int declare_group ()
{
adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, 10);
adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);
adios_select_method (m_adios_group, "MPI", "verbose=2", "");
adios_define_var (m_adios_group, "NX"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "t1"
,"", adios_double
,"NX", "100", "0");
adios_define_var (m_adios_group, "NX"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "t2"
,"", adios_double
,"NX", "100", "0");
return 0;
}
int declare_group ()
{
adios_set_max_buffer_size (10);
adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);
adios_select_method (m_adios_group, "MPI", "verbose=2", "");
adios_define_var (m_adios_group, "NX"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "t1"
,"", adios_double
,"NX", "100", "0");
adios_define_var (m_adios_group, "NX"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "t2"
,"", adios_double
,"NX", "100", "0");
return 0;
}
int main (int argc, char ** argv)
{
MPI_Comm comm = 0; // dummy mpi
/* ADIOS variables declarations for matching gwrite_temperature.ch */
uint64_t adios_groupsize, adios_totalsize;
int64_t g;
int64_t f;
int64_t Tid, Pid, Vid; // variable IDs
char dimstr[32];
sprintf (dimstr, "%d,%d", NX, NY);
adios_init_noxml (comm);
adios_set_max_buffer_size (1);
adios_declare_group (&g, "vars", "", adios_flag_yes);
adios_select_method (g, "POSIX", "", "");
Tid = adios_define_var (g, "T" ,"", adios_double, dimstr, dimstr, "0,0");
adios_set_transform (Tid, "none");
Pid = adios_define_var (g, "P" ,"", adios_double, dimstr, dimstr, "0,0");
adios_set_transform (Pid, "none");
Vid = adios_define_var (g, "V" ,"", adios_double, dimstr, dimstr, "0,0");
adios_set_transform (Vid, "none");
adios_read_init_method(ADIOS_READ_METHOD_BP,0,"");
if (adios_query_is_method_available (ADIOS_QUERY_METHOD_ALACRITY)) {
adios_set_transform (Tid, "alacrity");
adios_set_transform (Pid, "alacrity");
adios_set_transform (Vid, "alacrity");
printf ("Turned on ALACRITY transformation for array variables\n");
}
adios_open (&f, "vars", "vars.bp", "w", comm);
adios_groupsize = 3*NX*NY*sizeof(double);
adios_group_size (f, adios_groupsize, &adios_totalsize);
adios_write (f, "T", T);
adios_write (f, "P", P);
adios_write (f, "V", V);
adios_close (f);
adios_finalize (0);
return 0;
}
int output_define(int nx, int ny, int gnx, int gny, int offsx, int offsy)
{
char ldims[256], gdims[256], offs[256];
snprintf (ldims, sizeof(ldims), "%d,%d", nx, ny);
snprintf (gdims, sizeof(gdims), "%d,%d", gnx, gny);
snprintf (offs, sizeof(offs), "%d,%d", offsx, offsy);
adios_define_var (gh, "xy", "", adios_double, ldims, gdims, offs);
groupsize = nx*ny*sizeof(double);
return 0;
}
int main (int argc, char ** argv)
{
int size, i, block;
MPI_Comm comm = 0; // dummy mpi
/* ADIOS variables declarations for matching gwrite_temperature.ch */
uint64_t adios_groupsize, adios_totalsize;
int64_t g;
int64_t f;
char dimstr[32];
adios_init_noxml (comm);
adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, 1);
adios_declare_group (&g, "table", "", adios_flag_yes);
adios_select_method (g, "POSIX1", "", "");
sprintf (dimstr, "%d,%d", NX, NY);
adios_define_var (g, "A" ,"", adios_integer, dimstr, dimstr, "0,0");
sprintf (dimstr, "%d,%d", n_of_elements, Elements_length);
adios_define_var (g, "Elements" ,"", adios_byte, dimstr, dimstr, "0,0");
sprintf (dimstr, "%d,%d", NY, Columns_length);
adios_define_var (g, "Columns" ,"", adios_byte, dimstr, dimstr, "0,0");
adios_open (&f, "table", "table.bp", "w", comm);
adios_groupsize = NX*NY*sizeof(int32_t) /* size of A */
