eavlXGCImporter::eavlXGCImporter(const string &filename)
{
nNodes = 0;
nPlanes = 0;
nElems = 0;
fp = NULL;
mesh_fp = NULL;
points = NULL;
cells = NULL;
string::size_type i0 = filename.rfind("xgc.");
string::size_type i1 = filename.rfind(".bp");
string meshname = filename.substr(0,i0+4) + "mesh.bp";
MPI_Comm comm_dummy = 0;
fp = adios_read_open_file(filename.c_str(), ADIOS_READ_METHOD_BP, comm_dummy);
mesh_fp = adios_read_open_file(meshname.c_str(), ADIOS_READ_METHOD_BP, comm_dummy);
if (fp == NULL)
THROW(eavlException, "XGC variable file not found.");
if (mesh_fp == NULL)
THROW(eavlException, "XGC mesh file not found.");
Initialize();
}
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;
}
ToolsAdiosParallel::ToolsAdiosParallel(ProgramOptions &options, Dims &mpiTopology, std::ostream &outStream) :
ITools(options, mpiTopology, outStream), errorStream(std::cerr)
{
if (m_options.verbose)
errorStream << m_options.inputFile << std::endl;
comm = MPI_COMM_WORLD;
pFile = adios_read_open_file(m_options.inputFile.c_str(), ADIOS_READ_METHOD_BP, comm);
}
/// Test if the file is present. This function accomplishes its task by
/// actually attempting to open it. It returns true if the open attempt
/// was successful, returns false otherwise.
bool ADIOS_File::exists(const std::string& fileName)
{
ADIOS_FILE* f = adios_read_open_file
(fileName.c_str(), ADIOS_READ_METHOD_BP, MPI_COMM_WORLD);
if (f != 0) {
adios_read_close(f);
return true;
}
return false;
}
AdiosCheckpointInput::AdiosCheckpointInput(std::string& checkpoint_file)
{
adios_read_init(method, OHMMS::Controller->getMPI(), "verbose=3;abort_on_error");
adios_file_handle = adios_read_open_file(checkpoint_file.c_str(), method,
comm);
if (adios_file_handle == NULL)
{
qmcplusplus::app_error() << adios_errmsg() << std::endl;
}
//Select for local values
sel = adios_selection_writeblock (OHMMS::Controller->rank());
}
eavlXGCParticleImporter::eavlXGCParticleImporter(const string &filename)
{
timestep = 0;
maxnum = 0;
enphase = 0;
inphase = 0;
emaxgid = 0;
imaxgid = 0;
nvars = 0;
time = 0;
retVal = 0;
totalIParticles = 0;
totalEParticles = 0;
iphaseAvail = 0;
ephaseAvail = 0;
fp = NULL;
getR = true;
getZ = true;
getPhi = true;
getRho = true;
getW1 = true;
getW2 = true;
getMu = true;
getW0 = true;
getF0 = true;
getOriginNode = true;
std::string key (".restart");
std::size_t found = filename.find(key);
if(found != std::string::npos)
readingRestartFile = 1;
else
readingRestartFile = 0;
MPI_Comm comm_dummy = comm = 0;
char hostname[MPI_MAX_PROCESSOR_NAME];
char str [256];
int len = 0;
//Set local mpi vars so we know how many minions there are, and wich we are
MPI_Comm_size(comm,&numMPITasks);
MPI_Comm_rank(comm,&mpiRank);
MPI_Get_processor_name(hostname, &len);
fp = adios_read_open_file(filename.c_str(), ADIOS_READ_METHOD_BP, comm_dummy);
if(fp == NULL)
THROW(eavlException, "XGC variable file not found.");
Initialize();
}
bool ADIOS1CommonRead::Open()
{
if (m_OpenAsFile)
{
m_fh =
adios_read_open_file(m_FileName.c_str(), m_ReadMethod, m_MPIComm);
}
else
{
m_fh = adios_read_open(m_FileName.c_str(), m_ReadMethod, m_MPIComm,
ADIOS_LOCKMODE_CURRENT, 0.0);
}
return (m_fh != NULL);
}
static void test_file_mode_reads(const char *bp_filename) {
int i;
ADIOS_FILE *fp = adios_read_open_file(bp_filename, ADIOS_READ_METHOD_BP, COMM);
MPI_Assert(COMM, fp);
fprintf(stderr, "[rank %d/%d] Starting file-mode writeblock reads on %s\n", rank, size, bp_filename);
for (i = 0; i < fp->nvars; ++i) {
const char *varname = fp->var_namelist[i];
test_file_mode_reads_on_var(fp, bp_filename, varname);
MPI_Barrier(COMM);
}
adios_read_close(fp);
fprintf(stderr, "[rank %d/%d] Finished file-mode writeblock reads on %s\n", rank, size, bp_filename);
}
/// Open the named file in read-only mode. If a write operation is
/// desired, the caller is expected to close this file and call adios_open
/// explicitly. This object is used to carry the file name when any write
/// operations are to be performed. Furthermore, the file is always open
/// in streaming mode.
