mirror of
https://github.com/HDFGroup/hdf5.git
synced 2024-11-27 02:10:55 +08:00
ed7d456e51
Tested platform: Kagiso only since it is only a comment block change. If it works in one machine, it should work in all, I hope. Still need to check the parallel build on copper.
1133 lines
34 KiB
C
1133 lines
34 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the files COPYING and Copyright.html. COPYING can be found at the root *
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* of the source code distribution tree; Copyright.html can be found at the *
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* root level of an installed copy of the electronic HDF5 document set and *
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* is linked from the top-level documents page. It can also be found at *
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* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
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* access to either file, you may request a copy from help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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/*
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* Example of using the parallel HDF5 library to access datasets.
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* Last revised: April 24, 2001.
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*
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* This program contains two parts. In the first part, the mpi processes
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* collectively create a new parallel HDF5 file and create two fixed
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* dimension datasets in it. Then each process writes a hyperslab into
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* each dataset in an independent mode. All processes collectively
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* close the datasets and the file.
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* In the second part, the processes collectively open the created file
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* and the two datasets in it. Then each process reads a hyperslab from
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* each dataset in an independent mode and prints them out.
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* All processes collectively close the datasets and the file.
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*
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* The need of requirement of parallel file prefix is that in general
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* the current working directory in which compiling is done, is not suitable
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* for parallel I/O and there is no standard pathname for parallel file
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* systems. In some cases, the parallel file name may even needs some
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* parallel file type prefix such as: "pfs:/GF/...". Therefore, this
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* example requires an explicite parallel file prefix. See the usage
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* for more detail.
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*/
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#include <assert.h>
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#include "hdf5.h"
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#include <string.h>
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#include <stdlib.h>
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#ifdef H5_HAVE_PARALLEL
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/* Temporary source code */
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#define FAIL -1
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/* temporary code end */
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/* Define some handy debugging shorthands, routines, ... */
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/* debugging tools */
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#define MESG(x)\
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if (verbose) printf("%s\n", x);\
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#define MPI_BANNER(mesg)\
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{printf("--------------------------------\n");\
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printf("Proc %d: ", mpi_rank); \
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printf("*** %s\n", mesg);\
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printf("--------------------------------\n");}
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#define SYNC(comm)\
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{MPI_BANNER("doing a SYNC"); MPI_Barrier(comm); MPI_BANNER("SYNC DONE");}
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/* End of Define some handy debugging shorthands, routines, ... */
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/* Constants definitions */
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/* 24 is a multiple of 2, 3, 4, 6, 8, 12. Neat for parallel tests. */
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#define SPACE1_DIM1 24
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#define SPACE1_DIM2 24
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#define SPACE1_RANK 2
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#define DATASETNAME1 "Data1"
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#define DATASETNAME2 "Data2"
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#define DATASETNAME3 "Data3"
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/* hyperslab layout styles */
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#define BYROW 1 /* divide into slabs of rows */
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#define BYCOL 2 /* divide into blocks of columns */
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#define PARAPREFIX "HDF5_PARAPREFIX" /* file prefix environment variable name */
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/* dataset data type. Int's can be easily octo dumped. */
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typedef int DATATYPE;
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/* global variables */
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int nerrors = 0; /* errors count */
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#ifndef PATH_MAX
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#define PATH_MAX 512
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#endif /* !PATH_MAX */
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char testfiles[2][PATH_MAX];
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int mpi_size, mpi_rank; /* mpi variables */
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/* option flags */
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int verbose = 0; /* verbose, default as no. */
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int doread=1; /* read test */
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int dowrite=1; /* write test */
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int docleanup=1; /* cleanup */
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/* Prototypes */
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void slab_set(hsize_t start[], hsize_t count[], hsize_t stride[], int mode);
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void dataset_fill(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset);
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void dataset_print(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset);
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int dataset_vrfy(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset, DATATYPE *original);
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void phdf5writeInd(char *filename);
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void phdf5readInd(char *filename);
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void phdf5writeAll(char *filename);
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void phdf5readAll(char *filename);
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void test_split_comm_access(char filenames[][PATH_MAX]);
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int parse_options(int argc, char **argv);
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void usage(void);
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int mkfilenames(char *prefix);
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void cleanup(void);
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/*
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* Setup the dimensions of the hyperslab.
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* Two modes--by rows or by columns.
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* Assume dimension rank is 2.
