path: root/src/H5Fio.c

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Copyright by The HDF Group.                                               *
 * Copyright by the Board of Trustees of the University of Illinois.         *
 * All rights reserved.                                                      *
 *                                                                           *
 * This file is part of HDF5.  The full HDF5 copyright notice, including     *
 * terms governing use, modification, and redistribution, is contained in    *
 * the files COPYING and Copyright.html.  COPYING can be found at the root   *
 * of the source code distribution tree; Copyright.html can be found at the  *
 * root level of an installed copy of the electronic HDF5 document set and   *
 * is linked from the top-level documents page.  It can also be found at     *
 * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
 * access to either file, you may request a copy from help@hdfgroup.org.     *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

/*-------------------------------------------------------------------------
 *
 * Created:             H5Fio.c
 *                      Jan 10 2008
 *                      Quincey Koziol <koziol@hdfgroup.org>
 *
 * Purpose:             File I/O routines.
 *
 *-------------------------------------------------------------------------
 */

/****************/
/* Module Setup */
/****************/

#define H5F_PACKAGE		/*suppress error about including H5Fpkg	  */


/***********/
/* Headers */
/***********/
#include "H5private.h"		/* Generic Functions			*/
#include "H5Eprivate.h"		/* Error handling		  	*/
#include "H5Fpkg.h"             /* File access				*/
#include "H5FDprivate.h"	/* File drivers				*/
#include "H5Iprivate.h"		/* IDs			  		*/


/****************/
/* Local Macros */
/****************/


/******************/
/* Local Typedefs */
/******************/


/********************/
/* Package Typedefs */
/********************/


/********************/
/* Local Prototypes */
/********************/


/*********************/
/* Package Variables */
/*********************/


/*****************************/
/* Library Private Variables */
/*****************************/


/*******************/
/* Local Variables */
/*******************/



/*-------------------------------------------------------------------------
 * Function:	H5F_block_read
 *
 * Purpose:	Reads some data from a file/server/etc into a buffer.
 *		The data is contiguous.	 The address is relative to the base
 *		address for the file.
 *
 * Return:	Non-negative on success/Negative on failure
 *
 * Programmer:	Robb Matzke
 *		matzke@llnl.gov
 *		Jul 10 1997
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5F_block_read(const H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size,
    hid_t dxpl_id, void *buf/*out*/)
{
    H5F_io_info_t fio_info;             /* I/O info for operation */
    herr_t      ret_value = SUCCEED;    /* Return value */

    FUNC_ENTER_NOAPI(FAIL)
#ifdef QAK
HDfprintf(stderr, "%s: read from addr = %a, size = %Zu\n", FUNC, addr, size);
#endif /* QAK */

    HDassert(f);
    HDassert(f->shared);
    HDassert(buf);
    HDassert(H5F_addr_defined(addr));

    /* Check for attempting I/O on 'temporary' file address */
    if(H5F_addr_le(f->shared->tmp_addr, (addr + size)))
        HGOTO_ERROR(H5E_IO, H5E_BADRANGE, FAIL, "attempting I/O in temporary file space")

    /* Set up I/O info for operation */
    fio_info.f = f;
    if(NULL == (fio_info.dxpl = (H5P_genplist_t *)H5I_object(dxpl_id)))
        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get property list")

    /* Pass through metadata accumulator layer */
    if(H5F__accum_read(&fio_info, type, addr, size, buf) < 0)
        HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "read through metadata accumulator failed")

done:
    FUNC_LEAVE_NOAPI(ret_value)
} /* end H5F_block_read() */


/*-------------------------------------------------------------------------
 * Function:	H5F_block_write
 *
 * Purpose:	Writes some data from memory to a file/server/etc.  The
 *		data is contiguous.  The address is relative to the base
 *		address.
 *
 * Return:	Non-negative on success/Negative on failure
 *
 * Programmer:	Robb Matzke
 *		matzke@llnl.gov
 *		Jul 10 1997
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5F_block_write(const H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size,
    hid_t dxpl_id, const void *buf)
{
    H5F_io_info_t fio_info;             /* I/O info for operation */
    herr_t      ret_value = SUCCEED;    /* Return value */

    FUNC_ENTER_NOAPI(FAIL)
#ifdef QAK
HDfprintf(stderr, "%s: write to addr = %a, size = %Zu\n", FUNC, addr, size);
#endif /* QAK */

    HDassert(f);
    HDassert(f->shared);
    HDassert(H5F_INTENT(f) & H5F_ACC_RDWR);
    HDassert(buf);
    HDassert(H5F_addr_defined(addr));

