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
void adios_checkpoint_verify_variables(ADIOS_FILE* fp, const char* name, unsigned long origin)
{
ADIOS_VARINFO *vi;
int count = 1;
int size;
vi = adios_inq_var(fp, name);
if (vi->ndim > 0)
{
cout<<name<<" verification not passed, not a scalar"<<endl;
return;
}
size = count*adios_type_size(vi->type, vi->value);
unsigned long* mem= (unsigned long* )malloc(size);
adios_schedule_read(fp, NULL, name, 0, 1, mem);
adios_perform_reads(fp, 1);
if(mem[0] == origin)
{
cout<<name<<" verification passed"<<mem[0]<<endl;
}
else
{
cout<<name<<" verification not passed, readin: "<<mem[0]<<" writeout: "<<origin<<endl;
}
adios_free_varinfo (vi);
free(mem);
}
int read_file (char *fname)
{
ADIOS_SELECTION *sel;
ADIOS_FILE * f;
ADIOS_VARINFO * vi;
int err=0,i,n;
uint64_t start[1] = {0};
uint64_t count[2] = {NX};
uint64_t ndim;
reset_rarrays();
log ("Read and check data in %s\n", fname);
f = adios_read_open_file (fname, ADIOS_READ_METHOD_BP, comm);
if (f == NULL) {
printE ("Error at opening file: %s\n", adios_errmsg());
return 1;
}
sel = adios_selection_boundingbox (1, start, count);
adios_schedule_read (f, sel, "t1", 0, 1, r1);
adios_schedule_read (f, sel, "t2", 0, 1, r2);
adios_perform_reads (f, 1);
adios_selection_delete (sel);
CHECK_ARRAY (t, r1, NX);
CHECK_ARRAY (t, r2, NX);
endread:
adios_read_close(f);
MPI_Barrier (comm);
return err;
}
void adios_checkpoint_verify_variables(ADIOS_FILE* fp, const char* name, RealType* origin)
{
ADIOS_VARINFO *vi;
int count = 1;
int size;
vi = adios_inq_var(fp, name);
adios_inq_var_blockinfo (fp, vi);
if (vi->ndim > 0)
{
count*=vi->dims[0];
for (int j = 1; j < vi->ndim; j++)
{
count *= vi->dims[j];
}
}
size = count*adios_type_size(vi->type, vi->value);
RealType *mem= (RealType *)malloc(size);
adios_schedule_read(fp, NULL, name, 0, 1, mem);
adios_perform_reads(fp, 1);
for(int i=0; i<count; i++)
{
if(mem[i] == origin[i])
{
cout<<name<<"["<<i<<"]verification passed "<<mem[i]<<endl;
}
else
{
cout<<name<<"["<<i<<"]verification not passed, readin: "<<mem[i]<<" writeout: "<<origin[i]<<endl;
}
}
adios_free_varinfo (vi);
free(mem);
}
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;
}
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;
}
// 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 adios_checkpoint_verify_variables(ADIOS_FILE* fp, const char* name, int* origin)
{
ADIOS_VARINFO *vi;
int count = 1;
int size;
vi = adios_inq_var(fp, name);
if (vi->ndim > 0)
{
cout<<name<<" verification not passed, not a scalar"<<endl;
return;
}
size = count*adios_type_size(vi->type, vi->value);
int * mem= (int * )malloc(size);
ADIOS_SELECTION *sel = adios_selection_writeblock(OHMMS::Controller->rank());
adios_schedule_read(fp, sel, name, 0, 1, mem);
//adios_schedule_read(fp, NULL, name, 0, 1, mem);
adios_perform_reads(fp, 1);
if(mem[0] == *origin)
{
cout<<name<<" verification passed "<<mem[0]<<endl;
}
else
{
cout<<name<<" verification not passed, readin: "<<mem[0]<<" writeout: "<<*origin<<endl;
}
adios_free_varinfo (vi);
adios_selection_delete(sel);
free(mem);
}
/// 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 adios_checkpoint_verify_random_variables(ADIOS_FILE* fp, const char* name, uint_type* origin)
{
ADIOS_VARINFO *vi;
int count_int = 1;
int size;
uint64_t *start;
uint64_t *count;
vi = adios_inq_var(fp, name);
adios_inq_var_blockinfo (fp, vi);
if (vi->ndim > 0)
{
start = (uint64_t *)malloc(vi->ndim * sizeof(uint64_t));
count = (uint64_t *)malloc(vi->ndim * sizeof(uint64_t));
}
for (int j=0; j<vi->nblocks[0]; j++)
{
if(j == OHMMS::Controller->rank())
{
for (int k=0; k<vi->ndim; k++)
{
start[k] = vi->blockinfo[j].start[k];
count[k] = vi->blockinfo[j].count[k];
count_int *= count[k];
//cout<<OHMMS::Controller->rank()<<" count "<<start[k]<<" "<<count[k]<<endl;
}
}
}
size = count_int*adios_type_size(vi->type, vi->value);
uint_type *mem= (uint_type*)malloc(size);
ADIOS_SELECTION *sel = adios_selection_boundingbox(vi->ndim, start, count);
adios_schedule_read(fp, sel, name, 0, 1, mem);
adios_perform_reads(fp, 1);
int flag = 0;
for(int i=0; i<count_int; i++)
{
if(mem[i] == origin[i])
{
//cout<<name<<"["<<i<<"]verification passed "<<mem[i]<<endl;
}
else
{
flag = 1;
cout<<name<<"["<<i<<"]verification not passed, readin: "<<mem[i]<<" writeout: "<<origin[i]<<endl;
}
}
if (flag == 0) cout<<name<<" verification passed "<<endl;
else cout<<name<<" verification not passed "<<endl;
adios_free_varinfo (vi);
adios_selection_delete(sel);
free(start);
free(count);
free(mem);
}
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 ToolsAdiosParallel::convertToText()
{
if(m_options.data.size() == 0)
throw std::runtime_error("No datasets requested");
for (size_t i = 0; i < m_options.data.size(); ++i)
{
ADIOS_VARINFO *pVarInfo;
//get name of dataset to print
std::string nodeName = m_options.data[i];
uint8_t *P;
int varElement = 1;
int varTypeSize = 0;
adios_read_init_method(ADIOS_READ_METHOD_BP, comm, nodeName.c_str());
pVarInfo = adios_inq_var(pFile, nodeName.c_str());
varTypeSize = adios_type_size(pVarInfo->type, NULL);
// get number of elements combined in a dataset
for(int j = 0; j < pVarInfo->ndim; j++)
{
varElement = varElement * pVarInfo->dims[j];
