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, 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);
}
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);
}
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);
}
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 ADIOS1CommonRead::ScheduleReadCommon(const std::string &name,
const Dims &offs, const Dims &ldims,
const int fromStep, const int nSteps,
const bool readAsLocalValue,
const bool readAsJoinedArray,
void *data)
{
if (readAsLocalValue)
{
/* Get all the requested values from metadata now */
ADIOS_VARINFO *vi = adios_inq_var(m_fh, name.c_str());
if (vi)
{
adios_inq_var_stat(m_fh, vi, 0, 1);
int elemsize = adios_type_size(vi->type, nullptr);
long long blockidx = 0;
for (int i = 0; i < fromStep; i++)
{
blockidx += vi->nblocks[i];
}
char *dest = (char *)data;
for (int i = fromStep; i < fromStep + nSteps; i++)
{
for (int j = 0; j < vi->nblocks[i]; j++)
{
memcpy(dest, vi->statistics->blocks->mins[blockidx],
elemsize);
++blockidx;
dest += elemsize;
}
}
adios_free_varinfo(vi);
}
}
else
{
uint64_t start[32], count[32];
for (int i = 0; i < ldims.size(); i++)
{
start[i] = (uint64_t)offs[i];
count[i] = (uint64_t)ldims[i];
}
ADIOS_SELECTION *sel = nullptr;
if (ldims.size() > 0)
{
sel = adios_selection_boundingbox(ldims.size(), start, count);
}
adios_schedule_read(m_fh, sel, name.c_str(), (int)fromStep, (int)nSteps,
data);
adios_selection_delete(sel);
}
}
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::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 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);
}
int main (int argc, char ** argv)
{
char filename [256];
int rank, size, i, j, k, token;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Status status;
enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP;
ADIOS_SELECTION * sel;
void * data = NULL;
uint64_t start[3], count[3], step = 0;
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &rank);
MPI_Comm_size (comm, &size);
adios_read_init_method (method, comm, "verbose=3");
/* adios_read_open_file() allows for seeing all timesteps in the file */
ADIOS_FILE * f = adios_read_open_file ("adios_globaltime.bp", method, comm);
if (f == NULL)
{
printf ("%s\n", adios_errmsg());
return -1;
}
ADIOS_VARINFO * v = adios_inq_var (f, "temperature");
// read in two timesteps
data = malloc (2 * v->dims[0] * v->dims[1] * sizeof (double));
if (data == NULL)
{
fprintf (stderr, "malloc failed.\n");
return -1;
}
// read in timestep 'rank' (up to 12)
step = rank % 13;
start[0] = 0;
count[0] = v->dims[0];
start[1] = 0;
count[1] = v->dims[1];
/* Read a subset of the temperature array */
sel = adios_selection_boundingbox (v->ndim, start, count);
/* 2 steps from 'step' */
adios_schedule_read (f, sel, "temperature", step, 2, data);
adios_perform_reads (f, 1);
if (rank == 0)
printf ("Array size of temperature [0:%lld,0:%lld]\n", v->dims[0], v->dims[1]);
if (rank > 0) {
MPI_Recv (&token, 1, MPI_INT, rank-1, 0, comm, &status);
}
printf("------------------------------------------------\n", rank);
printf("rank=%d: \n", rank);
for (i = 0; i < 2; i++) {
printf ("step %lld = [\n", step+i);
for (j = 0; j < v->dims[0]; j++) {
printf (" [");
for (k = 0; k < v->dims[1]; k++) {
printf ("%g ", ((double *)data) [ i * v->dims[0] * v->dims[1] + j * v->dims[1] + k]);
}
printf ("]\n");
}
printf ("]\n");
}
printf ("\n");
if (rank < size-1) {
MPI_Send (&token, 1, MPI_INT, rank+1, 0, comm);
}
free (data);
adios_free_varinfo (v);
adios_read_close (f);
MPI_Barrier (comm);
adios_read_finalize_method (method);
MPI_Finalize ();
return 0;
}
int main (int argc, char ** argv)
{
