hdf5/src/H5MF.c
John Mainzer c100b0bf26 [svn-r11470] Purpose:
Repair synchronization bug in the metadata cache in PHDF5

Also repair numerous other bugs that surfaced in testing the
bug fix.


Description:

While operations modifying metadata must be collective, we allow
independant reads.  This allows metadata caches on different processes
to adjust to different sizes, and to place the entries on their dirty
lists in different orders.  Since only process 0 actually writes
metadata to disk (all other processes thought they did, but the writes
were discarded on the theory that they had to be collective), this made
it possible for another process to modify metadata, flush it, and then
read it back in in its original form (pre-modification) form.  The
possibilities for file corruption should be obvious.


Solution:

Make the policy that only process 0 can write to file explicit, and
visible to the metadata caches.  Thus only process 0 may flush dirty
entries -- all other caches must retain dirty entries until they are
informed by process 0 that the entries are clean.

Synchronization is handled by counting the bytes of dirty cache entries
created, and then synching up between the caches whenever the sum
exceeds an (eventually user specified) limit.  Dirty metadata creation
is consistent across all processes because all operations modifying
metadata must be collective.

This change uncovered may bugs which are repaired in this checkin.
It also required modification of H5HL and H5O to allocate file space
on insertion rather than on flush from cache.


Platforms tested:

H5committest, heping(parallel & serial)

