/*
* Reduce (add) distributions from multiple MPI processors.
*/
void Distribution::reduce(MPI::Intracomm& communicator, int root)
{
long* totHistogram = new long[nBin_];
communicator.Reduce(histogram_.cArray(), totHistogram, nBin_, MPI::LONG, MPI::SUM, root);
if (communicator.Get_rank() == root) {
for (int i=0; i < nBin_; ++i) {
histogram_[i] = totHistogram[i];
}
} else {
for (int i=0; i < nBin_; ++i) {
histogram_[i] = 0.0;
}
}
delete totHistogram;
long totSample;
communicator.Reduce(&nSample_, &totSample, 1, MPI::LONG, MPI::SUM, root);
if (communicator.Get_rank() == root) {
nSample_ = totSample;
} else {
nSample_ = 0;
}
long totReject;
communicator.Reduce(&nReject_, &totReject, 1, MPI::LONG, MPI::SUM, root);
if (communicator.Get_rank() == root) {
nReject_ = totReject;
} else {
nReject_ = 0;
}
}
int main(int argc, char* argv[]) {
MPI::Init(argc, argv);
rank = MPI::COMM_WORLD.Get_rank();
size = MPI::COMM_WORLD.Get_size();
if (size < 2) MPI::COMM_WORLD.Abort(1);
if (size < 1+COLS+ROWS) MPI::COMM_WORLD.Abort(1);
MPI::Group globalGroup = MPI::COMM_WORLD.Get_group();
if (0 == rank) {
int matrix[COLS][ROWS], xirtam[ROWS][COLS];
srand(time(0));
for (int i=0; i<COLS; i++)
for (int j=0; j<ROWS; j++) {
matrix[i][j] = 9 * (double)rand() / (double)RAND_MAX;
xirtam[j][i] = matrix[i][j];
}
cout << "random matrica: " << endl;
for (int i=0; i<COLS; i++) {
for (int j=0; j<ROWS; j++)
cout << matrix[i][j] << " ";
cout << endl;
}
}
else {
MPI::Group group;
MPI::Intracomm comm;
int j=0, k=0;
for (int i=1; i<size; i++)
if (i % 2) ranksA[j++] = i;
else ranksB[k++] = i;
if (rank % 2)
group = globalGroup.Incl(size / 2 + size % 2, ranksA);
else
group = globalGroup.Incl(size / 2, ranksB);
comm = MPI::COMM_WORLD.Create(group);
int newRank = comm.Get_rank();
pline(); cout << rank << ", " << newRank << ", " << powerSum << endl;
fflush(stdout);
group.Free();
comm.Free();
}
//comm.Free();
MPI::Finalize();
return 0;
}
/*
* Broadcast a buffer.
*/
void Buffer::bcast(MPI::Intracomm& comm, int source)
{
int comm_size = comm.Get_size();
int myRank = comm.Get_rank();
if (source > comm_size - 1 || source < 0) {
UTIL_THROW("Source rank out of bounds");
}
int sendBytes;
if (myRank == source) {
sendBytes = sendPtr_ - sendBufferBegin_;
comm.Bcast(&sendBytes, 1, MPI::INT, source);
comm.Bcast(sendBufferBegin_, sendBytes, MPI::CHAR, source);
sendPtr_ = sendBufferBegin_;
sendType_ = NONE;
} else {
comm.Bcast(&sendBytes, 1, MPI::INT, source);
comm.Bcast(recvBufferBegin_, sendBytes, MPI::CHAR, source);
recvPtr_ = recvBufferBegin_;
recvType_ = NONE;
}
if (sendBytes > maxSendLocal_) {
maxSendLocal_ = sendBytes;
}
}
void LocalScalar3D<real>::Dump(BlockManager& blockManager, const int step, const char* label) {
ImposeBoundaryCondition(blockManager);
MPI::Intracomm comm = blockManager.getCommunicator();
ostringstream ossFileNameTime;
ossFileNameTime << "./BIN/";
mkdir(ossFileNameTime.str().c_str(), 0755);
#ifdef _BLOCK_IS_LARGE_
#else
#endif
for (int id = 0; id < blockManager.getNumBlock(); ++id) {
BlockBase* block = blockManager.getBlock(id);
::Vec3i size = block->getSize();
Vec3d origin = block->getOrigin();
Vec3d blockSize = block->getBlockSize();
Vec3d cellSize = block->getCellSize();
int level = block->getLevel();
ostringstream ossFileName;
ossFileName << "./BIN/";
ossFileName << "dump-";
ossFileName << label;
ossFileName << "-";
ossFileName.width(5);
ossFileName.setf(ios::fixed);
ossFileName.fill('0');
ossFileName << comm.Get_rank();
ossFileName << "-";
ossFileName.width(5);
ossFileName.setf(ios::fixed);
ossFileName.fill('0');
ossFileName << id;
ossFileName << "-";
ossFileName.width(10);
ossFileName.setf(ios::fixed);
ossFileName.fill('0');
ossFileName << step;
ossFileName << ".bin";
int cx = size.x + 2*vc;
int cy = size.y + 2*vc;
int cz = size.z + 2*vc;
int iNE = 1;
real* pData = GetBlockData(block);
ofstream ofs;
ofs.open(ossFileName.str().c_str(), ios::out | ios::binary);
ofs.write((char*)&size.x, sizeof(int));
ofs.write((char*)&size.y, sizeof(int));
ofs.write((char*)&size.z, sizeof(int));
ofs.write((char*)&vc , sizeof(int));
ofs.write((char*)&iNE , sizeof(int));
ofs.write((char*)pData , sizeof(real)*cx*cy*cz);
ofs.close();
}
}
void MpiFileIo::setIoCommunicator(MPI::Intracomm& communicator)
{
communicatorPtr_ = &communicator;
if (communicator.Get_rank() == 0) {
isIoProcessor_ = true;
} else {
isIoProcessor_ = false;
}
}
int getRank() const
{
int rank = Network::INVALID_VALUE;
if ( intraComm != MPI::COMM_NULL)
{
rank = intraComm.Get_rank();
}else
{
log.Err() << "getRank() returns invalid\n";
}
return rank;
}
/*
* Compute, store and return total number of atoms on all processors.