void ADIOS_File::open(const std::string &fn, ADIOS_READ_METHOD rm,
float to, bool strm)
{
const char *cptr = (fn.empty() ? m_fname.c_str() : fn.c_str());
if (*cptr == 0) // can not proceed with a valid file name
return;
if (m_handle)
(void) adios_read_close(m_handle);
if (strm) { // variables are visible one step at a time
m_handle = adios_read_open_stream
(cptr, rm, m_comm, ADIOS_LOCKMODE_CURRENT, to);
if (m_handle != 0) { // successfully opened the stream for reading
if (m_fname.compare(cptr) != 0)
m_fname = cptr;
LOGGER(ibis::gVerbose > 4)
<< "ADIOS_File::open(" << m_fname
<< ") successfully opened the name file in streaming mode";
}
else {
LOGGER(ibis::gVerbose >= 0)
<< "Warning -- ADIOS_File::open(" << cptr
<< ") failed to locate an active stream";
}
}
else { // open_file makes all variables visible at once
if (m_fname.compare(cptr) != 0)
m_fname = cptr;
m_handle = adios_read_open_file(cptr, rm, m_comm);
if (m_handle != 0) {
LOGGER(ibis::gVerbose > 4)
<< "ADIOS_File::open(" << m_fname
<< ") opened the named file for reading";
}
else {
LOGGER(ibis::gVerbose >= 0)
<< "Warning -- ADIOS_File::open(" << cptr
<< ") failed to open the named file in read-only mode";
}
}
} // ADIOS_File::open
int main (int argc, char ** argv)
{
char filename [256];
int rank, size, i;
int NX = 4096;
double t[NX];
MPI_Comm comm = MPI_COMM_WORLD;
/* ADIOS variables declarations for matching gwrite_temperature.ch */
ADIOS_FILE *fp;
ADIOS_SELECTION *s;
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &rank);
MPI_Comm_size (comm, &size);
strcpy (filename, "adios_global.bp");
//adios_read_init_method (ADIOS_READ_METHOD_BP, comm, "");
fp = adios_read_open_file ("adios_global.bp", ADIOS_READ_METHOD_BP, comm);
#include "gread_temperature.ch"
adios_read_close (fp);
// Verify data
for (i = 0; i < NX; i++)
if (t[i] != rank*NX + i)
{
fprintf (stderr, "Error detected\n");
}
adios_read_finalize_method (ADIOS_READ_METHOD_BP);
MPI_Finalize ();
return 0;
}
int read_scalar ()
{
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 all instances of the scalar 'O' ------------\n");
f = adios_read_open_file (fname, ADIOS_READ_METHOD_BP, comm);
if (f == NULL) {
printf ("Error at opening file: %s\n", adios_errmsg());
retval = adios_errno;
}
else
{
/* Read the scalar O with writeblock selection */
print_scalar (f, "O");
adios_read_close (f);
}
adios_read_finalize_method (ADIOS_READ_METHOD_BP);
return retval;
}
int read_all ()
{
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 file ------------\n");
f = adios_read_open_file (fname, ADIOS_READ_METHOD_BP, comm);
if (f == NULL) {
printf ("Error at opening file: %s\n", adios_errmsg());
retval = adios_errno;
}
else
{
/* Processing all the steps at once */
print_varinfo (f, 0);
adios_read_close (f);
}
adios_read_finalize_method (ADIOS_READ_METHOD_BP);
return retval;
}
//Reads an adios restart file :: can only be instantiated if EAVL was built
//with MPI enabled!
