int read_file (char *fname) { ADIOS_SELECTION *sel; ADIOS_FILE * f; ADIOS_VARINFO * vi; int err=0,i,n; uint64_t start[1] = {0}; uint64_t count[2] = {NX}; uint64_t ndim; reset_rarrays(); log ("Read and check data in %s\n", fname); f = adios_read_open_file (fname, ADIOS_READ_METHOD_BP, comm); if (f == NULL) { printE ("Error at opening file: %s\n", adios_errmsg()); return 1; } sel = adios_selection_boundingbox (1, start, count); adios_schedule_read (f, sel, "t1", 0, 1, r1); adios_schedule_read (f, sel, "t2", 0, 1, r2); adios_perform_reads (f, 1); adios_selection_delete (sel); CHECK_ARRAY (t, r1, NX); CHECK_ARRAY (t, r2, NX); endread: adios_read_close(f); MPI_Barrier (comm); return err; }
void adios_checkpoint_verify_variables(ADIOS_FILE* fp, const char* name, int* origin) { ADIOS_VARINFO *vi; int count = 1; int size; vi = adios_inq_var(fp, name); if (vi->ndim > 0) { cout<<name<<" verification not passed, not a scalar"<<endl; return; } size = count*adios_type_size(vi->type, vi->value); int * mem= (int * )malloc(size); ADIOS_SELECTION *sel = adios_selection_writeblock(OHMMS::Controller->rank()); adios_schedule_read(fp, sel, name, 0, 1, mem); //adios_schedule_read(fp, NULL, name, 0, 1, mem); adios_perform_reads(fp, 1); if(mem[0] == *origin) { cout<<name<<" verification passed "<<mem[0]<<endl; } else { cout<<name<<" verification not passed, readin: "<<mem[0]<<" writeout: "<<*origin<<endl; } adios_free_varinfo (vi); adios_selection_delete(sel); free(mem); }
void adios_checkpoint_verify_variables(ADIOS_FILE* fp, const char* name, unsigned long origin) { ADIOS_VARINFO *vi; int count = 1; int size; vi = adios_inq_var(fp, name); if (vi->ndim > 0) { cout<<name<<" verification not passed, not a scalar"<<endl; return; } size = count*adios_type_size(vi->type, vi->value); unsigned long* mem= (unsigned long* )malloc(size); adios_schedule_read(fp, NULL, name, 0, 1, mem); adios_perform_reads(fp, 1); if(mem[0] == origin) { cout<<name<<" verification passed"<<mem[0]<<endl; } else { cout<<name<<" verification not passed, readin: "<<mem[0]<<" writeout: "<<origin<<endl; } adios_free_varinfo (vi); free(mem); }
void adios_checkpoint_verify_variables(ADIOS_FILE* fp, const char* name, RealType* origin) { ADIOS_VARINFO *vi; int count = 1; int size; vi = adios_inq_var(fp, name); adios_inq_var_blockinfo (fp, vi); if (vi->ndim > 0) { count*=vi->dims[0]; for (int j = 1; j < vi->ndim; j++) { count *= vi->dims[j]; } } size = count*adios_type_size(vi->type, vi->value); RealType *mem= (RealType *)malloc(size); adios_schedule_read(fp, NULL, name, 0, 1, mem); adios_perform_reads(fp, 1); for(int i=0; i<count; i++) { if(mem[i] == origin[i]) { cout<<name<<"["<<i<<"]verification passed "<<mem[i]<<endl; } else { cout<<name<<"["<<i<<"]verification not passed, readin: "<<mem[i]<<" writeout: "<<origin[i]<<endl; } } adios_free_varinfo (vi); free(mem); }
void adios_checkpoint_verify_random_variables(ADIOS_FILE* fp, const char* name, uint_type* origin) { ADIOS_VARINFO *vi; int count_int = 1; int size; uint64_t *start; uint64_t *count; vi = adios_inq_var(fp, name); adios_inq_var_blockinfo (fp, vi); if (vi->ndim > 0) { start = (uint64_t *)malloc(vi->ndim * sizeof(uint64_t)); count = (uint64_t *)malloc(vi->ndim * sizeof(uint64_t)); } for (int j=0; j<vi->nblocks[0]; j++) { if(j == OHMMS::Controller->rank()) { for (int k=0; k<vi->ndim; k++) { start[k] = vi->blockinfo[j].start[k]; count[k] = vi->blockinfo[j].count[k]; count_int *= count[k]; //cout<<OHMMS::Controller->rank()<<" count "<<start[k]<<" "<<count[k]<<endl; } } } size = count_int*adios_type_size(vi->type, vi->value); uint_type *mem= (uint_type*)malloc(size); ADIOS_SELECTION *sel = adios_selection_boundingbox(vi->ndim, start, count); adios_schedule_read(fp, sel, name, 0, 1, mem); adios_perform_reads(fp, 1); int flag = 0; for(int i=0; i<count_int; i++) { if(mem[i] == origin[i]) { //cout<<name<<"["<<i<<"]verification passed "<<mem[i]<<endl; } else { flag = 1; cout<<name<<"["<<i<<"]verification not passed, readin: "<<mem[i]<<" writeout: "<<origin[i]<<endl; } } if (flag == 0) cout<<name<<" verification passed "<<endl; else cout<<name<<" verification not passed "<<endl; adios_free_varinfo (vi); adios_selection_delete(sel); free(start); free(count); free(mem); }
void ADIOS1CommonRead::ScheduleReadCommon(const std::string &name, const Dims &offs, const Dims &ldims, const int fromStep, const int nSteps, const bool readAsLocalValue, const bool readAsJoinedArray, void *data) { if (readAsLocalValue) { /* Get all the requested values from metadata now */ ADIOS_VARINFO *vi = adios_inq_var(m_fh, name.c_str()); if (vi) { adios_inq_var_stat(m_fh, vi, 0, 1); int elemsize = adios_type_size(vi->type, nullptr); long long blockidx = 0; for (int i = 0; i < fromStep; i++) { blockidx += vi->nblocks[i]; } char *dest = (char *)data; for (int i = fromStep; i < fromStep + nSteps; i++) { for (int j = 0; j < vi->nblocks[i]; j++) { memcpy(dest, vi->statistics->blocks->mins[blockidx], elemsize); ++blockidx; dest += elemsize; } } adios_free_varinfo(vi); } } else { uint64_t start[32], count[32]; for (int i = 0; i < ldims.size(); i++) { start[i] = (uint64_t)offs[i]; count[i] = (uint64_t)ldims[i]; } ADIOS_SELECTION *sel = nullptr; if (ldims.size() > 0) { sel = adios_selection_boundingbox(ldims.size(), start, count); } adios_schedule_read(m_fh, sel, name.c_str(), (int)fromStep, (int)nSteps, data); adios_selection_delete(sel); } }
void ToolsAdiosParallel::convertToText() { if(m_options.data.size() == 0) throw std::runtime_error("No datasets requested"); for (size_t i = 0; i < m_options.data.size(); ++i) { ADIOS_VARINFO *pVarInfo; //get name of dataset to print std::string nodeName = m_options.data[i]; uint8_t *P; int varElement = 1; int varTypeSize = 0; adios_read_init_method(ADIOS_READ_METHOD_BP, comm, nodeName.c_str()); pVarInfo = adios_inq_var(pFile, nodeName.c_str()); varTypeSize = adios_type_size(pVarInfo->type, NULL); // get number of elements combined in a dataset for(int j = 0; j < pVarInfo->ndim; j++) { varElement = varElement * pVarInfo->dims[j]; } // allocate memory P = (uint8_t*) malloc (sizeof(uint8_t) * varTypeSize * varElement); adios_schedule_read(pFile, NULL, nodeName.c_str(), 0, 1, P); adios_perform_reads(pFile, 1); if(pVarInfo->ndim > 0) { for(int k = 0; k < varElement; k++) { printValue(pVarInfo->type, &P[k*varTypeSize]); } } else { printValue(pVarInfo->type, pVarInfo->value); } adios_free_varinfo(pVarInfo); } }
/** Read the skalar field and optionally the attribute into the values referenced by the pointers */ void operator()(ThreadParams& params, const std::string& name, T_Scalar* value, const std::string& attrName = "", T_Attribute* attribute = nullptr) { log<picLog::INPUT_OUTPUT> ("ADIOS: read %1%D scalars: %2%") % simDim % name; std::string datasetName = params.adiosBasePath + name; ADIOS_VARINFO* varInfo; ADIOS_CMD_EXPECT_NONNULL( varInfo = adios_inq_var(params.fp, datasetName.c_str()) ); if(varInfo->ndim != simDim) throw std::runtime_error(std::string("Invalid dimensionality for ") + name); if(varInfo->type != traits::PICToAdios<T_Scalar>().type) throw std::runtime_error(std::string("Invalid type for ") + name); DataSpace<simDim> gridPos = Environment<simDim>::get().GridController().getPosition(); uint64_t start[varInfo->ndim]; uint64_t count[varInfo->ndim]; for(int d = 0; d < varInfo->ndim; ++d) { /* \see adios_define_var: z,y,x in C-order */ start[d] = gridPos.revert()[d]; count[d] = 1; } ADIOS_SELECTION* fSel = adios_selection_boundingbox(varInfo->ndim, start, count); // avoid deadlock between not finished pmacc tasks and mpi calls in adios __getTransactionEvent().waitForFinished(); /* specify what we want to read, but start reading at below at `adios_perform_reads` */ /* magic parameters (0, 1): `from_step` (not used in streams), `nsteps` to read (must be 1 for stream) */ log<picLog::INPUT_OUTPUT > ("ADIOS: Schedule read skalar %1%)") % datasetName; ADIOS_CMD( adios_schedule_read(params.fp, fSel, datasetName.c_str(), 0, 1, (void*)value) ); /* start a blocking read of all scheduled variables */ ADIOS_CMD( adios_perform_reads(params.fp, 1) ); adios_selection_delete(fSel); adios_free_varinfo(varInfo); if(!attrName.empty()) { log<picLog::INPUT_OUTPUT> ("ADIOS: read attribute %1% for scalars: %2%") % attrName % name; *attribute = readAttribute<T_Attribute>(params.fp, datasetName, attrName); } }