}
// allocate memory
P = (uint8_t*) malloc (sizeof(uint8_t) * varTypeSize * varElement);
adios_schedule_read(pFile, NULL, nodeName.c_str(), 0, 1, P);
adios_perform_reads(pFile, 1);
if(pVarInfo->ndim > 0)
{
for(int k = 0; k < varElement; k++)
{
printValue(pVarInfo->type, &P[k*varTypeSize]);
}
}
else
{
printValue(pVarInfo->type, pVarInfo->value);
}
adios_free_varinfo(pVarInfo);
}
}
/** Read the skalar field and optionally the attribute into the values referenced by the pointers */
void operator()(ThreadParams& params,
const std::string& name, T_Scalar* value,
const std::string& attrName = "", T_Attribute* attribute = nullptr)
{
log<picLog::INPUT_OUTPUT> ("ADIOS: read %1%D scalars: %2%") % simDim % name;
std::string datasetName = params.adiosBasePath + name;
ADIOS_VARINFO* varInfo;
ADIOS_CMD_EXPECT_NONNULL( varInfo = adios_inq_var(params.fp, datasetName.c_str()) );
if(varInfo->ndim != simDim)
throw std::runtime_error(std::string("Invalid dimensionality for ") + name);
if(varInfo->type != traits::PICToAdios<T_Scalar>().type)
throw std::runtime_error(std::string("Invalid type for ") + name);
DataSpace<simDim> gridPos = Environment<simDim>::get().GridController().getPosition();
uint64_t start[varInfo->ndim];
uint64_t count[varInfo->ndim];
for(int d = 0; d < varInfo->ndim; ++d)
{
/* \see adios_define_var: z,y,x in C-order */
start[d] = gridPos.revert()[d];
count[d] = 1;
}
ADIOS_SELECTION* fSel = adios_selection_boundingbox(varInfo->ndim, start, count);
// avoid deadlock between not finished pmacc tasks and mpi calls in adios
__getTransactionEvent().waitForFinished();
/* specify what we want to read, but start reading at below at `adios_perform_reads` */
/* magic parameters (0, 1): `from_step` (not used in streams), `nsteps` to read (must be 1 for stream) */
log<picLog::INPUT_OUTPUT > ("ADIOS: Schedule read skalar %1%)") % datasetName;
ADIOS_CMD( adios_schedule_read(params.fp, fSel, datasetName.c_str(), 0, 1, (void*)value) );
/* start a blocking read of all scheduled variables */
ADIOS_CMD( adios_perform_reads(params.fp, 1) );
adios_selection_delete(fSel);
adios_free_varinfo(varInfo);
if(!attrName.empty())
{
log<picLog::INPUT_OUTPUT> ("ADIOS: read attribute %1% for scalars: %2%") % attrName % name;
*attribute = readAttribute<T_Attribute>(params.fp, datasetName, attrName);
}
}
void AdiosCheckpointInput::performReads()
{
for (int i = 0; i < read_queue.size(); i++)
{
const char* var_name = read_queue[i].c_str();
//grab the information from the metadata about this variable
ADIOS_VARINFO* adios_inq = adios_inq_var(adios_file_handle, var_name);
//Calculate the total size of the vector based on the metadata
uint64_t total_size = adios_type_size(adios_inq->type, NULL);
for (int i = 0; i < adios_inq->ndim; i++)
total_size *= adios_inq->dims[i];
//allocate and then store for when retrieve
void* buff = malloc(total_size);
buffers.push_back(buff);
//schedule the read
adios_schedule_read(adios_file_handle, sel, var_name, 0, 1, buff);
//Don't need the information about the variable anymore
adios_free_varinfo(adios_inq);
}
//perform the read
adios_perform_reads(adios_file_handle, 1);
}
void AdiosCheckpointInput::getVector(const std::string& var_name, vector<T>& buffer)
{
ADIOS_VARINFO* adios_inq = adios_inq_var(adios_file_handle, var_name.c_str());
//Check to make sure the T is the same size as the data type on the disk
if (adios_type_size(adios_inq->type, NULL) != sizeof(T))
{
qmcplusplus::app_error() << "Data type does not match data type found in file: " << std::endl;
APP_ABORT("qmcapp");
return ;
}
uint64_t total_size = 1;
for (int i = 0; i < adios_inq->ndim; i++)
total_size *= adios_inq->dims[i];
//make sure we have enough space to copy all the data from the file
buffer.reserve(total_size);
//schedule the read
adios_schedule_read(adios_file_handle, sel, var_name.c_str(), 0, 1, &(buffer[0]));
//perform the read
adios_perform_reads(adios_file_handle, 1);
//Don't need the information about the variable anymore
adios_free_varinfo(adios_inq);
}
void adios_trace_verify_local_variables(ADIOS_FILE* fp, const char* name, double* origin)
{
ADIOS_VARINFO *vi;
int count = 1;
unsigned long size = 1;
vi = adios_inq_var(fp, name);
adios_inq_var_blockinfo(fp, vi);
for (int j=0; j<vi->nblocks[0]; j++)
{
if(OHMMS::Controller->rank() == j)
{
for (int k=0; k<vi->ndim; k++)
{
count *= vi->blockinfo[j].count[k];
}
}
}
size = count * adios_type_size(vi->type, vi->value);
double* mem = (double*)malloc(size);
ADIOS_SELECTION *sel = adios_selection_writeblock(OHMMS::Controller->rank());
adios_schedule_read(fp, sel, name, 0, 1, mem);
adios_perform_reads(fp, 1);
int flag = 0;
for(int i=0; i<count; i++)
{
if(mem[i] == origin[i])
{
}
else
{
flag = 1;
cout<<OHMMS::Controller->rank()<<" "<<name<<"["<<i<<"]verification not passed, readin: "<<mem[i]<<" writeout: "<<origin[i]<<endl;
}
}
if(flag == 0) cout<<OHMMS::Controller->rank()<<" "<<name<<" verification passed"<<endl;
adios_selection_delete(sel);
adios_free_varinfo (vi);
free(mem);
}
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
int read_points ()
{
ADIOS_SELECTION *sel0,*sel1,*sel2,*sel3;
ADIOS_FILE * f;
ADIOS_VARINFO * vi;
int err=0,n,n1, i,j,k;
int nsteps_a, nsteps_b, nsteps_c;