+ n_of_elements * Elements_length /* size of Elements */
+ NY * Columns_length; /* size of Columns */
adios_group_size (f, adios_groupsize, &adios_totalsize);
adios_write (f, "A", A);
adios_write (f, "Elements", Elements);
adios_write (f, "Columns", Columns);
adios_close (f);
adios_finalize (0);
return 0;
}
int64_t defineAdiosVar(const char* name, int adiosType, uint64_t localDim, const char* globalStr, uint64_t offset)
{
char offsetStr[100] = "";
if (offset != 0) {
sprintf(offsetStr, "%" PRIu64, offset);
}
char dimStr[100];
sprintf(dimStr, "%" PRIu64, localDim);
int64_t id = adios_define_var (gAdios_group, name, "", adiosType, dimStr, globalStr, offsetStr);
printf("id = %ld \n", id);
return id;
}
void defineFastbitVar(int nblocks, const char* name, int64_t* ids, int adiosType, uint64_t* localDim, const char* globalStr, uint64_t* offset)
{
int i=0;
for (i = 0; i < nblocks; i++)
{
//int offset= i*5;
char offsetStr[100] = "";
if (offset != NULL) {
sprintf(offsetStr, "%" PRIu64, offset[i]);
}
char dimStr[100];
sprintf(dimStr, "%" PRIu64, localDim[i]);
ids[i] = adios_define_var (gAdios_group, name, "", adiosType, dimStr, globalStr, offsetStr);
//adios_set_transform (ids[i], "identity");
}
}
int main (int argc, char ** argv)
{
MPI_Comm comm = MPI_COMM_WORLD;
int rank;
int ndx, ndy; // size of array per processor
double * data;
double *X; //X coordinate
double *Y; //Y coordinate
// Offsets and sizes
int offs_x, offs_y; //offset in x and y direction
int nx_local, ny_local; //local address
int nx_global, ny_global; //global address
int posx, posy; // position index in the array
int i,j;
int64_t m_adios_group;
uint64_t adios_groupsize, adios_totalsize;
int64_t adios_handle;
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &rank);
MPI_Comm_size (comm, &nproc);
if (processArgs(argc, argv)) {
return 1;
}
//will work with each core writing ndx = 65, ndy = 129, (65*4,129*3) global
ndx = 65;
ndy = 129;
//2D array with block,block decomposition
posx = rank%npx; // 1st dim
posy = rank/npx; // 2nd dim
offs_x = posx * ndx;
offs_y = posy * ndy;
nx_local = ndx;
ny_local = ndy;
nx_global = npx * ndx;
ny_global = npy * ndy;
data = malloc (ndx * ndy * sizeof(double));
for( i = 0; i < ndx; i++ )
for( j = 0; j < ndy; j++)
data[i*ndy + j] = 1.0*rank;
X = malloc (ndx * ndy * sizeof(double));
for( i = 0; i < ndx; i++ )
for( j = 0; j < ndy; j++)
X[i*ndy + j] = offs_x + posy*ndx + i*ndx/ndx + (double)ndx*j/ndy;
Y = malloc (ndx * ndy * sizeof(double));
Y[0] = offs_y;
for( i = 0; i < ndx; i++ )
for( j = 0; j < ndy; j++)
Y[i*ndy + j] = offs_y + ndy*j/ndy;
char * schema_version = "1.1";
char * dimemsions = "nx_global,ny_global";
adios_init_noxml (comm);
adios_set_max_buffer_size (50);
adios_declare_group (&m_adios_group, "structured2d", "", adios_flag_yes);
adios_select_method (m_adios_group, "MPI", "", "");
adios_define_var (m_adios_group, "nx_global"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "ny_global"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "nproc"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "offs_x"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "offs_y"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "nx_local"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "ny_local"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "X"
,"", adios_double
,"nx_local,ny_local", "nx_global,ny_global", "offs_x,offs_y");
adios_define_var (m_adios_group, "Y"
,"", adios_double
,"nx_local,ny_local", "nx_global,ny_global", "offs_x,offs_y");