*/
void AtomStorage::computeNAtomTotal(MPI::Intracomm& communicator)
{
// If nAtomTotal is already set, do nothing and return.
// if (nAtomTotal_.isSet()) return;
int nAtomLocal = nAtom();
int nAtomTotal = 0;
communicator.Reduce(&nAtomLocal, &nAtomTotal, 1,
MPI::INT, MPI::SUM, 0);
if (communicator.Get_rank() !=0) {
nAtomTotal = 0;
}
nAtomTotal_.set(nAtomTotal);
}
/*
* Send a block (nonblocking)
*/
void MemoryOArchive::iSend(MPI::Intracomm& comm, MPI::Request& req, int dest)
{
int comm_size = comm.Get_size();
int myRank = comm.Get_rank();
// Preconditions
if (dest > comm_size - 1 || dest < 0) {
UTIL_THROW("Destination rank out of bounds");
}
if (dest == myRank) {
UTIL_THROW("Source and desination identical");
}
size_t sendBytes = cursor_ - buffer_;
size_t* sizePtr = (size_t*)buffer_;
*sizePtr = sendBytes;
req = comm.Isend(buffer_, sendBytes, MPI::UNSIGNED_CHAR, dest, 5);
}
/*
* Receive a block.
*/
void PackedData::recv(MPI::Intracomm& comm, int source)
{
MPI::Request request;
int myRank = comm.Get_rank();
int comm_size = comm.Get_size();
// Preconditons
if (source > comm_size - 1 || source < 0) {
UTIL_THROW("Source rank out of bounds");
}
if (source == myRank) {
UTIL_THROW("Source and desination identical");
}
request = comm.Irecv(begin_, capacity_, MPI::UNSIGNED_CHAR, source, 5);
request.Wait();
cursor_ = begin_;
}
void transfH_MPI(mblock<double>** Ap, mblock<float>** A, unsigned* seq_part)
{
unsigned rank = COMM_AHMED.Get_rank(),
nproc = COMM_AHMED.Get_size();
unsigned info[8];
if (rank==0) {
copyH(seq_part[1]-seq_part[0], Ap, A);
for (unsigned j=1; j<nproc; ++j) {
for (unsigned i=seq_part[j]; i<seq_part[j+1]; ++i) {
COMM_AHMED.Recv(info, 8, MPI::UNSIGNED, j, 7);
A[i] = new mblock<float>(info[0], info[1]);
float* tmp = NULL;
if (info[7]) {
tmp = new float[info[7]];
COMM_AHMED.Recv(tmp, info[7], MPI::FLOAT, j, 8);
}
A[i]->cpy_mbl(info+2, tmp);
delete [] tmp;
}
}
} else {
for (unsigned i=seq_part[rank]; i<seq_part[rank+1]; ++i) {
mblock<double>* p = Ap[i-seq_part[rank]];
info[0] = p->getn1();
info[1] = p->getn2();
p->get_prop(info+2);
info[7] = p->nvals();
COMM_AHMED.Send(info, 8, MPI::UNSIGNED, 0, 7);
if (info[7]) {
float* tmp = new float[info[7]];
for (unsigned i=0; i<info[7]; ++i) tmp[i] = (float) p->getdata()[i];
COMM_AHMED.Send(tmp, info[7], MPI::FLOAT, 0, 8);
delete [] tmp;
}
}
}
}
/*
* Send and receive buffer.
*/
void Buffer::sendRecv(MPI::Intracomm& comm, int source, int dest)
{
MPI::Request request[2];
int sendBytes = 0;
int myRank = comm.Get_rank();
int comm_size = comm.Get_size();
// Preconditions
if (dest > comm_size - 1 || dest < 0) {
UTIL_THROW("Destination rank out of bounds");
}
if (source > comm_size - 1 || source < 0) {
UTIL_THROW("Source rank out of bounds");
}
if (dest == myRank) {
UTIL_THROW("Destination and my rank are identical");
}
if (source == myRank) {
UTIL_THROW("Source and my rank are identical");
}
// Start nonblocking receive.
request[0] = comm.Irecv(recvBufferBegin_, bufferCapacity_ ,
MPI::CHAR, source, 5);
// Start nonblocking send.
sendBytes = sendPtr_ - sendBufferBegin_;
request[1] = comm.Isend(sendBufferBegin_, sendBytes , MPI::CHAR, dest, 5);
// Wait for completion of receive.
request[0].Wait();
recvPtr_ = recvBufferBegin_;
// Wait for completion of send.
request[1].Wait();
// Update statistics.
if (sendBytes > maxSendLocal_) {
maxSendLocal_ = sendBytes;
}
}
/*
* Receive a buffer.
*/
void Buffer::recv(MPI::Intracomm& comm, int source)
{
MPI::Request request;
int myRank = comm.Get_rank();
int comm_size = comm.Get_size();
// Preconditons
if (source > comm_size - 1 || source < 0) {
UTIL_THROW("Source rank out of bounds");
}
if (source == myRank) {
UTIL_THROW("Source and destination identical");
}
request = comm.Irecv(recvBufferBegin_, bufferCapacity_,
MPI::CHAR, source, 5);
request.Wait();
recvType_ = NONE;
recvPtr_ = recvBufferBegin_;
}
/*
* Send a block.
