/*
* modified by li.zhengbing, 2010-05-13 In JNI, if using
* GetStringUTFChars/GetXXXArrayElements, you must use
* ReleaseStringUTFChars/ReleaseXXXArrayElements to release resource.
* This modification adds ReleaseStringUTFChars/ReleaseXXXArrayElements.
*/
JNIEXPORT void JNICALL Java_gov_lbl_fastbit_FastBit_init
(JNIEnv * env, jobject jo, jstring jrcfile) {
jboolean iscopy;
const char *crcfile;
if (jrcfile != NULL)
crcfile = (*env)->GetStringUTFChars(env, jrcfile, &iscopy);
else
crcfile = NULL;
fastbit_init(crcfile);
(*env)->ReleaseStringUTFChars(env, jrcfile, crcfile);
} /* Java_gov_lbl_fastbit_FastBit_init */
int main(int argc, char **argv) {
int ierr, nhits, vselect;
const char *conffile;
const char *logfile;
FILE* output;
FastBitQueryHandle qh;
FastBitResultSetHandle rh;
ierr = 0;
vselect = 1;
logfile = 0;
conffile = 0;
#if defined(DEBUG) || defined(_DEBUG)
#if DEBUG + 0 > 10 || _DEBUG + 0 > 10
ierr = INT_MAX;
#elif DEBUG + 0 > 0
ierr += 7 * DEBUG;
#elif _DEBUG + 0 > 0
ierr += 5 * _DEBUG;
#else
ierr += 3;
#endif
#endif
/* process arguments started with - */
while (vselect < argc && argv[vselect][0] == '-') {
if (argv[vselect][1] == 'c' || argv[vselect][1] == 'C') {
if (vselect+1 < argc) {
conffile = argv[vselect+1];
vselect += 2;
}
else {
vselect += 1;
}
}
else if (argv[vselect][1] == 'h' || argv[vselect][1] == 'H') {
usage(*argv);
vselect += 1;
}
#if defined(TCAPI_USE_LOGFILE)
else if (argv[vselect][1] == 'l' || argv[vselect][1] == 'L') {
if (vselect+1 < argc) {
logfile = argv[vselect+1];
vselect += 2;
}
else {
vselect += 1;
}
}
#endif
else if (argv[vselect][1] == 'm' || argv[vselect][1] == 'M' ||
argv[vselect][1] == 'v' || argv[vselect][1] == 'V') {
if (vselect+1 < argc &&
(isdigit(argv[vselect+1][0]) != 0 ||
(argv[vselect+1][0] == '-' &&
isdigit(argv[vselect+1][1]) != 0))) {
ierr += atoi(argv[vselect+1]);
vselect += 2;
}
else {
ierr += 1;
vselect += 1;
}
}
else {
fprintf(stderr, "%s: unknown option %s\n", *argv, argv[vselect]);
++ vselect;
}
}
fastbit_init((const char*)conffile);
fastbit_set_verbose_level(ierr);
fastbit_set_logfile(logfile);
#if defined(TCAPI_USE_LOGFILE)
output = fastbit_get_logfilepointer();
printf("%s: output=0x%8.8x, stdout=0x%8.8x\n", *argv, output, stdout);
#else
output = stdout;
#endif
if (argc <= vselect) {
builtin(*argv, output);
return -1;
}
if (argc == vselect+1) /* buld indexes */
return fastbit_build_indexes(argv[vselect], (const char*)0);
qh = fastbit_build_query(0, argv[vselect], argv[vselect+1]);
if (qh == 0) {
fprintf(output, "%s failed to process query \"%s\" on data in %s\n",
argv[0], argv[vselect+1], argv[vselect]);
fastbit_cleanup();
return -2;
}
nhits = fastbit_get_result_rows(qh);
fprintf(output, "%s: applying \"%s\" on data in %s produced %d hit%s\n",
argv[0], argv[vselect+1], argv[vselect], nhits,
(nhits>1 ? "s" : ""));
if (nhits <= 0)
return 0;
/* print the selected values specified in the select clause. Since the
select clause was nil in the call to fastbit_build_query, there
would be nothing to print here! */