Misc. update:
2005-09-27 00:20:11 -05:00

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*-------------------------------------------------------------------------
*
* Created: H5MF.c
* Jul 11 1997
* Robb Matzke <matzke@llnl.gov>
*
* Purpose: File memory management functions.
*
* Modifications:
* Robb Matzke, 5 Aug 1997
* Added calls to H5E.
*
* Robb Matzke, 8 Jun 1998
* Implemented a very simple free list which is not persistent and which
* is lossy.
*
*-------------------------------------------------------------------------
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include "H5private.h"
#include "H5Eprivate.h"
#include "H5Fpkg.h"
#include "H5FDprivate.h"
#include "H5MFprivate.h"
/*-------------------------------------------------------------------------
* Function: H5MF_alloc
*
* Purpose: Allocate SIZE bytes of file memory and return the relative
* address where that contiguous chunk of file memory exists.
* The TYPE argument describes the purpose for which the storage
* is being requested.
*
* Return: Success: The file address of new chunk.
*
* Failure: HADDR_UNDEF
*
* Programmer: Robb Matzke
* matzke@llnl.gov
* Jul 11 1997
*
* Modifications:
* Robb Matzke, 1999-08-04
* Modified to work with the virtual file layer.
*-------------------------------------------------------------------------
*/
haddr_t
H5MF_alloc(H5F_t *f, H5FD_mem_t type, hid_t dxpl_id, hsize_t size)
{
haddr_t ret_value;
FUNC_ENTER_NOAPI(H5MF_alloc, HADDR_UNDEF);
/* check arguments */
assert(f);
assert(size > 0);
/* Fail if we don't have write access */
if (0==(f->intent & H5F_ACC_RDWR))
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, HADDR_UNDEF, "file is read-only");
/* Check that the file can address the new space */
if( H5MF_alloc_overflow(f, size) )
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, HADDR_UNDEF, "not enough address space in file");
/* Allocate space from the virtual file layer */
if (HADDR_UNDEF==(ret_value=H5FD_alloc(f->shared->lf, type, dxpl_id, size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, HADDR_UNDEF, "file allocation failed");
/* Convert absolute file address to relative file address */
assert(ret_value>=f->shared->base_addr);
/* Set return value */
ret_value -= f->shared->base_addr;
done:
FUNC_LEAVE_NOAPI(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5MF_xfree
*
* Purpose: Frees part of a file, making that part of the file
* available for reuse.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* matzke@llnl.gov
* Jul 17 1997
*
* Modifications:
* Robb Matzke, 1999-07-28
* The ADDR argument is passed by value
*
* Robb Matzke, 1999-08-03
* Modified to use the virtual file layer.
*-------------------------------------------------------------------------
*/
herr_t
H5MF_xfree(H5F_t *f, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, hsize_t size)
{
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOFUNC(H5MF_xfree);
/* check arguments */
assert(f);
if (!H5F_addr_defined(addr) || 0 == size)
HGOTO_DONE(SUCCEED);
assert(addr!=0);
/* Convert relative address to absolute address */
addr += f->shared->base_addr;
/* Allow virtual file layer to free block */
if (H5FD_free(f->shared->lf, type, dxpl_id, addr, size)<0) {
#ifdef H5MF_DEBUG
if (H5DEBUG(MF)) {
fprintf(H5DEBUG(MF),
"H5MF_free: lost %lu bytes of file storage\n",
(unsigned long)size);
}
#endif
}
done:
FUNC_LEAVE_NOAPI(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5MF_realloc
*
* Purpose: Changes the size of an allocated chunk, possibly moving it to
* a new address. The chunk to change is at address OLD_ADDR
* and is exactly OLD_SIZE bytes (if these are H5F_ADDR_UNDEF
* and zero then this function acts like H5MF_alloc). The new
* size will be NEW_SIZE and its address is the return value (if
* NEW_SIZE is zero then this function acts like H5MF_free and
* an undefined address is returned).
*
* If the new size is less than the old size then the new
* address will be the same as the old address (except for the
* special case where the new size is zero).
*
* If the new size is more than the old size then most likely a
* new address will be returned. However, under certain
* circumstances the library may return the same address.
*
* Return: Success: The relative file address of the new block.
*
* Failure: HADDR_UNDEF
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
* Robb Matzke, 1999-07-28
* The ORIG_ADDR is passed by value. The name of NEW_ADDR has
* been changed to NEW_ADDR_P
*
* Robb Matzke, 1999-08-04
* Modified to work with the virtual file layer.
*-------------------------------------------------------------------------
*/
haddr_t
H5MF_realloc(H5F_t *f, H5FD_mem_t type, hid_t dxpl_id, haddr_t old_addr, hsize_t old_size,
hsize_t new_size)
{
haddr_t ret_value;
FUNC_ENTER_NOAPI(H5MF_realloc, HADDR_UNDEF);
/* Convert old relative address to absolute address */
old_addr += f->shared->base_addr;
/* Check that the file can address the new space. */
/* In the worst case, this means adding new_size bytes to the end of the file. */
if( H5MF_alloc_overflow(f, new_size) )
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, HADDR_UNDEF, "not enough address space in file");
/* Reallocate memory from the virtual file layer */
ret_value = H5FD_realloc(f->shared->lf, type, dxpl_id, old_addr, old_size,
new_size);
if (HADDR_UNDEF==ret_value)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, HADDR_UNDEF, "unable to allocate new file memory");
/* Convert return value to relative address */
assert(ret_value>=f->shared->base_addr);
/* Set return value */
ret_value -= f->shared->base_addr;
done:
FUNC_LEAVE_NOAPI(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5MF_reserve
*