*/
void PackedData::send(MPI::Intracomm& comm, int dest)
{
MPI::Request request;
int sendBytes = 0;
int comm_size = comm.Get_size();
int myRank = comm.Get_rank();
// Preconditions
if (dest > comm_size - 1 || dest < 0) {
UTIL_THROW("Destination rank out of bounds");
}
if (dest == myRank) {
UTIL_THROW("Source and desination identical");
}
sendBytes = cursor_ - begin_;
request = comm.Isend(begin_, sendBytes, MPI::UNSIGNED_CHAR, dest, 5);
request.Wait();
}
/// Octree情報を他rankにブロードキャスト.
void BCMOctree::broadcast(MPI::Intracomm& comm)
{
assert(comm.Get_rank() == 0);
rootGrid->broadcast(comm);
int numLeafNode = leafNodeArray.size();
int ibuf[2];
ibuf[0] = numLeafNode;
ibuf[1] = ordering;
comm.Bcast(&ibuf, 2, MPI::INT, 0);
size_t size = Pedigree::GetSerializeSize();
unsigned char* buf = new unsigned char[size * numLeafNode];
size_t ip = 0;
for (int id = 0; id < rootGrid->getSize(); id++) {
packPedigrees(rootNodes[id], ip, buf);
}
comm.Bcast(buf, size*numLeafNode, MPI::BYTE, 0);
delete[] buf;
}
// Metropolis-Hastings population size resampling; not used anymore
void resample_popsizes_mh(ArgModel *model, const LocalTrees *trees,
bool sample_popsize_recomb, double heat) {
list<PopsizeConfigParam> &l = model->popsize_config.params;
double curr_like = sample_popsize_recomb ? calc_arg_prior(model, trees) :
calc_arg_prior_recomb_integrate(model, trees, NULL, NULL, NULL);
#ifdef ARGWEAVER_MPI
MPI::Intracomm *comm = model->mc3.group_comm;
int rank = comm->Get_rank();
comm->Reduce(rank == 0 ? MPI_IN_PLACE : &curr_like,
&curr_like, 1, MPI::DOUBLE, MPI_SUM, 0);
#endif
for (int rep=0; rep < model->popsize_config.numsample; rep++) {
int idx=0;
for (list<PopsizeConfigParam>::iterator it = l.begin();
it != l.end(); it++) {
curr_like =
resample_single_popsize_mh(model, trees, sample_popsize_recomb,
heat, it, curr_like, idx++);
}
}
}
/*
* Receive a block.
*/
void MemoryIArchive::recv(MPI::Intracomm& comm, int source)
{
int myRank = comm.Get_rank();
int comm_size = comm.Get_size();
// Preconditions
if (source > comm_size - 1 || source < 0) {
UTIL_THROW("Source rank out of bounds");
}
if (source == myRank) {
UTIL_THROW("Source and desination identical");
}
size_t recvCapacity = capacity_ + sizeof(size_t);
comm.Recv(buffer_, recvCapacity, MPI::UNSIGNED_CHAR, source, 5);
begin_ = buffer_ + sizeof(size_t);
cursor_ = begin_;
size_t* sizePtr = (size_t*) buffer_;
size_t size = *sizePtr;
end_ = buffer_ + size;
}
FullyDistSpVec<IT, IT> FullyDistSpVec<IT, NT>::sort()
{
MPI::Intracomm World = commGrid->GetWorld();
FullyDistSpVec<IT,IT> temp(commGrid);
IT nnz = getlocnnz();
pair<NT,IT> * vecpair = new pair<NT,IT>[nnz];
int nprocs = World.Get_size();
int rank = World.Get_rank();
IT * dist = new IT[nprocs];
dist[rank] = nnz;
World.Allgather(MPI::IN_PLACE, 1, MPIType<IT>(), dist, 1, MPIType<IT>());
IT sizeuntil = accumulate(dist, dist+rank, 0);
for(IT i=0; i< nnz; ++i)
{
vecpair[i].first = num[i]; // we'll sort wrt numerical values
vecpair[i].second = ind[i] + sizeuntil;
}
SpParHelper::MemoryEfficientPSort(vecpair, nnz, dist, World);
vector< IT > nind(nnz);
vector< IT > nnum(nnz);
for(IT i=0; i< nnz; ++i)
{
num[i] = vecpair[i].first; // sorted range (change the object itself)
nind[i] = ind[i]; // make sure the sparsity distribution is the same
nnum[i] = vecpair[i].second; // inverse permutation stored as numerical values
}
delete [] vecpair;
delete [] dist;
temp.NOT_FOUND = NOT_FOUND;
temp.glen = glen;
temp.ind = nind;
temp.num = nnum;
return temp;
}
/*
* Send a buffer.
