int main (int argc, char ** argv) {
//For varriable definitions:
//gbounds = global bounds string, lbounds = local bounds string, offs = offset string, tstring = temp string to hold temperary stuff
char gbounds[1007], lbounds[1007], offs[1007],tstring[100];
//size = number of cores, gidx = adios group index
int rank, size, gidx, i, j, k, ii;
//data = pointer to read-in data
void * data = NULL;
uint64_t s[] = {0,0,0,0,0,0,0,0,0,0}; //starting offset
uint64_t c[] = {1,1,1,1,1,1,1,1,1,1}; //chunk block array
uint64_t bytes_read = 0;
int element_size;
int64_t new_adios_group, m_adios_file;
uint64_t var_size; //portion_bound,
uint64_t adios_groupsize, adios_totalsize;
int read_buffer; //possible maximum size you the user would like for each chunk in MB
int write_buffer = 1536; //actual buffer size you use in MB
int itime;
int WRITEME=1;
uint64_t chunk_size; //chunk size in # of elements
char *var_path, *var_name; // full path cut into dir path and name
MPI_Init(&argc,&argv);
MPI_Comm_rank(comm,&rank);
MPI_Comm_size(comm,&size);
// timing numbers
// we will time:
// 0: adios_open, adios_group_size
// 1: the total time to read in the data
// 2: times around each write (will only work if we do NOT buffer....
// 3: the time in the close
// 4: fopen, fclose
// 5: total time
// timers: the total I/O time
int timers = 6;
double start_time[timers], end_time[timers], total_time[timers];
if (TIMING==100) {
for (itime=0;itime<timers;itime++) {
start_time[itime] = 0;
end_time[itime] = 0;
total_time[itime]=0;
}
//MPI_Barrier(MPI_COMM_WORLD);
start_time[5] = MPI_Wtime();
}
if(rank==0)
printf("converting...\n");
if (argc < 5) {
if (rank==0) printf("Usage: %s <BP-file> <ADIOS-file> read_buffer(MB) write_buffer(MB) METHOD (LUSTRE_strip_count) (LUSTRE_strip_size) (LUSTRE_block_size)\n", argv[0]);
return 1;
}
if(TIMING==100)
start_time[4] = MPI_Wtime();
ADIOS_FILE * f = adios_fopen (argv[1], MPI_COMM_SELF);
if(TIMING==100){
end_time[4] = MPI_Wtime();
total_time[4] = end_time[4]-start_time[4];
}
adios_init_noxml(comm); // no xml will be used to write the new adios file
read_buffer = atoi(argv[3]);
write_buffer = atoi(argv[4]);
adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, write_buffer); // allocate MB buffer
if (f == NULL) {
printf("rank=%d, file cant be opened\n", rank);
if (DEBUG) printf ("%s\n", adios_errmsg());
return -1;
}
for (gidx = 0; gidx < f->groups_count; gidx++) { //group part
adios_groupsize = 0;
ADIOS_GROUP * g = adios_gopen (f, f->group_namelist[gidx]);
if (g == NULL) {
if (DEBUG) printf ("%s\n", adios_errmsg());
printf("rank %d: group cannot be opened.\n", rank);
return -1;
}
/* First create all of the groups */
// now I need to create this group in the file that will be written
adios_declare_group(&new_adios_group,f->group_namelist[gidx],"",adios_flag_yes);
if(strcmp(argv[5],"MPI_LUSTRE")!=0) //see whether or not the user uses MPI_LUSTRE method
adios_select_method (new_adios_group, argv[5], "", ""); //non-MPI_LUSTRE methods... like MPI, POSIX....
else{
char lustre_pars[1000];
strcpy(lustre_pars, "");
strcat(lustre_pars, "stripe_count=");
sprintf(tstring, "%d", atoi(argv[6]));
strcat(lustre_pars, tstring);
strcat(lustre_pars, ",stripe_size=");
sprintf(tstring, "%d", atoi(argv[7]));
strcat(lustre_pars, tstring);
strcat(lustre_pars, ",block_size=");
sprintf(tstring, "%d", atoi(argv[8]));
strcat(lustre_pars, tstring);
if(rank==0)
printf("lustre_pars=%s\n", lustre_pars);
adios_select_method (new_adios_group, argv[5], lustre_pars, ""); //Use MPI Lustre method
}
// variable definition part
for (i = 0; i < g->vars_count; i++) {
ADIOS_VARINFO * v = adios_inq_var_byid (g, i);
getbasename (g->var_namelist[i], &var_path, &var_name);
if (v->ndim == 0)
{
// scalars: every process does them the same.
adios_define_var(new_adios_group,var_name,var_path,v->type,0,0,0);
getTypeInfo( v->type, &element_size); //element_size is size per element based on its type
if (v->type == adios_string) { //special case when the scalar is string.
adios_groupsize += strlen(v->value);
} else {
adios_groupsize += element_size;
}
}
else
{
// vector variables
getTypeInfo( v->type, &element_size);
var_size=1;
for (ii=0;ii<v->ndim;ii++) {
var_size*=v->dims[ii];
}
uint64_t total_size = var_size; //total_size tells you the total number of elements in the current vector variable
var_size*=element_size; //var_size tells you the size of the current vector variable in bytess
//re-initialize the s and c variables
for(j=0; j<v->ndim; j++){
s[j] = 0;
c[j] = 1;
}
//find the approximate chunk_size you would like to use.