void AdiosCheckpointInput::getVector(const std::string& var_name, vector<T>& buffer) { ADIOS_VARINFO* adios_inq = adios_inq_var(adios_file_handle, var_name.c_str()); //Check to make sure the T is the same size as the data type on the disk if (adios_type_size(adios_inq->type, NULL) != sizeof(T)) { qmcplusplus::app_error() << "Data type does not match data type found in file: " << std::endl; APP_ABORT("qmcapp"); return ; } uint64_t total_size = 1; for (int i = 0; i < adios_inq->ndim; i++) total_size *= adios_inq->dims[i]; //make sure we have enough space to copy all the data from the file buffer.reserve(total_size); //schedule the read adios_schedule_read(adios_file_handle, sel, var_name.c_str(), 0, 1, &(buffer[0])); //perform the read adios_perform_reads(adios_file_handle, 1); //Don't need the information about the variable anymore adios_free_varinfo(adios_inq); }
void adios_trace_verify_local_variables(ADIOS_FILE* fp, const char* name, double* origin) { ADIOS_VARINFO *vi; int count = 1; unsigned long size = 1; vi = adios_inq_var(fp, name); adios_inq_var_blockinfo(fp, vi); for (int j=0; j<vi->nblocks[0]; j++) { if(OHMMS::Controller->rank() == j) { for (int k=0; k<vi->ndim; k++) { count *= vi->blockinfo[j].count[k]; } } } size = count * adios_type_size(vi->type, vi->value); double* mem = (double*)malloc(size); ADIOS_SELECTION *sel = adios_selection_writeblock(OHMMS::Controller->rank()); adios_schedule_read(fp, sel, name, 0, 1, mem); adios_perform_reads(fp, 1); int flag = 0; for(int i=0; i<count; i++) { if(mem[i] == origin[i]) { } else { flag = 1; cout<<OHMMS::Controller->rank()<<" "<<name<<"["<<i<<"]verification not passed, readin: "<<mem[i]<<" writeout: "<<origin[i]<<endl; } } if(flag == 0) cout<<OHMMS::Controller->rank()<<" "<<name<<" verification passed"<<endl; adios_selection_delete(sel); adios_free_varinfo (vi); free(mem); }
void AdiosCheckpointInput::performReads() { for (int i = 0; i < read_queue.size(); i++) { const char* var_name = read_queue[i].c_str(); //grab the information from the metadata about this variable ADIOS_VARINFO* adios_inq = adios_inq_var(adios_file_handle, var_name); //Calculate the total size of the vector based on the metadata uint64_t total_size = adios_type_size(adios_inq->type, NULL); for (int i = 0; i < adios_inq->ndim; i++) total_size *= adios_inq->dims[i]; //allocate and then store for when retrieve void* buff = malloc(total_size); buffers.push_back(buff); //schedule the read adios_schedule_read(adios_file_handle, sel, var_name, 0, 1, buff); //Don't need the information about the variable anymore adios_free_varinfo(adios_inq); } //perform the read adios_perform_reads(adios_file_handle, 1); }
int main (int argc, char ** argv) { char filename [256]; int rank, size, i, j, k, token; MPI_Comm comm = MPI_COMM_WORLD; MPI_Status status; enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP; ADIOS_SELECTION * sel; void * data = NULL; uint64_t start[3], count[3], step = 0; MPI_Init (&argc, &argv); MPI_Comm_rank (comm, &rank); MPI_Comm_size (comm, &size); adios_read_init_method (method, comm, "verbose=3"); /* adios_read_open_file() allows for seeing all timesteps in the file */ ADIOS_FILE * f = adios_read_open_file ("adios_globaltime.bp", method, comm); if (f == NULL) { printf ("%s\n", adios_errmsg()); return -1; } ADIOS_VARINFO * v = adios_inq_var (f, "temperature"); // read in two timesteps data = malloc (2 * v->dims[0] * v->dims[1] * sizeof (double)); if (data == NULL) { fprintf (stderr, "malloc failed.\n"); return -1; } // read in timestep 'rank' (up to 12) step = rank % 13; start[0] = 0; count[0] = v->dims[0]; start[1] = 0; count[1] = v->dims[1]; /* Read a subset of the temperature array */ sel = adios_selection_boundingbox (v->ndim, start, count); /* 2 steps from 'step' */ adios_schedule_read (f, sel, "temperature", step, 2, data); adios_perform_reads (f, 1); if (rank == 0) printf ("Array size of temperature [0:%lld,0:%lld]\n", v->dims[0], v->dims[1]); if (rank > 0) { MPI_Recv (&token, 1, MPI_INT, rank-1, 0, comm, &status); } printf("------------------------------------------------\n", rank); printf("rank=%d: \n", rank); for (i = 0; i < 2; i++) { printf ("step %lld = [\n", step+i); for (j = 0; j < v->dims[0]; j++) { printf (" ["); for (k = 0; k < v->dims[1]; k++) { printf ("%g ", ((double *)data) [ i * v->dims[0] * v->dims[1] + j * v->dims[1] + k]); } printf ("]\n"); } printf ("]\n"); } printf ("\n"); if (rank < size-1) { MPI_Send (&token, 1, MPI_INT, rank+1, 0, comm); } free (data); adios_free_varinfo (v); adios_read_close (f); MPI_Barrier (comm); adios_read_finalize_method (method); MPI_Finalize (); return 0; }
int main (int argc, char ** argv) { int rank, size, i, j, npl, token; MPI_Comm comm = MPI_COMM_WORLD; MPI_Status status; enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP; ADIOS_SELECTION * sel; void * data = NULL; uint64_t start[1], count[1]; MPI_Init (&argc, &argv); MPI_Comm_rank (comm, &rank); MPI_Comm_size (comm, &size); adios_read_init_method (method, comm, "verbose=3"); ADIOS_FILE * f = adios_read_open ("adios_global_no_xml.bp", method, comm, ADIOS_LOCKMODE_NONE, 0); if (f == NULL) { printf ("%s\n", adios_errmsg()); return -1; } ADIOS_VARINFO * v = adios_inq_var (f, "temperature"); /* Using less readers to read the global array back, i.e., non-uniform */ uint64_t slice_size = v->dims[0]/size; start[0] = slice_size * rank; if (rank == size-1) /* last rank may read more lines */ slice_size = slice_size + v->dims[0]%size; count[0] = slice_size; data = malloc (slice_size * sizeof (double)); if (data == NULL) { fprintf (stderr, "malloc failed.\n"); return -1; } /* Read a subset of the temperature array */ sel = adios_selection_boundingbox (v->ndim, start, count); adios_schedule_read (f, sel, "temperature", 0, 1, data); adios_perform_reads (f, 1); if (rank > 0) { MPI_Recv (&token, 1, MPI_INT, rank-1, 0, comm, &status); } printf (" ======== Rank %d ========== \n", rank); npl = 10; for (i = 0; i < slice_size; i+=npl) { printf ("[%4.4" PRIu64 "] ", rank*slice_size+i); for (j= 0; j < npl; j++) { printf (" %6.6g", * ((double *)data + i + j)); } printf ("\n"); } fflush(stdout); sleep(1); if (rank < size-1) { MPI_Send (&token, 1, MPI_INT, rank+1, 0, comm); } free (data); adios_selection_delete (sel); adios_free_varinfo (v); adios_read_close (f); MPI_Barrier (comm); adios_read_finalize_method (method); MPI_Finalize (); return 0; }