*/
void Buffer::send(MPI::Intracomm& comm, int dest)
{
MPI::Request request;
int sendBytes = 0;
int comm_size = comm.Get_size();
int myRank = comm.Get_rank();
// Preconditions
if (dest > comm_size - 1 || dest < 0) {
UTIL_THROW("Destination rank out of bounds");
}
if (dest == myRank) {
UTIL_THROW("Source and destination identical");
}
sendBytes = sendPtr_ - sendBufferBegin_;
request = comm.Isend(sendBufferBegin_, sendBytes, MPI::CHAR, dest, 5);
request.Wait();
// Update statistics.
if (sendBytes > maxSendLocal_) {
maxSendLocal_ = sendBytes;
}
}
void mltaGeHVec_MPI(double d, mblock<double>** A, double* x, double* y,
unsigned p, unsigned *seq_part, blcluster** blList)
{
unsigned rank = COMM_AHMED.Get_rank();
unsigned info[3]; // nblcks, beg2, n2
if (rank == 0)
{
for (unsigned j=1; j<p; j++)
{
info[0] = seq_part[j+1] - seq_part[j];
dimsx_(blList+seq_part[j], info[0], info[1], info[2]);
COMM_AHMED.Send(info, 3, MPI::UNSIGNED, j, 1);
COMM_AHMED.Send(x+info[1], info[2], MPI::DOUBLE, j, 2);
}
// compute for processor 0
for (unsigned i=seq_part[0]; i<seq_part[1]; ++i)
{
unsigned idx = i-seq_part[0];
A[idx]->mltaVec(d, x+blList[i]->getb2(), y+blList[i]->getb1());
}
for (unsigned j=1; j<p; ++j)
{
unsigned dimsy[2];
COMM_AHMED.Recv(dimsy, 2, MPI::UNSIGNED, j, 3);
double* tmp = new double[dimsy[1]];
COMM_AHMED.Recv(tmp, dimsy[1], MPI::DOUBLE, j, 4);
blas::add(dimsy[1], tmp, y+dimsy[0]);
delete [] tmp;
}
}
else
{
COMM_AHMED.Recv(info, 3, MPI::UNSIGNED, 0, 1);
// receive required part of x
double* xp = new double[info[2]];
COMM_AHMED.Recv(xp, info[2], MPI::DOUBLE, 0, 2);
unsigned dimsy[2];
dimsy_(blList+seq_part[rank], info[0], dimsy[0], dimsy[1]);
double* tmp = new double[dimsy[1]];
blas::setzero(dimsy[1], tmp);
for (unsigned i=seq_part[rank]; i<seq_part[rank+1]; ++i)
{
unsigned idx = i-seq_part[rank];
A[idx]->mltaVec(d, xp+blList[i]->getb2()-info[1],
tmp+blList[i]->getb1()-dimsy[0]);
}
COMM_AHMED.Send(dimsy, 2, MPI::UNSIGNED, 0, 3);
COMM_AHMED.Send(tmp, dimsy[1], MPI::DOUBLE, 0, 4);
delete [] tmp;
delete [] xp;
}
}
// currently only hacked for spheres, with radius and sd as two parameters
bool HipGISAXS::fit_steepest_descent(real_t zcut,
real_t radius_min, real_t radius_max, real_t radius_num,
real_t sd_min, real_t sd_max, real_t sd_num,
unsigned int dim, MPI::Intracomm& world_comm,
int x_min, int x_max, int x_step) {
int mpi_rank = world_comm.Get_rank();
if(!init_steepest_fit(world_comm, zcut)) return false;
int num_alphai = 0, num_phi = 0, num_tilt = 0;;
real_t alphai_min, alphai_max, alphai_step;
HiGInput::instance().scattering_alphai(alphai_min, alphai_max, alphai_step);
if(alphai_max < alphai_min) alphai_max = alphai_min;
if(alphai_min == alphai_max || alphai_step == 0) num_alphai = 1;
else num_alphai = (alphai_max - alphai_min) / alphai_step + 1;
real_t phi_min, phi_max, phi_step;
HiGInput::instance().scattering_inplanerot(phi_min, phi_max, phi_step);
if(phi_step == 0) num_phi = 1;
else num_phi = (phi_max - phi_min) / phi_step + 1;
real_t tilt_min, tilt_max, tilt_step;
HiGInput::instance().scattering_tilt(tilt_min, tilt_max, tilt_step);
if(tilt_step == 0) num_tilt = 1;
else num_tilt = (tilt_max - tilt_min) / tilt_step + 1;
std::cout << "** Num alphai: " << num_alphai << std::endl
<< "** Num phi: " << num_phi << std::endl
<< "** Num tilt: " << num_tilt << std::endl;
// prepare parameters
std::vector<std::vector<real_t> > params;
int num_params = 2;
std::vector<real_t> temp;
real_t deltap = 0.0;
if(radius_num <= 1)
temp.push_back(radius_min);
else {
deltap = fabs(radius_max - radius_min) / (radius_num - 1);
for(int i = 0; i < radius_num; ++ i) {
temp.push_back(radius_min + i * deltap);
} // for
} // if-else
params.push_back(temp);
temp.clear();
if(sd_num <= 1)
temp.push_back(sd_min);
else {
deltap = fabs(sd_max - sd_min) / (sd_num - 1);
for(int i = 0; i < sd_num; ++ i) {
temp.push_back(sd_min + i * deltap);
} // for
} // if-else
params.push_back(temp);
temp.clear();
// this will work only on one shape and one structure
const real_t err_threshold = 1e-8;
const unsigned int max_iter = 200;
std::vector<real_t> param_vals;
//param_vals.push_back(16.0);
//param_vals.push_back(6.0);
param_vals.push_back(23.0);
param_vals.push_back(2.0);
std::vector<real_t> param_deltas;
param_deltas.push_back(0.05);
param_deltas.push_back(0.05);
real_t gamma_const = 0.05;
real_t qdeltay = QGrid::instance().delta_y();
real_t alpha_i = alphai_min;
// high level of parallelism here (alphai, phi, tilt) for dynamicity ...
