NAMD
Public Member Functions | Static Public Member Functions | Public Attributes | Protected Attributes | List of all members
Node Class Reference

#include <Node.h>

Inheritance diagram for Node:

Public Member Functions

 Node (GroupInitMsg *msg)
 
 ~Node (void)
 
void run ()
 
void enableScriptBarrier ()
 
void scriptBarrier (void)
 
void scriptParam (ScriptParamMsg *)
 
void reloadCharges (const char *filename)
 
void reloadCharges (float charge[], int n)
 
void reloadGridforceGrid (const char *key)
 
void reloadGridforceGrid (int gridnum)
 
void updateGridScale (const char *key, Vector scale)
 
void updateGridScale (int gridnum, float sx, float sy, float sz)
 
void reloadStructure (const char *, const char *)
 
void resendMolecule ()
 
void resendMolecule2 ()
 
void sendCheckpointReq (int remote, const char *key, int task, Lattice &lat, ControllerState &cs)
 
void recvCheckpointReq (CheckpointMsg *)
 
void recvCheckpointAck (CheckpointMsg *)
 
void sendEnableExitScheduler (void)
 
void recvEnableExitScheduler (void)
 
void enableExitScheduler (void)
 
void exitScheduler (void)
 
void sendEnableEarlyExit (void)
 
void recvEnableEarlyExit (void)
 
void enableEarlyExit (void)
 
void earlyExit (void)
 
void startup ()
 
void mallocTest (int)
 
void mallocTestQd (void)
 
float measureMemory ()
 
void BOCCheckIn ()
 
void awaitBOCCheckIn ()
 
void saveMolDataPointers (NamdState *)
 
void startHPM ()
 
void stopHPM ()
 
void traceBarrier (int turnOnTrace, int step)
 
void resumeAfterTraceBarrier (CkReductionMsg *msg)
 
void papiMeasureBarrier (int turnOnMeasure, int step)
 
void resumeAfterPapiMeasureBarrier (CkReductionMsg *msg)
 
void outputPatchComputeMaps (const char *filename, int tag)
 
ScriptTcl * getScript ()
 
int myid ()
 
int numNodes ()
 
void setScript (ScriptTcl *s)
 

Static Public Member Functions

static Node * Object ()
 
static Node * ObjectOnPe (int pe)
 
static void messageRun ()
 
static void messageStartUp ()
 
static void messageBOCCheckIn ()
 

Public Attributes

int mallocTest_size
 
float initVM
 
float initRSS
 
int curTimeStep
 
int curMFlopStep
 
bool specialTracing
 
WorkDistrib * workDistrib
 
ComputeMgr * computeMgr
 
Random * rand
 
Molecule * molecule
 
Parameters * parameters
 
SimParameters * simParameters
 
ConfigList * configList
 
PDB * pdb
 
NamdState * state
 
Output * output
 
IMDOutput * imd
 
colvarmodule * colvars
 
Vector * coords
 

Protected Attributes

AtomMap * atomMap
 
PatchMap * patchMap
 
ComputeMap * computeMap
 
LdbCoordinator * ldbCoordinator
 

Detailed Description

Definition at line 78 of file Node.h.

Constructor & Destructor Documentation

◆ Node()

Node::Node ( GroupInitMsg *  msg)

Definition at line 304 of file Node.C.

References atomMap, colvars, configList, DebugM, eventEndOfTimeStep, GroupInitMsg::group, imd, PatchMap::Instance(), AtomMap::Instance(), ComputeMap::Instance(), molecule, NAMD_bug(), output, parameters, patchMap, pdb, recvCheckpointCAck_handler(), recvCheckpointCReq_handler(), simParameters, specialTracing, and state.

305 {
306  DebugM(4,"Creating Node\n");
307 #if(CMK_CCS_AVAILABLE && CMK_WEB_MODE)
308  CApplicationInit();
309 #endif
310  if (CkpvAccess(Node_instance) == 0) {
311  CkpvAccess(Node_instance) = this;
312  eventEndOfTimeStep = traceRegisterUserEvent("EndOfTimeStep", 135);
313  } else {
314  NAMD_bug("Node::Node() - another instance of Node exists!");
315  }
316 
317  CkpvAccess(BOCclass_group) = msg->group;
318  delete msg;
319 
320  CkpvAccess(BOCclass_group).node = thisgroup;
321 
322  recvCheckpointCReq_index = CmiRegisterHandler((CmiHandler)recvCheckpointCReq_handler);
323  recvCheckpointCAck_index = CmiRegisterHandler((CmiHandler)recvCheckpointCAck_handler);
324 
325  startupPhase = 0;
326 
327  molecule = NULL;
328  parameters = NULL;
329  simParameters = NULL;
330  configList = NULL;
331  pdb = NULL;
332  state = NULL;
333  output = NULL;
334  imd = new IMDOutput;
335  colvars = 0;
336 
337 #if USE_HPM
338  // assumes that this will be done only on BG/P
339  TopoManager *tmgr = new TopoManager();
340  int x, y, z;
341  tmgr->rankToCoordinates(CkMyPe(), x, y, z, localRankOnNode);
342  delete tmgr;
343 #endif
344 
345  specialTracing = traceAvailable() && (traceIsOn()==0);
346 
347  DebugM(4,"Creating PatchMap, AtomMap, ComputeMap\n");
348  patchMap = PatchMap::Instance();
349  atomMap = AtomMap::Instance();
350  if ( CkMyRank() == 0 ) ComputeMap::Instance();
351 
352  //Note: Binding BOC vars such as workDistrib has been moved
353  //to the 1st phase of startup because the in-order message delivery
354  //is not always guaranteed --Chao Mei
355 #if defined(CMK_BALANCED_INJECTION_API) && CMK_BALANCED_INJECTION_API != 0
356  if(CkMyRank() == 0){
357  balancedInjectionLevel=ck_get_GNI_BIConfig();
358  // CkPrintf("[%d] get retrieved BI=%d\n",CkMyPe(),balancedInjectionLevel);
359  ck_set_GNI_BIConfig(20);
360  // CkPrintf("[%d] set retrieved BI=%d\n",CkMyPe(),ck_get_GNI_BIConfig());
361  }
362 #endif
363 
364 }
Node::specialTracing
bool specialTracing
Definition: Node.h:166
recvCheckpointCReq_handler
void recvCheckpointCReq_handler(envelope *)
Definition: Node.C:1397
GroupInitMsg::group
BOCgroup group
Definition: Node.h:68
Node::imd
IMDOutput * imd
Definition: Node.h:186
AtomMap::Instance
static AtomMap * Instance()
Definition: AtomMap.C:125
Node::output
Output * output
Definition: Node.h:185
Node::simParameters
SimParameters * simParameters
Definition: Node.h:181
DebugM
#define DebugM(x, y)
Definition: Debug.h:75
NAMD_bug
void NAMD_bug(const char *err_msg)
Definition: common.C:196
Node::state
NamdState * state
Definition: Node.h:184
Node::atomMap
AtomMap * atomMap
Definition: Node.h:202
Node::pdb
PDB * pdb
Definition: Node.h:183
Node::configList
ConfigList * configList
Definition: Node.h:182
Node::parameters
Parameters * parameters
Definition: Node.h:180
ComputeMap::Instance
static ComputeMap * Instance()
Definition: ComputeMap.C:24
recvCheckpointCAck_handler
void recvCheckpointCAck_handler(envelope *)
Definition: Node.C:1419
Node::patchMap
PatchMap * patchMap
Definition: Node.h:203
Node::colvars
colvarmodule * colvars
Definition: Node.h:187
eventEndOfTimeStep
int eventEndOfTimeStep
Definition: Node.C:299
PatchMap::Instance
static PatchMap * Instance()
Definition: PatchMap.C:32
Node::molecule
Molecule * molecule
Definition: Node.h:179

◆ ~Node()

Node::~Node ( void  )

Definition at line 369 of file Node.C.

References atomMap, computeMap, imd, output, patchMap, and rand.

370 {
371  delete imd;
372  delete output;
373  delete computeMap;
374  delete atomMap;
375  delete patchMap;
376  delete CkpvAccess(comm);
377  // BEGIN LA
378  delete rand;
379  // END LA
380 #ifdef MEASURE_NAMD_WITH_PAPI
381  delete CkpvAccess(papiEvents);
382 #endif
383 }
Node::imd
IMDOutput * imd
Definition: Node.h:186
Node::output
Output * output
Definition: Node.h:185
Node::computeMap
ComputeMap * computeMap
Definition: Node.h:204
Node::atomMap
AtomMap * atomMap
Definition: Node.h:202
Node::rand
Random * rand
Definition: Node.h:175
Node::patchMap
PatchMap * patchMap
Definition: Node.h:203

Member Function Documentation

◆ awaitBOCCheckIn()

void Node::awaitBOCCheckIn ( )

◆ BOCCheckIn()

void Node::BOCCheckIn ( )

◆ earlyExit()

void Node::earlyExit ( void  )

Definition at line 1472 of file Node.C.

References NAMD_die().

1472  {
1473  NAMD_die("Exiting prematurely; see error messages above.");
1474 }
NAMD_die
void NAMD_die(const char *err_msg)
Definition: common.C:148

◆ enableEarlyExit()

void Node::enableEarlyExit ( void  )

Definition at line 1464 of file Node.C.

References sendEnableEarlyExit().

Referenced by Sequencer::hardWallDrude(), Sequencer::maximumMove(), Sequencer::maximumMove_SOA(), Sequencer::rattle1(), Sequencer::rattle1_SOA(), and recvEnableEarlyExit().

1464  {
1465  if ( CkMyPe() ) {
1466  sendEnableEarlyExit();
1467  } else {
1468  CkStartQD(CkIndex_Node::earlyExit(),&thishandle);
1469  }
1470 }
Node::sendEnableEarlyExit
void sendEnableEarlyExit(void)
Definition: Node.C:1455

◆ enableExitScheduler()

void Node::enableExitScheduler ( void  )

Definition at line 1442 of file Node.C.

References sendEnableExitScheduler().

Referenced by BackEnd::awaken(), and recvEnableExitScheduler().

1442  {
1443  if ( CkMyPe() ) {
1444  sendEnableExitScheduler();
1445  } else {
1446  CkStartQD(CkIndex_Node::exitScheduler(), &thishandle);
1447  }
1448 }
Node::sendEnableExitScheduler
void sendEnableExitScheduler(void)
Definition: Node.C:1431

◆ enableScriptBarrier()

void Node::enableScriptBarrier ( )

Definition at line 1214 of file Node.C.

1214  {
1215  CkStartQD(CkIndex_Node::scriptBarrier(), &thishandle);
1216 }

◆ exitScheduler()

void Node::exitScheduler ( void  )

Definition at line 1450 of file Node.C.

1450  {
1451  //CmiPrintf("exitScheduler %d\n",CkMyPe());
1452  CsdExitScheduler();
1453 }

◆ getScript()

ScriptTcl * Node::getScript ( void  )

Definition at line 1659 of file Node.C.

References PatchData::script.

Referenced by Output::coordinate(), and Controller::printEnergies().

1659  {
1660 #ifndef NODEGROUP_FORCE_REGISTER
1661  return script;
1662 #else
1663  if(script == NULL){
1664  CProxy_PatchData cpdata(CkpvAccess(BOCclass_group).patchData);
1665  PatchData* patchData = cpdata.ckLocalBranch();
1666  return patchData->script;
1667  }else{
1668  return script;
1669  }
1670 #endif
1671 }
PatchData::script
ScriptTcl * script
Definition: PatchData.h:160

◆ mallocTest()

void Node::mallocTest ( int  step)

Definition at line 406 of file Node.C.

References NAMD_die().

Referenced by mallocTestQd().

406  {
407  int MB = 1024*1024;
408  int size = 100;
409  char* foo = (char*) malloc(size*MB);
410  if ( ! foo ) {
411  char buf[256];
412  sprintf(buf,"Malloc fails on Pe %d at %d MB.\n",CkMyPe(),step*size);
413  NAMD_die(buf);
414  }
415  memset(foo,0,size*MB*sizeof(char));
416 }
NAMD_die
void NAMD_die(const char *err_msg)
Definition: common.C:148

◆ mallocTestQd()

void Node::mallocTestQd ( void  )

Definition at line 418 of file Node.C.

References mallocTest(), and mallocTest_size.

418  {
419  if ( mallocTest_size ) {
420  CkPrintf("All PEs successfully allocated %d MB.\n", 100*mallocTest_size);
421  } else {
422  CkPrintf("Starting malloc test on all PEs.\n");
423  }
424  fflush(stdout);
425  ++mallocTest_size;
426  CkStartQD(CkIndex_Node::mallocTestQd(), &thishandle);
427  (CProxy_Node(CkpvAccess(BOCclass_group).node)).mallocTest(mallocTest_size);
428 }
Node::mallocTest
void mallocTest(int)
Definition: Node.C:406
Node::mallocTest_size
int mallocTest_size
Definition: Node.h:130

◆ measureMemory()

float Node::measureMemory ( )

◆ messageBOCCheckIn()

static void Node::messageBOCCheckIn ( )
static

◆ messageRun()

void Node::messageRun ( )
static

Definition at line 1167 of file Node.C.

References run().

Referenced by startup().

1167  {
1168  (CProxy_Node(CkpvAccess(BOCclass_group).node)).run();
1169 }
Node::run
void run()
Definition: Node.C:1176

◆ messageStartUp()

void Node::messageStartUp ( )
static

Definition at line 433 of file Node.C.

References startup().

433  {
434  (CProxy_Node(CkpvAccess(BOCclass_group).node)).startup();
435 }
Node::startup
void startup()
Definition: Node.C:465

◆ myid()

int Node::myid ( )
inline

Definition at line 191 of file Node.h.

Referenced by ComputeMgr::createComputes(), WorkDistrib::distributeHomePatches(), and LdbCoordinator::initialize().

191 { return CkMyPe(); }

◆ numNodes()

int Node::numNodes ( )
inline

Definition at line 192 of file Node.h.

Referenced by WorkDistrib::assignNodeToPatch(), and LdbCoordinator::initialize().

192 { return CkNumPes(); }

◆ Object()

static Node* Node::Object ( )
inlinestatic

Definition at line 86 of file Node.h.