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*/
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void
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slab_set(hsize_t start[], hsize_t count[], hsize_t stride[], int mode)
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{
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switch (mode){
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case BYROW:
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/* Each process takes a slabs of rows. */
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stride[0] = 1;
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stride[1] = 1;
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count[0] = SPACE1_DIM1/mpi_size;
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count[1] = SPACE1_DIM2;
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start[0] = mpi_rank*count[0];
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start[1] = 0;
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break;
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case BYCOL:
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/* Each process takes a block of columns. */
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stride[0] = 1;
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stride[1] = 1;
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count[0] = SPACE1_DIM1;
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count[1] = SPACE1_DIM2/mpi_size;
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start[0] = 0;
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start[1] = mpi_rank*count[1];
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break;
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default:
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/* Unknown mode. Set it to cover the whole dataset. */
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printf("unknown slab_set mode (%d)\n", mode);
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stride[0] = 1;
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stride[1] = 1;
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count[0] = SPACE1_DIM1;
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count[1] = SPACE1_DIM2;
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start[0] = 0;
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start[1] = 0;
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break;
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}
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}
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/*
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* Fill the dataset with trivial data for testing.
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* Assume dimension rank is 2 and data is stored contiguous.
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*/
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void
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dataset_fill(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset)
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{
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DATATYPE *dataptr = dataset;
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hsize_t i, j;
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/* put some trivial data in the data_array */
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for (i=0; i < count[0]; i++){
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for (j=0; j < count[1]; j++){
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*dataptr++ = (i*stride[0]+start[0])*100 + (j*stride[1]+start[1]+1);
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}
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}
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}
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/*
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* Print the content of the dataset.
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*/
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void dataset_print(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset)
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{
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DATATYPE *dataptr = dataset;
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hsize_t i, j;
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/* print the slab read */
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for (i=0; i < count[0]; i++){
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printf("Row %lu: ", (unsigned long)(i*stride[0]+start[0]));
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for (j=0; j < count[1]; j++){
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printf("%03d ", *dataptr++);
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}
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printf("\n");
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}
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}
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/*
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* Print the content of the dataset.
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*/
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int dataset_vrfy(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset, DATATYPE *original)
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{
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#define MAX_ERR_REPORT 10 /* Maximum number of errors reported */
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hsize_t i, j;
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int nerr;
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/* print it if verbose */
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if (verbose)
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dataset_print(start, count, stride, dataset);
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nerr = 0;
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for (i=0; i < count[0]; i++){
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for (j=0; j < count[1]; j++){
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if (*dataset++ != *original++){
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nerr++;
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if (nerr <= MAX_ERR_REPORT){
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printf("Dataset Verify failed at [%lu][%lu](row %lu, col %lu): expect %d, got %d\n",
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(unsigned long)i, (unsigned long)j,
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(unsigned long)(i*stride[0]+start[0]), (unsigned long)(j*stride[1]+start[1]),
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*(dataset-1), *(original-1));
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}
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}
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}
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}
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if (nerr > MAX_ERR_REPORT)
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printf("[more errors ...]\n");
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if (nerr)
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printf("%d errors found in dataset_vrfy\n", nerr);
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return(nerr);
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}
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/*
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* Example of using the parallel HDF5 library to create two datasets
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* in one HDF5 files with parallel MPIO access support.
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* The Datasets are of sizes (number-of-mpi-processes x DIM1) x DIM2.
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* Each process controls only a slab of size DIM1 x DIM2 within each
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* dataset.
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*/
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void
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phdf5writeInd(char *filename)
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{
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hid_t fid1; /* HDF5 file IDs */
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hid_t acc_tpl1; /* File access templates */
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hid_t sid1; /* Dataspace ID */
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hid_t file_dataspace; /* File dataspace ID */
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hid_t mem_dataspace; /* memory dataspace ID */
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hid_t dataset1, dataset2; /* Dataset ID */
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hsize_t dims1[SPACE1_RANK] =
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{SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */
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DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */
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hsize_t start[SPACE1_RANK]; /* for hyperslab setting */
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hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
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herr_t ret; /* Generic return value */
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MPI_Comm comm = MPI_COMM_WORLD;
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MPI_Info info = MPI_INFO_NULL;
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if (verbose)
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printf("Independent write test on file %s\n", filename);
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/* -------------------
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* START AN HDF5 FILE
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* -------------------*/
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/* setup file access template with parallel IO access. */
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acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS);
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assert(acc_tpl1 != FAIL);
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MESG("H5Pcreate access succeed");
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/* set Parallel access with communicator */
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ret = H5Pset_fapl_mpio(acc_tpl1, comm, info);
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assert(ret != FAIL);
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MESG("H5Pset_fapl_mpio succeed");
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/* create the file collectively */
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fid1=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl1);
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assert(fid1 != FAIL);
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MESG("H5Fcreate succeed");
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/* Release file-access template */
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ret=H5Pclose(acc_tpl1);
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assert(ret != FAIL);
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/* --------------------------
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* Define the dimensions of the overall datasets
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* and the slabs local to the MPI process.