for(int i = 0; i < num_alphai; i ++, alpha_i += alphai_step) {
real_t alphai = alpha_i * PI_ / 180;
real_t phi = phi_min;
for(int j = 0; j < num_phi; j ++, phi += phi_step) {
real_t tilt = tilt_min;
for(int k = 0; k < num_tilt; k ++, tilt += tilt_step) {
std::cout << "-- Computing reference GISAXS "
<< i * num_phi * num_tilt + j * num_tilt + k + 1 << " / "
<< num_alphai * num_phi * num_tilt
<< " [alphai = " << alpha_i << ", phi = " << phi
<< ", tilt = " << tilt << "] ..." << std::endl;
/* run the reference gisaxs simulation using input params */
real_t* ref_data = NULL;
if(!run_gisaxs(alpha_i, alphai, phi, tilt, ref_data, world_comm)) {
if(mpi_rank == 0) std::cerr << "error: could not finish successfully" << std::endl;
return false;
} // if
if(dim != 1) {
std::cerr << "uh-oh: only 1D is supported for now" << std::endl;
return false;
} // if
real_t* ref_z_cut = new (std::nothrow) real_t[nqy_];
for(unsigned int iy = 0; iy < nqy_; ++ iy) {
// assuming nqz_ == 1 ...
ref_z_cut[iy] = ref_data[nqx_ * iy + 0];
} // for
delete[] ref_data;
// this will store z cut values for each iteration for plotting later
real_t* z_cuts = new (std::nothrow) real_t[nqy_ * max_iter];
real_t* temp_zcuts = new (std::nothrow) real_t[nqy_];
// do some preprocessing
// start the main loop, bound by max_iter and err_threshold
// compute gisaxs for current parameter values
// compute the neighbors parameter values
// for 12 combinations of current and neighbors, compute gisaxs and error
// compute the derivatives (gradient) and error stuff
// update parameter values
// compute the error surface
real_t err = 10.0;
std::vector<real_t> param1_list;
std::vector<real_t> param2_list;
structure_iterator_t structure_iter = HiGInput::instance().structure_begin();
Structure* structure = &((*structure_iter).second);
Shape* shape = HiGInput::instance().shape(*structure);
shape_param_iterator_t shape_param = (*shape).param_begin();
real_t* data = NULL;
std::vector<real_t> param_error_data;
for(unsigned int iter = 0; iter < max_iter; ++ iter) {
param1_list.clear();
param1_list.push_back(param_vals[0] - 2 * param_deltas[0]); // p1mm
param1_list.push_back(param_vals[0] - param_deltas[0]); // p1m
param1_list.push_back(param_vals[0]); // p1
param1_list.push_back(param_vals[0] + param_deltas[0]); // p1p
param1_list.push_back(param_vals[0] + 2 * param_deltas[0]); // p1pp
param2_list.clear();
param2_list.push_back(param_vals[1] - 2 * param_deltas[1]); // p2mm
param2_list.push_back(param_vals[1] - param_deltas[1]); // p2m
param2_list.push_back(param_vals[1]); // p2
param2_list.push_back(param_vals[1] + param_deltas[1]); // p2p
param2_list.push_back(param_vals[1] + 2 * param_deltas[1]); // p2pp
// current point
(*shape_param).second.mean(param1_list[2]);
(*shape_param).second.deviation(param2_list[2]);
if(!run_gisaxs(alpha_i, alphai, phi, tilt, data, world_comm)) {
if(mpi_rank == 0)
std::cerr << "error: could not finish successfully" << std::endl;
return false;
} // if
for(unsigned int iy = 0; iy < nqy_; ++ iy) {
// assuming nqz_ == 1 ...
z_cuts[iter * nqy_ + iy] = data[nqx_ * iy];
} // for
delete[] data; data = NULL;
real_t err22 = compute_cut_fit_error(z_cuts + iter * nqy_, ref_z_cut, qdeltay);
// 12 neighbors
(*shape_param).second.mean(param1_list[0]);
(*shape_param).second.deviation(param2_list[2]);
if(!run_gisaxs(alpha_i, alphai, phi, tilt, data, world_comm)) {
if(mpi_rank == 0)
std::cerr << "error: could not finish successfully" << std::endl;
return false;
} // if
for(unsigned int iy = 0; iy < nqy_; ++ iy) {
// assuming nqz_ == 1 ...
temp_zcuts[iy] = data[nqx_ * iy];
} // for
delete[] data; data = NULL;
real_t err02 = compute_cut_fit_error(temp_zcuts, ref_z_cut, qdeltay);
(*shape_param).second.mean(param1_list[1]);
(*shape_param).second.deviation(param2_list[1]);
if(!run_gisaxs(alpha_i, alphai, phi, tilt, data, world_comm)) {
if(mpi_rank == 0)
std::cerr << "error: could not finish successfully" << std::endl;
return false;
} // if
for(unsigned int iy = 0; iy < nqy_; ++ iy) {
// assuming nqz_ == 1 ...
temp_zcuts[iy] = data[nqx_ * iy];
} // for
delete[] data; data = NULL;
real_t err11 = compute_cut_fit_error(temp_zcuts, ref_z_cut, qdeltay);
(*shape_param).second.mean(param1_list[1]);
(*shape_param).second.deviation(param2_list[2]);
if(!run_gisaxs(alpha_i, alphai, phi, tilt, data, world_comm)) {
if(mpi_rank == 0)
std::cerr << "error: could not finish successfully" << std::endl;
return false;
} // if
for(unsigned int iy = 0; iy < nqy_; ++ iy) {
// assuming nqz_ == 1 ...
temp_zcuts[iy] = data[nqx_ * iy];
} // for
delete[] data; data = NULL;
real_t err12 = compute_cut_fit_error(temp_zcuts, ref_z_cut, qdeltay);
(*shape_param).second.mean(param1_list[1]);
(*shape_param).second.deviation(param2_list[3]);
if(!run_gisaxs(alpha_i, alphai, phi, tilt, data, world_comm)) {
if(mpi_rank == 0)
std::cerr << "error: could not finish successfully" << std::endl;
return false;
} // if
for(unsigned int iy = 0; iy < nqy_; ++ iy) {
// assuming nqz_ == 1 ...