chunk_size = calcChunkSize(total_size, read_buffer*1024*1024/element_size, size);
//set the chunk block array with the total size as close to chunk_size as possible
calcC(chunk_size, v, c);
strcpy(lbounds,"");
for(j=0; j<v->ndim; j++){
sprintf(tstring, "%" PRId64 ",", c[j]);
strcat(lbounds, tstring);
}
printf("rank=%d, name=%s, chunk_size1=%" PRId64 " c[]=%s\n",rank,g->var_namelist[i],chunk_size,lbounds);
chunk_size = 1;
for(ii=0; ii<v->ndim; ii++) //reset chunk_size based on the created c. Now the chunk_size is exact.
chunk_size *= c[ii];
//current step points to where the process is in processing the vector. First sets with respect to rank.
uint64_t current_step = rank*chunk_size;
//First advance the starting point s by current_step. Of course, you don't do it if the current_step exceeds total_size.
if(current_step<total_size)
rS(v, s, current_step, rank);
uint64_t elements_defined = 0; //First, the number of elements you have defined is 0.
//You (the process) process your part of the vector when your current_step is smaller than the total_size
while(current_step < total_size)
{
//ts, temporary s, is introduced for the sake of the inner do while loop below. Copy s to ts.
uint64_t ts[] = {0,0,0,0,0,0,0,0,0,0};
arrCopy(s, ts);
//for every outer while iteration, you always have the whole chunk_size remained to process.
uint64_t remain_chunk = chunk_size;
if(current_step+chunk_size>total_size) //except when you are nearing the end of the vector....
remain_chunk = total_size-current_step;
//tc, temporary c, is introduced for the sake of the inner do while loop below. Copy s to tc.
uint64_t tc[] = {1,1,1,1,1,1,1,1,1,1};
arrCopy(c, tc);
do{
//how much of the remain chunk you wanna process? initially you think you can do all of it....
uint64_t used_chunk = remain_chunk;
//you feel like you should process the vector with tc block size, but given ts, you might go over bound.
uint64_t uc[] = {1,1,1,1,1,1,1,1,1,1};
//so you verify it by setting a new legit chunck block uc, and getting a new remain_chunk.
remain_chunk = checkBound(v, ts, tc, uc, remain_chunk);
//you check whether or not ts+uc goes over the bound. This is just checking to make sure there's no error.
//Thereotically, there should be no problem at all.
checkOverflow(0, v, ts, uc);
//the below code fragment simply calculates gbounds, and sets place holders for lbounds and offs.
strcpy(gbounds,"");
strcpy(lbounds,"");
strcpy(offs,"");
for(j=0; j<v->ndim-1; j++){
sprintf(tstring, "%d,", (int)v->dims[j]);
strcat(gbounds, tstring);
//sprintf(tstring, "ldim%d_%s,", j, var_name);
sprintf(tstring, "ldim%d,", j);
strcat(lbounds, tstring);
//sprintf(tstring, "offs%d_%s,", j, var_name);
sprintf(tstring, "offs%d,", j);
strcat(offs, tstring);
}
sprintf(tstring, "%d", (int)v->dims[v->ndim-1]);
strcat(gbounds, tstring);
//sprintf(tstring, "ldim%d_%s", v->ndim-1, var_name);
sprintf(tstring, "ldim%d", v->ndim-1);
strcat(lbounds, tstring);
//sprintf(tstring, "offs%d_%s", v->ndim-1, var_name);
sprintf(tstring, "offs%d", v->ndim-1);
strcat(offs, tstring);
//sprintf(tstring, "%d", v->ndim);
for(j=0; j<v->ndim; j++){
//sprintf(tstring, "ldim%d_%s", j, var_name);
sprintf(tstring, "ldim%d", j);
adios_define_var(new_adios_group, tstring, "bp2bp", adios_unsigned_long, 0, 0, 0);
//sprintf(tstring, "offs%d_%s", j, var_name);
sprintf(tstring, "offs%d", j);
adios_define_var(new_adios_group, tstring, "bp2bp", adios_unsigned_long, 0, 0, 0);
}
adios_define_var(new_adios_group,var_name,var_path,v->type,lbounds,gbounds,offs);
if (DEBUG){
strcpy(lbounds,"");
strcpy(offs,"");
for(j=0; j<v->ndim; j++){
sprintf(tstring, "%" PRId64 ",", ts[j]);
strcat(offs, tstring);
sprintf(tstring, "%" PRId64 ",", uc[j]);
strcat(lbounds, tstring);
}
printf("rank=%d, name=%s, gbounds=%s: lbounds=%s: offs=%s \n",rank,g->var_namelist[i],gbounds, lbounds, offs);
}
used_chunk -= remain_chunk; //you get the actual used_chunk here.
elements_defined += used_chunk;
if(remain_chunk!=0){
rS(v, ts, used_chunk, rank); //advance ts by used_chunk.
for(k=0; k<10; k++)
tc[k] = 1;
calcC(remain_chunk, v, tc); //based on the remain_chunk, calculate new tc chunk block remained to process.
