eavlField *
eavlXGCImporter::GetField(const string &name, const string &mesh, int chunk)
{
map<string, ADIOS_VARINFO*>::const_iterator it = variables.find(name);
if (it == variables.end())
THROW(eavlException, string("Variable not found: ")+name);
uint64_t s[3], c[3];
ADIOS_SELECTION *sel = MakeSelection(it->second, s, c);
int nt = 1;
for (int i = 0; i < it->second->ndim; i++)
nt *= c[i];
double *buff = new double[nt];
adios_schedule_read_byid(fp, sel, it->second->varid, 0, 1, buff);
int retval = adios_perform_reads(fp, 1);
adios_selection_delete(sel);
eavlFloatArray *arr = new eavlFloatArray(name, 1);
arr->SetNumberOfTuples(nt);
for (int i = 0; i < nt; i++)
arr->SetComponentFromDouble(i, 0, buff[i]);
delete [] buff;
eavlField *field = new eavlField(1, arr, eavlField::ASSOC_POINTS);
//field->PrintSummary(cout);
return field;
}
int read_write(int step)
{
int retval = 0;
int i;
uint64_t total_size;
// open output file
adios_open (&fh, group_namelist[0], outfilename, (step==1 ? "w" : "a"), comm);
adios_group_size (fh, write_total, &total_size);
for (i=0; i<f->nvars; i++)
{
if (varinfo[i].writesize != 0) {
// read variable subset
print ("rank %d: Read variable %d: %s\n", rank, i, f->var_namelist[i]);
ADIOS_SELECTION *sel = adios_selection_boundingbox (varinfo[i].v->ndim,
varinfo[i].start,
varinfo[i].count);
adios_schedule_read_byid (f, sel, i, 1, 1, readbuf);
adios_perform_reads (f, 1);
// write (buffer) variable
print ("rank %d: Write variable %d: %s\n", rank, i, f->var_namelist[i]);
adios_write(fh, f->var_namelist[i], readbuf);
}
}
adios_release_step (f); // this step is no longer needed to be locked in staging area
adios_close (fh); // write out output buffer to file
return retval;
}
// k is numbered from 1 to sum_nblocks
void verifyData(ADIOS_FILE* f, ADIOS_VARINFO* v, int k, int timestep)
{
uint64_t blockBytes = adios_type_size (v->type, v->value);
int j=0;
if (v->ndim <= 0) {
return;
}
//printf("verify block[%d]: ", k);
for (j=0; j<v->ndim; j++)
{
blockBytes *= v->blockinfo[k].count[j];
//printf("%" PRIu64 ":%" PRIu64 " ", v->blockinfo[k].start[j], v->blockinfo[k].count[j]);
}
void* data = NULL;
data = malloc(blockBytes);
ADIOS_SELECTION* sel = adios_selection_boundingbox (v->ndim, v->blockinfo[k].start, v->blockinfo[k].count);
int err = adios_schedule_read_byid(f, sel, v->varid, timestep, 1, data);
if (!err) {
err = adios_perform_reads(f, 1);
}
//fastbit_adios_util_printData(data, v->type, blockBytes/adios_type_size(v->type, v->value));
adios_selection_delete(sel);
free(data);
data = NULL;
}
void onBox(int rank, ADIOS_FILE* f, ADIOS_VARINFO* v, int timestep, uint64_t* start, uint64_t* count, FastBitDataType ft)
{
int i=0;
char selName[100];
sprintf(selName, "box-%lu", start[0]);
uint64_t totalCount = 1;
for (i = 0; i<v->ndim; i++) {
totalCount *= count[i];
}
double* data = (double *) calloc (totalCount, sizeof (double));
uint64_t currStart = 0;
ADIOS_SELECTION* boxSel = adios_selection_boundingbox(v->ndim, start, count);
int err = adios_schedule_read_byid(f, boxSel, v->varid, timestep, 1, data);
if (!err) {
err = adios_perform_reads(f, 1);
}
processData(data, totalCount, rank, timestep, selName, ft, v);
} // on box
/// Read a sub-array.
///
/// @Note The length of the buffer is assumed to be sufficiently large
/// if the argument bufLen is less or equal to 0. The caller is
/// responsible for allocating the buffer (@c buf) of the currect size.