int rank, size, i, j, npl, token;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Status status;
enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP;
ADIOS_SELECTION * sel;
void * data = NULL;
uint64_t start[1], count[1];
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &rank);
MPI_Comm_size (comm, &size);
adios_read_init_method (method, comm, "verbose=3");
ADIOS_FILE * f = adios_read_open ("adios_global_no_xml.bp", method,
comm, ADIOS_LOCKMODE_NONE, 0);
if (f == NULL)
{
printf ("%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;
data = malloc (slice_size * sizeof (double));
if (data == NULL)
{
fprintf (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);
if (rank > 0) {
MPI_Recv (&token, 1, MPI_INT, rank-1, 0, comm, &status);
}
printf (" ======== Rank %d ========== \n", rank);
npl = 10;
for (i = 0; i < slice_size; i+=npl) {
printf ("[%4.4" PRIu64 "] ", rank*slice_size+i);
for (j= 0; j < npl; j++) {
printf (" %6.6g", * ((double *)data + i + j));
}
printf ("\n");
}
fflush(stdout);
sleep(1);
if (rank < size-1) {
MPI_Send (&token, 1, MPI_INT, rank+1, 0, comm);
}
free (data);
adios_selection_delete (sel);
adios_free_varinfo (v);
adios_read_close (f);
MPI_Barrier (comm);
adios_read_finalize_method (method);
MPI_Finalize ();
return 0;
}
int main (int argc, char **argv){
int rank =0, size =0;
int NX = 0;
double *t = NULL;
// this is an array we expect as a reference array
double *t_ref = NULL;
MPI_Comm comm = MPI_COMM_WORLD;
diag_t diag = DIAG_OK; // to store the diagnostic information
struct test_info test_result = {TEST_PASSED, "1D_arr_global_noxml"};
struct err_counts err = { 0, 0};
struct adios_tsprt_opts adios_opts;
GET_ENTRY_OPTIONS(adios_opts, "Runs readers. It is recommended to run as many readers as writers.");
// adios read initialization
MPI_Init( &argc, &argv);
MPI_Comm_rank (comm, &rank);
// depending on the method
SET_ERROR_IF_NOT_ZERO(adios_read_init_method(adios_opts.method, comm, adios_opts.adios_options), err.adios);
RET_IF_ERROR(err.adios, rank);
// I will be working with streams so the lock mode is necessary,
// return immediately if the stream unavailable
ADIOS_FILE *adios_handle = adios_read_open(FILE_NAME, adios_opts.method, comm, ADIOS_LOCKMODE_NONE, 0.0);
if ( !adios_handle){
p_error("Quitting ... (%d) %s\n", adios_errno, adios_errmsg());
return DIAG_ERR;
}
// define portions of data how they will be read
ADIOS_SELECTION *sel = NULL;
ADIOS_VARINFO *avi = NULL;
// for storing the variables
char buf[STR_BUFFER_SIZE];
int step = 0;
// read how many processors wrote that array
avi = adios_inq_var (adios_handle, "size");
if (!avi){
p_error("rank %d: Quitting ... (%d) %s\n", rank, adios_errno, adios_errmsg());
diag = DIAG_ERR;
goto close_adios;
}
size = *((int*)avi->value);
adios_free_varinfo(avi);
avi = NULL;
// if I run the more readers than writers; just release
// the excessive readers
if (rank >= size){
p_info("rank %d: I am an excessive rank. Nothing to read ...\n", rank);
diag = DIAG_OK;
goto close_adios;
}
// read the size of the array
avi = adios_inq_var (adios_handle, "NX");
if (!avi){
p_error("rank %d: Quitting ... (%d) %s\n", rank, adios_errno, adios_errmsg());
diag = DIAG_ERR;
goto close_adios;
}
// I expect a scalar that will tell me the size of an array
assert(0 == avi->ndim);
assert(adios_integer == avi->type);
NX = *((int*)avi->value);
// I don't need that variable any more
adios_free_varinfo(avi);
assert(NX_DIM == NX);
avi = NULL;
// this will define the slice that we want to read; each rank should
// read its own slice written by a corresponding writer rank
uint64_t count[1] = { NX };
uint64_t start[1] = { 0 };