}
adios_groupsize+= used_chunk*element_size+2*v->ndim*8;
}while(remain_chunk!=0);
current_step += size*chunk_size; //once a whole chunk_size is processed, advance the current_step in roll-robin manner.
if(current_step<total_size){ //advance s in the same way.
rS(v, s, size*chunk_size, rank);
}
}
//beside checkOverflow above, here you check whether or not the total number of elements processed across processes matches
//the total number of elements in the original vector.
if(DEBUG){
uint64_t* sb = (uint64_t *) malloc(sizeof(uint64_t));
uint64_t* rb = (uint64_t *) malloc(sizeof(uint64_t));
sb[0] = elements_defined;
MPI_Reduce(sb,rb,1,MPI_UNSIGNED_LONG_LONG,MPI_SUM,0, comm);
if(rank==0 && rb[0]!=total_size)
printf("some array define mismatch. please use debug mode\n");
free(sb); free(rb);
}
}
free (var_name);
free (var_path);
} // finished declaring all of the variables
// Now we can define the attributes....
for (i = 0; i < g->attrs_count; i++) {
enum ADIOS_DATATYPES atype;
int asize;
void *adata;
adios_get_attr_byid (g, i, &atype, &asize, &adata);
// if (DEBUG) printf("attribute name=%s\n",g->attr_namelist[i]);
adios_define_attribute(new_adios_group,g->attr_namelist[i],"",atype,adata,0);
}
/*------------------------------ NOW WE WRITE -------------------------------------------- */
// Now we have everything declared... now we need to write them out!!!!!!
if (WRITEME==1) {
// open up the file for writing....
if (DEBUG) printf("rank=%d, opening file = %s, with group %s, size=%" PRId64 "\n",rank,argv[2],f->group_namelist[gidx],adios_groupsize);
if(TIMING==100)
start_time[0] = MPI_Wtime();
adios_open(&m_adios_file, f->group_namelist[gidx],argv[2],"w",comm);
adios_group_size( m_adios_file, adios_groupsize, &adios_totalsize);
//get both the total adios_totalsize and total adios_groupsize summed across processes.
uint64_t* sb = (uint64_t *) malloc(sizeof(uint64_t));;
uint64_t* rb = (uint64_t *) malloc(sizeof(uint64_t));
sb[0] = adios_groupsize;
MPI_Reduce(sb,rb,1,MPI_UNSIGNED_LONG_LONG,MPI_SUM,0, comm);
uint64_t* sb2 = (uint64_t *) malloc(sizeof(uint64_t));;
uint64_t* rb2 = (uint64_t *) malloc(sizeof(uint64_t));
sb2[0] = adios_totalsize;
MPI_Reduce(sb2,rb2,1,MPI_UNSIGNED_LONG_LONG,MPI_SUM,0, comm);
if(rank==0){
printf("total adios_totalsize = %" PRId64 "\n", *rb2);
printf("total adios_groupsize = %" PRId64 "\n", *rb);
}
free(sb); free(rb); free(sb2); free(rb2);
if (TIMING==100) {
end_time[0] = MPI_Wtime();
total_time[0]+=end_time[0] - start_time[0]; //variable definition time taken
}
// now we have to write out the variables.... since they are all declared now
// This will be the place we actually write out the data!!!!!!!!
for (i = 0; i < g->vars_count; i++) {
ADIOS_VARINFO * v = adios_inq_var_byid (g, i);
getbasename (g->var_namelist[i], &var_path, &var_name);
if (v->ndim == 0)
{
if (DEBUG) {
printf ("ADIOS WRITE SCALAR: rank=%d, name=%s value=",
rank,g->var_namelist[i]);
print_data (v->value, 0, v->type);
printf ("\n");
}
if (TIMING==100) {
start_time[2] = MPI_Wtime();
}
adios_write(m_adios_file,g->var_namelist[i],v->value);
if (TIMING==100) {
end_time[2] = MPI_Wtime();
total_time[2]+=end_time[2] - start_time[2]; //IO write time...
}
}
else
{
for(j=0; j<v->ndim; j++){
s[j] = 0;
c[j] = 1;
}
getTypeInfo( v->type, &element_size);
uint64_t total_size = 1;
for (ii=0;ii<v->ndim;ii++)
total_size*=v->dims[ii];
chunk_size = calcChunkSize(total_size, read_buffer*1024*1024/element_size, size);
calcC(chunk_size, v, c);
chunk_size = 1;
for(ii=0; ii<v->ndim; ii++)
chunk_size *= c[ii];
uint64_t current_step = rank*chunk_size;
if(current_step<total_size)
rS(v, s, current_step, rank);
uint64_t elements_written = 0;
while(current_step < total_size)
{
uint64_t ts[] = {0,0,0,0,0,0,0,0,0,0};
arrCopy(s, ts);
uint64_t remain_chunk = chunk_size;
if(current_step+chunk_size>total_size)
remain_chunk = total_size-current_step;
uint64_t tc[] = {1,1,1,1,1,1,1,1,1,1};
arrCopy(c, tc);
do{
uint64_t uc[] = {1,1,1,1,1,1,1,1,1,1};
uint64_t used_chunk = remain_chunk;
remain_chunk = checkBound(v, ts, tc, uc, remain_chunk);
checkOverflow(1, v, ts, uc);
used_chunk -= remain_chunk;
elements_written += used_chunk;
//allocated space for data read-in
data = (void *) malloc(used_chunk*element_size);
if (TIMING==100) {
start_time[1] = MPI_Wtime();
}
if(PERFORMANCE_CHECK) printf("rank=%d, read start\n",rank);
bytes_read = adios_read_var_byid(g,v->varid,ts,uc,data);
if(PERFORMANCE_CHECK) printf("rank=%d, read end\n",rank);
if (TIMING==100) {
end_time[1] = MPI_Wtime();
total_time[1]+=end_time[1] -start_time[1]; //IO read time
}
if (DEBUG)
printf ("ADIOS WRITE: rank=%d, name=%s datasize=%" PRId64 "\n",rank,g->var_namelist[i],bytes_read);
if (TIMING==100) {
start_time[2] = MPI_Wtime();
}
if (DEBUG){
printf("rank=%d, write ts=",rank);
int k;
for(k=0; k<v->ndim; k++)
printf("%" PRId64 ",", ts[k]);
printf(" uc=");
for(k=0; k<v->ndim; k++)
printf("%" PRId64 ",", uc[k]);
printf("\n");
}
//local bounds and offets placeholders are not written out with actual values.
