int read_stepbystep ()
{
ADIOS_FILE * f;
float timeout_sec = 0.0;
int steps = 0;
int retval = 0;
MPI_Comm comm = MPI_COMM_SELF;
adios_read_init_method (ADIOS_READ_METHOD_BP, comm, "verbose=3");
printf ("\n--------- Read as stream ------------\n");
f = adios_read_open (fname, ADIOS_READ_METHOD_BP,
comm, ADIOS_LOCKMODE_NONE, timeout_sec);
if (adios_errno == err_file_not_found)
{
printf ("Stream not found after waiting %f seconds: %s\n",
timeout_sec, adios_errmsg());
retval = adios_errno;
}
else if (adios_errno == err_end_of_stream)
{
printf ("Stream terminated before open. %s\n", adios_errmsg());
retval = adios_errno;
}
else if (f == NULL) {
printf ("Error at opening stream: %s\n", adios_errmsg());
retval = adios_errno;
}
else
{
/* 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
printf ("Step: %d\n", f->current_step);
print_varinfo (f, f->current_step);
// advance to 1) next available step with 2) blocking wait
adios_advance_step (f, 0, timeout_sec);
if (adios_errno == err_step_notready)
{
//printf ("No new step arrived within the timeout. Quit. %s\n",
// adios_errmsg());
break; // quit while loop
}
}
adios_read_close (f);
}
adios_read_finalize_method (ADIOS_READ_METHOD_BP);
//printf ("We have processed %d steps\n", steps);
return retval;
}
int
eavlXGCParticleImporter::AdvanceToTimeStep(int step, int timeout_sec)
{
int currentTimestep = timestep;
while(currentTimestep < step)
{
int err = adios_advance_step(fp, 0, timeout_sec);
if(err != 0)
{
return err;
}
currentTimestep++;
}
timestep = 0;
maxnum = 0;
enphase = 0;
inphase = 0;
emaxgid = 0;
imaxgid = 0;
nvars = 0;
time = 0;
retVal = 0;
totalIParticles = 0;
totalEParticles = 0;
map<string, ADIOS_VARINFO*>::const_iterator it;
for(it = ephase.begin(); it != ephase.end(); it++)
adios_free_varinfo(it->second);
ephase.clear();
for(it = iphase.begin(); it != iphase.end(); it++)
adios_free_varinfo(it->second);
iphase.clear();
for(it = egid.begin(); it != egid.end(); it++)
adios_free_varinfo(it->second);
egid.clear();
for(it = igid.begin(); it != igid.end(); it++)
adios_free_varinfo(it->second);
igid.clear();
Initialize();
return 0;
}
StepStatus ADIOS1CommonRead::AdvanceStep(const StepMode mode,
const float timeout_sec)
{
if (m_OpenAsFile)
{
throw std::invalid_argument("ERROR: ADIOS1Reader does not allow "
"Advance() on a file which was opened for "
"read as File\n");
}
if (mode != StepMode::NextAvailable && mode != StepMode::LatestAvailable)
{
throw std::invalid_argument(
"ERROR: ADIOS1Reader.Advance() only allows "
"for NextAvailable or LatestAvailable modes.\n");
}
int last = (mode == StepMode::NextAvailable ? 0 : 1);
float *to = const_cast<float *>(&timeout_sec);
adios_advance_step(m_fh, last, *to);
StepStatus status;
switch (adios_errno)
{
case err_no_error:
status = StepStatus::OK;
break;
case err_end_of_stream:
status = StepStatus::EndOfStream;
break;
case err_step_notready:
status = StepStatus::NotReady;
break;
default:
status = StepStatus::OtherError;
break;
}
return status;
}
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, 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 read_scalar_stepbystep ()
{
ADIOS_FILE * f;
float timeout_sec = 0.0;
int steps = 0;
int retval = 0;
MPI_Comm comm = MPI_COMM_SELF;
adios_read_init_method (ADIOS_READ_METHOD_BP, comm, "verbose=3");
printf ("\n--------- Read scalar in stream using varinfo->value ------------\n");
f = adios_read_open (fname, ADIOS_READ_METHOD_BP,
comm, ADIOS_LOCKMODE_NONE, timeout_sec);
if (adios_errno == err_file_not_found)
{
printf ("Stream not found after waiting %f seconds: %s\n",
timeout_sec, adios_errmsg());
retval = adios_errno;
}
else if (adios_errno == err_end_of_stream)
{
printf ("Stream terminated before open. %s\n", adios_errmsg());
retval = adios_errno;
}
else if (f == NULL) {
printf ("Error at opening stream: %s\n", adios_errmsg());
retval = adios_errno;
}
else
{
/* 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
printf ("Step: %d\n", f->current_step);
/* Check the scalar O with varinfo->value */
ADIOS_VARINFO * v = adios_inq_var (f, "NX");
int value = *(int*)v->value;
printf ("Scalar NX = %d", value);
if (value !=
block_count [f->current_step*nblocks_per_step*size])
{
printf ("\tERROR expected = %llu",
block_count [f->current_step*nblocks_per_step*size]);
nerrors++;
}
printf ("\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 ("No new step arrived within the timeout. Quit. %s\n",
// adios_errmsg());
break; // quit while loop
}
}
adios_read_close (f);
}
adios_read_finalize_method (ADIOS_READ_METHOD_BP);
//printf ("We have processed %d steps\n", steps);
return retval;
}
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;
}
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)
{
/* 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;
}
/// Advance to the next available step. Returns true if successful,
/// false otherwise.