    /* Check for attempting I/O on 'temporary' file address */
    if(H5F_addr_le(f->shared->tmp_addr, (addr + size)))
        HGOTO_ERROR(H5E_IO, H5E_BADRANGE, FAIL, "attempting I/O in temporary file space")

    /* Set up I/O info for operation */
    fio_info.f = f;
    if(NULL == (fio_info.dxpl = (H5P_genplist_t *)H5I_object(dxpl_id)))
        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get property list")

    /* Pass through metadata accumulator layer */
    if(H5F__accum_write(&fio_info, type, addr, size, buf) < 0)
        HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "write through metadata accumulator failed")

done:
    FUNC_LEAVE_NOAPI(ret_value)
} /* end H5F_block_write() */


/*-------------------------------------------------------------------------
 * Function:    H5F_flush_tagged_metadata
 *
 * Purpose:     Flushes metadata with specified tag in the metadata cache 
 *              to disk.
 *
 * Return:      Non-negative on success/Negative on failure
 *
 * Programmer:	Mike McGreevy
 *              September 9, 2010
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5F_flush_tagged_metadata(H5F_t * f, haddr_t tag, hid_t dxpl_id)
{
    H5F_io_info_t fio_info;             /* I/O info for operation */
    herr_t ret_value = SUCCEED;

    FUNC_ENTER_NOAPI(FAIL)

    /* Use tag to search for and flush associated metadata */
    if(H5AC_flush_tagged_metadata(f, tag, dxpl_id)<0)
        HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush tagged metadata")

    /* Set up I/O info for operation */
    fio_info.f = f;

    if(NULL == (fio_info.dxpl = (H5P_genplist_t *)H5I_object(dxpl_id)))
        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get property list")
    

    /* Flush and reset the accumulator */
    if(H5F__accum_reset(&fio_info, TRUE) < 0)
        HGOTO_ERROR(H5E_IO, H5E_CANTRESET, FAIL, "can't reset accumulator")

    /* Flush file buffers to disk. */
    if(H5FD_flush(f->shared->lf, dxpl_id, FALSE) < 0)
        HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "low level flush failed")

done:
    FUNC_LEAVE_NOAPI(ret_value);
} /* end H5F_flush_tagged_metadata */


/*-------------------------------------------------------------------------
 * Function:    H5F_evict_tagged_metadata
 *
 * Purpose:     Evicts metadata from the cache with specified tag.
 *
 * Return:      Non-negative on success/Negative on failure
 *
 * Programmer:	Mike McGreevy
 *              September 9, 2010
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5F_evict_tagged_metadata(H5F_t * f, haddr_t tag, hid_t dxpl_id)
{
    herr_t ret_value = SUCCEED;

    FUNC_ENTER_NOAPI(FAIL)

    /* Unpin the superblock, as this will be marked for eviction and it can't 
        be pinned. */
    if(H5AC_unpin_entry(f->shared->sblock) < 0)
        HGOTO_ERROR(H5E_CACHE, H5E_CANTUNPIN, FAIL, "unable to unpin superblock")
    f->shared->sblock = NULL;

    /* Evict the object's metadata */
    if(H5AC_evict_tagged_metadata(f, tag, dxpl_id)<0)
        HGOTO_ERROR(H5E_CACHE, H5E_CANTEXPUNGE, FAIL, "unable to evict tagged metadata")

    /* Re-read the superblock. */
    if(H5F__super_read(f, dxpl_id, FALSE) < 0)
	HGOTO_ERROR(H5E_FILE, H5E_READERROR, FAIL, "unable to read superblock")

done:
    FUNC_LEAVE_NOAPI(ret_value);
} /* end H5F_evict_tagged_metadata */


/*-------------------------------------------------------------------------
 * Function:    H5F_evict_cache_entries
 *
 * Purpose:     To revict all cache entries except the pinned superblock entry
 *
 * Return:      Non-negative on success/Negative on failure
 *
 * Programmer:	Vailin Choi; Dec 2013
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5F_evict_cache_entries(H5F_t *f, hid_t dxpl_id)
{
    unsigned status = 0;
    int32_t    cur_num_entries;
    herr_t ret_value = SUCCEED;

    FUNC_ENTER_NOAPI(FAIL)

    HDassert(f);
    HDassert(f->shared);

    /* Evict all except pinned entries in the cache */
    if(H5AC_evict(f, dxpl_id) < 0)
        HGOTO_ERROR(H5E_CACHE, H5E_CANTEXPUNGE, FAIL, "unable to evict all except pinned entries")

    /* Retrieve status of the superblock */
    if(H5AC_get_entry_status(f, (haddr_t)0, &status) < 0)
        HGOTO_ERROR(H5E_HEAP, H5E_CANTGET, FAIL, "unable to get entry status")

    /* Verify status of the superblock entry in the cache */
    if(!(status & H5AC_ES__IN_CACHE) || !(status & H5AC_ES__IS_PINNED))
        HGOTO_ERROR(H5E_HEAP, H5E_CANTGET, FAIL, "unable to get entry status")

    /* Get the number of cache entries */
    if(H5AC_get_cache_size(f->shared->cache, NULL, NULL, NULL, &cur_num_entries) < 0)
        HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "H5AC_get_cache_size() failed.")