temp_zcuts[iy] = data[nqx_ * iy];
} // for
delete[] data; data = NULL;
real_t err13 = compute_cut_fit_error(temp_zcuts, ref_z_cut, qdeltay);
(*shape_param).second.mean(param1_list[2]);
(*shape_param).second.deviation(param2_list[0]);
if(!run_gisaxs(alpha_i, alphai, phi, tilt, data, world_comm)) {
if(mpi_rank == 0)
std::cerr << "error: could not finish successfully" << std::endl;
return false;
} // if
for(unsigned int iy = 0; iy < nqy_; ++ iy) {
// assuming nqz_ == 1 ...
temp_zcuts[iy] = data[nqx_ * iy];
} // for
delete[] data; data = NULL;
real_t err20 = compute_cut_fit_error(temp_zcuts, ref_z_cut, qdeltay);
(*shape_param).second.mean(param1_list[2]);
(*shape_param).second.deviation(param2_list[1]);
if(!run_gisaxs(alpha_i, alphai, phi, tilt, data, world_comm)) {
if(mpi_rank == 0)
std::cerr << "error: could not finish successfully" << std::endl;
return false;
} // if
for(unsigned int iy = 0; iy < nqy_; ++ iy) {
// assuming nqz_ == 1 ...
temp_zcuts[iy] = data[nqx_ * iy];
} // for
delete[] data; data = NULL;
real_t err21 = compute_cut_fit_error(temp_zcuts, ref_z_cut, qdeltay);
(*shape_param).second.mean(param1_list[2]);
(*shape_param).second.deviation(param2_list[3]);
if(!run_gisaxs(alpha_i, alphai, phi, tilt, data, world_comm)) {
if(mpi_rank == 0)
std::cerr << "error: could not finish successfully" << std::endl;
return false;
} // if
for(unsigned int iy = 0; iy < nqy_; ++ iy) {
// assuming nqz_ == 1 ...
temp_zcuts[iy] = data[nqx_ * iy];
} // for
delete[] data; data = NULL;
real_t err23 = compute_cut_fit_error(temp_zcuts, ref_z_cut, qdeltay);
(*shape_param).second.mean(param1_list[2]);
(*shape_param).second.deviation(param2_list[4]);
if(!run_gisaxs(alpha_i, alphai, phi, tilt, data, world_comm)) {
if(mpi_rank == 0)
std::cerr << "error: could not finish successfully" << std::endl;
return false;
} // if
for(unsigned int iy = 0; iy < nqy_; ++ iy) {
// assuming nqz_ == 1 ...
temp_zcuts[iy] = data[nqx_ * iy];
} // for
delete[] data; data = NULL;
real_t err24 = compute_cut_fit_error(temp_zcuts, ref_z_cut, qdeltay);
(*shape_param).second.mean(param1_list[3]);
(*shape_param).second.deviation(param2_list[1]);
if(!run_gisaxs(alpha_i, alphai, phi, tilt, data, world_comm)) {
if(mpi_rank == 0)
std::cerr << "error: could not finish successfully" << std::endl;
return false;
} // if
for(unsigned int iy = 0; iy < nqy_; ++ iy) {
// assuming nqz_ == 1 ...
temp_zcuts[iy] = data[nqx_ * iy];
} // for
delete[] data; data = NULL;
real_t err31 = compute_cut_fit_error(temp_zcuts, ref_z_cut, qdeltay);
(*shape_param).second.mean(param1_list[3]);
(*shape_param).second.deviation(param2_list[2]);
if(!run_gisaxs(alpha_i, alphai, phi, tilt, data, world_comm)) {
if(mpi_rank == 0)
std::cerr << "error: could not finish successfully" << std::endl;
return false;
} // if
for(unsigned int iy = 0; iy < nqy_; ++ iy) {
// assuming nqz_ == 1 ...
temp_zcuts[iy] = data[nqx_ * iy];
} // for
delete[] data; data = NULL;
real_t err32 = compute_cut_fit_error(temp_zcuts, ref_z_cut, qdeltay);
(*shape_param).second.mean(param1_list[3]);
(*shape_param).second.deviation(param2_list[3]);
if(!run_gisaxs(alpha_i, alphai, phi, tilt, data, world_comm)) {
if(mpi_rank == 0)
std::cerr << "error: could not finish successfully" << std::endl;
return false;
} // if
for(unsigned int iy = 0; iy < nqy_; ++ iy) {
// assuming nqz_ == 1 ...
temp_zcuts[iy] = data[nqx_ * iy];
} // for
delete[] data; data = NULL;
real_t err33 = compute_cut_fit_error(temp_zcuts, ref_z_cut, qdeltay);
(*shape_param).second.mean(param1_list[4]);
(*shape_param).second.deviation(param2_list[2]);
if(!run_gisaxs(alpha_i, alphai, phi, tilt, data, world_comm)) {
if(mpi_rank == 0)
std::cerr << "error: could not finish successfully" << std::endl;
return false;
} // if
for(unsigned int iy = 0; iy < nqy_; ++ iy) {
// assuming nqz_ == 1 ...
