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[svn-r2652] Purpose:

Browse Source 
Maintainance & performance enhancements
Description:
    Re-arranged header files to protect private symbols better.

    Changed optimized regular hyperslab I/O to compute the offsets more
    efficiently from previous method of using matrix operations.

    Added sequential I/O operations at a more abstract level (at the same level
    as H5F_arr_read/write), to support the optimized hyperslab I/O.

Platforms tested:
    Solaris 2.6 (baldric) & FreeBSD 4.1.1 (hawkwind)
This commit is contained in:
Quincey Koziol 2000-10-10 02:43:38 -05:00
parent 428f04e82a
commit ba28c64ba7
59 changed files with 2023 additions and 717 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
src/H5.c
View File

@ -1823,8 +1823,8 @@ H5_trace (hbool_t returning, const char *func, const char *type, ...)
/*Save the rank of simple data spaces for arrays*/
{
H5S_t *space = H5I_object(obj);
if (H5S_SIMPLE==space->extent.type) {
asize[argno] = space->extent.u.simple.rank;
if (H5S_SIMPLE==H5S_get_simple_extent_type(space)) {
asize[argno] = H5S_get_simple_extent_ndims(space);
}
}
break;

5
src/H5A.c
View File

@ -17,6 +17,7 @@ static char RcsId[] = "$Revision$";
/* $Id$ */
#define H5A_PACKAGE /*suppress error about including H5Apkg */
#define H5S_PACKAGE /*suppress error about including H5Spkg */
/* Private header files */
#include <H5private.h> /* Generic Functions */
@ -29,6 +30,7 @@ static char RcsId[] = "$Revision$";
#include <H5MMprivate.h> /* Memory management */
#include <H5Pprivate.h> /* Property lists */
#include <H5Oprivate.h> /* Object Headers */
#include <H5Spkg.h> /* Data-space functions */
#include <H5Apkg.h> /* Attributes */
#define PABLO_MASK H5A_mask
@ -254,8 +256,7 @@ H5A_create(const H5G_entry_t *ent, const char *name, const H5T_t *type,
/* Compute the internal sizes */
attr->dt_size=(H5O_DTYPE[0].raw_size)(attr->ent.file,type);
attr->ds_size=(H5O_SDSPACE[0].raw_size)(attr->ent.file,
&(space->extent.u.simple));
attr->ds_size=(H5O_SDSPACE[0].raw_size)(attr->ent.file,&(space->extent.u.simple));
attr->data_size=H5S_get_simple_extent_npoints(space)*H5T_get_size(type);
/* Hold the symbol table entry (and file) open */

4
src/H5AC.c
View File

@ -23,9 +23,13 @@
*
*-------------------------------------------------------------------------
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h>
#include <H5ACprivate.h>
#include <H5Eprivate.h>
#include <H5Fpkg.h>
#include <H5FLprivate.h> /*Free Lists */
#include <H5MMprivate.h>

3
src/H5Apkg.h
View File

@ -23,8 +23,9 @@
# undef H5A_DEBUG
#endif
#include <H5HGprivate.h>
#include <H5Aprivate.h>
#include <H5HGprivate.h>
#include <H5Sprivate.h>
struct H5A_t {
uintn initialized;/* Indicate whether the attribute has been modified */

5
src/H5B.c
View File

@ -86,12 +86,15 @@
*
*-------------------------------------------------------------------------
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
/* private headers */
#include <H5private.h> /*library */
#include <H5ACprivate.h> /*cache */
#include <H5Bprivate.h> /*B-link trees */
#include <H5Eprivate.h> /*error handling */
#include <H5Fprivate.h> /*file access */
#include <H5Fpkg.h> /*file access */
#include <H5FLprivate.h> /*Free Lists */
#include <H5MFprivate.h> /*file memory management */
#include <H5MMprivate.h> /*core memory management */