int main (int argc, char **argv){ int rank =0, size =0; int NX = 0; double *t = NULL; // this is an array we expect as a reference array double *t_ref = NULL; MPI_Comm comm = MPI_COMM_WORLD; diag_t diag = DIAG_OK; // to store the diagnostic information struct test_info test_result = {TEST_PASSED, "1D_arr_global_noxml"}; struct err_counts err = { 0, 0}; struct adios_tsprt_opts adios_opts; GET_ENTRY_OPTIONS(adios_opts, "Runs readers. It is recommended to run as many readers as writers."); // adios read initialization MPI_Init( &argc, &argv); MPI_Comm_rank (comm, &rank); // depending on the method SET_ERROR_IF_NOT_ZERO(adios_read_init_method(adios_opts.method, comm, adios_opts.adios_options), err.adios); RET_IF_ERROR(err.adios, rank); // I will be working with streams so the lock mode is necessary, // return immediately if the stream unavailable ADIOS_FILE *adios_handle = adios_read_open(FILE_NAME, adios_opts.method, comm, ADIOS_LOCKMODE_NONE, 0.0); if ( !adios_handle){ p_error("Quitting ... (%d) %s\n", adios_errno, adios_errmsg()); return DIAG_ERR; } // define portions of data how they will be read ADIOS_SELECTION *sel = NULL; ADIOS_VARINFO *avi = NULL; // for storing the variables char buf[STR_BUFFER_SIZE]; int step = 0; // read how many processors wrote that array avi = adios_inq_var (adios_handle, "size"); if (!avi){ p_error("rank %d: Quitting ... (%d) %s\n", rank, adios_errno, adios_errmsg()); diag = DIAG_ERR; goto close_adios; } size = *((int*)avi->value); adios_free_varinfo(avi); avi = NULL; // if I run the more readers than writers; just release // the excessive readers if (rank >= size){ p_info("rank %d: I am an excessive rank. Nothing to read ...\n", rank); diag = DIAG_OK; goto close_adios; } // read the size of the array avi = adios_inq_var (adios_handle, "NX"); if (!avi){ p_error("rank %d: Quitting ... (%d) %s\n", rank, adios_errno, adios_errmsg()); diag = DIAG_ERR; goto close_adios; } // I expect a scalar that will tell me the size of an array assert(0 == avi->ndim); assert(adios_integer == avi->type); NX = *((int*)avi->value); // I don't need that variable any more adios_free_varinfo(avi); assert(NX_DIM == NX); avi = NULL; // this will define the slice that we want to read; each rank should // read its own slice written by a corresponding writer rank uint64_t count[1] = { NX }; uint64_t start[1] = { 0 }; start[0] = rank*NX; sel = adios_selection_boundingbox(1,start, count); if( !sel ){ p_error("rank %d: Quitting ... (%d) %s\n", rank, adios_errno, adios_errmsg()); diag = DIAG_ERR; goto close_adios; } // make the reference array with reference values I expect to get t_ref = calloc(NX, sizeof(double)); if (gen_1D_array(t_ref, NX, rank) == DIAG_ERR){ p_error("Generating 1D array. Quitting ...\n"); diag = DIAG_ERR; goto close_adios; } // allocate the memory for the actual array to be read t = calloc(NX, sizeof(double)); if (adios_schedule_read(adios_handle, sel, "var_1d_array",0,1,t) != 0){ p_error("rank %d: Quitting ...(%d) %s\n", rank, adios_errno, adios_errmsg()); diag = DIAG_ERR; goto just_clean; } // not sure if this assumption is correct; difficult to find in the ADIOS sources if (adios_perform_reads(adios_handle, 1) != 0){ p_error("rank %d: Quitting ...(%d) %s\n", rank, adios_errno, adios_errmsg()); diag = DIAG_ERR; goto just_clean; } sprintf(buf, "Rank %d: var_1d_array: step %d: t: ", rank, step); int i = 0; for(i=0; i < NX; ++i){ if( t[i] != t_ref[i] ){ p_test_failed("%s: rank %d: for t[%d] (expected %.1f, got %.1f)\n", test_result.name, rank, i, t_ref[i], t[i] ); test_result.result = TEST_FAILED; break; } } if (TEST_PASSED == test_result.result) p_test_passed("%s: rank %d\n", test_result.name, rank); just_clean: // clean everything adios_selection_delete(sel); sel = NULL; free(t); t = NULL; free(t_ref); t_ref = NULL; close_adios: CLOSE_ADIOS_READER(adios_handle, adios_opts.method); if ((DIAG_OK == diag) && (TEST_PASSED == test_result.result)) { return 0; } else { return 1; } }
int read_points () { ADIOS_SELECTION *sel0,*sel1,*sel2,*sel3; ADIOS_FILE * f; ADIOS_VARINFO * vi; int err=0,n,n1, i,j,k; int nsteps_a, nsteps_b, nsteps_c; int v; uint64_t *pts1; uint64_t *pts2; uint64_t *pts3; uint64_t start[3] = {offs1,offs2,offs3}; uint64_t count[3] = {ldim1,ldim2,ldim3}; pts1 = (uint64_t*) malloc (1*sizeof(uint64_t)*ldim1); pts2 = (uint64_t*) malloc (2*sizeof(uint64_t)*ldim1*ldim2); pts3 = (uint64_t*) malloc (3*sizeof(uint64_t)*ldim1*ldim2*ldim3); for (i=0; i<ldim1; i++) { pts1[i] = offs1 + i; for (j=0; j<ldim2; j++) { pts2[i*2*ldim2 + 2*j] = offs1 + i; pts2[i*2*ldim2 + 2*j+1] = j; for (k=0; k<ldim3; k++) { pts3[i*3*ldim2*ldim3+j*3*ldim3+3*k] = offs1 + i; pts3[i*3*ldim2*ldim3+j*3*ldim3+3*k+1] = j; pts3[i*3*ldim2*ldim3+j*3*ldim3+3*k+2] = k; } } } //Force error on very last point: pts3[3*ldim1*ldim2*ldim3-1] = 0; reset_readvars(); log ("Read and check data in %s using point selections\n", FILENAME); f = adios_read_open (FILENAME, read_method, comm, ADIOS_LOCKMODE_CURRENT, 0.0); if (f == NULL) { printE ("Error at opening file: %s\n", rank, adios_errmsg()); return 1; } sel1 = adios_selection_points (1, ldim1, pts1); sel2 = adios_selection_points (2, ldim1*ldim2, pts2); sel3 = adios_selection_points (3, ldim1*ldim2*ldim3, pts3); #ifdef DEBUG_PRINTS fprintf(stderr, "1D selection: {"); for (i=0; i<ldim1; i++) { fprintf (stderr, "%d ", i, i, pts1[i]); } fprintf(stderr, "}\n"); fprintf(stderr, "2D selection :\n"); for (i=0; i<ldim1; i++) { fprintf (stderr, "i=%d, idx=%2d- = ", i, i*2*ldim2); for (j=0; j<ldim2; j++) { n = i*2*ldim2+2*j; fprintf (stderr, "{%d,%d} ", pts2[n], pts2[n+1]); } fprintf(stderr, "\n"); } fprintf(stderr, "3D selection :\n"); for (i=0; i<ldim1; i++) { for (j=0; j<ldim2; j++) { fprintf (stderr, "i=%d, j=%d, idx=%3d- = ", i, j, i*3*ldim2*ldim3+j*3*ldim3); for (k=0; k<ldim3; k++) { n = i*3*ldim2*ldim3+j*3*ldim3+3*k; fprintf (stderr, "{%d,%d,%d} ", pts3[n], pts3[n+1], pts3[n+2]); } fprintf(stderr, "\n"); } } #endif n1=0; while (n1 < NSTEPS && adios_errno != err_end_of_stream) { n1++; log (" Step %d\n", f->current_step); log (" Check 1D variable a1...\n"); adios_schedule_read (f, sel1, "a1", 0, 1, r1); adios_perform_reads (f, 1); #ifdef DEBUG_PRINTS fprintf(stderr, "1D result: {"); for (i=0; i<ldim1; i++) { fprintf (stderr, "%d ", i, i, r1[i]); } fprintf(stderr, "}\n"); #endif for (i=0; i<ldim1; i++) { v = VALUE1D(rank,f->current_step,i); if (r1[i] != v) { printE ("Error: a1[%d]=%d != read=%d\n", i, v, r1[i]); //goto endread; } } log (" Check 2D variable a2...\n"); adios_schedule_read (f, sel2, "a2", 0, 1, r2); adios_perform_reads (f, 1); #ifdef DEBUG_PRINTS fprintf(stderr, "2D result :\n"); n = 0; for (i=0; i<ldim1; i++) { fprintf (stderr, "row=%2d- = {", i); for (j=0; j<ldim2; j++) { fprintf (stderr, "%d ", r2[n]); n++; } fprintf(stderr, "}\n"); } #endif n = 0; for (i=0; i<ldim1; i++) { for (j=0; j<ldim2; j++) { v = VALUE2D(rank,f->current_step,i,j); if (v != r2[n]) { printE ("Error: a2[%d,%d]=%d != read=%d\n", i, j, v, r2[n]); //goto endread; } n++; } } log (" Check 3D variable a3...\n"); adios_schedule_read (f, sel3, "a3", 0, 1, r3); adios_perform_reads (f, 1); #ifdef DEBUG_PRINTS fprintf(stderr, "3D selection :\n"); n=0; for (i=0; i<ldim1; i++) { for (j=0; j<ldim2; j++) { fprintf (stderr, "[%d,%d] = {", i, j); for (k=0; k<ldim3; k++) { fprintf (stderr, "%d ", r3[n]); n++; } fprintf(stderr, "}\n"); } } #endif n = 0; for (i=0; i<ldim1; i++) { for (j=0; j<ldim2; j++) { for (k=0; k<ldim3; k++) { v = VALUE3D(rank,f->current_step,i,j,k); if (v != r3[n]) { printE ("Error: a3[%d,%d,%d]=%d != read=%d\n", i, j, k, v, r3[n]); //goto endread; } n++; } } } if (n1 < NSTEPS) { adios_advance_step (f, 0, -1.0); } } endread: adios_selection_delete (sel1); adios_selection_delete (sel2); adios_selection_delete (sel3); free(pts1); free(pts2); free(pts3); adios_read_close(f); MPI_Barrier (comm); return err; }