if(PERFORMANCE_CHECK) printf("rank=%d, adios write start\n", rank);
for(k=0; k<v->ndim; k++){
//sprintf(tstring, "ldim%d_%s", k, var_name);
sprintf(tstring, "ldim%d", k);
if (DEBUG) {
printf ("ADIOS WRITE DIMENSION: rank=%d, name=%s value=",
rank,tstring);
print_data (&uc[k], 0, adios_unsigned_long);
printf ("\n");
}
adios_write(m_adios_file, tstring, &uc[k]);
//sprintf(tstring, "offs%d_%s", k, var_name);
sprintf(tstring, "offs%d", k);
if (DEBUG) {
printf ("ADIOS WRITE OFFSET: rank=%d, name=%s value=",
rank,tstring);
print_data (&ts[k], 0, adios_unsigned_long);
printf ("\n");
}
adios_write(m_adios_file, tstring, &ts[k]);
}
adios_write(m_adios_file,g->var_namelist[i],data);
if(PERFORMANCE_CHECK) printf("rank=%d, adios write end\n", rank);
if (TIMING==100) {
end_time[2] = MPI_Wtime();
total_time[2]+=end_time[2] - start_time[2]; //IO write time
}
free(data);
if(remain_chunk!=0){
rS(v, ts, used_chunk, rank);
for(k=0; k<10; k++)
tc[k] = 1;
calcC(remain_chunk, v, tc);
}
}while(remain_chunk!=0);
current_step += size*chunk_size;
if(current_step<total_size)
rS(v, s, size*chunk_size,rank);
}
if(DEBUG){
uint64_t* sb = (uint64_t *) malloc(sizeof(uint64_t));;
uint64_t* rb = (uint64_t *) malloc(sizeof(uint64_t));
sb[0] = elements_written;
MPI_Reduce(sb,rb,1,MPI_UNSIGNED_LONG_LONG,MPI_SUM,0, comm);
if(rank==0 && rb[0]!=total_size)
printf("some array read mismatch. please use debug mode\n");
free(sb); free(rb);
}
}
free (var_name);
free (var_path);
}// end of the writing of the variable..
if (TIMING==100) {
start_time[3] = MPI_Wtime();
}
if(PERFORMANCE_CHECK) printf("rank=%d, adios_close start\n", rank);
adios_close(m_adios_file);
if(PERFORMANCE_CHECK) printf("rank=%d, adios_close end\n", rank);
if (TIMING==100) {
end_time[3] = MPI_Wtime();
total_time[3]+=end_time[3] - start_time[3];
}
adios_gclose(g);
} //end of WRITEME
} // end of all of the groups
if(rank==0)
printf("conversion done!\n");
if(TIMING==100)
start_time[4] = MPI_Wtime();
adios_fclose(f);
if(TIMING==100){
end_time[4] = MPI_Wtime();
total_time[4] = total_time[4]+end_time[4]-start_time[4];
}
adios_finalize(rank);
// now, we write out the timing data, for each category, we give max, min, avg, std, all in seconds, across all processes.
if(TIMING==100){
// 0: adios_open, adios_group_size
// 1: the total time to read in the data
// 2: times around each write (will only work if we do NOT buffer....