44
src/H5D.c
View File

@ -76,6 +76,32 @@ const H5D_create_t H5D_create_dflt = {
{0, 0, NULL} /* No filters in pipeline */
};
/* Default data transfer property list */
/* Not const anymore because some of the VFL drivers modify this struct - QAK */
H5D_xfer_t H5D_xfer_dflt = {
1024*1024, /*Temporary buffer size */
NULL, /*Type conversion buffer or NULL */
NULL, /*Background buffer or NULL */
H5T_BKG_NO, /*Type of background buffer needed */
{0.1, 0.5, 0.9}, /*B-tree node splitting ratios */
#ifndef H5_HAVE_PARALLEL
1, /*Cache the hyperslab blocks */
#else
0, /*Don't cache the hyperslab blocks */
#endif /* H5_HAVE_PARALLEL */
0, /*No limit on hyperslab block size to cache */
NULL, /*Use malloc() for VL data allocations */
NULL, /*No information needed for malloc() calls */
NULL, /*Use free() for VL data frees */
NULL, /*No information needed for free() calls */
-2, /*See H5Pget_driver() */
NULL, /*No file driver-specific information yet */
#ifdef COALESCE_READS
0, /*coalesce single reads into a read */
/*transaction */
#endif
};
/* Interface initialization? */
static intn interface_initialize_g = 0;
#define INTERFACE_INIT H5D_init_interface
@ -1407,7 +1433,7 @@ H5D_open_oid(H5G_entry_t *ent)
* This is especially important for parallel I/O where the B-tree must
* be fully populated before I/O can happen.
*/
if ((dataset->ent.file->intent & H5F_ACC_RDWR) &&
if ((H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR) &&
H5D_CHUNKED==dataset->layout.type) {
if (H5D_init_storage(dataset, space)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
@ -1526,7 +1552,7 @@ herr_t
H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, hid_t dxpl_id, void *buf/*out*/)
{
const H5F_xfer_t *xfer_parms = NULL;
const H5D_xfer_t *xfer_parms = NULL;
hssize_t nelmts; /*number of elements */
size_t smine_start; /*strip mine start loc */
size_t n, smine_nelmts; /*elements per strip */
@ -1566,7 +1592,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
/* Get the dataset transfer property list */
if (H5P_DEFAULT == dxpl_id) {
xfer_parms = &H5F_xfer_dflt;
xfer_parms = &H5D_xfer_dflt;
} else if (H5P_DATA_XFER != H5P_get_class(dxpl_id) ||
NULL == (xfer_parms = H5I_object(dxpl_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms");
@ -1902,7 +1928,7 @@ herr_t
H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, hid_t dxpl_id, const void *buf)
{
const H5F_xfer_t *xfer_parms = NULL;
const H5D_xfer_t *xfer_parms = NULL;
hssize_t nelmts; /*total number of elmts */
size_t smine_start; /*strip mine start loc */
size_t n, smine_nelmts; /*elements per strip */
@ -1967,13 +1993,13 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
/* Get the dataset transfer property list */
if (H5P_DEFAULT == dxpl_id) {
xfer_parms = &H5F_xfer_dflt;
xfer_parms = &H5D_xfer_dflt;
} else if (H5P_DATA_XFER != H5P_get_class(dxpl_id) ||
NULL == (xfer_parms = H5I_object(dxpl_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms");
}
if (0==(dataset->ent.file->intent & H5F_ACC_RDWR)) {
if (0==(H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR)) {
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL,
"no write intent on file");
}
@ -2768,8 +2794,8 @@ H5Diterate(void *buf, hid_t type_id, hid_t space_id, H5D_operator_t op,
herr_t
H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void *buf)
{
H5F_xfer_t tmp_xfer_parms; /* Temporary copy of the default xfer parms */
H5F_xfer_t *xfer_parms = NULL; /* xfer parms as iterator op_data */
H5D_xfer_t tmp_xfer_parms; /* Temporary copy of the default xfer parms */
H5D_xfer_t *xfer_parms = NULL; /* xfer parms as iterator op_data */
herr_t ret_value=FAIL;
FUNC_ENTER(H5Dvlen_reclaim, FAIL);
@ -2784,7 +2810,7 @@ H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void *buf)
/* Retrieve dataset transfer property list */
if (H5P_DEFAULT == plist_id) {
HDmemcpy(&tmp_xfer_parms,&H5F_xfer_dflt,sizeof(H5F_xfer_t));
HDmemcpy(&tmp_xfer_parms,&H5D_xfer_dflt,sizeof(H5D_xfer_t));
xfer_parms = &tmp_xfer_parms;
} else if (H5P_DATA_XFER != H5P_get_class(plist_id) ||
NULL == (xfer_parms = H5I_object(plist_id))) {

