOfTimeStep, GroupInitMsg::group, imd, ComputeMap::Instance(), AtomMap::Instance(), PatchMap::Instance(), ldbCoordinator, molecule, NAMD_bug(), output, parameters, patchMap, pdb, simParameters, state, and workDistrib. 00089 {
00090 DebugM(4,"Creating Node\n");
00091 #if(CMK_CCS_AVAILABLE && CMK_WEB_MODE)
00092 CApplicationInit();
00093 #endif
00094 if (CpvAccess(Node_instance) == 0) {
00095 CpvAccess(Node_instance) = this;
00096 eventEndOfTimeStep = traceRegisterUserEvent("EndOfTimeStep");
00097 } else {
00098 NAMD_bug("Node::Node() - another instance of Node exists!");
00099 }
00100
00101 CpvAccess(BOCclass_group) = msg->group;
00102 delete msg;
00103
00104 CpvAccess(BOCclass_group).node = thisgroup;
00105
00106 startupPhase = 0;
00107
00108 molecule = NULL;
00109 parameters = NULL;
00110 simParameters = NULL;
00111 configList = NULL;
00112 pdb = NULL;
00113 state = NULL;
00114 output = NULL;
00115 imd = new IMDOutput;
00116
00117 DebugM(4,"Creating PatchMap, AtomMap, ComputeMap\n");
00118 patchMap = PatchMap::Instance();
00119 atomMap = AtomMap::Instance();
00120 computeMap = ComputeMap::Instance();
00121
00122 DebugM(4,"Binding to BOC's\n");
00123 CProxy_PatchMgr pm(CpvAccess(BOCclass_group).patchMgr);
00124 patchMgr = pm.ckLocalBranch();
00125 CProxy_ProxyMgr prm(CpvAccess(BOCclass_group).proxyMgr);
00126 proxyMgr = prm.ckLocalBranch();
00127 CProxy_WorkDistrib wd(CpvAccess(BOCclass_group).workDistrib);
00128 workDistrib = wd.ckLocalBranch();
00129 CProxy_ComputeMgr cm(CpvAccess(BOCclass_group).computeMgr);
00130 computeMgr = cm.ckLocalBranch();
00131 CProxy_LdbCoordinator lc(CpvAccess(BOCclass_group).ldbCoordinator);
00132 ldbCoordinator = lc.ckLocalBranch();
00133
00134 }
|
|
|
Definition at line 139 of file Node.C. 00140 {
00141 delete output;
00142 delete computeMap;
00143 delete atomMap;
00144 delete patchMap;
00145 delete CpvAccess(comm);
00146 }
|
|
|
|
|
|
|
|
|
Definition at line 636 of file Node.C. References BackEnd::exit(), iERROR(), and iout. 00636 {
00637 iout << iERROR << "Exiting prematurely.\n" << endi;
00638 BackEnd::exit();
00639 delete msg;
00640 }
|
|
|
Definition at line 624 of file Node.C. References sendEnableEarlyExit(). Referenced by Sequencer::maximumMove(), Sequencer::rattle1(), and recvEnableEarlyExit(). 00624 {
00625 if ( CkMyPe() ) {
00626 sendEnableEarlyExit();
00627 } else {
00628 #if CHARM_VERSION > 050402
00629 CkStartQD(CkIndex_Node::earlyExit((CkQdMsg*)0),&thishandle);
00630 #else
00631 CkStartQD(CProxy_Node::ckIdx_earlyExit((CkQdMsg*)0),&thishandle);
00632 #endif
00633 }
00634 }
|
|
|
Definition at line 591 of file Node.C. References sendEnableExitScheduler(). Referenced by BackEnd::awaken(), and recvEnableExitScheduler(). 00591 {
00592 if ( CkMyPe() ) {
00593 sendEnableExitScheduler();
00594 } else {
00595 #if CHARM_VERSION > 050402
00596 CkStartQD(CkIndex_Node::exitScheduler((CkQdMsg*)0),&thishandle);
00597 #else
00598 CkStartQD(CProxy_Node::ckIdx_exitScheduler((CkQdMsg*)0),&thishandle);
00599 #endif
00600 }
00601 }
|
|
|
Definition at line 534 of file Node.C. 00534 {
00535 #if CHARM_VERSION > 050402
00536 CkStartQD(CkIndex_Node::scriptBarrier((CkQdMsg*)0),&thishandle);
00537 #else
00538 CkStartQD(CProxy_Node::ckIdx_scriptBarrier((CkQdMsg*)0),&thishandle);
00539 #endif
00540 }
|
|
|
Definition at line 603 of file Node.C. 00603 {
00604 //CmiPrintf("exitScheduler %d\n",CkMyPe());