Referenced by HomePatch::addForceToMomentum(), HomePatch::addForceToMomentum3(), Sequencer::addMovDragToPosition(), Sequencer::addRotDragToPosition(), HomePatch::addVelocityToPosition(), after_backend_init(), Controller::algorithm(), CollectionMaster::CollectVectorInstanceDcdSelection::append(), WorkDistrib::assignNodeToPatch(), BackEnd::awaken(), PmeZPencil::backward_fft(), PmeYPencil::backward_fft(), PmeXPencil::backward_fft(), LdbCoordinator::barrier(), HomePatch::boxClosed(), HomePatch::buildRattleList(), HomePatch::buildRattleList_SOA(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), Controller::calcPressure(), colvarproxy_namd::calculate(), ComputeQMMgr::calcUSR(), ComputePmeMgr::chargeGridSubmitted(), colvarproxy_namd::check_atom_id(), colvarproxy_namd::check_volmap_by_id(), ComputeGridForce::checkGridForceRatio(), CudaPmeOneDevice::checkPatchLevelLatticeCompatibilityAndComputeOffsets(), SimParameters::close_dcdfile(), SimParameters::close_veldcdfile(), colvarproxy_namd::colvarproxy_namd(), Controller::compareChecksums(), CudaPmeOneDevice::compute(), colvarproxy_namd::compute_volmap(), ComputeCylindricalBC::ComputeCylindricalBC(), ComputeEwald::ComputeEwald(), OneFourNbTholeElem::computeForce(), AngleElem::computeForce(), ImproperElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), TholeElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), ComputeFullDirect::ComputeFullDirect(), ComputeGlobal::ComputeGlobal(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), ComputeLCPO::ComputeLCPO(), LjPmeCompute::computeLJpotential(), ComputeMsm::ComputeMsm(), LjPmeCompute::computeNonbonded(), ComputeNonbondedPair::ComputeNonbondedPair(), ComputeNonbondedSelf::ComputeNonbondedSelf(), ComputePme::ComputePme(), ComputeRestraints::ComputeRestraints(), ComputeSphericalBC::ComputeSphericalBC(), ComputeStir::ComputeStir(), ComputeTclBC::ComputeTclBC(), Controller::Controller(), Output::coordinate(), Output::coordinateNeeded(), ComputeMgr::createComputes(), ComputeCUDAMgr::createCudaComputeNonbonded(), ComputeCUDAMgr::createCudaGlobalMaster(), ComputeCUDAMgr::createCudaPmeOneDevice(), ComputeGridForce::createGridForcedIdxList(), ParallelIOMgr::createHomePatches(), LdbCoordinator::createLoadBalancer(), CudaComputeNonbonded::CudaComputeNonbonded(), CudaPmeOneDevice::CudaPmeOneDevice(), HomePatch::depositMigration(), CollectionMaster::disposeForces(), CollectionMaster::disposePositions(), CollectionMaster::disposeVelocities(), ComputeConsForce::doForce(), ComputeEField::doForce(), ComputeConsTorque::doForce(), ComputeStir::doForce(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), ComputeGridForce::doForce(), ComputeRestraints::doForce(), HomePatch::doGroupSizeCheck(), HomePatch::doGroupSizeCheck_SOA(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), HomePatch::doPairlistCheck(), ComputePme::doQMWork(), ComputeTclBC::doWork(), ComputeGBISser::doWork(), ComputeGlobal::doWork(), CudaComputeNonbonded::doWork(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), dumpbench(), HomePatch::exchangeAtoms(), HomePatch::exchangeCheckpoint(), CudaPmeOneDevice::finishReduction(), Output::force(), Patch::forceBoxClosed(), Output::forceNeeded(), PmeZPencil::forward_fft(), PmeYPencil::forward_fft(), PmeXPencil::forward_fft(), ComputePmeCUDADevice::gatherForce(), ComputePmeCUDADevice::gatherForceDone(), HomePatch::gbisComputeAfterP1(), HomePatch::gbisComputeAfterP2(), GlobalMasterIMD::get_vmd_forces(), GlobalMaster::getCurrentReduction(), CudaComputeNonbonded::getCurrentReduction(), ComputeLjPmeSerialMgr::getLJparameters(), Controller::getTotalPotentialEnergy(), GlobalMaster::GlobalMaster(), GlobalMasterEasy::GlobalMasterEasy(), GlobalMasterFreeEnergy::GlobalMasterFreeEnergy(), GlobalMasterIMD::GlobalMasterIMD(), GlobalMasterServer::GlobalMasterServer(), GlobalMasterSymmetry::GlobalMasterSymmetry(), GlobalMasterTMD::GlobalMasterTMD(), ComputePmeMgr::gridCalc2R(), Sequencer::hardWallDrude(), HomePatch::hardWallDrude(), colvarproxy_namd::init_atom_group(), colvarproxy_namd::init_atoms_map(), colvarproxy_namd::init_tcl_pointers(), colvarproxy_namd::init_volmap_by_name(), ComputeCUDAMgr::initialize(), ComputePmeCUDA::initialize(), LjPmeCompute::initialize(), LdbCoordinator::initialize(), ComputeQM::initialize(), CudaComputeNonbonded::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize(), ComputePmeCUDADevice::initialize(), ComputePmeMgr::initialize_computes(), ComputePmeMgr::initialize_pencils(), Controller::integrate(), Sequencer::integrate(), Sequencer::integrate_SOA(), isPmeProcessor(), Sequencer::langevinPiston(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), CudaComputeNonbonded::launchWork(), LJTable::LJTable(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), HomePatch::loweAndersenVelocities(), WorkDistrib::mapComputes(), Sequencer::maximumMove(), Sequencer::maximumMove_SOA(), ScriptTcl::measure(), ComputePmeCUDADevice::mergeForcesOnPatch(), Sequencer::minimize(), HomePatch::minimize_rattle2(), HomePatch::mollyAverage(), HomePatch::mollyMollify(), Controller::monteCarloPressure_accept(), Controller::multigatorCalcEnthalpy(), NAMD_bug(), NAMD_die(), NAMD_err(), NAMD_quit(), NamdHybridLB::NamdHybridLB(), CudaComputeNonbonded::openBoxesOnPe(), PmePencil< CBase_PmeZPencil >::order_init(), Patch::Patch(), PatchDataSOA_set_buffer(), PatchDataSOA_set_size(), WorkDistrib::patchMapInit(), Compute::patchReady(), PmeXPencil::pme_kspace(), Patch::positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), Controller::printEnergies(), Controller::printMinimizeEnergies(), HomePatch::qmSwapAtoms(), Sequencer::rattle1(), HomePatch::rattle1(), Sequencer::rattle1_SOA(), HomePatch::rattle1_SOA(), HomePatch::rattle1old(), HomePatch::rattle2(), ParallelIOMgr::readInfoForParOutDcdSelection(), LdbCoordinator::rebalance(), Controller::rebalanceLoad(), ProxyPatch::receiveAll(), ProxyPatch::receiveData(), CollectionMaster::receiveDataStream(), CollectionMaster::receiveForces(), CollectionMaster::receivePositions(), CollectionMaster::receivePositionsDcdSelection(), Controller::receivePressure(), CollectionMaster::receiveVelocities(), recursive_bisect_with_curve(), ComputePmeCUDADevice::recvAtoms(), ParallelIOMgr::recvAtomsCntPerPatch(), ComputePmeCUDADevice::recvAtomsFromNeighbor(), recvCheckpointCAck_handler(), recvCheckpointCReq_handler(), HomePatch::recvCheckpointLoad(), ComputeMgr::recvComputeConsForceMsg(), ComputeExtMgr::recvCoord(), ComputeMsmSerialMgr::recvCoord(), ComputeLjPmeSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeGBISserMgr::recvCoord(), ComputeMgr::recvCudaGlobalMasterCreateMsg(), ComputeMgr::recvCudaGlobalMasterRemoveMsg(), ComputeMgr::recvCudaGlobalMasterUpdateMsg(), ParallelIOMgr::recvDcdParams(), HomePatch::recvExchangeMsg(), ComputeQMMgr::recvPartQM(), ComputeQMMgr::recvPntChrg(), recvReplicaDcdData(), recvReplicaDcdInit(), ComputeGlobal::recvResults(), Sequencer::reloadCharges(), Controller::rescaleaccelMD(), Sequencer::rescaleSoluteCharges(), CudaComputeNonbonded::reSortTileLists(), HomePatch::revert(), ScriptTcl::run(), ComputeQM::saveResults(), ComputeGlobal::saveTotalForces(), ComputePmeUtil::select(), ComputeNonbondedUtil::select(), PmeZPencil::send_all_ungrid(), GlobalMasterIMD::send_energies(), GlobalMasterIMD::send_fcoords(), PmeZPencil::send_trans(), PmeYPencil::send_trans(), PmeYPencil::send_untrans(), PmeXPencil::send_untrans(), ComputePmeCUDADevice::sendAtomsToNeighbor(), ComputeMgr::sendComputeGlobalData(), ComputeMgr::sendComputeGlobalResults(), ParallelIOMgr::sendDcdParams(), ComputePmeCUDADevice::sendForcesToNeighbors(), ComputePmeMgr::sendTrans(), ComputePmeMgr::sendUngrid(), ComputePmeMgr::sendUntrans(), HomePatch::setGBISIntrinsicRadii(), PatchMgr::setLattice(), HomePatch::setLcpoType(), ComputeLjPmeSerialMgr::setLJparameters(), ComputePmeCUDAMgr::setupPencils(), SimpleBroadcastObject< Tensor >::SimpleBroadcastObject(), NamdHybridLB::splitComputes(), ComputePmeCUDADevice::spreadCharge(), CollectionMaster::startNextRoundOutputForce(), CollectionMaster::startNextRoundOutputPos(), CollectionMaster::startNextRoundOutputVel(), NamdCentLB::Strategy(), CollectionMgr::submitForces(), CollectionMgr::submitPositions(), ExclElem::submitReductionData(), PmePencilXYZ::submitReductions(), PmePencilZ::submitReductions(), ComputePmeMgr::submitReductions(), CollectionMgr::submitVelocities(), Tcl_centerOfMass(), Tcl_centerOfNumber(), Tcl_loadCoords(), Tcl_radiusOfGyration(), Sequencer::tcoupleVelocities(), ComputePme::ungridForces(), colvarproxy_namd::update_atom_properties(), colvarproxy_namd::update_atoms_map(), colvarproxy_namd::update_group_properties(), ComputeLonepairsCUDA::updateAtoms(), ComputeMgr::updateLocalComputes4(), Output::velocity(), Output::velocityNeeded(), ReductionMgr::willRequire(), ReductionMgr::willSubmit(), wrap_coor_int(), wrap_coor_int_dcd_selection(), and CollectionMaster::wrapCoorFinished().

86 {return CkpvAccess(Node_instance);}

◆ ObjectOnPe()

static Node* Node::ObjectOnPe ( int  pe)
inlinestatic

Definition at line 87 of file Node.h.

87 {return CkpvAccessOther(Node_instance, CmiRankOf(pe));}

◆ outputPatchComputeMaps()

void Node::outputPatchComputeMaps ( const char *  filename,
int  tag 
)

Definition at line 1620 of file Node.C.

References Patch::getNumAtoms(), gNAMDBinaryName, PatchMap::gridsize_a(), PatchMap::gridsize_b(), PatchMap::gridsize_c(), NAMD_die(), ComputeMap::node(), PatchMap::node(), ComputeMap::numComputes(), PatchMap::numPatches(), PatchMap::Object(), ComputeMap::Object(), SimParameters::outputMaps, PatchMap::patch(), ComputeMap::pid(), simParameters, SimParameters::simulatedNodeSize, SimParameters::simulatedPEs, SimParameters::simulateInitialMapping, and ComputeMap::type().

Referenced by Controller::rebalanceLoad(), and startup().

1620  {
1621  if(!simParameters->outputMaps && !simParameters->simulateInitialMapping) return;
1622 
1623  int numpes = CkNumPes();
1624  int nodesize = CkMyNodeSize();
1625  if(simParameters->simulateInitialMapping) {
1626  numpes = simParameters->simulatedPEs;
1627  nodesize = simParameters->simulatedNodeSize;
1628  }
1629 
1630  char fname[128];
1631  sprintf(fname, "mapdump_%s.%d_%d_%d_%s", filename, numpes, nodesize, tag, gNAMDBinaryName);
1632 
1633  FILE *fp = fopen(fname, "w");
1634  if(fp == NULL) {
1635  NAMD_die("Error in outputing PatchMap and ComputeMap info!\n");
1636  return;
1637  }
1638  PatchMap *pMap = PatchMap::Object();
1639  ComputeMap *cMap = ComputeMap::Object();
1640  int numPatches = pMap->numPatches();
1641  int numComputes = cMap->numComputes();
1642  fprintf(fp, "%d %d %d %d %d %d %d\n", numpes, nodesize, numPatches, numComputes,
1643  pMap->gridsize_a(), pMap->gridsize_b(), pMap->gridsize_c());
1644  //output PatchMap info
1645  for(int i=0; i<numPatches; i++) {
1646  #ifdef MEM_OPT_VERSION
1647  fprintf(fp, "%d %d\n", pMap->numAtoms(i), pMap->node(i));
1648  #else
1649  fprintf(fp, "%d %d\n", pMap->patch(i)->getNumAtoms(), pMap->node(i));
1650  #endif
1651  }
1652 
1653  //output ComputeMap info
1654  for(int i=0; i<numComputes; i++) {
1655  fprintf(fp, "%d %d %d %d\n", cMap->node(i), cMap->type(i), cMap->pid(i,0), cMap->pid(i,1));
1656  }
1657 }
SimParameters::simulateInitialMapping
Bool simulateInitialMapping
Definition: SimParameters.h:232
Patch::getNumAtoms
int getNumAtoms() const
Definition: Patch.h:105
ComputeMap::numComputes
int numComputes(void)
Definition: ComputeMap.h:103
PatchMap::Object
static PatchMap * Object()
Definition: PatchMap.h:27
Node::simParameters
SimParameters * simParameters
Definition: Node.h:181
PatchMap::patch
Patch * patch(PatchID pid)
Definition: PatchMap.h:244
PatchMap::gridsize_c
int gridsize_c(void) const
Definition: PatchMap.h:66
PatchMap::gridsize_a
int gridsize_a(void) const
Definition: PatchMap.h:64
PatchMap::numPatches
int numPatches(void) const
Definition: PatchMap.h:59
gNAMDBinaryName
char * gNAMDBinaryName
Definition: BackEnd.C:247
ComputeMap::type
ComputeType type(ComputeID cid)
Definition: ComputeMap.C:118
NAMD_die
void NAMD_die(const char *err_msg)
Definition: common.C:148
ComputeMap::Object
static ComputeMap * Object()
Definition: ComputeMap.h:91
ComputeMap::node
int node(ComputeID cid)
Definition: ComputeMap.h:108
PatchMap::gridsize_b
int gridsize_b(void) const
Definition: PatchMap.h:65
ComputeMap::pid
int pid(ComputeID cid, int i)
Definition: ComputeMap.C:107
PatchMap::node
int node(int pid) const
Definition: PatchMap.h:114

◆ papiMeasureBarrier()

void Node::papiMeasureBarrier ( int  turnOnMeasure,
int  step 
)

Definition at line 1525 of file Node.C.

