mirror/hdf5
2
0
Fork 0
mirror of https://github.com/HDFGroup/hdf5.git synced 2025-03-07 16:37:56 +08:00
Code Issues Packages Projects Releases Wiki Activity

[svn-r17045] Description:

Browse Source 
Update the metadata accumulator code:
        - Fix a bug where we were adding 2, instead of multiplying by 2 :-/
        - Put an upper limit on the size of the metadata accumulator
        - Allocate the accumulator in powers of 2, instead of random sizes
        - Roll out the writes from the accumulator in a more I/O friendly way

Tested on:
    FreeBSD/32 6.3 (duty) in debug mode
    FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
    Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
        in debug mode
    Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
        w/C++ & FORTRAN, in production mode
    Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
        w/szip filter, in production mode
    Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
        in production mode
    Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
    Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
    Mac OS X/32 10.5.7 (amazon) in debug mode
    Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe,
        in production mode
This commit is contained in:
Quincey Koziol 2009-06-12 10:28:34 -05:00
parent dc8650cfeb
commit c9b6d5bf85
1 changed files with 150 additions and 56 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

206
src/H5Faccum.c
View File

@ -40,6 +40,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5Fpkg.h" /* File access */
#include "H5FDprivate.h" /* File drivers */
#include "H5Vprivate.h" /* Vectors and arrays */
/****************/
@ -49,12 +50,19 @@
/* Metadata accumulator controls */
#define H5F_ACCUM_THROTTLE 8
#define H5F_ACCUM_THRESHOLD 2048
#define H5F_ACCUM_MAX_SIZE (1024 *1024) /* Max. accum. buf size (max. I/Os will be 1/2 this size) */
/******************/
/* Local Typedefs */
/******************/
/* Enumerated type to indicate how data will be added to accumulator */
typedef enum {
H5F_ACCUM_PREPEND, /* Data will be prepended to accumulator */
H5F_ACCUM_APPEND /* Data will be appended to accumulator */
} H5F_accum_adjust_t;
/********************/
/* Package Typedefs */
@ -112,7 +120,8 @@ H5F_accum_read(const H5F_t *f, hid_t dxpl_id, H5FD_mem_t type, haddr_t addr,
HDassert(buf);
/* Check if this information is in the metadata accumulator */
if((f->shared->feature_flags & H5FD_FEAT_ACCUMULATE_METADATA) && type != H5FD_MEM_DRAW) {
if((f->shared->feature_flags & H5FD_FEAT_ACCUMULATE_METADATA) && type != H5FD_MEM_DRAW
&& size < H5F_ACCUM_MAX_SIZE) {
/* Current read overlaps with metadata accumulator */
if(H5F_addr_overlap(addr, size, f->shared->accum.loc, f->shared->accum.size)) {
unsigned char *read_buf = (unsigned char *)buf; /* Pointer to the buffer being read in */
@ -195,12 +204,17 @@ H5F_accum_read(const H5F_t *f, hid_t dxpl_id, H5FD_mem_t type, haddr_t addr,
/* Cache the new piece of metadata */
/* Check if we need to resize the buffer */
if(size > f->shared->accum.alloc_size) {
size_t new_size; /* New size of accumulator */
/* Adjust the buffer size to be a power of 2 that is large enough to hold data */
new_size = (size_t)1 << (1 + H5V_log2_gen(size - 1));
/* Grow the metadata accumulator buffer */
if(NULL == (f->shared->accum.buf = H5FL_BLK_REALLOC(meta_accum, f->shared->accum.buf, size)))
if(NULL == (f->shared->accum.buf = H5FL_BLK_REALLOC(meta_accum, f->shared->accum.buf, new_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate metadata accumulator buffer")
/* Note the new buffer size */