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* ------------------------- */
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/* setup dimensionality object */
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sid1 = H5Screate_simple (SPACE1_RANK, dims1, NULL);
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assert (sid1 != FAIL);
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MESG("H5Screate_simple succeed");
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/* create a dataset collectively */
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dataset1 = H5Dcreate(fid1, DATASETNAME1, H5T_NATIVE_INT, sid1,
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H5P_DEFAULT);
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assert(dataset1 != FAIL);
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MESG("H5Dcreate succeed");
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/* create another dataset collectively */
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dataset2 = H5Dcreate(fid1, DATASETNAME2, H5T_NATIVE_INT, sid1,
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H5P_DEFAULT);
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assert(dataset2 != FAIL);
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MESG("H5Dcreate succeed");
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/* set up dimensions of the slab this process accesses */
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start[0] = mpi_rank*SPACE1_DIM1/mpi_size;
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start[1] = 0;
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count[0] = SPACE1_DIM1/mpi_size;
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count[1] = SPACE1_DIM2;
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stride[0] = 1;
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stride[1] =1;
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if (verbose)
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printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n",
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(unsigned long)start[0], (unsigned long)start[1],
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(unsigned long)count[0], (unsigned long)count[1],
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(unsigned long)(count[0]*count[1]));
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/* put some trivial data in the data_array */
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dataset_fill(start, count, stride, &data_array1[0][0]);
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MESG("data_array initialized");
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/* create a file dataspace independently */
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file_dataspace = H5Dget_space (dataset1);
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assert(file_dataspace != FAIL);
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MESG("H5Dget_space succeed");
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ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride,
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count, NULL);
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assert(ret != FAIL);
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MESG("H5Sset_hyperslab succeed");
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/* create a memory dataspace independently */
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mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL);
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assert (mem_dataspace != FAIL);
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/* write data independently */
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ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
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H5P_DEFAULT, data_array1);
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assert(ret != FAIL);
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MESG("H5Dwrite succeed");
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/* write data independently */
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ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
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H5P_DEFAULT, data_array1);
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assert(ret != FAIL);
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MESG("H5Dwrite succeed");
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/* release dataspace ID */
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H5Sclose(file_dataspace);
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/* close dataset collectively */
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ret=H5Dclose(dataset1);
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assert(ret != FAIL);
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MESG("H5Dclose1 succeed");
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ret=H5Dclose(dataset2);
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assert(ret != FAIL);
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MESG("H5Dclose2 succeed");
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/* release all IDs created */
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H5Sclose(sid1);
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/* close the file collectively */
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H5Fclose(fid1);
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}
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/* Example of using the parallel HDF5 library to read a dataset */
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void
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phdf5readInd(char *filename)
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{
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hid_t fid1; /* HDF5 file IDs */
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hid_t acc_tpl1; /* File access templates */
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hid_t file_dataspace; /* File dataspace ID */
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hid_t mem_dataspace; /* memory dataspace ID */
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hid_t dataset1, dataset2; /* Dataset ID */
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DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */
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DATATYPE data_origin1[SPACE1_DIM1][SPACE1_DIM2]; /* expected data buffer */
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hsize_t start[SPACE1_RANK]; /* for hyperslab setting */
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hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
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herr_t ret; /* Generic return value */
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MPI_Comm comm = MPI_COMM_WORLD;
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MPI_Info info = MPI_INFO_NULL;
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if (verbose)
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printf("Independent read test on file %s\n", filename);