int main (int argc, char ** argv) { int rank, j; int NX, NY; double *t; MPI_Comm comm = MPI_COMM_WORLD; MPI_Init (&argc, &argv); MPI_Comm_rank (comm, &rank); adios_read_init_method(ADIOS_READ_METHOD_FLEXPATH, comm, ""); ADIOS_SELECTION *global_range_select; ADIOS_SELECTION scalar_block_select; scalar_block_select.type = ADIOS_SELECTION_WRITEBLOCK; scalar_block_select.u.block.index = 0; /* schedule_read of a scalar. */ int test_scalar = -1; ADIOS_FILE* afile = adios_read_open("arrays", ADIOS_READ_METHOD_FLEXPATH, comm, ADIOS_LOCKMODE_NONE, 0.0); int i; for(i=0; i<afile->nvars; i++){ printf("var: %s\n", afile->var_namelist[i]); } int ii = 0; while(adios_errno != err_end_of_stream){ /* get a bounding box - rank 0 for now*/ ADIOS_VARINFO *nx_info = adios_inq_var( afile, "/scalar/dim/NX"); ADIOS_VARINFO *ny_info = adios_inq_var( afile, "/scalar/dim/NY"); ADIOS_VARINFO *size_info = adios_inq_var( afile, "size"); ADIOS_VARINFO *arry = adios_inq_var( afile, "var_2d_array"); int nx_val = *((int*)nx_info->value); int ny_val = *((int*)ny_info->value); int size_val = *((int*)size_info->value); printf("nx: %d, ny: %d, size: %d\n", nx_val, ny_val, size_val); uint64_t xcount = arry->dims[0]; uint64_t ycount = arry->dims[1]; uint64_t starts[] = {0,0}; uint64_t counts[] = {xcount, ycount}; global_range_select = adios_selection_boundingbox(2, starts, counts); int nelem = xcount*ycount; if(nx_info->value) { NX = *((int *)nx_info->value); } if(ny_info->value){ NY= *((int*)ny_info->value); } if(rank == 0){ int n; printf("dims: [ "); for(n=0; n<arry->ndim; n++){ printf("%d ", (int)arry->dims[n]); } printf("]\n"); } /* Allocate space for the arrays */ int arr_size = sizeof(double) * nelem; t = (double *) malloc (arr_size); memset(t, 0, arr_size); //fprintf(stderr, "t %p\n", t); /* Read the arrays */ adios_schedule_read (afile, global_range_select, "var_2d_array", 0, 1, t); adios_schedule_read (afile, &scalar_block_select, "test_scalar", 0, 1, &test_scalar); adios_perform_reads (afile, 1); //sleep(20); printf("Rank=%d: test_scalar: %d step: %d, t[0,5+x] = [", rank, test_scalar, ii); for(j=0; j<nelem; j++) { printf(", %6.2f", t[j]); } printf("]\n\n"); adios_release_step(afile); adios_advance_step(afile, 0, 30); ii++; //MPI_Barrier (comm); //sleep(1); } // adios_read_close(afile); adios_read_finalize_method(ADIOS_READ_METHOD_FLEXPATH); MPI_Finalize (); return 0; }
int main (int argc, char ** argv) { char filename [256] = "stream.bp"; int rank, size; int NX, NY; int len, off; double *t = NULL; MPI_Comm comm = MPI_COMM_WORLD; int64_t adios_handle; uint64_t adios_groupsize, adios_totalsize; uint64_t start[2], count[2]; ADIOS_SELECTION *sel; int steps = 0; MPI_Init (&argc, &argv); MPI_Comm_rank (comm, &rank); MPI_Comm_size (comm, &size); // ADIOS read init adios_read_init_method (ADIOS_READ_METHOD_BP, comm, "verbose=3"); ADIOS_FILE* fp = adios_read_open_file ("kstar.bp", ADIOS_READ_METHOD_BP, comm); assert(fp != NULL); ADIOS_VARINFO* nx_info = adios_inq_var( fp, "N"); ADIOS_VARINFO* ny_info = adios_inq_var( fp, "L"); NX = *((int *)nx_info->value); NY= *((int*)ny_info->value); len = NX / size; off = len * rank; if (rank == size-1) len = len + NX % size; printf("\trank=%d: NX,NY,len,off = %d\t%d\t%d\t%d\n", rank, NX, NY, len, off); assert(len > 0); t = (double *) malloc(sizeof(double) * len * NY); memset(t, '\0', sizeof(double) * len * NY); assert(t != NULL); start[0] = off; start[1] = 0; count[0] = len; count[1] = NY; sel = adios_selection_boundingbox (2, start, count); // ADIOS write init adios_init ("adios.xml", comm); remove (filename); //int ii; //for(ii = 0; ii<10; ii++){ // for (i = 0; i < len * NY; i++) // t[i] = ii*1000 + rank; while(adios_errno != err_end_of_stream && adios_errno != err_step_notready) { steps++; // Reading adios_schedule_read (fp, sel, "var", 0, 1, t); adios_perform_reads (fp, 1); // Debugging //for (i = 0; i < len*NY; i++) t[i] = off * NY + i; printf("step=%d\trank=%d\t[%d,%d]\n", steps, rank, len, NY); // Writing adios_open (&adios_handle, "writer", filename, "a", comm); adios_groupsize = 4*4 + 8*len*NY; adios_group_size (adios_handle, adios_groupsize, &adios_totalsize); adios_write (adios_handle, "NX", &NX); adios_write (adios_handle, "NY", &NY); adios_write (adios_handle, "len", &len); adios_write (adios_handle, "off", &off); adios_write (adios_handle, "var_2d_array", t); adios_close (adios_handle); // Advance MPI_Barrier (comm); adios_advance_step(fp, 0, TIMEOUT_SEC); } free(t); MPI_Barrier (comm); adios_read_close(fp); if (rank==0) printf ("We have processed %d steps\n", steps); MPI_Barrier (comm); adios_read_finalize_method(ADIOS_READ_METHOD_BP); adios_finalize (rank); MPI_Finalize (); return 0; }
int main(int argc, char ** argv) { int rank, size, varid, numvars; int bins, step, mod; char *filename, *in_stream, *data_var_name; MPI_Comm comm = MPI_COMM_WORLD; enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_FLEXPATH; //enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP; ADIOS_SELECTION * global_range_select; double *data; uint64_t tstep, global_size, mysize, mystart, sz; MPI_Init (&argc, &argv); MPI_Comm_rank(comm, &rank); MPI_Comm_size(comm, &size); /* Command line parsing */ if (rank == 0 && argc < 4) { fprintf(stderr, "\nHistogram usage: <exec> input-stream-name num-bins" " arr1 [arr2] [arr3] [...]\n" "\t where arr1, arr2, arr3 ... are the names of the arrays to be analyzed.\n"); MPI_Abort(comm, -1); } MPI_Barrier(comm); in_stream = argv[1]; //Parse cmd line bins = atoi(argv[2]); numvars = argc - 3; const char *vars[numvars]; for (varid=0; varid < numvars; varid++) { vars[varid] = argv[varid + 3]; } /* Adios open and init */ adios_read_init_method (method, comm, "verbose=1"); ADIOS_FILE * f = adios_read_open (in_stream, method, comm, ADIOS_LOCKMODE_ALL, -1); step = 0; //not used now while (adios_errno != err_end_of_stream){ //resource monitor /*loop over different arrays inside stream*/ for (varid = 0; varid < numvars; varid++){ #ifdef ENABLE_MONITOR //double t1 = wfgettimeofday(); lib_mem_init(); ind_timer_start(0, "whole timestep"); #endif //Init variables.... global_size = 0; tstep = 0; mod = 0; mysize = 0; mystart = 0; adios_schedule_read (f, NULL, "ntimestep", 0, 1, &tstep); adios_perform_reads (f, 1); ADIOS_VARINFO * glob_info = adios_inq_var (f, vars[varid]); global_size = glob_info->dims[0]; //printf("[DEBUG] global_size = %" PRIu64 " ntimestep = %" PRIu64 "\n", // global_size, tstep); //printf("[HIST%d] received data for timestep %" PRIu64 " with ndim: %d and globalsize:%" // PRIu64 " \n", rank, tstep, ndim, global_size); //sleep(800); //debug //Array slice computation mod = global_size % size;//size = MPI size if (mod == 0){ mysize = global_size / size; mystart = mysize * rank; } else { mysize = global_size / (size); if (rank < mod){ mysize++; mystart = mysize * rank; } else { mystart = (mod * (mysize + 1)) + ((rank - mod) * mysize); } } #ifdef ENABLE_MONITOR nohandler_mem(rank); #endif //printf("[HISTO%d]: mysize = %" PRIu64" mystart = %" PRIu64 "\n", rank, mysize, mystart); //debug //if (step == 0) sleep(800); uint64_t starts[] = {mystart}; uint64_t counts[] = {mysize}; global_range_select = adios_selection_boundingbox (1, starts, counts); //Allocate space for arrays uint64_t msize = ((uint64_t) sizeof(double) * mysize); //printf("[DEBUG] mysize = %" PRIu64 " msize= %" PRIu64" \n", mysize, msize); //data = (double *) malloc(sizeof(double) * mysize); data = new double[mysize]; if (data == NULL){ //printf("DEBUG: malloc returned NULL, size was %d\n", msize); } else { if (rank == 0) printf("[HIST0] DEBUG: malloc successful, size was %d\n", mysize); } //memset (data, 0, sizeof(double) * mysize); //Read data adios_schedule_read (f, global_range_select, vars[varid], 0, 1, data); adios_perform_reads (f, 1); #ifdef ENABLE_MONITOR nohandler_mem(rank); #endif //printf("PERFORM_READS success of variable: %s\n", vars[varid]); /* Data check if (step == 4) { FILE *fp; char *log; asprintf(&log, "histo-input%d-%d.log", step, rank); fp = fopen(log, "w"); fprintf(fp, "timestep: %" PRIu64 " mysize: %"PRIu64 "\n", tstep, mysize); for (i=0; i<(int)mysize; i++){ fprintf(fp, "%lf\n", data[i]); } fclose(fp); sleep(800); } */ // find max and min sz = 0; sz = mysize; double min = data[0]; double max = data[0]; for (uint64_t i = 1; i < sz; ++i) { if (data[i] > max) max = data[i]; if (data[i] < min) min = data[i]; }//local max, min found. //local data should just use shared mem. double g_min, g_max; // Find the global max/min MPI_Allreduce (&min, &g_min, 1, MPI_DOUBLE, MPI_MIN, comm); MPI_Allreduce (&max, &g_max, 1, MPI_DOUBLE, MPI_MAX, comm); //printf("[HIST%d] glob-min: %f, glob-max: %f\n", rank, g_min, g_max); nohandler_mem(rank); double width = (g_max - g_min)/bins; std::vector<uint64_t> hist(bins); for (uint64_t i = 0; i < sz; ++i)//fill local bins { //printf("[HISTO%d] local filling adding index %" PRIu64 "\n", rank, i); int idx = int((data[i] - g_min)/width);//discover index if (idx == bins) // we hit the max --idx; //printf("[%d]: %f -> %d\n", rank, data[i], idx); ++hist[idx]; } delete[] data; // Global reduce histograms std::vector<uint64_t> g_hist(bins); MPI_Reduce(&hist[0], &g_hist[0], bins, MPI_UINT64_T, MPI_SUM, 0, comm); //debug //printf("[Completed histogram routine]\n"); if (rank == 0) //print histogram to file { FILE *fp; const char *log = "histograms.log"; fp = fopen(log, "a"); fprintf(fp, "Histogram for %s, timestep %" PRIu64"\n", vars[varid], tstep); for (int i = 0; i < bins; ++i) fprintf(fp, " %f-%f: %" PRIu64 "\n", g_min + i*width, g_min + (i+1)*width, g_hist[i]); fclose (fp); } #ifdef ENABLE_MONITOR nohandler_mem(rank); #endif if (rank == 0) //print histogram to terminal { printf("Histogram for %s, timestep %" PRIu64"\n", vars[varid], tstep); for (int i = 0; i < bins; ++i) printf(" %f-%f: %" PRIu64 "\n", g_min + i*width, g_min + (i+1)*width, g_hist[i]); } //resource monitor #ifdef ENABLE_MONITOR //double t2 = wfgettimeofday(); ind_timer_end(0); char monitor_title[40]; sprintf(monitor_title, "histogram-%s", vars[varid]); monitor_out (rank, size, tstep, msize, t1, t2, comm, monitor_title); #endif } //end of read + analysis for 3 variables adios_release_step(f); //delete[] data; if (rank == 0) printf("[HIST%d] read and wrote data for timestep %" PRIu64 "\n", rank, tstep); step++; adios_advance_step(f, 0, -1); /* if (step == 6){ double t1 = wfgettimeofday(); FILE *tfp; tfp = fopen("time.log", "a"); fprintf(tfp, "rank %d histogram end time: %f\n", rank, t1); fclose(tfp); } */ }//end of adios stream while loop if (rank == 0) printf("[HIST%d] out of read loop\n", rank); /* performance measurement */ /* if (rank == 0){ double t3 = wfgettimeofday(); FILE *tfp; tfp = fopen("time.log", "a"); fprintf(tfp, "master histogram end time: %f\n", t3); fclose(tfp); } */ #ifdef ENABLE_MONITOR outer_timer_end(rank, "histogram"); #endif adios_read_close(f); adios_read_finalize_method(method); MPI_Finalize(); return 0; }
void performQuery(ADIOS_QUERY_TEST_INFO *queryInfo, ADIOS_FILE *f, int use_streaming, int print_points, int read_results) { int timestep = 0 ; ADIOS_VARINFO * tempVar = adios_inq_var(f, queryInfo->varName); if (use_streaming) for (timestep = 0; timestep < queryInfo->fromStep; ++timestep) assert(adios_advance_step(f, 0, 0) == 0); fprintf(stderr,"times steps for variable is: [%d, %d], batch size is %" PRIu64 "\n", queryInfo->fromStep, queryInfo->fromStep + queryInfo->numSteps, queryInfo->batchSize); for (timestep = queryInfo->fromStep; timestep < queryInfo->fromStep + queryInfo->numSteps; timestep ++) { fprintf(stderr, "querying on timestep %d \n", timestep); ADIOS_SELECTION* currBatch = NULL; while (adios_query_evaluate(queryInfo->query, queryInfo->outputSelection, use_streaming ? 0 : timestep, queryInfo->batchSize, &currBatch) >= 0) { if (currBatch == NULL) { break; } assert(currBatch->type ==ADIOS_SELECTION_POINTS); const ADIOS_SELECTION_POINTS_STRUCT * retrievedPts = &(currBatch->u.points); /* fprintf(stderr,"retrieved points %" PRIu64 " \n", retrievedPts->npoints); */ if (print_points) { printPoints(retrievedPts, timestep); } if (read_results) { int elmSize = adios_type_size(tempVar->type, NULL); void *data = malloc(retrievedPts->npoints * elmSize); // read returned temp data adios_schedule_read (f, currBatch, queryInfo->varName, use_streaming ? 0 : timestep, 1, data); adios_perform_reads(f, 1); free(data); } fprintf(stderr,"Total data retrieved:%"PRIu64"\n", retrievedPts->npoints); /* if (tempVar->type == adios_double) { */ /* for (i = 0; i < retrievedPts->npoints; i++) { */ /* fprintf(stderr,"%.6f\t", ((double*)data)[i]); */ /* } */ /* fprintf(stderr,"\n"); */ /* } */ /* else if (tempVar->type == adios_real) { */ /* for (i = 0; i < retrievedPts->npoints; i++) { */ /* fprintf(stderr,"%.6f\t", ((float*)data)[i]); */ /* } */ /* fprintf(stderr,"\n"); */ /* } */ adios_selection_delete(currBatch); currBatch = NULL; } if (use_streaming) { const int err = adios_advance_step(f, 0, 0); if (timestep < queryInfo->fromStep + queryInfo->numSteps - 1) { assert(err == 0); } else { assert(err == err_end_of_stream || err == err_step_notready); } } } adios_query_free(queryInfo->query); }
int main (int argc, char ** argv) { char filename [256]; int rank; MPI_Comm comm = MPI_COMM_WORLD; enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP; ADIOS_SELECTION * sel1=NULL; int8_t v1 = 0; int16_t v2 = 0; int32_t v3 = 0; int64_t v4 = 0; uint8_t v5 = 0; uint16_t v6 = 0; uint32_t v7 = 0; uint64_t v8 = 0; float v9 = 0.0; double v10 = 0.0; char v11[256]; complex v12; v12.r = 0.0; v12.i = 0.0; double_complex v13; v13.r = 0.0; v13.i = 0.0; MPI_Init (&argc, &argv); MPI_Comm_rank (comm, &rank); strcpy (filename, "scalars.bp"); adios_read_init_method (method, comm, "verbose=3"); ADIOS_FILE * f = adios_read_open (filename, method, comm, ADIOS_LOCKMODE_NONE, 0.0); adios_schedule_read (f, sel1, "var_byte", 0, 1, &v1); adios_schedule_read (f, sel1, "var_short", 0, 1, &v2); adios_schedule_read (f, sel1, "var_int", 0, 1, &v3); adios_schedule_read (f, sel1, "var_long", 0, 1, &v4); adios_schedule_read (f, sel1, "var_ubyte", 0, 1, &v5); adios_schedule_read (f, sel1, "var_ushort", 0, 1, &v6); adios_schedule_read (f, sel1, "var_uint", 0, 1, &v7); adios_schedule_read (f, sel1, "var_ulong", 0, 1, &v8); adios_schedule_read (f, sel1, "var_real", 0, 1, &v9); adios_schedule_read (f, sel1, "var_double", 0, 1, &v10); /* note that a string is an array and thus v11 a pointer already, so we pass the v11 instead of &v11 here */ adios_schedule_read (f, sel1, "var_string", 0, 1, v11); adios_schedule_read (f, sel1, "var_complex", 0, 1, &v12); adios_schedule_read (f, sel1, "var_double_complex", 0, 1, &v13); adios_perform_reads (f,1); if (rank == 0) { printf("byte v1 = %d\n", v1); printf("short v2 = %d\n", v2); printf("integer v3 = %d\n", v3); printf("long v4 = %" PRId64 "\n", v4); printf("uns.byte v5 = %u\n", v5); printf("uns.short v6 = %u\n", v6); printf("uns.int v7 = %u\n", v7); printf("uns.long v8 = %" PRIu64 "\n", v8); printf("float v9 = %g\n", v9); printf("double v10 = %g\n", v10); printf("string v11 = %s\n", v11); printf("complex v12 = (%g, i%g)\n", v12.r, v12.i); printf("dbl-complex v13 = (%g, i%g)\n", v13.r, v13.i); } adios_read_close (f); MPI_Barrier (comm); adios_read_finalize_method (ADIOS_READ_METHOD_BP); MPI_Finalize (); return 0; }
int main (int argc, char ** argv) { int rank, size; int NX, NY; int len, off; double *t = NULL; MPI_Comm comm = MPI_COMM_WORLD; uint64_t start[2], count[2]; ADIOS_SELECTION *sel; int steps = 0; #ifdef _USE_GNUPLOT int i, j; double *tmp; FILE *pipe; #else // Variables for ADIOS write int64_t adios_handle; uint64_t adios_groupsize, adios_totalsize; char outfn[256]; #endif MPI_Init (&argc, &argv); MPI_Comm_rank (comm, &rank); MPI_Comm_size (comm, &size); adios_read_init_method(ADIOS_READ_METHOD_FLEXPATH, comm, ""); ADIOS_FILE* fp = adios_read_open("stream.bp", ADIOS_READ_METHOD_FLEXPATH, comm, ADIOS_LOCKMODE_NONE, 0.0); assert(fp != NULL); ADIOS_VARINFO* nx_info = adios_inq_var( fp, "NX"); ADIOS_VARINFO* ny_info = adios_inq_var( fp, "NY"); NX = *((int *)nx_info->value); NY= *((int*)ny_info->value); len = NX / size; off = len * rank; if (rank == size-1) len = len + NX % size; printf("\trank=%d: NX,NY,len,off = %d\t%d\t%d\t%d\n", rank, NX, NY, len, off); assert(len > 0); t = (double *) malloc(sizeof(double) * len * NY); memset(t, '\0', sizeof(double) * len * NY); assert(t != NULL); start[0] = off; start[1] = 0; count[0] = len; count[1] = NY; // Not working ... //sel = adios_selection_boundingbox (2, start, count); sel = malloc(sizeof(ADIOS_SELECTION)); sel->type=ADIOS_SELECTION_WRITEBLOCK; sel->u.block.index = rank; #ifdef _USE_GNUPLOT if ((NX % size) > 0) { fprintf(stderr, "Equal distribution is required\n"); return -1; } if (rank == 0) { pipe = popen("gnuplot", "w"); fprintf(pipe, "set view map\n"); fprintf(pipe, "set xrange [0:%d]\n", NX-1); tmp = (double *) malloc(sizeof(double) * NX * NY); assert(tmp != NULL); } #else // ADIOS write init adios_init ("adios.xml", comm); #endif //while(adios_errno != err_end_of_stream && adios_errno != err_step_notready) while(1) { steps++; // Reading adios_schedule_read (fp, sel, "var_2d_array", 0, 1, t); adios_perform_reads (fp, 1); printf("step=%d\trank=%d\tfp->current_step=%d\t[%d,%d]\n", steps, rank, fp->current_step, len, NY); /* // Debugging for (i=0; i<len; i++) { printf("%d: rank=%d: t[%d,0:4] = ", steps, rank, off+i); for (j=0; j<5; j++) { printf(", %g", t[i*NY + j]); } printf(" ...