start[0] = rank*NX;
sel = adios_selection_boundingbox(1,start, count);
if( !sel ){
p_error("rank %d: Quitting ... (%d) %s\n", rank, adios_errno, adios_errmsg());
diag = DIAG_ERR;
goto close_adios;
}
// make the reference array with reference values I expect to get
t_ref = calloc(NX, sizeof(double));
if (gen_1D_array(t_ref, NX, rank) == DIAG_ERR){
p_error("Generating 1D array. Quitting ...\n");
diag = DIAG_ERR;
goto close_adios;
}
// allocate the memory for the actual array to be read
t = calloc(NX, sizeof(double));
if (adios_schedule_read(adios_handle, sel, "var_1d_array",0,1,t) != 0){
p_error("rank %d: Quitting ...(%d) %s\n", rank, adios_errno, adios_errmsg());
diag = DIAG_ERR;
goto just_clean;
}
// not sure if this assumption is correct; difficult to find in the ADIOS sources
if (adios_perform_reads(adios_handle, 1) != 0){
p_error("rank %d: Quitting ...(%d) %s\n", rank, adios_errno, adios_errmsg());
diag = DIAG_ERR;
goto just_clean;
}
sprintf(buf, "Rank %d: var_1d_array: step %d: t: ", rank, step);
int i = 0;
for(i=0; i < NX; ++i){
if( t[i] != t_ref[i] ){
p_test_failed("%s: rank %d: for t[%d] (expected %.1f, got %.1f)\n", test_result.name, rank, i, t_ref[i], t[i] );
test_result.result = TEST_FAILED;
break;
}
}
if (TEST_PASSED == test_result.result)
p_test_passed("%s: rank %d\n", test_result.name, rank);
just_clean:
// clean everything
adios_selection_delete(sel);
sel = NULL;
free(t);
t = NULL;
free(t_ref);
t_ref = NULL;
close_adios:
CLOSE_ADIOS_READER(adios_handle, adios_opts.method);
if ((DIAG_OK == diag) && (TEST_PASSED == test_result.result)) {
return 0;
} else {
return 1;
}
}
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;
}
int main (int argc, char ** argv)
{
int rank, j;
int NX, NY;
double *t;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &rank);
adios_read_init_method(ADIOS_READ_METHOD_FLEXPATH, comm, "");
ADIOS_SELECTION *global_range_select;
ADIOS_SELECTION scalar_block_select;
scalar_block_select.type = ADIOS_SELECTION_WRITEBLOCK;
scalar_block_select.u.block.index = 0;
/* schedule_read of a scalar. */
int test_scalar = -1;
ADIOS_FILE* afile = adios_read_open("arrays",
ADIOS_READ_METHOD_FLEXPATH,
comm,
ADIOS_LOCKMODE_NONE, 0.0);
int i;
for(i=0; i<afile->nvars; i++){
printf("var: %s\n", afile->var_namelist[i]);
}
int ii = 0;
while(adios_errno != err_end_of_stream){
/* get a bounding box - rank 0 for now*/
ADIOS_VARINFO *nx_info = adios_inq_var( afile, "/scalar/dim/NX");
ADIOS_VARINFO *ny_info = adios_inq_var( afile, "/scalar/dim/NY");
ADIOS_VARINFO *size_info = adios_inq_var( afile, "size");
ADIOS_VARINFO *arry = adios_inq_var( afile, "var_2d_array");
int nx_val = *((int*)nx_info->value);
int ny_val = *((int*)ny_info->value);
int size_val = *((int*)size_info->value);
printf("nx: %d, ny: %d, size: %d\n", nx_val, ny_val, size_val);
uint64_t xcount = arry->dims[0];
uint64_t ycount = arry->dims[1];
uint64_t starts[] = {0,0};
uint64_t counts[] = {xcount, ycount};
global_range_select = adios_selection_boundingbox(2, starts, counts);
int nelem = xcount*ycount;
if(nx_info->value) {
NX = *((int *)nx_info->value);
}
if(ny_info->value){
NY= *((int*)ny_info->value);
}
if(rank == 0){
int n;
printf("dims: [ ");
for(n=0; n<arry->ndim; n++){
printf("%d ", (int)arry->dims[n]);
}
printf("]\n");
}
/* Allocate space for the arrays */
int arr_size = sizeof(double) * nelem;
t = (double *) malloc (arr_size);
memset(t, 0, arr_size);
//fprintf(stderr, "t %p\n", t);
/* Read the arrays */
adios_schedule_read (afile,
global_range_select,
"var_2d_array",
0, 1, t);
adios_schedule_read (afile,
&scalar_block_select,
"test_scalar",
0, 1, &test_scalar);