* Purpose: Sets aside file space that has not yet been allocated, but will
* be (or might be in the worst case). This number is used to
* ensure that there is room in the file when it is flushed to disk.
*
* Nothing changes (and no error is generated) if the file is opened
* as read-only.
*
* Return: Success: 0
*
* Failure: negative
*
* Programmer: James Laird
* Nat Furrer
* Thursday, May 27, 2004
*
* Modifications:
*-------------------------------------------------------------------------
*/
herr_t
H5MF_reserve(H5F_t *f, hsize_t size)
{
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(H5MF_reserve, FAIL);
/* Check arguments */
assert(f);
/* Check that there is room in the file to reserve this space */
if( H5MF_alloc_overflow( f, size ) )
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "not enough address space in file");
f->shared->lf->reserved_alloc += size;
done:
FUNC_LEAVE_NOAPI(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5MF_free_reserved
*
* Purpose: Releases the file space set aside by H5MF_reserve. This should
* be called immediately before allocating the file space for which
* the space was reserved.
*
* Return: None
*
* Programmer: James Laird
* Nat Furrer
* Thursday, May 27, 2004
*
* Modifications:
*-------------------------------------------------------------------------
*/
herr_t
H5MF_free_reserved(H5F_t *f, hsize_t size)
{
FUNC_ENTER_NOAPI_NOFUNC(H5MF_free_reserved)
/* Check arguments */
assert(f);
/* If this assert breaks, it means that HDF5 is trying to free file space
* that was never reserved.
*/
assert(size <= f->shared->lf->reserved_alloc);
f->shared->lf->reserved_alloc -= size;
FUNC_LEAVE_NOAPI(SUCCEED)
}
/*-------------------------------------------------------------------------
* Function: H5MF_alloc_overflow
*
* Purpose: Checks if an allocation of file space would cause an overflow.
* F is the file whose space is being allocated, SIZE is the amount
* of space needed.
*
* Return: 0 if no overflow would result
* 1 if overflow would result (the allocation should not be allowed)
*
* Programmer: James Laird
* Nat Furrer
* Tuesday, June 1, 2004
*
* Modifications:
*-------------------------------------------------------------------------
*/
hbool_t
H5MF_alloc_overflow(H5F_t *f, hsize_t size)
{
hsize_t space_needed; /* Accumulator variable */
size_t c; /* Local index variable */
hbool_t ret_value; /* Return value */
FUNC_ENTER_NOAPI_NOFUNC(H5MF_alloc_overflow)
/* Start with the current end of the file's address. */
space_needed = (hsize_t)H5F_get_eoa(f);
HDassert(H5F_addr_defined(space_needed));
/* Subtract the file's base address to get the actual amount of
* space being used:
* (end of allocated space - beginning of allocated space)
*/
HDassert(H5F_BASE_ADDR(f) < space_needed);
space_needed -= (hsize_t)H5F_BASE_ADDR(f);
/* Add the amount of space requested for this allocation */
space_needed += size;
/* Also add space that is "reserved" for data to be flushed
* to disk (e.g., for object headers and the heap).
* This is the total amount of file space that will be
* allocated.
*/
space_needed += f->shared->lf->reserved_alloc;
/* Ensure that this final number is less than the file's
* address space. We do this by shifting in multiples
* of 16 bits because some systems will do nothing if
* we shift by the size of a long long (64 bits) all at
* once (<cough> Linux <cough>). Thus, we break one shift
* into several smaller shifts.
*/
for(c=0; c < H5F_SIZEOF_ADDR(f); c += 2)
space_needed = space_needed >> 16;
if(space_needed != 0)
ret_value=TRUE;
else
ret_value=FALSE;
FUNC_LEAVE_NOAPI(ret_value)
}
/*-------------------------------------------------------------------------
* Function: H5MF_can_extend
*
* Purpose: Check if a block in the file can be extended.
*
* Return: Success: TRUE(1)/FALSE(0)
*
* Failure: FAIL
*
* Programmer: Quincey Koziol
* Friday, June 11, 2004
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
htri_t
H5MF_can_extend(H5F_t *f, H5FD_mem_t type, haddr_t addr, hsize_t size, hsize_t extra_requested)
{
htri_t ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5MF_can_extend, FAIL);
/* Convert old relative address to absolute address */
addr += H5F_BASE_ADDR(f);
/* Pass the request down to the virtual file layer */
if((ret_value=H5FD_can_extend(f->shared->lf, type, addr, size, extra_requested))<0)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate new file memory");
/* Make sure there is enough addressable space to satisfy the request */
if (ret_value == TRUE)
ret_value = !H5MF_alloc_overflow(f, extra_requested);
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5MF_can_extend() */
/*-------------------------------------------------------------------------
* Function: H5MF_extend
*
* Purpose: Extend a block in the file.
*
* Return: Success: Non-negative
*
* Failure: Negative
*
* Programmer: Quincey Koziol
* Saturday, June 12, 2004
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5MF_extend(H5F_t *f, H5FD_mem_t type, haddr_t addr, hsize_t size, hsize_t extra_requested)
{
herr_t ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5MF_extend, FAIL);
/* Make sure there is enough addressable space to satisfy the request */
if ( H5MF_alloc_overflow(f, extra_requested) )
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate new file memory: out of address space");
/* Convert old relative address to absolute address */
addr += H5F_BASE_ADDR(f);
/* Pass the request down to the virtual file layer */
if((ret_value=H5FD_extend(f->shared->lf, type, addr, size, extra_requested))<0)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate new file memory");
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5MF_extend() */