582 lines
22 KiB
C
582 lines
22 KiB
C
/******************************************************************************\
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* *
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* Copyright (c) 2003, The Regents of the University of California *
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* See the file COPYRIGHT for a complete copyright notice and license. *
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* *
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********************************************************************************
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*
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* CVS info:
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* $RCSfile: aiori-HDF5.c,v $
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* $Revision: 1.2 $
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* $Date: 2008/12/02 17:12:14 $
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* $Author: rklundt $
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*
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* Purpose:
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* Implementation of abstract I/O interface for HDF5.
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*
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\******************************************************************************/
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#include "aiori.h" /* abstract IOR interface */
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#include <errno.h> /* sys_errlist */
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#include <stdio.h> /* only for fprintf() */
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#include <stdlib.h>
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#include <sys/stat.h>
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#include <hdf5.h>
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#define NUM_DIMS 1 /* number of dimensions to data set */
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/******************************************************************************/
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/*
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* HDF5_CHECK will display a custom error message and then exit the program
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*/
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/*
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* should use MPI_Abort(), not exit(), in this macro; some versions of
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* MPI, however, hang with HDF5 property lists et al. left unclosed
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*/
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/*
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* for versions later than hdf5-1.6, the H5Eget_[major|minor]() functions
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* have been deprecated and replaced with H5Eget_msg()
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*/
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#if H5_VERS_MAJOR > 1 && H5_VERS_MINOR > 6
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#define HDF5_CHECK(HDF5_RETURN, MSG) do { \
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char resultString[1024]; \
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\
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if (HDF5_RETURN < 0) { \
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fprintf(stdout, "** error **\n"); \
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fprintf(stdout, "ERROR in %s (line %d): %s.\n", \
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__FILE__, __LINE__, MSG); \
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strcpy(resultString, H5Eget_major((H5E_major_t)HDF5_RETURN)); \
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if (strcmp(resultString, "Invalid major error number") != 0) \
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fprintf(stdout, "HDF5 %s\n", resultString); \
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strcpy(resultString, H5Eget_minor((H5E_minor_t)HDF5_RETURN)); \
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if (strcmp(resultString, "Invalid minor error number") != 0) \
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fprintf(stdout, "%s\n", resultString); \
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fprintf(stdout, "** exiting **\n"); \
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exit(-1); \
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} \
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} while(0)
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#else /* ! (H5_VERS_MAJOR > 1 && H5_VERS_MINOR > 6) */
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#define HDF5_CHECK(HDF5_RETURN, MSG) do { \
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char resultString[1024]; \
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\
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if (HDF5_RETURN < 0) { \
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fprintf(stdout, "** error **\n"); \
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fprintf(stdout, "ERROR in %s (line %d): %s.\n", \
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__FILE__, __LINE__, MSG); \
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/* \
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* H5Eget_msg(hid_t mesg_id, H5E_type_t* mesg_type, \
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* char* mesg, size_t size) \
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*/ \
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fprintf(stdout, "** exiting **\n"); \
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exit(-1); \
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} \
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} while(0)
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#endif /* H5_VERS_MAJOR > 1 && H5_VERS_MINOR > 6 */
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/**************************** P R O T O T Y P E S *****************************/
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IOR_offset_t SeekOffset_HDF5 (void *, IOR_offset_t, IOR_param_t *);
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void SetHints (MPI_Info *, char *);
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void SetupDataSet_HDF5(void *, IOR_param_t *);
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void ShowHints (MPI_Info *);
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/************************** D E C L A R A T I O N S ***************************/
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extern int errno, /* error number */
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rank,
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rankOffset,
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verbose; /* verbose output */
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extern MPI_Comm testComm;
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static hid_t xferPropList; /* xfer property list */
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hid_t dataSet; /* data set id */
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hid_t dataSpace; /* data space id */
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hid_t fileDataSpace; /* file data space id */
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hid_t memDataSpace; /* memory data space id */
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int newlyOpenedFile; /* newly opened file */
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/***************************** F U N C T I O N S ******************************/
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/******************************************************************************/
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/*
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* Create and open a file through the HDF5 interface.
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*/
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void *
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IOR_Create_HDF5(char * testFileName,
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IOR_param_t * param)
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{
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return IOR_Open_HDF5(testFileName, param);
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} /* IOR_Create_HDF5() */
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/******************************************************************************/
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/*
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* Open a file through the HDF5 interface.
