void CParam::S4_alpha_i(CData &Data) {
is_accept_vec(3) = 0 ;
// if ( normC < 0 ) normC = normC_fn(Beta, Data) ; // Ver_1_4_1
for (int i_pheno=0; i_pheno<n_pheno; i_pheno++){ // V_1_3_5 ; Update each alpha_i
arma::mat Beta_prop = Beta ;
RandVec = Rcpp::rnorm(1, Beta(i_pheno,i_pheno), Data.stepsize_alpha ) ;
Beta_prop(i_pheno,i_pheno) = RandVec(0) ;
double logP_numer = R::dnorm(Beta_prop(i_pheno,i_pheno), Data.theta_alpha, sqrt(Data.tau2_alpha),1) ; // log=TRUE
double logP_denom = R::dnorm(Beta(i_pheno,i_pheno), Data.theta_alpha, sqrt(Data.tau2_alpha),1) ; // log=TRUE
double normC_prop = normC_fn(Beta_prop, Data) ;
for (int i_SNP=0; i_SNP<n_SNP; i_SNP++){
double e_it = E_mat(i_pheno,i_SNP) ;
logP_numer = logP_numer + log( normC ) + Beta_prop(i_pheno,i_pheno) * e_it ;
logP_denom = logP_denom + log( normC_prop ) + Beta(i_pheno,i_pheno) * e_it ;
}
double accept_prob = exp( logP_numer - logP_denom ) ;
accept_prob_vec(3) = accept_prob ;
RandVec = Rcpp::runif(1, 0, 1) ;
if ( accept_prob >= RandVec(0) ){
Beta = Beta_prop ; normC = normC_prop ;
is_accept_vec(3) = is_accept_vec(3) + 1 ;
}
} // for (int i=0; i<n_pheno; i++){
is_accept_vec(3) = 1.0 / n_pheno * is_accept_vec(3) ;
}
void CParam::S1_e_it(CData &Data) {
for (int i_SNP=0; i_SNP<n_SNP; i_SNP++){
for (int i=0; i<n_pheno; i++){
if ( ( Data.Y(i,i_SNP) > 0 ) & ( Data.Y(i,i_SNP) <= Data.threshold_on ) ){
// V 1.3.1 -> other case: e_it is fixed in CParam::Initialize,
// i.e., e_it=0 if y_it<=0 and 1 if y_it>=Data.threshold_on
double unnorm_logprob0 = 0.0 ;
double unnorm_logprob1 = Beta(i,i) ;
for (int j=0; j<n_pheno; j++){
if (G_mat(i,j)==1) unnorm_logprob1 = unnorm_logprob1 + Beta(i,j) * E_mat(j,i_SNP) ;
}
// Note: Not count G_mat(i,j)=0 or G_mat(i,j)=9,i.e., diagonal
unnorm_logprob0 = unnorm_logprob0 + R::dnorm(Data.Y(i,i_SNP),0,1,1) ; // log = T
unnorm_logprob1 = unnorm_logprob1 + R::dlnorm(Data.Y(i,i_SNP),mu_vec(i),sqrt(sig2_vec(i)),1) ; // log = T
double prob_e_it = 1.0 / ( 1.0 + exp(unnorm_logprob0-unnorm_logprob1) ) ;
// Note: p1 = f1/(f1+f0) = 1 / (1+f0/f1) = 1 / (1+exp(log f0 - log f1))
RandVec = Rcpp::runif(1,0,1) ;
if ( prob_e_it >= RandVec(0) ){
E_mat(i,i_SNP) = 1 ;
} else {
E_mat(i,i_SNP) = 0 ;
}
}
// To check loglikelihood
if (E_mat(i,i_SNP)==1){
loglikelihood = loglikelihood + R::dlnorm(Data.Y(i,i_SNP),mu_vec(i),sqrt(sig2_vec(i)),1) ;
} else {
loglikelihood = loglikelihood + R::dnorm(Data.Y(i,i_SNP),0,1,1) ;
}
}
}
is_accept_vec(0) = 1 ;
}
double CParam::rtruncNorm_uppertail_fn(double mean, double sd, double lowerlimit){
RandVec = Rcpp::runif(1,0,1) ;
double std_lowerlimit = (lowerlimit-mean) / sd ;
double temp_pnorm = (1.0-R::pnorm(std_lowerlimit,0,1,1,0)) * RandVec(0) ; // x,mu,sigma,lt,lg
double std_x = -1.0 * R::qnorm(temp_pnorm,0,1,1,0) ; // p,mu,sigma,lt,lg
return( mean + std_x * sd ) ;
}
double CParam::rinvgamma(double alpha, double beta){
RandVec = Rcpp::rgamma(1, alpha, (1.0/beta) ) ;
return ( 1.0 / RandVec(0) ) ;
// Note that b in Rcpp::rgamma(a,b) is scale,
// i.e., its mean is ab, NOT a/b
// If X ~ Gamma(a,b), then 1/X ~ IG(a,1/b)
}
void CParam::S5_beta_ij(CData &Data) {
is_accept_vec(4) = 0 ;
int w_cur = 0 ; // just for calculation of is_accept_vec( )