int64_t
ADIOS_Var::readData(void* buf, int64_t bufLen,
const uint64_t* start,
const uint64_t* count)
{
uint64_t total_elm = 1;
for (int i=0; i<getNumDimension(); i++) {
total_elm *= count[i];
#ifdef DEBUG
LOGGER(ibis::gVerbose > 5)
<< "ADIOS_Var::readData: [" << i << "] start=" << start[i]
<< ", count=" << count[i];
#endif
}
{
uint64_t total_bytes = total_elm *
adios_type_size(getType(), readValue());
if (bufLen > 0 && (uint64_t)bufLen < total_bytes) {
LOGGER(ibis::gVerbose > 0)
<< "Warning -- ADIOS_Var::readData: bufLen (" << bufLen
<< ") < total_bytes (" << total_bytes << ")";
return -1;
}
}
ADIOS_SELECTION *sel = adios_selection_boundingbox
(m_handle->ndim, start, count);
if (sel == 0) {
LOGGER(ibis::gVerbose > 1)
<< "Warning -- ADIOS_Var::readData failed to create a selection";
return -2;
}
IBIS_BLOCK_GUARD(adios_selection_delete, sel);
int ierr = adios_schedule_read_byid
(getFile(), sel, index(), getFile()->current_step, 1, buf);
if (ierr != 0) {
LOGGER(ibis::gVerbose > 0)
<< "Warning -- ADIOS_Var::readData call to "
"adios_schedule_read_byid failed due to " << adios_errmsg();
return -3;
}
ierr = adios_perform_reads(getFile(), 1); // 1 == blocking
if (ierr != 0) {
LOGGER(ibis::gVerbose > 0)
<< "Warning -- ADIOS_Var::readData call to adios_perform_reads on "
<< getFileName() << " failed due to " << adios_errmsg();
return -4;
}
LOGGER(ibis::gVerbose > 5)
<< "ADIOS_Var::readData: competeled reading " << total_elm
<< " element" << (total_elm>1?"s":"") << " for " << getName()
<< " from " << getFileName();
return total_elm;
} // ADIOS_Var::readData
void onBlock(int rank, ADIOS_FILE* f, ADIOS_VARINFO* v, int i, int j, int blockCounter, FastBitDataType ft)
{
char bmsVarName[100];
char keyVarName[100];
char offsetName[100];
int64_t var_ids_bms[v->nblocks[i]];
int64_t var_ids_key[v->nblocks[i]];
int64_t var_ids_offset[v->nblocks[i]];
sprintf(bmsVarName, "bms-%d-%d-%d", v->varid, i, j);
sprintf(keyVarName, "key-%d-%d-%d", v->varid, i, j);
sprintf(offsetName, "offset-%d-%d-%d", v->varid, i, j);
uint64_t blockSize = fastbit_adios_util_getBlockSize(v, i, j);
uint64_t blockDataByteSize = adios_type_size (v->type, v->value) * blockSize;
char notes[100];
logTime(NULL); logTimeMillis(NULL);
sprintf(notes, " reading data from adios on varid=%d, time=%d, block: %d, size=%ld bytes=%ld", v->varid, i, j, blockSize, blockDataByteSize);
logTime(notes); logTimeMillis(notes);
localtime(&indexRefresh);
//printf(" %d th block / (%d), size= %" PRIu64 " bytes=%" PRIu64, j, blockSize, blockCounter, blockDataByteSize);
void* data = malloc (blockDataByteSize);
ADIOS_SELECTION* blockSel = adios_selection_writeblock(j);
//adios_selcton_writeblock(num), 0 <= num < nblocks[timestep]
//ADIOS_SELECTION* blockSel = adios_selection_writeblock(blockCounter);
int err = adios_schedule_read_byid(f, blockSel, v->varid, i, 1, data);
if (!err) {
err = adios_perform_reads(f, 1);
} else {
printf("Unable to read block %d at timestep: %d \n", j, i);
return;
//break;
}
//fastbit_adios_util_printData(data, v->type, blockSize);
char selName[20];
sprintf(selName, "block-%d", j);
processData(data, blockSize, rank, i, selName, ft, v);
//processData(void* data, uint64_t dataCount, int rank, int timestep, char* selName, FastBitDataType ft, ADIOS_VARINFO* v)
adios_selection_delete(blockSel);
verifyData(f, v, blockCounter, i);
} // onblock
void onMultiBlock(int rank, ADIOS_FILE* f, ADIOS_VARINFO* v, int timestep, int blockStart, int blockEnd, FastBitDataType ft)
{
int i=0;
char selName[100];
sprintf(selName, "block-%d", blockStart, blockEnd);
uint64_t blockSizeArray[blockEnd-blockStart];
uint64_t totalCount = 0;
for (i = blockStart; i< blockEnd; i++) {
blockSizeArray[i-blockStart] = fastbit_adios_util_getBlockSize(v, timestep, i);
//totalBytes += blockSizeArray[i-blockStart] * adios_type_size (v->type, v->value);
totalCount += blockSizeArray[i-blockStart];
}
//void* data = malloc (totalBytes);
double* data = (double *) calloc (totalCount, sizeof (double));
uint64_t currStart = 0;
for (i = blockStart; i < blockEnd; i++) {
ADIOS_SELECTION* blockSel = adios_selection_writeblock(i);
int err = adios_schedule_read_byid(f, blockSel, v->varid, timestep, 1, &data[currStart]);
currStart += blockSizeArray[i-blockStart];
if (!err) {
err = adios_perform_reads(f, 1);
} else {
printf("Unable to read block %d at timestep: %d \n", i, timestep);
return;
//break;
}
}
processData(data, totalCount, rank, timestep, selName, ft, v);
//processData(void* data, uint64_t dataCount, int rank, int timestep, char* selName, FastBitDataType ft, ADIOS_VARINFO* v)
} // on multi block
