diff options
Diffstat (limited to 'testpar/testphdf5.c')
| -rw-r--r-- | testpar/testphdf5.c | 947 |
1 files changed, 51 insertions, 896 deletions
diff --git a/testpar/testphdf5.c b/testpar/testphdf5.c index 03c3d92..1d8b632 100644 --- a/testpar/testphdf5.c +++ b/testpar/testphdf5.c @@ -1,84 +1,16 @@ - /* $Id$ */ /* - * Example of using the parallel HDF5 library to access datasets. - * - * This program contains two parts. In the first part, the mpi processes - * collectively create a new parallel HDF5 file and create two fixed - * dimension datasets in it. Then each process writes a hyperslab into - * each dataset in an independent mode. All processes collectively - * close the datasets and the file. - * In the second part, the processes collectively open the created file - * and the two datasets in it. Then each process reads a hyperslab from - * each dataset in an independent mode and prints them out. - * All processes collectively close the datasets and the file. + * Main driver of the Parallel HDF5 tests */ -#include <assert.h> -#include <hdf5.h> -#include <mpi.h> -#include <mpio.h> - -/* Temporary source code */ -#define FAIL -1 -/* temporary code end */ - -/* Define some handy debugging shorthands, routines, ... */ -/* debugging tools */ - -#define MESG(x) \ - if (verbose) printf("%s\n", x); \ - -#define VRFY(val, mesg) do { \ - if (val) { \ - if (*mesg != '\0'){ \ - MESG(mesg); \ - } \ - } \ - else{ \ - printf("*** Assertion failed (%s) at line %4d in %s\n", \ - mesg, (int)__LINE__, __FILE__); \ - nerrors++; \ - H5Eprint (stdout); \ - if (!verbose) exit(nerrors); \ - } \ - H5Eclear(); \ -} while(0) - -#define MPI_BANNER(mesg)\ - {printf("--------------------------------\n");\ - printf("Proc %d: ", mpi_rank); \ - printf("*** %s\n", mesg);\ - printf("--------------------------------\n");} - -#define SYNC(comm)\ - {MPI_BANNER("doing a SYNC"); MPI_Barrier(comm); MPI_BANNER("SYNC DONE");} -/* End of Define some handy debugging shorthands, routines, ... */ - -/* Constants definitions */ -/* 24 is a multiple of 2, 3, 4, 6, 8, 12. Neat for parallel tests. */ -#define SPACE1_DIM1 24 -#define SPACE1_DIM2 24 -#define SPACE1_RANK 2 -#define DATASETNAME1 "Data1" -#define DATASETNAME2 "Data2" -#define DATASETNAME3 "Data3" -/* hyperslab layout styles */ -#define BYROW 1 /* divide into slabs of rows */ -#define BYCOL 2 /* divide into blocks of columns */ - - -/* dataset data type. Int's can be easily octo dumped. */ -typedef int DATATYPE; +#include <testphdf5.h> /* global variables */ int nerrors = 0; /* errors count */ - -int mpi_size, mpi_rank; /* mpi variables */ - -/* option flags */ int verbose = 0; /* verbose, default as no. */ + +/* other option flags */ int doread=1; /* read test */ int dowrite=1; /* write test */ @@ -89,8 +21,7 @@ int dowrite=1; /* write test */ /* continue. */ #include <sys/types.h> #include <sys/stat.h> -void pause_proc(MPI_Comm comm, int mpi_rank, char* mpi_name, int mpi_namelen, - int argc, char **argv) +void pause_proc(MPI_Comm comm, int argc, char **argv) { int pid; @@ -100,14 +31,22 @@ void pause_proc(MPI_Comm comm, int mpi_rank, char* mpi_name, int mpi_namelen, int loops = 0; int time_int = 10; + /* mpi variables */ + int mpi_size, mpi_rank; + int mpi_namelen; + char mpi_name[MPI_MAX_PROCESSOR_NAME]; + #ifdef DISABLED /* check if an pause interval option is given */ if (--argc > 0 && isdigit(*++argv)) time_int = atoi(*argv); #endif pid = getpid(); + MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); + MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); + MPI_Get_processor_name(mpi_name, &mpi_namelen); - if (mpi_rank == 0) + if (MAINPROCESS) while ((stat(greenlight, &statbuf) == -1) && loops < maxloop){ if (!loops++){ printf("Proc %d (%*s, %d): You may attach %d for debugging.