int v;
uint64_t *pts1;
uint64_t *pts2;
uint64_t *pts3;
uint64_t start[3] = {offs1,offs2,offs3};
uint64_t count[3] = {ldim1,ldim2,ldim3};
pts1 = (uint64_t*) malloc (1*sizeof(uint64_t)*ldim1);
pts2 = (uint64_t*) malloc (2*sizeof(uint64_t)*ldim1*ldim2);
pts3 = (uint64_t*) malloc (3*sizeof(uint64_t)*ldim1*ldim2*ldim3);
for (i=0; i<ldim1; i++)
{
pts1[i] = offs1 + i;
for (j=0; j<ldim2; j++)
{
pts2[i*2*ldim2 + 2*j] = offs1 + i;
pts2[i*2*ldim2 + 2*j+1] = j;
for (k=0; k<ldim3; k++)
{
pts3[i*3*ldim2*ldim3+j*3*ldim3+3*k] = offs1 + i;
pts3[i*3*ldim2*ldim3+j*3*ldim3+3*k+1] = j;
pts3[i*3*ldim2*ldim3+j*3*ldim3+3*k+2] = k;
}
}
}
//Force error on very last point: pts3[3*ldim1*ldim2*ldim3-1] = 0;
reset_readvars();
log ("Read and check data in %s using point selections\n", FILENAME);
f = adios_read_open (FILENAME, read_method, comm,
ADIOS_LOCKMODE_CURRENT, 0.0);
if (f == NULL) {
printE ("Error at opening file: %s\n", rank, adios_errmsg());
return 1;
}
sel1 = adios_selection_points (1, ldim1, pts1);
sel2 = adios_selection_points (2, ldim1*ldim2, pts2);
sel3 = adios_selection_points (3, ldim1*ldim2*ldim3, pts3);
#ifdef DEBUG_PRINTS
fprintf(stderr, "1D selection: {");
for (i=0; i<ldim1; i++) {
fprintf (stderr, "%d ", i, i, pts1[i]);
}
fprintf(stderr, "}\n");
fprintf(stderr, "2D selection :\n");
for (i=0; i<ldim1; i++) {
fprintf (stderr, "i=%d, idx=%2d- = ", i, i*2*ldim2);
for (j=0; j<ldim2; j++) {
n = i*2*ldim2+2*j;
fprintf (stderr, "{%d,%d} ", pts2[n], pts2[n+1]);
}
fprintf(stderr, "\n");
}
fprintf(stderr, "3D selection :\n");
for (i=0; i<ldim1; i++) {
for (j=0; j<ldim2; j++) {
fprintf (stderr, "i=%d, j=%d, idx=%3d- = ", i, j, i*3*ldim2*ldim3+j*3*ldim3);
for (k=0; k<ldim3; k++) {
n = i*3*ldim2*ldim3+j*3*ldim3+3*k;
fprintf (stderr, "{%d,%d,%d} ", pts3[n], pts3[n+1], pts3[n+2]);
}
fprintf(stderr, "\n");
}
}
#endif
n1=0;
while (n1 < NSTEPS && adios_errno != err_end_of_stream) {
n1++;
log (" Step %d\n", f->current_step);
log (" Check 1D variable a1...\n");
adios_schedule_read (f, sel1, "a1", 0, 1, r1);
adios_perform_reads (f, 1);
#ifdef DEBUG_PRINTS
fprintf(stderr, "1D result: {");
for (i=0; i<ldim1; i++) {
fprintf (stderr, "%d ", i, i, r1[i]);
}
fprintf(stderr, "}\n");
#endif
for (i=0; i<ldim1; i++) {
v = VALUE1D(rank,f->current_step,i);
if (r1[i] != v) {
printE ("Error: a1[%d]=%d != read=%d\n", i, v, r1[i]);
//goto endread;
}
}
log (" Check 2D variable a2...\n");
adios_schedule_read (f, sel2, "a2", 0, 1, r2);
adios_perform_reads (f, 1);
#ifdef DEBUG_PRINTS
fprintf(stderr, "2D result :\n");
n = 0;
for (i=0; i<ldim1; i++) {
fprintf (stderr, "row=%2d- = {", i);
for (j=0; j<ldim2; j++) {
fprintf (stderr, "%d ", r2[n]);
n++;
}
fprintf(stderr, "}\n");
}
#endif
n = 0;
for (i=0; i<ldim1; i++) {
for (j=0; j<ldim2; j++) {
v = VALUE2D(rank,f->current_step,i,j);
if (v != r2[n]) {
printE ("Error: a2[%d,%d]=%d != read=%d\n", i, j, v, r2[n]);
//goto endread;
}
n++;
}
}
log (" Check 3D variable a3...\n");
adios_schedule_read (f, sel3, "a3", 0, 1, r3);
adios_perform_reads (f, 1);
#ifdef DEBUG_PRINTS
fprintf(stderr, "3D selection :\n");
n=0;
for (i=0; i<ldim1; i++) {
for (j=0; j<ldim2; j++) {
fprintf (stderr, "[%d,%d] = {", i, j);
for (k=0; k<ldim3; k++) {
fprintf (stderr, "%d ", r3[n]);
n++;
}
fprintf(stderr, "}\n");
}
}
#endif
n = 0;
for (i=0; i<ldim1; i++) {
for (j=0; j<ldim2; j++) {
for (k=0; k<ldim3; k++) {
v = VALUE3D(rank,f->current_step,i,j,k);
if (v != r3[n]) {
printE ("Error: a3[%d,%d,%d]=%d != read=%d\n", i, j, k, v, r3[n]);
//goto endread;
}
n++;
}
}
}
if (n1 < NSTEPS)
{
adios_advance_step (f, 0, -1.0);
}
}
endread:
adios_selection_delete (sel1);
adios_selection_delete (sel2);
adios_selection_delete (sel3);
free(pts1);
free(pts2);
free(pts3);
adios_read_close(f);
MPI_Barrier (comm);
return err;
}
static void test_file_mode_reads_on_var(ADIOS_FILE *fp, const char *bp_filename, const char *varname) {
int i;
ADIOS_VARINFO *varinfo = adios_inq_var(fp, varname);
MPI_Assert(COMM, varinfo);
if (varinfo->value != NULL) {
//if (rank == 0) fprintf(stderr, "(skipping scalar variable '%s')\n", varname);
adios_free_varinfo(varinfo);
return;
}
fprintf(stderr, "[rank %d/%d] Starting file-mode writeblock reads on %s:/%s\n", rank, size, bp_filename, varname);
adios_inq_var_blockinfo(fp, varinfo);
MPI_Assert(COMM, varinfo->blockinfo);
const enum ADIOS_DATATYPES datatype = varinfo->type;
const int datatypesize = adios_get_type_size(datatype, NULL);
int timestep, timestep_blockidx, blockidx = 0;
for (timestep = 0; timestep < varinfo->nsteps; ++timestep) {
for (timestep_blockidx = 0; timestep_blockidx < varinfo->nblocks[timestep]; ++timestep_blockidx, ++blockidx) {
if (blockidx % size != rank) continue;
const ADIOS_VARBLOCK *vb = &varinfo->blockinfo[blockidx];
ADIOS_SELECTION *block_bb = adios_selection_boundingbox(varinfo->ndim, vb->start, vb->count);
ADIOS_SELECTION *block_wb = adios_selection_writeblock(timestep_blockidx);
ADIOS_SELECTION *block_abs_wb = adios_selection_writeblock(blockidx);
block_abs_wb->u.block.is_absolute_index = 1;
uint64_t blocksize = datatypesize;
for (i = 0; i < varinfo->ndim; ++i)
blocksize *= vb->count[i];
void *buf_bb = malloc(blocksize);
void *buf_wb = malloc(blocksize);
void *buf_abs_wb = malloc(blocksize);