rh = fastbit_build_result_set(qh);
if (rh != 0) {
int ncols = fastbit_get_result_columns(qh);
fprintf(output, "%s\n", fastbit_get_select_clause(qh));
while (fastbit_result_set_next(rh) == 0) {
int i;
fprintf(output, "%s", fastbit_result_set_getString(rh, 0));
for (i = 1; i < ncols; ++ i)
fprintf(output, ", %s", fastbit_result_set_getString(rh, i));
fprintf(output, "\n");
}
fastbit_destroy_result_set(rh);
}
fflush(output);
vselect += 2;
/* print attributes explicitly specified on the command line */
if (argc > vselect) {
int i, j;
for (i = vselect; i < argc; i += 2) {
char t = (i+1<argc ? argv[i+1][0] : 'i');
switch (t) {
default:
case 'i':
case 'I': {
const int32_t *tmp = fastbit_get_qualified_ints(qh, argv[i]);
if (tmp != 0) {
fprintf(output, "%s[%d]=", argv[i], nhits);
for (j = 0; j < nhits; ++ j)
fprintf(output, "%d ", (int)tmp[j]);
fprintf(output, "\n");
}
else {
fprintf(output, "%s: failed to retrieve values for "
"column %s (requested type %c)\n",
argv[0], argv[i], t);
}
break;}
case 'u':
case 'U': {
const uint32_t *tmp = fastbit_get_qualified_uints(qh, argv[i]);
if (tmp != 0) {
fprintf(output, "%s[%d]=", argv[i], nhits);
for (j = 0; j < nhits; ++ j)
fprintf(output, "%u ", (unsigned)tmp[j]);
fprintf(output, "\n");
}
else {
fprintf(output, "%s: failed to retrieve value for "
"column %s (requested type %c)\n",
argv[0], argv[i], t);
}
break;}
case 'l':
case 'L': {
const int64_t *tmp = fastbit_get_qualified_longs(qh, argv[i]);
if (tmp != 0) {
fprintf(output, "%s[%d]=", argv[i], nhits);
for (j = 0; j < nhits; ++ j)
fprintf(output, "%lld ", (long long)tmp[j]);
fprintf(output, "\n");
}
else {
fprintf(output, "%s: failed to retrieve value for "
"column %s (requested type %c)\n",
argv[0], argv[i], t);
}
break;}
case 'r':
case 'R':
case 'f':
case 'F': {
const float *tmp = fastbit_get_qualified_floats(qh, argv[i]);
if (tmp != 0) {
fprintf(output, "%s[%d]=", argv[i], nhits);
for (j = 0; j < nhits; ++ j)
fprintf(output, "%g ", tmp[j]);
fprintf(output, "\n");
}
else {
fprintf(output, "%s: failed to retrieve value for "
"column %s (requested type %c)\n",
argv[0], argv[i], t);
}
break;}
case 'd':
case 'D': {
const double *tmp = fastbit_get_qualified_doubles(qh, argv[i]);
if (tmp != 0) {
fprintf(output, "%s[%d]=", argv[i], nhits);
for (j = 0; j < nhits; ++ j)
fprintf(output, "%lG ", tmp[j]);
fprintf(output, "\n");
}
else {
fprintf(output, "%s: failed to retrieve value for "
"column %s (requested type %c)\n",
argv[0], argv[i], t);
}
break;}
case 's':
case 'S':
case 't':
case 'T': {
const char **tmp = fastbit_get_qualified_strings(qh, argv[i]);
if (tmp != 0) {
fprintf(output, "%s[%d]=", argv[i], nhits);
for (j = 0; j < nhits; ++ j)
fprintf(output, "\"%s\" ", tmp[j]);
fprintf(output, "\n");
}
else {
fprintf(output, "%s: failed to retrieve value for "
"column %s (requested type %c)\n",
argv[0], argv[i], t);
}
break;}
}
}
}
ierr = fastbit_destroy_query(qh);
fastbit_cleanup();
return ierr;
} /* main */
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;
}
