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);
}
}
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;
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_file("adios_stat.bp", method, comm);
if (f == NULL)
{
fprintf (stderr, "%s\n", adios_errmsg());
return -1;
}
ADIOS_VARINFO * v = adios_inq_var (f, "temperature");
if (v) {
/* get statistics, for each individual time-step */
adios_inq_var_stat (f, v, 1, 0);
printf("Global MIN of temperature: %lf\n", * (double *) v->statistics->min);
printf("Global MAX of temperature: %lf\n", * (double *) v->statistics->max);
printf("Global AVG of temperature: %lf\n", * (double *) v->statistics->avg);
printf("Global STD DEV of temperature: %lf\n", * (double *) v->statistics->std_dev);
printf("\n");
printf("---------------------------------------------------------------------------\n");
if (v->statistics->steps) {
printf("MIN\t\tMAX\t\tAVG\t\tSTD_DEV\t\tHISTOGRAM\n");
for(i = 0; i < v->nsteps; i++)
{
if (v->statistics->steps->mins[i])
printf("%lf\t", * (double *) v->statistics->steps->mins[i]);
else
printf("--\t\t");
if (v->statistics->steps->maxs[i])
printf("%lf\t", * (double *) v->statistics->steps->maxs[i]);
else
printf("--\t\t");
if (v->statistics->steps->avgs[i])
printf("%lf\t", * (double *) v->statistics->steps->avgs[i]);
else
printf("--\t\t");
if (v->statistics->steps->std_devs[i])
printf("%lf\t", * (double *) v->statistics->steps->std_devs[i]);
else
printf("--\t\t");
if (v->statistics->histogram) {
for(j = 0; j <= v->statistics->histogram->num_breaks; j++) {
printf("%d ", v->statistics->histogram->frequencies[i][j]);
}
printf("\n");
} else {
printf("--\t\t");
}
printf("\n");
}
} else {
printf ("Per step statistics is missing\n");
}
printf("---------------------------------------------------------------------------\n");
printf("\n");
if (v->statistics->histogram) {
printf("Break points:\t\t\t");
for(j = 0; j < v->statistics->histogram->num_breaks; j++)
printf("%6.2lf\t", v->statistics->histogram->breaks[j]);
printf("\n");
printf("Frequencies:\t\t\t");
for(j = 0; j <= v->statistics->histogram->num_breaks; j++)
printf("%6d\t", v->statistics->histogram->gfrequencies[j]);
}
printf("\n\n");
#if 0
printf ("Auto covariance of MIN values of temperature over time: %lf\n", adios_stat_cov (v, v, "min", 0, 12, 0));
printf ("Auto correlation of MAX values of temperature over time, with lag 2 units: %lf\n", adios_stat_cor (v, v, "max", 0, 8, 2));
printf("\n\n");
#endif
adios_free_varinfo (v);
} else {
fprintf (stderr, "ERROR: Cannot inquire statistics of variable 'temperature': %s\n", adios_errmsg());
}
v = adios_inq_var (f, "complex");
if (v) {
adios_inq_var_stat (f, v, 1, 0);
double *C = v->statistics->min;
printf("Global Minimum of variable complex - Magnitude: %lf\n", C[0]);
printf("Global Minimum of variable complex - Real part: %lf\n", C[1]);
printf("Global Minimum of variable complex - Imaginary part: %lfi\n", C[2]);
double ** Cmin;
Cmin = (double **) v->statistics->steps->mins;
printf("\nMagnitude\t\tReal\t\t\tImaginary\n");
for (j = 0; j < v->nsteps; j++)
{
printf ("%lf\t\t%lf\t\t%lf\n", Cmin[j][0], Cmin[j][1], Cmin[j][2]);
}
printf("\n");
adios_free_varinfo (v);
} else {
fprintf (stderr, "ERROR: Cannot inquire statistics of variable 'complex': %s\n", adios_errmsg());
}
adios_read_close (f);
MPI_Barrier (comm);
adios_read_finalize_method (method);
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)
{
int i, j, k,l;
MPI_Comm comm_dummy = 0; /* MPI_Comm is defined through adios_read.h */
if (argc < 2) {
printf("Usage: %s <BP-file>\n", argv[0]);
return 1;
}
adios_read_init_method (ADIOS_READ_METHOD_BP, comm_dummy, "show_hidden_attrs");
ADIOS_FILE * f;
f = adios_read_open_file (argv[1], ADIOS_READ_METHOD_BP, comm_dummy);
if (f == NULL) {
printf ("%s\n", adios_errmsg());
return -1;
}
/* For all variables */
printf(" Variables=%d:\n", f->nvars);
for (i = 0; i < f->nvars; i++) {
ADIOS_VARINFO * v = adios_inq_var_byid (f, i);
adios_inq_var_stat (f, v, 0, 1);
adios_inq_var_blockinfo (f, v);
uint64_t total_size = adios_type_size (v->type, v->value);
for (j = 0; j < v->ndim; j++)
total_size *= v->dims[j];
printf(" %-9s %s", adios_type_to_string(v->type), f->var_namelist[i]);
if (v->ndim == 0) {
/* Scalars do not need to be read in, we get it from the metadata
when using adios_inq_var */
printf(" = %s\n", value_to_string(v->type, v->value, 0));
} else {
/* Arrays, print min/max statistics*/
printf("[%lld",v->dims[0]);
for (j = 1; j < v->ndim; j++)
printf(", %lld",v->dims[j]);
//printf("] = \n");
if (v->type == adios_integer)