\n"); } */ // Do something #ifdef _USE_GNUPLOT // Option 1: plotting MPI_Gather(t, len * NY, MPI_DOUBLE, tmp, len * NY, MPI_DOUBLE, 0, comm); if (rank == 0) { fprintf(pipe, "set title 'Soft X-Rray Signal (shot #%d)'\n", steps); fprintf(pipe, "set xlabel 'Channel#'\n"); fprintf(pipe, "set ylabel 'Timesteps'\n"); fprintf(pipe, "set cblabel 'Voltage (eV)'\n"); # ifndef _GNUPLOT_INTERACTIVE fprintf(pipe, "set terminal png\n"); fprintf(pipe, "set output 'fig%03d.png'\n", steps); # endif fprintf(pipe, "splot '-' matrix with image\n"); //fprintf(pipe, "plot '-' with lines, '-' with lines, '-' with lines\n"); double *sum = calloc(NX, sizeof(double)); for (j = 0; j < NY; j++) { for (i = 0; i < NX; i++) { sum[i] += tmp[i * NY + j]; } } for (j = 0; j < NY; j++) { for (i = 0; i < NX; i++) { fprintf (pipe, "%g ", (-tmp[i * NY + j] + sum[i]/NY)/3276.8); } fprintf(pipe, "\n"); } fprintf(pipe, "e\n"); fprintf(pipe, "e\n"); fflush (pipe); # ifdef _GNUPLOT_INTERACTIVE printf ("Press [Enter] to continue . . ."); fflush (stdout); getchar (); # endif free(sum); } #else // Option 2: BP writing snprintf (outfn, sizeof(outfn), "reader_%3.3d.bp", steps); adios_open (&adios_handle, "reader", outfn, "w", comm); adios_groupsize = 4 * sizeof(int) + sizeof(double) * len * NY; adios_group_size (adios_handle, adios_groupsize, &adios_totalsize); adios_write (adios_handle, "NX", &NX); adios_write (adios_handle, "NY", &NY); adios_write (adios_handle, "len", &len); adios_write (adios_handle, "off", &off); adios_write (adios_handle, "var", t); adios_close (adios_handle); #endif // Advance MPI_Barrier (comm); adios_advance_step(fp, 0, TIMEOUT_SEC); if (adios_errno == err_end_of_stream) { printf("rank %d, Stream terminated. Quit\n", rank); break; // quit while loop } else if (adios_errno == err_step_notready) { printf ("rank %d: No new step arrived within the timeout. Quit.\n", rank); break; // quit while loop } else if (adios_errno != err_no_error) { printf("ADIOS returned code=%d, msg:%s\n", adios_errno, adios_get_last_errmsg()); break; // quit while loop } } // free(t); adios_read_close(fp); //printf("rank %d, Successfully closed stream\n", rank); adios_read_finalize_method(ADIOS_READ_METHOD_FLEXPATH); //printf("rank %d, Successfully finalized read method\n", rank); #ifndef _USE_GNUPLOT adios_finalize (rank); //printf("rank %d, Successfully finalized adios\n", rank); #else if (rank==0) { free(tmp); pclose(pipe); } #endif MPI_Finalize (); return 0; }
int main (int argc, char ** argv) { /* application data structures */ int rank; int NX, NY; double *t; int *p; /* MPI and ADIOS data structures */ MPI_Comm comm = MPI_COMM_WORLD; /* MPI and ADIOS setup */ MPI_Init (&argc, &argv); MPI_Comm_rank (comm, &rank); adios_read_init_method(ADIOS_READ_METHOD_FLEXPATH, comm, ""); /* First read in the scalars to calculate the size of the arrays */ /* get everything from single process - rank 0 for now*/ ADIOS_SELECTION process_select; process_select.type=ADIOS_SELECTION_WRITEBLOCK; process_select.u.block.index = rank; /* read the size of arrays using local inq_var */ /* Note: at this moment, timeout is not handled. It blocks until writer appears */ ADIOS_FILE* afile = adios_read_open("arrays", ADIOS_READ_METHOD_FLEXPATH, comm, ADIOS_LOCKMODE_NONE, 30.0); /* Read arrays for each time step */ while(adios_errno != err_end_of_stream){ ADIOS_VARINFO* nx_info = adios_inq_var( afile, "NX"); if(nx_info->value) { NX = *((int *)nx_info->value); } ADIOS_VARINFO* ny_info = adios_inq_var( afile, "NY"); if(ny_info->value) { NY = *((int *)ny_info->value); } /* Allocate space for the arrays */ t = (double *) malloc (NX*NY*sizeof(double)); p = (int *) malloc (NX*sizeof(int)); memset(t, 0, NX*NY*sizeof(double)); memset(p, 0, NX*sizeof(int)); /* schedule a read of the arrays */ adios_schedule_read (afile, &process_select, "var_double_2Darray", 0, 1, t); adios_schedule_read (afile, &process_select, "var_int_1Darray", 0, 1, p); /* commit request and retrieve data */ adios_perform_reads (afile, 1); /* print result */ printf("Results Rank=%d Step=%d p[] = [%d, %d,...] t[][] = [%.2f, %.2f]\n", rank, afile->current_step, p[0], p[1], t[0], t[1]); /* block until next step is available (30 sec timeout unsupported) */ adios_release_step(afile); adios_advance_step(afile, 0, 30); MPI_Barrier (comm); /* shutdown ADIOS and MPI */ } adios_read_close(afile); /* wait until all readers finish */ adios_read_finalize_method(ADIOS_READ_METHOD_FLEXPATH); MPI_Finalize (); return 0; }
int main (int argc, char ** argv) { int i, j, datasize; MPI_Comm comm = MPI_COMM_WORLD; enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP; ADIOS_SELECTION * sel1; double * data = NULL; uint64_t start[2], count[2]; MPI_Init (&argc, &argv); #ifdef WITH_NCSU_TIMER timer_init(); #endif adios_read_init_method (method, comm, NULL); ADIOS_FILE * f = adios_read_open_file ("adios_global.bp", method, comm); ADIOS_VARINFO * varinfo = adios_inq_var (f, "temperature"); if (varinfo) { int nranks; assert(varinfo->ndim == 2); nranks = varinfo->dims[0]; assert(nranks % 4 == 0); assert(varinfo->dims[1] == 10); datasize = (nranks / 2) * varinfo->dims[1] * sizeof(double); data = malloc (datasize); start[0] = nranks / 4; start[1] = 2; count[0] = nranks / 2; count[1] = 6; sel1 = adios_selection_boundingbox (varinfo->ndim, start, count); adios_schedule_read (f, sel1, "temperature", 0, 1, data); adios_perform_reads (f, 1); printf("Subvolume at (%" PRIu64 ",%" PRIu64 ") of size (%" PRIu64 ",%" PRIu64 "):\n", start[0], start[1], count[0], count[1]); for (i = 0; i < count[0]; i++) { printf("[ "); for (j = 0; j < count[1]; j++) { printf("%.0lf ", data[i * count[1] + j]); } printf("]\n"); } adios_selection_delete (sel1); } adios_free_varinfo (varinfo); adios_read_close (f); adios_read_finalize_method (ADIOS_READ_METHOD_BP); #ifdef WITH_NCSU_TIMER printf("[TIMERS] "); timer_result_t *results = timer_get_results_sorted(); for (i = 0; i < timer_get_num_timers(); i++) { printf("%s: %0.4lf ", results[i].name, results[i].time); } printf("\n"); free(results); #endif #ifdef WITH_NCSU_TIMER timer_finalize(); #endif MPI_Finalize (); return 0; }