memset(buf_bb, 0, blocksize);
memset(buf_wb, 1, blocksize);
memset(buf_abs_wb, 2, blocksize);
MPI_Assert(COMM, buf_bb && buf_wb && buf_abs_wb);
adios_schedule_read(fp, block_bb, varname, timestep, 1, buf_bb );
adios_schedule_read(fp, block_wb, varname, timestep, 1, buf_wb );
adios_schedule_read(fp, block_abs_wb, varname, timestep, 1, buf_abs_wb);
adios_perform_reads(fp, 1);
fprintf(stderr, "[rank %d/%d] Checking file-mode blockidx %d BB vs. WB...\n", rank, size, blockidx);
MPI_Assert(COMM, memcmp(buf_bb, buf_wb, blocksize) == 0);
fprintf(stderr, "[rank %d/%d] Checking file-mode blockidx %d BB vs. abs-WB...\n", rank, size, blockidx);
MPI_Assert(COMM, memcmp(buf_bb, buf_abs_wb, blocksize) == 0);
free(buf_bb); free(buf_wb); free(buf_abs_wb);
adios_selection_delete(block_bb);
adios_selection_delete(block_wb);
adios_selection_delete(block_abs_wb);
}
}
adios_free_varinfo(varinfo);
fprintf(stderr, "[rank %d/%d] Finished file-mode writeblock reads on %s:/%s\n", rank, size, bp_filename, varname);
}
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;
}
int main (int argc, char ** argv)
{
int rank, size, i, j;
MPI_Comm comm = MPI_COMM_WORLD;
ADIOS_FILE * f;
ADIOS_VARINFO * v;
ADIOS_SELECTION * sel;
int steps = 0;
int retval = 0;
float timeout_sec = 1.0;
void * data = NULL;
uint64_t start[2], count[2];
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &rank);
MPI_Comm_size (comm, &size);
adios_read_init_method (ADIOS_READ_METHOD_BP, comm, "verbose=3");
f = adios_read_open ("adios_globaltime.bp", ADIOS_READ_METHOD_BP,
comm, ADIOS_LOCKMODE_NONE, timeout_sec);
if (adios_errno == err_file_not_found)
{
printf ("rank %d: Stream not found after waiting %f seconds: %s\n",
rank, timeout_sec, adios_errmsg());
retval = adios_errno;
}
else if (adios_errno == err_end_of_stream)
{
printf ("rank %d: Stream terminated before open. %s\n", rank, adios_errmsg());
retval = adios_errno;
}
else if (f == NULL) {
printf ("rank %d: Error at opening stream: %s\n", rank, adios_errmsg());
retval = adios_errno;
}
else
{
/* process file here... */
v = adios_inq_var (f, "temperature");
adios_inq_var_blockinfo (f, v);
printf ("ndim = %d\n", v->ndim);
//printf ("nsteps = %d\n", v->nsteps);
printf ("dims[%llu][%llu]\n", v->dims[0], v->dims[1]);
uint64_t slice_size = v->dims[0]/size;
if (rank == size-1)
slice_size = slice_size + v->dims[0]%size;
start[0] = rank * slice_size;
count[0] = slice_size;
start[1] = 0;
count[1] = v->dims[1];
data = malloc (slice_size * v->dims[1] * 8);
/* Processing loop over the steps (we are already in the first one) */
while (adios_errno != err_end_of_stream) {
steps++; // steps start counting from 1
sel = adios_selection_boundingbox (v->ndim, start, count);
adios_schedule_read (f, sel, "temperature", 0, 1, data);
adios_perform_reads (f, 1);
if (rank == 0)
printf ("--------- Step: %d --------------------------------\n",
f->current_step);
printf("rank=%d: [0:%lld,0:%lld] = [", rank, v->dims[0], v->dims[1]);
for (i = 0; i < slice_size; i++) {
printf (" [");
for (j = 0; j < v->dims[1]; j++) {
printf ("%g ", *((double *)data + i * v->dims[1] + j));
}
printf ("]");
}
printf (" ]\n\n");
// advance to 1) next available step with 2) blocking wait
adios_advance_step (f, 0, timeout_sec);
if (adios_errno == err_step_notready)
{
printf ("rank %d: No new step arrived within the timeout. Quit. %s\n",
rank, adios_errmsg());
break; // quit while loop
}
}
adios_read_close (f);
}
if (rank==0)
printf ("We have processed %d steps\n", steps);
adios_read_finalize_method (ADIOS_READ_METHOD_BP);
free (data);
MPI_Finalize ();
return retval;
}
int worker(int argc, char* argv[]) {
TAU_PROFILE_TIMER(timer, __func__, __FILE__, TAU_USER);
TAU_PROFILE_START(timer);
my_printf("%d of %d In worker B\n", myrank, commsize);
static bool announced = false;
/* validate input */
validate_input(argc, argv);
my_printf("Worker B will execute until it sees n iterations.\n", iterations);
/* ADIOS: These declarations are required to match the generated
* gread_/gwrite_ functions. (And those functions are
* generated by calling 'gpp.py adios_config.xml') ...
* EXCEPT THAT THE generation of Reader code is broken.
* So, we will write the reader code manually.
*/
uint64_t adios_groupsize;
uint64_t adios_totalsize;
uint64_t adios_handle;
void * data = NULL;
uint64_t start[2], count[2];
int i, j, steps = 0;
int NX = 10;
int NY = 1;
double t[NX];
double p[NX];
/* ADIOS: Can duplicate, split the world, whatever.
* This allows you to have P writers to N files.
* With no splits, everyone shares 1 file, but
* can write lock-free by using different areas.
*/
MPI_Comm adios_comm, adios_comm_b_to_c;
adios_comm = MPI_COMM_WORLD;
//MPI_Comm_dup(MPI_COMM_WORLD, &adios_comm);
adios_comm_b_to_c = MPI_COMM_WORLD;
//MPI_Comm_dup(MPI_COMM_WORLD, &adios_comm_b_to_c);
enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_FLEXPATH;
adios_read_init_method(method, adios_comm, "verbose=3");
if (adios_errno != err_no_error) {
fprintf (stderr, "rank %d: Error %d at init: %s\n", myrank, adios_errno, adios_errmsg());
exit(4);
}
if (send_to_c) {
adios_init("adios_config.xml", adios_comm);
}
/* ADIOS: Set up the adios communications and buffers, open the file.
