/* * Print the content of the dataset. */ int dataset_vrfy(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset, DATATYPE *original) { #define MAX_ERR_REPORT 10 /* Maximum number of errors reported */ hsize_t i, j; int nerr; /* print it if verbose */ if (verbose) dataset_print(start, count, stride, dataset); nerr = 0; for (i=0; i < count[0]; i++){ for (j=0; j < count[1]; j++){ if (*dataset++ != *original++){ nerr++; if (nerr <= MAX_ERR_REPORT){ printf("Dataset Verify failed at [%lu][%lu](row %lu, col %lu): expect %d, got %d\n", (unsigned long)i, (unsigned long)j, (unsigned long)(i*stride[0]+start[0]), (unsigned long)(j*stride[1]+start[1]), *(dataset-1), *(original-1)); } } } } if (nerr > MAX_ERR_REPORT) printf("[more errors ...]\n"); if (nerr) printf("%d errors found in dataset_vrfy\n", nerr); return(nerr); }
int main(int argc, char *argv[]) { if (dataset_init(argc, argv) == -1) { dataset_usage(); return EXIT_FAILURE; } int size; int *buf = malloc(SSORT_MAX_NUMS * sizeof(int)); if (buf == NULL) { pexit(progname); } size = dataset_get(buf, SSORT_MAX_NUMS); if (size == -1) { pexit(progname); } selection_sort(buf, size); dataset_print(buf, size); free(buf); return EXIT_SUCCESS; }
void external_dataset_sort(external_dataset_t* data) { struct runtime rt; void* results = NULL; size_t i; stream_t* tmp; stream_t* stream = data->stream; stream_seek(stream, 0); tmp = stream_create(stream->config, "tmp.stream"); stream_open(tmp, O_CREAT | O_TRUNC | O_RDWR | O_SYNC); /* sort each individual chunk of memory size */ for(i = 0; i < data->n_records / MEMORY_RECORDS(stream); i++) { memory_read(stream, RECORDS(data->mem), MEMORY_RECORDS(stream)); N_RECORDS(data->mem) = MEMORY_RECORDS(stream); results = NULL; start_timing(&rt); fp_im_sort(data->context, RECORDS(data->mem), N_RECORDS(data->mem), &results); stop_timing(&rt); printf("Sort time: %f\n", get_runtime(rt)); memory_write(tmp, RECORDS(data->mem), N_RECORDS(data->mem)); dataset_print(data->mem, TRUE); } if(data->n_records % MEMORY_RECORDS(stream)) { memory_read(stream, RECORDS(data->mem), data->n_records % MEMORY_RECORDS(stream)); N_RECORDS(data->mem) = data->n_records % MEMORY_RECORDS(stream); start_timing(&rt); results = NULL; fp_im_sort(data->context, RECORDS(data->mem), N_RECORDS(data->mem), &results); stop_timing(&rt); memory_write(tmp, RECORDS(data->mem), N_RECORDS(data->mem)); dataset_print(data->mem, TRUE); } /* merge memory chunks block by block */ }
int main(int argc, char** argv) { /* configuration for the visualization program */ visualize_config_t config; /* reference to the loaded dataset */ dataset_t* dataset; group_list_t* groups = NULL; configure(&config, argc, argv); /* load dataset from input file */ dataset = dataset_load(config.input); if(dataset) { /* if a group list is defined, load that one too */ if(config.have_groups) groups = group_list_load(config.grpfile); /* if the dataset is supposed to be printed to stdout in text format, * then do so */ if(config.print) dataset_print(dataset); /* now draw the dataset */ dataset_draw(&config, dataset, groups); /* release group list from memory if there is one */ if(groups) group_list_destroy(groups); /* release dataset from memory */ dataset_destroy(&dataset); } return 0; }
void phdf5readAll(char *filename) { hid_t fid1; /* HDF5 file IDs */ hid_t acc_tpl1; /* File access templates */ hid_t xfer_plist; /* Dataset transfer properties list */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */ DATATYPE data_origin1[SPACE1_DIM1][SPACE1_DIM2]; /* expected data buffer */ hsize_t start[SPACE1_RANK]; /* for hyperslab setting */ hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; if (verbose) printf("Collective read test on file %s\n", filename); /* ------------------- * OPEN AN HDF5 FILE * -------------------*/ /* setup file access template with parallel IO access. */ acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS); assert(acc_tpl1 != FAIL); MESG("H5Pcreate access succeed"); /* set Parallel access with communicator */ ret = H5Pset_fapl_mpio(acc_tpl1, comm, info); assert(ret != FAIL); MESG("H5Pset_fapl_mpio succeed"); /* open the file collectively */ fid1=H5Fopen(filename,H5F_ACC_RDWR,acc_tpl1); assert(fid1 != FAIL); MESG("H5Fopen succeed"); /* Release file-access template */ ret=H5Pclose(acc_tpl1); assert(ret != FAIL); /* -------------------------- * Open the datasets in it * ------------------------- */ /* open the dataset1 collectively */ dataset1 = H5Dopen2(fid1, DATASETNAME1, H5P_DEFAULT); assert(dataset1 != FAIL); MESG("H5Dopen2 succeed"); /* open another dataset collectively */ dataset2 = H5Dopen2(fid1, DATASETNAME2, H5P_DEFAULT); assert(dataset2 != FAIL); MESG("H5Dopen2 2 succeed"); /* * Set up dimensions of the slab this process accesses. */ /* Dataset1: each process takes a block of columns. */ slab_set(start, count, stride, BYCOL); if (verbose) printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], (unsigned long)(count[0]*count[1])); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); assert(file_dataspace != FAIL); MESG("H5Dget_space succeed"); ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); assert(ret != FAIL); MESG("H5Sset_hyperslab succeed"); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); assert (mem_dataspace != FAIL); /* fill dataset with test data */ dataset_fill(start, count, stride, &data_origin1[0][0]); MESG("data_array initialized"); if (verbose){ MESG("data_array created"); dataset_print(start, count, stride, &data_array1[0][0]); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate (H5P_DATASET_XFER); assert(xfer_plist != FAIL); ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); assert(ret != FAIL); MESG("H5Pcreate xfer succeed"); /* read data collectively */ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); assert(ret != FAIL); MESG("H5Dread succeed"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]); assert(ret != FAIL); /* release all temporary handles. */ /* Could have used them for dataset2 but it is cleaner */ /* to create them again.*/ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* Dataset2: each process takes a block of rows. */ slab_set(start, count, stride, BYROW); if (verbose) printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], (unsigned long)(count[0]*count[1])); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); assert(file_dataspace != FAIL); MESG("H5Dget_space succeed"); ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); assert(ret != FAIL); MESG("H5Sset_hyperslab succeed"); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); assert (mem_dataspace != FAIL); /* fill dataset with test data */ dataset_fill(start, count, stride, &data_origin1[0][0]); MESG("data_array initialized"); if (verbose){ MESG("data_array created"); dataset_print(start, count, stride, &data_array1[0][0]); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate (H5P_DATASET_XFER); assert(xfer_plist != FAIL); ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); assert(ret != FAIL); MESG("H5Pcreate xfer succeed"); /* read data independently */ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); assert(ret != FAIL); MESG("H5Dread succeed"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]); assert(ret != FAIL); /* release all temporary handles. */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* * All reads completed. Close datasets collectively */ ret=H5Dclose(dataset1); assert(ret != FAIL); MESG("H5Dclose1 succeed"); ret=H5Dclose(dataset2); assert(ret != FAIL); MESG("H5Dclose2 succeed"); /* close the file collectively */ H5Fclose(fid1); }
void phdf5writeAll(char *filename) { hid_t fid1; /* HDF5 file IDs */ hid_t acc_tpl1; /* File access templates */ hid_t xfer_plist; /* Dataset transfer properties list */ hid_t sid1; /* Dataspace ID */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ hsize_t dims1[SPACE1_RANK] = {SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */ DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */ hsize_t start[SPACE1_RANK]; /* for hyperslab setting */ hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; /* in support of H5Tuner Test */ MPI_Comm comm_test = MPI_COMM_WORLD; MPI_Info info_test ; int i_test, nkeys_test, flag_test; char key[MPI_MAX_INFO_KEY], value[MPI_MAX_INFO_VAL+1]; char *libtuner_file = getenv("LD_PRELOAD"); /* in support of H5Tuner Test */ if (verbose) printf("Collective write test on file %s\n", filename); /* ------------------- * START AN HDF5 FILE * -------------------*/ /* setup file access template with parallel IO access. */ acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS); assert(acc_tpl1 != FAIL); MESG("H5Pcreate access succeed"); /* set Parallel access with communicator */ ret = H5Pset_fapl_mpio(acc_tpl1, comm, info); assert(ret != FAIL); MESG("H5Pset_fapl_mpio succeed"); /* create the file collectively */ fid1=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl1); assert(fid1 != FAIL); MESG("H5Fcreate succeed"); // ------------------------------------------------ // H5Tuner tests // ------------------------------------------------ // Retrieve MPI parameters set via the H5Tuner printf("\n\n--------------------------------------------------\n"); if ( (libtuner_file != NULL) && (strlen(libtuner_file) > 1) ){ printf("Version of the H5Tuner loaded: \n%s\n", libtuner_file); } else { printf("No H5Tuner currently loaded.