References curMFlopStep.

1525  {
1526 #ifdef MEASURE_NAMD_WITH_PAPI
1527  curMFlopStep = step;
1528  double results[NUM_PAPI_EVENTS+1];
1529 
1530  if(turnOnMeasure){
1531  CkpvAccess(papiEvents)[NUM_PAPI_EVENTS]=CmiWallTimer();
1532 
1533  long long counters[NUM_PAPI_EVENTS+1];
1534  int ret=PAPI_start_counters(CkpvAccess(papiEvents), NUM_PAPI_EVENTS);
1535  if(ret==PAPI_OK)
1536  {
1537  // CkPrintf("traceBarrier start counters (%d) at step %d called on proc %d\n", turnOnMeasure, step, CkMyPe());
1538  }
1539  else
1540  {
1541  CkPrintf("error PAPI_start_counters (%d) at step %d called on proc %d\n",ret , step, CkMyPe());
1542  }
1543  if(PAPI_read_counters(counters, NUM_PAPI_EVENTS)!=PAPI_OK)
1544  {
1545  CkPrintf("error PAPI_read_counters %d\n",PAPI_read_counters(counters, NUM_PAPI_EVENTS));
1546  };
1547  }else{
1548  long long counters[NUM_PAPI_EVENTS+1];
1549  for(int i=0;i<NUM_PAPI_EVENTS;i++) counters[i]=0LL;
1550  if(PAPI_read_counters(counters, NUM_PAPI_EVENTS)==PAPI_OK)
1551  {
1552 #if !MEASURE_PAPI_SPP
1553  results[0] = (double)counters[0]/1e6;
1554  results[1] = (double)counters[1]/1e6;
1555 #else
1556  for(int i=0;i<NUM_PAPI_EVENTS;i++) results[i] = counters[i]/1e6;
1557 #endif
1558  // for(int i=0;i<NUM_PAPI_EVENTS;i++) CkPrintf("[%d] counter %d is %ld\n",CkMyPe(),i,counters[i]);
1559  }
1560  else
1561  {
1562  // CkPrintf("error PAPI_read_counters %d\n",PAPI_read_counters(counters, NUM_PAPI_EVENTS));
1563  }
1564  // CkPrintf("traceBarrier stop counters (%d) at step %d called on proc %d\n", turnOnMeasure, step, CkMyPe());
1565 
1566  PAPI_stop_counters(counters, NUM_PAPI_EVENTS);
1567  }
1568  if(CkMyPe()==0)
1569  // CkPrintf("traceBarrier (%d) at step %d called on proc %d\n", turnOnMeasure, step, CkMyPe());
1570  results[NUM_PAPI_EVENTS]=CkpvAccess(papiEvents)[NUM_PAPI_EVENTS]; //starttime
1571  CProxy_Node nd(CkpvAccess(BOCclass_group).node);
1572  CkCallback cb(CkIndex_Node::resumeAfterPapiMeasureBarrier(NULL), nd[0]);
1573  contribute(sizeof(double)*(NUM_PAPI_EVENTS+1), &results, CkReduction::sum_double, cb);
1574 #endif
1575 }
Node::curMFlopStep
int curMFlopStep
Definition: Node.h:157

◆ recvCheckpointAck()

void Node::recvCheckpointAck ( CheckpointMsg *  msg)

Definition at line 1425 of file Node.C.

References CheckpointMsg::checkpoint, Controller::recvCheckpointAck(), and state.

Referenced by recvCheckpointCAck_handler().

1425  {
1426  state->controller->recvCheckpointAck(msg->checkpoint);
1427  delete msg;
1428 }
CheckpointMsg::checkpoint
Controller::checkpoint checkpoint
Definition: Node.C:102
Node::state
NamdState * state
Definition: Node.h:184
Controller::recvCheckpointAck
void recvCheckpointAck(checkpoint &cp)
Definition: Controller.C:4976

◆ recvCheckpointReq()

void Node::recvCheckpointReq ( CheckpointMsg *  msg)

Definition at line 1403 of file Node.C.

References CheckpointMsg::checkpoint, CheckpointMsg::key, Controller::recvCheckpointReq(), CheckpointMsg::replica, state, and CheckpointMsg::task.

Referenced by recvCheckpointCReq_handler().

1403  {
1404  state->controller->recvCheckpointReq(msg->key,msg->task,msg->checkpoint);
1405 
1406  int remote = msg->replica;
1407  msg->replica = CmiMyPartition();
1408  envelope *env = UsrToEnv(CheckpointMsg::pack(msg));
1409  CmiSetHandler(env,recvCheckpointCAck_index);
1410 #if CMK_HAS_PARTITION
1411  CmiInterSyncSendAndFree(CkMyPe(),remote,env->getTotalsize(),(char*)env);
1412 #else
1413  CmiSyncSendAndFree(CkMyPe(),env->getTotalsize(),(char*)env);
1414 #endif
1415 }
Controller::recvCheckpointReq
void recvCheckpointReq(const char *key, int task, checkpoint &cp)
Definition: Controller.C:4946
CheckpointMsg::task
int task
Definition: Node.C:100
CheckpointMsg::replica
int replica
Definition: Node.C:101
CheckpointMsg::checkpoint
Controller::checkpoint checkpoint
Definition: Node.C:102
Node::state
NamdState * state
Definition: Node.h:184
CheckpointMsg::key
char * key
Definition: Node.C:103

◆ recvEnableEarlyExit()

void Node::recvEnableEarlyExit ( void  )

Definition at line 1460 of file Node.C.

References enableEarlyExit().

1460  {
1461  enableEarlyExit();
1462 }
Node::enableEarlyExit
void enableEarlyExit(void)
Definition: Node.C:1464

◆ recvEnableExitScheduler()

void Node::recvEnableExitScheduler ( void  )

Definition at line 1437 of file Node.C.

References enableExitScheduler().

1437  {
1438  //CmiPrintf("recvEnableExitScheduler\n");
1439  enableExitScheduler();
1440 }
Node::enableExitScheduler
void enableExitScheduler(void)
Definition: Node.C:1442

◆ reloadCharges() [1/2]

void Node::reloadCharges ( const char *  filename)

Definition at line 1227 of file Node.C.

References molecule, NAMD_die(), and Molecule::numAtoms.

1227  {
1228  FILE *file = fopen(filename,"r");
1229  if ( ! file ) NAMD_die("node::reloadCharges():Error opening charge file.");
1230 
1231  int n = molecule->numAtoms;
1232  float *charge = new float[n];
1233 
1234  for ( int i = 0; i < n; ++i ) {
1235  if ( ! fscanf(file,"%f",&charge[i]) )
1236  NAMD_die("Node::reloadCharges():Not enough numbers in charge file.");
1237  }
1238 
1239  fclose(file);
1240  CProxy_Node(thisgroup).reloadCharges(charge,n);
1241 #ifdef NODEGROUP_FORCE_REGISTER
1242  if(CkMyPe()==0)
1243  {
1244  CProxy_PatchData cpdata(CkpvAccess(BOCclass_group).patchData);
1245  cpdata.setDeviceKernelUpdateCounter();
1246  }
1247 #endif
1248  delete [] charge;
1249 }
Molecule::numAtoms
int numAtoms
Definition: Molecule.h:586
NAMD_die
void NAMD_die(const char *err_msg)
Definition: common.C:148
Node::molecule
Molecule * molecule
Definition: Node.h:179

◆ reloadCharges() [2/2]

void Node::reloadCharges ( float  charge[],
int  n 
)

Definition at line 1251 of file Node.C.

References molecule, and Molecule::reloadCharges().

1251  {
1252  molecule->reloadCharges(charge,n);
1253 }
Molecule::reloadCharges
void reloadCharges(float charge[], int n)
Node::molecule
Molecule * molecule
Definition: Node.h:179

◆ reloadGridforceGrid() [1/2]

void Node::reloadGridforceGrid ( const char *  key)

Definition at line 1257 of file Node.C.

References DebugM, endi(), MGridforceParamsList::find_key(), Molecule::get_gridfrc_grid(), MGridforceParamsList::index_for_key(), SimParameters::mgridforcelist, MGRIDFORCEPARAMS_DEFAULTKEY, molecule, NAMD_bug(), NAMD_die(), GridforceGrid::reinitialize(), and simParameters.

1257  {
1258  DebugM(4, "reloadGridforceGrid(const char*) called on node " << CkMyPe() << "\n" << endi);
1259 
1260  int gridnum;
1261  MGridforceParams *mgridParams;
1262  if (key == NULL) {
1263  gridnum = simParameters->mgridforcelist.index_for_key(MGRIDFORCEPARAMS_DEFAULTKEY);
1264  mgridParams = simParameters->mgridforcelist.find_key(MGRIDFORCEPARAMS_DEFAULTKEY);
1265  } else {
1266  gridnum = simParameters->mgridforcelist.index_for_key(key);
1267  mgridParams = simParameters->mgridforcelist.find_key(key);
1268  }
1269 
1270  if (gridnum < 0 || mgridParams == NULL) {
1271  NAMD_die("Node::reloadGridforceGrid(const char*):Could not find grid.");
1272  }
1273 
1274  GridforceGrid *grid = molecule->get_gridfrc_grid(gridnum);
1275  if (grid == NULL) {
1276  NAMD_bug("Node::reloadGridforceGrid(const char*):grid not found");
1277  }
1278  grid->reinitialize(simParameters, mgridParams);
1279 
1280  CProxy_Node(thisgroup).reloadGridforceGrid(gridnum);
1281 #ifdef NODEGROUP_FORCE_REGISTER
1282  if(CkMyPe()==0)
1283  {
1284  CProxy_PatchData cpdata(CkpvAccess(BOCclass_group).patchData);
1285  cpdata.setDeviceKernelUpdateCounter();
1286  }
1287 #endif
1288  DebugM(4, "reloadGridforceGrid(const char*) finished\n" << endi);
1289 }
Molecule::get_gridfrc_grid
GridforceGrid * get_gridfrc_grid(int gridnum) const
Definition: Molecule.h:1368
Node::simParameters
SimParameters * simParameters
Definition: Node.h:181
DebugM
#define DebugM(x, y)
Definition: Debug.h:75
endi
std::ostream & endi(std::ostream &s)
Definition: InfoStream.C:54
GridforceGrid::reinitialize
virtual void reinitialize(SimParameters *simParams, MGridforceParams *mgridParams)=0
MGridforceParamsList::index_for_key
int index_for_key(const char *key)
Definition: MGridforceParams.C:33
NAMD_bug
void NAMD_bug(const char *err_msg)
Definition: common.C:196
MGRIDFORCEPARAMS_DEFAULTKEY
#define MGRIDFORCEPARAMS_DEFAULTKEY
Definition: MGridforceParams.h:19
MGridforceParamsList::find_key
MGridforceParams * find_key(const char *key)
Definition: MGridforceParams.C:14
NAMD_die
void NAMD_die(const char *err_msg)
Definition: common.C:148
SimParameters::mgridforcelist
MGridforceParamsList mgridforcelist
Definition: SimParameters.h:358
Node::molecule
Molecule * molecule
Definition: Node.h:179

◆ reloadGridforceGrid() [2/2]

void Node::reloadGridforceGrid ( int  gridnum)

Definition at line 1338 of file Node.C.

References ALLBUTME, BUFSIZE, DebugM, MOStream::end(), endi(), Molecule::get_gridfrc_grid(), GRIDFORCEGRIDTAG, molecule, NAMD_bug(), GridforceGrid::pack_grid(), Molecule::set_gridfrc_grid(), and GridforceGrid::unpack_grid().

1338  {
1339  if (CmiMyRank()) return;
1340  DebugM(4, "reloadGridforceGrid(int) called on node " << CkMyPe() << "\n" << endi);
1341 
1342  GridforceGrid *grid = molecule->get_gridfrc_grid(gridnum);
1343  if (grid == NULL) {
1344  NAMD_bug("Node::reloadGridforceGrid(int):grid not found");
1345  }
1346 
1347  if (CkMyPe()) {
1348  // not node 0 -> receive grid
1349  DebugM(4, "Receiving grid\n");
1350 
1351  delete grid;
1352 
1353  MIStream *msg = CkpvAccess(comm)->newInputStream(0, GRIDFORCEGRIDTAG);
1354  grid = GridforceGrid::unpack_grid(gridnum, msg);
1355  molecule->set_gridfrc_grid(gridnum, grid);
1356  delete msg;
1357  } else {
1358  // node 0 -> send grid
1359  DebugM(4, "Sending grid\n");
1360 
1361  MOStream *msg = CkpvAccess(comm)->newOutputStream(ALLBUTME, GRIDFORCEGRIDTAG, BUFSIZE);
1362  GridforceGrid::pack_grid(grid, msg);
1363  msg->end();
1364  delete msg;
1365  }
1366 #ifdef NODEGROUP_FORCE_REGISTER
1367  if(CkMyPe()==0)
1368  {
1369  CProxy_PatchData cpdata(CkpvAccess(BOCclass_group).patchData);
1370  cpdata.setDeviceKernelUpdateCounter();
1371  }
1372 #endif
1373  DebugM(4, "reloadGridforceGrid(int) finished\n" << endi);
1374 }
GRIDFORCEGRIDTAG
#define GRIDFORCEGRIDTAG
Definition: common.h:183
Molecule::get_gridfrc_grid
GridforceGrid * get_gridfrc_grid(int gridnum) const
Definition: Molecule.h:1368
MOStream::end
void end(void)
Definition: MStream.C:176
GridforceGrid::pack_grid
static void pack_grid(GridforceGrid *grid, MOStream *msg)
Definition: GridForceGrid.C:50
DebugM
#define DebugM(x, y)
Definition: Debug.h:75
endi
std::ostream & endi(std::ostream &s)
Definition: InfoStream.C:54
ALLBUTME
#define ALLBUTME
Definition: Communicate.h:14
NAMD_bug
void NAMD_bug(const char *err_msg)
Definition: common.C:196
BUFSIZE
#define BUFSIZE
Definition: Communicate.h:15
GridforceGrid::unpack_grid
static GridforceGrid * unpack_grid(int gridnum, MIStream *msg)
Definition: GridForceGrid.C:60
Molecule::set_gridfrc_grid
int set_gridfrc_grid(int gridnum, GridforceGrid *grid)
Definition: Molecule.h:1377
Node::molecule
Molecule * molecule
Definition: Node.h:179

◆ reloadStructure()

void Node::reloadStructure ( const char *  fname,
const char *  pdbname 
)

Definition at line 1071 of file Node.C.