adios_perform_reads (afile, 1);
//sleep(20);
printf("Rank=%d: test_scalar: %d step: %d, t[0,5+x] = [", rank, test_scalar, ii);
for(j=0; j<nelem; j++) {
printf(", %6.2f", t[j]);
}
printf("]\n\n");
adios_release_step(afile);
adios_advance_step(afile, 0, 30);
ii++;
//MPI_Barrier (comm);
//sleep(1);
}
//
adios_read_close(afile);
adios_read_finalize_method(ADIOS_READ_METHOD_FLEXPATH);
MPI_Finalize ();
return 0;
}
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, 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;
}
void performQuery(ADIOS_QUERY_TEST_INFO *queryInfo, ADIOS_FILE *f, int use_streaming, int print_points, int read_results)
{
int timestep = 0 ;
ADIOS_VARINFO * tempVar = adios_inq_var(f, queryInfo->varName);
if (use_streaming)
for (timestep = 0; timestep < queryInfo->fromStep; ++timestep)
assert(adios_advance_step(f, 0, 0) == 0);
fprintf(stderr,"times steps for variable is: [%d, %d], batch size is %" PRIu64 "\n", queryInfo->fromStep, queryInfo->fromStep + queryInfo->numSteps, queryInfo->batchSize);
for (timestep = queryInfo->fromStep; timestep < queryInfo->fromStep + queryInfo->numSteps; timestep ++) {
fprintf(stderr, "querying on timestep %d \n", timestep);
ADIOS_SELECTION* currBatch = NULL;
while (adios_query_evaluate(queryInfo->query, queryInfo->outputSelection, use_streaming ? 0 : timestep, queryInfo->batchSize, &currBatch) >= 0) {
if (currBatch == NULL) {
break;
}
assert(currBatch->type ==ADIOS_SELECTION_POINTS);
const ADIOS_SELECTION_POINTS_STRUCT * retrievedPts = &(currBatch->u.points);
/* fprintf(stderr,"retrieved points %" PRIu64 " \n", retrievedPts->npoints); */
if (print_points) {
printPoints(retrievedPts, timestep);
}
if (read_results) {
int elmSize = adios_type_size(tempVar->type, NULL);
void *data = malloc(retrievedPts->npoints * elmSize);
// read returned temp data
adios_schedule_read (f, currBatch, queryInfo->varName, use_streaming ? 0 : timestep, 1, data);
adios_perform_reads(f, 1);
free(data);
}
fprintf(stderr,"Total data retrieved:%"PRIu64"\n", retrievedPts->npoints);
/* if (tempVar->type == adios_double) { */
/* for (i = 0; i < retrievedPts->npoints; i++) { */
/* fprintf(stderr,"%.6f\t", ((double*)data)[i]); */
/* } */
/* fprintf(stderr,"\n"); */
/* } */
/* else if (tempVar->type == adios_real) { */
/* for (i = 0; i < retrievedPts->npoints; i++) { */
/* fprintf(stderr,"%.6f\t", ((float*)data)[i]); */
/* } */
/* fprintf(stderr,"\n"); */
/* } */
adios_selection_delete(currBatch);
currBatch = NULL;
}
if (use_streaming) {
const int err = adios_advance_step(f, 0, 0);
if (timestep < queryInfo->fromStep + queryInfo->numSteps - 1) {
assert(err == 0);
} else {
assert(err == err_end_of_stream || err == err_step_notready);
}
}
}
adios_query_free(queryInfo->query);
}
int main (int argc, char ** argv)
{
char filename [256];
int rank;
MPI_Comm comm = MPI_COMM_WORLD;
enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP;
ADIOS_SELECTION * sel1=NULL;
int8_t v1 = 0;
int16_t v2 = 0;
int32_t v3 = 0;
int64_t v4 = 0;
uint8_t v5 = 0;
uint16_t v6 = 0;
uint32_t v7 = 0;
uint64_t v8 = 0;
float v9 = 0.0;
double v10 = 0.0;
char v11[256];
complex v12;
v12.r = 0.0;
v12.i = 0.0;
double_complex v13;
v13.r = 0.0;
v13.i = 0.0;
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &rank);
strcpy (filename, "scalars.bp");
adios_read_init_method (method, comm, "verbose=3");
ADIOS_FILE * f = adios_read_open (filename, method, comm, ADIOS_LOCKMODE_NONE, 0.0);
adios_schedule_read (f, sel1, "var_byte", 0, 1, &v1);
adios_schedule_read (f, sel1, "var_short", 0, 1, &v2);
adios_schedule_read (f, sel1, "var_int", 0, 1, &v3);
adios_schedule_read (f, sel1, "var_long", 0, 1, &v4);