adios_define_var (m_adios_group, "data"
,"", adios_double
,"nx_local,ny_local", "nx_global,ny_global", "offs_x,offs_y");
adios_define_schema_version (m_adios_group, schema_version);
adios_define_mesh_structured (dimemsions, "X,Y", "2", m_adios_group, "structuredmesh");
adios_define_mesh_timevarying ("no", m_adios_group, "structuredmesh");
adios_define_var_mesh (m_adios_group, "data", "structuredmesh");
adios_define_var_centering (m_adios_group, "data", "point");
adios_open (&adios_handle, "structured2d", "structured2d_noxml.bp", "w", comm);
adios_groupsize = 7*sizeof(int) \
+ 3*sizeof(double) * (nx_local*ny_local);
adios_group_size (adios_handle, adios_groupsize, &adios_totalsize);
adios_write (adios_handle, "nproc", &nproc);
adios_write (adios_handle, "nx_global", &nx_global);
adios_write (adios_handle, "ny_global", &ny_global);
adios_write (adios_handle, "offs_x", &offs_x);
adios_write (adios_handle, "offs_y", &offs_y);
adios_write (adios_handle, "nx_local", &nx_local);
adios_write (adios_handle, "ny_local", &ny_local);
adios_write (adios_handle, "X", X);
adios_write (adios_handle, "Y", Y);
adios_write (adios_handle, "data", data);
adios_close (adios_handle);
MPI_Barrier (comm);
free (data);
free (X);
free (Y);
adios_finalize (rank);
MPI_Finalize ();
return 0;
}
int main (int argc, char ** argv)
{
int err,i,M;
int iconnect;
MPI_Init (&argc, &argv);
MPI_Comm_rank (wcomm, &wrank);
MPI_Comm_size (wcomm, &wsize);
if (argc < 2) { Usage(); return 1; }
errno = 0;
M = strtol (argv[1], NULL, 10);
if (errno || M < 1 || M > wsize) {
printE("Invalid 1st argument %s\n", argv[1]); Usage(); return 1;
}
iconnect = (wrank >= wsize-M); // connect to server from ranks N-M, N-M+1, ..., N
MPI_Comm_split (wcomm, iconnect, wrank+M-wsize, &subcomm);
MPI_Comm_rank (subcomm, &subrank);
MPI_Comm_size (subcomm, &subsize);
if (iconnect) {
if (subsize != M) {
printE ("Something wrong with communicator split: N=%d, M=%d, splitted size=%d\n",
wsize, M, subsize);
return 2;
}
log ("connect as subrank %d\n", subrank);
}
alloc_vars();
adios_read_init_method(ADIOS_READ_METHOD_DATASPACES, subcomm, "verbose=4");
adios_init_noxml (subcomm);
adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, 1);
if (iconnect)
{
adios_declare_group (&m_adios_group, "connect", "iter", adios_flag_yes);
adios_select_method (m_adios_group, "DATASPACES", "verbose=4", "");
adios_define_var (m_adios_group, "ldim1", "", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, "gdim1", "", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, "offs1", "", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, "a1", "", adios_integer,
"ldim1", "gdim1", "offs1");
for (i=0; i<NSTEPS; i++) {
if (!err) {
set_vars (i);
err = write_file (i);
}
}
}
log ("done with work, sync with others...\n");
MPI_Barrier (wcomm);
log ("call adios_finalize...\n");
adios_finalize (wrank);
log ("call adios_read_finalize_method...\n");
adios_read_finalize_method (ADIOS_READ_METHOD_DATASPACES);
fini_vars();
MPI_Finalize ();
return err;
}
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);
}
int write_blocks ()
{
int NX, G, O;
double *t;
/* ADIOS variables declarations for matching gwrite_temperature.ch */
int it, i, r;
uint64_t adios_groupsize, adios_totalsize;
if (!rank) printf ("------- Write blocks -------\n");
// We will have "3 steps * 2 blocks per process * number of processes" blocks
nsteps = 3;
nblocks_per_step = 2;
block_offset = (uint64_t*) malloc (sizeof(uint64_t) * nsteps * nblocks_per_step * size);