eavlField *
eavlXGCParticleImporter::GetField(const string &name, const string &mesh, int chunk)
{
int idx = 0;
eavlField *field;
uint64_t s[3], c[3];
map<string, ADIOS_VARINFO*>::const_iterator it;
if(name.compare("ephase") == 0 && ephaseAvail)
{
eavlFloatArray *arr = new eavlFloatArray(name, 1);
arr->SetNumberOfTuples(totalEParticles*9);
for(it = ephase.begin(); it != ephase.end(); it++)
{
int nt = 1;
ADIOS_SELECTION *sel;
if(readingRestartFile)
sel = MakeSelection(it->second, s, c);
else
sel = MakeLimitedSelection(it->second, s, c, 0);
for(int i = 0; i < it->second->ndim; i++)
nt *= c[i];
double *buff = new double[nt];
adios_schedule_read_byid(fp, sel, it->second->varid, 0, 1, buff);
int retval = adios_perform_reads(fp, 1);
adios_selection_delete(sel);
for(int i = 0; i < nt; i++)
{
arr->SetComponentFromDouble(idx, 0, buff[i]);
idx++;
}
delete [] buff;
}
field = new eavlField(1, arr, eavlField::ASSOC_POINTS);
}
else if(name.compare("iphase") == 0 && iphaseAvail)
{
eavlFloatArray *arr = new eavlFloatArray(name, 1);
arr->SetNumberOfTuples(totalIParticles*9);
for(it = iphase.begin(); it != iphase.end(); it++)
{
int nt = 1;
ADIOS_SELECTION *sel;
if(readingRestartFile)
sel = MakeSelection(it->second, s, c);
else
sel = MakeLimitedSelection(it->second, s, c, 1);
for (int i = 0; i < it->second->ndim; i++)
nt *= c[i];
double *buff = new double[nt];
adios_schedule_read_byid(fp, sel, it->second->varid, 0, 1, buff);
int retval = adios_perform_reads(fp, 1);
adios_selection_delete(sel);
for(int i = 0; i < nt; i++)
{
arr->SetComponentFromDouble(idx, 0, buff[i]);
idx++;
}
delete [] buff;
}
field = new eavlField(1, arr, eavlField::ASSOC_POINTS);
}
else if(name.compare("igid") == 0 && iphaseAvail)
{
eavlIntArray *arr = new eavlIntArray(name, 1);
arr->SetNumberOfTuples(totalIParticles);
for(it = igid.begin(); it != igid.end(); it++)
{
int nt = 1;
ADIOS_SELECTION *sel;
if(readingRestartFile)
sel = MakeSelection(it->second, s, c);
else
sel = MakeLimitedSelection(it->second, s, c, 1);
for(int i = 0; i < it->second->ndim; i++)
nt *= c[i];
long long *buff = new long long[nt];
adios_schedule_read_byid(fp, sel, it->second->varid, 0, 1, buff);
int retval = adios_perform_reads(fp, 1);
adios_selection_delete(sel);
for(int i = 0; i < nt; i++)
{
arr->SetValue(idx, (int)buff[i]);
idx++;
}
delete [] buff;
}
field = new eavlField(1, arr, eavlField::ASSOC_POINTS);
}
else if((name.compare("egid") == 0) && ephaseAvail )
{
eavlIntArray *arr = new eavlIntArray(name, 1);
arr->SetNumberOfTuples(totalEParticles);
for (it = egid.begin(); it != egid.end(); it++)
{
int nt = 1;
ADIOS_SELECTION *sel;
if(readingRestartFile)
sel = MakeSelection(it->second, s, c);
else
sel = MakeLimitedSelection(it->second, s, c, 0);
for(int i = 0; i < it->second->ndim; i++)
nt *= c[i];
long long *buff = new long long[nt];
adios_schedule_read_byid(fp, sel, it->second->varid, 0, 1, buff);
int retval = adios_perform_reads(fp, 1);
adios_selection_delete(sel);
for(int i = 0; i < nt; i++)
{
arr->SetValue(idx, (int)buff[i]);
idx++;
}
delete [] buff;
}
field = new eavlField(1, arr, eavlField::ASSOC_POINTS);
}
else
{
THROW(eavlException, string("Variable not found: ")+name);
}
return field;
}
eavlDataSet *
eavlXGCParticleImporter::GetMesh(const string &name, int chunk)
{
eavlDataSet *ds = new eavlDataSet;
if(name == "iMesh" && iphaseAvail)
{
ds->SetNumPoints(totalIParticles);
eavlCoordinatesCartesian *coords = new eavlCoordinatesCartesian(NULL,
eavlCoordinatesCartesian::X,
eavlCoordinatesCartesian::Y,
eavlCoordinatesCartesian::Z);
ds->AddCoordinateSystem(coords);
coords->SetAxis(0, new eavlCoordinateAxisField("xcoords", 0));
coords->SetAxis(1, new eavlCoordinateAxisField("ycoords", 0));
coords->SetAxis(2, new eavlCoordinateAxisField("zcoords", 0));
eavlArray *axisValues[3] = {
new eavlFloatArray("xcoords", 1),
new eavlFloatArray("ycoords", 1),
new eavlFloatArray("zcoords", 1)
};
axisValues[0]->SetNumberOfTuples(totalIParticles);
axisValues[1]->SetNumberOfTuples(totalIParticles);
axisValues[2]->SetNumberOfTuples(totalIParticles);
//Set all of the axis values to the x, y, z coordinates of the
//iphase particles; set computational node origin
eavlIntArray *originNode;
if(getOriginNode && readingRestartFile)
originNode = new eavlIntArray("originNode", 1, totalIParticles);
eavlFloatArray *r;
if(getR)
r = new eavlFloatArray("R", 1, totalIParticles);
eavlFloatArray *z;
if(getZ)
z = new eavlFloatArray("Z", 1, totalIParticles);
eavlFloatArray *phi;
if(getPhi)
phi = new eavlFloatArray("phi", 1, totalIParticles);
eavlFloatArray *rho;
if(getRho)
rho = new eavlFloatArray("rho", 1, totalIParticles);