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/* setup file access template */
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acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS);
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assert(acc_tpl1 != FAIL);
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/* set Parallel access with communicator */
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ret = H5Pset_fapl_mpio(acc_tpl1, comm, info);
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assert(ret != FAIL);
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/* open the file collectively */
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fid1=H5Fopen(filename,H5F_ACC_RDWR,acc_tpl1);
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assert(fid1 != FAIL);
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/* Release file-access template */
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ret=H5Pclose(acc_tpl1);
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assert(ret != FAIL);
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/* open the dataset1 collectively */
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dataset1 = H5Dopen(fid1, DATASETNAME1);
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assert(dataset1 != FAIL);
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/* open another dataset collectively */
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dataset2 = H5Dopen(fid1, DATASETNAME1);
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assert(dataset2 != FAIL);
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/* set up dimensions of the slab this process accesses */
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start[0] = mpi_rank*SPACE1_DIM1/mpi_size;
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start[1] = 0;
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count[0] = SPACE1_DIM1/mpi_size;
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count[1] = SPACE1_DIM2;
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stride[0] = 1;
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stride[1] =1;
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if (verbose)
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printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n",
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(unsigned long)start[0], (unsigned long)start[1],
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(unsigned long)count[0], (unsigned long)count[1],
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(unsigned long)(count[0]*count[1]));
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/* create a file dataspace independently */
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file_dataspace = H5Dget_space (dataset1);
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assert(file_dataspace != FAIL);
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ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride,
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count, NULL);
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assert(ret != FAIL);
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/* create a memory dataspace independently */
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mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL);
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assert (mem_dataspace != FAIL);
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/* fill dataset with test data */
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dataset_fill(start, count, stride, &data_origin1[0][0]);
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/* read data independently */
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ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
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H5P_DEFAULT, data_array1);
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assert(ret != FAIL);
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/* verify the read data with original expected data */
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ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
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assert(ret != FAIL);
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/* read data independently */
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ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
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H5P_DEFAULT, data_array1);
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assert(ret != FAIL);
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/* verify the read data with original expected data */
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ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
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assert(ret == 0);
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/* close dataset collectively */
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ret=H5Dclose(dataset1);
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assert(ret != FAIL);
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ret=H5Dclose(dataset2);
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assert(ret != FAIL);
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/* release all IDs created */
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H5Sclose(file_dataspace);
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/* close the file collectively */
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H5Fclose(fid1);
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}
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/*
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|
* 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; /* 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;
|
|
|
|
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");
|
|
|
|
/* 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[]=(%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);
|
|
}
|
|
|
|
/*
|
|
* 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; /* 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 = 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[]=(%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);
|
|
}
|
|
|
|
/*
|
|
* 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[][PATH_MAX])
|
|
{
|
|
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]);
|
|
|
|
color = mpi_rank%2;
|
|
mrc = MPI_Comm_split (MPI_COMM_WORLD, color, mpi_rank, &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 (mpi_rank == 0){
|
|
mrc = MPI_File_delete(filenames[color], info);
|
|
assert(mrc==MPI_SUCCESS);
|
|
}
|
|
}
|
|
|
|
/*
|
|
* Show command usage
|
|
*/
|
|
void
|
|
usage(void)
|
|
{
|
|
printf("Usage: testphdf5 [-f <prefix>] [-r] [-w] [-v]\n");
|
|
printf("\t-f\tfile prefix for parallel test files.\n");
|
|
printf("\t \te.g. pfs:/PFS/myname\n");
|
|
printf("\t \tcan be set via $" PARAPREFIX ".\n");
|
|
printf("\t \tDefault is current directory.\n");
|
|
printf("\t-c\tno cleanup\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");
|
|
}
|
|
|
|
|
|
/*
|
|
* compose the test filename with the prefix supplied.
|
|
* return code: 0 if no error
|
|
* 1 otherwise.