temp_zcuts[iy] = data[nqx_ * iy];
} // for
delete[] data; data = NULL;
real_t err42 = compute_cut_fit_error(temp_zcuts, ref_z_cut, qdeltay);
// 22 0
// 02 1mm
// 11 1m2m
// 12 1m
// 13 1m2p
// 20 2mm
// 21 2m
// 23 2p
// 24 2pp
// 31 1p2m
// 32 1p
// 33 1p2p
// 42 1pp
real_t derr1 = (err32 - err12) / (2 * param_deltas[0]);
real_t derr2 = (err23 - err21) / (2 * param_deltas[1]);
err = sqrt(derr1 * derr1 + derr2 * derr2);
std::cout << "++ Iteration: " << iter << ", Error: " << err << std::endl;
std::cout << "++ Parameter 1: " << param_vals[0]
<< ", Parameter 2: " << param_vals[1] << std::endl;
param_error_data.push_back(iter);
param_error_data.push_back(param_vals[0]);
param_error_data.push_back(param_vals[1]);
param_error_data.push_back(err);
if(err < err_threshold) break;
real_t herr11 = (err42 + err02 - 2 * err22) /
(4 * param_deltas[0] * param_deltas[0]);
real_t herr12 = (err33 - err13 - (err31 - err11)) /
(4 * param_deltas[0] * param_deltas[1]);
real_t herr21 = (err33 - err13 - (err31 - err11)) /
(4 * param_deltas[0] * param_deltas[1]);
real_t herr22 = (err24 + err20 - 2 * err22) /
(4 * param_deltas[1] * param_deltas[1]);
real_t* herr = new (std::nothrow) real_t[2 * 2];
herr[0] = herr11;
herr[1] = herr12;
herr[2] = herr21;
herr[3] = herr22;
real_t* herrinv;
mldivide(2, herr, herrinv);
param_vals[0] -= gamma_const * (herrinv[0] * derr1 + herrinv[1] * derr2);
param_vals[1] -= gamma_const * (herrinv[2] * derr1 + herrinv[3] * derr2);
delete[] herrinv;
delete[] herr;
} // for
// compute the error surface
std::vector<std::vector<real_t> >::iterator mean_iter = params.begin();
std::vector<std::vector<real_t> >::iterator sd_iter = mean_iter + 1;
std::vector<real_t> err_surface;
for(std::vector<real_t>::iterator curr_mean = (*mean_iter).begin();
curr_mean != (*mean_iter).end(); ++ curr_mean) {
for(std::vector<real_t>::iterator curr_sd = (*sd_iter).begin();
curr_sd != (*sd_iter).end(); ++ curr_sd) {
(*shape_param).second.mean(*curr_mean);
(*shape_param).second.deviation(*curr_sd);
if(!run_gisaxs(alpha_i, alphai, phi, tilt, data, world_comm)) {
if(mpi_rank == 0)
std::cerr << "error: could not finish successfully" << std::endl;
return false;
} // if
for(unsigned int iy = 0; iy < nqy_; ++ iy) {
// assuming nqz_ == 1 ...
temp_zcuts[iy] = data[nqx_ * iy];
} // for
delete[] data; data = NULL;
real_t curr_err = compute_cut_fit_error(temp_zcuts, ref_z_cut, qdeltay);
err_surface.push_back(*curr_mean);
err_surface.push_back(*curr_sd);
err_surface.push_back(curr_err);
} // for
} // for
// write data to files
// define output filename
std::stringstream alphai_b, phi_b, tilt_b;
std::string alphai_s, phi_s, tilt_s;
alphai_b << alpha_i; alphai_s = alphai_b.str();
phi_b << phi; phi_s = phi_b.str();
tilt_b << tilt; tilt_s = tilt_b.str();
std::string param_error_file(HiGInput::instance().param_pathprefix() +
"/" + HiGInput::instance().runname() +
"/param_error_ai=" + alphai_s + "_rot=" + phi_s +
"_tilt=" + tilt_s + ".dat");
std::string z_cut_file(HiGInput::instance().param_pathprefix() +
"/" + HiGInput::instance().runname() +
"/z_cut_ai=" + alphai_s + "_rot=" + phi_s +
"_tilt=" + tilt_s + ".dat");
std::string err_surf_file(HiGInput::instance().param_pathprefix() +
"/" + HiGInput::instance().runname() +
"/err_surf_ai=" + alphai_s + "_rot=" + phi_s +
"_tilt=" + tilt_s + ".dat");
// write param_error_data
std::ofstream param_error_f(param_error_file.c_str());
for(std::vector<real_t>::iterator pei = param_error_data.begin();
pei != param_error_data.end(); pei += 4) {
param_error_f << *pei << "\t" << *(pei + 1) << "\t" << *(pei + 2) << "\t"
<< *(pei + 3) << std::endl;
} // for
param_error_f.close();
// write ref_z_cut and z_cuts
std::ofstream zcut_f(z_cut_file.c_str());
for(unsigned int yy = 0; yy < nqy_; ++ yy) {
zcut_f << ref_z_cut[yy] << "\t";
} // for
zcut_f << std::endl;
for(unsigned int i = 0; i < max_iter; ++ i) {
for(unsigned int yy = 0; yy < nqy_; ++ yy) {
zcut_f << z_cuts[i * nqy_ + yy] << "\t";
} // for
zcut_f << std::endl;
} // for
zcut_f.close();
// write error surface
std::ofstream err_surf_f(err_surf_file.c_str());
for(std::vector<real_t>::iterator surfi = err_surface.begin();
surfi != err_surface.end(); surfi += 3) {
err_surf_f << *surfi << "\t" << *(surfi + 1) << "\t" << *(surfi + 2) << std::endl;
} // for
err_surf_f.close();
(*shape_param).second.mean(22.0);
(*shape_param).second.deviation(7.0);
param_error_data.clear();
delete[] temp_zcuts;
delete[] z_cuts;
delete[] ref_z_cut;
