void NSDFWriter::flush()
{
// We need to update the tend on each write since we do not know
// when the simulation is getting over and when it is just paused.
writeScalarAttr<string>(filehandle_, "tend", iso_time(NULL));
// append all uniform data
for (map< string, hid_t>::iterator it = classFieldToUniform_.begin();
it != classFieldToUniform_.end(); ++it){
map< string, vector < unsigned int > >::iterator idxit = classFieldToSrcIndex_.find(it->first);
if (idxit == classFieldToSrcIndex_.end()){
cerr << "Error: NSDFWriter::flush - could not find entry for " << it->first <<endl;
break;
}
if (data_.size() == 0 || data_[0].size() == 0){
break;
}
double * buffer = (double*)calloc(idxit->second.size() * steps_, sizeof(double));
vector< double > values;
for (unsigned int ii = 0; ii < idxit->second.size(); ++ii){
for (unsigned int jj = 0; jj < steps_; ++jj){
buffer[ii * steps_ + jj] = data_[idxit->second[ii]][jj];
}
data_[idxit->second[ii]].clear();
}
hid_t filespace = H5Dget_space(it->second);
if (filespace < 0){
break;
}
hsize_t dims[2];
hsize_t maxdims[2];
// retrieve current datset dimensions
herr_t status = H5Sget_simple_extent_dims(filespace, dims, maxdims);
hsize_t newdims[] = {dims[0], dims[1] + steps_}; // new column count
status = H5Dset_extent(it->second, newdims); // extend dataset to new column count
H5Sclose(filespace);
filespace = H5Dget_space(it->second); // get the updated filespace
hsize_t start[2] = {0, dims[1]};
dims[1] = steps_; // change dims for memspace & hyperslab
hid_t memspace = H5Screate_simple(2, dims, NULL);
H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, NULL, dims, NULL);
status = H5Dwrite(it->second, H5T_NATIVE_DOUBLE, memspace, filespace, H5P_DEFAULT, buffer);
H5Sclose(memspace);
H5Sclose(filespace);
free(buffer);
}
// append all event data
for (unsigned int ii = 0; ii < eventSrc_.size(); ++ii){
appendToDataset(getEventDataset(eventSrc_[ii], eventSrcFields_[ii]),
events_[ii]);
events_[ii].clear();
}
// flush HDF5 nodes.
HDF5DataWriter::flush();
}
void HDF5DataWriter::flush()
{
if (filehandle_ < 0){
cerr << "HDF5DataWriter::flush() - "
"Filehandle invalid. Cannot write data." << endl;
return;
}
for (unsigned int ii = 0; ii < datasets_.size(); ++ii){
herr_t status = appendToDataset(datasets_[ii], data_[ii]);
data_[ii].clear();
if (status < 0){
cerr << "Warning: appending data for object " << src_[ii]
<< " returned status " << status << endl;
}
}
HDF5WriterBase::flush();
H5Fflush(filehandle_, H5F_SCOPE_LOCAL);
}
void HDF5DataWriter::flush()
{
if (filehandle_ < 0){
cerr << "HDF5DataWriter::flush() - Filehandle invalid. Cannot write data." << endl;
return;
}
for (map < string, vector < double > >::iterator ii = datamap_.begin(); ii != datamap_.end(); ++ ii){
hid_t dataset = nodemap_[ii->first];
if (dataset < 0){
dataset = get_dataset(ii->first);
nodemap_[ii->first] = dataset;
}
herr_t status = appendToDataset(dataset, ii->second);
if (status < 0){
cerr << "Warning: appending data for object " << ii->first << " returned status " << status << endl;
}
ii->second.clear();
}
H5Fflush(filehandle_, H5F_SCOPE_LOCAL);
}
/**
Write data to datasets in HDF5 file. Clear all data in the table
objects associated with this object. */
void HDF5DataWriter::process(const Eref & e, ProcPtr p)
{
if (filehandle_ < 0){
return;
}
// cout << "HDF5DataWriter::process: currentTime=" << p->currTime << endl;
requestOut()->send(e, recvDataBuf()->getFid());
for (map<string, vector < double > >:: iterator data_it = datamap_.begin(); data_it != datamap_.end(); ++data_it){
string path = data_it->first;
// if (data_it->second.size() >= flushLimit_){
map < string, hid_t >::iterator node_it = nodemap_.find(path);
assert (node_it != nodemap_.end());
if (node_it->second < 0){
nodemap_[path] = get_dataset(path);
}
herr_t status = appendToDataset(nodemap_[path], data_it->second);
if (status < 0){
cerr << "Warning: appending data for object " << data_it->first << " returned status " << status << endl;
}
data_it->second.clear();
}
}
/**
Write data to datasets in HDF5 file. Clear all data in the table
objects associated with this object. */
void HDF5DataWriter::process(const Eref & e, ProcPtr p)
{
if (filehandle_ < 0){
return;
}
vector <double> dataBuf;
requestOut()->send(e, &dataBuf);
for (unsigned int ii = 0; ii < dataBuf.size(); ++ii){
data_[ii].push_back(dataBuf[ii]);
}
++steps_;
if (steps_ >= flushLimit_){
steps_ = 0;
for (unsigned int ii = 0; ii < datasets_.size(); ++ii){
herr_t status = appendToDataset(datasets_[ii], data_[ii]);
data_[ii].clear();
if (status < 0){
cerr << "Warning: appending data for object " << src_[ii]
<< " returned status " << status << endl;
}
}
}
}