int worker(int argc, char* argv[]) { TAU_PROFILE_TIMER(timer, __func__, __FILE__, TAU_USER); TAU_PROFILE_START(timer); my_printf("%d of %d In worker B\n", myrank, commsize); static bool announced = false; /* validate input */ validate_input(argc, argv); my_printf("Worker B will execute until it sees n iterations.\n", iterations); /* ADIOS: These declarations are required to match the generated * gread_/gwrite_ functions. (And those functions are * generated by calling 'gpp.py adios_config.xml') ... * EXCEPT THAT THE generation of Reader code is broken. * So, we will write the reader code manually. */ uint64_t adios_groupsize; uint64_t adios_totalsize; uint64_t adios_handle; void * data = NULL; uint64_t start[2], count[2]; int i, j, steps = 0; int NX = 10; int NY = 1; double t[NX]; double p[NX]; /* ADIOS: Can duplicate, split the world, whatever. * This allows you to have P writers to N files. * With no splits, everyone shares 1 file, but * can write lock-free by using different areas. */ MPI_Comm adios_comm, adios_comm_b_to_c; adios_comm = MPI_COMM_WORLD; //MPI_Comm_dup(MPI_COMM_WORLD, &adios_comm); adios_comm_b_to_c = MPI_COMM_WORLD; //MPI_Comm_dup(MPI_COMM_WORLD, &adios_comm_b_to_c); enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_FLEXPATH; adios_read_init_method(method, adios_comm, "verbose=3"); if (adios_errno != err_no_error) { fprintf (stderr, "rank %d: Error %d at init: %s\n", myrank, adios_errno, adios_errmsg()); exit(4); } if (send_to_c) { adios_init("adios_config.xml", adios_comm); } /* ADIOS: Set up the adios communications and buffers, open the file. */ ADIOS_FILE *fp; // file handler ADIOS_VARINFO *vi; // information about one variable ADIOS_SELECTION * sel; char adios_filename_a_to_b[256]; char adios_filename_b_to_c[256]; enum ADIOS_LOCKMODE lock_mode = ADIOS_LOCKMODE_NONE; double timeout_sec = 1.0; sprintf(adios_filename_a_to_b, "adios_a_to_b.bp"); sprintf(adios_filename_b_to_c, "adios_b_to_c.bp"); my_printf ("rank %d: Worker B opening file: %s\n", myrank, adios_filename_a_to_b); fp = adios_read_open(adios_filename_a_to_b, method, adios_comm, lock_mode, timeout_sec); if (adios_errno == err_file_not_found) { fprintf (stderr, "rank %d: Stream not found after waiting %d seconds: %s\n", myrank, timeout_sec, adios_errmsg()); exit(1); } else if (adios_errno == err_end_of_stream) { // stream has been gone before we tried to open fprintf (stderr, "rank %d: Stream terminated before open. %s\n", myrank, adios_errmsg()); exit(2); } else if (fp == NULL) { // some other error happened fprintf (stderr, "rank %d: Error %d at opening: %s\n", myrank, adios_errno, adios_errmsg()); exit(3); } else { my_printf("Found file %s\n", adios_filename_a_to_b); my_printf ("File info:\n"); my_printf (" current step: %d\n", fp->current_step); my_printf (" last step: %d\n", fp->last_step); my_printf (" # of variables: %d:\n", fp->nvars); vi = adios_inq_var(fp, "temperature"); adios_inq_var_blockinfo(fp, vi); printf ("ndim = %d\n", vi->ndim); printf ("nsteps = %d\n", vi->nsteps); printf ("dims[%llu][%llu]\n", vi->dims[0], vi->dims[1]); uint64_t slice_size = vi->dims[0]/commsize; if (myrank == commsize-1) { slice_size = slice_size + vi->dims[0]%commsize; } start[0] = myrank * slice_size; count[0] = slice_size; start[1] = 0; count[1] = vi->dims[1]; data = malloc (slice_size * vi->dims[1] * 8); /* Processing loop over the steps (we are already in the first one) */ while (adios_errno != err_end_of_stream && steps < iterations) { steps++; // steps start counting from 1 TAU_PROFILE_TIMER(adios_recv_timer, "ADIOS recv", __FILE__, TAU_USER); TAU_PROFILE_START(adios_recv_timer); sel = adios_selection_boundingbox (vi->ndim, start, count); adios_schedule_read (fp, sel, "temperature", 0, 1, data); adios_perform_reads (fp, 1); if (myrank == 0) printf ("--------- B Step: %d --------------------------------\n", fp->current_step); #if 0 printf("B rank=%d: [0:%lld,0:%lld] = [", myrank, vi->dims[0], vi->dims[1]); for (i = 0; i < slice_size; i++) { printf (" ["); for (j = 0; j < vi->dims[1]; j++) { printf ("%g ", *((double *)data + i * vi->dims[1] + j)); } printf ("]"); } printf (" ]\n\n"); #endif // advance to 1) next available step with 2) blocking wait adios_advance_step (fp, 0, timeout_sec); if (adios_errno == err_step_notready) { printf ("B rank %d: No new step arrived within the timeout. Quit. %s\n", myrank, adios_errmsg()); break; // quit while loop } TAU_PROFILE_STOP(adios_recv_timer); /* Do some exchanges with neighbors */ //do_neighbor_exchange(); /* "Compute" */ compute(steps); for (i = 0; i < NX; i++) { t[i] = steps*100.0 + myrank*NX + i; } for (i = 0; i < NY; i++) { p[i] = steps*1000.0 + myrank*NY + i; } if (send_to_c) { TAU_PROFILE_TIMER(adios_send_timer, "ADIOS send", __FILE__, TAU_USER); TAU_PROFILE_START(adios_send_timer); /* ADIOS: write to the next application in the workflow */ if (steps == 0) { adios_open(&adios_handle, "b_to_c", adios_filename_b_to_c, "w", adios_comm_b_to_c); } else { adios_open(&adios_handle, "b_to_c", adios_filename_b_to_c, "a", adios_comm_b_to_c); } /* ADIOS: Actually write the data out. * Yes, this is the recommended method, and this way, changes in * configuration with the .XML file will, even in the worst-case * scenario, merely require running 'gpp.py adios_config.xml' * and typing 'make'. */ #include "gwrite_b_to_c.ch" /* ADIOS: Close out the file completely and finalize. * If MPI is being used, this must happen before MPI_Finalize(). */ adios_close(adios_handle); TAU_PROFILE_STOP(adios_send_timer); #if 1 if (!announced) { SOS_val foo; foo.i_val = NX; SOS_pack(example_pub, "NX", SOS_VAL_TYPE_INT, foo); SOS_announce(example_pub); SOS_publish(example_pub); announced = true; } #endif } MPI_Barrier(adios_comm_b_to_c); } MPI_Barrier(MPI_COMM_WORLD); adios_read_close(fp); /* ADIOS: Close out the file completely and finalize. * If MPI is being used, this must happen before MPI_Finalize(). */ adios_read_finalize_method(method); } if (send_to_c) { adios_finalize(myrank); } free(data); //MPI_Comm_free(&adios_comm); //MPI_Comm_free(&adios_comm_b_to_c); TAU_PROFILE_STOP(timer); /* exit */ return 0; }
int main (int argc, char ** argv) { int rank, size, i, j; MPI_Comm comm = MPI_COMM_WORLD; ADIOS_FILE * f; ADIOS_VARINFO * v; ADIOS_SELECTION * sel; int steps = 0; int retval = 0; float timeout_sec = 1.0; void * data = NULL; uint64_t start[2], count[2]; MPI_Init (&argc, &argv); MPI_Comm_rank (comm, &rank); MPI_Comm_size (comm, &size); adios_read_init_method (ADIOS_READ_METHOD_BP, comm, "verbose=3"); f = adios_read_open ("adios_globaltime.bp", ADIOS_READ_METHOD_BP, comm, ADIOS_LOCKMODE_NONE, timeout_sec); if (adios_errno == err_file_not_found) { printf ("rank %d: Stream not found after waiting %f seconds: %s\n", rank, timeout_sec, adios_errmsg()); retval = adios_errno; } else if (adios_errno == err_end_of_stream) { printf ("rank %d: Stream terminated before open. %s\n", rank, adios_errmsg()); retval = adios_errno; } else if (f == NULL) { printf ("rank %d: Error at opening stream: %s\n", rank, adios_errmsg()); retval = adios_errno; } else { /* process file here... */ v = adios_inq_var (f, "temperature"); adios_inq_var_blockinfo (f, v); printf ("ndim = %d\n", v->ndim); //printf ("nsteps = %d\n", v->nsteps); printf ("dims[%llu][%llu]\n", v->dims[0], v->dims[1]); uint64_t slice_size = v->dims[0]/size; if (rank == size-1) slice_size = slice_size + v->dims[0]%size; start[0] = rank * slice_size; count[0] = slice_size; start[1] = 0; count[1] = v->dims[1]; data = malloc (slice_size * v->dims[1] * 8); /* Processing loop over the steps (we are already in the first one) */ while (adios_errno != err_end_of_stream) { steps++; // steps start counting from 1 sel = adios_selection_boundingbox (v->ndim, start, count); adios_schedule_read (f, sel, "temperature", 0, 1, data); adios_perform_reads (f, 1); if (rank == 0) printf ("--------- Step: %d --------------------------------\n", f->current_step); printf("rank=%d: [0:%lld,0:%lld] = [", rank, v->dims[0], v->dims[1]); for (i = 0; i < slice_size; i++) { printf (" ["); for (j = 0; j < v->dims[1]; j++) { printf ("%g ", *((double *)data + i * v->dims[1] + j)); } printf ("]"); } printf (" ]\n\n"); // advance to 1) next available step with 2) blocking wait adios_advance_step (f, 0, timeout_sec); if (adios_errno == err_step_notready) { printf ("rank %d: No new step arrived within the timeout. Quit. %s\n", rank, adios_errmsg()); break; // quit while loop } } adios_read_close (f); } if (rank==0) printf ("We have processed %d steps\n", steps); adios_read_finalize_method (ADIOS_READ_METHOD_BP); free (data); MPI_Finalize (); return retval; }