// 3: the time in the close
// 4: fopen, fclose
// 5: total time
end_time[5] = MPI_Wtime();
total_time[5] = end_time[5] - start_time[5];
double sb[7];
sb[0] = total_time[1]; sb[1] = total_time[4]; //read_var, fopen+fclose
sb[2] = sb[0]+sb[1];
sb[3] = total_time[0]; sb[4] = total_time[2]+total_time[3]; //adios_open+adios_group_size, write+close
sb[5] = sb[3]+sb[4];
sb[6] = total_time[5]; //total
double * rb = NULL;
if(rank==0)
rb = (double *)malloc(size*7*sizeof(double));
//MPI_Barrier(comm);
MPI_Gather(sb, 7, MPI_DOUBLE, rb, 7, MPI_DOUBLE, 0, comm);
if(rank==0){
double read_avg1 = 0;
double read_avg2 = 0;
double tread_avg = 0;
double write_avg1 = 0;
double write_avg2 = 0;
double twrite_avg = 0;
double total_avg = 0;
for(j=0; j<size; j++){
read_avg1 += rb[7*j];
read_avg2 += rb[7*j+1];
tread_avg += rb[7*j+2];
write_avg1 += rb[7*j+3];
write_avg2 += rb[7*j+4];
twrite_avg += rb[7*j+5];
total_avg += rb[7*j+6];
}
read_avg1 /= size;
read_avg2 /= size;
tread_avg /= size;
write_avg1 /= size;
write_avg2 /= size;
twrite_avg /= size;
total_avg /= size;
double read1_max = rb[0];
double read1_min = rb[0];
double read1_std = rb[0]-read_avg1; read1_std *= read1_std;
double read2_max = rb[1];
double read2_min = rb[1];
double read2_std = rb[1]-read_avg2; read2_std *= read2_std;
double tread_max = rb[2];
double tread_min = rb[2];
double tread_std = rb[2]-tread_avg; tread_std *= tread_std;
double write1_max = rb[3];
double write1_min = rb[3];
double write1_std = rb[3]-write_avg1; write1_std *= write1_std;
double write2_max = rb[4];
double write2_min = rb[4];
double write2_std = rb[4]-write_avg2; write2_std *= write2_std;
double twrite_max = rb[5];
double twrite_min = rb[5];
double twrite_std = rb[5]-twrite_avg; twrite_std *= twrite_std;
double total_max = rb[6];
double total_min = rb[6];
double total_std = rb[6]-total_avg; total_std *= total_std;
for(j=1; j<size; j++){
if(rb[7*j]>read1_max)
read1_max = rb[7*j];
else if(rb[7*j]<read1_min)
read1_min = rb[7*j];
double std = rb[7*j]-read_avg1; std *= std;
read1_std += std;
if(rb[7*j+1]>read2_max)
read2_max = rb[7*j+1];
else if(rb[7*j+1]<read2_min)
read2_min = rb[7*j+1];
std = rb[7*j+1]-read_avg2; std *= std;
read2_std += std;
if(rb[7*j+2]>tread_max)
tread_max = rb[7*j+2];
else if(rb[7*j+2]<tread_min)
tread_min = rb[7*j+2];
std = rb[7*j+2]-tread_avg; std *= std;
tread_std += std;
if(rb[7*j+3]>write1_max)
write1_max = rb[7*j+3];
else if(rb[7*j+3]<write1_min)
write1_min = rb[7*j+3];
std = rb[7*j+3]-write_avg1; std *= std;
write1_std += std;
if(rb[7*j+4]>write2_max)
write2_max = rb[7*j+4];
else if(rb[7*j+4]<write2_min)
write2_min = rb[7*j+4];
std = rb[7*j+4]-write_avg2; std *= std;
write2_std += std;
if(rb[7*j+5]>twrite_max)
twrite_max = rb[7*j+5];
else if(rb[7*j+5]<twrite_min)
twrite_min = rb[7*j+5];
std = rb[7*j+5]-twrite_avg; std *= std;
twrite_std += std;
if(rb[7*j+6]>total_max)
total_max = rb[7*j+6];
else if(rb[7*j+6]<total_min)
total_min = rb[7*j+6];
std = rb[7*j+6]-total_avg; std *= std;
total_std += std;
}
read1_std /= size; read1_std = sqrt(read1_std);
read2_std /= size; read2_std = sqrt(read2_std);
tread_std /= size; tread_std = sqrt(tread_std);
write1_std /= size; write1_std = sqrt(write1_std);
write2_std /= size; write2_std = sqrt(write2_std);
twrite_std /= size; twrite_std = sqrt(twrite_std);
total_std /= size; total_std = sqrt(total_std);
printf("---type--- max\tmin\tavg\tstd\n");
printf("---read_var--- %lf\t%lf\t%lf\t%lf\n", read1_max, read1_min, read_avg1, read1_std);
printf("---fopen+fclose--- %lf\t%lf\t%lf\t%lf\n", read2_max, read2_min, read_avg2, read2_std);
printf("---total_read--- %lf\t%lf\t%lf\t%lf\n", tread_max, tread_min, tread_avg, tread_std);
printf("---adios_open+adios_groupsize--- %lf\t%lf\t%lf\t%lf\n", write1_max, write1_min, write_avg1, write1_std);
printf("---write+close--- %lf\t%lf\t%lf\t%lf\n", write2_max, write2_min, write_avg2, write2_std);
printf("---total_write--- %lf\t%lf\t%lf\t%lf\n", twrite_max, twrite_min, twrite_avg, twrite_std);
printf("---total--- %lf\t%lf\t%lf\t%lf\n", total_max, total_min, total_avg, total_std);
free(rb);
}
}
// if (TIMING==100 && rank==0) {
// printf("------------------------------------------------------------------\n");
// printf("Define variables = %lf\n",total_time[0]);
// printf("Read variables = %lf\n",total_time[1]);
// printf("Write variables = %lf\n",total_time[2]);
// printf("Close File for write = %lf\n",total_time[3]);
// printf("Total write time = %lf\n",total_time[2] + total_time[3]);
// for (itime=0;itime<timers-1;itime++)
// total_time[timers-1]+=total_time[itime];
// printf("Total I/O time = %lf\n",total_time[timers-1]);
// }
MPI_Finalize();
return(0);
}
bool
ADIOSFileObject::Open()
{
if (IsOpen())
return true;
#ifdef PARALLEL
fp = adios_fopen(fileName.c_str(), (MPI_Comm)VISIT_MPI_COMM);
#else
fp = adios_fopen(fileName.c_str(), 0);
#endif
char errmsg[1024];
if (fp == NULL)
{
sprintf(errmsg, "Error opening bp file %s:\n%s", fileName.c_str(), adios_errmsg());
EXCEPTION1(InvalidDBTypeException, errmsg);
}
ADIOS_VARINFO *avi;
gps = (ADIOS_GROUP **) malloc(fp->groups_count * sizeof(ADIOS_GROUP *));
if (gps == NULL)
EXCEPTION1(InvalidDBTypeException, "The file could not be opened. Not enough memory");
debug5 << "ADIOS BP file: " << fileName << endl;
debug5 << "# of groups: " << fp->groups_count << endl;
debug5 << "# of variables: " << fp->vars_count << endl;
debug5 << "# of attributes:" << fp->attrs_count << endl;
debug5 << "time steps: " << fp->ntimesteps << " from " << fp->tidx_start << endl;
//Read in variables/scalars.