f->shared->accum.alloc_size = size;
f->shared->accum.alloc_size = new_size;
} /* end if */
else {
/* Check if we should shrink the accumulator buffer */
@ -244,6 +258,111 @@ done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5F_accum_read() */
/*-------------------------------------------------------------------------
* Function: H5F_accum_adjust
*
* Purpose: Adjust accumulator size, if necessary
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* koziol@hdfgroup.org
* Jun 11 2009
*
*-------------------------------------------------------------------------
*/
static herr_t
H5F_accum_adjust(H5F_meta_accum_t *accum, H5FD_t *lf, hid_t dxpl_id,
H5F_accum_adjust_t adjust, size_t size)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5F_accum_adjust)
HDassert(accum);
HDassert(lf);
HDassert(size > 0);
HDassert(size <= H5F_ACCUM_MAX_SIZE);
/* Check if we need more buffer space */
if((size + accum->size) > accum->alloc_size) {
size_t new_size; /* New size of accumulator */
/* Adjust the buffer size to be a power of 2 that is large enough to hold data */
new_size = (size_t)1 << (1 + H5V_log2_gen((size + accum->size) - 1));
/* Check for accumulator getting too big */
if(new_size > H5F_ACCUM_MAX_SIZE) {
size_t shrink_size; /* Amount to shrink accumulator by */
size_t remnant_size; /* Amount left in accumulator */
/* Cap the accumulator's growth, leaving some room */
/* Determine the amounts to work with */
if(size > (H5F_ACCUM_MAX_SIZE / 2)) {
new_size = H5F_ACCUM_MAX_SIZE;
shrink_size = accum->size;
remnant_size = 0;
} /* end if */
else {
new_size = (H5F_ACCUM_MAX_SIZE / 2);
shrink_size = (H5F_ACCUM_MAX_SIZE / 2);
remnant_size = accum->size - shrink_size;
} /* end else */
/* Check if we need to flush accumulator data to file */
if(accum->dirty) {
/* Check whether to accumulator will be prepended or appended */
if(H5F_ACCUM_PREPEND == adjust) {
/* Write out upper part of the existing metadata accumulator, with dispatch to driver */
if(H5FD_write(lf, dxpl_id, H5FD_MEM_DEFAULT, (accum->loc + remnant_size), shrink_size, (accum->buf + remnant_size)) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed")
} /* end if */
else {
/* Sanity check */
HDassert(H5F_ACCUM_APPEND == adjust);
/* Write out lower part of the existing metadata accumulator, with dispatch to driver */
if(H5FD_write(lf, dxpl_id, H5FD_MEM_DEFAULT, accum->loc, shrink_size, accum->buf) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed")
/* Move remnant of accumulator down */
HDmemmove(accum->buf, (accum->buf + shrink_size), remnant_size);
/* Adjust accumulator's location */
accum->loc += shrink_size;
} /* end else */
/* Reset accumulator dirty flag (in case of error) */
accum->dirty = FALSE;
} /* end if */
/* Trim the accumulator's use of its buffer */
accum->size = remnant_size;
} /* end if */
/* Check for accumulator needing to be reallocated */
if(new_size > accum->alloc_size) {
unsigned char *new_buf; /* New buffer to hold the accumulated metadata */
/* Reallocate the metadata accumulator buffer */
if(NULL == (new_buf = H5FL_BLK_REALLOC(meta_accum, accum->buf, new_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate metadata accumulator buffer")
/* Update accumulator info */
accum->buf = new_buf;
accum->alloc_size = new_size;
#ifdef H5_CLEAR_MEMORY
HDmemset(accum->buf + accum->size, 0, (accum->alloc_size - (accum->size + size)));
#endif /* H5_CLEAR_MEMORY */
} /* end if */
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5F_accum_adjust() */
/*-------------------------------------------------------------------------
* Function: H5F_accum_write
@ -273,23 +392,15 @@ H5F_accum_write(const H5F_t *f, hid_t dxpl_id, H5FD_mem_t type, haddr_t addr,