eavlXGCParticleImporter::eavlXGCParticleImporter( const string &filename,
ADIOS_READ_METHOD method,
MPI_Comm communicator,
ADIOS_LOCKMODE mode,
int timeout_sec
)
{
timestep = 0;
maxnum = 0;
enphase = 0;
inphase = 0;
emaxgid = 0;
imaxgid = 0;
nvars = 0;
time = 0;
retVal = 0;
totalIParticles = 0;
totalEParticles = 0;
fp = NULL;
fp = NULL;
getR = true;
getZ = true;
getPhi = true;
getRho = true;
getW1 = true;
getW2 = true;
getMu = true;
getW0 = true;
getF0 = true;
getOriginNode = true;
comm = communicator;
std::string key (".restart");
std::size_t found = filename.find(key);
if(found != std::string::npos)
readingRestartFile = 1;
else
readingRestartFile = 0;
char hostname[MPI_MAX_PROCESSOR_NAME];
char str [256];
int len = 0;
//Set local mpi vars so we know how many minions there are, and wich we are
MPI_Comm_size(comm,&numMPITasks);
MPI_Comm_rank(comm,&mpiRank);
MPI_Get_processor_name(hostname, &len);
if(method == ADIOS_READ_METHOD_BP) //do not open stream if not staging
fp = adios_read_open_file(filename.c_str(), method, comm);
else
fp = adios_read_open(filename.c_str(), method, comm, mode, timeout_sec);
if (fp == NULL)
{
cerr << __LINE__ << endl;
if(adios_errno == err_end_of_stream)
{
printf ("End of stream, no more steps expected. Quit. %s\n",
adios_errmsg()
);
}
else
{
printf ("No new step arrived within the timeout. Quit. %s\n",
adios_errmsg()
);
THROW(eavlException, "XGC variable file not found.");
}
}
Initialize();
}
int main (int argc, char** argv)
{
fastbit_init(0);
fastbit_set_verbose_level(0);
ADIOS_FILE * f;
//MPI_Comm comm_dummy = 0; // MPI_Comm is defined through adios_read.h
MPI_Comm comm_dummy = MPI_COMM_WORLD;
int rank, size;
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm_dummy, &rank);
MPI_Comm_size (comm_dummy, &size);
adios_init_noxml (comm_dummy);
if (argc < 2) {
printf("Usage: index_fastbit fileName (attrName)");
return 0;
}
f = adios_read_open_file (argv[1], ADIOS_READ_METHOD_BP, comm_dummy);
if (f == NULL) {
printf ("::%s\n", adios_errmsg());
return -1;
}
/*
adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, (f->file_size)*2/1048576 + 5); // +5MB for extra room in buffer
adios_declare_group (&gAdios_group, gGroupNameFastbitIdx, "", adios_flag_yes);
adios_select_method (gAdios_group, "MPI", "", "");
*/
gIdxFileName = fastbit_adios_util_getFastbitIndexFileName(argv[1]);
unlink(gIdxFileName);
adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, 500); // +5MB for extra room in buffer
adios_declare_group (&gAdios_group, gGroupNameFastbitIdx, "", adios_flag_yes);
adios_select_method (gAdios_group, "MPI", "", "");
adios_open (&gAdios_write_file, gGroupNameFastbitIdx, gIdxFileName, "w", MPI_COMM_WORLD);
#ifdef MULTI_BLOCK
int testid = adios_define_var (gAdios_group, "pack", "", adios_integer , 0, 0, 0);
#endif
#ifdef BOX
int testid = adios_define_var (gAdios_group, "elements", "", adios_integer , 0, 0, 0);
#endif
//uint64_t estimatedbytes = (nb+nk+no)*adios_type_size(adios_double, NULL);
int jobCounter = getJobCounter(f);
uint64_t estimatedbytes = getByteEstimationOnFile(f, rank);
if (size > 1) {
int maxJobsPP = jobCounter/size + 1;
estimatedbytes = estimatedbytes * maxJobsPP /jobCounter +1048576;
}
estimatedbytes += 1048576;
uint64_t adios_totalsize; // adios_group_size needs to be call before any write_byid, Otherwise write_byid does nothing
adios_group_size (gAdios_write_file, estimatedbytes , &adios_totalsize);
printf("=> .. adios open output file: %s, rank %d allocated %" PRIu64 " bytes... \n", gIdxFileName, rank, adios_totalsize);