int main (int argc, char ** argv) { int rank, size, i, j; MPI_Comm comm = MPI_COMM_WORLD; enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP; ADIOS_SELECTION * sel; void * data = NULL; uint64_t start[2], count[2]; MPI_Init (&argc, &argv); MPI_Comm_rank (comm, &rank); MPI_Comm_size (comm, &size); adios_read_init_method (method, comm, "verbose=4"); adios_logger_open ("log_read_C", rank); ADIOS_FILE * f = adios_read_open ("global_array_C.bp", method, comm, ADIOS_LOCKMODE_NONE, 0); if (f == NULL) { log_error ("%s\n", adios_errmsg()); return -1; } ADIOS_VARINFO * v = adios_inq_var (f, "temperature"); /* Using less readers to read the global array back, i.e., non-uniform */ uint64_t slice_size = v->dims[0]/size; start[0] = slice_size * rank; if (rank == size-1) /* last rank may read more lines */ slice_size = slice_size + v->dims[0]%size; count[0] = slice_size; start[1] = 0; count[1] = v->dims[1]; data = malloc (slice_size * v->dims[1] * sizeof (double)); if (data == NULL) { log_error (stderr, "malloc failed.\n"); return -1; } /* Read a subset of the temperature array */ sel = adios_selection_boundingbox (v->ndim, start, count); adios_schedule_read (f, sel, "temperature", 0, 1, data); adios_perform_reads (f, 1); for (i = 0; i < slice_size; i++) { log_test ("rank %d: [%lld,%d:%lld]", rank, start[0]+i, 0, slice_size); for (j = 0; j < v->dims[1]; j++) log_test (" %6.6g", * ((double *)data + i * v->dims[1] + j)); log_test ("\n"); } free (data); adios_read_close (f); MPI_Barrier (comm); adios_read_finalize_method (method); adios_logger_close(); MPI_Finalize (); return 0; }
static void test_file_mode_reads_on_var(ADIOS_FILE *fp, const char *bp_filename, const char *varname) { int i; ADIOS_VARINFO *varinfo = adios_inq_var(fp, varname); MPI_Assert(COMM, varinfo); if (varinfo->value != NULL) { //if (rank == 0) fprintf(stderr, "(skipping scalar variable '%s')\n", varname); adios_free_varinfo(varinfo); return; } fprintf(stderr, "[rank %d/%d] Starting file-mode writeblock reads on %s:/%s\n", rank, size, bp_filename, varname); adios_inq_var_blockinfo(fp, varinfo); MPI_Assert(COMM, varinfo->blockinfo); const enum ADIOS_DATATYPES datatype = varinfo->type; const int datatypesize = adios_get_type_size(datatype, NULL); int timestep, timestep_blockidx, blockidx = 0; for (timestep = 0; timestep < varinfo->nsteps; ++timestep) { for (timestep_blockidx = 0; timestep_blockidx < varinfo->nblocks[timestep]; ++timestep_blockidx, ++blockidx) { if (blockidx % size != rank) continue; const ADIOS_VARBLOCK *vb = &varinfo->blockinfo[blockidx]; ADIOS_SELECTION *block_bb = adios_selection_boundingbox(varinfo->ndim, vb->start, vb->count); ADIOS_SELECTION *block_wb = adios_selection_writeblock(timestep_blockidx); ADIOS_SELECTION *block_abs_wb = adios_selection_writeblock(blockidx); block_abs_wb->u.block.is_absolute_index = 1; uint64_t blocksize = datatypesize; for (i = 0; i < varinfo->ndim; ++i) blocksize *= vb->count[i]; void *buf_bb = malloc(blocksize); void *buf_wb = malloc(blocksize); void *buf_abs_wb = malloc(blocksize); memset(buf_bb, 0, blocksize); memset(buf_wb, 1, blocksize); memset(buf_abs_wb, 2, blocksize); MPI_Assert(COMM, buf_bb && buf_wb && buf_abs_wb); adios_schedule_read(fp, block_bb, varname, timestep, 1, buf_bb ); adios_schedule_read(fp, block_wb, varname, timestep, 1, buf_wb ); adios_schedule_read(fp, block_abs_wb, varname, timestep, 1, buf_abs_wb); adios_perform_reads(fp, 1); fprintf(stderr, "[rank %d/%d] Checking file-mode blockidx %d BB vs. WB...\n", rank, size, blockidx); MPI_Assert(COMM, memcmp(buf_bb, buf_wb, blocksize) == 0); fprintf(stderr, "[rank %d/%d] Checking file-mode blockidx %d BB vs. abs-WB...\n", rank, size, blockidx); MPI_Assert(COMM, memcmp(buf_bb, buf_abs_wb, blocksize) == 0); free(buf_bb); free(buf_wb); free(buf_abs_wb); adios_selection_delete(block_bb); adios_selection_delete(block_wb); adios_selection_delete(block_abs_wb); } } adios_free_varinfo(varinfo); fprintf(stderr, "[rank %d/%d] Finished file-mode writeblock reads on %s:/%s\n", rank, size, bp_filename, varname); }
void performQuery(ADIOS_QUERY_TEST_INFO *queryInfo, ADIOS_FILE *f, int use_streaming, int print_points, int read_results) { int timestep = 0 ; ADIOS_VARINFO * tempVar = adios_inq_var(f, queryInfo->varName); adios_inq_var_blockinfo(f, tempVar); if (use_streaming) for (timestep = 0; timestep < queryInfo->fromStep; ++timestep) assert(adios_advance_step(f, 0, 0) == 0); fprintf(stderr,"times steps for variable is: [%d, %d], batch size is %" PRIu64 "\n", queryInfo->fromStep, queryInfo->fromStep + queryInfo->numSteps, queryInfo->batchSize); for (timestep = queryInfo->fromStep; timestep < queryInfo->fromStep + queryInfo->numSteps; timestep ++) { fprintf(stderr, "querying on timestep %d \n", timestep); while (1) { ADIOS_QUERY_RESULT *currBatch = NULL; currBatch = adios_query_evaluate( queryInfo->query, queryInfo->outputSelection, use_streaming ? 0 : timestep, queryInfo->batchSize ); if (currBatch == NULL) { fprintf(stderr, "Unexpected error status in querying evaluation, returned NULL as result. " "ADIOS error message: %s \n", adios_errmsg()); break; } if (currBatch->status == ADIOS_QUERY_RESULT_ERROR) { fprintf(stderr, "ERROR in querying evaluation: %s \n", adios_errmsg()); break; } if (currBatch->nselections == 0) { /* this is normal, we processed everything in previous loop or there is 0 total result */ break; } int n; if (currBatch->selections->type == ADIOS_SELECTION_POINTS) { for (n = 0; n < currBatch->nselections; n++) { const ADIOS_SELECTION_POINTS_STRUCT * retrievedPts = &(currBatch->selections[n].u.points); /* fprintf(stderr,"retrieved points %" PRIu64 " \n", retrievedPts->npoints); */ uint64_t * wboffs = calloc (retrievedPts->ndim, sizeof(uint64_t)); if (retrievedPts->container_selection && retrievedPts->container_selection->type == ADIOS_SELECTION_WRITEBLOCK) { int i; int blockidx = retrievedPts->container_selection->u.block.index; if (use_streaming) { adios_inq_var_blockinfo(f, tempVar); } else { for (i = 0; i < timestep-1; i++) blockidx += tempVar->nblocks[i]; } for (i = 0; i < retrievedPts->ndim; ++i) { wboffs[i] = tempVar->blockinfo[blockidx].start[i]; } } if (print_points) { printPoints(retrievedPts, timestep, wboffs); } free (wboffs); if (read_results) { int elmSize = adios_type_size(tempVar->type, NULL); void *data = malloc(retrievedPts->npoints * elmSize); // read returned temp data adios_schedule_read (f, &currBatch->selections[n], queryInfo->varName, use_streaming ? 0 : timestep, 1, data); adios_perform_reads(f, 1); free(data); } fprintf(stderr,"Total points retrieved %"PRIu64" in %d blocks\n", currBatch->npoints, currBatch->nselections); /* if (tempVar->type == adios_double) { */ /* for (i = 0; i < retrievedPts->npoints; i++) { */ /* fprintf(stderr,"%.6f\t", ((double*)data)[i]); */ /* } */ /* fprintf(stderr,"\n"); */ /* } */ /* else if (tempVar->type == adios_real) { */ /* for (i = 0; i < retrievedPts->npoints; i++) { */ /* fprintf(stderr,"%.6f\t", ((float*)data)[i]); */ /* } */ /* fprintf(stderr,"\n"); */ /* } */ } } else if (currBatch->selections->type == ADIOS_SELECTION_WRITEBLOCK) { fprintf(stderr,"Number of blocks retrieved: %d\n", currBatch->nselections); if (print_points) { for (n = 0; n < currBatch->nselections; n++) { fprintf(stdout,"%d %d\n", timestep, currBatch->selections[n].u.block.index); } } } free(currBatch->selections); if (currBatch->status == ADIOS_QUERY_NO_MORE_RESULTS) { free (currBatch); break; } free(currBatch); } if (use_streaming) { const int err = adios_advance_step(f, 0, 0); if (timestep < queryInfo->fromStep + queryInfo->numSteps - 1) { assert(err == 0); } else { assert(err == err_end_of_stream || err == err_step_notready); } } } adios_query_free(queryInfo->query); }