13
src/H5Dcontig.c
View File

@ -11,9 +11,12 @@
* H5F_seg_read/write.
*
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5Fprivate.h>
#include <H5Fpkg.h>
#include <H5FDprivate.h> /*file driver */
#include <H5MMprivate.h>
@ -244,8 +247,8 @@ H5F_contig_write(H5F_t *f, H5FD_mem_t type, haddr_t addr, hsize_t size,
f->shared->sieve_size=0;
} /* end if */
/* Write directly from the user's buffer */
if (H5F_block_write(f, H5FD_MEM_DRAW, addr, size, dxpl_id, buf)<0) {
/* Write directly to the user's buffer */
if (H5F_block_write(f, type, addr, size, dxpl_id, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"block write failed");
}
@ -293,7 +296,7 @@ H5F_contig_write(H5F_t *f, H5FD_mem_t type, haddr_t addr, hsize_t size,
else {
/* Check if we can actually hold the I/O request in the sieve buffer */
if(size>f->shared->sieve_buf_size) {
if (H5F_block_write(f, H5FD_MEM_DRAW, addr, size, dxpl_id, buf)<0) {
if (H5F_block_write(f, type, addr, size, dxpl_id, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"block write failed");
}
@ -330,7 +333,7 @@ H5F_contig_write(H5F_t *f, H5FD_mem_t type, haddr_t addr, hsize_t size,
} /* end else */
} /* end if */
else {
if (H5F_block_write(f, H5FD_MEM_DRAW, addr, size, dxpl_id, buf)<0) {
if (H5F_block_write(f, type, addr, size, dxpl_id, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"block write failed");
}

13
src/H5Distore.c
View File

@ -29,10 +29,13 @@
* entries near the front of the list to make room for the new
* entry which is added to the end of the list.
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h>
#include <H5Dprivate.h>
#include <H5Eprivate.h>
#include <H5Fprivate.h>
#include <H5Fpkg.h>
#include <H5FLprivate.h> /*Free Lists */
#include <H5Iprivate.h>
#include <H5MFprivate.h>
@ -1498,8 +1501,8 @@ H5F_istore_lock(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
ent->chunk = chunk;
{
H5F_xfer_t *dxpl;
dxpl = (H5P_DEFAULT==dxpl_id) ? &H5F_xfer_dflt : (H5F_xfer_t *)H5I_object(dxpl_id);
H5D_xfer_t *dxpl;
dxpl = (H5P_DEFAULT==dxpl_id) ? &H5D_xfer_dflt : (H5D_xfer_t *)H5I_object(dxpl_id);
ent->split_ratios[0] = dxpl->split_ratios[0];
ent->split_ratios[1] = dxpl->split_ratios[1];
ent->split_ratios[2] = dxpl->split_ratios[2];
@ -1640,8 +1643,8 @@ H5F_istore_unlock(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
x.alloc_size = x.chunk_size;
x.chunk = chunk;
{
H5F_xfer_t *dxpl;
dxpl = (H5P_DEFAULT==dxpl_id) ? &H5F_xfer_dflt : (H5F_xfer_t *)H5I_object(dxpl_id);
H5D_xfer_t *dxpl;
dxpl = (H5P_DEFAULT==dxpl_id) ? &H5D_xfer_dflt : (H5D_xfer_t *)H5I_object(dxpl_id);
x.split_ratios[0] = dxpl->split_ratios[0];
x.split_ratios[1] = dxpl->split_ratios[1];
x.split_ratios[2] = dxpl->split_ratios[2];

24
src/H5Dprivate.h
View File

@ -22,6 +22,7 @@
#include <H5private.h>
#include <H5Fprivate.h> /*for the H5F_t type */
#include <H5Gprivate.h> /*symbol tables */
#include <H5MMpublic.h> /*for H5MM_allocate_t and H5MM_free_t types */
#include <H5Oprivate.h> /*object Headers */
#include <H5Sprivate.h> /*for the H5S_t type */
#include <H5Tprivate.h> /*for the H5T_t type */
@ -50,9 +51,32 @@ typedef struct H5D_create_t {
H5O_pline_t pline; /*data filter pipeline */
} H5D_create_t;
/* Data transfer property list */
typedef struct H5D_xfer_t {
size_t buf_size; /*max temp buffer size */
void *tconv_buf; /*type conversion buffer or null */
void *bkg_buf; /*background buffer or null */
H5T_bkg_t need_bkg; /*type of background buffer needed */
double split_ratios[3];/*B-tree node splitting ratios */
uintn cache_hyper; /*cache hyperslab blocks during I/O? */
uintn block_limit; /*largest hyperslab block to cache */
H5MM_allocate_t vlen_alloc; /*VL datatype allocation function */
void *alloc_info; /*VL datatype allocation information */
H5MM_free_t vlen_free; /*VL datatype free function */
void *free_info; /*VL datatype free information */
hid_t driver_id; /*File driver ID */
void *driver_info; /*File driver specific information */
#ifdef COALESCE_READS
uintn gather_reads; /*coalesce single reads into a read */
/*transaction */
#endif
} H5D_xfer_t;
typedef struct H5D_t H5D_t;
/* library variables */
__DLLVAR__ const H5D_create_t H5D_create_dflt;
__DLLVAR__ H5D_xfer_t H5D_xfer_dflt;
/* Functions defined in H5D.c */
__DLL__ herr_t H5D_init(void);