00605 CsdExitScheduler();
00606 delete msg;
00607 }
|
|
|
Definition at line 153 of file Node.h. Referenced by Output::coordinate(), and Controller::printEnergies(). 00153 { return script; }
|
|
|
|
|
|
Definition at line 497 of file Node.C. Referenced by startup(). 00497 {
00498 (CProxy_Node(CpvAccess(BOCclass_group).node)).run();
00499 }
|
|
|
Definition at line 151 of file Node.C. 00151 {
00152 (CProxy_Node(CpvAccess(BOCclass_group).node)).startup();
00153 }
|
|
|
Definition at line 149 of file Node.h. Referenced by ComputeMgr::createComputes(), WorkDistrib::distributeHomePatches(), WorkDistrib::initAndSendHomePatch(), and LdbCoordinator::initialize(). 00149 { return CkMyPe(); }
|
|
|
Definition at line 150 of file Node.h. Referenced by WorkDistrib::assignNodeToPatch(), LdbCoordinator::initialize(), and LdbCoordinator::nodeDone(). 00150 { return CkNumPes(); }
|
|
|
|
Definition at line 619 of file Node.C. References enableEarlyExit(). 00619 {
00620 delete msg;
00621 enableEarlyExit();
00622 }
|
|
|
Definition at line 585 of file Node.C. References enableExitScheduler(). 00585 {
00586 //CmiPrintf("recvEnableExitScheduler\n");
00587 delete msg;
00588 enableExitScheduler();
00589 }
|
|
||||||||||||
|
Definition at line 569 of file Node.C. References charge, molecule, and Molecule::reloadCharges(). 00569 {
00570 molecule->reloadCharges(charge,n);
00571 }
|
|
|
Definition at line 552 of file Node.C. References charge, molecule, NAMD_die(), Molecule::numAtoms, and Molecule::reloadCharges(). 00552 {
00553 FILE *file = fopen(filename,"r");
00554 if ( ! file ) NAMD_die("node::reloadCharges():Error opening charge file.");
00555
00556 int n = molecule->numAtoms;
00557 float *charge = new float[n];
00558
00559 for ( int i = 0; i < n; ++i ) {
00560 if ( ! fscanf(file,"%f",&charge[i]) )
00561 NAMD_die("Node::reloadCharges():Not enough numbers in charge file.");
00562 }
00563
00564 fclose(file);
00565 CProxy_Node(thisgroup).reloadCharges(charge,n);
00566 delete [] charge;
00567 }
|
|
|
Definition at line 506 of file Node.C. References ResizeArrayIter< T >::begin(), DebugM, ResizeArrayIter< T >::end(), PatchMap::homePatchList(), HomePatchList, iINFO(), iout, memusage(), PatchMap::Object(), NamdState::runController(), HomePatch::runSequencer(), and state. 00507 {
00508 // Start Controller (aka scalar Sequencer) on Pe(0)
00509 if ( ! CkMyPe() ) {
00510 state->runController();
00511 }
00512
00513 DebugM(4, "Starting Sequencers\n");
00514 // Run Sequencer on each HomePatch - i.e. start simulation
00515 HomePatchList *hpl = PatchMap::Object()->homePatchList();
00516 ResizeArrayIter<HomePatchElem> ai(*hpl);
00517 for (ai=ai.begin(); ai != ai.end(); ai++) {
00518 HomePatch *patch = (*ai).patch;
00519 patch->runSequencer();
00520 }
00521
00522 if (!CkMyPe()) {
00523 iout << iINFO << "Finished startup with " <<
00524 (memusage()/1024) << " kB of memory in use.\n" << endi;
00525 }
00526
00527 }
|
|
|
Definition at line 646 of file Node.C. References NamdState::configList, configList, NamdState::molecule, molecule, NamdState::parameters, parameters, NamdState::pdb, pdb, NamdState::simParameters, and simParameters. 00647 {
00648 this->molecule = state->molecule;
00649 this->parameters = state->parameters;
00650 this->simParameters = state->simParameters;
00651 this->configList = state->configList;
00652 this->pdb = state->pdb;
00653 this->state = state;
00654 }