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*/
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void *
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IOR_Open_HDF5(char * testFileName,
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IOR_param_t * param)
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{
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hid_t accessPropList,
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createPropList;
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hsize_t memStart[NUM_DIMS],
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dataSetDims[NUM_DIMS],
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memStride[NUM_DIMS],
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memCount[NUM_DIMS],
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memBlock[NUM_DIMS],
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memDataSpaceDims[NUM_DIMS];
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int tasksPerDataSet;
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unsigned fd_mode = (unsigned)0;
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hid_t *fd;
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MPI_Comm comm;
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MPI_Info mpiHints = MPI_INFO_NULL;
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fd = (hid_t *)malloc(sizeof(hid_t));
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if (fd == NULL) ERR("Unable to malloc file descriptor");
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/*
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* HDF5 uses different flags than those for POSIX/MPIIO
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*/
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if (param->open == WRITE) { /* WRITE flags */
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param->openFlags = IOR_TRUNC;
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} else { /* READ or check WRITE/READ flags */
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param->openFlags = IOR_RDONLY;
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}
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/* set IOR file flags to HDF5 flags */
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/* -- file open flags -- */
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if (param->openFlags & IOR_RDONLY) {fd_mode |= H5F_ACC_RDONLY;}
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if (param->openFlags & IOR_WRONLY) {
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fprintf(stdout, "File write only not implemented in HDF5\n");
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}
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if (param->openFlags & IOR_RDWR) {fd_mode |= H5F_ACC_RDWR;}
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if (param->openFlags & IOR_APPEND) {
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fprintf(stdout, "File append not implemented in HDF5\n");
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}
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if (param->openFlags & IOR_CREAT) {fd_mode |= H5F_ACC_CREAT;}
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if (param->openFlags & IOR_EXCL) {fd_mode |= H5F_ACC_EXCL;}
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if (param->openFlags & IOR_TRUNC) {fd_mode |= H5F_ACC_TRUNC;}
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if (param->openFlags & IOR_DIRECT) {
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fprintf(stdout, "O_DIRECT not implemented in HDF5\n");
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}
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/* set up file creation property list */
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createPropList = H5Pcreate(H5P_FILE_CREATE);
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HDF5_CHECK(createPropList, "cannot create file creation property list");
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/* set size of offset and length used to address HDF5 objects */
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HDF5_CHECK(H5Pset_sizes(createPropList, sizeof(hsize_t), sizeof(hsize_t)),
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"cannot set property list properly");
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/* set up file access property list */
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accessPropList = H5Pcreate(H5P_FILE_ACCESS);
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HDF5_CHECK(accessPropList, "cannot create file access property list");
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/*
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* someday HDF5 implementation will allow subsets of MPI_COMM_WORLD
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*/
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/* store MPI communicator info for the file access property list */
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if (param->filePerProc) {
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comm = MPI_COMM_SELF;
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} else {
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comm = testComm;
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}
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SetHints(&mpiHints, param->hintsFileName);
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/*
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* note that with MP_HINTS_FILTERED=no, all key/value pairs will
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* be in the info object. The info object that is attached to
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* the file during MPI_File_open() will only contain those pairs
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* deemed valid by the implementation.
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*/
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/* show hints passed to file */
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if (rank == 0 && param->showHints) {
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fprintf(stdout, "\nhints passed to access property list {\n");
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ShowHints(&mpiHints);
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fprintf(stdout, "}\n");
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}
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HDF5_CHECK(H5Pset_fapl_mpio(accessPropList, comm, mpiHints),
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"cannot set file access property list");
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/* set alignment */
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HDF5_CHECK(H5Pset_alignment(accessPropList, param->setAlignment,
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param->setAlignment), "cannot set alignment");
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/* open file */
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if (param->open == WRITE) { /* WRITE */
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*fd = H5Fcreate(testFileName, fd_mode,
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createPropList, accessPropList);
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HDF5_CHECK(*fd, "cannot create file");
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} else { /* READ or CHECK */
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*fd = H5Fopen(testFileName, fd_mode, accessPropList);