References NamdState::loadStructure(), molecule, pdb, and state.

1071  {
1072  delete molecule;
1073  molecule = state->molecule = 0;
1074  delete pdb;
1075  pdb = state->pdb = 0;
1076  state->loadStructure(fname,pdbname,1);
1077  this->molecule = state->molecule;
1078  this->pdb = state->pdb;
1079  CProxy_Node nodeProxy(thisgroup);
1080  nodeProxy.resendMolecule();
1081 }
NamdState::loadStructure
int loadStructure(const char *, const char *, int)
Definition: NamdState.C:165
Node::state
NamdState * state
Definition: Node.h:184
Node::pdb
PDB * pdb
Definition: Node.h:183
Node::molecule
Molecule * molecule
Definition: Node.h:179

◆ resendMolecule()

void Node::resendMolecule ( )

Definition at line 1084 of file Node.C.

References ALLBUTME, BUFSIZE, molecule, MOLECULETAG, node_molecule, node_parameters, SimParameters::nonbonded_select(), Molecule::numAtoms, parameters, SimParameters::pme_select(), SimParameters::PMEOn, Molecule::receive_Molecule(), Parameters::receive_Parameters(), Molecule::send_Molecule(), Parameters::send_Parameters(), simParameters, and STATICPARAMSTAG.

1084  {
1085  if ( CmiMyRank() ) {
1086  return;
1087  }
1088  if ( CmiMyPe() == 0 ) {
1089  int bufSize = BUFSIZE;
1090  MOStream *conv_msg;
1091  conv_msg = CkpvAccess(comm)->newOutputStream(ALLBUTME, STATICPARAMSTAG, bufSize);
1092  parameters->send_Parameters(conv_msg);
1093  if(molecule->numAtoms>=1000000) bufSize = 16*BUFSIZE;
1094  conv_msg = CkpvAccess(comm)->newOutputStream(ALLBUTME, MOLECULETAG, bufSize);
1095  molecule->send_Molecule(conv_msg);
1096  } else {
1097  MIStream *conv_msg;
1098  delete parameters;
1099  parameters = new Parameters;
1100  conv_msg = CkpvAccess(comm)->newInputStream(0, STATICPARAMSTAG);
1101  parameters->receive_Parameters(conv_msg);
1102  delete molecule;
1103  molecule = new Molecule(simParameters,parameters);
1104  conv_msg = CkpvAccess(comm)->newInputStream(0, MOLECULETAG);
1105  molecule->receive_Molecule(conv_msg);
1106  }
1107  node_parameters = parameters;
1108  node_molecule = molecule;
1109  SimParameters::nonbonded_select();
1110  if ( simParameters->PMEOn ) SimParameters::pme_select();
1111  CProxy_Node nodeProxy(thisgroup);
1112  for ( int i=0; i<CmiMyNodeSize(); ++i ) {
1113  nodeProxy[CmiMyPe()+i].resendMolecule2();
1114  }
1115 }
Molecule::send_Molecule
void send_Molecule(MOStream *)
Definition: Molecule.C:5665
Node::simParameters
SimParameters * simParameters
Definition: Node.h:181
ALLBUTME
#define ALLBUTME
Definition: Communicate.h:14
STATICPARAMSTAG
#define STATICPARAMSTAG
Definition: common.h:178
node_molecule
Molecule * node_molecule
Definition: Node.C:439
Molecule
Molecule stores the structural information for the system.
Definition: Molecule.h:174
SimParameters::pme_select
static void pme_select()
Definition: SimParameters.C:477
Molecule::numAtoms
int numAtoms
Definition: Molecule.h:586
BUFSIZE
#define BUFSIZE
Definition: Communicate.h:15
SimParameters::nonbonded_select
static void nonbonded_select()
Definition: SimParameters.C:473
Parameters::send_Parameters
void send_Parameters(MOStream *)
Definition: Parameters.C:6560
Node::parameters
Parameters * parameters
Definition: Node.h:180
node_parameters
Parameters * node_parameters
Definition: Node.C:438
MOLECULETAG
#define MOLECULETAG
Definition: common.h:179
Molecule::receive_Molecule
void receive_Molecule(MIStream *)
Definition: Molecule.C:6031
Node::molecule
Molecule * molecule
Definition: Node.h:179
Parameters::receive_Parameters
void receive_Parameters(MIStream *)
Definition: Parameters.C:6936

◆ resendMolecule2()

void Node::resendMolecule2 ( )

Definition at line 1117 of file Node.C.

References AtomMap::allocateMap(), molecule, node_molecule, node_parameters, Molecule::numAtoms, AtomMap::Object(), and parameters.

1117  {
1118  parameters = node_parameters;
1119  molecule = node_molecule;
1120  AtomMap::Object()->allocateMap(molecule->numAtoms);
1121 }
AtomMap::allocateMap
void allocateMap(int nAtomIDs)
Definition: AtomMap.C:161
node_molecule
Molecule * node_molecule
Definition: Node.C:439
Molecule::numAtoms
int numAtoms
Definition: Molecule.h:586
AtomMap::Object
static AtomMap * Object()
Definition: AtomMap.h:37
Node::parameters
Parameters * parameters
Definition: Node.h:180
node_parameters
Parameters * node_parameters
Definition: Node.C:438
Node::molecule
Molecule * molecule
Definition: Node.h:179

◆ resumeAfterPapiMeasureBarrier()

void Node::resumeAfterPapiMeasureBarrier ( CkReductionMsg *  msg)

Definition at line 1577 of file Node.C.

References curMFlopStep, simParameters, and state.

1577  {
1578 #ifdef MEASURE_NAMD_WITH_PAPI
1579 
1580  if(simParameters->papiMeasureStartStep != curMFlopStep) {
1581  double *results = (double *)msg->getData();
1582  double endtime=CmiWallTimer();
1583  int bstep = simParameters->papiMeasureStartStep;
1584  int estep = bstep + simParameters->numPapiMeasureSteps;
1585 #if MEASURE_PAPI_SPP
1586  CkPrintf("SPP INFO: PAPI_FP_OPS timestep %d to %d is %lf(1e6)\n", bstep,estep,results[0]);
1587  CkPrintf("SPP INFO: PAPI_TOT_INS timestep %d to %d is %lf(1e6)\n", bstep,estep,results[1]);
1588  CkPrintf("SPP INFO: perf::PERF_COUNT_HW_CACHE_LL:MISS timestep %d to %d is %lf(1e6)\n", bstep,estep,results[2]);
1589  CkPrintf("SPP INFO: DATA_PREFETCHER:ALL timestep %d to %d is %lf(1e6)\n", bstep,estep,results[3]);
1590  CkPrintf("SPP INFO: PAPI_L1_DCA timestep %d to %d is %lf(1e6)\n", bstep,estep,results[4]);
1591  CkPrintf("SPP INFO: PAPI_TOT_CYC timestep %d to % is %lf(1e6)\n", bstep,estep,results[5]);
1592  // CkPrintf("SPP INFO: INSTRUCTION_FETCH_STALL timestep %d to %d is %lf(1e6)\n", bstep,estep,results[6]);
1593  // CkPrintf("SPP INFO: WALLtime timestep %d to %d is %lf\n", bstep,estep,endtime-results[NUM_PAPI_EVENTS]/CkNumPes());
1594  CkPrintf("SPP INFO: WALLtime timestep %d to %d is %lf\n", bstep,estep,endtime-results[NUM_PAPI_EVENTS]);
1595  CkPrintf("SPP INFO: endtime %lf avgtime %lf tottime %lf\n", endtime,results[NUM_PAPI_EVENTS]/CkNumPes(),results[NUM_PAPI_EVENTS] );
1596 #else
1597  if(CkpvAccess(papiEvents)[0] == PAPI_FP_INS){
1598  double totalFPIns = results[0];
1599  if(CkpvAccess(papiEvents)[1] == PAPI_FMA_INS) totalFPIns += (results[1]*2);
1600  CkPrintf("FLOPS INFO: from timestep %d to %d, the total FP instruction of NAMD is %lf(x1e6) per processor\n",
1601  bstep, estep, totalFPIns/CkNumPes());
1602  }else{
1603  char nameBuf[PAPI_MAX_STR_LEN];
1604  CkPrintf("PAPI COUNTERS INFO: from timestep %d to %d, ",
1605  bstep, estep);
1606  for(int i=0; i<NUM_PAPI_EVENTS; i++) {
1607  PAPI_event_code_to_name(CkpvAccess(papiEvents)[i], nameBuf);
1608  CkPrintf("%s is %lf(x1e6), ", nameBuf, results[i]/CkNumPes());
1609  }
1610  CkPrintf("per processor\n");
1611  }
1612 #endif
1613  }
1614  delete msg;
1615  state->controller->resumeAfterPapiMeasureBarrier(curMFlopStep);
1616 #endif
1617 }
Node::simParameters
SimParameters * simParameters
Definition: Node.h:181
Node::curMFlopStep
int curMFlopStep
Definition: Node.h:157
Node::state
NamdState * state
Definition: Node.h:184

◆ resumeAfterTraceBarrier()

void Node::resumeAfterTraceBarrier ( CkReductionMsg *  msg)

Definition at line 1519 of file Node.C.

References curTimeStep, Controller::resumeAfterTraceBarrier(), and state.

1519  {
1520  CmiAssert(CmiMyPe()==0);
1521  delete msg;
1522  state->controller->resumeAfterTraceBarrier(curTimeStep);
1523 }
Node::curTimeStep
int curTimeStep
Definition: Node.h:152
Node::state
NamdState * state
Definition: Node.h:184
Controller::resumeAfterTraceBarrier
void resumeAfterTraceBarrier(int)
Definition: Controller.C:5016

◆ run()

void Node::run ( void  )

Definition at line 1176 of file Node.C.

References ResizeArrayIter< T >::begin(), DebugM, ResizeArrayIter< T >::end(), endi(), PatchMap::homePatchList(), iINFO(), iout, memusage_MB(), PatchMap::Object(), NamdState::runController(), HomePatch::runSequencer(), startupTime, and state.

Referenced by messageRun().

1177 {
1178 // NAMD_EVENT_START(1, NamdProfileEvent::NODE_RUN);
1179 
1180  // Start Controller (aka scalar Sequencer) on Pe(0)
1181 // printf("\n\n I am in Node.C in run method about to call state->runController\n\n");
1182  if ( ! CkMyPe() ) {
1183  state->runController();
1184  }
1185 
1186  DebugM(4, "Starting Sequencers\n");
1187  // Run Sequencer on each HomePatch - i.e. start simulation
1188  HomePatchList *hpl = PatchMap::Object()->homePatchList();
1189  ResizeArrayIter<HomePatchElem> ai(*hpl);
1190  for (ai=ai.begin(); ai != ai.end(); ai++) {
1191  HomePatch *patch = (*ai).patch;
1192 //CkPrintf("Proc#%d in Node calling Sequencer ",CkMyPe());
1193  patch->runSequencer();
1194  }
1195 
1196  if (!CkMyPe()) {
1197  double newTime = CmiWallTimer();
1198  iout << iINFO << "Startup phase " << startupPhase-1 << " took "
1199  << newTime - startupTime << " s, "
1200  << memusage_MB() << " MB of memory in use\n";
1201  iout << iINFO << "Finished startup at " << newTime << " s, "
1202  << memusage_MB() << " MB of memory in use\n\n" << endi;
1203  fflush(stdout);
1204  }
1205 
1206 // NAMD_EVENT_STOP(1, NamdProfileEvent::NODE_RUN);
1207 }
iINFO
std::ostream & iINFO(std::ostream &s)
Definition: InfoStream.C:81
HomePatch::runSequencer
void runSequencer(void)
Definition: HomePatch.C:305
PatchMap::Object
static PatchMap * Object()
Definition: PatchMap.h:27
DebugM
#define DebugM(x, y)
Definition: Debug.h:75
startupTime
double startupTime
Definition: Node.C:300
PatchMap::homePatchList
HomePatchList * homePatchList()
Definition: PatchMap.C:438
endi
std::ostream & endi(std::ostream &s)
Definition: InfoStream.C:54
iout
#define iout
Definition: InfoStream.h:51
NamdState::runController
void runController(void)
Definition: NamdState.C:83
memusage_MB
double memusage_MB()
Definition: memusage.h:13
Node::state
NamdState * state
Definition: Node.h:184

◆ saveMolDataPointers()

void Node::saveMolDataPointers ( NamdState *  state)

Definition at line 1480 of file Node.C.

References configList, molecule, parameters, pdb, simParameters, and state.

1481 {
1482  this->molecule = state->molecule;
1483  this->parameters = state->parameters;
1484  this->simParameters = state->simParameters;
1485  this->configList = state->configList;
1486  this->pdb = state->pdb;
1487  this->state = state;
1488 }
Node::simParameters
SimParameters * simParameters
Definition: Node.h:181
Node::state
NamdState * state
Definition: Node.h:184
Node::pdb
PDB * pdb
Definition: Node.h:183
Node::configList
ConfigList * configList
Definition: Node.h:182
Node::parameters
Parameters * parameters
Definition: Node.h:180
Node::molecule
Molecule * molecule
Definition: Node.h:179

◆ scriptBarrier()

void Node::scriptBarrier ( void  )

Definition at line 1218 of file Node.C.