|
|
|
Definition at line 542 of file Node.C. 00542 {
00543 delete qmsg;
00544 //script->awaken();
00545 }
|
|
|
Definition at line 547 of file Node.C. References ScriptParamMsg::param, SimParameters::scriptSet(), simParameters, and ScriptParamMsg::value. 00547 {
00548 simParameters->scriptSet(msg->param,msg->value);
00549 delete msg;
00550 }
|
|
|
Definition at line 451 of file Node.C. References NAMD_die(). 00451 {
00452 #ifdef CHARMIZE_NAMD
00453 if(CkMyPe()){
00454 atomDisArr = msg->atomsDis;
00455 }
00456 delete msg;
00457 #else
00458 NAMD_die("sendCharmArrProxies should not be called in this case!");
00459 #endif
00460 }
|
|
|
Definition at line 609 of file Node.C. Referenced by enableEarlyExit(). 00609 {
00610 CkQdMsg *msg = new CkQdMsg;
00611 #if CHARM_VERSION > 050402
00612 CProxy_Node nodeProxy(thisgroup);
00613 nodeProxy[0].recvEnableEarlyExit(msg);
00614 #else
00615 CProxy_Node(thisgroup).recvEnableEarlyExit(msg,0);
00616 #endif
00617 }
|
|
|
Definition at line 574 of file Node.C. Referenced by enableExitScheduler(). 00574 {
00575 //CmiPrintf("sendEnableExitScheduler\n");
00576 CkQdMsg *msg = new CkQdMsg;
00577 #if CHARM_VERSION > 050402
00578 CProxy_Node nodeProxy(thisgroup);
00579 nodeProxy[0].recvEnableExitScheduler(msg);
00580 #else
00581 CProxy_Node(thisgroup).recvEnableExitScheduler(msg,0);
00582 #endif
00583 }
|
|
|
Definition at line 152 of file Node.h. Referenced by main(). 00152 { script = s; }
|
|
|
Definition at line 155 of file Node.C. 00155 {
00156 delete qmsg;
00157 (CProxy_Node(CpvAccess(BOCclass_group).node)).startup();
00158 }
|
|
|
Definition at line 166 of file Node.C. References AtomMap::allocateMap(), WorkDistrib::assignNodeToPatch(), ProxyMgr::buildProxySpanningTree(), computeMap, computeMgr, ComputeMgr::createComputes(), WorkDistrib::createHomePatches(), LdbCoordinator::createLoadBalancer(), ProxyMgr::createProxies(), DebugM, WorkDistrib::distributeHomePatches(), SimParameters::enableProxyRecvST, SimParameters::enableProxySendST, SimParameters::freeEnergyOn, iINFO(), WorkDistrib::initAndSendHomePatch(), LdbCoordinator::initialize(), iout, WorkDistrib::mapComputes(), SlaveInitMsg::master, memusage(), messageRun(), molecule, NAMD_bug(), Molecule::numAtoms, Sync::Object(), LdbCoordinator::Object(), ComputeMap::Object(), ProxyMgr::Object(), AtomMap::Object(), CollectionMasterHandler::Object(), Sync::openSync(), output, parameters, patchMap, WorkDistrib::patchMapInit(), pdb, SimParameters::PMEOn, WorkDistrib::preCreateHomePatches(), ComputeMap::printComputeMap(), proxySendSpanning, registerUserEventsForAllComputeObjs(), WorkDistrib::sendMaps(), CollectionMasterHandler::setRealMaster(), ProxyMgr::setRecvSpanning(), ProxyMgr::setSendSpanning(), SimParameters::shiftIOToOne, simParameters, workDistrib, SimParameters::wrapAll, and SimParameters::wrapWater. 00166 {
00167 int gotoRun = false;
00168
00169 if (!CkMyPe()) {
00170 iout << iINFO << "Entering startup phase " << startupPhase << " with " <<
00171 (memusage()/1024) << " kB of memory in use.\n" << endi;
00172 fflush(stdout);
00173 }
00174
00175 switch (startupPhase) {
00176
00177 case 0:
00178 #ifdef CHARMIZE_NAMD
00179 populateAtomDisArrs(startupPhase);
00180 #endif
00181
00182 namdOneCommInit(); // Namd1.X style
00183 break;
00184
00185 case 1:
00186 // send & receive molecule, simparameters... (Namd1.X style)
00187 if (CkMyPe()) {
00188 namdOneRecv();