HDassert(buf);
/* Check for accumulating metadata */
if((f->shared->feature_flags & H5FD_FEAT_ACCUMULATE_METADATA) && type != H5FD_MEM_DRAW) {
if((f->shared->feature_flags & H5FD_FEAT_ACCUMULATE_METADATA) && type != H5FD_MEM_DRAW
&& size < H5F_ACCUM_MAX_SIZE) {
/* Check if there is already metadata in the accumulator */
if(f->shared->accum.size > 0) {
/* Check if the new metadata adjoins the beginning of the current accumulator */
if((addr + size) == f->shared->accum.loc) {
/* Check if we need more buffer space */
if((size + f->shared->accum.size) > f->shared->accum.alloc_size) {
/* Adjust the buffer size, by doubling it */
f->shared->accum.alloc_size = MAX(f->shared->accum.alloc_size * 2, size + f->shared->accum.size);
/* Reallocate the metadata accumulator buffer */
if(NULL == (f->shared->accum.buf = H5FL_BLK_REALLOC(meta_accum, f->shared->accum.buf, f->shared->accum.alloc_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate metadata accumulator buffer")
#ifdef H5_CLEAR_MEMORY
HDmemset(f->shared->accum.buf + f->shared->accum.size, 0, (f->shared->accum.alloc_size - (f->shared->accum.size + size)));
#endif /* H5_CLEAR_MEMORY */
} /* end if */
/* Check if we need to adjust accumulator size */
if(H5F_accum_adjust(&f->shared->accum, f->shared->lf, dxpl_id, H5F_ACCUM_PREPEND, size) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTRESIZE, FAIL, "can't adjust metadata accumulator")
/* Move the existing metadata to the proper location */
HDmemmove(f->shared->accum.buf + size, f->shared->accum.buf, f->shared->accum.size);
@ -306,18 +417,9 @@ HDmemset(f->shared->accum.buf + f->shared->accum.size, 0, (f->shared->accum.allo
} /* end if */
/* Check if the new metadata adjoins the end of the current accumulator */
else if(addr == (f->shared->accum.loc + f->shared->accum.size)) {
/* Check if we need more buffer space */
if((size + f->shared->accum.size) > f->shared->accum.alloc_size) {
/* Adjust the buffer size, by doubling it */
f->shared->accum.alloc_size = MAX(f->shared->accum.alloc_size * 2, size + f->shared->accum.size);
/* Reallocate the metadata accumulator buffer */
if(NULL == (f->shared->accum.buf = H5FL_BLK_REALLOC(meta_accum, f->shared->accum.buf, f->shared->accum.alloc_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate metadata accumulator buffer")
#ifdef H5_CLEAR_MEMORY
HDmemset(f->shared->accum.buf + f->shared->accum.size + size, 0, (f->shared->accum.alloc_size - (f->shared->accum.size + size)));
#endif /* H5_CLEAR_MEMORY */
} /* end if */
/* Check if we need to adjust accumulator size */
if(H5F_accum_adjust(&f->shared->accum, f->shared->lf, dxpl_id, H5F_ACCUM_APPEND, size) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTRESIZE, FAIL, "can't adjust metadata accumulator")
/* Copy the new metadata to the end */
HDmemcpy(f->shared->accum.buf + f->shared->accum.size, buf, size);
@ -347,18 +449,9 @@ HDmemset(f->shared->accum.buf + f->shared->accum.size + size, 0, (f->shared->acc
/* Calculate the new accumulator size, based on the amount of overlap */
H5_ASSIGN_OVERFLOW(new_size, (f->shared->accum.loc - addr) + f->shared->accum.size, hsize_t, size_t);
/* Check if we need more buffer space */
if(new_size > f->shared->accum.alloc_size) {
/* Adjust the buffer size, by doubling it */
f->shared->accum.alloc_size = MAX(f->shared->accum.alloc_size + 2, new_size);
/* Reallocate the metadata accumulator buffer */
if(NULL == (f->shared->accum.buf = H5FL_BLK_REALLOC(meta_accum, f->shared->accum.buf, f->shared->accum.alloc_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate metadata accumulator buffer")
#ifdef H5_CLEAR_MEMORY