block_count = (uint64_t*) malloc (sizeof(uint64_t) * nsteps * nblocks_per_step * size);
gdims = (uint64_t*) malloc (sizeof(uint64_t) * nsteps);
adios_init_noxml (comm);
adios_set_max_buffer_size (10);
int64_t m_adios_group;
int64_t m_adios_file;
adios_declare_group (&m_adios_group, "restart", "", adios_flag_yes);
adios_select_method (m_adios_group, "MPI", "", "");
adios_define_var (m_adios_group, "NX"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "G"
,"", adios_integer
,0, 0, 0);
/* have to define O and temperature as many times as we
write them within one step (twice) */
for (it=0; it < nblocks_per_step; it++) {
adios_define_var (m_adios_group, "O"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "t"
,"", adios_double
,"NX", "G", "O");
}
for (it =0; it < nsteps; it++) {
if (!rank) printf ("Step %d:\n", it);
NX = 10+it;
G = nblocks_per_step * NX * size;
t = (double *) malloc (NX*sizeof(double));
for (i = 0; i < NX; i++)
t[i] = rank + it*0.1 + 0.01;
MPI_Barrier (comm);
if (it==0)
adios_open (&m_adios_file, "restart", fname, "w", comm);
else
adios_open (&m_adios_file, "restart", fname, "a", comm);
adios_groupsize = 4 + 4 + 4 + NX * 8
+ 4 + 4 + 4 + NX * 8;
adios_group_size (m_adios_file, adios_groupsize, &adios_totalsize);
adios_write(m_adios_file, "NX", (void *) &NX);
adios_write(m_adios_file, "G", (void *) &G);
O = rank * nblocks_per_step * NX;
adios_write(m_adios_file, "O", (void *) &O);
adios_write(m_adios_file, "t", t);
printf ("rank %d: block 1: size=%d, offset=%d\n", rank, NX, O);
for (r = 0; r < size; r++) {
block_count [it*nblocks_per_step*size + nblocks_per_step*r] = NX;
block_offset [it*nblocks_per_step*size + nblocks_per_step*r] = r * nblocks_per_step * NX;
}
for (i = 0; i < NX; i++)
t[i] += 0.01;
O = rank * nblocks_per_step * NX + NX;
adios_write(m_adios_file, "O", (void *) &O);
adios_write(m_adios_file, "t", t);
printf ("rank %d: block 2: size=%d, offset=%d\n", rank, NX, O);
for (r = 0; r < size; r++) {
block_count [it*nblocks_per_step*size + nblocks_per_step*r + 1] = NX;
block_offset [it*nblocks_per_step*size + nblocks_per_step*r + 1] = r * nblocks_per_step * NX + NX;
}
gdims [it] = G;
adios_close (m_adios_file);
MPI_Barrier (comm);
free(t);
}
adios_finalize (rank);
return 0;
}
int main (int argc, char ** argv)
{
char filename [256];
int rank, size, i, block;
int NX = 100, Global_bounds, Offsets;
double t[NX];
int sub_blocks = 3;
MPI_Comm comm = MPI_COMM_WORLD;
/* ADIOS variables declarations for matching gwrite_temperature.ch */
uint64_t adios_groupsize, adios_totalsize;
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &rank);
MPI_Comm_size (comm, &size);
Global_bounds = sub_blocks * NX * size;
strcpy (filename, "adios_global_no_xml.bp");
adios_init_noxml (comm);
adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, 10);
int64_t m_adios_group;
int64_t m_adios_file;
adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);
adios_select_method (m_adios_group, "MPI", "", "");
adios_define_var (m_adios_group, "NX"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "Global_bounds"
,"", adios_integer
,0, 0, 0);
for (i=0;i<sub_blocks;i++) {
adios_define_var (m_adios_group, "Offsets"
,"", adios_integer
,0, 0, 0);
int64_t varid;
varid = adios_define_var (m_adios_group, "temperature"
,"", adios_double
,"NX", "Global_bounds", "Offsets");
adios_set_transform (varid, "none");
}
adios_open (&m_adios_file, "restart", filename, "w", comm);
adios_groupsize = sub_blocks * (4 + 4 + 4 + NX * 8);
adios_group_size (m_adios_file, adios_groupsize, &adios_totalsize);
