diff options
| -rw-r--r-- | examples/Makefile.in | 7 | ||||
| -rw-r--r-- | examples/ph5example.c | 1018 |
2 files changed, 1024 insertions, 1 deletions
diff --git a/examples/Makefile.in b/examples/Makefile.in index fa5d93b..b36f86a 100644 --- a/examples/Makefile.in +++ b/examples/Makefile.in @@ -16,7 +16,8 @@ LIBHDF5=../src/libhdf5.la ## These are the programs that `make all' or `make tests' will build and which ## `make check' will run. List them in the order they should be run. TEST_PROGS= h5_write h5_read h5_extend_write h5_chunk_read h5_compound \ - h5_group h5_select h5_attribute h5_mount h5_reference + h5_group h5_select h5_attribute h5_mount h5_reference \ + ph5example ## These are the files that `make clean' (and derivatives) will remove from ## this directory. @@ -62,4 +63,8 @@ h5_mount: h5_mount.lo h5_reference: h5_reference.lo @$(LT_LINK_EXE) $(CFLAGS) -o $@ h5_reference.lo $(LIBHDF5) $(LDFLAGS) $(LIBS) + +ph5example: ph5example.lo + @$(LT_LINK_EXE) $(CFLAGS) -o $@ $@.lo $(LIBHDF5) $(LDFLAGS) $(LIBS) + @CONCLUDE@ diff --git a/examples/ph5example.c b/examples/ph5example.c new file mode 100644 index 0000000..2adffbc --- /dev/null +++ b/examples/ph5example.c @@ -0,0 +1,1018 @@ +/* + * Example of using the parallel HDF5 library to access datasets. + * Last revised: March 22, 2001 for v1.4.0. + * + * 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. + */ + +#include <assert.h> +#include <hdf5.h> + +#ifdef H5_HAVE_PARALLEL +/* 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 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; + +/* global variables */ +int nerrors = 0; /* errors count */ + +int mpi_size, mpi_rank; /* mpi variables */ + +/* option flags */ +int verbose = 0; /* verbose, default as no. */ +int doread=1; /* read test */ +int dowrite=1; /* write test */ + + + +/* + * 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; + 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]; + 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; + break; + } +} + + +/* + * 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); + } + } +} + + +/* + * 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 slab read */ + for (i=0; i < count[0]; i++){ + printf("Row %d: ", (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, nerrors; + + /* print it if verbose */ + if (verbose) + dataset_print(start, count, stride, dataset); + + nerrors = 0; + for (i=0; i < count[0]; i++){ + for (j=0; j < count[1]; j++){ + if (*dataset++ != *original++){ + nerrors++; + if (nerrors <= 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]), + *(dataset-1), *(original-1)); + } + } + } + } + if (nerrors > MAX_ERR_REPORT) + printf("[more errors ...]\n"); + if (nerrors) + printf("%d errors found in dataset_vrfy\n", nerrors); + return(nerrors); +} + + +/* + * 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); + 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"); + + /* Release file-access template */ + ret=H5Pclose(acc_tpl1); + assert(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); + assert (sid1 != FAIL); + MESG("H5Screate_simple succeed"); + + + /* create a dataset collectively */ + dataset1 = H5Dcreate(fid1, DATASETNAME1, H5T_NATIVE_INT, sid1, + H5P_DEFAULT); + assert(dataset1 != FAIL); + MESG("H5Dcreate succeed"); + + /* create another dataset collectively */ + dataset2 = H5Dcreate(fid1, DATASETNAME2, H5T_NATIVE_INT, sid1, + H5P_DEFAULT); + assert(dataset2 != FAIL); + MESG("H5Dcreate succeed"); + + + + /* set up dimensions of the slab this process accesses */ + start[0] = mpi_rank*SPACE1_DIM1/mpi_size; + start[1] = 0; + count[0] = SPACE1_DIM1/mpi_size; + count[1] = SPACE1_DIM2; + stride[0] = 1; + stride[1] =1; +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]); + + /* 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); + 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); + + /* write data independently */ + ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, + H5P_DEFAULT, data_array1); + assert(ret != FAIL); + MESG("H5Dwrite succeed"); + + /* write data independently */ + ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, + H5P_DEFAULT, data_array1); + assert(ret != FAIL); + MESG("H5Dwrite succeed"); + + /* release dataspace ID */ + H5Sclose(file_dataspace); + + /* close dataset 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); +} + +/* 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); + assert(acc_tpl1 != FAIL); + /* set Parallel access with communicator */ + ret = H5Pset_fapl_mpio(acc_tpl1, comm, info); + assert(ret != FAIL); + + + /* open the file collectively */ + fid1=H5Fopen(filename,H5F_ACC_RDWR,acc_tpl1); + assert(fid1 != FAIL); + + /* Release file-access template */ + ret=H5Pclose(acc_tpl1); + assert(ret != FAIL); + + /* open the dataset1 collectively */ + dataset1 = H5Dopen(fid1, DATASETNAME1); + assert(dataset1 != FAIL); + + /* open another dataset collectively */ + dataset2 = H5Dopen(fid1, DATASETNAME1); + assert(dataset2 != FAIL); + + + /* set up dimensions of the slab this process accesses */ + start[0] = mpi_rank*SPACE1_DIM1/mpi_size; + start[1] = 0; + count[0] = SPACE1_DIM1/mpi_size; + count[1] = SPACE1_DIM2; + stride[0] = 1; + stride[1] =1; +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]); + + /* create a file dataspace independently */ + file_dataspace = H5Dget_space (dataset1); + assert(file_dataspace != FAIL); + ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, + count, NULL); + assert(ret != FAIL); + + /* 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]); + + /* read data independently */ + ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, + H5P_DEFAULT, data_array1); + assert(ret != FAIL); + + /* 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); + + /* read data independently */ + ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, + H5P_DEFAULT, data_array1); + assert(ret != FAIL); + + /* verify the read data with original expected data */ + ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]); + assert(ret == 0); + + /* close dataset collectively */ + ret=H5Dclose(dataset1); + assert(ret != FAIL); + ret=H5Dclose(dataset2); + assert(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 */ + 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); + 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"); + + /* 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 = H5Dcreate(fid1, DATASETNAME1, H5T_NATIVE_INT, sid1, H5P_DEFAULT); + assert(dataset1 != FAIL); + MESG("H5Dcreate succeed"); + + /* create another dataset collectively */ + dataset2 = H5Dcreate(fid1, DATASETNAME2, H5T_NATIVE_INT, sid1, H5P_DEFAULT); + assert(dataset2 != FAIL); + MESG("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); +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]); + + /* 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[]=(%d,%d), count[]=(%d,%d), total datapoints=%d\n", + start[0], start[1], count[0], count[1], 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); +} + +/* + * 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); + 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 = H5Dopen(fid1, DATASETNAME1); + assert(dataset1 != FAIL); + MESG("H5Dopen succeed"); + + /* open another dataset collectively */ + dataset2 = H5Dopen(fid1, DATASETNAME1); + assert(dataset2 != FAIL); + MESG("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); +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]); + + /* 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[]=(%d,%d), count[]=(%d,%d), total datapoints=%d\n", + start[0], start[1], count[0], count[1], 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); +} + +/* + * 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 *filenames[]) +{ + int mpi_size, myrank; + 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("Independent write test on file %s %s\n", + filenames[0], filenames[1]); + + /* set up MPI parameters */ + MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); + MPI_Comm_rank(MPI_COMM_WORLD,&myrank); + color = myrank%2; + mrc = MPI_Comm_split (MPI_COMM_WORLD, color, myrank, &comm); + assert(mrc==MPI_SUCCESS); + MPI_Comm_size(comm,&newprocs); + MPI_Comm_rank(comm,&newrank); + + if (color){ + /* odd-rank processes */ + mrc = MPI_Barrier(comm); + assert(mrc==MPI_SUCCESS); + }else{ + /* even-rank processes */ + /* setup file access template */ + acc_tpl = H5Pcreate (H5P_FILE_ACCESS); + assert(acc_tpl != FAIL); + + /* set Parallel access with communicator */ + ret = H5Pset_fapl_mpio(acc_tpl, comm, info); + assert(ret != FAIL); + + /* create the file collectively */ + fid=H5Fcreate(filenames[color],H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl); + assert(fid != FAIL); + MESG("H5Fcreate succeed"); + + /* Release file-access template */ + ret=H5Pclose(acc_tpl); + assert(ret != FAIL); + + ret=H5Fclose(fid); + assert(ret != FAIL); + } + if (myrank == 0){ + mrc = MPI_File_delete(filenames[color], info); + assert(mrc==MPI_SUCCESS); + } +} + +/* + * Show command usage + */ +void +usage() +{ + printf("Usage: testphdf5 [-r] [-w] [-v]\n"); + printf("\t-r\tno read\n"); + printf("\t-w\tno write\n"); + printf("\t-v\tverbose on\n"); + printf("\tdefault do write then read\n"); + printf("\n"); +} + + +/* + * parse the command line options + */ +int +parse_options(int argc, char **argv){ + while (--argc){ + if (**(++argv) != '-'){ + break; + }else{ + switch(*(*argv+1)){ + case 'r': doread = 0; + break; + case 'w': dowrite = 0; + break; + case 'v': verbose = 1; + break; + default: usage(); + nerrors++; + return(1); + } + } + } + return(0); +} + + +int +main(int argc, char **argv) +{ + char *filenames[]={ "ParaEg1.h5f", "ParaEg2.h5f" }; + + int mpi_namelen; + char mpi_name[MPI_MAX_PROCESSOR_NAME]; + + 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); + nerrors++; + goto finish; + } + + if (parse_options(argc, argv) != 0) + goto finish; + + if (dowrite){ + MPI_BANNER("testing PHDF5 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]); + } + if (doread){ + MPI_BANNER("testing PHDF5 dataset independent read..."); + phdf5readInd(filenames[0]); + MPI_BANNER("testing PHDF5 dataset collective read..."); + phdf5readAll(filenames[1]); + } + + if (!(dowrite || doread)){ + usage(); + nerrors++; + } + +finish: + if (mpi_rank == 0){ /* only process 0 reports */ + if (nerrors) + printf("***PHDF5 tests detected %d errors***\n", nerrors); + else{ + printf("===================================\n"); + printf("PHDF5 tests finished with no errors\n"); + printf("===================================\n"); + } + } + MPI_Finalize(); + + return(nerrors); +} + +#else /* H5_HAVE_PARALLEL */ +/* dummy program since H5_HAVE_PARALLE is not configured in */ +int +main() +{ +printf("No PHDF5 example because parallel is not configured in\n"); +return(0); +} +#endif /* H5_HAVE_PARALLEL */ |