\n", @@ -121,806 +60,6 @@ void pause_proc(MPI_Comm comm, int mpi_rank, char* mpi_name, int mpi_namelen, } #endif /* USE_PAUSE */ -/* - * Setup the dimensions of the hyperslab. - * Two modes--by rows or by columns. - * Assume dimension rank is 2. - */ -void -slab_set(hssize_t start[], hsize_t count[], hsize_t stride[], int mode) -{ - switch (mode){ - case BYROW: - /* Each process takes a slabs of rows. */ - stride[0] = 1; - stride[1] = 1; - count[0] = SPACE1_DIM1/mpi_size; - count[1] = SPACE1_DIM2; - start[0] = mpi_rank*count[0]; - start[1] = 0; -if (verbose) printf("slab_set BYROW\n"); - break; - case BYCOL: - /* Each process takes a block of columns. */ - stride[0] = 1; - stride[1] = 1; - count[0] = SPACE1_DIM1; - count[1] = SPACE1_DIM2/mpi_size; - start[0] = 0; - start[1] = mpi_rank*count[1]; -#ifdef DISABLED - /* change the above macro to #ifndef if you want to test */ - /* zero elements access. */ - printf("set to size 0\n"); - if (!(mpi_rank % 3)) - count[1]=0; -#endif -if (verbose) printf("slab_set BYCOL\n"); - break; - default: - /* Unknown mode. Set it to cover the whole dataset. */ - printf("unknown slab_set mode (%d)\n", mode); - stride[0] = 1; - stride[1] = 1; - count[0] = SPACE1_DIM1; - count[1] = SPACE1_DIM2; - start[0] = 0; - start[1] = 0; -if (verbose) printf("slab_set wholeset\n"); - break; - } -if (verbose){ - printf("start[]=(%d,%d), count[]=(%d,%d), total datapoints=%d\n", - start[0], start[1], count[0], count[1], count[0]*count[1]); - } -} - - -/* - * Fill the dataset with trivial data for testing. - * Assume dimension rank is 2 and data is stored contiguous. - */ -void -dataset_fill(hssize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset) -{ - DATATYPE *dataptr = dataset; - int i, j; - - /* put some trivial data in the data_array */ - for (i=0; i < count[0]; i++){ - for (j=0; j < count[1]; j++){ - *dataptr = (i*stride[0]+start[0])*100 + (j*stride[1]+start[1]+1); - dataptr++; - } - } -} - - -/* - * Print the content of the dataset. - */ -void dataset_print(hssize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset) -{ - DATATYPE *dataptr = dataset; - int i, j; - - /* print the column heading */ - printf("%-8s", "Cols:"); - for (j=0; j < count[1]; j++){ - printf("%3d ", start[1]+j); - } - printf("\n"); - - /* print the slab data */ - for (i=0; i < count[0]; i++){ - printf("Row %2d: ", (int)(i*stride[0]+start[0])); - for (j=0; j < count[1]; j++){ - printf("%03d ", *dataptr++); - } - printf("\n"); - } -} - - -/* - * Print the content of the dataset. - */ -int dataset_vrfy(hssize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset, DATATYPE *original) -{ -#define MAX_ERR_REPORT 10 /* Maximum number of errors reported */ - DATATYPE *dataptr = dataset; - DATATYPE *originptr = original; - - int i, j, vrfyerrs; - - /* print it if verbose */ - if (verbose) - dataset_print(start, count, stride, dataset); - - vrfyerrs = 0; - for (i=0; i < count[0]; i++){ - for (j=0; j < count[1]; j++){ - if (*dataset != *original){ - if (vrfyerrs++ < MAX_ERR_REPORT){ - printf("Dataset Verify failed at [%d][%d](row %d, col %d): expect %d, got %d\n", - i, j, - (int)(i*stride[0]+start[0]), (int)(j*stride[1]+start[1]), - *(original), *(dataset)); - } - dataset++; - original++; - } - } - } - if (vrfyerrs > MAX_ERR_REPORT) - printf("[more errors ...]