adios_write(m_adios_file, "NX", (void *) &NX);
adios_write(m_adios_file, "Global_bounds", (void *) &Global_bounds);
/* now we will write the data for each sub block */
for (block=0;block<sub_blocks;block++) {
Offsets = rank * sub_blocks * NX + block*NX;
adios_write(m_adios_file, "Offsets", (void *) &Offsets);
for (i = 0; i < NX; i++)
t[i] = Offsets + i;
adios_write(m_adios_file, "temperature", t);
}
adios_close (m_adios_file);
MPI_Barrier (comm);
adios_finalize (rank);
MPI_Finalize ();
return 0;
}
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)
{
char filename [256];
int rank, size, i, j;
int NX = 100, gb, offset; //local/global/offset
double t[NX];
int nblocks = 3;
MPI_Comm comm = MPI_COMM_WORLD;
char g_str[100], o_str[100], l_str[100];
// attributes (from C variables)
int someints[5] = {5,4,3,2,1};
double somedoubles[5] = {5.55555, 4.4444, 3.333, 2.22, 1.1};
/* ADIOS variables declarations for matching gwrite_temperature.ch */
uint64_t adios_groupsize, adios_totalsize;
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &rank);
MPI_Comm_size (comm, &size);
gb = nblocks * NX * size;
sprintf (g_str, "%d", gb);
sprintf (l_str, "%d", NX);
strcpy (filename, "no_xml_write_byid.bp");
adios_init_noxml (comm);
adios_set_max_buffer_size (10);
int64_t m_adios_group;
int64_t m_adios_file;
int64_t var_ids[nblocks];
adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);
adios_select_method (m_adios_group, "MPI", "", "");
for (i = 0; i < nblocks; i++)
{
offset = rank * nblocks * NX + i * NX;
sprintf (o_str, "%d", offset);
var_ids[i] = adios_define_var (m_adios_group, "temperature"
,"", adios_double
,l_str, g_str, o_str
);
adios_set_transform (var_ids[i], "none");
// This is here just for fun
uint64_t varsize = adios_expected_var_size(var_ids[i]);
// adios_expected_var_size() works here because the definition of the variable
// does not depend on any dimension variable (but defined with numerical dimensions)
fprintf (stderr, "Temperature block %d is %" PRIu64 " bytes\n", i, varsize);
}
// add some attributes
adios_define_attribute_byvalue (m_adios_group,
"single_string","", adios_string, 1, "A single string attribute");
char *strings[] = {"X","Yy","ZzZ"};
adios_define_attribute_byvalue (m_adios_group,
"three_strings","", adios_string_array, 3, strings);
adios_define_attribute_byvalue (m_adios_group,
"single_int", "", adios_integer, 1, &someints);
adios_define_attribute_byvalue (m_adios_group,
"single_double","", adios_double, 1, &somedoubles);
adios_define_attribute_byvalue (m_adios_group,
"five_ints", "", adios_integer, 5, &someints);
adios_define_attribute_byvalue (m_adios_group,
"five_double", "", adios_double, 5, &somedoubles);
adios_open (&m_adios_file, "restart", filename, "w", comm);
adios_groupsize = nblocks * (4 + 4 + 4 + NX * 8);
adios_group_size (m_adios_file, adios_groupsize, &adios_totalsize);
/* now we will write the data for each sub block */
for (i = 0; i < nblocks; i++)
{
offset = rank * nblocks * NX + i * NX;
for (j = 0; j < NX; j++)
t[j] = offset + j;
adios_write_byid(m_adios_file, var_ids[i], t);
}
adios_close (m_adios_file);
MPI_Barrier (comm);
adios_finalize (rank);
MPI_Finalize ();
return 0;
}
int main (int argc, char ** argv)
{
char filename [256];
char color_str[256];
int rank, size, i, color;
int NX = 100, Global_bounds, Offsets;
double t[NX];
MPI_Comm comm = MPI_COMM_WORLD;
/* ADIOS variables declarations for matching gwrite_temperature.ch */
uint64_t adios_groupsize, adios_totalsize;
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &rank);