*/
ADIOS_FILE *fp; // file handler
ADIOS_VARINFO *vi; // information about one variable
ADIOS_SELECTION * sel;
char adios_filename_a_to_b[256];
char adios_filename_b_to_c[256];
enum ADIOS_LOCKMODE lock_mode = ADIOS_LOCKMODE_NONE;
double timeout_sec = 1.0;
sprintf(adios_filename_a_to_b, "adios_a_to_b.bp");
sprintf(adios_filename_b_to_c, "adios_b_to_c.bp");
my_printf ("rank %d: Worker B opening file: %s\n", myrank, adios_filename_a_to_b);
fp = adios_read_open(adios_filename_a_to_b, method, adios_comm, lock_mode, timeout_sec);
if (adios_errno == err_file_not_found) {
fprintf (stderr, "rank %d: Stream not found after waiting %d seconds: %s\n",
myrank, timeout_sec, adios_errmsg());
exit(1);
} else if (adios_errno == err_end_of_stream) {
// stream has been gone before we tried to open
fprintf (stderr, "rank %d: Stream terminated before open. %s\n", myrank, adios_errmsg());
exit(2);
} else if (fp == NULL) {
// some other error happened
fprintf (stderr, "rank %d: Error %d at opening: %s\n", myrank, adios_errno, adios_errmsg());
exit(3);
} else {
my_printf("Found file %s\n", adios_filename_a_to_b);
my_printf ("File info:\n");
my_printf (" current step: %d\n", fp->current_step);
my_printf (" last step: %d\n", fp->last_step);
my_printf (" # of variables: %d:\n", fp->nvars);
vi = adios_inq_var(fp, "temperature");
adios_inq_var_blockinfo(fp, vi);
printf ("ndim = %d\n", vi->ndim);
printf ("nsteps = %d\n", vi->nsteps);
printf ("dims[%llu][%llu]\n", vi->dims[0], vi->dims[1]);
uint64_t slice_size = vi->dims[0]/commsize;
if (myrank == commsize-1) {
slice_size = slice_size + vi->dims[0]%commsize;
}
start[0] = myrank * slice_size;
count[0] = slice_size;
start[1] = 0;
count[1] = vi->dims[1];
data = malloc (slice_size * vi->dims[1] * 8);
/* Processing loop over the steps (we are already in the first one) */
while (adios_errno != err_end_of_stream && steps < iterations) {
steps++; // steps start counting from 1
TAU_PROFILE_TIMER(adios_recv_timer, "ADIOS recv", __FILE__, TAU_USER);
TAU_PROFILE_START(adios_recv_timer);
sel = adios_selection_boundingbox (vi->ndim, start, count);
adios_schedule_read (fp, sel, "temperature", 0, 1, data);
adios_perform_reads (fp, 1);
if (myrank == 0)
printf ("--------- B Step: %d --------------------------------\n",
fp->current_step);
#if 0
printf("B rank=%d: [0:%lld,0:%lld] = [", myrank, vi->dims[0], vi->dims[1]);
for (i = 0; i < slice_size; i++) {
printf (" [");
for (j = 0; j < vi->dims[1]; j++) {
printf ("%g ", *((double *)data + i * vi->dims[1] + j));
}
printf ("]");
}
printf (" ]\n\n");
#endif
// advance to 1) next available step with 2) blocking wait
adios_advance_step (fp, 0, timeout_sec);
if (adios_errno == err_step_notready)
{
printf ("B rank %d: No new step arrived within the timeout. Quit. %s\n",
myrank, adios_errmsg());
break; // quit while loop
}
TAU_PROFILE_STOP(adios_recv_timer);
/* Do some exchanges with neighbors */
//do_neighbor_exchange();
/* "Compute" */
compute(steps);
for (i = 0; i < NX; i++) {
t[i] = steps*100.0 + myrank*NX + i;
}
for (i = 0; i < NY; i++) {
p[i] = steps*1000.0 + myrank*NY + i;
}
if (send_to_c) {
TAU_PROFILE_TIMER(adios_send_timer, "ADIOS send", __FILE__, TAU_USER);
TAU_PROFILE_START(adios_send_timer);
/* ADIOS: write to the next application in the workflow */
if (steps == 0) {
adios_open(&adios_handle, "b_to_c", adios_filename_b_to_c, "w", adios_comm_b_to_c);
} else {
adios_open(&adios_handle, "b_to_c", adios_filename_b_to_c, "a", adios_comm_b_to_c);
}
/* ADIOS: Actually write the data out.
* Yes, this is the recommended method, and this way, changes in
* configuration with the .XML file will, even in the worst-case
* scenario, merely require running 'gpp.py adios_config.xml'
* and typing 'make'.
*/
#include "gwrite_b_to_c.ch"
/* ADIOS: Close out the file completely and finalize.
* If MPI is being used, this must happen before MPI_Finalize().
*/
adios_close(adios_handle);
TAU_PROFILE_STOP(adios_send_timer);
#if 1
if (!announced) {
SOS_val foo;
foo.i_val = NX;
SOS_pack(example_pub, "NX", SOS_VAL_TYPE_INT, foo);
SOS_announce(example_pub);
SOS_publish(example_pub);
announced = true;
}
#endif
}
MPI_Barrier(adios_comm_b_to_c);
}
MPI_Barrier(MPI_COMM_WORLD);
adios_read_close(fp);
/* ADIOS: Close out the file completely and finalize.
* If MPI is being used, this must happen before MPI_Finalize().