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HDF5_CHECK(*fd, "cannot open file");
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}
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/* show hints actually attached to file handle */
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if (param->showHints || (1) /* WEL - this needs fixing */) {
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if (rank == 0 && (param->showHints) /* WEL - this needs fixing */) {
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WARN("showHints not working for HDF5");
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}
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} else {
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MPI_Info mpiHintsCheck = MPI_INFO_NULL;
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hid_t apl;
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apl = H5Fget_access_plist(*fd);
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HDF5_CHECK(H5Pget_fapl_mpio(apl, &comm, &mpiHintsCheck),
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"cannot get info object through HDF5");
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if (rank == 0) {
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fprintf(stdout,
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"\nhints returned from opened file (HDF5) {\n");
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ShowHints(&mpiHintsCheck);
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fprintf(stdout, "}\n");
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if (1 == 1) { /* request the MPIIO file handle and its hints */
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MPI_File * fd_mpiio;
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HDF5_CHECK(H5Fget_vfd_handle(*fd, apl, (void **)&fd_mpiio),
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"cannot get MPIIO file handle");
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MPI_CHECK(MPI_File_get_info(*fd_mpiio, &mpiHintsCheck),
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"cannot get info object through MPIIO");
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fprintf(stdout,
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"\nhints returned from opened file (MPIIO) {\n");
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ShowHints(&mpiHintsCheck);
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fprintf(stdout, "}\n");
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}
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}
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MPI_CHECK(MPI_Barrier(testComm), "barrier error");
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}
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/* this is necessary for resetting various parameters
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needed for reopening and checking the file */
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newlyOpenedFile = TRUE;
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HDF5_CHECK(H5Pclose(createPropList), "cannot close creation property list");
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HDF5_CHECK(H5Pclose(accessPropList), "cannot close access property list");
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/* create property list for serial/parallel access */
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xferPropList = H5Pcreate(H5P_DATASET_XFER);
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HDF5_CHECK(xferPropList, "cannot create transfer property list");
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/* set data transfer mode */
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if (param->collective) {
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HDF5_CHECK(H5Pset_dxpl_mpio(xferPropList, H5FD_MPIO_COLLECTIVE),
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"cannot set collective data transfer mode");
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} else {
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HDF5_CHECK(H5Pset_dxpl_mpio(xferPropList, H5FD_MPIO_INDEPENDENT),
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"cannot set independent data transfer mode");
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}
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/* set up memory data space for transfer */
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memStart[0] = (hsize_t)0;
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memCount[0] = (hsize_t)1;
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memStride[0] = (hsize_t)(param->transferSize / sizeof(IOR_size_t));
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memBlock[0] = (hsize_t)(param->transferSize / sizeof(IOR_size_t));
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memDataSpaceDims[0] = (hsize_t)param->transferSize;
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memDataSpace = H5Screate_simple(NUM_DIMS, memDataSpaceDims, NULL);
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HDF5_CHECK(memDataSpace, "cannot create simple memory data space");
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/* define hyperslab for memory data space */
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HDF5_CHECK(H5Sselect_hyperslab(memDataSpace, H5S_SELECT_SET,
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memStart, memStride, memCount, memBlock),
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"cannot create hyperslab");
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/* set up parameters for fpp or different dataset count */
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if (param->filePerProc) {
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tasksPerDataSet = 1;
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} else {
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if (param->individualDataSets) {
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/* each task in segment has single data set */
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tasksPerDataSet = 1;
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} else {
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/* share single data set across all tasks in segment */
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tasksPerDataSet = param->numTasks;
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}
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}
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dataSetDims[0] = (hsize_t)((param->blockSize / sizeof(IOR_size_t))
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* tasksPerDataSet);
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/* create a simple data space containing information on size
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and shape of data set, and open it for access */
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dataSpace = H5Screate_simple(NUM_DIMS, dataSetDims, NULL);
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HDF5_CHECK(dataSpace, "cannot create simple data space");
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return(fd);
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} /* IOR_Open_HDF5() */
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/******************************************************************************/
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/*
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* Write or read access to file using the HDF5 interface.