MPI_Comm_size (comm, &size);
Global_bounds = NX * size;
strcpy (filename, "adios_global_aggregate_by_color.bp");
adios_init_noxml (comm);
adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, 10);
int64_t m_adios_group;
int64_t m_adios_file;
adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);
// split into 2 groups
color = (rank % 2 == 0 ? 0 : 1);
sprintf (color_str, "color=%d", color);
adios_select_method (m_adios_group, "MPI", color_str, "");
adios_define_var (m_adios_group, "NX"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "Global_bounds"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "Offsets"
,"", adios_integer
,0, 0, 0);
adios_define_var (m_adios_group, "temperature"
,"", adios_double
,"NX", "Global_bounds", "Offsets");
adios_open (&m_adios_file, "restart", filename, "w", comm);
adios_groupsize = 4 + 4 + 4 + NX * 8;
adios_group_size (m_adios_file, adios_groupsize, &adios_totalsize);
adios_write(m_adios_file, "NX", (void *) &NX);
adios_write(m_adios_file, "Global_bounds", (void *) &Global_bounds);
Offsets = rank * NX;
adios_write(m_adios_file, "Offsets", (void *) &Offsets);
for (i = 0; i < NX; i++)
t[i] = Offsets + i;
adios_write(m_adios_file, "temperature", t);
adios_close (m_adios_file);
MPI_Barrier (comm);
adios_finalize (rank);
MPI_Finalize ();
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;
}
/**
* Define variables and write data
*/
SEXP R_write(SEXP R_filename,
SEXP R_group,
SEXP R_groupname,
SEXP R_nvars, // number of vars
SEXP R_varname_list, // var names
SEXP R_var_list, // var values
SEXP R_varlength_list, // length of var values
SEXP R_ndim, // number of dims
SEXP R_type,
SEXP R_comm,
SEXP R_p,
SEXP R_adios_rank)
{
const char *filename = CHARPT(R_filename, 0);
int64_t m_adios_group = (int64_t)(REAL(R_group)[0]);
const char *groupname = CHARPT(R_groupname, 0);
int nvars = asInteger(R_nvars);
MPI_Comm comm = MPI_Comm_f2c(INTEGER(R_comm)[0]);
int size = asInteger(R_p);
int rank = asInteger(R_adios_rank);
int i, j;
int Global_bounds, Offsets;
uint64_t adios_groupsize, adios_totalsize;
int64_t m_adios_file;
// variable to store the value converted from integer
char str[256];
// Define variables
for(i = 0; i < nvars; i++) {
const char *varname = CHAR(asChar(VECTOR_ELT(R_varname_list,i)));
int *length = INTEGER(VECTOR_ELT(R_varlength_list, i));
int *vndim = INTEGER(VECTOR_ELT(R_ndim, i));
int *typetag = INTEGER(VECTOR_ELT(R_type, i));
if((length[0] == 1) && (vndim[0] == 1)){
// scalar
if(typetag[0] == 0) {
adios_define_var (m_adios_group, varname, "", adios_integer, 0, 0, 0);
}else {
adios_define_var (m_adios_group, varname, "", adios_double, 0, 0, 0);
}
}else {
// define dimensions, global_dimensions, local_offsets and the variable
int temp_var_length = strlen(varname) + 8;
char* local_var = (char*)malloc(vndim[0]*temp_var_length);
char* global_var = (char*)malloc(vndim[0]*temp_var_length);
char* offset_var = (char*)malloc(vndim[0]*temp_var_length);
// initialize char variables
strcpy(local_var, "");
strcpy(global_var, "");
strcpy(offset_var, "");
// j = 0
j = 0;
sprintf(str, "%d", j);
char* local = (char*)malloc(temp_var_length);
strcpy(local, varname);
strcat(local, "_nx_");
strcat(local, str);
strcat(local_var, local);
char* global = (char*)malloc(temp_var_length);
strcpy(global, varname);
strcat(global, "_gx_");
strcat(global, str);
strcat(global_var, global);
char* offset = (char*)malloc(temp_var_length);
strcpy(offset, varname);
strcat(offset, "_off_");
strcat(offset, str);
strcat(offset_var, offset);