eavlFloatArray *w1;
if(getW1)
w1 = new eavlFloatArray("w1", 1, totalIParticles);
eavlFloatArray *w2;
if(getW2)
w2 = new eavlFloatArray("w2", 1, totalIParticles);
eavlFloatArray *mu;
if(getMu)
mu = new eavlFloatArray("mu", 1, totalIParticles);
eavlFloatArray *w0;
if(getW0)
w0 = new eavlFloatArray("w0", 1, totalIParticles);
eavlFloatArray *f0;
if(getF0)
f0 = new eavlFloatArray("f0", 1, totalIParticles);
uint64_t s[3], c[3];
double *buff;
int nt = 1, idx = 0;
map<string, ADIOS_VARINFO*>::const_iterator it;
for(it = iphase.begin(); it != iphase.end(); it++)
{
ADIOS_SELECTION *sel;
if(readingRestartFile)
sel = MakeSelection(it->second, s, c);
else
sel = MakeLimitedSelection(it->second, s, c, 1);
nt = 1;
for (int i = 0; i < it->second->ndim; i++)
nt *= c[i];
buff = new double[nt];
adios_schedule_read_byid(fp, sel, it->second->varid, 0, 1, buff);
adios_perform_reads(fp, 1);
adios_selection_delete(sel);
string nodeNum;
if(getOriginNode && readingRestartFile) nodeNum = it->first.substr(it->first.find("_",1,1)+1, 5);
for(int i = 0; i < nt; i+=9)
{
if(getR) r->SetValue(idx, buff[i]);
if(getZ) z->SetValue(idx, buff[i+1]);
if(getPhi) phi->SetValue(idx, buff[i+2]);
if(getRho) rho->SetValue(idx, buff[i+3]);
if(getW1) w1->SetValue(idx, buff[i+4]);
if(getW2) w2->SetValue(idx, buff[i+5]);
if(getMu) mu->SetValue(idx, buff[i+6]);
if(getW0) w0->SetValue(idx, buff[i+7]);
if(getF0) f0->SetValue(idx, buff[i+8]);
axisValues[0]->SetComponentFromDouble(idx, 0, r->GetValue(idx)*cos(phi->GetValue(idx)));
axisValues[1]->SetComponentFromDouble(idx, 0, r->GetValue(idx)*sin(phi->GetValue(idx)));
axisValues[2]->SetComponentFromDouble(idx, 0, z->GetValue(idx));
if(getOriginNode && readingRestartFile) originNode->SetValue(idx, atoi(nodeNum.c_str()));
idx++;
}
delete [] buff;
}
ds->AddField(new eavlField(1, axisValues[0], eavlField::ASSOC_POINTS));
ds->AddField(new eavlField(1, axisValues[1], eavlField::ASSOC_POINTS));
ds->AddField(new eavlField(1, axisValues[2], eavlField::ASSOC_POINTS));
if(getOriginNode && readingRestartFile)
ds->AddField(new eavlField(1, originNode, eavlField::ASSOC_POINTS));
if(getR) ds->AddField(new eavlField(1, r, eavlField::ASSOC_POINTS));
if(getZ) ds->AddField(new eavlField(1, z, eavlField::ASSOC_POINTS));
if(getPhi) ds->AddField(new eavlField(1, phi, eavlField::ASSOC_POINTS));
if(getRho) ds->AddField(new eavlField(1, rho, eavlField::ASSOC_POINTS));
if(getW1) ds->AddField(new eavlField(1, w1, eavlField::ASSOC_POINTS));
if(getW2) ds->AddField(new eavlField(1, w2, eavlField::ASSOC_POINTS));
if(getMu) ds->AddField(new eavlField(1, mu, eavlField::ASSOC_POINTS));
if(getW0) ds->AddField(new eavlField(1, w0, eavlField::ASSOC_POINTS));
if(getF0) ds->AddField(new eavlField(1, f0, eavlField::ASSOC_POINTS));
eavlCellSet *cellSet = new eavlCellSetAllPoints(name + "_cells", totalIParticles);
ds->AddCellSet(cellSet);
//-- END set axis values
//----Set the ids of all axis values
idx = 0;
long long *idBuff;
eavlIntArray *axisIds = new eavlIntArray("id", 1, totalIParticles);
for(it = igid.begin(); it != igid.end(); it++)
{
ADIOS_SELECTION *sel;
if(readingRestartFile)
sel = MakeSelection(it->second, s, c);
else
sel = MakeLimitedSelection(it->second, s, c, 1);
nt = 1;
for (int i = 0; i < it->second->ndim; i++)
nt *= c[i];
idBuff = new long long[nt];
adios_schedule_read_byid(fp, sel, it->second->varid, 0, 1, idBuff);
adios_perform_reads(fp, 1);
adios_selection_delete(sel);
for(int i = 0; i < nt; i++)
{
axisIds->SetValue(idx, (int)idBuff[i]);
idx++;
}
delete [] idBuff;
}
ds->AddField(new eavlField(1, axisIds, eavlField::ASSOC_POINTS));
//-- END set ids
}
else if(name == "eMesh" && ephaseAvail)
{
ds->SetNumPoints(totalEParticles);
eavlCoordinatesCartesian *coords = new eavlCoordinatesCartesian(NULL,
eavlCoordinatesCartesian::X,
eavlCoordinatesCartesian::Y,
eavlCoordinatesCartesian::Z);
ds->AddCoordinateSystem(coords);
coords->SetAxis(0, new eavlCoordinateAxisField("xcoords", 0));
coords->SetAxis(1, new eavlCoordinateAxisField("ycoords", 0));
coords->SetAxis(2, new eavlCoordinateAxisField("zcoords", 0));
eavlArray *axisValues[3] = {
new eavlFloatArray("xcoords", 1),
new eavlFloatArray("ycoords", 1),
new eavlFloatArray("zcoords", 1)
};
axisValues[0]->SetNumberOfTuples(totalEParticles);
axisValues[1]->SetNumberOfTuples(totalEParticles);
axisValues[2]->SetNumberOfTuples(totalEParticles);
//Set all of the axis values to the x, y, z coordinates of the
//ephase particles; set computational node origin
eavlIntArray *originNode;
if(getOriginNode && readingRestartFile)
originNode = new eavlIntArray("originNode", 1, totalIParticles);