for (int i=0; i<(n_pheno-1); i++){
for (int j=(i+1); j<n_pheno; j++){
if ( G_mat(i,j)==1 ){
w_cur ++ ;
arma::mat Beta_prop = Beta ;
double temp_beta_prop = 0.0 ;
while ( temp_beta_prop <= 0.0 ){
temp_beta_prop = rtruncNorm_uppertail_fn(Beta(i,j), Data.stepsize_beta, 0) ;
}
Beta_prop(i,j) = temp_beta_prop ;
Beta_prop(j,i) = temp_beta_prop ;
double logP_numer = R::dgamma(Beta_prop(i,j),Data.a_beta,(1.0/Data.b_beta),1) ; // (shape,scale,log), i.e., b_beta = rate // V_1_3_5
double logP_denom = R::dgamma(Beta(i,j),Data.a_beta,(1.0/Data.b_beta),1) ; //
double normC_prop = normC_fn(Beta_prop, Data) ;
for (int i_SNP=0; i_SNP<n_SNP; i_SNP++){
double e_it = E_mat(i,i_SNP) ;
double e_jt = E_mat(j,i_SNP) ;
logP_numer = logP_numer + log(normC) + Beta_prop(i,j) * e_it * e_jt ;
logP_denom = logP_denom + log(normC_prop) + Beta(i,j) * e_it * e_jt ;
}
double logQ_numer = log( dtruncnorm_uppertail_fn(Beta(i,j), 0, Beta_prop(i,j), Data.stepsize_beta) ) ; // CHECK
double logQ_denom = log( dtruncnorm_uppertail_fn(Beta_prop(i,j), 0, Beta(i,j), Data.stepsize_beta) ) ;
double accept_prob = exp( logP_numer - logP_denom + logQ_numer - logQ_denom ) ;
accept_prob_vec(4) = accept_prob ;
RandVec = Rcpp::runif(1, 0, 1) ;
if ( accept_prob >= RandVec(0) ){
Beta = Beta_prop ; normC = normC_prop ;
is_accept_vec(4) = is_accept_vec(4) + 1 ;
}
}
}
}
if ( w_cur == 0 ){
is_accept_vec(4) = 0.2 ;
} else {
is_accept_vec(4) = 1.0 / w_cur * is_accept_vec(4) ;
}
}
void CParam::S2_mu_i(CData &Data) {
for (int i=0; i<n_pheno; i++){
double sig2_i = sig2_vec(i) ;
arma::vec e_i = E_mat.row(i).t() ;
double n_i = sum(e_i) ;
arma::vec logy_i = Data.logY.row(i).t() ;
arma::vec e1_logy = logy_i % e_i ;
double sum_e1_logy = sum(e1_logy) ;
// Note: % Schur product: element-wise multiplication of two objects
// sum of log_y_it with e_it=1
double mean_star = (sig2_i * Data.theta_mu + Data.tau2_mu * sum_e1_logy) / (sig2_i + Data.tau2_mu * n_i) ;
double var_star = (sig2_i * Data.tau2_mu)/(sig2_i + Data.tau2_mu * n_i) ;
RandVec = Rcpp::rnorm(1, mean_star, sqrt(var_star)) ;
mu_vec(i) = RandVec(0) ;
}
is_accept_vec(1) = 1 ;
}
// Generate a random point uniformly distrbuted within the domain
void pDomain::Generate(pVector &pos) const
{
switch (type)
{
case PDPoint:
pos = p1;
break;
case PDLine:
pos = p1 + p2 * drand48();
break;
case PDBox:
// Scale and translate [0,1] random to fit box
pos.x = p1.x + (p2.x - p1.x) * drand48();
pos.y = p1.y + (p2.y - p1.y) * drand48();
pos.z = p1.z + (p2.z - p1.z) * drand48();
break;
case PDTriangle:
{
float r1 = drand48();
float r2 = drand48();
if(r1 + r2 < 1.0f)
pos = p1 + u * r1 + v * r2;
else
pos = p1 + u * (1.0f-r1) + v * (1.0f-r2);
}
break;
case PDRectangle:
pos = p1 + u * drand48() + v * drand48();
break;
case PDPlane: // How do I sensibly make a point on an infinite plane?
pos = p1;
break;
case PDSphere:
// Place on [-1..1] sphere
pos = RandVec() - vHalf;
pos.normalize();
// Scale unit sphere pos by [0..r] and translate
// (should distribute as r^2 law)
if(radius1 == radius2)
pos = p1 + pos * radius1;
else
pos = p1 + pos * (radius2 + drand48() * (radius1 - radius2));
break;
case PDCylinder:
case PDCone:
{
// For a cone, p2 is the apex of the cone.