// define local dim, global dim and offset for each dimension
adios_define_var (m_adios_group, local,
"", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, global,
"", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, offset,
"", adios_integer, 0, 0, 0);
Free(local);
Free(global);
Free(offset);
for(j = 1; j < vndim[0]; j++) {
sprintf(str, "%d", j);
strcat(local_var, ",");
char* local = (char*)malloc(temp_var_length);
strcpy(local, varname);
strcat(local, "_nx_");
strcat(local, str);
strcat(local_var, local);
strcat(global_var, ",");
char* global = (char*)malloc(temp_var_length);
strcpy(global, varname);
strcat(global, "_gx_");
strcat(global, str);
strcat(global_var, global);
strcat(offset_var, ",");
char* offset = (char*)malloc(temp_var_length);
strcpy(offset, varname);
strcat(offset, "_off_");
strcat(offset, str);
strcat(offset_var, offset);
// define local dim, global dim and offset for each dimension
adios_define_var (m_adios_group, local,
"", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, global,
"", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, offset,
"", adios_integer, 0, 0, 0);
Free(local);
Free(global);
Free(offset);
}
// define variable
if(typetag[0] == 0) {
adios_define_var (m_adios_group, varname, "", adios_integer,
local_var, global_var, offset_var);
}else {
adios_define_var (m_adios_group, varname, "", adios_double,
local_var, global_var, offset_var);
}
Free(local_var);
Free(global_var);
Free(offset_var);
}
}
// Open ADIOS
adios_open (&m_adios_file, groupname, filename, "w", comm);
adios_groupsize = 0;
for(i = 0; i < nvars; i++) {
int *length = INTEGER(VECTOR_ELT(R_varlength_list, i));
int *vndim = INTEGER(VECTOR_ELT(R_ndim, i));
int *typetag = INTEGER(VECTOR_ELT(R_type, i));
// calculate the length of the variable
int temp = 1;
for(j = 0; j < vndim[0]; j++)
temp *= length[j];
if((length[0] == 1) && (vndim[0] == 1)){
// scalar
if(typetag[0] == 0) {
adios_groupsize += 4;
}else {
adios_groupsize += 8;
}
}else {
if(typetag[0] == 0) {
adios_groupsize += (12 * vndim[0] + temp * 4);
}else {
adios_groupsize += (12 * vndim[0] + temp * 8);
}
}
}
adios_group_size (m_adios_file, adios_groupsize, &adios_totalsize);
// Write data into variables
for(i = 0; i < nvars; i++) {
const char *varname = CHAR(asChar(VECTOR_ELT(R_varname_list,i)));
int *length = INTEGER(VECTOR_ELT(R_varlength_list, i));
int *vndim = INTEGER(VECTOR_ELT(R_ndim, i));
int *typetag = INTEGER(VECTOR_ELT(R_type, i));
if((length[0] == 1) && (vndim[0] == 1)){
// scalar
}else {
// var
int temp_var_length = strlen(varname) + 8;
j = 0;
sprintf(str, "%d", j);
char* local = (char*)malloc(temp_var_length);
strcpy(local, varname);
strcat(local, "_nx_");
strcat(local, str);
char* global = (char*)malloc(temp_var_length);
strcpy(global, varname);
strcat(global, "_gx_");
strcat(global, str);
char* offset = (char*)malloc(temp_var_length);
strcpy(offset, varname);
strcat(offset, "_off_");
strcat(offset, str);
adios_write(m_adios_file, local, (void *) &(length[j]));
Global_bounds = length[j] * size;
adios_write(m_adios_file, global, (void *) &Global_bounds);
Offsets = rank * length[j];
adios_write(m_adios_file, offset, (void *) &Offsets);
Free(local);
Free(global);
Free(offset);
for(j = 1; j < vndim[0]; j++) {
sprintf(str, "%d", j);
char* local = (char*)malloc(temp_var_length);
strcpy(local, varname);
strcat(local, "_nx_");
strcat(local, str);
char* global = (char*)malloc(temp_var_length);
strcpy(global, varname);
strcat(global, "_gx_");
strcat(global, str);
char* offset = (char*)malloc(temp_var_length);
strcpy(offset, varname);