bool ADIOS_File::nextStep(float to) {
if (m_handle == 0) return false;
adios_release_step(m_handle);
return (0 == adios_advance_step(m_handle, 0, to));
} // ADIOS_File::nextStep
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)
{
int err;
int steps = 0, curr_step;
int retval = 0;
MPI_Init (&argc, &argv);
comm = MPI_COMM_WORLD;
MPI_Comm_rank (comm, &rank);
MPI_Comm_size (comm, &numproc);
if (processArgs(argc, argv)) {
return 1;
}
print0("Input stream = %s\n", infilename);
print0("Output stream = %s\n", outfilename);
print0("Read method = %s (id=%d)\n", rmethodname, read_method);
print0("Read method parameters = \"%s\"\n", rmethodparams);
print0("Write method = %s\n", wmethodname);
print0("Write method parameters = \"%s\"\n", wmethodparams);
err = adios_read_init_method(read_method, comm,
"max_chunk_size=100; "
"app_id =32767; \n"
"verbose= 3;"
"poll_interval = 100;"
);
if (!err) {
print0 ("%s\n", adios_errmsg());
}
adios_init_noxml(comm);
print0 ("Waiting to open stream %s...\n", infilename);
f = adios_read_open_stream (infilename, read_method, comm,
ADIOS_LOCKMODE_ALL, timeout_sec);
if (adios_errno == err_file_not_found)
{
print ("rank %d: Stream not found after waiting %d seconds: %s\n",
rank, timeout_sec, adios_errmsg());
retval = adios_errno;
}
else if (adios_errno == err_end_of_stream)
{
print ("rank %d: Stream terminated before open. %s\n", rank, adios_errmsg());
retval = adios_errno;
}
else if (f == NULL) {
print ("rank %d: Error at opening stream: %s\n", rank, adios_errmsg());
retval = adios_errno;
}
else
{
// process steps here...
if (f->current_step != 0) {
print ("rank %d: WARNING: First %d steps were missed by open.\n",
rank, f->current_step);
}
while (1)
{
steps++; // start counting from 1
print0 ("File info:\n");
print0 (" current step: %d\n", f->current_step);
print0 (" last step: %d\n", f->last_step);
print0 (" # of variables: %d:\n", f->nvars);
retval = process_metadata(steps);
if (retval) break;
retval = read_write(steps);
if (retval) break;
// advance to 1) next available step with 2) blocking wait
curr_step = f->current_step; // save for final bye print
adios_advance_step (f, 0, timeout_sec);
if (adios_errno == err_end_of_stream)
{
break; // quit while loop
}
else if (adios_errno == err_step_notready)
{
print ("rank %d: No new step arrived within the timeout. Quit. %s\n",
rank, adios_errmsg());
break; // quit while loop
}
else if (f->current_step != curr_step+1)
{
// we missed some steps
print ("rank %d: WARNING: steps %d..%d were missed when advancing.\n",
rank, curr_step+1, f->current_step-1);
}
}
adios_read_close (f);
}
print0 ("Bye after processing %d steps\n", steps);
adios_read_finalize_method (read_method);
adios_finalize (rank);
MPI_Finalize ();
return retval;
}
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;
}
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);
}