1218  {
1219  //script->awaken();
1220 }

◆ scriptParam()

void Node::scriptParam ( ScriptParamMsg *  msg)

Definition at line 1222 of file Node.C.

References ScriptParamMsg::param, SimParameters::scriptSet(), simParameters, and ScriptParamMsg::value.

1222  {
1223  simParameters->scriptSet(msg->param,msg->value);
1224  delete msg;
1225 }
Node::simParameters
SimParameters * simParameters
Definition: Node.h:181
SimParameters::scriptSet
void scriptSet(const char *, const char *)
Definition: SimParameters.C:177
ScriptParamMsg::value
char value[MAX_SCRIPT_PARAM_SIZE]
Definition: Node.h:75
ScriptParamMsg::param
char param[MAX_SCRIPT_PARAM_SIZE]
Definition: Node.h:74

◆ sendCheckpointReq()

void Node::sendCheckpointReq ( int  remote,
const char *  key,
int  task,
Lattice &  lat,
ControllerState &  cs 
)

Definition at line 1379 of file Node.C.

References CheckpointMsg::checkpoint, CheckpointMsg::key, Controller::checkpoint::lattice, CheckpointMsg::replica, Controller::checkpoint::state, and CheckpointMsg::task.

Referenced by Controller::algorithm().

1379  {
1380  CheckpointMsg *msg = new (1+strlen(key),0) CheckpointMsg;
1381  msg->replica = CmiMyPartition();
1382  msg->task = task;
1383  msg->checkpoint.lattice = lat;
1384  msg->checkpoint.state = cs;
1385  strcpy(msg->key,key);
1386  envelope *env = UsrToEnv(CheckpointMsg::pack(msg));
1387  CmiSetHandler(env,recvCheckpointCReq_index);
1388 #if CMK_HAS_PARTITION
1389  CmiInterSyncSendAndFree(CkMyPe(),remote,env->getTotalsize(),(char*)env);
1390 #else
1391  CmiSyncSendAndFree(CkMyPe(),env->getTotalsize(),(char*)env);
1392 #endif
1393 }
Controller::checkpoint::state
ControllerState state
Definition: Controller.h:388
CheckpointMsg::task
int task
Definition: Node.C:100
CheckpointMsg::replica
int replica
Definition: Node.C:101
CheckpointMsg::checkpoint
Controller::checkpoint checkpoint
Definition: Node.C:102
CheckpointMsg::key
char * key
Definition: Node.C:103

◆ sendEnableEarlyExit()

void Node::sendEnableEarlyExit ( void  )

Definition at line 1455 of file Node.C.

Referenced by enableEarlyExit().

1455  {
1456  CProxy_Node nodeProxy(thisgroup);
1457  nodeProxy[0].recvEnableEarlyExit();
1458 }

◆ sendEnableExitScheduler()

void Node::sendEnableExitScheduler ( void  )

Definition at line 1431 of file Node.C.

Referenced by enableExitScheduler().

1431  {
1432  //CmiPrintf("sendEnableExitScheduler\n");
1433  CProxy_Node nodeProxy(thisgroup);
1434  nodeProxy[0].recvEnableExitScheduler();
1435 }

◆ setScript()

void Node::setScript ( ScriptTcl *  s)
inline

Definition at line 194 of file Node.h.

Referenced by after_backend_init().

194 { script = s; }

◆ startHPM()

void Node::startHPM ( )

Definition at line 1491 of file Node.C.

1491  {
1492 #if USE_HPM
1493  HPM_Start("500 steps", localRankOnNode);
1494 #endif
1495 }

◆ startup()

void Node::startup ( )

Definition at line 465 of file Node.C.

References Lattice::a_p(), AtomMap::allocateMap(), WorkDistrib::assignNodeToPatch(), Lattice::b_p(), ProxyMgr::buildProxySpanningTree(), Lattice::c_p(), computeMap, computeMgr, ComputeMgr::createComputes(), WorkDistrib::createHomePatches(), LdbCoordinator::createLoadBalancer(), ProxyMgr::createProxies(), SimParameters::CUDASOAintegrate, SimParameters::dcdSelectionOn, DebugM, WorkDistrib::distributeHomePatches(), endi(), BackEnd::exit(), PDB::get_extremes(), ProxyMgr::getRecvSpanning(), ProxyMgr::getSendSpanning(), iINFO(), SynchronousCollectives::initAllScope(), LdbCoordinator::initialize(), initializeGPUResident(), iout, SimParameters::isRecvSpanningTreeOn(), SimParameters::isSendSpanningTreeOn(), SimParameters::lattice, SimParameters::mallocTest, mallocTest_size, WorkDistrib::mapComputes(), memusage_MB(), messageRun(), molecule, SimParameters::MSMOn, SimParameters::MsmSerialOn, NAMD_bug(), NAMD_EVENT_START, NAMD_EVENT_STOP, node_molecule, node_parameters, node_simParameters, SimParameters::nonbonded_select(), Molecule::numAtoms, ComputeMap::numComputes(), PatchMap::Object(), AtomMap::Object(), Sync::Object(), SynchronousCollectives::Object(), ComputeMap::Object(), LdbCoordinator::Object(), ProxyMgr::Object(), Sync::openSync(), output, outputPatchComputeMaps(), parameters, WorkDistrib::patchMapInit(), pdb, SimParameters::pme_select(), SimParameters::PMEOn, PRIORITY_SIZE, proxyRecvSpanning, proxySendSpanning, SimParameters::proxyTreeBranchFactor, rand, SimParameters::randomSeed, registerUserEventsForAllComputeObjs(), WorkDistrib::sendComputeMap(), WorkDistrib::sendPatchMap(), SEQ_STK_SZ, WorkDistrib::setPatchMapArrived(), ProxyMgr::setProxyTreeBranchFactor(), ProxyMgr::setRecvSpanning(), ProxyMgr::setSendSpanning(), simParameters, SimParameters::simulatedNodeSize, SimParameters::simulatedPEs, SimParameters::simulateInitialMapping, MsmInitMsg::smax, MsmInitMsg::smin, Random::split(), startupTime, SimParameters::useCkLoop, SimParameters::usePMECUDA, and workDistrib.

Referenced by messageStartUp().