float dist = drand48(); // Distance between base and tip
float theta = drand48() * 2.0f * float(M_PI); // Angle around axis
// Distance from axis
float r = radius2 + drand48() * (radius1 - radius2);
float x = r * cosf(theta); // Weighting of each frame vector
float y = r * sinf(theta);
// Scale radius along axis for cones
if(type == PDCone)
{
x *= dist;
y *= dist;
}
pos = p1 + p2 * dist + u * x + v * y;
}
break;
case PDBlob:
pos.x = p1.x + NRand(radius1);
pos.y = p1.y + NRand(radius1);
pos.z = p1.z + NRand(radius1);
break;
case PDDisc:
{
float theta = drand48() * 2.0f * float(M_PI); // Angle around normal
// Distance from center
float r = radius2 + drand48() * (radius1 - radius2);
float x = r * cosf(theta); // Weighting of each frame vector
float y = r * sinf(theta);
pos = p1 + u * x + v * y;
}
break;
default:
pos = pVector(0,0,0);
}
}
int CParam::rDiscrete(int max_no){
// generate an integer from 0 to (max_no-1)
double max_no_ = 1.0 * max_no ;
RandVec = Rcpp::runif(1, 0.0, max_no_) ;
return ( floor(RandVec(0)) ) ;
}
void CParam::check_random_generate(CData &Data){
RandVec = Rcpp::rnorm(2,2,1000) ;
std::cout << RandVec(0) << " " << RandVec(1) << std::endl ;
// std::cout << pow(10,-3) << std::endl ;
}
void CParam::S6_G_beta_ij(CData &Data) {
arma::mat G_prop = G_mat ; arma::mat Beta_prop = Beta ;
double logQ_numer, logQ_denom ;
double logP_numer, logP_denom ;
double normC_prop ;
bool is_forcein_edge_selected = false ;
// double P_G_q, P_G ; // For updated E(i,j)
// Step 1
int w_cur = 0 ; int w_max = 0 ; int w_prop ;
for (int i=0; i<(n_pheno-1); i++){
for (int j=(i+1); j<n_pheno; j++){
w_max ++ ; w_cur = w_cur + G_mat(i,j) ;
}
}
if ( w_cur==0 ){ w_prop = 1 ; logQ_numer = log(0.5) ; logQ_denom = log(1.0) ; } // q(w|w^q) // q(w^q|w)
if ( w_cur==w_max ){ w_prop = w_max - 1 ; logQ_numer = log(0.5) ; logQ_denom = log(1.0) ; } // q(w|w^q) // q(w^q|w)
if ( (w_cur > 0) && (w_cur < w_max) ){
RandVec = Rcpp::runif(1, 0, 1) ;
if ( RandVec(0) < 0.5 ){ w_prop = w_cur + 1 ; } else { w_prop = w_cur - 1 ; }
logQ_denom = log(0.5) ; // q(w^q|w)
if ( (w_prop==0) || (w_prop==w_max) ){ logQ_numer = log(1.0) ; } else { logQ_numer = log(0.5) ; } // q(w|w^q)
}
// Step 2
if ( w_prop > w_cur ){ // step 2-a
int id_added = rDiscrete(w_max-w_cur) + 1 ; // 1 ~ total. of empty edges
int count_empty_edge = 0 ;
for (int i=0; i<(n_pheno-1); i++){
for (int j=(i+1); j<n_pheno; j++){
if ( G_mat(i,j)==0 ){
count_empty_edge++;
if ( id_added==count_empty_edge ){
G_prop(i,j) = 1 ; G_prop(j,i) = G_prop(i,j) ;
RandVec = Rcpp::rgamma(1, Data.a_betaG, 1.0/Data.b_betaG) ; // q(beta_ij^q)
Beta_prop(i,j) = RandVec(0) ;
Beta_prop(j,i) = Beta_prop(i,j) ;
id_added = -9 ;
// if ( Data.PriorSetting==2 ){
// P_G = 1.0 - Data.priorprob_G(i,j) ; // Bernoulli(E_ij=0; p_ij)
// P_G_q = Data.priorprob_G(i,j) ; // Bernoulli(E_ij^q=1; p_ij)
// }
logP_numer = R::dgamma(Beta_prop(i,j),Data.a_beta,(1.0/Data.b_beta),1) ; // f(beta_ij^q|G_ij^q)
logP_denom = 0 ; // f(beta_ij|G_ij) cancelled with q(beta_ij)
normC_prop = normC_fn(Beta_prop, Data) ;
for (int i_SNP=0; i_SNP<n_SNP; i_SNP++){
double e_it = E_mat(i,i_SNP) ;
double e_jt = E_mat(j,i_SNP) ;
logP_numer = logP_numer - log(normC_prop) + Beta_prop(i,j) * e_it * e_jt ; // f(e_t|alpha,beta^q,G^q)
logP_denom = logP_denom - log(normC) + Beta(i,j) * e_it * e_jt ; // f(e_t|alpha,beta,G)
}
logQ_numer = logQ_numer + 0 ; // q(beta_ij) cancelled with f(beta_ij|G_ij)
logQ_denom = logQ_denom + R::dgamma(Beta_prop(i,j),Data.a_betaG,(1.0/Data.b_betaG),1) ; // q(beta_ij^q)
} // if ( id_added==count_empty_edge )
} // for ( G_mat(i,j)==0 )
} // for (j)
} // for (i)
logQ_numer = logQ_numer - log(w_cur) ; // q(G|G^q,w)
logQ_denom = logQ_denom - log(w_max-w_cur) ; // q(G^q|G,w^q)
} else { // step 2-b
int id_deleted = rDiscrete(w_cur)+1 ; // 1 ~ total no. of connected edges
int count_connected_edge = 0 ;