printf("] : min=%d max=%d\n",
(*(int*)v->statistics->min), (*(int*)v->statistics->max));
else if (v->type == adios_double)
printf("] : min=%lg max=%lg\n",
(*(double*)v->statistics->min), (*(double*)v->statistics->max));
/* Print block info */
for (l=0; l<v->nsteps; l++) {
printf(" step %3d: \n", l);
for (j=0; j<v->nblocks[l]; j++) {
printf(" block %3d: [", j);
for (k=0; k<v->ndim; k++) {
printf("%3lld:%3lld", v->blockinfo[j].start[k],
v->blockinfo[j].start[k]+v->blockinfo[j].count[k]-1);
if (k<v->ndim-1)
printf(", ");
}
printf("]\n");
}
}
}
adios_free_varinfo (v);
} /* variables */
/* For all attributes */
printf(" Attributes=%d:\n", f->nattrs);
for (i = 0; i < f->nattrs; i++) {
enum ADIOS_DATATYPES atype;
int asize;
void *adata;
adios_get_attr_byid (f, i, &atype, &asize, &adata);
printf(" %-9s %s = %s\n", adios_type_to_string(atype),
f->attr_namelist[i], value_to_string(atype, adata, 0));
free(adata);
} /* attributes */
adios_read_close (f);
return 0;
}
int main (int argc, char ** argv)
{
int i, j, k, l, t;
MPI_Comm comm_dummy = 0; /* MPI_Comm is defined through adios_read.h */
void * data = NULL;
uint64_t start[] = {0,0,0,0,0,0,0,0,0,0};
uint64_t count[10];
ADIOS_SELECTION *sel;
if (argc < 2) {
printf("Usage: %s <BP-file>\n", argv[0]);
return 1;
}
ADIOS_FILE * f;
//int step;
//for (step=0; step < 2; step++) {
f = adios_read_open_file (argv[1], ADIOS_READ_METHOD_BP, comm_dummy);
if (f == NULL) {
printf ("%s\n", adios_errmsg());
return -1;
}
/* For all variables */
printf(" Variables=%d:\n", f->nvars);
for (i = 0; i < f->nvars; i++) {
ADIOS_VARINFO * v = adios_inq_var_byid (f, i);
adios_inq_var_stat (f, v, 0, 0);
uint64_t total_size = adios_type_size (v->type, v->value);
for (j = 0; j < v->ndim; j++)
total_size *= v->dims[j];
printf(" %-9s %s", adios_type_to_string(v->type), f->var_namelist[i]);
if (v->ndim == 0) {
/* Scalars do not need to be read in, we get it from the metadata
when using adios_inq_var */
printf(" = %s\n", value_to_string(v->type, v->value, 0));
} else {
/* Arrays have to be read in from the file */
if (v->nsteps > 1) {
printf(" %d*",v->nsteps);
}
printf("[%" PRIu64,v->dims[0]);
for (j = 1; j < v->ndim; j++)
printf(", %" PRIu64,v->dims[j]);
//printf("] = \n");
if (v->type == adios_integer)
printf("] = min=%d max=%d\n", (*(int*)v->statistics->min), (*(int*)v->statistics->max));
else if (v->type == adios_double)
printf("] = min=%lg max=%lg\n", (*(double*)v->statistics->min), (*(double*)v->statistics->max));
if (total_size > 1024*1024*1024) {
printf(" // too big, do not read in\n");
} else {
data = malloc (total_size);
if (data == NULL) {
fprintf (stderr, "malloc failed.\n");
return -1;
}
for (j = 0; j < v->ndim; j++)
count[j] = v->dims[j];
for (t=0; t<v->nsteps; t++) {
sel = adios_selection_boundingbox (v->ndim, start, count);
adios_schedule_read_byid (f, sel, i, t, 1, data);
adios_perform_reads (f, 1);
printf(" Step %d:\n", t);
if (adios_errno) {
printf ("%s\n", adios_errmsg());
} else if (total_size > 1024*1024) {
printf ("Too big to print\n");
} else if (v->ndim == 1) {
printf (" [");
for (j = 0; j < v->dims[0]; j++)
printf("%s ", value_to_string(v->type, data, j));
printf ("]\n");
} else if (v->ndim == 2) {
for (j = 0; j < v->dims[0]; j++) {
printf (" row %d: [", j);
for (k = 0; k < v->dims[1]; k++)
printf("%s ", value_to_string(v->type, data, j*v->dims[1] + k));
printf ("]\n");
}
} else if (v->ndim == 3) {
for (j = 0; j < v->dims[0]; j++) {
printf (" block %d: \n", j);
for (k = 0; k < v->dims[1]; k++) {
printf (" row %d: [", k);
for (l = 0; l < v->dims[2]; l++) {
// NCSU ALACRITY-ADIOS - Fixed bug, k*v->dims[1] changed to k*v->dims[2]
printf("%s ", value_to_string(v->type, data, j*v->dims[1]*v->dims[2] + k*v->dims[2] + l));
}
printf ("]\n");
}
printf ("\n");
}
} else {
printf (" cannot print arrays with >3 dimensions\n");
}
}
free (data);
}
}
adios_free_varinfo (v);
} /* variables */
/* For all attributes */
printf(" Attributes=%d:\n", f->nattrs);
for (i = 0; i < f->nattrs; i++) {
enum ADIOS_DATATYPES atype;
int asize;
void *adata;
adios_get_attr_byid (f, i, &atype, &asize, &adata);
int type_size = adios_type_size (atype, adata);
int nelems = asize / type_size;
printf(" %-9s %s = ", adios_type_to_string(atype), f->attr_namelist[i]);
char *p = (char*)adata;
if (nelems>1) printf("{");
for (j=0; j<nelems; j++) {
if (j>0) printf(", ");
printf ("%s", value_to_string(atype, p, 0));
p += type_size;
}
if (nelems>1) printf("}");
printf("\n");
free(adata);
} /* attributes */
adios_read_close (f);
//} /* loop 'step' */
return 0;
}