\n"); - if (vrfyerrs) - printf("%d errors found in dataset_vrfy\n", vrfyerrs); - return(vrfyerrs); -} - - -/* - * Example of using the parallel HDF5 library to create two datasets - * in one HDF5 files with parallel MPIO access support. - * The Datasets are of sizes (number-of-mpi-processes x DIM1) x DIM2. - * Each process controls only a slab of size DIM1 x DIM2 within each - * dataset. - */ - -void -phdf5writeInd(char *filename) -{ - hid_t fid1, fid2; /* HDF5 file IDs */ - hid_t acc_tpl1; /* File access templates */ - hid_t sid1,sid2; /* Dataspace ID */ - hid_t file_dataspace; /* File dataspace ID */ - hid_t mem_dataspace; /* memory dataspace ID */ - hid_t dataset1, dataset2; /* Dataset ID */ - int rank = SPACE1_RANK; /* Logical rank of dataspace */ - hsize_t dims1[SPACE1_RANK] = - {SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */ - hsize_t dimslocal1[SPACE1_RANK] = - {SPACE1_DIM1,SPACE1_DIM2}; /* local dataspace dim sizes */ - DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */ - - hssize_t start[SPACE1_RANK]; /* for hyperslab setting */ - hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */ - - herr_t ret; /* Generic return value */ - int i, j; - int mpi_size, mpi_rank; - char *fname; - int mrc; /* mpi return code */ - - MPI_Comm comm = MPI_COMM_WORLD; - MPI_Info info = MPI_INFO_NULL; - - if (verbose) - printf("Independent write test on file %s\n", filename); - - /* set up MPI parameters */ - MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); - MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); - - /* ------------------- - * START AN HDF5 FILE - * -------------------*/ - /* setup file access template with parallel IO access. */ - acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS); - VRFY((acc_tpl1 != FAIL), "H5Pcreate access succeed"); - /* set Parallel access with communicator */ - ret = H5Pset_mpi(acc_tpl1, comm, info); - VRFY((ret != FAIL), "H5Pset_mpi succeed"); - - /* create the file collectively */ - fid1=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl1); - VRFY((fid1 != FAIL), "H5Fcreate succeed"); - - /* Release file-access template */ - ret=H5Pclose(acc_tpl1); - VRFY((ret != FAIL), ""); - - - /* -------------------------- - * Define the dimensions of the overall datasets - * and the slabs local to the MPI process. - * ------------------------- */ - /* setup dimensionality object */ - sid1 = H5Screate_simple (SPACE1_RANK, dims1, NULL); - VRFY((sid1 != FAIL), "H5Screate_simple succeed"); - - - /* create a dataset collectively */ - dataset1 = H5Dcreate(fid1, DATASETNAME1, H5T_NATIVE_INT, sid1, - H5P_DEFAULT); - VRFY((dataset1 != FAIL), "H5Dcreate succeed"); - - /* create another dataset collectively */ - dataset2 = H5Dcreate(fid1, DATASETNAME2, H5T_NATIVE_INT, sid1, - H5P_DEFAULT); - VRFY((dataset2 != FAIL), "H5Dcreate succeed"); - - - - /* set up dimensions of the slab this process accesses */ - slab_set(start, count, stride, BYROW); - - /* put some trivial data in the data_array */ - dataset_fill(start, count, stride, &data_array1[0][0]); - MESG("data_array initialized"); - - /* create a file dataspace independently */ - file_dataspace = H5Dget_space (dataset1); - VRFY((file_dataspace != FAIL), "H5Dget_space succeed"); - ret=H5Sset_hyperslab(file_dataspace, start, count, stride); - VRFY((ret != FAIL), "H5Sset_hyperslab succeed"); - - /* create a memory dataspace independently */ - mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); - VRFY((mem_dataspace != FAIL), ""); - - /* write data independently */ - ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, - H5P_DEFAULT, data_array1); - VRFY((ret != FAIL), "H5Dwrite succeed"); - - /* write data independently */ - ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, - H5P_DEFAULT, data_array1); - VRFY((ret != FAIL), "H5Dwrite succeed"); - - /* release dataspace ID */ - H5Sclose(file_dataspace); - - /* close dataset collectively */ - ret=H5Dclose(dataset1); - VRFY((ret != FAIL), "H5Dclose1 