// IMPORTANT:
// can only call open/close once in a process
// otherwise data is tangled or only the data in the last open/close call is recorded
#ifdef MULTI_BLOCK
adios_write_byid(gAdios_write_file, testid, &pack);
#endif
#ifdef BOX
adios_write_byid(gAdios_write_file, testid, &recommended_index_ele);
#endif
sumLogTime(-1);
sumLogTimeMillis(-1);
if (argc >= 3) {
int i=2;
while (i<argc) {
const char* varName = argv[i];
if(strstr(varName, "<binning prec") != NULL) {
if (gBinningOption == NULL) {
gBinningOption = argv[i];
}
if (argc == 3) {
buildIndexOnAllVar(f, rank, size);
break;
}
i++;
continue;
} else {
ADIOS_VARINFO * v = adios_inq_var(f, varName);
if (v == NULL) {
printf("No such variable: %s\n", varName);
return 0;
}
printf("building fastbit index on variable: %s\n", varName);
buildIndex_mpi(f, v, rank, size);
adios_free_varinfo(v);
i++;
}
}
} else {
buildIndexOnAllVar(f, rank, size);
}
sumLogTime(0);
sumLogTimeMillis(0);
adios_close(gAdios_write_file);
adios_read_close(f);
//
// writing file clean up
//
// read back:
f = adios_read_open_file (gIdxFileName, ADIOS_READ_METHOD_BP, comm_dummy);
if (f == NULL) {
printf("No such file: %s \n", gIdxFileName);
return 0;
}
int numVars = f->nvars;
int i=0;
int k=0;
int j=0;
for (i=0; i<numVars; i++) {
char* varName = f->var_namelist[i];
ADIOS_VARINFO* v = adios_inq_var(f, varName);
adios_inq_var_blockinfo(f,v);
int timestep = 0;
for (k=0; k<v->sum_nblocks; k++) {
verifyData(f, v, k, timestep);
}
adios_free_varinfo(v);
}
adios_read_close(f);
if (rank == 0) {
printf(" ==> index file is at: %s\n", gIdxFileName);
}
// clean up
MPI_Barrier (comm_dummy);
adios_finalize (rank);
MPI_Finalize ();
free (gIdxFileName);
fastbit_cleanup();
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 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 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) {
char xmlFileName[256];
enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP;
MPI_Comm comm = MPI_COMM_WORLD;
ADIOS_QUERY_TEST_INFO *queryInfo;
ADIOS_FILE *f;
MPI_Init(&argc, &argv);
if (argc < 4 || argc > 7) {
fprintf(stderr," usage: %s {input bp file} {xml file} {query engine (ALACRITY/FASTBIT)} [mode (FILE/stream)] [print points? (TRUE/false)] [read results? (true/FALSE)]\n", argv[0]);
MPI_Abort(comm, 1);
}
else {
strcpy(xmlFileName, argv[2]);
}
enum ADIOS_QUERY_METHOD query_method = ADIOS_QUERY_METHOD_UNKNOWN;
if (strcasecmp(argv[3], "ALACRITY") == 0) {
// init with ALACRITY
//adios_query_init(ADIOS_QUERY_TOOL_ALACRITY);
query_method = ADIOS_QUERY_METHOD_ALACRITY;
}
else if (strcasecmp(argv[3], "FASTBIT") == 0) {
// init with FastBit
query_method = ADIOS_QUERY_METHOD_FASTBIT;
//fprintf(stderr,"FastBit not supported in this test yet, exiting...\n");
//MPI_Abort(comm, 1);
}
else {
fprintf(stderr,"Unsupported query engine %s, exiting...\n", argv[3]);
MPI_Abort(comm, 1);
}
const int use_streaming = (argc >= 5) && (strcasecmp(argv[4], "stream") == 0);
const int read_results = (argc >= 6) && (strcasecmp(argv[5], "true") == 0);
const int print_points = !(argc >= 7) || (strcasecmp(argv[6], "true") == 0);
fprintf(stderr, "NOTE: Running the query in %s mode\n", use_streaming ? "STREAM" : "FILE");
fprintf(stderr, "NOTE: %s print query result points\n", print_points ? "WILL" : "WILL NOT");
fprintf(stderr, "NOTE: %s read data using query result point selection\n", read_results ? "WILL" : "WILL NOT");
// ADIOS init
adios_read_init_method(method, comm, NULL);
f = use_streaming ?
