// 'demographicPara' is a 1x6 matrix.
double MaxPosterior::computeJointDensity_MPI_overSubSample(Eigen::MatrixXd demographicPara, IM im, popTree* poptree, Chain coldCh, unsigned int nProcs, unsigned int crr_procID)
{
// REMOVE
//if(crr_procID == 0)
// std::cout << "\n In MaxPosterior::computeJointDensity_MPI_overSubSample\n";
poptree->replacePara(demographicPara);
coldCh.compute_partialJointPosteriorDensity_overSubSample(poptree, im, crr_procID, nProcs);
std::vector<long double> expectationOfEachCoalProb = coldCh.get_expectationOfCoalProb();
unsigned int nloci = coldCh.GetNumLoci();
double posterior = 1;
if(nloci != expectationOfEachCoalProb.size())
{
std::cout << "** Error In MaxPosterior::computeJointDensity_MPI_overSubSample() **\n";
std::cout << "nloci = " << nloci
<< " expectationOfEachCoalProb.size() = " << expectationOfEachCoalProb.size() <<"\n\n";
}
for(unsigned int lc=0; lc< nloci; lc++)
{
double each_local = expectationOfEachCoalProb.at(lc);
double each_global =0;
MPI::COMM_WORLD.Barrier();
MPI::COMM_WORLD.Allreduce(&each_local, &each_global, 1, MPI_DOUBLE, MPI_SUM);
MPI::COMM_WORLD.Barrier();
if(crr_procID ==0)
{
posterior *=each_global;
}
MPI::COMM_WORLD.Barrier();
}
if(crr_procID ==0)
{
Eigen::Vector3d paraMax = im.get_paraMax();
double priorPopTree = poptree->computeJointPrior(paraMax);
posterior *=priorPopTree;
}
if(crr_procID ==0)
{
totalComputingTime_eigen += coldCh.get_eachComputingTime_eigen();
totalComputingTime_condiProb += coldCh.get_eachComputingTime_condiProb();
totalNum_eigenFunctionCalls++;
totalNum_condiProbFunctionCalls += coldCh.get_countCondiProbFunctionCalls();
// std::cout << "totalComputingTime_eigen = " << totalComputingTime_eigen.count()/1000 << "milliseconds\n";
}
return posterior;
}
// 3/16/2016
// 'demographicPara' is a 1x6 matrix.
long double MaxPosterior::computeLogJointDensity_MPI_overSubLoci_ESS(Eigen::MatrixXd demographicPara, IM im, popTree* poptree, Chain coldCh, unsigned int nProcs, unsigned int crr_procID)
{
// REMOVE
// if(crr_procID == 0)
// std::cout << "\n In MaxPosterior::computeJointDensity_MPI_overSubSample\n";
poptree->replacePara(demographicPara);
coldCh.compute_partialJointPosteriorDensity_overSubLoci_ESS(poptree, im, crr_procID, nProcs);
std::vector<long double> logExpectationOfEachCoalProb = coldCh.get_logExpectationOfCoalProb();
std::vector<long double> logExpectationOfEachCoalProbSquared = coldCh.get_logExpectationOfCoalProbSquared();
unsigned int numSubLoci = coldCh.getNumSubLoci();
long double posterior = 1;
long double posteriorSquared = 1;
if(numSubLoci != logExpectationOfEachCoalProb.size())
{
std::cout << "** Error In MaxPosterior::computeJointDensity_MPI_overSubSample() **\n";
std::cout << "numSubLoci = " << numSubLoci
<< " expectationOfEachCoalProb.size() = " << logExpectationOfEachCoalProb.size() <<"\n\n";
}
long double local_logPosterior_subLoci =0;
// long double local_logPosteriorSquared_subLoci =0;
long double local_sumESS =0;
long double global_logPosterior = 0;
// long double global_logPosteriorSquared = 0;
long double global_sumESS =0;
for(unsigned int lc=0; lc< numSubLoci; lc++)
{
local_logPosterior_subLoci += logExpectationOfEachCoalProb.at(lc);
local_sumESS += coldCh.GetNumIterations()*exp(2*logExpectationOfEachCoalProb.at(lc)-logExpectationOfEachCoalProbSquared.at(lc));
// local_logPosteriorSquared_subLoci += logExpectationOfEachCoalProbSquared.at(lc);
// std::cout<<"crrProcID="<<crr_procID<< "lc = " << lc <<" local_logPosterior_subLoci = "<< local_logPosterior_subLoci
// <<" local_logPosteriorSquared_subLoci = "<< local_logPosteriorSquared_subLoci <<"\n";
//std::cout <<"crrProcID="<<crr_procID<< " lc = " << lc <<" nMCMC="<<coldCh.GetNumIterations()
// << " each ESS= "<< coldCh.GetNumIterations()*exp(2*logExpectationOfEachCoalProb.at(lc)-logExpectationOfEachCoalProbSquared.at(lc)) <<"\n";
}
MPI::COMM_WORLD.Barrier();
MPI::COMM_WORLD.Allreduce(&local_logPosterior_subLoci, &global_logPosterior, 1, MPI_LONG_DOUBLE, MPI_SUM);
MPI::COMM_WORLD.Barrier();
MPI::COMM_WORLD.Allreduce(&local_sumESS, &global_sumESS, 1, MPI_LONG_DOUBLE, MPI_SUM);
// MPI::COMM_WORLD.Allreduce(&local_logPosteriorSquared_subLoci, &global_logPosteriorSquared, 1, MPI_LONG_DOUBLE, MPI_SUM);
MPI::COMM_WORLD.Barrier();
long double logPosterior = 0;
long double ESS = 0;
if(crr_procID ==0)
{
Eigen::Vector3d paraMax = im.get_paraMax();
double priorPopTree = poptree->computeJointPrior(paraMax);
//posterior = exp(global_logPosterior+log(priorPopTree));
logPosterior = global_logPosterior +log(priorPopTree);
ESS = global_sumESS/coldCh.GetNumLoci();
// ESS = coldCh.GetNumIterations()*exp(2*global_logPosterior - global_logPosteriorSquared);
// ESS = n(\bar w)^2 / \bar w^2
/*
std::cout << "coldCh.GetNumIterations()=" <<coldCh.GetNumIterations()
<<" global_logPosterior = " << global_logPosterior
<<" global_logPosteriorSquared="<< global_logPosteriorSquared<<"\n";
*/
std::cout << "Average effective sample size (ESS) of the importance sampling is "<< ESS
<< "(<"<<coldCh.GetNumIterations() << ", "<<ESS/coldCh.GetNumIterations()*100 <<"%).\n";
// std::cout << "Effective sample size of the importance sampling (product of sum, log) is "<< coldCh.GetNumLoci()*log(coldCh.GetNumIterations())+2*global_logPosterior - global_logPosteriorSquared <<".\n";
}
if(crr_procID ==0)
{
totalComputingTime_eigen += coldCh.get_eachComputingTime_eigen();
totalComputingTime_condiProb += coldCh.get_eachComputingTime_condiProb();
totalNum_eigenFunctionCalls++;
totalNum_condiProbFunctionCalls += coldCh.get_countCondiProbFunctionCalls();
// std::cout << "totalComputingTime_eigen = " << totalComputingTime_eigen.count()/1000 << "milliseconds\n";
}
// std::cout << "crr_procID=" << crr_procID << " logPosterior = " << logPosterior <<"\n";
return logPosterior;
}