adios_schedule_read (f, sel1, "var_ubyte", 0, 1, &v5);
adios_schedule_read (f, sel1, "var_ushort", 0, 1, &v6);
adios_schedule_read (f, sel1, "var_uint", 0, 1, &v7);
adios_schedule_read (f, sel1, "var_ulong", 0, 1, &v8);
adios_schedule_read (f, sel1, "var_real", 0, 1, &v9);
adios_schedule_read (f, sel1, "var_double", 0, 1, &v10);
/* note that a string is an array and thus v11 a pointer already,
so we pass the v11 instead of &v11 here */
adios_schedule_read (f, sel1, "var_string", 0, 1, v11);
adios_schedule_read (f, sel1, "var_complex", 0, 1, &v12);
adios_schedule_read (f, sel1, "var_double_complex", 0, 1, &v13);
adios_perform_reads (f,1);
if (rank == 0) {
printf("byte v1 = %d\n", v1);
printf("short v2 = %d\n", v2);
printf("integer v3 = %d\n", v3);
printf("long v4 = %" PRId64 "\n", v4);
printf("uns.byte v5 = %u\n", v5);
printf("uns.short v6 = %u\n", v6);
printf("uns.int v7 = %u\n", v7);
printf("uns.long v8 = %" PRIu64 "\n", v8);
printf("float v9 = %g\n", v9);
printf("double v10 = %g\n", v10);
printf("string v11 = %s\n", v11);
printf("complex v12 = (%g, i%g)\n", v12.r, v12.i);
printf("dbl-complex v13 = (%g, i%g)\n", v13.r, v13.i);
}
adios_read_close (f);
MPI_Barrier (comm);
adios_read_finalize_method (ADIOS_READ_METHOD_BP);
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)
{
/* application data structures */
int rank;
int NX, NY;
double *t;
int *p;
/* MPI and ADIOS data structures */
MPI_Comm comm = MPI_COMM_WORLD;
/* MPI and ADIOS setup */
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &rank);
adios_read_init_method(ADIOS_READ_METHOD_FLEXPATH, comm, "");
/* First read in the scalars to calculate the size of the arrays */
/* get everything from single process - rank 0 for now*/
ADIOS_SELECTION process_select;
process_select.type=ADIOS_SELECTION_WRITEBLOCK;
process_select.u.block.index = rank;
/* read the size of arrays using local inq_var */
/* Note: at this moment, timeout is not handled. It blocks until writer appears */
ADIOS_FILE* afile = adios_read_open("arrays", ADIOS_READ_METHOD_FLEXPATH, comm,
ADIOS_LOCKMODE_NONE, 30.0);
/* Read arrays for each time step */
while(adios_errno != err_end_of_stream){
ADIOS_VARINFO* nx_info = adios_inq_var( afile, "NX");
if(nx_info->value) {
NX = *((int *)nx_info->value);
}
ADIOS_VARINFO* ny_info = adios_inq_var( afile, "NY");
if(ny_info->value) {
NY = *((int *)ny_info->value);
}
/* Allocate space for the arrays */
t = (double *) malloc (NX*NY*sizeof(double));
p = (int *) malloc (NX*sizeof(int));
memset(t, 0, NX*NY*sizeof(double));
memset(p, 0, NX*sizeof(int));
/* schedule a read of the arrays */
adios_schedule_read (afile, &process_select, "var_double_2Darray", 0, 1, t);
adios_schedule_read (afile, &process_select, "var_int_1Darray", 0, 1, p);
/* commit request and retrieve data */
adios_perform_reads (afile, 1);
/* print result */
printf("Results Rank=%d Step=%d p[] = [%d, %d,...] t[][] = [%.2f, %.2f]\n",
rank, afile->current_step, p[0], p[1], t[0], t[1]);
/* block until next step is available (30 sec timeout unsupported) */
adios_release_step(afile);
adios_advance_step(afile, 0, 30);
MPI_Barrier (comm);
/* shutdown ADIOS and MPI */
}
adios_read_close(afile);
/* wait until all readers finish */
adios_read_finalize_method(ADIOS_READ_METHOD_FLEXPATH);
MPI_Finalize ();
return 0;
}
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 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;
}
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 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;
}
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);
}