HDmemset(f->shared->accum.buf + f->shared->accum.size, 0, (f->shared->accum.alloc_size - f->shared->accum.size));
#endif /* H5_CLEAR_MEMORY */
} /* end if */
/* Check if we need to adjust accumulator size */
if(H5F_accum_adjust(&f->shared->accum, f->shared->lf, dxpl_id, H5F_ACCUM_PREPEND, (new_size - f->shared->accum.size)) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTRESIZE, FAIL, "can't adjust metadata accumulator")
/* Calculate the proper offset of the existing metadata */
H5_ASSIGN_OVERFLOW(old_offset, (addr + size) - f->shared->accum.loc, hsize_t, size_t);
@ -381,18 +474,9 @@ HDmemset(f->shared->accum.buf + f->shared->accum.size, 0, (f->shared->accum.allo
/* Calculate the new accumulator size, based on the amount of overlap */
H5_ASSIGN_OVERFLOW(new_size, (addr - f->shared->accum.loc) + size, hsize_t, size_t);
/* Check if we need more buffer space */
if(new_size > f->shared->accum.alloc_size) {
/* Adjust the buffer size, by doubling it */
f->shared->accum.alloc_size = MAX(f->shared->accum.alloc_size * 2, new_size);
/* Reallocate the metadata accumulator buffer */
if(NULL == (f->shared->accum.buf = H5FL_BLK_REALLOC(meta_accum, f->shared->accum.buf, f->shared->accum.alloc_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate metadata accumulator buffer")
#ifdef H5_CLEAR_MEMORY
HDmemset(f->shared->accum.buf + f->shared->accum.size, 0, (f->shared->accum.alloc_size - f->shared->accum.size));
#endif /* H5_CLEAR_MEMORY */
} /* end if */
/* Check if we need to adjust accumulator size */
if(H5F_accum_adjust(&f->shared->accum, f->shared->lf, dxpl_id, H5F_ACCUM_APPEND, (new_size - f->shared->accum.size)) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTRESIZE, FAIL, "can't adjust metadata accumulator")
/* Copy the new metadata to the end */
HDmemcpy(f->shared->accum.buf + (addr - f->shared->accum.loc), buf, size);
@ -421,12 +505,17 @@ HDmemset(f->shared->accum.buf + f->shared->accum.size, 0, (f->shared->accum.allo
/* Cache the new piece of metadata */
/* Check if we need to resize the buffer */
if(size > f->shared->accum.alloc_size) {
size_t new_size; /* New size of accumulator */
/* Adjust the buffer size to be a power of 2 that is large enough to hold data */
new_size = (size_t)1 << (1 + H5V_log2_gen(size - 1));
/* Grow the metadata accumulator buffer */
if(NULL == (f->shared->accum.buf = H5FL_BLK_REALLOC(meta_accum, f->shared->accum.buf, size)))
if(NULL == (f->shared->accum.buf = H5FL_BLK_REALLOC(meta_accum, f->shared->accum.buf, new_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate metadata accumulator buffer")
/* Note the new buffer size */
f->shared->accum.alloc_size = size;
f->shared->accum.alloc_size = new_size;
#ifdef H5_CLEAR_MEMORY
{
size_t clear_size = MAX(f->shared->accum.size, size);
@ -462,12 +551,17 @@ HDmemset(f->shared->accum.buf + clear_size, 0, (f->shared->accum.alloc_size - cl
else {
/* Check if we need to reallocate the buffer */
if(size > f->shared->accum.alloc_size) {
size_t new_size; /* New size of accumulator */
/* Adjust the buffer size to be a power of 2 that is large enough to hold data */
new_size = (size_t)1 << (1 + H5V_log2_gen(size - 1));
/* Reallocate the metadata accumulator buffer */
if(NULL == (f->shared->accum.buf = H5FL_BLK_REALLOC(meta_accum, f->shared->accum.buf, size)))
if(NULL == (f->shared->accum.buf = H5FL_BLK_REALLOC(meta_accum, f->shared->accum.buf, new_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate metadata accumulator buffer")
/* Note the new buffer size */
f->shared->accum.alloc_size = size;
f->shared->accum.alloc_size = new_size;
} /* end if */
/* Update the metadata accumulator information */