eavlFloatArray *r;
if(getR)
r = new eavlFloatArray("R", 1, totalIParticles);
eavlFloatArray *z;
if(getZ)
z = new eavlFloatArray("Z", 1, totalIParticles);
eavlFloatArray *phi;
if(getPhi)
phi = new eavlFloatArray("phi", 1, totalIParticles);
eavlFloatArray *rho;
if(getRho)
rho = new eavlFloatArray("rho", 1, totalIParticles);
eavlFloatArray *w1;
if(getW1)
w1 = new eavlFloatArray("w1", 1, totalIParticles);
eavlFloatArray *w2;
if(getW2)
w2 = new eavlFloatArray("w2", 1, totalIParticles);
eavlFloatArray *mu;
if(getMu)
mu = new eavlFloatArray("mu", 1, totalIParticles);
eavlFloatArray *w0;
if(getW0)
w0 = new eavlFloatArray("w0", 1, totalIParticles);
eavlFloatArray *f0;
if(getF0)
f0 = new eavlFloatArray("f0", 1, totalIParticles);
uint64_t s[3], c[3];
int nt = 1, idx = 0;
double *buff;
map<string, ADIOS_VARINFO*>::const_iterator it;
for(it = ephase.begin(); it != ephase.end(); it++)
{
ADIOS_SELECTION *sel;
if(readingRestartFile)
sel = MakeSelection(it->second, s, c);
else
sel = MakeLimitedSelection(it->second, s, c, 0);
nt = 1;
for(int i = 0; i < it->second->ndim; i++)
nt *= c[i];
buff = new double[nt];
adios_schedule_read_byid(fp, sel, it->second->varid, 0, 1, buff);
adios_perform_reads(fp, 1);
adios_selection_delete(sel);
string nodeNum;
if(getOriginNode && readingRestartFile) nodeNum = it->first.substr(it->first.find("_",1,1)+1, 5);
for(int i = 0; i < nt; i+=9)
{
if(getR) r->SetValue(idx, buff[i]);
if(getZ) z->SetValue(idx, buff[i+1]);
if(getPhi) phi->SetValue(idx, buff[i+2]);
if(getRho) rho->SetValue(idx, buff[i+3]);
if(getW1) w1->SetValue(idx, buff[i+4]);
if(getW2) w2->SetValue(idx, buff[i+5]);
if(getMu) mu->SetValue(idx, buff[i+6]);
if(getW0) w0->SetValue(idx, buff[i+7]);
if(getF0) f0->SetValue(idx, buff[i+8]);
axisValues[0]->SetComponentFromDouble(idx, 0, r->GetValue(idx)*cos(phi->GetValue(idx)));
axisValues[1]->SetComponentFromDouble(idx, 0, r->GetValue(idx)*sin(phi->GetValue(idx)));
axisValues[2]->SetComponentFromDouble(idx, 0, z->GetValue(idx));
if(getOriginNode && readingRestartFile) originNode->SetValue(idx, atoi(nodeNum.c_str()));
idx++;
}
delete [] buff;
}
ds->AddField(new eavlField(1, axisValues[0], eavlField::ASSOC_POINTS));
ds->AddField(new eavlField(1, axisValues[1], eavlField::ASSOC_POINTS));
ds->AddField(new eavlField(1, axisValues[2], eavlField::ASSOC_POINTS));
if(getOriginNode && readingRestartFile)
ds->AddField(new eavlField(1, originNode, eavlField::ASSOC_POINTS));
if(getR) ds->AddField(new eavlField(1, r, eavlField::ASSOC_POINTS));
if(getZ) ds->AddField(new eavlField(1, z, eavlField::ASSOC_POINTS));
if(getPhi) ds->AddField(new eavlField(1, phi, eavlField::ASSOC_POINTS));
if(getRho) ds->AddField(new eavlField(1, rho, eavlField::ASSOC_POINTS));
if(getW1) ds->AddField(new eavlField(1, w1, eavlField::ASSOC_POINTS));
if(getW2) ds->AddField(new eavlField(1, w2, eavlField::ASSOC_POINTS));
if(getMu) ds->AddField(new eavlField(1, mu, eavlField::ASSOC_POINTS));
if(getW0) ds->AddField(new eavlField(1, w0, eavlField::ASSOC_POINTS));
if(getF0) ds->AddField(new eavlField(1, f0, eavlField::ASSOC_POINTS));
eavlCellSet *cellSet = new eavlCellSetAllPoints(name + "_cells", totalEParticles);
ds->AddCellSet(cellSet);
//-- END set axis values
//----Set the ids of all axis values
idx = 0;
long long *idBuff;
eavlIntArray *axisIds = new eavlIntArray("id", 1, totalEParticles);
for(it = egid.begin(); it != egid.end(); it++)
{
ADIOS_SELECTION *sel;
if(readingRestartFile)
sel = MakeSelection(it->second, s, c);
else
sel = MakeLimitedSelection(it->second, s, c, 0);
nt = 1;
for (int i = 0; i < it->second->ndim; i++)
nt *= c[i];
idBuff = new long long[nt];
adios_schedule_read_byid(fp, sel, it->second->varid, 0, 1, idBuff);
adios_perform_reads(fp, 1);
adios_selection_delete(sel);
for(int i = 0; i < nt; i++)
{
axisIds->SetValue(idx, (int)idBuff[i]);
idx++;
}
delete [] idBuff;
}
ds->AddField(new eavlField(1, axisIds, eavlField::ASSOC_POINTS));
}
return ds;
}
int print_scalar (ADIOS_FILE *f, char * name)
{
ADIOS_VARINFO * v;
int i,j,k;
v = adios_inq_var (f, name);
adios_inq_var_blockinfo (f, v);
printf ("Scalar '%s':\n", name);
printf ("nsteps = %d\n", v->nsteps);
printf ("nblocks per step = %d\n", v->nblocks[0]);
int err;
/* Read one writeblock across all timesteps */
int *data = (int*) calloc (v->nsteps, sizeof(int));
ADIOS_SELECTION *s;
printf ("Read same instance across all timesteps:\n");
for (i=0; i < v->nblocks[0]; i++) {
s = adios_selection_writeblock(i);
err = adios_schedule_read_byid(f, s, v->varid, 0, v->nsteps, data);
if (!err)
{
err = adios_perform_reads(f, 1);
if (!err)
{
err = 0;
printf (" block %d = [", i);