\n"); } printf("--------------------------------------------------\n"); // Retrieve HDF5 Threshold and Alignment hsize_t alignment[2]; size_t sieve_buf_size; alignment[0]= 0; // threshold value alignment[1]= 0; // alignment value int ierr = H5Pget_alignment(acc_tpl1, &alignment[0], &alignment[1]); printf("\n\n--------------------------------------------------\n"); printf("Testing values for Threshold and Alignment\n"); printf("--------------------------------------------------\n"); printf("Test value set to:88 \nRetrieved Threshold=%lu\n", alignment[0]); printf("Test value set to:44 \nRetrieved Alignment=%lu\n", alignment[1]); // Check Threshold if ( alignment[0] == 88 ) { printf("PASSED: Threshold Test\n"); } else { printf("FAILED: Threshold Test\n"); } // Check Alignment if ( alignment[1] == 44 ) { printf("PASSED: Alignment Test\n"); } else { printf("FAILED: Alignment Test\n"); } printf("--------------------------------------------------\n\n"); // Retrieve HDF5 sieve buffer size ierr = H5Pget_sieve_buf_size(acc_tpl1, &sieve_buf_size); printf("\n\n--------------------------------------------------\n"); printf("Testing values for Sieve Buffer Size\n"); printf("--------------------------------------------------\n"); printf("Test value set to:77 \nRetrieved Sieve Buffer Size=%lu\n", sieve_buf_size); // Check sieve buffer size if ( (int) sieve_buf_size == 77 ) { printf("PASSED: Sieve Buffer Size Test\n"); } else { printf("FAILED: Sieve Buffer Size Test\n"); } printf("--------------------------------------------------\n\n"); // Retrieve MPI parameters set via the H5Tuner MPI_Info_create(&info_test); ret = H5Pget_fapl_mpio(acc_tpl1, &comm_test, &info_test); assert(ret != FAIL); MESG("H5Pget_fapl_mpio succeed"); printf("-------------------------------------------------\n" ); printf("Testing parameters values via MPI_Info\n" ); printf("-------------------------------------------------\n" ); if(info_test == MPI_INFO_NULL) { printf("MPI info object is null. No keys are available.\n"); } else { MPI_Info_get_nkeys(info_test, &nkeys_test); //printf("MPI info has %d keys\n", nkeys_test); if (nkeys_test <= 0) { printf("MPI info has no keys\n"); } else { printf("MPI info has %d keys\n", nkeys_test); for ( i_test=0; i_test < nkeys_test; i_test++) { MPI_Info_get_nthkey( info_test, i_test, key ); MPI_Info_get( info_test, key, MPI_MAX_INFO_VAL, value, &flag_test ); printf( "Retrieved value for key %s is %s\n", key, value ); //fflush(stdout); } } printf("-------------------------------------------------\n" ); MPI_Info_free(&info_test); } // end of H5Tuner tests // --------------------------------------- /* Release file-access template */ ret=H5Pclose(acc_tpl1); assert(ret != FAIL); /* -------------------------- * Define the dimensions of the overall datasets * and create the dataset * ------------------------- */ /* setup dimensionality object */ sid1 = H5Screate_simple (SPACE1_RANK, dims1, NULL); assert (sid1 != FAIL); MESG("H5Screate_simple succeed"); /* create a dataset collectively */ dataset1 = H5Dcreate2(fid1, DATASETNAME1, H5T_NATIVE_INT, sid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); assert(dataset1 != FAIL); MESG("H5Dcreate2 succeed"); /* create another dataset collectively */ dataset2 = H5Dcreate2(fid1, DATASETNAME2, H5T_NATIVE_INT, sid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); assert(dataset2 != FAIL); MESG("H5Dcreate2 2 succeed"); /* * Set up dimensions of the slab this process accesses. */ /* Dataset1: each process takes a block of rows. */ slab_set(start, count, stride, BYROW); if (verbose) printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], (unsigned long)(count[0]*count[1])); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); assert(file_dataspace != FAIL); MESG("H5Dget_space succeed"); ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); assert(ret != FAIL); MESG("H5Sset_hyperslab succeed"); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); assert (mem_dataspace != FAIL); /* fill the local slab with some trivial data */ dataset_fill(start, count, stride, &data_array1[0][0]); MESG("data_array initialized"); if (verbose){ MESG("data_array created"); dataset_print(start, count, stride, &data_array1[0][0]); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate (H5P_DATASET_XFER); assert(xfer_plist != FAIL); ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); assert(ret != FAIL); MESG("H5Pcreate xfer succeed"); /* write data collectively */ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); assert(ret != FAIL); MESG("H5Dwrite succeed"); /* release all temporary handles. */ /* Could have used them for dataset2 but it is cleaner */ /* to create them again.