std::cout << "parameter values: " << param_vals[0] << ", " << param_vals[1]
<< " [error: " << err << "]" << std::endl;
// synchronize all procs after each run
world_comm.Barrier();
} // for tilt
} // for phi
} // for alphai
return true;
} // HipGISAXS::fit_all_gisaxs()
ifstream& FullyDistSpVec<IT,NT>::ReadDistribute (ifstream& infile, int master)
{
IT total_nnz;
MPI::Intracomm World = commGrid->GetWorld();
int neighs = World.Get_size(); // number of neighbors (including oneself)
int buffperneigh = MEMORYINBYTES / (neighs * (sizeof(IT) + sizeof(NT)));
int * displs = new int[neighs];
for (int i=0; i<neighs; ++i)
displs[i] = i*buffperneigh;
int * curptrs = NULL;
int recvcount = 0;
IT * inds = NULL;
NT * vals = NULL;
int rank = World.Get_rank();
if(rank == master) // 1 processor only
{
inds = new IT [ buffperneigh * neighs ];
vals = new NT [ buffperneigh * neighs ];
curptrs = new int[neighs];
fill_n(curptrs, neighs, 0); // fill with zero
if (infile.is_open())
{
infile.clear();
infile.seekg(0);
infile >> glen >> total_nnz;
World.Bcast(&glen, 1, MPIType<IT>(), master);
IT tempind;
NT tempval;
double loadval;
IT cnz = 0;
while ( (!infile.eof()) && cnz < total_nnz)
{
infile >> tempind;
//infile >> tempval;
infile >> loadval;
tempval = static_cast<NT>(loadval);
tempind--;
IT locind;
int rec = Owner(tempind, locind); // recipient (owner) processor
inds[ rec * buffperneigh + curptrs[rec] ] = locind;
vals[ rec * buffperneigh + curptrs[rec] ] = tempval;
++ (curptrs[rec]);
if(curptrs[rec] == buffperneigh || (cnz == (total_nnz-1)) ) // one buffer is full, or file is done !
{
// first, send the receive counts ...
World.Scatter(curptrs, 1, MPI::INT, &recvcount, 1, MPI::INT, master);
// generate space for own recv data ... (use arrays because vector<bool> is cripled, if NT=bool)
IT * tempinds = new IT[recvcount];
NT * tempvals = new NT[recvcount];
// then, send all buffers that to their recipients ...
World.Scatterv(inds, curptrs, displs, MPIType<IT>(), tempinds, recvcount, MPIType<IT>(), master);
World.Scatterv(vals, curptrs, displs, MPIType<NT>(), tempvals, recvcount, MPIType<NT>(), master);
// now push what is ours to tuples
for(IT i=0; i< recvcount; ++i)
{
ind.push_back( tempinds[i] ); // already offset'd by the sender
num.push_back( tempvals[i] );
}
// reset current pointers so that we can reuse {inds,vals} buffers
fill_n(curptrs, neighs, 0);
DeleteAll(tempinds, tempvals);
}
++ cnz;
}
assert (cnz == total_nnz);
// Signal the end of file to other processors along the diagonal
fill_n(curptrs, neighs, numeric_limits<int>::max());
World.Scatter(curptrs, 1, MPI::INT, &recvcount, 1, MPI::INT, master);
}
void LocalScalar3D<real>::Load2(BlockManager& blockManager, const int step, const char* label) {
MPI::Intracomm comm = blockManager.getCommunicator();
ostringstream ossFileName;
ossFileName << "./BIN/";
ossFileName << "dump-";
ossFileName << label;
ossFileName << "-";
ossFileName.width(5);
ossFileName.setf(ios::fixed);
ossFileName.fill('0');
ossFileName << comm.Get_rank();
ossFileName << "-";
ossFileName.width(10);
ossFileName.setf(ios::fixed);
ossFileName.fill('0');
ossFileName << step;
ossFileName << ".bin";
int nx = 0;
int ny = 0;
int nz = 0;
int nv = 0;
int ne = 0;
int nb = 0;
ifstream ifs;
ifs.open(ossFileName.str().c_str(), ios::in | ios::binary);
ifs.read((char*)&nx, sizeof(int));
ifs.read((char*)&ny, sizeof(int));
ifs.read((char*)&nz, sizeof(int));
ifs.read((char*)&nv, sizeof(int));
ifs.read((char*)&ne, sizeof(int));
ifs.read((char*)&nb, sizeof(int));
int cx = nx + 2*nv;
int cy = ny + 2*nv;
int cz = nz + 2*nv;
BlockBase* block = blockManager.getBlock(0);
::Vec3i size = block->getSize();
if( nx == size.x && ny == size.y && nz == size.z && nv == vc && ne == 1 && nb == blockManager.getNumBlock() ) {
for (int id = 0; id < blockManager.getNumBlock(); ++id) {
block = blockManager.getBlock(id);
real* pData = GetBlockData(block);
ifs.read((char*)pData, sizeof(real)*cx*cy*cz);
}
} else if( 2*nx == size.x && 2*ny == size.y && 2*nz == size.z && nv == vc && ne == 1 && nb == blockManager.getNumBlock() ) {
real *pDataS = new real [cx*cy*cz];
for (int id = 0; id < blockManager.getNumBlock(); ++id) {
block = blockManager.getBlock(id);
real* pData = GetBlockData(block);
ifs.read((char*)pDataS, sizeof(real)*cx*cy*cz);
int sz[3] = {2*nx, 2*ny, 2*nz};
sf3d_copy_x2_(
(real*)pData,
(real*)pDataS,
(int*)sz,
(int*)&vc);
}
delete [] pDataS;
} else {
Exit(0);
}
ifs.close();
ImposeBoundaryCondition(blockManager);
}