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*/
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IOR_offset_t
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IOR_Xfer_HDF5(int access,
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void * fd,
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IOR_size_t * buffer,
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IOR_offset_t length,
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IOR_param_t * param)
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{
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static int firstReadCheck = FALSE,
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startNewDataSet;
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IOR_offset_t segmentPosition,
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segmentSize;
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/*
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* this toggle is for the read check operation, which passes through
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* this function twice; note that this function will open a data set
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* only on the first read check and close only on the second
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*/
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if (access == READCHECK) {
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if (firstReadCheck == TRUE) {
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firstReadCheck = FALSE;
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} else {
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firstReadCheck = TRUE;
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}
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}
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/* determine by offset if need to start new data set */
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if (param->filePerProc == TRUE) {
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segmentPosition = (IOR_offset_t)0;
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segmentSize = param->blockSize;
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} else {
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segmentPosition = (IOR_offset_t)((rank + rankOffset) % param->numTasks)
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* param->blockSize;
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segmentSize = (IOR_offset_t)(param->numTasks) * param->blockSize;
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}
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if ((IOR_offset_t)((param->offset - segmentPosition) % segmentSize) == 0) {
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/*
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* ordinarily start a new data set, unless this is the
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* second pass through during a read check
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*/
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startNewDataSet = TRUE;
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if (access == READCHECK && firstReadCheck != TRUE) {
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startNewDataSet = FALSE;
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}
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}
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/* create new data set */
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if (startNewDataSet == TRUE) {
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/* if just opened this file, no data set to close yet */
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if (newlyOpenedFile != TRUE) {
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HDF5_CHECK(H5Dclose(dataSet), "cannot close data set");
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HDF5_CHECK(H5Sclose(fileDataSpace),
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"cannot close file data space");
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}
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SetupDataSet_HDF5(fd, param);
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}
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SeekOffset_HDF5(fd, param->offset, param);
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/* this is necessary to reset variables for reaccessing file */
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startNewDataSet = FALSE;
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newlyOpenedFile = FALSE;
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/* access the file */
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if (access == WRITE) { /* WRITE */
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HDF5_CHECK(H5Dwrite(dataSet, H5T_NATIVE_LLONG,
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memDataSpace, fileDataSpace,
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xferPropList, buffer),
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"cannot write to data set");
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} else { /* READ or CHECK */
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HDF5_CHECK(H5Dread(dataSet, H5T_NATIVE_LLONG,
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memDataSpace, fileDataSpace,
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xferPropList, buffer),
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"cannot read from data set");
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}
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return(length);
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} /* IOR_Xfer_HDF5() */
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/******************************************************************************/
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/*
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* Perform fsync().
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*/
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void
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IOR_Fsync_HDF5(void * fd, IOR_param_t * param)
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{
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;
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} /* IOR_Fsync_HDF5() */
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/******************************************************************************/
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/*
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* Close a file through the HDF5 interface.
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*/
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void
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IOR_Close_HDF5(void * fd,
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IOR_param_t * param)
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{
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if (param->fd_fppReadCheck == NULL) {
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HDF5_CHECK(H5Dclose(dataSet), "cannot close data set");
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HDF5_CHECK(H5Sclose(dataSpace), "cannot close data space");
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HDF5_CHECK(H5Sclose(fileDataSpace), "cannot close file data space");
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HDF5_CHECK(H5Sclose(memDataSpace), "cannot close memory data space");
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HDF5_CHECK(H5Pclose(xferPropList),
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" cannot close transfer property list");
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}
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HDF5_CHECK(H5Fclose(*(hid_t *)fd), "cannot close file");
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free(fd);
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} /* IOR_Close_HDF5() */
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/******************************************************************************/
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/*
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* Delete a file through the HDF5 interface.
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*/
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void
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IOR_Delete_HDF5(char * testFileName, IOR_param_t * param)
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{
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if (unlink(testFileName) != 0) WARN("cannot delete file");
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} /* IOR_Delete_HDF5() */
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/******************************************************************************/
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/*
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* Determine api version.
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*/
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void
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IOR_SetVersion_HDF5(IOR_param_t *test)
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{
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unsigned major, minor, release;
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if (H5get_libversion(&major, &minor, &release) < 0) {
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WARN("cannot get HDF5 library version");
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} else {
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sprintf(test->apiVersion, "%s-%u.%u.%u",
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test->api, major, minor, release);
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}
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#ifndef H5_HAVE_PARALLEL
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strcat(test->apiVersion, " (Serial)");
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#else /* H5_HAVE_PARALLEL */
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strcat(test->apiVersion, " (Parallel)");
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#endif /* not H5_HAVE_PARALLEL */
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} /* IOR_SetVersion_HDF5() */
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/************************ L O C A L F U N C T I O N S ***********************/
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/******************************************************************************/
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/*
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* Seek to offset in file using the HDF5 interface and set up hyperslab.