variables.clear();
scalars.clear();
for (int gr=0; gr<fp->groups_count; gr++)
{
debug5 << " group " << fp->group_namelist[gr] << ":" << endl;
gps[gr] = adios_gopen_byid(fp, gr);
if (gps[gr] == NULL)
{
sprintf(errmsg, "Error opening group %s in bp file %s:\n%s", fp->group_namelist[gr], fileName.c_str(), adios_errmsg());
EXCEPTION1(InvalidDBTypeException, errmsg);
}
for (int vr=0; vr<gps[gr]->vars_count; vr++)
{
avi = adios_inq_var_byid(gps[gr], vr);
if (avi == NULL)
{
sprintf(errmsg, "Error opening inquiring variable %s in group %s of bp file %s:\n%s",
gps[gr]->var_namelist[vr], fp->group_namelist[gr], fileName.c_str(), adios_errmsg());
EXCEPTION1(InvalidDBTypeException, errmsg);
}
if (SupportedVariable(avi))
{
//Scalar
if (avi->ndim == 0)
{
ADIOSScalar s(gps[gr]->var_namelist[vr], avi);
scalars[s.Name()] = s;
debug5<<" added scalar "<<s<<endl;
}
//Variable
else
{
// add variable to map, map id = variable path without the '/' in the beginning
ADIOSVar v(gps[gr]->var_namelist[vr], gr, avi);
variables[v.name] = v;
debug5<<" added variable "<< v.name<<endl;
}
}
else
debug5<<"Skipping variable: "<<gps[gr]->var_namelist[vr]<<" dim= "<<avi->ndim
<<" timedim= "<<avi->timedim
<<" type= "<<adios_type_to_string(avi->type)<<endl;
adios_free_varinfo(avi);
}
//Read in attributes.
for (int a = 0; a < gps[gr]->attrs_count; a++)
{
int sz;
void *data = NULL;
ADIOS_DATATYPES attrType;
if (adios_get_attr_byid(gps[gr], a, &attrType, &sz, &data) != 0)
{
debug5<<"Failed to get attr: "<<gps[gr]->attr_namelist[a]<<endl;
continue;
}
ADIOSAttr attr(gps[gr]->attr_namelist[a], attrType, data);
attributes[attr.Name()] = attr;
free(data);
}
adios_gclose(gps[gr]);
gps[gr] = NULL;
}
return true;
}
int main (int argc, char ** argv)
{
int gidx, i, j, k,l;
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];
int64_t bytes_read = 0;
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_fopen (argv[1], comm_dummy);
if (f == NULL) {
printf ("%s\n", adios_errmsg());
return -1;
}
/* For all groups */
for (gidx = 0; gidx < f->groups_count; gidx++) {
printf("Group %s:\n", f->group_namelist[gidx]);
ADIOS_GROUP * g = adios_gopen (f, f->group_namelist[gidx]);
if (g == NULL) {
printf ("%s\n", adios_errmsg());
return -1;
}
/* For all variables */
printf(" Variables=%d:\n", g->vars_count);
for (i = 0; i < g->vars_count; i++) {
ADIOS_VARINFO * v = adios_inq_var_byid (g, i);
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), g->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 */
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 timedim=%d\n", (*(int*)v->gmin), (*(int*)v->gmax), v->timedim);
else if (v->type == adios_double)
printf("] = min=%lg max=%lg timedim=%d\n", (*(double*)v->gmin), (*(double*)v->gmax), v->timedim);
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];
bytes_read = adios_read_var_byid (g, i, start, count, data);
if (bytes_read < 0) {
printf ("%s\n", adios_errmsg());
} else if (bytes_read > 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++) {
printf("%s ", value_to_string(v->type, data, j*v->dims[1]*v->dims[2] + k*v->dims[1] + 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", g->attrs_count);
for (i = 0; i < g->attrs_count; i++) {
enum ADIOS_DATATYPES atype;
int asize;
void *adata;
adios_get_attr_byid (g, i, &atype, &asize, &adata);
printf(" %-9s %s = %s\n", adios_type_to_string(atype),
g->attr_namelist[i], value_to_string(atype, adata, 0));
free(adata);
} /* attributes */
adios_gclose (g);
} /* groups */
adios_fclose (f);
//} /* loop 'step' */
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 process_metadata(int step)
{
int retval = 0;
int i, j;
char gdims[256], ldims[256], offs[256];
uint64_t sum_count;
ADIOS_VARINFO *v; // shortcut pointer
if (step > 1)
{
// right now, nothing to prepare in later steps
print("Step %d. return immediately\n",step);
return 0;
}
/* First step processing */
// get groupname of stream, then declare for output
adios_get_grouplist(f, &group_namelist);
print0("Group name is %s\n", group_namelist[0]);
adios_declare_group(&gh,group_namelist[0],"",adios_flag_yes);
varinfo = (VarInfo *) malloc (sizeof(VarInfo) * f->nvars);
