mirror of
https://github.com/HDFGroup/hdf5.git
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427ff7da28
Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-)
Description:
Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation. So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.
I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
FreeBSD 4.10 (sleipnir) w/threadsafe
FreeBSD 4.10 (sleipnir) w/backward compatibility
Solaris 2.7 (arabica) w/"purify options"
Solaris 2.8 (sol) w/FORTRAN & C++
AIX 5.x (copper) w/parallel & FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN
Linux 2.4 (heping) w/FORTRAN & C++
Misc. update:
1132 lines
34 KiB
C
1132 lines
34 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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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://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
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* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
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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 */
|
|
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; /* 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 */
|