for (int i=0; i<(n_pheno-1); i++){
for (int j=(i+1); j<n_pheno; j++){
if ( G_mat(i,j)==1 ){
count_connected_edge++;
if ( id_deleted==count_connected_edge ){
G_prop(i,j) = 0 ; G_prop(j,i) = G_prop(i,j) ;
Beta_prop(i,j) = 0 ; // q(beta_ij^q)
Beta_prop(j,i) = Beta_prop(i,j) ;
id_deleted = -9 ;
if (Data.isforcein==true){
if (Data.E_forcein_mat(i,j)==1) is_forcein_edge_selected = true ;
}
// if ( Data.PriorSetting==2 ){
// P_G = Data.priorprob_G(i,j) ; // Bernoulli(E_ij=1; p_ij)
// P_G_q = 1.0 - Data.priorprob_G(i,j) ; // Bernoulli(E_ij^q=0; p_ij)
// }
logP_numer = 0 ; // f(beta_ij^q|G_ij^q) cancelled with q(beta_ij^q)
logP_denom = R::dgamma(Beta(i,j),Data.a_beta,(1.0/Data.b_beta),1) ; // f(beta_ij|G_ij)
normC_prop = normC_fn(Beta_prop, Data) ;
for (int i_SNP=0; i_SNP<n_SNP; i_SNP++){
double e_it = E_mat(i,i_SNP) ;
double e_jt = E_mat(j,i_SNP) ;
logP_numer = logP_numer - log(normC_prop) + Beta_prop(i,j) * e_it * e_jt ; // f(e_t|alpha,beta^q,G^q)
logP_denom = logP_denom - log(normC) + Beta(i,j) * e_it * e_jt ; // f(e_t|alpha,beta,G)
}
logQ_numer = logQ_numer + R::dgamma(Beta(i,j),Data.a_betaG,(1.0/Data.b_betaG),1) ; // q(beta_ij)
logQ_denom = logQ_denom + 0 ; // q(beta_ij^q) cancelled with f(beta_ij^q|G_ij^q)
}
}
}
}
logQ_numer = logQ_numer - log(w_max-w_cur) ; // q(G|G^q,w)
logQ_denom = logQ_denom - log(w_cur) ; // q(G^q|G,w^q)
}
// if ( Data.PriorSetting==1 ){
if ( w_prop > 0 ) logP_numer = logP_numer - log(w_prop) ; // f(G^q) // if w_prop=0, let 1/w_prop = 1, so that log(w_prop) = 0
if ( w_cur > 0 ) logP_denom = logP_denom - log(w_cur) ; // f(G) // if w_cur=0, let 1/w_cur = 1, so that log(w_cur) = 0
// }
// if ( Data.PriorSetting==2 ){
// if ( w_prop > 0 ) logP_numer = logP_numer + log(P_G_q) ;
// if ( w_cur > 0 ) logP_denom = logP_denom + log(P_G) ;
// }
// Step 3
double accept_prob = exp( logP_numer - logP_denom + logQ_numer - logQ_denom ) ;
if (is_forcein_edge_selected==true) accept_prob = 0 ;
accept_prob_vec(5) = accept_prob ;
RandVec = Rcpp::runif(1, 0, 1) ;
if ( accept_prob >= RandVec(0) ){
Beta = Beta_prop ; G_mat = G_prop ; normC = normC_prop ;
is_accept_vec(5) = 1 ;
} else {
is_accept_vec(5) = 0 ;
}
}
int main(int argc, char *argv[])
{
int ierr = 0, i, j, forierr = 0;
#ifdef EPETRA_MPI
// Initialize MPI
MPI_Init(&argc,&argv);
Epetra_MpiComm Comm( MPI_COMM_WORLD );
#else
Epetra_SerialComm Comm;
#endif
bool verbose = false;
// Check if we should print results to standard out
if (argc>1) if (argv[1][0]=='-' && argv[1][1]=='v') verbose = true;
//char tmp;
//if (Comm.MyPID()==0) cout << "Press any key to continue..."<< endl;
//if (Comm.MyPID()==0) cin >> tmp;
//Comm.Barrier();
Comm.SetTracebackMode(0); // This should shut down any error traceback reporting
int MyPID = Comm.MyPID();
int NumProc = Comm.NumProc();
if (verbose && MyPID==0)
cout << Epetra_Version() << endl << endl;
if (verbose) cout << "Processor "<<MyPID<<" of "<< NumProc
<< " is alive."<<endl;
// Redefine verbose to only print on PE 0
if (verbose && Comm.MyPID()!=0) verbose = false;
int NumMyEquations = 20;
long long NumGlobalEquations = NumMyEquations*NumProc+EPETRA_MIN(NumProc,3);
if (MyPID < 3) NumMyEquations++;
// Construct a Source Map that puts approximately the same Number of equations on each processor in
// uniform global ordering
Epetra_Map SourceMap(NumGlobalEquations, NumMyEquations, 0LL, Comm);
// Get update list and number of local equations from newly created Map
int NumMyElements = SourceMap.NumMyElements();
long long * SourceMyGlobalElements = new long long[NumMyElements];
SourceMap.MyGlobalElements(SourceMyGlobalElements);
// Construct a Target Map that will contain:
// some unchanged elements (relative to the soure map),
// some permuted elements
// some off-processor elements
Epetra_Vector RandVec(SourceMap);
RandVec.Random(); // This creates a vector of random numbers between negative one and one.