if (!varinfo) {
print("ERROR: rank %d cannot allocate %lu bytes\n", rank, sizeof(VarInfo)*f->nvars);
return 1;
}
write_total = 0;
largest_block = 0;
// Decompose each variable and calculate output buffer size
for (i=0; i<f->nvars; i++)
{
print0 ("Get info on variable %d: %s\n", i, f->var_namelist[i]);
varinfo[i].v = adios_inq_var_byid (f, i);
v = varinfo[i].v; // just a shortcut
if (v == NULL) {
print ("rank %d: ERROR: Variable %s inquiry failed: %s\n",
rank, f->var_namelist[i], adios_errmsg());
return 1;
}
// print variable type and dimensions
print0(" %-9s %s", adios_type_to_string(v->type), f->var_namelist[i]);
if (v->ndim > 0) {
print0("[%llu", v->dims[0]);
for (j = 1; j < v->ndim; j++)
print0(", %llu", v->dims[j]);
print0("] :\n");
} else {
print0("\tscalar\n");
}
// determine subset we will write
decompose (numproc, rank, v->ndim, v->dims, decomp_values,
varinfo[i].count, varinfo[i].start, &sum_count);
varinfo[i].writesize = sum_count * adios_type_size(v->type, v->value);
if (varinfo[i].writesize != 0) {
write_total += varinfo[i].writesize;
if (largest_block < varinfo[i].writesize)
largest_block = varinfo[i].writesize;
}
}
// determine output buffer size and allocate it
uint64_t bufsize = write_total + f->nvars*128 + f->nattrs*32 + 1024;
if (bufsize > max_write_buffer_size) {
print ("ERROR: rank %d: write buffer size needs to hold about %llu bytes, "
"but max is set to %d\n", rank, bufsize, max_write_buffer_size);
return 1;
}
print0 ("Rank %d: allocate %llu MB for output buffer\n", rank, bufsize/1048576+1);
adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, bufsize/1048576+1);
// allocate read buffer
bufsize = largest_block + 128;
if (bufsize > max_read_buffer_size) {
print ("ERROR: rank %d: read buffer size needs to hold at least %llu bytes, "
"but max is set to %d\n", rank, bufsize, max_read_buffer_size);
return 1;
}
print0 ("Rank %d: allocate %g MB for input buffer\n", rank, (double)bufsize/1048576.0);
readbuf = (char *) malloc ((size_t)bufsize);
if (!readbuf) {
print ("ERROR: rank %d: cannot allocate %llu bytes for read buffer\n",
rank, bufsize);
return 1;
}
// Select output method
adios_select_method (gh, wmethodname, wmethodparams, "");
// Define variables for output based on decomposition
char *vpath, *vname;
for (i=0; i<f->nvars; i++)
{
v = varinfo[i].v;
if (varinfo[i].writesize != 0) {
// define variable for ADIOS writes
getbasename (f->var_namelist[i], &vpath, &vname);
if (v->ndim > 0)
{
int64s_to_str (v->ndim, v->dims, gdims);
int64s_to_str (v->ndim, varinfo[i].count, ldims);
int64s_to_str (v->ndim, varinfo[i].start, offs);
print ("rank %d: Define variable path=\"%s\" name=\"%s\" "
"gdims=%s ldims=%s offs=%s\n",
rank, vpath, vname, gdims, ldims, offs);
adios_define_var (gh, vname, vpath, v->type, ldims, gdims, offs);
}
else
{
print ("rank %d: Define scalar path=\"%s\" name=\"%s\"\n",
rank, vpath, vname);
adios_define_var (gh, vname, vpath, v->type, "", "", "");
}
free(vpath);
free(vname);
}
}
if (rank == 0)
{
// get and define attributes
enum ADIOS_DATATYPES attr_type;
void * attr_value;
char * attr_value_str;
int attr_size;
for (i=0; i<f->nattrs; i++)
{
adios_get_attr_byid (f, i, &attr_type, &attr_size, &attr_value);
attr_value_str = (char *)value_to_string (attr_type, attr_value, 0);
getbasename (f->attr_namelist[i], &vpath, &vname);
if (vpath && !strcmp(vpath,"/__adios__")) {
// skip on /__adios/... attributes
print ("rank %d: Ignore this attribute path=\"%s\" name=\"%s\" value=\"%s\"\n",
rank, vpath, vname, attr_value_str);
} else {
adios_define_attribute (gh, vname, vpath,
attr_type, attr_value_str, "");
print ("rank %d: Define attribute path=\"%s\" name=\"%s\" value=\"%s\"\n",
rank, vpath, vname, attr_value_str);
free (attr_value);
}
}
}
return retval;
}
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;
}
int main (int argc, char ** argv)
{
char filename [256];
int rank, size, gidx, i, j, k,l;
MPI_Comm comm_dummy = MPI_COMM_WORLD; /* MPI_Comm is defined through adios_read.h */
enum ADIOS_DATATYPES attr_type;
void * data = NULL;
uint64_t start[] = {0,0,0,0,0,0,0,0,0,0};