465  {
466  NAMD_EVENT_START(1, NamdProfileEvent::NAMD_STARTUP);
467 
468  int gotoRun = false;
469  double newTime;
470 
471  if (!CkMyPe()) {
472  if (!startupPhase) {
473  iout << iINFO << "\n";
474  startupTime = CmiWallTimer();
475  iout << iINFO << "Entering startup at " << startupTime << " s, ";
476  } else {
477  newTime = CmiWallTimer();
478  iout << iINFO << "Startup phase " << startupPhase-1 << " took "
479  << newTime - startupTime << " s, ";
480  startupTime = newTime;
481  }
482  iout << memusage_MB() << " MB of memory in use\n" << endi;
483  fflush(stdout);
484  }
485  switch (startupPhase) {
486 
487  case 0:
488  computeMap = ComputeMap::Object();
489  namdOneCommInit(); // Namd1.X style
490  break;
491 
492  case 1:
493  bindBocVars();
494 
495  // send & receive molecule, simparameters... (Namd1.X style)
496  if (CkMyPe()) {
497  namdOneRecv();
498  } else {
499  namdOneSend();
500  }
501  break;
502 
503  case 2:
504  // fix up one-per-node objects (for SMP version)
505  simParameters = node_simParameters;
506  parameters = node_parameters;
507  molecule = node_molecule;
508 
509  SimParameters::nonbonded_select();
510  if ( simParameters->PMEOn ) SimParameters::pme_select();
511 
512  #if !CMK_SMP || ! USE_CKLOOP
513  //the CkLoop library should be only used in SMP mode
514  simParameters->useCkLoop = 0;
515  #else
516  if ( CkNumPes() < 2 * CkNumNodes() ) simParameters->useCkLoop = 0;
517  #endif
518 
519 
520  if ( simParameters->mallocTest ) {
521  if (!CkMyPe()) {
522  mallocTest_size = 0;
523  CkStartQD(CkIndex_Node::mallocTestQd(), &thishandle);
524  }
525  return;
526  }
527 
528 
529  #ifdef MEASURE_NAMD_WITH_PAPI
530  if(simParameters->papiMeasure) namdInitPapiCounters();
531  #endif
532 
533  #ifdef MEM_OPT_VERSION
534  //At this point, each Node object has received the simParameters,
535  //parameters and the atom signatures info from the master Node
536  //(proc 0). It's time to initialize the parallel IO manager and
537  //read the binary per-atom file --Chao Mei
538 
539  //Step 1: initialize the parallel IO manager per Node
540  ioMgr->initialize(this);
541  #endif
542 
543  break;
544 
545  case 3:
546 
547  #ifdef MEM_OPT_VERSION
548  //Step 2: read the binary per-atom files (signater index, coordinates etc.)
549  ioMgr->readPerAtomInfo();
550  if(simParameters->dcdSelectionOn)
551  if(!CkMyPe())
552  ioMgr->sendDcdParams();
553  #endif
554 
555  break;
556 
557  case 4:
558 
559  #ifdef MEM_OPT_VERSION
560  //Step 3: update counters of tuples and exclusions inside Molecule object
561  ioMgr->updateMolInfo();
562 
563  //Step 4: prepare distributing the atoms to neighboring procs if necessary
564  ioMgr->migrateAtomsMGrp();
565 
566  //step 5: initialize patchMap and send it to every other processors
567  //to decide atoms to patch distribution on every input processor
568  if(!CkMyPe()) {
569  workDistrib->patchMapInit(); // create space division
570  workDistrib->sendPatchMap();
571  }
572  #endif
573 
574  #if USE_HPM
575  HPM_Init(localRankOnNode);
576  #endif
577 
578  // take care of inital thread setting
579  threadInit();
580 
581  // create blank AtomMap
582  AtomMap::Object()->allocateMap(molecule->numAtoms);
583 
584  if (!CkMyPe()) {
585 #if defined(NAMD_CUDA) || defined(NAMD_HIP)
586  if (simParameters->usePMECUDA) {
587  // computePmeCUDAMgr was created in BackEnd.C
588  // This empty branch is to avoid initializing ComputePmeMgr
589  } else
590 #endif
591  if (simParameters->PMEOn) {
592  CkpvAccess(BOCclass_group).computePmeMgr = CProxy_ComputePmeMgr::ckNew();
593  }
594  #ifdef OPENATOM_VERSION
595  if ( simParameters->openatomOn ) {
596  CkpvAccess(BOCclass_group).computeMoaMgr = CProxy_ComputeMoaMgr::ckNew();
597  }
598  #endif // OPENATOM_VERSION
599 
600  }
601 
602  #ifdef OPENATOM_VERSION
603  if ( simParameters->openatomOn ) {
604  // if ( ! CkMyPe() ) {
605  CkCallback doneMoaStart(CkIndexmain::doneMoaSetup(), thishandle);
606  startOA(simParameters->moaDriverFile, simParameters->moaPhysicsFile, doneMoaStart);
607  // }
608  }
609  #endif // OPENATOM_VERSION
610 
611  // BEGIN LA
612  rand = new Random(simParameters->randomSeed);
613  rand->split(CkMyPe(), CkNumPes());
614  // END LA
615 
616  break;
617 
618  case 5:
619  #ifdef MEM_OPT_VERSION
620  //Now, every input proc has received all the atoms necessary
621  //to decide the patches those atoms belong to
622 
623  //step 1: integrate the migrated atoms into the atom list that
624  //contains the initally distributed atoms, and sort the atoms
625  //based on hydrogenList value
626  ioMgr->integrateMigratedAtoms();
627 
628  //step 2: integrate the cluster size of each atom on each output proc
629  ioMgr->integrateClusterSize();
630 
631  //step 3: calculate the number of atoms in each patch on every
632  //input procs (atoms belonging to a patch may lie on different
633  //procs), and reduce such info on proc 0. Such info is required
634  //for determing which node a particular patch is assigned to.
635  ioMgr->calcAtomsInEachPatch();
636 
637  //set to false to re-send PatchMap later
638  workDistrib->setPatchMapArrived(false);
639  #endif
640  break;
641  case 6:
642  if(simParameters->isSendSpanningTreeOn()) {
643  ProxyMgr::Object()->setSendSpanning();
644  }
645  if(simParameters->isRecvSpanningTreeOn()) {
646  ProxyMgr::Object()->setRecvSpanning();
647  }
648  if(simParameters->proxyTreeBranchFactor) {
649  ProxyMgr::Object()->setProxyTreeBranchFactor(simParameters->proxyTreeBranchFactor);
650  }
651  #ifdef PROCTRACE_DEBUG
652  DebugFileTrace::Instance("procTrace");
653  #endif
654 
655  if (!CkMyPe()) {
656  output = new Output; // create output object just on PE(0)
657 
658  #ifndef MEM_OPT_VERSION
659  workDistrib->patchMapInit(); // create space division
660  workDistrib->createHomePatches(); // load atoms into HomePatch(es)
661  #endif
662 
663  workDistrib->assignNodeToPatch();
664  workDistrib->mapComputes();
665  //ComputeMap::Object()->printComputeMap();
666 
667  // For MIC runs, take the additional step after the compute map has been created to
668  // assign the various computes to either the host or the device. This info will
669  // be distributed across the PEs.
670  #if defined(NAMD_MIC)
671  mic_initHostDeviceLDB();
672  #endif
673 
674  if(simParameters->simulateInitialMapping) {
675  iout << iINFO << "Simulating initial mapping with " << simParameters->simulatedPEs
676  << " PEs with " << simParameters->simulatedNodeSize << " PEs per node\n" << endi;
677  outputPatchComputeMaps("init_mapping", 0);
678  iout << iINFO << "Simulating initial mapping is done, now NAMD exits\n" << endi;
679  BackEnd::exit();
680  }
681 
682  registerUserEventsForAllComputeObjs();
683 
684  //in MEM_OPT_VERSION, patchMap is resent
685  //because they have been updated since creation including
686  //#atoms per patch, the proc a patch should stay etc. --Chao Mei
687  workDistrib->sendPatchMap();
688  #if defined(NODEAWARE_PROXY_SPANNINGTREE) && defined(USE_NODEPATCHMGR)
689  CProxy_NodeProxyMgr npm(CkpvAccess(BOCclass_group).nodeProxyMgr);
690  //a node broadcast
691  npm.createProxyInfo(PatchMap::Object()->numPatches());
692  #endif
693  }
694  {
695  #if defined(NODEAWARE_PROXY_SPANNINGTREE) && defined(USE_NODEPATCHMGR)
696  CProxy_NodeProxyMgr npm(CkpvAccess(BOCclass_group).nodeProxyMgr);
697  if(CkMyRank()==0) {
698  //just need to register once
699  npm[CkMyNode()].ckLocalBranch()->registerLocalProxyMgr(CkpvAccess(BOCclass_group).proxyMgr);
700  }
701  npm[CkMyNode()].ckLocalBranch()->registerLocalPatchMap(CkMyRank(), PatchMap::Object());
702  #endif
703  }
704  break;
705 
706  case 7:
707 #ifdef CHARM_HAS_MSA
708  if ( simParameters->MSMOn && ! simParameters->MsmSerialOn ) {
709  CProxy_ComputeMsmMsaMgr msm(CkpvAccess(BOCclass_group).computeMsmMsaMgr);
710  msm[CkMyPe()].initialize(new CkQdMsg);
711  }
712 #else
713  if ( simParameters->MSMOn && ! simParameters->MsmSerialOn ) {
714  CProxy_ComputeMsmMgr msm(CkpvAccess(BOCclass_group).computeMsmMgr);
715  MsmInitMsg *msg = new MsmInitMsg;
716  Lattice lattice = simParameters->lattice; // system lattice vectors
717  ScaledPosition smin=0, smax=0;
718  if (lattice.a_p() && lattice.b_p() && lattice.c_p()) {
719  msg->smin = smin;
720  msg->smax = smax;
721  msm[CkMyPe()].initialize(msg); // call from my own PE
722  }
723  else if ( ! CkMyPe() ) {
724  pdb->get_extremes(smin, smax); // only available on PE 0
725  msg->smin = smin;
726  msg->smax = smax;
727  msm.initialize(msg); // broadcast to chare group
728  }
729 
730  /*
731  CProxy_Node nd(CkpvAccess(BOCclass_group).node);
732  Node *node = nd.ckLocalBranch();
733  ScaledPosition smin, smax;
734  node->pdb->get_extremes(smin, smax);
735  msg->smin = smin; // extreme positions in system
736  msg->smax = smax;
737  msm[CkMyPe()].initialize(msg);
738  */
739  }
740 #endif
741 
742  if ( simParameters->PMEOn ) {
743  #ifdef OPENATOM_VERSION
744  if ( simParameters->openatomOn ) {
745  CProxy_ComputeMoaMgr moa(CkpvAccess(BOCclass_group).computeMoaMgr);
746  moa[CkMyPe()].initialize(new CkQdMsg);
747  }
748  #endif // OPENATOM_VERSION
749 #if defined(NAMD_CUDA) || defined(NAMD_HIP)
750  if ( simParameters->usePMECUDA ) {
751  if(CkMyRank()==0) {
752  CProxy_ComputePmeCUDAMgr pme(CkpvAccess(BOCclass_group).computePmeCUDAMgr);
753  pme.ckLocalBranch()->initialize(new CkQdMsg); // must run on pe 0 to call ckNew
754  }
755  } else
756 #endif
757  {
758  CProxy_ComputePmeMgr pme(CkpvAccess(BOCclass_group).computePmeMgr);
759  pme[CkMyPe()].initialize(new CkQdMsg);
760  }
761  }
762  break;
763 
764  case 8:
765 #if defined(NAMD_CUDA) || defined(NAMD_HIP)
766  if ( CkMyRank()==0 ) {
767  CProxy_ComputeCUDAMgr nb(CkpvAccess(BOCclass_group).computeCUDAMgr);
768  nb.ckLocalBranch()->initialize(new CkQdMsg);
769  }
770 #endif
771  break;
772 
773  case 9:
774  workDistrib->sendComputeMap();
775  break;
776 
777  case 10:
778  #ifdef MEM_OPT_VERSION
779  //migrate atoms to HomePatch processors
780  ioMgr->sendAtomsToHomePatchProcs();
781  #endif
782  break;
783 
784  case 11:
785  // part 2 of MSM init
786  if ( simParameters->MSMOn && ! simParameters->MsmSerialOn ) {
787  CProxy_ComputeMsmMgr msm(CkpvAccess(BOCclass_group).computeMsmMgr);
788  msm[CkMyPe()].initialize_create(); // call from my own PE
789  }
790 
791  if ( simParameters->PMEOn ) {
792  #ifdef OPENATOM_VERSION
793  if ( simParameters->openatomOn ) {
794  CProxy_ComputeMoaMgr moa(CkpvAccess(BOCclass_group).computeMoaMgr);
795  moa[CkMyPe()].initWorkers(new CkQdMsg);
796  }
797  #endif // OPENATOM_VERSION
798 #if defined(NAMD_CUDA) || defined(NAMD_HIP)
799  if ( simParameters->usePMECUDA ) {
800  if(CkMyRank()==0) {
801  CProxy_ComputePmeCUDAMgr pme(CkpvAccess(BOCclass_group).computePmeCUDAMgr);
802  pme[CkMyNode()].initialize_pencils(new CkQdMsg);
803  }
804  } else
805 #endif
806  {
807  CProxy_ComputePmeMgr pme(CkpvAccess(BOCclass_group).computePmeMgr);
808  pme[CkMyPe()].initialize_pencils(new CkQdMsg);
809  }
810  }
811 #ifdef CHARM_HAS_MSA
812  else if ( simParameters->MSMOn && ! simParameters->MsmSerialOn ) {
813  CProxy_ComputeMsmMsaMgr msm(CkpvAccess(BOCclass_group).computeMsmMsaMgr);
814  msm[CkMyPe()].initWorkers(new CkQdMsg);
815  }
816 #else
817  else if ( simParameters->MSMOn && ! simParameters->MsmSerialOn ) {
818  CProxy_ComputeMsmMgr msm(CkpvAccess(BOCclass_group).computeMsmMgr);
819  msm[CkMyPe()].update(new CkQdMsg);
820  }
821 #endif
822 
823  #ifdef MEM_OPT_VERSION
824  //Now every processor has all the atoms it needs to create the HomePatches.
825  //The HomePatches are created in parallel on every home patch procs.
826  ioMgr->createHomePatches();
827  #else
828  if (!CkMyPe()) {
829  workDistrib->distributeHomePatches();
830  }
831  #endif
832  break;
833 
834  case 12:
835  if ( simParameters->PMEOn ) {
836  #ifdef OPENATOM_VERSION
837  if ( simParameters->openatomOn ) {
838  CProxy_ComputeMoaMgr moa(CkpvAccess(BOCclass_group).computeMoaMgr);
839  moa[CkMyPe()].startWorkers(new CkQdMsg);
840  }
841  #endif // OPENATOM_VERSION
842 #if defined(NAMD_CUDA) || defined(NAMD_HIP)
843  if ( simParameters->usePMECUDA ) {
844  if(CkMyRank()==0) {
845  CProxy_ComputePmeCUDAMgr pme(CkpvAccess(BOCclass_group).computePmeCUDAMgr);
846  pme[CkMyNode()].activate_pencils(new CkQdMsg);
847  }
848  } else
849 #endif
850  {
851  CProxy_ComputePmeMgr pme(CkpvAccess(BOCclass_group).computePmeMgr);
852  pme[CkMyPe()].activate_pencils(new CkQdMsg);
853  }
854  }
855 #ifdef CHARM_HAS_MSA
856  else if ( simParameters->MSMOn && ! simParameters->MsmSerialOn ) {
857  CProxy_ComputeMsmMsaMgr msm(CkpvAccess(BOCclass_group).computeMsmMsaMgr);
858  msm[CkMyPe()].startWorkers(new CkQdMsg);
859  }
860 #else
861  /*
862  else if ( simParameters->MSMOn && ! simParameters->MsmSerialOn ) {
863  CProxy_ComputeMsmMgr msm(CkpvAccess(BOCclass_group).computeMsmMgr);
864  //msm[CkMyPe()].startWorkers(new CkQdMsg);
865  }
866  */
867 #endif
868 
869  proxyMgr->createProxies(); // need Home patches before this
870  if (!CkMyPe()) LdbCoordinator::Object()->createLoadBalancer();
871 
872 #ifdef NAMD_TCL
873  // TclInitSubsystems() has a race condition so we create one interp per node here
874  if (CkMyPe() && CkMyNodeSize() > 1 && ! CkMyRank()) Tcl_DeleteInterp(Tcl_CreateInterp());
875 #endif
876 
877 #ifdef USE_NODEPATCHMGR
878  //at this point, PatchMap info has been recved on PEs. It is time to create
879  //the home patch spanning tree for receiving proxy list info
880  if(proxyMgr->getSendSpanning() || proxyMgr->getRecvSpanning()) {
881  if(CkMyRank()==0) {
882  CProxy_NodeProxyMgr npm(CkpvAccess(BOCclass_group).nodeProxyMgr);
883  npm[CkMyNode()].ckLocalBranch()->createSTForHomePatches(PatchMap::Object());
884  }
885  }
886 #endif
887 
888  break;
889 
890  case 13:
891 #if defined(NAMD_CUDA) || defined(NAMD_HIP)
892  // Initialize the collective synchronization object before the sequencers are created
893  if (simParameters->CUDASOAintegrate) {
894  SynchronousCollectives* syncColl = SynchronousCollectives::Object();
895  syncColl->initAllScope();
896  // Sync between all PEs so that expectedBarrierAll and currentBarrierAll are set
897  }
898 #endif
899  break;
900 
901  case 14:
902 #if defined(NAMD_CUDA) || defined(NAMD_HIP)
903  if (simParameters->CUDASOAintegrate) {
904  gpuResInitThread = CthCreate((CthVoidFn) &(initializeGPUResident), nullptr, SEQ_STK_SZ);
905  gpuResInitThreadPriority = 0;
906  CthSetStrategyDefault(gpuResInitThread);
907  CthAwakenPrio(gpuResInitThread, CK_QUEUEING_IFIFO, PRIORITY_SIZE, &gpuResInitThreadPriority);
908  CthSuspend();
909  }
910 #endif
911  break;
912 
913  case 15:
914  // Make sure that the GPU resident initialization threads have finished
915  break;
916 
917  case 16:
918 
919  // DMK - DEBUG - If, in MIC runs, the debug option to dump all the compute maps to files
920  // for debugging/verification purposes has been enabled, have each PE do so now.
921  #if defined(NAMD_MIC)
922  mic_dumpHostDeviceComputeMap();
923  #endif
924 
925  if (!CkMyPe()) {
926  iout << iINFO << "CREATING " << ComputeMap::Object()->numComputes()
927  << " COMPUTE OBJECTS\n" << endi;
928  }
929  DebugM(4,"Creating Computes\n");
930  computeMgr->createComputes(ComputeMap::Object());
931  DebugM(4,"Building Sequencers\n");
932  buildSequencers();
933  DebugM(4,"Initializing LDB\n");
934  LdbCoordinator::Object()->initialize(PatchMap::Object(),ComputeMap::Object());
935  break;
936 
937  case 17:
938  // computes may create proxies on the fly so put these in separate phase
939  Sync::Object()->openSync(); // decide if to open local Sync
940  if (proxySendSpanning || proxyRecvSpanning ) proxyMgr->buildProxySpanningTree();
941 #if defined(CMK_BALANCED_INJECTION_API) && CMK_BALANCED_INJECTION_API != 0
942  if(CkMyRank() == 0){
943  // CkPrintf("[%d] get retrieved BI=%d\n",CkMyPe(),balancedInjectionLevel);
944  ck_set_GNI_BIConfig(balancedInjectionLevel);
945  // CkPrintf("[%d] set retrieved BI=%d\n",CkMyPe(),ck_get_GNI_BIConfig());
946  }
947 #endif
948 
949  break;
950 
951  case 18:
952  {
953  //For debugging
954  /*if(!CkMyPe()){
955  FILE *dumpFile = fopen("/tmp/NAMD_Bench.dump", "w");
956  dumpbench(dumpFile);
957  NAMD_die("Normal execution\n");
958  }*/
959  }
960  #ifdef MEM_OPT_VERSION
961  if(simParameters->dcdSelectionOn)
962  ioMgr->readInfoForParOutDcdSelection();
963  //free space in the Molecule object that are not used anymore
964  ioMgr->freeMolSpace();
965  #endif
966  gotoRun = true;
967  break;
968 
969  default:
970  NAMD_bug("Startup Phase has a bug - check case statement");
971  break;
972 
973  }
974 
975  startupPhase++;
976  if (!CkMyPe()) {
977  if (!gotoRun) {
978  CkStartQD(CkCallback(CkIndex_Node::startup(), thisgroup));
979  } else {
980  Node::messageRun();
981  }
982  }
983 
984  NAMD_EVENT_STOP(1, NamdProfileEvent::NAMD_STARTUP);
985 }
AtomMap::allocateMap
void allocateMap(int nAtomIDs)
Definition: AtomMap.C:161
NAMD_EVENT_STOP
#define NAMD_EVENT_STOP(eon, id)
Definition: NamdEventsProfiling.h:318
iINFO
std::ostream & iINFO(std::ostream &s)
Definition: InfoStream.C:81
SimParameters::simulateInitialMapping
Bool simulateInitialMapping
Definition: SimParameters.h:232
WorkDistrib::setPatchMapArrived
void setPatchMapArrived(bool s)
Definition: WorkDistrib.h:108
ProxyMgr::createProxies
void createProxies(void)
Definition: ProxyMgr.C:416
ProxyMgr::setRecvSpanning
void setRecvSpanning()
Definition: ProxyMgr.C:370
proxyRecvSpanning
int proxyRecvSpanning
Definition: ProxyMgr.C:45
ComputeMap::numComputes
int numComputes(void)
Definition: ComputeMap.h:103
ProxyMgr::getRecvSpanning
int getRecvSpanning()
Definition: ProxyMgr.C:375
ProxyMgr::Object
static ProxyMgr * Object()
Definition: ProxyMgr.h:394
Lattice::c_p
NAMD_HOST_DEVICE int c_p() const
Definition: Lattice.h:291
PatchMap::Object
static PatchMap * Object()
Definition: PatchMap.h:27
BackEnd::exit
static void exit(int status=0)
Definition: BackEnd.C:284
Vector
Definition: Vector.h:72
Node::output
Output * output
Definition: Node.h:185
Node::simParameters
SimParameters * simParameters
Definition: Node.h:181
ProxyMgr::setSendSpanning
void setSendSpanning()
Definition: ProxyMgr.C:361
DebugM
#define DebugM(x, y)
Definition: Debug.h:75
LdbCoordinator::createLoadBalancer
void createLoadBalancer()
Definition: LdbCoordinator.C:198
startupTime
double startupTime
Definition: Node.C:300
endi
std::ostream & endi(std::ostream &s)
Definition: InfoStream.C:54
ProxyMgr::getSendSpanning
int getSendSpanning()
Definition: ProxyMgr.C:366
initializeGPUResident
void initializeGPUResident()
Definition: Node.C:450
iout
#define iout
Definition: InfoStream.h:51
node_molecule
Molecule * node_molecule
Definition: Node.C:439
Node::outputPatchComputeMaps
void outputPatchComputeMaps(const char *filename, int tag)
Definition: Node.C:1620
ComputeMgr::createComputes
void createComputes(ComputeMap *map)
Definition: ComputeMgr.C:1037
Lattice::b_p
NAMD_HOST_DEVICE int b_p() const
Definition: Lattice.h:290
Random::split
void split(int iStream, int numStreams)
Definition: Random.h:77
WorkDistrib::patchMapInit
void patchMapInit(void)
Definition: WorkDistrib.C:1238
Sync::openSync
void openSync()
Definition: Sync.C:63
Node::computeMap
ComputeMap * computeMap
Definition: Node.h:204
memusage_MB
double memusage_MB()
Definition: memusage.h:13
SEQ_STK_SZ
#define SEQ_STK_SZ
Definition: Thread.h:11
WorkDistrib::sendComputeMap
void sendComputeMap(void)
Definition: WorkDistrib.C:1211
PRIORITY_SIZE
#define PRIORITY_SIZE
Definition: Priorities.h:13
Output
Definition: Output.h:35
LdbCoordinator::initialize
void initialize(PatchMap *pmap, ComputeMap *cmap, int reinit=0)
Definition: LdbCoordinator.C:213
Random
Definition: Random.h:37
NAMD_EVENT_START
#define NAMD_EVENT_START(eon, id)
Definition: NamdEventsProfiling.h:312
ProxyMgr::buildProxySpanningTree
void buildProxySpanningTree()
Definition: ProxyMgr.C:558
WorkDistrib::createHomePatches
void createHomePatches(void)
Definition: WorkDistrib.C:989
NAMD_bug
void NAMD_bug(const char *err_msg)
Definition: common.C:196
MsmInitMsg::smax
ScaledPosition smax
Definition: ComputeMsm.h:21
SimParameters::pme_select
static void pme_select()
Definition: SimParameters.C:477
Node::messageRun
static void messageRun()
Definition: Node.C:1167
Sync::Object
static Sync * Object()
Definition: Sync.h:52
PDB::get_extremes
void get_extremes(ScaledPosition &xmin, ScaledPosition &xmax) const
Definition: PDB.h:104
Lattice::a_p
NAMD_HOST_DEVICE int a_p() const
Definition: Lattice.h:289
Molecule::numAtoms
int numAtoms
Definition: Molecule.h:586
Node::pdb
PDB * pdb
Definition: Node.h:183
LdbCoordinator::Object
static LdbCoordinator * Object()
Definition: LdbCoordinator.h:93
AtomMap::Object
static AtomMap * Object()
Definition: AtomMap.h:37
SimParameters::nonbonded_select
static void nonbonded_select()
Definition: SimParameters.C:473
WorkDistrib::sendPatchMap
void sendPatchMap(void)
Definition: WorkDistrib.C:1111
SimParameters::isRecvSpanningTreeOn
int isRecvSpanningTreeOn()
Definition: SimParameters.h:1229
Node::parameters
Parameters * parameters
Definition: Node.h:180
SimParameters::randomSeed
unsigned int randomSeed
Definition: SimParameters.h:828
Node::workDistrib
WorkDistrib * workDistrib
Definition: Node.h:169
node_parameters
Parameters * node_parameters
Definition: Node.C:438
node_simParameters
SimParameters * node_simParameters
Definition: Node.C:437
Node::rand
Random * rand
Definition: Node.h:175
WorkDistrib::mapComputes
void mapComputes(void)
Definition: WorkDistrib.C:2407
registerUserEventsForAllComputeObjs
void registerUserEventsForAllComputeObjs(void)
Definition: ComputeMgr.C:853
ComputeMap::Object
static ComputeMap * Object()
Definition: ComputeMap.h:91
MsmInitMsg::smin
ScaledPosition smin
Definition: ComputeMsm.h:21
WorkDistrib::distributeHomePatches
void distributeHomePatches(void)
Definition: WorkDistrib.C:1063
ProxyMgr::setProxyTreeBranchFactor
void setProxyTreeBranchFactor(int dim)
Definition: ProxyMgr.C:379
SimParameters::isSendSpanningTreeOn
int isSendSpanningTreeOn()
Definition: SimParameters.h:1227
Node::computeMgr
ComputeMgr * computeMgr
Definition: Node.h:172
Node::mallocTest_size
int mallocTest_size
Definition: Node.h:130
Node::molecule
Molecule * molecule
Definition: Node.h:179
SynchronousCollectives::Object
static SynchronousCollectives * Object()
Definition: SynchronousCollectives.h:63
WorkDistrib::assignNodeToPatch
void assignNodeToPatch(void)
Definition: WorkDistrib.C:1456
proxySendSpanning
int proxySendSpanning
Definition: ProxyMgr.C:44