long long *TargetMyGlobalElements = new long long[NumMyElements];
long long MinGID = SourceMap.MinMyGID64();
for (i=0; i< NumMyEquations/2; i++) TargetMyGlobalElements[i] = i + MinGID; // Half will be the same...
for (i=NumMyEquations/2; i<NumMyEquations; i++) {
int index = abs((int)(((double) (NumGlobalEquations-1) ) * RandVec[i]));
TargetMyGlobalElements[i] = EPETRA_MIN(NumGlobalEquations-1,(long long) EPETRA_MAX(0,index));
}
int NumSameIDs = 0;
int NumPermutedIDs = 0;
int NumRemoteIDs = 0;
bool StillContiguous = true;
for (i=0; i < NumMyEquations; i++) {
if (SourceMyGlobalElements[i]==TargetMyGlobalElements[i] && StillContiguous)
NumSameIDs++;
else if (SourceMap.MyGID(TargetMyGlobalElements[i])) {
StillContiguous = false;
NumPermutedIDs++;
}
else {
StillContiguous = false;
NumRemoteIDs++;
}
}
EPETRA_TEST_ERR(!(NumMyEquations==NumSameIDs+NumPermutedIDs+NumRemoteIDs),ierr);
Epetra_Map TargetMap((long long) -1, NumMyElements, TargetMyGlobalElements, 0LL, Comm);
// Create a multivector whose elements are GlobalID * (column number +1)
int NumVectors = 3;
Epetra_MultiVector SourceMultiVector(SourceMap, NumVectors);
for (j=0; j < NumVectors; j++)
for (i=0; i < NumMyElements; i++)
SourceMultiVector[j][i] = (double) SourceMyGlobalElements[i]*(j+1);
// Create a target multivector that we will fill using an Import
Epetra_MultiVector TargetMultiVector(TargetMap, NumVectors);
Epetra_Import Importer(TargetMap, SourceMap);
EPETRA_TEST_ERR(!(TargetMultiVector.Import(SourceMultiVector, Importer, Insert)==0),ierr);
// Test Target against expected values
forierr = 0;
for (j=0; j < NumVectors; j++)
for (i=0; i < NumMyElements; i++) {
if (TargetMultiVector[j][i]!= (double) TargetMyGlobalElements[i]*(j+1))
cout << "TargetMultiVector["<<i<<"]["<<j<<"] = " << TargetMultiVector[j][i]
<< " TargetMyGlobalElements[i]*(j+1) = " << TargetMyGlobalElements[i]*(j+1) << endl;
forierr += !(TargetMultiVector[j][i]== (double) TargetMyGlobalElements[i]*(j+1));
}
EPETRA_TEST_ERR(forierr,ierr);
if (verbose) cout << "MultiVector Import using Importer Check OK" << endl << endl;
//////////////////////////////////////////////////////////////////////////////
// Now use Importer to do an export
Epetra_Vector TargetVector(SourceMap);
Epetra_Vector ExpectedTarget(SourceMap);
Epetra_Vector SourceVector(TargetMap);
NumSameIDs = Importer.NumSameIDs();
int NumPermuteIDs = Importer.NumPermuteIDs();
int NumExportIDs = Importer.NumExportIDs();
int *PermuteFromLIDs = Importer.PermuteFromLIDs();
int *ExportLIDs = Importer.ExportLIDs();
int *ExportPIDs = Importer.ExportPIDs();
for (i=0; i < NumSameIDs; i++) ExpectedTarget[i] = (double) (MyPID+1);
for (i=0; i < NumPermuteIDs; i++) ExpectedTarget[PermuteFromLIDs[i]] =
(double) (MyPID+1);
for (i=0; i < NumExportIDs; i++) ExpectedTarget[ExportLIDs[i]] +=
(double) (ExportPIDs[i]+1);
for (i=0; i < NumMyElements; i++) SourceVector[i] = (double) (MyPID+1);
EPETRA_TEST_ERR(!(TargetVector.Export(SourceVector, Importer, Add)==0),ierr);
forierr = 0;
for (i=0; i < NumMyElements; i++) {
if (TargetVector[i]!= ExpectedTarget[i])
cout << " TargetVector["<<i<<"] = " << TargetVector[i]
<< " ExpectedTarget["<<i<<"] = " << ExpectedTarget[i] << " on PE " << MyPID << endl;
forierr += !(TargetVector[i]== ExpectedTarget[i]);
}
EPETRA_TEST_ERR(forierr,ierr);
if (verbose) cout << "Vector Export using Importer Check OK" << endl << endl;
//////////////////////////////////////////////////////////////////////////////
// Now use Importer to create a reverse exporter
TargetVector.PutScalar(0.0);
Epetra_Export ReversedImport(Importer);
EPETRA_TEST_ERR(!(TargetVector.Export(SourceVector, ReversedImport, Add)==0),ierr);
forierr = 0;
for (i=0; i < NumMyElements; i++) {
if (TargetVector[i]!= ExpectedTarget[i])
cout << " TargetVector["<<i<<"] = " << TargetVector[i]
<< " ExpectedTarget["<<i<<"] = " << ExpectedTarget[i] << " on PE " << MyPID << endl;
forierr += !(TargetVector[i]== ExpectedTarget[i]);
}
EPETRA_TEST_ERR(forierr,ierr);
if (verbose) cout << "Vector Export using Reversed Importer Check OK" << endl << endl;
//////////////////////////////////////////////////////////////////////////////
// Now use Exporter to create a reverse importer
TargetVector.PutScalar(0.0);
Epetra_Import ReversedExport(ReversedImport);
EPETRA_TEST_ERR(!(TargetVector.Export(SourceVector, ReversedExport, Add)==0),ierr);
forierr = 0;
for (i=0; i < NumMyElements; i++) {
if (TargetVector[i]!= ExpectedTarget[i])
cout << " TargetVector["<<i<<"] = " << TargetVector[i]
<< " ExpectedTarget["<<i<<"] = " << ExpectedTarget[i] << " on PE " << MyPID << endl;
forierr += !(TargetVector[i]== ExpectedTarget[i]);
}
EPETRA_TEST_ERR(forierr,ierr);
if (verbose) cout << "Vector Export using Reversed Exporter Check OK" << endl << endl;
//////////////////////////////////////////////////////////////////////////////////////////
// Build a tridiagonal system two ways:
// 1) From "standard" matrix view where equations are uniquely owned.