for (j=0; j < v->nsteps; j++) {
printf ("%d", data[j]);
if (data[j] !=
block_offset [j*nblocks_per_step*size + i])
{
err = 1;
}
if (j < v->nsteps-1) printf(",");
}
printf("]");
if (err)
{
nerrors++;
printf ("\tERROR expected = [");
for (j=0; j < v->nsteps; j++) {
printf ("%llu", block_offset [j*nblocks_per_step*size + i]);
if (j < v->nsteps-1) printf(",");
}
printf("]");
}
printf("\n");
} else {
printf ("ERROR at reading scalar '%s': %s\n", name, adios_errmsg());
}
} else {
printf ("ERROR at scheduling read for scalar '%s': %s\n", name, adios_errmsg());
}
adios_selection_delete(s);
}
/* Now read piecewise, one writeblock at a time */
printf ("Read each instance individually:\n");
for (j=0; j < v->nsteps; j++) {
printf (" step %d: \n", j);
for (i=0; i < v->nblocks[j]; i++) {
s = adios_selection_writeblock(i);
err = adios_schedule_read_byid(f, s, v->varid, j, 1, data);
if (!err)
{
err = adios_perform_reads(f, 1);
if (!err)
{
printf (" block %d = %d", i, data[0]);
if (data[0] !=
block_offset [j*nblocks_per_step*size + i])
{
printf ("\tERROR expected = %llu",
block_offset [j*nblocks_per_step*size + i]);
nerrors++;
}
printf ("\n");
} else {
printf ("ERROR at reading scalar '%s': %s\n", name, adios_errmsg());
}
} else {
printf ("ERROR at scheduling read for scalar '%s': %s\n", name, adios_errmsg());
}
adios_selection_delete(s);
}
}
/* Now get them piecewise, but not with reading but through statistics */
printf ("Get each instance individually from available statistics:\n");
adios_inq_var_stat (f, v, 0, 1);
if (v->statistics && v->statistics->blocks) {
ADIOS_VARSTAT *stat = v->statistics;
int blockid = 0;
for (j=0; j < v->nsteps; j++) {
printf (" step %d: \n", j);
for (i=0; i < v->nblocks[j]; i++) {
printf (" block %d = %d", i, *(int*)stat->blocks->mins[blockid]);
if (*(int*)stat->blocks->mins[blockid] !=
block_offset [j*nblocks_per_step*size + i])
{
printf ("\tERROR expected = %llu",
block_offset [j*nblocks_per_step*size + i]);
nerrors++;
}
printf ("\n");
blockid++;
}
}
}
adios_free_varinfo (v);
free(data);
}
eavlDataSet *ReadPsiMesh(const string &filename)
{
MPI_Comm comm_dummy = 0;
ADIOS_FILE *fp = adios_read_open_file(filename.c_str(), ADIOS_READ_METHOD_BP, comm_dummy);
int nNodes = 0, nElems = 0, ptID = -1, elemID = -1;
ADIOS_VARINFO *points = NULL, *cells = NULL, *psi;
for (int i = 0; i < fp->nvars; i++)
{
ADIOS_VARINFO *avi = adios_inq_var_byid(fp, i);
string varNm(&fp->var_namelist[i][1]);
if (varNm == "n_t")
{
nElems = (int)(*(int *)avi->value);
adios_free_varinfo(avi);
}
else if (varNm == "n_n")
{
nNodes = (int)(*(int *)avi->value);
adios_free_varinfo(avi);
}
else if (varNm == "coordinates/values")
points = avi;
else if (varNm == "cell_set[0]/node_connect_list")
cells = avi;
else if (varNm == "psi")
psi = avi;
else
adios_free_varinfo(avi);
}
cout<<"nNodes= "<<nNodes<<" nTri= "<<nElems<<endl;
eavlDataSet *out = new eavlDataSet;
out->SetNumPoints(nNodes);
eavlCoordinatesCartesian *coords = new eavlCoordinatesCartesian(NULL,
eavlCoordinatesCartesian::X,
eavlCoordinatesCartesian::Y);
out->AddCoordinateSystem(coords);
coords->SetAxis(0, new eavlCoordinateAxisField("xcoords", 0));
coords->SetAxis(1, new eavlCoordinateAxisField("ycoords", 0));
eavlArray *axisValues[2] = {new eavlFloatArray("xcoords", 1),
new eavlFloatArray("ycoords", 1)};
axisValues[0]->SetNumberOfTuples(nNodes);
axisValues[1]->SetNumberOfTuples(nNodes);
//read points.
double *buff = new double[2*nNodes];
uint64_t s[3], c[3];
ADIOS_SELECTION *sel = MakeSelection(points, s, c);
adios_schedule_read_byid(fp, sel, points->varid, 0, 1, buff);
int retval = adios_perform_reads(fp, 1);
adios_selection_delete(sel);
adios_free_varinfo(points);
for (int i = 0; i < nNodes; i++)
{
axisValues[0]->SetComponentFromDouble(i, 0, buff[i*2 +0]);
axisValues[1]->SetComponentFromDouble(i, 0, buff[i*2 +1]);
}
out->AddField(new eavlField(1, axisValues[0], eavlField::ASSOC_POINTS));
out->AddField(new eavlField(1, axisValues[1], eavlField::ASSOC_POINTS));
delete [] buff;
eavlCellSetExplicit *cellSet = new eavlCellSetExplicit("2D_cells", 2);
eavlExplicitConnectivity conn;
//read cells
int *nodeList = new int[nElems*3];
sel = MakeSelection(cells, s, c);
adios_schedule_read_byid(fp, sel, cells->varid, 0, 1, nodeList);
retval = adios_perform_reads(fp, 1);
adios_selection_delete(sel);
int nodes[3];
for (int i = 0; i < nElems; i++)
{
nodes[0] = nodeList[i*3+0];
nodes[1] = nodeList[i*3+1];
nodes[2] = nodeList[i*3+2];
conn.AddElement(EAVL_TRI, 3, nodes);
}
delete [] nodeList;
cellSet->SetCellNodeConnectivity(conn);
out->AddCellSet(cellSet);
//read psi.