succeed"); - ret=H5Dclose(dataset2); - VRFY((ret != FAIL), "H5Dclose2 succeed"); - - /* release all IDs created */ - H5Sclose(sid1); - - /* close the file collectively */ - H5Fclose(fid1); -} - -/* Example of using the parallel HDF5 library to read a dataset */ -void -phdf5readInd(char *filename) -{ - hid_t fid1, fid2; /* HDF5 file IDs */ - hid_t acc_tpl1; /* File access templates */ - hid_t sid1,sid2; /* Dataspace ID */ - hid_t file_dataspace; /* File dataspace ID */ - hid_t mem_dataspace; /* memory dataspace ID */ - hid_t dataset1, dataset2; /* Dataset ID */ - int rank = SPACE1_RANK; /* Logical rank of dataspace */ - hsize_t dims1[] = {SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */ - DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */ - DATATYPE data_origin1[SPACE1_DIM1][SPACE1_DIM2]; /* expected data buffer */ - - hssize_t start[SPACE1_RANK]; /* for hyperslab setting */ - hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */ - - herr_t ret; /* Generic return value */ - int i, j; - int mpi_size, mpi_rank; - - MPI_Comm comm = MPI_COMM_WORLD; - MPI_Info info = MPI_INFO_NULL; - - if (verbose) - printf("Independent read test on file %s\n", filename); - - /* set up MPI parameters */ - MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); - MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); - - - /* setup file access template */ - acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS); - VRFY((acc_tpl1 != FAIL), ""); - /* set Parallel access with communicator */ - ret = H5Pset_mpi(acc_tpl1, comm, info); - VRFY((ret != FAIL), ""); - - - /* open the file collectively */ - fid1=H5Fopen(filename,H5F_ACC_RDWR,acc_tpl1); - VRFY((fid1 != FAIL), ""); - - /* Release file-access template */ - ret=H5Pclose(acc_tpl1); - VRFY((ret != FAIL), ""); - - /* open the dataset1 collectively */ - dataset1 = H5Dopen(fid1, DATASETNAME1); - VRFY((dataset1 != FAIL), ""); - - /* open another dataset collectively */ - dataset2 = H5Dopen(fid1, DATASETNAME1); - VRFY((dataset2 != FAIL), ""); - - - /* set up dimensions of the slab this process accesses */ - slab_set(start, count, stride, BYROW); - - /* create a file dataspace independently */ - file_dataspace = H5Dget_space (dataset1); - VRFY((file_dataspace != FAIL), ""); - ret=H5Sset_hyperslab(file_dataspace, start, count, stride); - VRFY((ret != FAIL), ""); - - /* create a memory dataspace independently */ - mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); - VRFY((mem_dataspace != FAIL), ""); - - /* fill dataset with test data */ - dataset_fill(start, count, stride, &data_origin1[0][0]); - - /* read data independently */ - ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, - H5P_DEFAULT, data_array1); - VRFY((ret != FAIL), ""); - - /* verify the read data with original expected data */ - ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]); - if (ret) nerrors++; - - /* read data independently */ - ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, - H5P_DEFAULT, data_array1); - VRFY((ret != FAIL), ""); - - /* verify the read data with original expected data */ - ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]); - if (ret) nerrors++; - - /* close dataset collectively */ - ret=H5Dclose(dataset1); - VRFY((ret != FAIL), ""); - ret=H5Dclose(dataset2); - VRFY((ret != FAIL), ""); - - /* release all IDs created */ - H5Sclose(file_dataspace); - - /* close the file collectively */ - H5Fclose(fid1); -} - - -/* - * Example of using the parallel HDF5 library to create two datasets - * in one HDF5 file with collective parallel access support. - * The Datasets are of sizes (number-of-mpi-processes x DIM1) x DIM2. - * Each process controls only a slab of size