*/
adios_read_finalize_method(method);
}
if (send_to_c) {
adios_finalize(myrank);
}
free(data);
//MPI_Comm_free(&adios_comm);
//MPI_Comm_free(&adios_comm_b_to_c);
TAU_PROFILE_STOP(timer);
/* exit */
return 0;
}
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 main (int argc, char ** argv)
{
int i, j, datasize;
MPI_Comm comm = MPI_COMM_WORLD;
enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP;
ADIOS_SELECTION * sel1;
double * data = NULL;
uint64_t start[2], count[2];
MPI_Init (&argc, &argv);
#ifdef WITH_NCSU_TIMER
timer_init();
#endif
adios_read_init_method (method, comm, NULL);
ADIOS_FILE * f = adios_read_open_file ("adios_global.bp", method, comm);
ADIOS_VARINFO * varinfo = adios_inq_var (f, "temperature");
if (varinfo)
{
int nranks;
assert(varinfo->ndim == 2);
nranks = varinfo->dims[0];
assert(nranks % 4 == 0);
assert(varinfo->dims[1] == 10);
datasize = (nranks / 2) * varinfo->dims[1] * sizeof(double);
data = malloc (datasize);
start[0] = nranks / 4;
start[1] = 2;
count[0] = nranks / 2;
count[1] = 6;
sel1 = adios_selection_boundingbox (varinfo->ndim, start, count);
adios_schedule_read (f, sel1, "temperature", 0, 1, data);
adios_perform_reads (f, 1);
printf("Subvolume at (%" PRIu64 ",%" PRIu64 ") of size (%" PRIu64 ",%" PRIu64 "):\n", start[0], start[1], count[0], count[1]);
for (i = 0; i < count[0]; i++) {
printf("[ ");
for (j = 0; j < count[1]; j++) {
printf("%.0lf ", data[i * count[1] + j]);
}
printf("]\n");
}
adios_selection_delete (sel1);
}
adios_free_varinfo (varinfo);
adios_read_close (f);
adios_read_finalize_method (ADIOS_READ_METHOD_BP);
#ifdef WITH_NCSU_TIMER
printf("[TIMERS] ");
timer_result_t *results = timer_get_results_sorted();
for (i = 0; i < timer_get_num_timers(); i++) {
printf("%s: %0.4lf ", results[i].name, results[i].time);
}
printf("\n");
free(results);
#endif
#ifdef WITH_NCSU_TIMER
timer_finalize();
#endif
MPI_Finalize ();
return 0;
}
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);
}
int main (int argc, char ** argv)
{
char filename [256] = "stream.bp";
int rank, size;
int NX, NY;
int len, off;
double *t = NULL;
MPI_Comm comm = MPI_COMM_WORLD;
int64_t adios_handle;
uint64_t adios_groupsize, adios_totalsize;
uint64_t start[2], count[2];
ADIOS_SELECTION *sel;
int steps = 0;
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &rank);
MPI_Comm_size (comm, &size);
// ADIOS read init
adios_read_init_method (ADIOS_READ_METHOD_BP, comm, "verbose=3");
ADIOS_FILE* fp = adios_read_open_file ("kstar.bp",
ADIOS_READ_METHOD_BP,
comm);
assert(fp != NULL);
ADIOS_VARINFO* nx_info = adios_inq_var( fp, "N");
ADIOS_VARINFO* ny_info = adios_inq_var( fp, "L");
NX = *((int *)nx_info->value);
NY= *((int*)ny_info->value);
len = NX / size;
off = len * rank;
if (rank == size-1)
len = len + NX % size;
printf("\trank=%d: NX,NY,len,off = %d\t%d\t%d\t%d\n", rank, NX, NY, len, off);
assert(len > 0);
t = (double *) malloc(sizeof(double) * len * NY);
memset(t, '\0', sizeof(double) * len * NY);
assert(t != NULL);
start[0] = off;
start[1] = 0;
count[0] = len;
count[1] = NY;
sel = adios_selection_boundingbox (2, start, count);
// ADIOS write init
adios_init ("adios.xml", comm);
remove (filename);
//int ii;
//for(ii = 0; ii<10; ii++){
// for (i = 0; i < len * NY; i++)
// t[i] = ii*1000 + rank;
while(adios_errno != err_end_of_stream && adios_errno != err_step_notready)
{
steps++;
// Reading
adios_schedule_read (fp, sel, "var", 0, 1, t);
adios_perform_reads (fp, 1);
// Debugging
//for (i = 0; i < len*NY; i++) t[i] = off * NY + i;
printf("step=%d\trank=%d\t[%d,%d]\n", steps, rank, len, NY);
// Writing
adios_open (&adios_handle, "writer", filename, "a", comm);
adios_groupsize = 4*4 + 8*len*NY;
adios_group_size (adios_handle, adios_groupsize, &adios_totalsize);
adios_write (adios_handle, "NX", &NX);
adios_write (adios_handle, "NY", &NY);
adios_write (adios_handle, "len", &len);
adios_write (adios_handle, "off", &off);
adios_write (adios_handle, "var_2d_array", t);
adios_close (adios_handle);
// Advance
MPI_Barrier (comm);
adios_advance_step(fp, 0, TIMEOUT_SEC);
}
free(t);
MPI_Barrier (comm);
adios_read_close(fp);
if (rank==0)
printf ("We have processed %d steps\n", steps);
MPI_Barrier (comm);
adios_read_finalize_method(ADIOS_READ_METHOD_BP);
adios_finalize (rank);
MPI_Finalize ();
return 0;
}
int main (int argc, char ** argv)
{
int rank, size;
int NX, NY;
int len, off;
double *t = NULL;
MPI_Comm comm = MPI_COMM_WORLD;
uint64_t start[2], count[2];
ADIOS_SELECTION *sel;
int steps = 0;
#ifdef _USE_GNUPLOT
int i, j;
double *tmp;
FILE *pipe;
#else
// Variables for ADIOS write
int64_t adios_handle;
uint64_t adios_groupsize, adios_totalsize;
char outfn[256];
#endif
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &rank);
MPI_Comm_size (comm, &size);
adios_read_init_method(ADIOS_READ_METHOD_FLEXPATH, comm, "");
ADIOS_FILE* fp = adios_read_open("stream.bp",
ADIOS_READ_METHOD_FLEXPATH,
comm, ADIOS_LOCKMODE_NONE, 0.0);
assert(fp != NULL);
ADIOS_VARINFO* nx_info = adios_inq_var( fp, "NX");
ADIOS_VARINFO* ny_info = adios_inq_var( fp, "NY");
NX = *((int *)nx_info->value);
NY= *((int*)ny_info->value);
len = NX / size;
off = len * rank;
if (rank == size-1)
len = len + NX % size;
printf("\trank=%d: NX,NY,len,off = %d\t%d\t%d\t%d\n", rank, NX, NY, len, off);
assert(len > 0);
t = (double *) malloc(sizeof(double) * len * NY);
memset(t, '\0', sizeof(double) * len * NY);
assert(t != NULL);
start[0] = off;
start[1] = 0;
count[0] = len;
count[1] = NY;
// Not working ...