buff = new double[nNodes];
sel = MakeSelection(psi, s, c);
adios_schedule_read_byid(fp, sel, psi->varid, 0, 1, buff);
retval = adios_perform_reads(fp, 1);
adios_selection_delete(sel);
adios_free_varinfo(psi);
eavlArray *psiValues = new eavlFloatArray("psi", 1);
psiValues->SetNumberOfTuples(nNodes);
for (int i = 0; i < nNodes; i++)
psiValues->SetComponentFromDouble(i, 0, buff[i]);
out->AddField(new eavlField(1, psiValues, eavlField::ASSOC_POINTS));
delete [] buff;
return out;
}
eavlDataSet *
eavlXGCImporter::GetMesh(const string &name, int chunk)
{
eavlDataSet *ds = new eavlDataSet;
if (name == "mesh2D")
{
ds->SetNumPoints(nNodes);
eavlCoordinatesCartesian *coords = new eavlCoordinatesCartesian(NULL,
eavlCoordinatesCartesian::X,
eavlCoordinatesCartesian::Y);
ds->AddCoordinateSystem(coords);
coords->SetAxis(0, new eavlCoordinateAxisField("xcoords", 0));
coords->SetAxis(1, new eavlCoordinateAxisField("ycoords", 0));
eavlArray *axisValues[2] = {new eavlFloatArray("xcoords", 1),
new eavlFloatArray("ycoords", 1)};
axisValues[0]->SetNumberOfTuples(nNodes);
axisValues[1]->SetNumberOfTuples(nNodes);
//read points
double *buff = new double[2*nNodes];
uint64_t s[3], c[3];
ADIOS_SELECTION *sel = MakeSelection(points, s, c);
adios_schedule_read_byid(mesh_fp, sel, points->varid, 0, 1, buff);
int retval = adios_perform_reads(mesh_fp, 1);
adios_selection_delete(sel);
for (int i = 0; i < nNodes; i++)
{
axisValues[0]->SetComponentFromDouble(i, 0, buff[i*2 +0]);
axisValues[1]->SetComponentFromDouble(i, 0, buff[i*2 +1]);
}
ds->AddField(new eavlField(1, axisValues[0], eavlField::ASSOC_POINTS));
ds->AddField(new eavlField(1, axisValues[1], eavlField::ASSOC_POINTS));
delete [] buff;
eavlCellSetExplicit *cellSet = new eavlCellSetExplicit(name + "_Cells", 2);
eavlExplicitConnectivity conn;
//read cells
int *nodeList = new int[nElems*3];
sel = MakeSelection(cells, s, c);
adios_schedule_read_byid(mesh_fp, sel, cells->varid, 0, 1, nodeList);
retval = adios_perform_reads(mesh_fp, 1);
adios_selection_delete(sel);
int nodes[3];
for (int i = 0; i < nElems; i++)
{
nodes[0] = nodeList[i*3+0];
nodes[1] = nodeList[i*3+1];
nodes[2] = nodeList[i*3+2];
conn.AddElement(EAVL_TRI, 3, nodes);
}
delete [] nodeList;
cellSet->SetCellNodeConnectivity(conn);
ds->AddCellSet(cellSet);
}
else if (name == "mesh3D")
{
int nPts = nNodes*nPlanes;
ds->SetNumPoints(nPts);
eavlCoordinatesCartesian *coords = new eavlCoordinatesCartesian(NULL,
eavlCoordinatesCartesian::X,
eavlCoordinatesCartesian::Y,
eavlCoordinatesCartesian::Z);
ds->AddCoordinateSystem(coords);
coords->SetAxis(0, new eavlCoordinateAxisField("xcoords", 0));
coords->SetAxis(1, new eavlCoordinateAxisField("ycoords", 0));
coords->SetAxis(2, new eavlCoordinateAxisField("zcoords", 0));
eavlArray *axisValues[3] = {new eavlFloatArray("xcoords", 1),
new eavlFloatArray("ycoords", 1),
new eavlFloatArray("zcoords", 1)};
axisValues[0]->SetNumberOfTuples(nPts);
axisValues[1]->SetNumberOfTuples(nPts);
axisValues[2]->SetNumberOfTuples(nPts);
//read points
double *buff = new double[2*nNodes];
uint64_t s[3], c[3];
ADIOS_SELECTION *sel = MakeSelection(points, s, c);
adios_schedule_read_byid(mesh_fp, sel, points->varid, 0, 1, buff);
int retval = adios_perform_reads(mesh_fp, 1);
adios_selection_delete(sel);
int idx = 0;
double dPhi = 2.0*M_PI/(double)nPlanes;
//double dPhi = 2.0*M_PI/(double)32;
for (int i = 0; i < nPlanes; i++)
{
double phi = (double)i * dPhi;
for (int j = 0; j < nNodes; j++)
{
double R = buff[j*2 +0];
double Z = buff[j*2 +1];
axisValues[0]->SetComponentFromDouble(idx, 0, R*cos(phi));
axisValues[1]->SetComponentFromDouble(idx, 0, R*sin(phi));
axisValues[2]->SetComponentFromDouble(idx, 0, Z);
idx++;
}
}
ds->AddField(new eavlField(1, axisValues[0], eavlField::ASSOC_POINTS));
ds->AddField(new eavlField(1, axisValues[1], eavlField::ASSOC_POINTS));
ds->AddField(new eavlField(1, axisValues[2], eavlField::ASSOC_POINTS));
delete [] buff;
eavlCellSetExplicit *cellSet = new eavlCellSetExplicit(name + "_Cells", 3);
eavlExplicitConnectivity conn;
//read cells
int *nodeList = new int[nElems*3];
sel = MakeSelection(cells, s, c);
adios_schedule_read_byid(mesh_fp, sel, cells->varid, 0, 1, nodeList);