strcat(offset, "_off_");
strcat(offset, str);
adios_write(m_adios_file, local, (void *) &(length[j]));
Global_bounds = length[j];
adios_write(m_adios_file, global, (void *) &Global_bounds);
Offsets = 0;
adios_write(m_adios_file, offset, (void *) &Offsets);
Free(local);
Free(global);
Free(offset);
}
}
// write var data
if(typetag[0] == 0) {
adios_write(m_adios_file, varname, (void *) INTEGER(VECTOR_ELT(R_var_list, i)));
}else {
adios_write(m_adios_file, varname, (void *) REAL(VECTOR_ELT(R_var_list, i)));
}
}
adios_close (m_adios_file);
MPI_Barrier (comm);
return R_NilValue;
}
void define_vars ()
{
int i;
adios_define_var (m_adios_group, "ldim1", "", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, "ldim2", "", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, "ldim3", "", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, "gdim1", "", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, "gdim2", "", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, "gdim3", "", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, "offs1", "", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, "offs2", "", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, "offs3", "", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, "a0", "", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, "a1", "", adios_integer,
"ldim1", "gdim1", "offs1");
adios_define_var (m_adios_group, "a2", "", adios_integer,
"ldim1,ldim2", "gdim1,gdim2", "offs1,offs2");
adios_define_var (m_adios_group, "a3", "", adios_integer,
"ldim1,ldim2,ldim3", "gdim1,gdim2,gdim3", "offs1,offs2,offs3");
}
int main (int argc, char ** argv)
{
char filename [256];
int rank, size, i, j, step, block;
int Offset;
int NX = 2; // number of records written per step per process
int Width=20;
int sub_blocks = 2; // number of record-blocks written per process in one step
int steps = 3;
char t[NX][Width];
MPI_Comm comm = MPI_COMM_WORLD;
/* ADIOS variables declarations for matching gwrite_temperature.ch */
int adios_err;
uint64_t adios_groupsize, adios_totalsize;
int64_t adios_handle;
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &rank);
MPI_Comm_size (comm, &size);
//Global_bounds = sub_blocks * NX * size;
strcpy (filename, "steps.bp");
adios_init_noxml (comm);
adios_set_max_buffer_size (1);
int64_t m_adios_group;
int64_t m_adios_file;
adios_declare_group (&m_adios_group, "steps", "", adios_flag_yes);
adios_select_method (m_adios_group, "MPI", "", "");
adios_define_var (m_adios_group, "NX" ,"", adios_integer ,0, 0, 0);
adios_define_var (m_adios_group, "Width" ,"", adios_integer ,0, 0, 0);
adios_define_var (m_adios_group, "nproc" ,"", adios_integer ,0, 0, 0);
for (i=0;i<sub_blocks;i++) {
adios_define_var (m_adios_group, "record" ,"", adios_byte ,"NX,Width", "", "");
}
for (step=0; step<steps; step++) {
adios_open (&m_adios_file, "steps", filename, "a", comm);
adios_groupsize = sub_blocks * (4 + 4 + 4 + (uint64_t) NX * (uint64_t)Width);
adios_group_size (m_adios_file, adios_groupsize, &adios_totalsize);
adios_write(m_adios_file, "nproc", (void *) &size);
adios_write(m_adios_file, "NX", (void *) &NX);
adios_write(m_adios_file, "Width", (void *) &Width);
/* now we will write the data for each sub block */
for (block=0;block<sub_blocks;block++) {
for (i = 0; i < NX; i++)
//print 19 chars here + '\0'
sprintf (t[i], "r%2d b%2d s%2d i%2d ", rank, block, step, i);
adios_write(m_adios_file, "record", t);
}
adios_close (m_adios_file);
}
MPI_Barrier (comm);
adios_finalize (rank);
MPI_Finalize ();
return 0;
}