//sel = adios_selection_boundingbox (2, start, count);
sel = malloc(sizeof(ADIOS_SELECTION));
sel->type=ADIOS_SELECTION_WRITEBLOCK;
sel->u.block.index = rank;
#ifdef _USE_GNUPLOT
if ((NX % size) > 0)
{
fprintf(stderr, "Equal distribution is required\n");
return -1;
}
if (rank == 0) {
pipe = popen("gnuplot", "w");
fprintf(pipe, "set view map\n");
fprintf(pipe, "set xrange [0:%d]\n", NX-1);
tmp = (double *) malloc(sizeof(double) * NX * NY);
assert(tmp != NULL);
}
#else
// ADIOS write init
adios_init ("adios.xml", comm);
#endif
//while(adios_errno != err_end_of_stream && adios_errno != err_step_notready)
while(1)
{
steps++;
// Reading
adios_schedule_read (fp, sel, "var_2d_array", 0, 1, t);
adios_perform_reads (fp, 1);
printf("step=%d\trank=%d\tfp->current_step=%d\t[%d,%d]\n",
steps, rank, fp->current_step, len, NY);
/*
// Debugging
for (i=0; i<len; i++) {
printf("%d: rank=%d: t[%d,0:4] = ", steps, rank, off+i);
for (j=0; j<5; j++) {
printf(", %g", t[i*NY + j]);
}
printf(" ...\n");
}
*/
// Do something
#ifdef _USE_GNUPLOT // Option 1: plotting
MPI_Gather(t, len * NY, MPI_DOUBLE, tmp, len * NY, MPI_DOUBLE, 0, comm);
if (rank == 0)
{
fprintf(pipe, "set title 'Soft X-Rray Signal (shot #%d)'\n", steps);
fprintf(pipe, "set xlabel 'Channel#'\n");
fprintf(pipe, "set ylabel 'Timesteps'\n");
fprintf(pipe, "set cblabel 'Voltage (eV)'\n");
# ifndef _GNUPLOT_INTERACTIVE
fprintf(pipe, "set terminal png\n");
fprintf(pipe, "set output 'fig%03d.png'\n", steps);
# endif
fprintf(pipe, "splot '-' matrix with image\n");
//fprintf(pipe, "plot '-' with lines, '-' with lines, '-' with lines\n");
double *sum = calloc(NX, sizeof(double));
for (j = 0; j < NY; j++) {
for (i = 0; i < NX; i++) {
sum[i] += tmp[i * NY + j];
}
}
for (j = 0; j < NY; j++) {
for (i = 0; i < NX; i++) {
fprintf (pipe, "%g ", (-tmp[i * NY + j] + sum[i]/NY)/3276.8);
}
fprintf(pipe, "\n");
}
fprintf(pipe, "e\n");
fprintf(pipe, "e\n");
fflush (pipe);
# ifdef _GNUPLOT_INTERACTIVE
printf ("Press [Enter] to continue . . .");
fflush (stdout);
getchar ();
# endif
free(sum);
}
#else // Option 2: BP writing
snprintf (outfn, sizeof(outfn), "reader_%3.3d.bp", steps);
adios_open (&adios_handle, "reader", outfn, "w", comm);
adios_groupsize = 4 * sizeof(int) + sizeof(double) * len * NY;
adios_group_size (adios_handle, adios_groupsize, &adios_totalsize);
adios_write (adios_handle, "NX", &NX);
adios_write (adios_handle, "NY", &NY);
adios_write (adios_handle, "len", &len);
adios_write (adios_handle, "off", &off);
adios_write (adios_handle, "var", t);
adios_close (adios_handle);
#endif
// Advance
MPI_Barrier (comm);
adios_advance_step(fp, 0, TIMEOUT_SEC);
if (adios_errno == err_end_of_stream)
{
printf("rank %d, Stream terminated. Quit\n", rank);
break; // quit while loop
}
else if (adios_errno == err_step_notready)
{
printf ("rank %d: No new step arrived within the timeout. Quit.\n", rank);
break; // quit while loop
}
else if (adios_errno != err_no_error) {
printf("ADIOS returned code=%d, msg:%s\n",
adios_errno, adios_get_last_errmsg());
break; // quit while loop
}
}
//
free(t);
adios_read_close(fp);
//printf("rank %d, Successfully closed stream\n", rank);
adios_read_finalize_method(ADIOS_READ_METHOD_FLEXPATH);
//printf("rank %d, Successfully finalized read method\n", rank);
#ifndef _USE_GNUPLOT
adios_finalize (rank);
//printf("rank %d, Successfully finalized adios\n", rank);
#else
if (rank==0) {
free(tmp);
pclose(pipe);
}
#endif
MPI_Finalize ();
return 0;
}
int main(int argc, char ** argv)
{
int rank, size, varid, numvars;
int bins, step, mod;
char *filename, *in_stream, *data_var_name;
MPI_Comm comm = MPI_COMM_WORLD;
enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_FLEXPATH;
//enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP;
ADIOS_SELECTION * global_range_select;
double *data;
uint64_t tstep, global_size, mysize, mystart, sz;
MPI_Init (&argc, &argv);
MPI_Comm_rank(comm, &rank);
MPI_Comm_size(comm, &size);
/* Command line parsing */
if (rank == 0 && argc < 4) {
fprintf(stderr, "\nHistogram usage: <exec> input-stream-name num-bins"
" arr1 [arr2] [arr3] [...]\n"
"\t where arr1, arr2, arr3 ... are the names of the arrays to be analyzed.\n");
MPI_Abort(comm, -1);
}
MPI_Barrier(comm);
in_stream = argv[1];
//Parse cmd line
bins = atoi(argv[2]);
numvars = argc - 3;
const char *vars[numvars];
for (varid=0; varid < numvars; varid++)
{
vars[varid] = argv[varid + 3];
}
/* Adios open and init */
adios_read_init_method (method, comm, "verbose=1");
ADIOS_FILE * f = adios_read_open (in_stream, method, comm, ADIOS_LOCKMODE_ALL, -1);
step = 0; //not used now
while (adios_errno != err_end_of_stream){
//resource monitor
/*loop over different arrays inside stream*/
for (varid = 0; varid < numvars; varid++){
#ifdef ENABLE_MONITOR
//double t1 = wfgettimeofday();
lib_mem_init();
ind_timer_start(0, "whole timestep");
#endif
//Init variables....