◆ stopHPM()

void Node::stopHPM ( )

Definition at line 1497 of file Node.C.

1497  {
1498 #if USE_HPM
1499  HPM_Stop("500 steps", localRankOnNode);
1500  HPM_Print(CkMyPe(), localRankOnNode);
1501 #endif
1502 }

◆ traceBarrier()

void Node::traceBarrier ( int  turnOnTrace,
int  step 
)

Definition at line 1504 of file Node.C.

References curTimeStep.

1504  {
1505  curTimeStep = step;
1506  if(turnOnTrace) traceBegin();
1507  else traceEnd();
1508 
1509  if(turnOnTrace) CmiTurnOnStats();
1510  else CmiTurnOffStats();
1511 
1512  //CkPrintf("traceBarrier (%d) at step %d called on proc %d\n", turnOnTrace, step, CkMyPe());
1513  CProxy_Node nd(CkpvAccess(BOCclass_group).node);
1514  CkCallback cb(CkIndex_Node::resumeAfterTraceBarrier(NULL), nd[0]);
1515  contribute(0, NULL, CkReduction::sum_int, cb);
1516 
1517 }
Node::curTimeStep
int curTimeStep
Definition: Node.h:152

◆ updateGridScale() [1/2]

void Node::updateGridScale ( const char *  key,
Vector  scale 
)

Definition at line 1291 of file Node.C.

References DebugM, endi(), MGridforceParamsList::find_key(), Molecule::get_gridfrc_grid(), MGridforceParamsList::index_for_key(), SimParameters::mgridforcelist, MGRIDFORCEPARAMS_DEFAULTKEY, molecule, NAMD_bug(), NAMD_die(), simParameters, Vector::x, Vector::y, and Vector::z.

1291  {
1292  DebugM(4, "updateGridScale(char*, Vector) called on node " << CkMyPe() << "\n" << endi);
1293 
1294  int gridnum;
1295  MGridforceParams* mgridParams;
1296  if (key == NULL) {
1297  gridnum = simParameters->mgridforcelist.index_for_key(MGRIDFORCEPARAMS_DEFAULTKEY);
1298  mgridParams = simParameters->mgridforcelist.find_key(MGRIDFORCEPARAMS_DEFAULTKEY);
1299  } else {
1300  gridnum = simParameters->mgridforcelist.index_for_key(key);
1301  mgridParams = simParameters->mgridforcelist.find_key(key);
1302  }
1303 
1304  if (gridnum < 0 || mgridParams == NULL) {
1305  NAMD_die("Node::updateGridScale(char*, Vector): Could not find grid.");
1306  }
1307 
1308  GridforceGrid* grid = molecule->get_gridfrc_grid(gridnum);
1309  if (grid == NULL) {
1310  NAMD_bug("Node::updateGridScale(char*, Vector): grid not found");
1311  }
1312  CProxy_Node(thisgroup).updateGridScale(gridnum, scale.x, scale.y, scale.z);
1313 
1314  DebugM(4, "updateGridScale(char*, Vector) finished\n" << endi);
1315 }
Molecule::get_gridfrc_grid
GridforceGrid * get_gridfrc_grid(int gridnum) const
Definition: Molecule.h:1368
Node::simParameters
SimParameters * simParameters
Definition: Node.h:181
DebugM
#define DebugM(x, y)
Definition: Debug.h:75
endi
std::ostream & endi(std::ostream &s)
Definition: InfoStream.C:54
Vector::z
BigReal z
Definition: Vector.h:74
MGridforceParamsList::index_for_key
int index_for_key(const char *key)
Definition: MGridforceParams.C:33
NAMD_bug
void NAMD_bug(const char *err_msg)
Definition: common.C:196
MGRIDFORCEPARAMS_DEFAULTKEY
#define MGRIDFORCEPARAMS_DEFAULTKEY
Definition: MGridforceParams.h:19
MGridforceParamsList::find_key
MGridforceParams * find_key(const char *key)
Definition: MGridforceParams.C:14
Vector::x
BigReal x
Definition: Vector.h:74
NAMD_die
void NAMD_die(const char *err_msg)
Definition: common.C:148
SimParameters::mgridforcelist
MGridforceParamsList mgridforcelist
Definition: SimParameters.h:358
Vector::y
BigReal y
Definition: Vector.h:74
Node::molecule
Molecule * molecule
Definition: Node.h:179

◆ updateGridScale() [2/2]

void Node::updateGridScale ( int  gridnum,
float  sx,
float  sy,
float  sz 
)

Definition at line 1316 of file Node.C.

References MGridforceParamsList::at_index(), DebugM, endi(), Molecule::get_gridfrc_grid(), MGridforceParams::gridforceScale, SimParameters::mgridforcelist, molecule, NAMD_bug(), GridforceGrid::set_scale(), and simParameters.

1316  {
1317  if (CmiMyRank()) return;
1318  DebugM(4, "updateGridScale(char*, int, float, float, float) called on node " << CkMyPe() << "\n" << endi);
1319 
1320  GridforceGrid *grid = molecule->get_gridfrc_grid(gridnum);
1321  if (grid == NULL) {
1322  NAMD_bug("Node::updateGridScale(char*, int, float, float, float):grid not found");
1323  }
1324 
1325  Vector scale(sx,sy,sz);
1326  simParameters->mgridforcelist.at_index(gridnum)->gridforceScale = scale;
1327  grid->set_scale( scale );
1328 #ifdef NODEGROUP_FORCE_REGISTER
1329  if(CkMyPe()==0)
1330  {
1331  CProxy_PatchData cpdata(CkpvAccess(BOCclass_group).patchData);
1332  cpdata.setDeviceKernelUpdateCounter();
1333  }
1334 #endif
1335  DebugM(4, "updateGridScale(char*, int, float, float, float) finished\n" << endi);
1336 }
Molecule::get_gridfrc_grid
GridforceGrid * get_gridfrc_grid(int gridnum) const
Definition: Molecule.h:1368
Vector
Definition: Vector.h:72
Node::simParameters
SimParameters * simParameters
Definition: Node.h:181
DebugM
#define DebugM(x, y)
Definition: Debug.h:75
endi
std::ostream & endi(std::ostream &s)
Definition: InfoStream.C:54
NAMD_bug
void NAMD_bug(const char *err_msg)
Definition: common.C:196
SimParameters::mgridforcelist
MGridforceParamsList mgridforcelist
Definition: SimParameters.h:358
MGridforceParamsList::at_index
MGridforceParams * at_index(int idx)
Definition: MGridforceParams.C:54
Node::molecule
Molecule * molecule
Definition: Node.h:179
GridforceGrid::set_scale
virtual void set_scale(Vector s)=0

Member Data Documentation

◆ atomMap

AtomMap* Node::atomMap
protected

Definition at line 202 of file Node.h.

Referenced by Node(), and ~Node().

◆ colvars

colvarmodule* Node::colvars

Definition at line 187 of file Node.h.

Referenced by colvarproxy_namd::colvarproxy_namd(), and Node().

◆ computeMap

ComputeMap* Node::computeMap
protected

Definition at line 204 of file Node.h.

Referenced by startup(), and ~Node().

◆ computeMgr

ComputeMgr* Node::computeMgr

Definition at line 172 of file Node.h.

Referenced by Sequencer::integrate(), Sequencer::integrate_SOA(), Sequencer::minimize(), and startup().

◆ configList

ConfigList* Node::configList

Definition at line 182 of file Node.h.

Referenced by colvarproxy_namd::colvarproxy_namd(), WorkDistrib::createAtomLists(), GlobalMasterSymmetry::GlobalMasterSymmetry(), Node(), ComputeQMMgr::recvPntChrg(), and saveMolDataPointers().

◆ coords

Vector* Node::coords

Definition at line 188 of file Node.h.

Referenced by ScriptTcl::measure(), Tcl_centerOfMass(), Tcl_centerOfNumber(), Tcl_loadCoords(), and Tcl_radiusOfGyration().

◆ curMFlopStep

int Node::curMFlopStep

Definition at line 157 of file Node.h.

Referenced by papiMeasureBarrier(), and resumeAfterPapiMeasureBarrier().

◆ curTimeStep

int Node::curTimeStep

Definition at line 152 of file Node.h.

Referenced by resumeAfterTraceBarrier(), and traceBarrier().