|
|
*/
|
|
int
|
|
mkfilenames(char *prefix)
|
|
{
|
|
int i, n;
|
|
size_t strsize;
|
|
|
|
/* filename will be prefix/ParaEgN.h5 where N is 0 to 9. */
|
|
/* So, string must be big enough to hold the prefix, / and 10 more chars */
|
|
/* and the terminating null. */
|
|
strsize = strlen(prefix) + 12;
|
|
if (strsize > PATH_MAX){
|
|
printf("File prefix too long; Use a short path name.\n");
|
|
return(1);
|
|
}
|
|
n = sizeof(testfiles)/sizeof(testfiles[0]);
|
|
if (n > 9){
|
|
printf("Warning: Too many entries in testfiles. "
|
|
"Need to adjust the code to accommodate the large size.\n");
|
|
}
|
|
for (i=0; i<n; i++){
|
|
sprintf(testfiles[i], "%s/ParaEg%d.h5", prefix, i);
|
|
}
|
|
return(0);
|
|
|
|
}
|
|
|
|
|
|
/*
|
|
* parse the command line options
|
|
*/
|
|
int
|
|
parse_options(int argc, char **argv){
|
|
int i, n;
|
|
|
|
/* initialize testfiles to nulls */
|
|
n = sizeof(testfiles)/sizeof(testfiles[0]);
|
|
for (i=0; i<n; i++){
|
|
testfiles[i][0] = '\0';
|
|
}
|
|
|
|
while (--argc){
|
|
if (**(++argv) != '-'){
|
|
break;
|
|
}else{
|
|
switch(*(*argv+1)){
|
|
case 'f': ++argv;
|
|
if (--argc < 1){
|
|
usage();
|
|
nerrors++;
|
|
return(1);
|
|
}
|
|
if (mkfilenames(*argv)){
|
|
nerrors++;
|
|
return(1);
|
|
}
|
|
break;
|
|
case 'c': docleanup = 0; /* no cleanup */
|
|
break;
|
|
case 'r': doread = 0;
|
|
break;
|
|
case 'w': dowrite = 0;
|
|
break;
|
|
case 'v': verbose = 1;
|
|
break;
|
|
default: usage();
|
|
nerrors++;
|
|
return(1);
|
|
}
|
|
}
|
|
}
|
|
|
|
/* check the file prefix */
|
|
if (testfiles[0][0] == '\0'){
|
|
/* try get it from environment variable HDF5_PARAPREFIX */
|
|
char *env;
|
|
char *env_default = "."; /* default to current directory */
|
|
if ((env=getenv(PARAPREFIX))==NULL){
|
|
env = env_default;
|
|
}
|
|
mkfilenames(env);
|
|
}
|
|
return(0);
|
|
}
|
|
|
|
|
|
/*
|
|
* cleanup test files created
|
|
*/
|
|
void
|
|
cleanup(void)
|
|
{
|
|
int i, n;
|
|
|
|
n = sizeof(testfiles)/sizeof(testfiles[0]);
|
|
for (i=0; i<n; i++){
|
|
MPI_File_delete(testfiles[i], MPI_INFO_NULL);
|
|
}
|
|
}
|
|
|
|
|
|
/* Main Program */
|
|
int
|
|
main(int argc, char **argv)
|
|
{
|
|
int mpi_namelen;
|
|
char mpi_name[MPI_MAX_PROCESSOR_NAME];
|
|
int i, 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);
|
|
nerrors++;
|
|
goto finish;
|
|
}
|
|
|
|
if (parse_options(argc, argv) != 0)
|
|
goto finish;
|
|
|
|
/* show test file names */
|
|
if (mpi_rank == 0){
|
|
n = sizeof(testfiles)/sizeof(testfiles[0]);
|
|
printf("Parallel test files are:\n");
|
|
for (i=0; i<n; i++){
|
|
printf(" %s\n", testfiles[i]);
|
|
}
|
|
}
|
|
|
|
if (dowrite){
|
|
MPI_BANNER("testing PHDF5 dataset using split communicators...");
|
|
test_split_comm_access(testfiles);
|
|
MPI_BANNER("testing PHDF5 dataset independent write...");
|
|
phdf5writeInd(testfiles[0]);
|
|
MPI_BANNER("testing PHDF5 dataset collective write...");
|
|
phdf5writeAll(testfiles[1]);
|
|
}
|
|
if (doread){
|
|
MPI_BANNER("testing PHDF5 dataset independent read...");
|
|
phdf5readInd(testfiles[0]);
|
|
MPI_BANNER("testing PHDF5 dataset collective read...");
|
|
phdf5readAll(testfiles[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");
|
|
}
|
|
}
|
|
if (docleanup)
|
|
cleanup();
|
|
MPI_Finalize();
|
|
|
|
return(nerrors);
|
|
}
|
|
|
|
#else /* H5_HAVE_PARALLEL */
|
|
/* dummy program since H5_HAVE_PARALLE is not configured in */
|
|
int
|
|
main(void)
|
|
{
|
|
printf("No PHDF5 example because parallel is not configured in\n");
|
|
return(0);
|
|
}
|
|
#endif /* H5_HAVE_PARALLEL */
|