// 2) From 1D PDE view where nodes (equations) between processors are shared and partial contributions are done
// in parallel, then merged together at the end of the construction process.
//
//////////////////////////////////////////////////////////////////////////////////////////
// Construct a Standard Map that puts approximately the same number of equations on each processor in
// uniform global ordering
Epetra_Map StandardMap(NumGlobalEquations, NumMyEquations, 0LL, Comm);
// Get update list and number of local equations from newly created Map
NumMyElements = StandardMap.NumMyElements();
long long * StandardMyGlobalElements = new long long[NumMyElements];
StandardMap.MyGlobalElements(StandardMyGlobalElements);
// Create a standard Epetra_CrsGraph
Epetra_CrsGraph StandardGraph(Copy, StandardMap, 3);
EPETRA_TEST_ERR(StandardGraph.IndicesAreGlobal(),ierr);
EPETRA_TEST_ERR(StandardGraph.IndicesAreLocal(),ierr);
// Add rows one-at-a-time
// Need some vectors to help
// Off diagonal Values will always be -1
long long *Indices = new long long[2];
int NumEntries;
forierr = 0;
for (i=0; i<NumMyEquations; i++)
{
if (StandardMyGlobalElements[i]==0)
{
Indices[0] = 1;
NumEntries = 1;
}
else if (StandardMyGlobalElements[i] == NumGlobalEquations-1)
{
Indices[0] = NumGlobalEquations-2;
NumEntries = 1;
}
else
{
Indices[0] = StandardMyGlobalElements[i]-1;
Indices[1] = StandardMyGlobalElements[i]+1;
NumEntries = 2;
}
forierr += !(StandardGraph.InsertGlobalIndices(StandardMyGlobalElements[i], NumEntries, Indices)==0);
forierr += !(StandardGraph.InsertGlobalIndices(StandardMyGlobalElements[i], 1, StandardMyGlobalElements+i)==0); // Put in the diagonal entry
}
EPETRA_TEST_ERR(forierr,ierr);
// Finish up
EPETRA_TEST_ERR(!(StandardGraph.IndicesAreGlobal()),ierr);
EPETRA_TEST_ERR(!(StandardGraph.FillComplete()==0),ierr);
EPETRA_TEST_ERR(!(StandardGraph.IndicesAreLocal()),ierr);
EPETRA_TEST_ERR(StandardGraph.StorageOptimized(),ierr);
StandardGraph.OptimizeStorage();
EPETRA_TEST_ERR(!(StandardGraph.StorageOptimized()),ierr);
EPETRA_TEST_ERR(StandardGraph.UpperTriangular(),ierr);
EPETRA_TEST_ERR(StandardGraph.LowerTriangular(),ierr);
// Create Epetra_CrsMatrix using the just-built graph
Epetra_CrsMatrix StandardMatrix(Copy, StandardGraph);
EPETRA_TEST_ERR(StandardMatrix.IndicesAreGlobal(),ierr);
EPETRA_TEST_ERR(!(StandardMatrix.IndicesAreLocal()),ierr);
// Add rows one-at-a-time
// Need some vectors to help
// Off diagonal Values will always be -1
double *Values = new double[2];
Values[0] = -1.0; Values[1] = -1.0;
double two = 2.0;
forierr = 0;
for (i=0; i<NumMyEquations; i++)
{
if (StandardMyGlobalElements[i]==0)
{
Indices[0] = 1;
NumEntries = 1;
}
else if (StandardMyGlobalElements[i] == NumGlobalEquations-1)
{
Indices[0] = NumGlobalEquations-2;
NumEntries = 1;
}
else
{
Indices[0] = StandardMyGlobalElements[i]-1;
Indices[1] = StandardMyGlobalElements[i]+1;
NumEntries = 2;
}
forierr += !(StandardMatrix.ReplaceGlobalValues(StandardMyGlobalElements[i], NumEntries, Values, Indices)==0);
// Put in the diagonal entry
forierr += !(StandardMatrix.ReplaceGlobalValues(StandardMyGlobalElements[i], 1, &two, StandardMyGlobalElements+i)==0);
}
EPETRA_TEST_ERR(forierr,ierr);
// Finish up
EPETRA_TEST_ERR(!(StandardMatrix.IndicesAreLocal()),ierr);
EPETRA_TEST_ERR(!(StandardMatrix.FillComplete()==0),ierr);
EPETRA_TEST_ERR(!(StandardMatrix.IndicesAreLocal()),ierr);
// EPETRA_TEST_ERR((StandardMatrix.StorageOptimized()),ierr);
EPETRA_TEST_ERR((StandardMatrix.OptimizeStorage()),ierr);
EPETRA_TEST_ERR(!(StandardMatrix.StorageOptimized()),ierr);
EPETRA_TEST_ERR(StandardMatrix.UpperTriangular(),ierr);
EPETRA_TEST_ERR(StandardMatrix.LowerTriangular(),ierr);
// Construct an Overlapped Map of StandardMap that include the endpoints from two neighboring processors.