uint64_t count[MAX_DIMS], hcount[MAX_DIMS], bytes_read = 0;
herr_t h5_err;
char h5name[256],aname[256],fname[256];
int dims [MAX_DIMS];
int h5rank[MAX_DIMS];
int h5i, level;
hid_t grp_id [GMAX+1], space_id, dataset_id;
hid_t memspace_id, dataspace_id, att_id;
char ** grp_name;
hid_t type_id;
hid_t h5_type_id;
hsize_t adims;
if (argc < 2) {
printf("Usage: %s <BP-file> <HDF5-file>\n", argv[0]);
return 1;
}
MPI_Init(&argc, &argv);
h5_err = H5Eset_auto(NULL, NULL );
ADIOS_FILE * f = adios_fopen (argv[1], comm_dummy);
HDF5_FILE = H5Fcreate(argv[2],H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/* create the complex types for HDF5 */
complex_real_id = H5Tcreate (H5T_COMPOUND, sizeof (complex_real_t));
H5Tinsert (complex_real_id, "real", HOFFSET(complex_real_t,re), H5T_NATIVE_FLOAT);
H5Tinsert (complex_real_id, "imaginary", HOFFSET(complex_real_t,im), H5T_NATIVE_FLOAT);
complex_double_id = H5Tcreate (H5T_COMPOUND, sizeof (complex_double_t));
H5Tinsert (complex_double_id, "real", HOFFSET(complex_double_t,re), H5T_NATIVE_DOUBLE);
H5Tinsert (complex_double_id, "imaginary", HOFFSET(complex_double_t,im), H5T_NATIVE_DOUBLE);
if (f == NULL) {
if (DEBUG) printf ("%s\n", adios_errmsg());
return -1;
}
/* For all groups */
for (gidx = 0; gidx < f->groups_count; gidx++) {
if (DEBUG) printf("Group %s:\n", f->group_namelist[gidx]);
ADIOS_GROUP * g = adios_gopen (f, f->group_namelist[gidx]);
if (g == NULL) {
if (DEBUG) printf ("%s\n", adios_errmsg());
return -1;
}
/* First create all of the groups */
grp_id [0] = HDF5_FILE;
for (i = 0; i < g->vars_count; i++) {
ADIOS_VARINFO * v = adios_inq_var_byid (g, i);
strcpy(h5name,g->var_namelist[i]);
grp_name = bp_dirparser (h5name, &level);
for (j = 0; j < level-1; j++) {
grp_id [j + 1] = H5Gopen (grp_id [j], grp_name [j]);
if (grp_id [j + 1] < 0) {
grp_id [j + 1] = H5Gcreate (grp_id [j], grp_name [j], 0);
}
}
for (j=1; j<level; j++) {
H5Gclose(grp_id[j]);
}
}
/* Now we can write data into these scalars */
/* For all variables */
if (DEBUG) printf(" Variables=%d:\n", g->vars_count);
for (i = 0; i < g->vars_count; i++) {
ADIOS_VARINFO * v = adios_inq_var_byid (g, i);
uint64_t total_size = adios_type_size (v->type, v->value);
for (j = 0; j < v->ndim; j++)
total_size *= v->dims[j];
strcpy(h5name,g->var_namelist[i]);
if (DEBUG) printf(" %-9s %s", adios_type_to_string(v->type), g->var_namelist[i]);
h5_err = bp_getH5TypeId (v->type, &h5_type_id);
if (v->type==adios_string) H5Tset_size(h5_type_id,strlen(v->value));
if (v->ndim == 0) {
/* Scalars do not need to be read in, we get it from the metadata
when using adios_inq_var */
if (DEBUG) printf(" = %s\n", value_to_string(v->type, v->value, 0));
// add the hdf5 dataset, these are scalars
for (h5i = 0;h5i<MAX_DIMS;h5i++)
count[0] = 0;
count[0] = 1; // we are writing just 1 element, RANK=1
h5_err = bp_getH5TypeId (v->type, &h5_type_id);
H5LTmake_dataset(HDF5_FILE,h5name,1,count,h5_type_id,v->value);
} else {
h5_err = readVar(g, v, h5name);
}
adios_free_varinfo (v);
} /* variables */
/* For all attributes */
if (DEBUG) printf(" Attributes=%d:\n", g->attrs_count);
for (i = 0; i < g->attrs_count; i++) {
enum ADIOS_DATATYPES atype;
int asize;
void *adata;
adios_get_attr_byid (g, i, &atype, &asize, &adata);
grp_name = bp_dirparser (g->attr_namelist[i], &level);
strcpy(aname,grp_name[level-1]);
// the name of the attribute is the last in the array
// we then need to concat the rest together
strcpy(fname,"/");
for (j=0;j<level-1;j++) {
strcat(fname,grp_name[j]);
}
h5_err = bp_getH5TypeId (atype, &h5_type_id);
// let's create the attribute
adims = 1;
if (atype==adios_string) H5Tset_size(h5_type_id,strlen(adata));
space_id = H5Screate(H5S_SCALAR); // just a scalar
att_id = H5Acreate(HDF5_FILE, g->attr_namelist[i], h5_type_id, space_id,H5P_DEFAULT);
h5_err = H5Awrite(att_id, h5_type_id, adata);
h5_err = H5Aclose(att_id);
h5_err = H5Sclose(space_id);
if (DEBUG) printf(" %-9s %s = %s\n", adios_type_to_string(atype),
g->attr_namelist[i], value_to_string(atype, adata, 0));
free(adata);
} /* attributes */
adios_gclose (g);
} /* groups */
adios_fclose (f);
h5_err = H5Fclose(HDF5_FILE);
MPI_Finalize();
return 0;
}