00189 } else {
00190 namdOneSend();
00191 }
00192
00193 #ifdef CHARMIZE_NAMD
00194 //send charm array proxies
00195 if(!CkMyPe()){
00196 AllCharmArrsMsg *arrsMsg = new AllCharmArrsMsg;
00197 arrsMsg->atomsDis = atomDisArr;
00198 ((CProxy_Node)thisgroup).sendCharmArrProxies(arrsMsg);
00199 }
00200 #endif
00201 break;
00202
00203 case 2:
00204 // fix up one-per-node objects
00205 simParameters = node_simParameters;
00206 parameters = node_parameters;
00207 molecule = node_molecule;
00208
00209 #ifdef MEM_OPT_VERSION
00210 //Allocate CollectionMaster which handles I/O depending on the shiftIOToOne parameter
00211 if(!CkMyPe()){
00212 CkChareID collectionMaster;
00213 if(CkNumPes()>1 && simParameters->shiftIOToOne)
00214 collectionMaster = CProxy_CollectionMaster::ckNew(1);
00215 else
00216 collectionMaster = CProxy_CollectionMaster::ckNew(0);
00217
00218 //set CollectionMgr and CollectionMasterHandler's field for CollectionMaster
00219 CollectionMasterHandler::Object()->setRealMaster(collectionMaster);
00220 CProxy_CollectionMgr cmgr(CpvAccess(BOCclass_group).collectionMgr);
00221 SlaveInitMsg *bcmaster = new SlaveInitMsg;
00222 bcmaster->master = collectionMaster;
00223 cmgr.setCollectionMaster(bcmaster);
00224 }
00225 #endif
00226
00227 // take care of inital thread setting
00228 threadInit();
00229
00230 // create blank AtomMap
00231 AtomMap::Object()->allocateMap(molecule->numAtoms);
00232 break;
00233
00234 case 3:
00235 if(simParameters->enableProxySendST) {
00236 ProxyMgr::Object()->setSendSpanning();
00237 }
00238 if(simParameters->enableProxyRecvST) {
00239 ProxyMgr::Object()->setRecvSpanning();
00240 }
00241 #ifdef PROCTRACE_DEBUG
00242 DebugFileTrace::Instance("procTrace");
00243 #endif
00244
00245 if (!CkMyPe()) {
00246 output = new Output; // create output object just on PE(0)
00247 workDistrib->patchMapInit(); // create space division
00248
00249 #ifdef MEM_OPT_VERSION
00250 //create patches without populating them with atoms
00251 workDistrib->preCreateHomePatches();
00252 #else
00253 workDistrib->createHomePatches(); // load atoms into HomePatch(es)
00254 #endif
00255
00256 workDistrib->assignNodeToPatch();
00257 workDistrib->mapComputes();
00258 ComputeMap::Object()->printComputeMap();
00259
00260 registerUserEventsForAllComputeObjs();
00261
00262 workDistrib->sendMaps();
00263 }
00264 break;
00265
00266 case 4:
00267 if ( simParameters->PMEOn ) {
00268 CProxy_ComputePmeMgr pme(CpvAccess(BOCclass_group).computePmeMgr);
00269 #if CHARM_VERSION > 050402
00270 pme[CkMyPe()].initialize(new CkQdMsg);
00271 #else
00272 pme.initialize(new CkQdMsg, CkMyPe());
00273 #endif
00274 }
00275 break;
00276
00277 case 5:
00278 if ( simParameters->PMEOn ) {
00279 CProxy_ComputePmeMgr pme(CpvAccess(BOCclass_group).computePmeMgr);
00280 pme[CkMyPe()].initialize_pencils(new CkQdMsg);
00281 }
00282 if (!CkMyPe()) {
00283 #ifdef MEM_OPT_VERSION
00284 workDistrib->initAndSendHomePatch();
00285 #else
00286 workDistrib->distributeHomePatches();
00287 #endif
00288 }
00289 break;
00290
00291 case 6:
00292 if ( simParameters->PMEOn ) {
00293 CProxy_ComputePmeMgr pme(CpvAccess(BOCclass_group).computePmeMgr);
00294 pme[CkMyPe()].activate_pencils(new CkQdMsg);
00295 }
00296 proxyMgr->createProxies(); // need Home patches before this
00297 if (!CkMyPe()) LdbCoordinator::Object()->createLoadBalancer();
00298 break;
00299
00300 case 7:
00301 if (!CkMyPe()) {
00302 ComputeMap::Object()->printComputeMap();
00303 }
00304 Sync::Object()->openSync(); // decide if to open local Sync
00305 if (proxySendSpanning || proxyRecvSpanning )
00306 proxyMgr->buildProxySpanningTree();
00307 DebugM(4,"Creating Computes\n");
00308 computeMgr->createComputes(ComputeMap::Object());
00309 DebugM(4,"Building Sequencers\n");
00310 buildSequencers();
00311 DebugM(4,"Initializing LDB\n");
00312 LdbCoordinator::Object()->initialize(patchMap,computeMap);
00313 break;
00314
00315 case 8:
00316 {
00317 //For debugging
00318 /*if(!CkMyPe()){
00319 FILE *dumpFile = fopen("/tmp/NAMD_Bench.dump", "w");
00320 dumpbench(dumpFile);
00321 NAMD_die("Normal execution\n");
00322 }*/
00323 }
00324 #ifdef MEM_OPT_VERSION
00325 if(!CkMyPe()){
00326 molecule->delEachAtomSigs();
00327 molecule->delChargeSpace();
00328 if(!simParameters->freeEnergyOn)
00329 molecule->delMassSpace();
00330 molecule->delOtherEachAtomStructs();
00331 //we can free the pdb data here to save memory because output
00332 //is always in the binary format thus saving 3 doubles * numAtoms bytes.
00333 pdb->delPDBCoreData();
00334 }
00335 //decide whether to free memory space for cluster information
00336 //the condition could be referred to comment for function
00337 //wrap_coor_int in Output.C
00338 if(simParameters->wrapAll || simParameters->wrapWater){
00339 int peOfCollectionMaster = 0;
00340 if(CkNumPes()>1 && simParameters->shiftIOToOne) peOfCollectionMaster = 1;
00341 if(CkNumPes()>1 && CkMyPe()!=peOfCollectionMaster)
00342 molecule->delClusterSigs();
00343 }else{
00344 molecule->delClusterSigs();
00345 }
00346 #endif
00347 gotoRun = true;
00348 break;
00349
00350 default:
00351 NAMD_bug("Startup Phase has a bug - check case statement");
00352 break;
00353
00354 }
00355
00356 startupPhase++;
00357 if (!CkMyPe()) {
00358 if (!gotoRun) {
00359 #if CHARM_VERSION > 050402
00360 CkStartQD(CkIndex_Node::startUp((CkQdMsg*)0),&thishandle);
00361 #else
00362 CkStartQD(CProxy_Node::ckIdx_startUp((CkQdMsg*)0),&thishandle);
00363 #endif
00364 } else {
00365 Node::messageRun();
00366 }
00367 }
00368 }
|
|
|
Definition at line 157 of file Node.h. Referenced by Node(). |
|
|
|
|
|
Definition at line 130 of file Node.h. Referenced by Sequencer::integrate(), Node(), and startup(). |
|
|
Definition at line 136 of file Node.h. Referenced by WorkDistrib::createAtomLists(), WorkDistrib::initAndSendHomePatch(), Node(), and saveMolDataPointers(). |
|
|
|
|
|
Definition at line 140 of file Node.h. Referenced by Output::coordinate(), GlobalMasterIMD::get_vmd_forces(), GlobalMasterIMD::GlobalMasterIMD(), Node(), and Controller::printEnergies(). |
|
|
Definition at line 160 of file Node.h. Referenced by Node(). |
|
|
|
Definition at line 139 of file Node.h. Referenced by CollectionMaster::disposePositions(), CollectionMaster::disposeVelocities(), Node(), and startup(). |
|
|
Definition at line 134 of file Node.h. Referenced by LJTable::LJTable(), ComputeHomeTuples< BondElem, Bond, BondValue >::loadTuples(), Node(), saveMolDataPointers(), and startup(). |
|
|
|
|
|
Definition at line 137 of file Node.h. Referenced by WorkDistrib::caclNumAtomsInEachPatch(), WorkDistrib::createAtomLists(), WorkDistrib::fillOnePatchAtoms(), WorkDistrib::initAndSendHomePatch(), Node(), WorkDistrib::patchMapInit(), saveMolDataPointers(), and startup(). |
|
|
|
|
|
|
|
1.3.9.1