DIM1 x DIM2 within each - * dataset. [Note: not so yet. Datasets are of sizes DIM1xDIM2 and - * each process controls a hyperslab within.] - */ - -void -phdf5writeAll(char *filename) -{ - hid_t fid1, fid2; /* HDF5 file IDs */ - hid_t acc_tpl1; /* File access templates */ - hid_t xfer_plist; /* Dataset transfer properties list */ - hid_t sid1,sid2; /* Dataspace ID */ - hid_t file_dataspace; /* File dataspace ID */ - hid_t mem_dataspace; /* memory dataspace ID */ - hid_t dataset1, dataset2; /* Dataset ID */ - hid_t datatype; /* Datatype ID */ - int rank = SPACE1_RANK; /* Logical rank of dataspace */ - hsize_t dims1[SPACE1_RANK] = - {SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */ - DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */ - - hssize_t start[SPACE1_RANK]; /* for hyperslab setting */ - hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */ - - herr_t ret; /* Generic return value */ - int mpi_size, mpi_rank; - - MPI_Comm comm = MPI_COMM_WORLD; - MPI_Info info = MPI_INFO_NULL; - - if (verbose) - printf("Collective write test on file %s\n", filename); - - /* set up MPI parameters */ - MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); - MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); - - /* ------------------- - * START AN HDF5 FILE - * -------------------*/ - /* setup file access template with parallel IO access. */ - acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS); - VRFY((acc_tpl1 != FAIL), "H5Pcreate access succeed"); - /* set Parallel access with communicator */ - ret = H5Pset_mpi(acc_tpl1, comm, info); - VRFY((ret != FAIL), "H5Pset_mpi succeed"); - - /* create the file collectively */ - fid1=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl1); - VRFY((fid1 != FAIL), "H5Fcreate succeed"); - - /* Release file-access template */ - ret=H5Pclose(acc_tpl1); - VRFY((ret != FAIL), ""); - - - /* -------------------------- - * Define the dimensions of the overall datasets - * and create the dataset - * ------------------------- */ - /* setup dimensionality object */ - sid1 = H5Screate_simple (SPACE1_RANK, dims1, NULL); - VRFY((sid1 != FAIL), "H5Screate_simple succeed"); - - - /* create a dataset collectively */ - dataset1 = H5Dcreate(fid1, DATASETNAME1, H5T_NATIVE_INT, sid1, H5P_DEFAULT); - VRFY((dataset1 != FAIL), "H5Dcreate succeed"); - - /* create another dataset collectively */ - datatype = H5Tcopy(H5T_NATIVE_INT32); - ret = H5Tset_order(datatype, H5T_ORDER_LE); - VRFY((ret != FAIL), "H5Tset_order succeed"); - - dataset2 = H5Dcreate(fid1, DATASETNAME2, datatype, sid1, H5P_DEFAULT); - VRFY((dataset2 != FAIL), "H5Dcreate 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); - - /* create a file dataspace independently */ - file_dataspace = H5Dget_space (dataset1); - VRFY((file_dataspace != FAIL), "H5Dget_space succeed"); - ret=H5Sset_hyperslab(file_dataspace, start, count, stride); - VRFY((ret != FAIL), "H5Sset_hyperslab succeed"); - - /* create a memory dataspace independently */ - mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); - VRFY((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); - VRFY((xfer_plist != FAIL), ""); - ret=H5Pset_xfer(xfer_plist, H5D_XFER_COLLECTIVE); - VRFY((ret != FAIL), "H5Pcreate xfer succeed"); - - /* write data collectively */ - ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, - xfer_plist, data_array1); - VRFY((ret != FAIL), "H5Dwrite dataset1 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); - - /* 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); - VRFY((file_dataspace != FAIL), "H5Dget_space succeed"); - ret=H5Sset_hyperslab(file_dataspace, start, count, stride); - VRFY((ret != FAIL), "H5Sset_hyperslab