adios_read_open(argv[1], method, comm, ADIOS_LOCKMODE_ALL, -1) :
adios_read_open_file(argv[1], method, comm);
if (f == NULL) {
fprintf(stderr," can not open file %s \n", argv[1]);
MPI_Abort(comm, 1);
}
// Parse the xml file to generate query info
queryInfo = parseXml(xmlFileName, f);
// perform query
adios_query_set_method(queryInfo->query, query_method);
performQuery(queryInfo, f, use_streaming, print_points, read_results);
adios_read_close(f);
adios_read_finalize_method(ADIOS_READ_METHOD_BP);
MPI_Finalize();
return 0;
}
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 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;
}
eavlDataSet *ReadPsiMesh(const string &filename)
{
MPI_Comm comm_dummy = 0;
ADIOS_FILE *fp = adios_read_open_file(filename.c_str(), ADIOS_READ_METHOD_BP, comm_dummy);
int nNodes = 0, nElems = 0, ptID = -1, elemID = -1;
ADIOS_VARINFO *points = NULL, *cells = NULL, *psi;
for (int i = 0; i < fp->nvars; i++)
{
ADIOS_VARINFO *avi = adios_inq_var_byid(fp, i);
string varNm(&fp->var_namelist[i][1]);
if (varNm == "n_t")
{
nElems = (int)(*(int *)avi->value);
adios_free_varinfo(avi);
}
else if (varNm == "n_n")
{
nNodes = (int)(*(int *)avi->value);
adios_free_varinfo(avi);
}
else if (varNm == "coordinates/values")
points = avi;
else if (varNm == "cell_set[0]/node_connect_list")
cells = avi;
else if (varNm == "psi")
psi = avi;
else
adios_free_varinfo(avi);
}
cout<<"nNodes= "<<nNodes<<" nTri= "<<nElems<<endl;
eavlDataSet *out = new eavlDataSet;
out->SetNumPoints(nNodes);
eavlCoordinatesCartesian *coords = new eavlCoordinatesCartesian(NULL,
eavlCoordinatesCartesian::X,
eavlCoordinatesCartesian::Y);
out->AddCoordinateSystem(coords);
coords->SetAxis(0, new eavlCoordinateAxisField("xcoords", 0));
coords->SetAxis(1, new eavlCoordinateAxisField("ycoords", 0));
eavlArray *axisValues[2] = {new eavlFloatArray("xcoords", 1),
new eavlFloatArray("ycoords", 1)};
axisValues[0]->SetNumberOfTuples(nNodes);
axisValues[1]->SetNumberOfTuples(nNodes);
//read points.
double *buff = new double[2*nNodes];
uint64_t s[3], c[3];
ADIOS_SELECTION *sel = MakeSelection(points, s, c);
adios_schedule_read_byid(fp, sel, points->varid, 0, 1, buff);
int retval = adios_perform_reads(fp, 1);
adios_selection_delete(sel);
adios_free_varinfo(points);
for (int i = 0; i < nNodes; i++)
{
axisValues[0]->SetComponentFromDouble(i, 0, buff[i*2 +0]);
axisValues[1]->SetComponentFromDouble(i, 0, buff[i*2 +1]);
}
out->AddField(new eavlField(1, axisValues[0], eavlField::ASSOC_POINTS));
out->AddField(new eavlField(1, axisValues[1], eavlField::ASSOC_POINTS));
delete [] buff;
eavlCellSetExplicit *cellSet = new eavlCellSetExplicit("2D_cells", 2);
eavlExplicitConnectivity conn;
//read cells
int *nodeList = new int[nElems*3];
sel = MakeSelection(cells, s, c);
adios_schedule_read_byid(fp, sel, cells->varid, 0, 1, nodeList);
retval = adios_perform_reads(fp, 1);
adios_selection_delete(sel);
int nodes[3];
for (int i = 0; i < nElems; i++)
{
nodes[0] = nodeList[i*3+0];
nodes[1] = nodeList[i*3+1];
nodes[2] = nodeList[i*3+2];
conn.AddElement(EAVL_TRI, 3, nodes);
}
delete [] nodeList;
cellSet->SetCellNodeConnectivity(conn);
out->AddCellSet(cellSet);
//read psi.
buff = new double[nNodes];
sel = MakeSelection(psi, s, c);
adios_schedule_read_byid(fp, sel, psi->varid, 0, 1, buff);
retval = adios_perform_reads(fp, 1);
adios_selection_delete(sel);
adios_free_varinfo(psi);
eavlArray *psiValues = new eavlFloatArray("psi", 1);
psiValues->SetNumberOfTuples(nNodes);
for (int i = 0; i < nNodes; i++)
psiValues->SetComponentFromDouble(i, 0, buff[i]);
out->AddField(new eavlField(1, psiValues, eavlField::ASSOC_POINTS));
delete [] buff;
return out;
}
int main (int argc, char ** argv)
{
int 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;
}