void performQuery(ADIOS_QUERY_TEST_INFO *queryInfo, ADIOS_FILE *f, int use_streaming, int print_points, int read_results)
{
int timestep = 0 ;
ADIOS_VARINFO * tempVar = adios_inq_var(f, queryInfo->varName);
adios_inq_var_blockinfo(f, tempVar);
if (use_streaming)
for (timestep = 0; timestep < queryInfo->fromStep; ++timestep)
assert(adios_advance_step(f, 0, 0) == 0);
fprintf(stderr,"times steps for variable is: [%d, %d], batch size is %" PRIu64 "\n", queryInfo->fromStep, queryInfo->fromStep + queryInfo->numSteps, queryInfo->batchSize);
for (timestep = queryInfo->fromStep; timestep < queryInfo->fromStep + queryInfo->numSteps; timestep ++) {
fprintf(stderr, "querying on timestep %d \n", timestep);
while (1)
{
ADIOS_QUERY_RESULT *currBatch = NULL;
currBatch = adios_query_evaluate(
queryInfo->query,
queryInfo->outputSelection,
use_streaming ? 0 : timestep,
queryInfo->batchSize
);
if (currBatch == NULL) {
fprintf(stderr, "Unexpected error status in querying evaluation, returned NULL as result. "
"ADIOS error message: %s \n", adios_errmsg());
break;
}
if (currBatch->status == ADIOS_QUERY_RESULT_ERROR) {
fprintf(stderr, "ERROR in querying evaluation: %s \n", adios_errmsg());
break;
}
if (currBatch->nselections == 0) {
/* this is normal, we processed everything in previous loop or there is 0 total result */
break;
}
int n;
if (currBatch->selections->type == ADIOS_SELECTION_POINTS)
{
for (n = 0; n < currBatch->nselections; n++)
{
const ADIOS_SELECTION_POINTS_STRUCT * retrievedPts = &(currBatch->selections[n].u.points);
/* fprintf(stderr,"retrieved points %" PRIu64 " \n", retrievedPts->npoints); */
uint64_t * wboffs = calloc (retrievedPts->ndim, sizeof(uint64_t));
if (retrievedPts->container_selection &&
retrievedPts->container_selection->type == ADIOS_SELECTION_WRITEBLOCK)
{
int i;
int blockidx = retrievedPts->container_selection->u.block.index;
if (use_streaming) {
adios_inq_var_blockinfo(f, tempVar);
} else {
for (i = 0; i < timestep-1; i++)
blockidx += tempVar->nblocks[i];
}
for (i = 0; i < retrievedPts->ndim; ++i) {
wboffs[i] = tempVar->blockinfo[blockidx].start[i];
}
}
if (print_points) {
printPoints(retrievedPts, timestep, wboffs);
}
free (wboffs);
if (read_results) {
int elmSize = adios_type_size(tempVar->type, NULL);
void *data = malloc(retrievedPts->npoints * elmSize);
// read returned temp data
adios_schedule_read (f, &currBatch->selections[n], queryInfo->varName, use_streaming ? 0 : timestep, 1, data);
adios_perform_reads(f, 1);
free(data);
}
fprintf(stderr,"Total points retrieved %"PRIu64" in %d blocks\n",
currBatch->npoints, currBatch->nselections);
/* if (tempVar->type == adios_double) { */
/* for (i = 0; i < retrievedPts->npoints; i++) { */
/* fprintf(stderr,"%.6f\t", ((double*)data)[i]); */
/* } */
/* fprintf(stderr,"\n"); */
/* } */
/* else if (tempVar->type == adios_real) { */
/* for (i = 0; i < retrievedPts->npoints; i++) { */
/* fprintf(stderr,"%.6f\t", ((float*)data)[i]); */
/* } */
/* fprintf(stderr,"\n"); */
/* } */
}
}
else if (currBatch->selections->type == ADIOS_SELECTION_WRITEBLOCK)
{
fprintf(stderr,"Number of blocks retrieved: %d\n", currBatch->nselections);
if (print_points) {
for (n = 0; n < currBatch->nselections; n++)
{
fprintf(stdout,"%d %d\n", timestep, currBatch->selections[n].u.block.index);
}
}
}
free(currBatch->selections);
if (currBatch->status == ADIOS_QUERY_NO_MORE_RESULTS) {
free (currBatch);
break;
}
free(currBatch);
}
if (use_streaming) {
const int err = adios_advance_step(f, 0, 0);
if (timestep < queryInfo->fromStep + queryInfo->numSteps - 1) {
assert(err == 0);
} else {
assert(err == err_end_of_stream || err == err_step_notready);
}
}
}
adios_query_free(queryInfo->query);
}