    /* Should be the only one left in the cache */
    if(cur_num_entries != 1)
        HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "number of cache entries is not correct")

done:
    FUNC_LEAVE_NOAPI(ret_value);
} /* end H5F_evict_cache_entries() */


/*-------------------------------------------------------------------------
 * Function:    H5F_get_checksums
 *
 * Purpose:   	Decode checksum stored in the buffer
 *		Calculate checksum for the data in the buffer
 *
 * Note:	Assumes that the checksum is the last data in the buffer
 *
 * Return:      Non-negative on success/Negative on failure
 *
 * Programmer:	Vailin Choi; Sept 2013
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5F_get_checksums(const uint8_t *buf, size_t buf_size, uint32_t *s_chksum/*out*/, uint32_t *c_chksum/*out*/)
{
    FUNC_ENTER_NOAPI_NOINIT_NOERR

    /* Check arguments */
    HDassert(buf);
    HDassert(buf_size);

    /* Return the stored checksum */
    if(s_chksum) {
        const uint8_t *chk_p;      	/* Pointer into raw data buffer */

        /* Offset to the checksum in the buffer */
        chk_p = buf + buf_size - H5_SIZEOF_CHKSUM;

        /* Decode the checksum stored in the buffer */
        UINT32DECODE(chk_p, *s_chksum);
    } /* end if */

    /* Return the computed checksum for the buffer */
    if(c_chksum)
	*c_chksum = H5_checksum_metadata(buf, buf_size - H5_SIZEOF_CHKSUM, 0);

    FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5F_get_chksums() */


/*-------------------------------------------------------------------------
 * Function:    H5F_read_check_meatadata
 *
 * Purpose:   	Attempts to read and validate a piece of meatadata that has
 *		checksum as follows:
 * 		  a) read the piece of metadata
 * 		  b) calculate checksum for the buffer of metadata
 * 		  c) decode the checksum stored in the buffer of metadata
 *		  d) compare the computed checksum with its stored checksum
 *
 *	       	The library will perform (a) to (d) above for "f->read_attempts"
 *		times or until the checksum comparison in (d) passes.
 *		This routine also records the # of retries via 
 *		H5F_track_metadata_read_retries()
 *
 * Return:      Non-negative on success/Negative on failure
 *
 * Programmer:	Vailin Choi; Sept 2013
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5F_read_check_metadata(H5F_t *f, hid_t dxpl_id, H5FD_mem_t type,
    unsigned actype, haddr_t addr, size_t read_size, size_t chk_size,
    uint8_t *buf/*out*/)
{
    unsigned tries, max_tries;	/* The # of read attempts */
    unsigned retries;		/* The # of retries */
    uint32_t stored_chksum;  	/* Stored metadata checksum value */
    uint32_t computed_chksum; 	/* Computed metadata checksum value */
    herr_t ret_value = SUCCEED;	/* Return value */

    FUNC_ENTER_NOAPI(FAIL)

    /* Get the # of read attempts */
    max_tries = tries = H5F_GET_READ_ATTEMPTS(f);

    do {
        /* Read header from disk */
        if(H5F_block_read(f, type, addr, read_size, dxpl_id, buf) < 0)
	    HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read metadata")

	/* Get stored and computed checksums */
	H5F_get_checksums(buf, chk_size, &stored_chksum, &computed_chksum);

        /* Verify checksum */
        if(stored_chksum == computed_chksum)
            break;
    } while(--tries);

    /* Check for too many tries */
    if(tries == 0)
        HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "incorrect metadatda checksum after all read attempts (%u) for %u bytes:c_chksum=%u, s_chkum=%u", 
	    max_tries, chk_size, computed_chksum, stored_chksum)

    /* Calculate and track the # of retries */
    retries = max_tries - tries;
    if(retries)         /* Does not track 0 retry */
	if(H5F_track_metadata_read_retries(f, actype, retries) < 0)
            HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, FAIL, "cannot track read tries = %u ", retries)

done:
    FUNC_LEAVE_NOAPI(ret_value);
} /* end H5F_read_check_metadata */