retval = adios_perform_reads(mesh_fp, 1);
adios_selection_delete(sel);
int nodes[6];
for (int i = 0; i < nPlanes; i++)
{
int cellCnt = 0;
for (int j = 0; j < nElems*3; j+=3)
{
int off = i*nNodes;
nodes[0] = nodeList[j+0] + off;
nodes[1] = nodeList[j+1] + off;
nodes[2] = nodeList[j+2] + off;
off = ((i==nPlanes-1) ? 0 : (i+1)*nNodes);
nodes[3] = nodeList[j+0] + off;
nodes[4] = nodeList[j+1] + off;
nodes[5] = nodeList[j+2] + off;
conn.AddElement(EAVL_WEDGE, 6, nodes);
}
}
delete [] nodeList;
cellSet->SetCellNodeConnectivity(conn);
ds->AddCellSet(cellSet);
}
//ds->PrintSummary(cout);
return ds;
}
int main (int argc, char ** argv)
{
int i, j, k, l, t;
MPI_Comm comm_dummy = 0; /* MPI_Comm is defined through adios_read.h */
void * data = NULL;
uint64_t start[] = {0,0,0,0,0,0,0,0,0,0};
uint64_t count[10];
ADIOS_SELECTION *sel;
if (argc < 2) {
printf("Usage: %s <BP-file>\n", argv[0]);
return 1;
}
ADIOS_FILE * f;
//int step;
//for (step=0; step < 2; step++) {
f = adios_read_open_file (argv[1], ADIOS_READ_METHOD_BP, comm_dummy);
if (f == NULL) {
printf ("%s\n", adios_errmsg());
return -1;
}
/* For all variables */
printf(" Variables=%d:\n", f->nvars);
for (i = 0; i < f->nvars; i++) {
ADIOS_VARINFO * v = adios_inq_var_byid (f, i);
adios_inq_var_stat (f, v, 0, 0);
uint64_t total_size = adios_type_size (v->type, v->value);
for (j = 0; j < v->ndim; j++)
total_size *= v->dims[j];
printf(" %-9s %s", adios_type_to_string(v->type), f->var_namelist[i]);
if (v->ndim == 0) {
/* Scalars do not need to be read in, we get it from the metadata
when using adios_inq_var */
printf(" = %s\n", value_to_string(v->type, v->value, 0));
} else {
/* Arrays have to be read in from the file */
if (v->nsteps > 1) {
printf(" %d*",v->nsteps);
}
printf("[%" PRIu64,v->dims[0]);
for (j = 1; j < v->ndim; j++)
printf(", %" PRIu64,v->dims[j]);
//printf("] = \n");
if (v->type == adios_integer)
printf("] = min=%d max=%d\n", (*(int*)v->statistics->min), (*(int*)v->statistics->max));
else if (v->type == adios_double)
printf("] = min=%lg max=%lg\n", (*(double*)v->statistics->min), (*(double*)v->statistics->max));
if (total_size > 1024*1024*1024) {
printf(" // too big, do not read in\n");
} else {
data = malloc (total_size);
if (data == NULL) {
fprintf (stderr, "malloc failed.\n");
return -1;
}
for (j = 0; j < v->ndim; j++)
count[j] = v->dims[j];
for (t=0; t<v->nsteps; t++) {
sel = adios_selection_boundingbox (v->ndim, start, count);
adios_schedule_read_byid (f, sel, i, t, 1, data);
adios_perform_reads (f, 1);
printf(" Step %d:\n", t);
if (adios_errno) {
printf ("%s\n", adios_errmsg());
} else if (total_size > 1024*1024) {
printf ("Too big to print\n");
} else if (v->ndim == 1) {
printf (" [");
for (j = 0; j < v->dims[0]; j++)
printf("%s ", value_to_string(v->type, data, j));
printf ("]\n");
} else if (v->ndim == 2) {
for (j = 0; j < v->dims[0]; j++) {
printf (" row %d: [", j);
for (k = 0; k < v->dims[1]; k++)
printf("%s ", value_to_string(v->type, data, j*v->dims[1] + k));
printf ("]\n");
}
} else if (v->ndim == 3) {
for (j = 0; j < v->dims[0]; j++) {
printf (" block %d: \n", j);
for (k = 0; k < v->dims[1]; k++) {
printf (" row %d: [", k);
for (l = 0; l < v->dims[2]; l++) {
// NCSU ALACRITY-ADIOS - Fixed bug, k*v->dims[1] changed to k*v->dims[2]
printf("%s ", value_to_string(v->type, data, j*v->dims[1]*v->dims[2] + k*v->dims[2] + l));
}
printf ("]\n");
}
printf ("\n");
}
} else {
printf (" cannot print arrays with >3 dimensions\n");
}
}
free (data);
}
}
adios_free_varinfo (v);
} /* variables */
/* For all attributes */
printf(" Attributes=%d:\n", f->nattrs);
for (i = 0; i < f->nattrs; i++) {
enum ADIOS_DATATYPES atype;
int asize;
void *adata;
adios_get_attr_byid (f, i, &atype, &asize, &adata);
int type_size = adios_type_size (atype, adata);
int nelems = asize / type_size;
printf(" %-9s %s = ", adios_type_to_string(atype), f->attr_namelist[i]);
char *p = (char*)adata;
if (nelems>1) printf("{");
for (j=0; j<nelems; j++) {
if (j>0) printf(", ");
printf ("%s", value_to_string(atype, p, 0));
p += type_size;
}
if (nelems>1) printf("}");
printf("\n");
free(adata);
} /* attributes */
adios_read_close (f);
//} /* loop 'step' */
return 0;
}