int OverlapNumMyElements;
long long OverlapMinMyGID;
OverlapNumMyElements = NumMyElements + 1;
if (MyPID==0) OverlapNumMyElements--;
if (MyPID==0) OverlapMinMyGID = StandardMap.MinMyGID64();
else OverlapMinMyGID = StandardMap.MinMyGID64()-1;
long long * OverlapMyGlobalElements = new long long[OverlapNumMyElements];
for (i=0; i< OverlapNumMyElements; i++) OverlapMyGlobalElements[i] = OverlapMinMyGID + i;
Epetra_Map OverlapMap((long long) -1, OverlapNumMyElements, OverlapMyGlobalElements, 0LL, Comm);
// Create the Overlap Epetra_Matrix
Epetra_CrsMatrix OverlapMatrix(Copy, OverlapMap, 4);
EPETRA_TEST_ERR(OverlapMatrix.IndicesAreGlobal(),ierr);
EPETRA_TEST_ERR(OverlapMatrix.IndicesAreLocal(),ierr);
// Add matrix element one cell at a time.
// Each cell does an incoming and outgoing flux calculation
double pos_one = 1.0;
double neg_one = -1.0;
forierr = 0;
for (i=0; i<OverlapNumMyElements; i++)
{
long long node_left = OverlapMyGlobalElements[i]-1;
long long node_center = node_left + 1;
long long node_right = node_left + 2;
if (i>0) {
if (node_left>-1)
forierr += !(OverlapMatrix.InsertGlobalValues(node_center, 1, &neg_one, &node_left)==0);
forierr += !(OverlapMatrix.InsertGlobalValues(node_center, 1, &pos_one, &node_center)==0);
}
if (i<OverlapNumMyElements-1) {
forierr += !(OverlapMatrix.InsertGlobalValues(node_center, 1, &pos_one, &node_center)==0);
if (node_right<NumGlobalEquations)
forierr += !(OverlapMatrix.InsertGlobalValues(node_center, 1, &neg_one, &node_right)==0);
}
}
EPETRA_TEST_ERR(forierr,ierr);
// Handle endpoints
if (MyPID==0) {
long long node_center = 0;
EPETRA_TEST_ERR(!(OverlapMatrix.InsertGlobalValues(node_center, 1, &pos_one, &node_center)==0),ierr);
}
if (MyPID==NumProc-1) {
long long node_center = OverlapMyGlobalElements[OverlapNumMyElements-1];
EPETRA_TEST_ERR(!(OverlapMatrix.InsertGlobalValues(node_center, 1, &pos_one, &node_center)==0),ierr);
}
EPETRA_TEST_ERR(!(OverlapMatrix.FillComplete()==0),ierr);
// Make a gathered matrix from OverlapMatrix. It should be identical to StandardMatrix
Epetra_CrsMatrix GatheredMatrix(Copy, StandardGraph);
Epetra_Export Exporter(OverlapMap, StandardMap);
EPETRA_TEST_ERR(!(GatheredMatrix.Export(OverlapMatrix, Exporter, Add)==0),ierr);
EPETRA_TEST_ERR(!(GatheredMatrix.FillComplete()==0),ierr);
// Check if entries of StandardMatrix and GatheredMatrix are identical
int StandardNumEntries, GatheredNumEntries;
int * StandardIndices, * GatheredIndices;
double * StandardValues, * GatheredValues;
int StandardNumMyNonzeros = StandardMatrix.NumMyNonzeros();
int GatheredNumMyNonzeros = GatheredMatrix.NumMyNonzeros();
EPETRA_TEST_ERR(!(StandardNumMyNonzeros==GatheredNumMyNonzeros),ierr);
int StandardNumMyRows = StandardMatrix.NumMyRows();
int GatheredNumMyRows = GatheredMatrix.NumMyRows();
EPETRA_TEST_ERR(!(StandardNumMyRows==GatheredNumMyRows),ierr);
forierr = 0;
for (i=0; i< StandardNumMyRows; i++)
{
forierr += !(StandardMatrix.ExtractMyRowView(i, StandardNumEntries, StandardValues, StandardIndices)==0);
forierr += !(GatheredMatrix.ExtractMyRowView(i, GatheredNumEntries, GatheredValues, GatheredIndices)==0);
forierr += !(StandardNumEntries==GatheredNumEntries);
for (j=0; j < StandardNumEntries; j++) {
//if (StandardIndices[j]!=GatheredIndices[j])
// cout << "MyPID = " << MyPID << " i = " << i << " StandardIndices[" << j << "] = " << StandardIndices[j]
// << " GatheredIndices[" << j << "] = " << GatheredIndices[j] << endl;