succeed"); - - /* create a memory dataspace independently */ - mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); - VRFY((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); - VRFY((xfer_plist != FAIL), ""); - ret=H5Pset_xfer(xfer_plist, H5D_XFER_COLLECTIVE); - VRFY((ret != FAIL), "H5Pcreate xfer succeed"); - - /* write data independently */ -printf("WRITING TO DATASET2\n"); - ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, - xfer_plist, data_array1); - VRFY((ret != FAIL), "H5Dwrite dataset2 succeed"); - - /* release all temporary handles. */ - H5Sclose(file_dataspace); - H5Sclose(mem_dataspace); - H5Pclose(xfer_plist); - - - /* - * All writes completed. Close datasets collectively - */ - ret=H5Dclose(dataset1); - VRFY((ret != FAIL), "H5Dclose1 succeed"); - ret=H5Dclose(dataset2); - VRFY((ret != FAIL), "H5Dclose2 succeed"); - - /* release all IDs created */ - H5Sclose(sid1); - - /* close the file collectively */ - H5Fclose(fid1); -} - -/* - * Example of using the parallel HDF5 library to read two datasets - * in one HDF5 file with collective parallel access support. - * The Datasets are of sizes (number-of-mpi-processes x DIM1) x DIM2. - * Each process controls only a slab of size DIM1 x DIM2 within each - * dataset. [Note: not so yet. Datasets are of sizes DIM1xDIM2 and - * each process controls a hyperslab within.] - */ - -void -phdf5readAll(char *filename) -{ - hid_t fid1, fid2; /* HDF5 file IDs */ - hid_t acc_tpl1; /* File access templates */ - hid_t xfer_plist; /* Dataset transfer properties list */ - hid_t sid1,sid2; /* Dataspace ID */ - hid_t file_dataspace; /* File dataspace ID */ - hid_t mem_dataspace; /* memory dataspace ID */ - hid_t dataset1, dataset2; /* Dataset ID */ - int rank = SPACE1_RANK; /* Logical rank of dataspace */ - hsize_t dims1[] = {SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */ - DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */ - DATATYPE data_origin1[SPACE1_DIM1][SPACE1_DIM2]; /* expected data buffer */ - - hssize_t start[SPACE1_RANK]; /* for hyperslab setting */ - hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */ - - herr_t ret; /* Generic return value */ - int mpi_size, mpi_rank; - - MPI_Comm comm = MPI_COMM_WORLD; - MPI_Info info = MPI_INFO_NULL; - - if (verbose) - printf("Collective read test on file %s\n", filename); - - /* set up MPI parameters */ - MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); - MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); - - /* ------------------- - * OPEN AN HDF5 FILE - * -------------------*/ - /* setup file access template with parallel IO access. */ - acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS); - VRFY((acc_tpl1 != FAIL), "H5Pcreate access succeed"); - /* set Parallel access with communicator */ - ret = H5Pset_mpi(acc_tpl1, comm, info); - VRFY((ret != FAIL), "H5Pset_mpi succeed"); - - /* open the file collectively */ - fid1=H5Fopen(filename,H5F_ACC_RDWR,acc_tpl1); - VRFY((fid1 != FAIL), "H5Fopen succeed"); - - /* Release file-access template */ - ret=H5Pclose(acc_tpl1); - VRFY((ret != FAIL), ""); - - - /* -------------------------- - * Open the datasets in it - * ------------------------- */ - /* open the dataset1 collectively */ - dataset1 = H5Dopen(fid1, DATASETNAME1); - VRFY((dataset1 != FAIL), "H5Dopen succeed"); - - /* open another dataset collectively */ - dataset2 = H5Dopen(fid1, DATASETNAME2); - VRFY((dataset2 != FAIL), "H5Dopen 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); - - /* create a file dataspace independently */ - file_dataspace = H5Dget_space (dataset1); - VRFY((file_dataspace != FAIL), "H5Dget_space succeed"); - ret=H5Sset_hyperslab(file_dataspace, start, count, stride); - VRFY((ret != FAIL), "H5Sset_hyperslab succeed"); - - /* create a memory dataspace independently */ - mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); - VRFY((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_origin1[0][0]); - } - - /* set up the collective transfer properties list */ - xfer_plist = H5Pcreate (H5P_DATASET_XFER); - VRFY((xfer_plist != FAIL), ""); - ret=H5Pset_xfer(xfer_plist, H5D_XFER_COLLECTIVE); - VRFY((ret != FAIL), "H5Pcreate xfer succeed"); - - /* read data collectively */ - ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, - xfer_plist, data_array1); - VRFY((ret != FAIL), "H5Dread succeed"); - - /* verify the read data with original expected data */ - ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]); - if (ret) nerrors++; - - /* 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); - - /* create a file dataspace independently */ - file_dataspace = H5Dget_space (dataset1); - VRFY((file_dataspace != FAIL), "H5Dget_space succeed"); - ret=H5Sset_hyperslab(file_dataspace, start, count, stride); - VRFY((ret != FAIL), "H5Sset_hyperslab succeed"); - - /* create a memory dataspace independently */ - mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); - VRFY((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_origin1[0][0]); - } - - /* set up the collective transfer properties list */ - xfer_plist = H5Pcreate (H5P_DATASET_XFER); - VRFY((xfer_plist != FAIL), ""); - ret=H5Pset_xfer(xfer_plist, H5D_XFER_COLLECTIVE); - VRFY((ret != FAIL), "H5Pcreate xfer succeed"); - - /* read data independently */ - ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, - xfer_plist, data_array1); - VRFY((ret != FAIL), "H5Dread succeed"); - - /* verify the read data with original expected data */ - ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]); - if (ret) nerrors++; - - /* release all temporary handles. */ - H5Sclose(file_dataspace); - H5Sclose(mem_dataspace); - H5Pclose(xfer_plist); - - - /* - * All reads completed. Close datasets collectively - */ - ret=H5Dclose(dataset1); - VRFY((ret != FAIL), "H5Dclose1 succeed"); - ret=H5Dclose(dataset2); - VRFY((ret != FAIL), "H5Dclose2 succeed"); - - /* close the file collectively */ - H5Fclose(fid1); -} - -/* - * test file access by communicator besides COMM_WORLD. - * Split COMM_WORLD into two, one (even_comm) contains the original - * processes of even ranks. The other (odd_comm) contains the original - * processes of odd ranks. Processes in even_comm creates a file, then - * cloose it, using even_comm. Processes in old_comm just do a barrier - * using odd_comm. Then they all do a barrier using COMM_WORLD. - * If the file creation and cloose does not do correct collective action - * according to the communicator argument, the processes will freeze up - * sooner or later due to barrier mixed up. - */ -void -test_split_comm_access(char *filename[]) -{ - int mpi_size, mpi_rank; - MPI_Comm comm; - MPI_Info info = MPI_INFO_NULL; - int color, mrc; - int newrank, newprocs; - hid_t fid; /* file IDs */ - hid_t acc_tpl; /* File access properties */ - herr_t ret; /* generic return value */ - - if (verbose) - printf("Split Communicator access test on file %s %s\n", - filename[0], filename[1]); - - /* set up MPI parameters */ - MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); - MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); - color = mpi_rank%2; - mrc = MPI_Comm_split (MPI_COMM_WORLD, color, mpi_rank, &comm); - VRFY((mrc==MPI_SUCCESS), ""); - MPI_Comm_size(comm,&newprocs); - MPI_Comm_rank(comm,&newrank); - - if (color){ - /* odd-rank processes */ - mrc = MPI_Barrier(comm); - VRFY((mrc==MPI_SUCCESS), ""); - }else{ - /* even-rank