*/ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* Dataset2: each process takes a block of columns. */ slab_set(start, count, stride, BYCOL); if (verbose) printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], (unsigned long)(count[0]*count[1])); /* put some trivial data in the data_array */ dataset_fill(start, count, stride, &data_array1[0][0]); MESG("data_array initialized"); if (verbose){ MESG("data_array created"); dataset_print(start, count, stride, &data_array1[0][0]); } /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); assert(file_dataspace != FAIL); MESG("H5Dget_space succeed"); ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); assert(ret != FAIL); MESG("H5Sset_hyperslab succeed"); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); assert (mem_dataspace != FAIL); /* fill the local slab with some trivial data */ dataset_fill(start, count, stride, &data_array1[0][0]); MESG("data_array initialized"); if (verbose){ MESG("data_array created"); dataset_print(start, count, stride, &data_array1[0][0]); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate (H5P_DATASET_XFER); assert(xfer_plist != FAIL); ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); assert(ret != FAIL); MESG("H5Pcreate xfer succeed"); /* write data independently */ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); assert(ret != FAIL); MESG("H5Dwrite succeed"); /* release all temporary handles. */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* * All writes completed. Close datasets collectively */ ret=H5Dclose(dataset1); assert(ret != FAIL); MESG("H5Dclose1 succeed"); ret=H5Dclose(dataset2); assert(ret != FAIL); MESG("H5Dclose2 succeed"); /* release all IDs created */ H5Sclose(sid1); /* close the file collectively */ H5Fclose(fid1); }
void phdf5write2(char *filename, hio_context_t context) { hid_t fid1; /* HDF5 file IDs */ hid_t acc_tpl1; /* File access templates */ hid_t sid1; /* Dataspace ID */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ hsize_t dims1[SPACE1_RANK] = {SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */ DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */ hsize_t start[SPACE1_RANK]; /* for hyperslab setting */ hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ ssize_t bytes_written; hio_request_t req; if (verbose) printf("Collective write test on file %s\n", filename); /* ------------------- * START AN HDF5 FILE * -------------------*/ /* setup file access template with hio IO access. */ acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS); assert(acc_tpl1 != FAIL); MESG("H5Pcreate access succeed"); H5FD_hio_set_write_io(&settings, H5FD_HIO_STRIDED); H5FD_hio_set_write_blocking(&settings, H5FD_HIO_NONBLOCKING); H5FD_hio_set_request(&settings, &req); ret = H5Pset_fapl_hio(acc_tpl1, &settings); assert(ret != FAIL); MESG("H5Pset_fapl_hio succeed"); /* create the file collectively */ fid1=H5Fcreate(filename,0,H5P_DEFAULT,acc_tpl1); assert(fid1 != FAIL); MESG("H5Fcreate succeed"); /* Release file-access template */ ret=H5Pclose(acc_tpl1); assert(ret != FAIL); /* -------------------------- * Define the dimensions of the overall datasets * and create the dataset * ------------------------- */ /* setup dimensionality object */ sid1 = H5Screate_simple (SPACE1_RANK, dims1, NULL); assert (sid1 != FAIL); MESG("H5Screate_simple succeed"); /* create a dataset collectively */ dataset1 = H5Dcreate2(fid1, DATASETNAME1, H5T_NATIVE_INT, sid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); assert(dataset1 != FAIL); MESG("H5Dcreate2 succeed"); /* create another dataset collectively */ dataset2 = H5Dcreate2(fid1, DATASETNAME2, H5T_NATIVE_INT, sid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); assert(dataset2 != FAIL); MESG("H5Dcreate2 2 succeed"); /* * Set up dimensions of the slab this process accesses. */ /* Dataset1: each process takes a block of rows. */ slab_set(start, count, stride, BYROW); if (verbose) printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], (unsigned long)(count[0]*count[1])); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); assert(file_dataspace != FAIL); MESG("H5Dget_space succeed"); ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); assert(ret != FAIL); MESG("H5Sset_hyperslab succeed"); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); assert (mem_dataspace != FAIL); /* fill the local slab with some trivial data */ dataset_fill(start, count, stride, &data_array1[0][0]); MESG("data_array initialized"); if (verbose){ MESG("data_array created"); dataset_print(start, count, stride, &data_array1[0][0]); } /* write data strided and blocking*/ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); assert(ret != FAIL); MESG("H5Dwrite succeed"); //Wait for the request to finish hio_request_wait(&req, 1, &bytes_written); /* release all temporary handles. */ /* Could have used them for dataset2 but it is cleaner */ /* to create them again.*/ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); /* Dataset2: each process takes a block of columns. */ slab_set(start, count, stride, BYCOL); if (verbose) printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], (unsigned long)(count[0]*count[1])); /* put some trivial data in the data_array */ dataset_fill(start, count, stride, &data_array1[0][0]); MESG("data_array initialized"); if (verbose){ MESG("data_array created"); dataset_print(start, count, stride, &data_array1[0][0]); } /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); assert(file_dataspace != FAIL); MESG("H5Dget_space succeed"); ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); assert(ret != FAIL); MESG("H5Sset_hyperslab succeed"); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); assert (mem_dataspace != FAIL); /* fill the local slab with some trivial data */ dataset_fill(start, count, stride, &data_array1[0][0]); MESG("data_array initialized"); if (verbose){ MESG("data_array created"); dataset_print(start, count, stride, &data_array1[0][0]); } /* write data contiguous and blocking */ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); assert(ret != FAIL); MESG("H5Dwrite succeed"); /* release all temporary handles. */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); /* * All writes completed. Close datasets collectively */ ret=H5Dclose(dataset1); assert(ret != FAIL); MESG("H5Dclose1 succeed"); ret=H5Dclose(dataset2); assert(ret != FAIL); MESG("H5Dclose2 succeed"); /* release all IDs created */ H5Sclose(sid1); /* close the file collectively */ H5Fclose(fid1); }
int main(int argc, char** argv) { FILE* f; metadata_t* meta; fp_context_t* context; struct sort_config sc; dataset_t* ds; char target[256]; stream_t* stream; config_t conf; external_dataset_t* ext; int i; if(argc < 2) { printf("Barf!\n"); exit(-1); } if((f = fopen(argv[1], "r")) == NULL) { printf("Cannot open dataset file %s.\n", argv[1]); return -1; } meta = metadata_read(f); sc.verbose = 1; sc.normalize = 0; sc.denormalize = 0; sc.benchmark = 1; sc.find_order = ITERATIVE; sc.index = KEEP; sc.cmp = HILBERT; sc.print = stdout; context = fp_create_context(&sc, meta->dimz, meta->dimf, meta->start_order); ds = dataset_read(f, meta, context); fclose(f); dataset_print(ds, FALSE); strcpy(target, argv[1]); strcat(target, ".stream"); printf("Number of records: %d\n", ds->n_records); printf("Record size: %d\n", context->record_size); conf.memory_size = 1000; conf.block_size = 0x100; conf.record_size = context->record_size; stream = stream_create(&conf, target); stream_open(stream, O_CREAT | O_TRUNC | O_SYNC | O_WRONLY); dataset_convert(ds, stream); stream_close(stream); stream_open(stream, O_SYNC | O_RDONLY); ext = external_dataset_create(stream, meta, ds->n_records); for(i = 0; i < ds->n_records / MEMORY_RECORDS(stream); i++) { memory_read(stream, ext->mem->records, MEMORY_RECORDS(stream)); ext->mem->n_records = MEMORY_RECORDS(stream); dataset_print(ext->mem, FALSE); } if(ds->n_records % MEMORY_RECORDS(stream)) { memory_read(stream, ext->mem->records, ds->n_records % MEMORY_RECORDS(stream)); ext->mem->n_records = ds->n_records % MEMORY_RECORDS(stream); dataset_print(ext->mem, FALSE); } printf("Stream position: %ld vs. %ld\n", stream->pos, stream_tell(stream)); external_dataset_sort(ext); external_dataset_destroy(ext); stream_destroy(stream); stats_print(); dataset_destroy(ds); fp_destroy_context(context); metadata_destroy(meta); return 0; }