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*/
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IOR_offset_t
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SeekOffset_HDF5(void *fd,
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IOR_offset_t offset,
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IOR_param_t * param)
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{
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IOR_offset_t segmentSize;
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hsize_t hsStride[NUM_DIMS],
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hsCount[NUM_DIMS],
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hsBlock[NUM_DIMS];
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hsize_t hsStart[NUM_DIMS];
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if (param->filePerProc == TRUE) {
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segmentSize = (IOR_offset_t)param->blockSize;
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} else {
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segmentSize = (IOR_offset_t)(param->numTasks) * param->blockSize;
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}
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/* create a hyperslab representing the file data space */
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if (param->individualDataSets) {
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/* start at zero offset if not */
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hsStart[0] = (hsize_t)((offset % param->blockSize)
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/ sizeof(IOR_size_t));
|
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} else {
|
|
/* start at a unique offset if shared */
|
|
hsStart[0] = (hsize_t)((offset % segmentSize) / sizeof(IOR_size_t));
|
|
}
|
|
hsCount[0] = (hsize_t)1;
|
|
hsStride[0] = (hsize_t)(param->transferSize / sizeof(IOR_size_t));
|
|
hsBlock[0] = (hsize_t)(param->transferSize / sizeof(IOR_size_t));
|
|
|
|
/* retrieve data space from data set for hyperslab */
|
|
fileDataSpace = H5Dget_space(dataSet);
|
|
HDF5_CHECK(fileDataSpace, "cannot get data space from data set");
|
|
HDF5_CHECK(H5Sselect_hyperslab(fileDataSpace, H5S_SELECT_SET,
|
|
hsStart, hsStride, hsCount, hsBlock),
|
|
"cannot select hyperslab");
|
|
return(offset);
|
|
} /* SeekOffset_HDF5() */
|
|
|
|
|
|
/******************************************************************************/
|
|
/*
|
|
* Create HDF5 data set.
|
|
*/
|
|
|
|
void
|
|
SetupDataSet_HDF5(void * fd,
|
|
IOR_param_t * param)
|
|
{
|
|
char dataSetName[MAX_STR];
|
|
hid_t dataSetPropList;
|
|
int dataSetID;
|
|
static int dataSetSuffix = 0;
|
|
|
|
/* may want to use an extendable dataset (H5S_UNLIMITED) someday */
|
|
/* may want to use a chunked dataset (H5S_CHUNKED) someday */
|
|
|
|
/* need to reset suffix counter if newly-opened file */
|
|
if (newlyOpenedFile) dataSetSuffix = 0;
|
|
|
|
/* may want to use individual access to each data set someday */
|
|
if (param->individualDataSets) {
|
|
dataSetID = (rank + rankOffset) % param->numTasks;
|
|
} else {
|
|
dataSetID = 0;
|
|
}
|
|
|
|
sprintf(dataSetName, "%s-%04d.%04d", "Dataset", dataSetID, dataSetSuffix++);
|
|
|
|
if (param->open == WRITE) { /* WRITE */
|
|
/* create data set */
|
|
dataSetPropList = H5Pcreate(H5P_DATASET_CREATE);
|
|
/* check if hdf5 available */
|
|
#if defined (H5_VERS_MAJOR) && defined (H5_VERS_MINOR)
|
|
/* no-fill option not available until hdf5-1.6.x */
|
|
#if (H5_VERS_MAJOR > 0 && H5_VERS_MINOR > 5)
|
|
if (param->noFill == TRUE) {
|
|
if (rank == 0 && verbose >= VERBOSE_1) {
|
|
fprintf(stdout, "\nusing 'no fill' option\n");
|
|
}
|
|
HDF5_CHECK(H5Pset_fill_time(dataSetPropList,
|
|
H5D_FILL_TIME_NEVER),
|
|
"cannot set fill time for property list");
|
|
}
|
|
#else
|
|
char errorString[MAX_STR];
|
|
sprintf(errorString, "'no fill' option not available in %s", test->apiVersion);
|
|
ERR(errorString);
|
|
#endif
|
|
#else
|
|
WARN("unable to determine HDF5 version for 'no fill' usage");
|
|
#endif
|
|
dataSet = H5Dcreate(*(hid_t *)fd, dataSetName, H5T_NATIVE_LLONG,
|
|
dataSpace, dataSetPropList);
|
|
HDF5_CHECK(dataSet, "cannot create data set");
|
|
} else { /* READ or CHECK */
|
|
dataSet = H5Dopen(*(hid_t *)fd, dataSetName);
|
|
HDF5_CHECK(dataSet, "cannot create data set");
|
|
}
|
|
|
|
} /* SetupDataSet_HDF5() */
|
|
|
|
|
|
/******************************************************************************/
|
|
/*
|
|
* Use MPIIO call to get file size.
|
|
*/
|
|
|
|
IOR_offset_t
|
|
IOR_GetFileSize_HDF5(IOR_param_t * test,
|
|
MPI_Comm testComm,
|
|
char * testFileName)
|
|
{
|
|
return(IOR_GetFileSize_MPIIO(test, testComm, testFileName));
|
|
} /* IOR_GetFileSize_HDF5() */
|