//if (StandardValues[j]!=GatheredValues[j])
//cout << "MyPID = " << MyPID << " i = " << i << " StandardValues[" << j << "] = " << StandardValues[j]
// << " GatheredValues[" << j << "] = " << GatheredValues[j] << endl;
forierr += !(StandardIndices[j]==GatheredIndices[j]);
forierr += !(StandardValues[j]==GatheredValues[j]);
}
}
EPETRA_TEST_ERR(forierr,ierr);
if (verbose) cout << "Matrix Export Check OK" << endl << endl;
//Do Again with use of Epetra_OffsetIndex object for speed
Epetra_OffsetIndex OffsetIndex( OverlapMatrix.Graph(), GatheredMatrix.Graph(), Exporter );
EPETRA_TEST_ERR(!(GatheredMatrix.Export(OverlapMatrix, Exporter, Add)==0),ierr);
if (verbose) cout << "Optimized Matrix Export Check OK" << endl << endl;
bool passed;
Epetra_LongLongVector v1(StandardMap); v1.PutValue(2);
Epetra_LongLongVector v2(StandardMap); v2.PutValue(3);
Epetra_Export identExporter(StandardMap,StandardMap); // Identity exporter
EPETRA_TEST_ERR(!(v2.Export(v1, identExporter, Insert)==0),ierr);
passed = (v2.MinValue()==2);
EPETRA_TEST_ERR(!passed,ierr);
v1.PutValue(1);
Epetra_Import identImporter(StandardMap,StandardMap); // Identity importer
EPETRA_TEST_ERR(!(v2.Import(v1, identExporter, Insert)==0),ierr);
passed = passed && (v2.MaxValue()==1);
EPETRA_TEST_ERR(!passed,ierr);
if (verbose) {
if (passed) cout << "Identity Import/Export Check OK" << endl << endl;
else cout << "Identity Import/Export Check Failed" << endl << endl;
}
int NumSubMapElements = StandardMap.NumMyElements()/2;
int SubStart = Comm.MyPID();
NumSubMapElements = EPETRA_MIN(NumSubMapElements,StandardMap.NumMyElements()-SubStart);
Epetra_Map SubMap((long long) -1, NumSubMapElements, StandardMyGlobalElements+SubStart, 0LL, Comm);
Epetra_LongLongVector v3(View, SubMap, SubMap.MyGlobalElements64()); // Fill v3 with GID values for variety
Epetra_Export subExporter(SubMap, StandardMap); // Export to a subset of indices of standard map
EPETRA_TEST_ERR(!(v2.Export(v3,subExporter,Insert)==0),ierr);
forierr = 0;
for (i=0; i<SubMap.NumMyElements(); i++) {
int i1 = StandardMap.LID(SubMap.GID64(i));
forierr += !(v3[i]==v2[i1]);
}
EPETRA_TEST_ERR(forierr,ierr);
Epetra_Import subImporter(StandardMap, SubMap); // Import to a subset of indices of standard map
EPETRA_TEST_ERR(!(v1.Import(v3,subImporter,Insert)==0),ierr);
for (i=0; i<SubMap.NumMyElements(); i++) {
int i1 = StandardMap.LID(SubMap.GID64(i));
forierr += !(v3[i]==v1[i1]);
}
EPETRA_TEST_ERR(forierr,ierr);
if (verbose) {
if (forierr==0) cout << "SubMap Import/Export Check OK" << endl << endl;
else cout << "SubMap Import/Export Check Failed" << endl << endl;
}
#ifdef DOESNT_WORK_IN_PARALLEL
forierr = special_submap_import_test(Comm);
EPETRA_TEST_ERR(forierr, ierr);
if (verbose) {
if (forierr==0) cout << "Special SubMap Import Check OK" << endl << endl;
else cout << "Special SubMap Import Check Failed" << endl << endl;
}
#endif
forierr = alternate_import_constructor_test(Comm);
EPETRA_TEST_ERR(forierr, ierr);
if (verbose) {
if (forierr==0) cout << "Alternative Import Constructor Check OK" << endl << endl;
else cout << "Alternative Import Constructor Check Failed" << endl << endl;
}
// Release all objects
delete [] SourceMyGlobalElements;
delete [] TargetMyGlobalElements;
delete [] OverlapMyGlobalElements;
delete [] StandardMyGlobalElements;
delete [] Values;
delete [] Indices;
#ifdef EPETRA_MPI
MPI_Finalize() ;
#endif
/* end main
*/
return ierr ;
}