processes */ - int sub_mpi_rank; /* rank in the sub-comm */ - MPI_Comm_rank(comm,&sub_mpi_rank); - - /* setup file access template */ - acc_tpl = H5Pcreate (H5P_FILE_ACCESS); - VRFY((acc_tpl != FAIL), ""); - - /* set Parallel access with communicator */ - ret = H5Pset_mpi(acc_tpl, comm, info); - VRFY((ret != FAIL), ""); - - /* create the file collectively */ - fid=H5Fcreate(filename[color],H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl); - VRFY((fid != FAIL), "H5Fcreate succeed"); - - /* Release file-access template */ - ret=H5Pclose(acc_tpl); - VRFY((ret != FAIL), ""); - - /* close the file */ - ret=H5Fclose(fid); - VRFY((ret != FAIL), ""); - - /* detele the test file */ - if (sub_mpi_rank == 0){ - mrc = MPI_File_delete(filename[color], info); - VRFY((mrc==MPI_SUCCESS), ""); - } - } -} /* * Show command usage @@ -965,43 +104,59 @@ parse_options(int argc, char **argv){ main(int argc, char **argv) { - char *filenames[]={ "ParaEg1.h5f", "ParaEg2.h5f" }; + char *filenames[]={ "ParaEg1.h5f", + "ParaEg2.h5f", + "ParaEg3.h5f" + }; - int mpi_namelen; - char mpi_name[MPI_MAX_PROCESSOR_NAME]; + int mpi_size, mpi_rank; /* mpi variables */ + + MPI_Init(&argc, &argv); + MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); + MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); + + if (MAINPROCESS){ + printf("===================================\n"); + printf("PHDF5 TESTS START\n"); + printf("===================================\n"); + } - MPI_Init(&argc,&argv); - MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); - MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); - MPI_Get_processor_name(mpi_name,&mpi_namelen); /* Make sure datasets can be divided into equal chunks by the processes */ - if ((SPACE1_DIM1 % mpi_size) || (SPACE1_DIM2 % mpi_size)){ - printf("DIM1(%d) and DIM2(%d) must be multiples of processes (%d)\n", - SPACE1_DIM1, SPACE1_DIM2, mpi_size); + if ((DIM1 % mpi_size) || (DIM2 % mpi_size)){ + if (MAINPROCESS) + printf("DIM1(%d) and DIM2(%d) must be multiples of processes(%d)\n", + DIM1, DIM2, mpi_size); nerrors++; goto finish; } #ifdef USE_PAUSE - pause_proc(MPI_COMM_WORLD, mpi_rank, mpi_name, mpi_namelen, argc, argv); + pause_proc(MPI_COMM_WORLD, argc, argv); #endif if (parse_options(argc, argv) != 0) goto finish; if (dowrite){ - MPI_BANNER("testing PHDF5 dataset using split communicators..."); + MPI_BANNER("testing dataset using split communicators..."); test_split_comm_access(filenames); - MPI_BANNER("testing PHDF5 dataset independent write..."); - phdf5writeInd(filenames[0]); - MPI_BANNER("testing PHDF5 dataset collective write..."); - phdf5writeAll(filenames[1]); + + MPI_BANNER("testing dataset independent write..."); + dataset_writeInd(filenames[0]); + + MPI_BANNER("testing dataset collective write..."); + dataset_writeAll(filenames[1]); + MPI_BANNER("testing extendable dataset independent write..."); + extend_writeInd(filenames[2]); } if (doread){ - MPI_BANNER("testing PHDF5 dataset independent read..."); - phdf5readInd(filenames[0]); - MPI_BANNER("testing PHDF5 dataset collective read..."); - phdf5readAll(filenames[1]); + MPI_BANNER("testing dataset independent read..."); + dataset_readInd(filenames[0]); + + MPI_BANNER("testing dataset collective read..."); + dataset_readAll(filenames[1]); + MPI_BANNER("testing extendable dataset independent read..."); + extend_readInd(filenames[2]); } if (!(dowrite || doread)){ @@ -1010,7 +165,7 @@ main(int argc, char **argv) } finish: - if (mpi_rank == 0){ /* only process 0 reports */ + if (MAINPROCESS){ /* only process 0 reports */ printf("===================================\n"); if (nerrors){ printf("***PHDF5 tests detected %d errors***\n", nerrors); |