global_size = 0; tstep = 0;
mod = 0; mysize = 0; mystart = 0;
adios_schedule_read (f, NULL, "ntimestep", 0, 1, &tstep);
adios_perform_reads (f, 1);
ADIOS_VARINFO * glob_info = adios_inq_var (f, vars[varid]);
global_size = glob_info->dims[0];
//printf("[DEBUG] global_size = %" PRIu64 " ntimestep = %" PRIu64 "\n",
// global_size, tstep);
//printf("[HIST%d] received data for timestep %" PRIu64 " with ndim: %d and globalsize:%"
// PRIu64 " \n", rank, tstep, ndim, global_size);
//sleep(800);
//debug
//Array slice computation
mod = global_size % size;//size = MPI size
if (mod == 0){
mysize = global_size / size;
mystart = mysize * rank;
}
else {
mysize = global_size / (size);
if (rank < mod){
mysize++;
mystart = mysize * rank;
}
else {
mystart = (mod * (mysize + 1)) +
((rank - mod) * mysize);
}
}
#ifdef ENABLE_MONITOR
nohandler_mem(rank);
#endif
//printf("[HISTO%d]: mysize = %" PRIu64" mystart = %" PRIu64 "\n", rank, mysize, mystart);
//debug
//if (step == 0) sleep(800);
uint64_t starts[] = {mystart};
uint64_t counts[] = {mysize};
global_range_select = adios_selection_boundingbox (1, starts, counts);
//Allocate space for arrays
uint64_t msize = ((uint64_t) sizeof(double) * mysize);
//printf("[DEBUG] mysize = %" PRIu64 " msize= %" PRIu64" \n", mysize, msize);
//data = (double *) malloc(sizeof(double) * mysize);
data = new double[mysize];
if (data == NULL){
//printf("DEBUG: malloc returned NULL, size was %d\n", msize);
}
else {
if (rank == 0)
printf("[HIST0] DEBUG: malloc successful, size was %d\n", mysize);
}
//memset (data, 0, sizeof(double) * mysize);
//Read data
adios_schedule_read (f,
global_range_select,
vars[varid],
0, 1, data);
adios_perform_reads
(f, 1);
#ifdef ENABLE_MONITOR
nohandler_mem(rank);
#endif
//printf("PERFORM_READS success of variable: %s\n", vars[varid]);
/*
Data check
if (step == 4) {
FILE *fp;
char *log;
asprintf(&log, "histo-input%d-%d.log", step, rank);
fp = fopen(log, "w");
fprintf(fp, "timestep: %" PRIu64 " mysize: %"PRIu64 "\n",
tstep, mysize);
for (i=0; i<(int)mysize; i++){
fprintf(fp, "%lf\n", data[i]);
}
fclose(fp);
sleep(800);
}
*/
// find max and min
sz = 0;
sz = mysize;
double min = data[0];
double max = data[0];
for (uint64_t i = 1; i < sz; ++i)
{
if (data[i] > max) max = data[i];
if (data[i] < min) min = data[i];
}//local max, min found.
//local data should just use shared mem.
double g_min, g_max;
// Find the global max/min
MPI_Allreduce (&min, &g_min, 1, MPI_DOUBLE, MPI_MIN, comm);
MPI_Allreduce (&max, &g_max, 1, MPI_DOUBLE, MPI_MAX, comm);
//printf("[HIST%d] glob-min: %f, glob-max: %f\n", rank, g_min, g_max);
nohandler_mem(rank);
double width = (g_max - g_min)/bins;
std::vector<uint64_t> hist(bins);
for (uint64_t i = 0; i < sz; ++i)//fill local bins
{
//printf("[HISTO%d] local filling adding index %" PRIu64 "\n", rank, i);
int idx = int((data[i] - g_min)/width);//discover index
if (idx == bins) // we hit the max
--idx;
//printf("[%d]: %f -> %d\n", rank, data[i], idx);
++hist[idx];
}
delete[] data;
// Global reduce histograms
std::vector<uint64_t> g_hist(bins);
MPI_Reduce(&hist[0], &g_hist[0], bins, MPI_UINT64_T, MPI_SUM, 0, comm);
//debug
//printf("[Completed histogram routine]\n");
if (rank == 0) //print histogram to file
{
FILE *fp;
const char *log = "histograms.log";
fp = fopen(log, "a");
fprintf(fp, "Histogram for %s, timestep %" PRIu64"\n", vars[varid], tstep);
for (int i = 0; i < bins; ++i)
fprintf(fp, " %f-%f: %" PRIu64 "\n", g_min + i*width, g_min + (i+1)*width, g_hist[i]);
fclose (fp);
}
#ifdef ENABLE_MONITOR
nohandler_mem(rank);
#endif
if (rank == 0) //print histogram to terminal
{
printf("Histogram for %s, timestep %" PRIu64"\n", vars[varid], tstep);
for (int i = 0; i < bins; ++i)
printf(" %f-%f: %" PRIu64 "\n",
g_min + i*width, g_min + (i+1)*width, g_hist[i]);
}
//resource monitor
#ifdef ENABLE_MONITOR
//double t2 = wfgettimeofday();
ind_timer_end(0);
char monitor_title[40];
sprintf(monitor_title, "histogram-%s", vars[varid]);
monitor_out (rank, size, tstep, msize, t1, t2, comm, monitor_title);
#endif
}
//end of read + analysis for 3 variables
adios_release_step(f);
//delete[] data;
if (rank == 0) printf("[HIST%d] read and wrote data for timestep %" PRIu64 "\n", rank, tstep);
step++;
adios_advance_step(f, 0, -1);
/*
if (step == 6){
double t1 = wfgettimeofday();
FILE *tfp;
tfp = fopen("time.log", "a");
fprintf(tfp, "rank %d histogram end time: %f\n", rank, t1);
fclose(tfp);
}
*/
}//end of adios stream while loop
if (rank == 0) printf("[HIST%d] out of read loop\n", rank);
/* performance measurement */
/*
if (rank == 0){
double t3 = wfgettimeofday();
FILE *tfp;
tfp = fopen("time.log", "a");
fprintf(tfp, "master histogram end time: %f\n", t3);
fclose(tfp);
}
*/
#ifdef ENABLE_MONITOR
outer_timer_end(rank, "histogram");
#endif
adios_read_close(f);
adios_read_finalize_method(method);
MPI_Finalize();
return 0;
}
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;
}
int main (int argc, char ** argv)
{
int rank, size, i, j;
MPI_Comm comm = MPI_COMM_WORLD;
enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP;
ADIOS_SELECTION * sel;
void * data = NULL;
uint64_t start[2], count[2];
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &rank);
MPI_Comm_size (comm, &size);
adios_read_init_method (method, comm, "verbose=4");
adios_logger_open ("log_read_C", rank);
ADIOS_FILE * f = adios_read_open ("global_array_C.bp", method, comm, ADIOS_LOCKMODE_NONE, 0);
if (f == NULL)
{
log_error ("%s\n", adios_errmsg());
return -1;
}
ADIOS_VARINFO * v = adios_inq_var (f, "temperature");
/* Using less readers to read the global array back, i.e., non-uniform */
uint64_t slice_size = v->dims[0]/size;
start[0] = slice_size * rank;
if (rank == size-1) /* last rank may read more lines */
slice_size = slice_size + v->dims[0]%size;
count[0] = slice_size;
start[1] = 0;
count[1] = v->dims[1];
data = malloc (slice_size * v->dims[1] * sizeof (double));
if (data == NULL)
{
log_error (stderr, "malloc failed.\n");
return -1;
}
/* Read a subset of the temperature array */
sel = adios_selection_boundingbox (v->ndim, start, count);
adios_schedule_read (f, sel, "temperature", 0, 1, data);
adios_perform_reads (f, 1);
for (i = 0; i < slice_size; i++) {
log_test ("rank %d: [%lld,%d:%lld]", rank, start[0]+i, 0, slice_size);
for (j = 0; j < v->dims[1]; j++)
log_test (" %6.6g", * ((double *)data + i * v->dims[1] + j));
log_test ("\n");
}
free (data);
adios_read_close (f);
MPI_Barrier (comm);
adios_read_finalize_method (method);
adios_logger_close();
MPI_Finalize ();
return 0;
}