◆ imd

IMDOutput* Node::imd

Definition at line 186 of file Node.h.

Referenced by Output::coordinate(), Output::coordinateNeeded(), Output::force(), GlobalMasterIMD::get_vmd_forces(), GlobalMasterIMD::GlobalMasterIMD(), Node(), Controller::printEnergies(), Output::velocity(), and ~Node().

◆ initRSS

float Node::initRSS

Definition at line 136 of file Node.h.

◆ initVM

float Node::initVM

Definition at line 136 of file Node.h.

◆ ldbCoordinator

LdbCoordinator* Node::ldbCoordinator
protected

Definition at line 205 of file Node.h.

◆ mallocTest_size

int Node::mallocTest_size

Definition at line 130 of file Node.h.

Referenced by mallocTestQd(), and startup().

◆ molecule

Molecule* Node::molecule

Definition at line 179 of file Node.h.

Referenced by Sequencer::addMovDragToPosition(), Sequencer::addRotDragToPosition(), CollectionMaster::CollectVectorInstanceDcdSelection::append(), WorkDistrib::assignNodeToPatch(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), colvarproxy_namd::calculate(), ComputeQMMgr::calcUSR(), colvarproxy_namd::check_atom_id(), colvarproxy_namd::check_volmap_by_id(), ComputeGridForce::checkGridForceRatio(), SimParameters::close_dcdfile(), Controller::compareChecksums(), colvarproxy_namd::compute_volmap(), AngleElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), TholeElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), LjPmeCompute::computeNonbonded(), Controller::Controller(), Output::coordinate(), Output::coordinateNeeded(), WorkDistrib::createAtomLists(), ComputeMgr::createComputes(), ComputeGridForce::createGridForcedIdxList(), CudaPmeOneDevice::CudaPmeOneDevice(), ComputeConsForce::doForce(), ComputeConsTorque::doForce(), ComputeStir::doForce(), ComputeGridForce::doForce(), ComputeRestraints::doForce(), ComputePme::doQMWork(), dumpbench(), ComputeLjPmeSerialMgr::getLJparameters(), Controller::getTotalPotentialEnergy(), GlobalMasterEasy::GlobalMasterEasy(), GlobalMasterFreeEnergy::GlobalMasterFreeEnergy(), GlobalMasterSymmetry::GlobalMasterSymmetry(), GlobalMasterTMD::GlobalMasterTMD(), HomePatch::hardWallDrude(), colvarproxy_namd::init_atom_group(), colvarproxy_namd::init_atoms_map(), colvarproxy_namd::init_volmap_by_name(), ComputeQM::initialize(), ParallelIOMgr::initialize(), Sequencer::integrate_SOA(), Sequencer::langevinPiston(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), LJTable::LJTable(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), HomePatch::loweAndersenVelocities(), HomePatch::minimize_rattle2(), HomePatch::mollyAverage(), HomePatch::mollyMollify(), Controller::monteCarloPressure_accept(), Controller::multigatorCalcEnthalpy(), Node(), WorkDistrib::patchMapInit(), Controller::printEnergies(), Controller::printMinimizeEnergies(), HomePatch::qmSwapAtoms(), HomePatch::rattle1old(), HomePatch::rattle2(), ParallelIOMgr::readInfoForParOutDcdSelection(), Controller::receivePressure(), ComputeMgr::recvComputeConsForceMsg(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), ComputeLjPmeSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeGBISserMgr::recvCoord(), ParallelIOMgr::recvDcdParams(), ComputeQMMgr::recvPartQM(), reloadCharges(), Sequencer::reloadCharges(), reloadGridforceGrid(), reloadStructure(), Controller::rescaleaccelMD(), Sequencer::rescaleSoluteCharges(), resendMolecule(), resendMolecule2(), saveMolDataPointers(), ComputeQM::saveResults(), ComputeNonbondedUtil::select(), ParallelIOMgr::sendDcdParams(), HomePatch::setGBISIntrinsicRadii(), HomePatch::setLcpoType(), startup(), Tcl_centerOfMass(), Tcl_centerOfNumber(), Tcl_loadCoords(), Tcl_radiusOfGyration(), Sequencer::tcoupleVelocities(), colvarproxy_namd::update_atom_properties(), colvarproxy_namd::update_atoms_map(), colvarproxy_namd::update_group_properties(), ComputeLonepairsCUDA::updateAtoms(), updateGridScale(), wrap_coor_int(), and wrap_coor_int_dcd_selection().

◆ output

Output* Node::output

Definition at line 185 of file Node.h.

Referenced by SimParameters::close_dcdfile(), SimParameters::close_veldcdfile(), CollectionMaster::disposeForces(), CollectionMaster::disposePositions(), CollectionMaster::disposeVelocities(), Node(), recvReplicaDcdData(), recvReplicaDcdInit(), startup(), and ~Node().

◆ parameters

Parameters* Node::parameters

Definition at line 180 of file Node.h.

Referenced by ComputeNonbondedPair::ComputeNonbondedPair(), ComputeNonbondedSelf::ComputeNonbondedSelf(), ComputeLjPmeSerialMgr::getLJparameters(), LJTable::LJTable(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Node(), ComputeLjPmeSerialMgr::recvCoord(), resendMolecule(), resendMolecule2(), saveMolDataPointers(), ComputeNonbondedUtil::select(), and startup().

◆ patchMap

PatchMap* Node::patchMap
protected

Definition at line 203 of file Node.h.

Referenced by Node(), and ~Node().

◆ pdb

PDB* Node::pdb

Definition at line 183 of file Node.h.

Referenced by WorkDistrib::createAtomLists(), Node(), WorkDistrib::patchMapInit(), reloadStructure(), saveMolDataPointers(), and startup().

◆ rand

Random* Node::rand

Definition at line 175 of file Node.h.

Referenced by ComputeNonbondedPair::ComputeNonbondedPair(), ComputeNonbondedSelf::ComputeNonbondedSelf(), startup(), and ~Node().

◆ simParameters

SimParameters* Node::simParameters

Definition at line 181 of file Node.h.

Referenced by HomePatch::addForceToMomentum(), HomePatch::addForceToMomentum3(), HomePatch::addVelocityToPosition(), WorkDistrib::assignNodeToPatch(), PmeZPencil::backward_fft(), PmeYPencil::backward_fft(), PmeXPencil::backward_fft(), LdbCoordinator::barrier(), HomePatch::boxClosed(), HomePatch::buildRattleList(), HomePatch::buildRattleList_SOA(), ComputePmeMgr::chargeGridSubmitted(), CudaPmeOneDevice::checkPatchLevelLatticeCompatibilityAndComputeOffsets(), colvarproxy_namd::colvarproxy_namd(), CudaPmeOneDevice::compute(), ComputeCylindricalBC::ComputeCylindricalBC(), ComputeEwald::ComputeEwald(), OneFourNbTholeElem::computeForce(), AngleElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), CrosstermElem::computeForce(), AnisoElem::computeForce(), TholeElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), ComputeFullDirect::ComputeFullDirect(), ComputeGlobal::ComputeGlobal(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), ComputeLCPO::ComputeLCPO(), LjPmeCompute::computeLJpotential(), ComputeMsm::ComputeMsm(), ComputeNonbondedPair::ComputeNonbondedPair(), ComputeNonbondedSelf::ComputeNonbondedSelf(), ComputePme::ComputePme(), ComputeRestraints::ComputeRestraints(), ComputeSphericalBC::ComputeSphericalBC(), ComputeStir::ComputeStir(), ComputeTclBC::ComputeTclBC(), Output::coordinate(), Output::coordinateNeeded(), WorkDistrib::createAtomLists(), ComputeMgr::createComputes(), ComputeCUDAMgr::createCudaComputeNonbonded(), ComputeCUDAMgr::createCudaGlobalMaster(), ComputeCUDAMgr::createCudaPmeOneDevice(), LdbCoordinator::createLoadBalancer(), CudaComputeNonbonded::CudaComputeNonbonded(), CudaPmeOneDevice::CudaPmeOneDevice(), HomePatch::depositMigration(), CollectionMaster::disposePositions(), ComputeConsForce::doForce(), ComputeEField::doForce(), ComputeConsTorque::doForce(), ComputeStir::doForce(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), ComputeGridForce::doForce(), ComputeRestraints::doForce(), HomePatch::doGroupSizeCheck(), HomePatch::doGroupSizeCheck_SOA(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), HomePatch::doPairlistCheck(), ComputeTclBC::doWork(), ComputeGBISser::doWork(), ComputeGlobal::doWork(), CudaComputeNonbonded::doWork(), dumpbench(), HomePatch::exchangeAtoms(), HomePatch::exchangeCheckpoint(), PmeZPencil::fft_init(), PmeYPencil::fft_init(), PmeXPencil::fft_init(), CudaPmeOneDevice::finishReduction(), Output::force(), Output::forceNeeded(), PmeZPencil::forward_fft(), PmeYPencil::forward_fft(), PmeXPencil::forward_fft(), ComputePmeCUDADevice::gatherForce(), ComputePmeCUDADevice::gatherForceDone(), HomePatch::gbisComputeAfterP1(), HomePatch::gbisComputeAfterP2(), GlobalMasterIMD::get_vmd_forces(), GlobalMaster::getCurrentReduction(), CudaComputeNonbonded::getCurrentReduction(), ComputeLjPmeSerialMgr::getLJparameters(), GlobalMaster::GlobalMaster(), GlobalMasterFreeEnergy::GlobalMasterFreeEnergy(), GlobalMasterIMD::GlobalMasterIMD(), GlobalMasterServer::GlobalMasterServer(), GlobalMasterSymmetry::GlobalMasterSymmetry(), GlobalMasterTMD::GlobalMasterTMD(), HomePatch::hardWallDrude(), ComputePmeCUDA::initialize(), ComputeCUDAMgr::initialize(), LjPmeCompute::initialize(), LdbCoordinator::initialize(), ComputeQM::initialize(), CudaComputeNonbonded::initialize(), ParallelIOMgr::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize(), ComputePmeCUDADevice::initialize(), ComputePmeMgr::initialize_computes(), ComputePmeMgr::initialize_pencils(), isPmeProcessor(), CudaComputeNonbonded::launchWork(), LJTable::LJTable(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), HomePatch::loweAndersenVelocities(), WorkDistrib::mapComputes(), ComputePmeCUDADevice::mergeForcesOnPatch(), HomePatch::minimize_rattle2(), HomePatch::mollyAverage(), HomePatch::mollyMollify(), Controller::multigatorCalcEnthalpy(), NamdHybridLB::NamdHybridLB(), Node(), PmePencil< CBase_PmeZPencil >::order_init(), outputPatchComputeMaps(), Patch::Patch(), PatchDataSOA_set_buffer(), PatchDataSOA_set_size(), WorkDistrib::patchMapInit(), Compute::patchReady(), Patch::positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), HomePatch::qmSwapAtoms(), HomePatch::rattle1(), HomePatch::rattle1_SOA(), HomePatch::rattle1old(), HomePatch::rattle2(), ProxyPatch::receiveAll(), ProxyPatch::receiveData(), CollectionMaster::receiveDataStream(), recursive_bisect_with_curve(), ComputePmeCUDADevice::recvAtoms(), ComputePmeCUDADevice::recvAtomsFromNeighbor(), HomePatch::recvCheckpointLoad(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), ComputeLjPmeSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeMgr::recvCudaGlobalMasterCreateMsg(), ComputeMgr::recvCudaGlobalMasterRemoveMsg(), ComputeMgr::recvCudaGlobalMasterUpdateMsg(), HomePatch::recvExchangeMsg(), ComputeQMMgr::recvPartQM(), ComputeGlobal::recvResults(), reloadGridforceGrid(), resendMolecule(), CudaComputeNonbonded::reSortTileLists(), resumeAfterPapiMeasureBarrier(), HomePatch::revert(), ScriptTcl::run(), saveMolDataPointers(), WorkDistrib::savePatchMap(), ComputeGlobal::saveTotalForces(), scriptParam(), ComputePmeUtil::select(), ComputeNonbondedUtil::select(), PmeZPencil::send_all_ungrid(), GlobalMasterIMD::send_energies(), GlobalMasterIMD::send_fcoords(), PmeZPencil::send_trans(), PmeYPencil::send_trans(), PmeYPencil::send_untrans(), PmeXPencil::send_untrans(), ComputePmeCUDADevice::sendAtomsToNeighbor(), ComputeMgr::sendComputeGlobalData(), ComputeMgr::sendComputeGlobalResults(), ComputePmeCUDADevice::sendForcesToNeighbors(), WorkDistrib::sendPatchMap(), ComputePmeMgr::sendTrans(), ComputePmeMgr::sendUngrid(), ComputePmeMgr::sendUntrans(), HomePatch::setGBISIntrinsicRadii(), PatchMgr::setLattice(), ComputeLjPmeSerialMgr::setLJparameters(), ComputePmeCUDAMgr::setupPencils(), SimpleBroadcastObject< Tensor >::SimpleBroadcastObject(), NamdHybridLB::splitComputes(), ComputePmeCUDADevice::spreadCharge(), startup(), NamdCentLB::Strategy(), CollectionMgr::submitForces(), CollectionMgr::submitPositions(), ExclElem::submitReductionData(), PmePencilXYZ::submitReductions(), PmePencilZ::submitReductions(), ComputePmeMgr::submitReductions(), CollectionMgr::submitVelocities(), ComputePme::ungridForces(), updateGridScale(), ComputeMgr::updateLocalComputes4(), Output::velocity(), Output::velocityNeeded(), ReductionMgr::willRequire(), ReductionMgr::willSubmit(), wrap_coor_int(), and wrap_coor_int_dcd_selection().

◆ specialTracing

bool Node::specialTracing

Definition at line 166 of file Node.h.

Referenced by Node().

◆ state

NamdState* Node::state

Definition at line 184 of file Node.h.

Referenced by colvarproxy_namd::calculate(), Node(), recvCheckpointAck(), recvCheckpointReq(), reloadStructure(), resumeAfterPapiMeasureBarrier(), resumeAfterTraceBarrier(), run(), and saveMolDataPointers().

◆ workDistrib

WorkDistrib* Node::workDistrib

Definition at line 169 of file Node.h.

Referenced by ParallelIOMgr::createHomePatches(), and startup().

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