494
src/H5Dseq.c Normal file
View File

@ -0,0 +1,494 @@
/*
* Copyright (C) 2000 NCSA
* All rights reserved.
*
* Programmer: Quincey Koziol <koziol@ncsa.uiuc.edu>
* Thursday, September 28, 2000
*
* Purpose: Provides I/O facilities for sequences of bytes stored with various
* layout policies. These routines are similar to the H5Farray.c routines,
* these deal in terms of byte offsets and lengths, not coordinates and
* hyperslab sizes.
*
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h>
#include <H5Dprivate.h>
#include <H5Eprivate.h>
#include <H5Fpkg.h>
#include <H5FDprivate.h> /*file driver */
#include <H5Iprivate.h>
#include <H5MFprivate.h>
#include <H5MMprivate.h> /*memory management */
#include <H5Oprivate.h>
#include <H5Pprivate.h>
#include <H5Vprivate.h>
/* MPIO driver functions are needed for some special checks */
#include <H5FDmpio.h>
/* Interface initialization */
#define PABLO_MASK H5Fseq_mask
#define INTERFACE_INIT NULL
static intn interface_initialize_g = 0;
/*-------------------------------------------------------------------------
* Function: H5F_seq_read
*
* Purpose: Reads a sequence of bytes from a file dataset into a buffer in
* in memory. The data is read from file F and the array's size and
* storage information is in LAYOUT. External files are described
* according to the external file list, EFL. The sequence offset is
* FILE_OFFSET in the file and MEM_OFFSET in memory (offsets are
* in terms of bytes) and the size of the hyperslab is SEQ_LEN. The
* total size of the file array is implied in the LAYOUT argument.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, September 28, 2000
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5F_seq_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline, const H5O_fill_t *fill,
const struct H5O_efl_t *efl, const H5S_t *file_space, size_t elmt_size,
hsize_t seq_len, hssize_t mem_offset, hssize_t file_offset,
void *_buf/*out*/)
{
uint8_t *buf = (uint8_t*)_buf; /*cast for arithmetic */
hsize_t dset_dims[H5O_LAYOUT_NDIMS]; /* dataspace dimensions */
hssize_t coords[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in dataspace */
hsize_t hslab_size[H5O_LAYOUT_NDIMS]; /* hyperslab size in dataspace*/
intn ndims;
haddr_t addr; /*address in file */
intn i; /*counters */
#ifdef H5_HAVE_PARALLEL
H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
#endif
FUNC_ENTER(H5F_seq_read, FAIL);
/* Check args */
assert(f);
assert(layout);
assert(buf);
#ifdef H5_HAVE_PARALLEL
{
/* Get the transfer mode */
H5F_xfer_t *dxpl;
H5FD_mpio_dxpl_t *dx;
if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
H5FD_MPIO==dxpl->driver_id && (dx=dxpl->driver_info) &&
H5FD_MPIO_INDEPENDENT!=dx->xfer_mode) {
xfer_mode = dx->xfer_mode;
}
}
/* Collective MPIO access is unsupported for non-contiguous datasets */
if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) {
HRETURN_ERROR (H5E_DATASET, H5E_READERROR, FAIL,
"collective access on non-contiguous datasets not supported yet");
}
#endif
switch (layout->type) {
case H5D_CONTIGUOUS:
/* Filters cannot be used for contiguous data. */
if (pline && pline->nfilters>0) {
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
"filters are not allowed for contiguous data");
}
/*
* Initialize loop variables. The loop is a multi-dimensional loop
* that counts from SIZE down to zero and IDX is the counter. Each
* element of IDX is treated as a digit with IDX[0] being the least
* significant digit.
*/
if (efl && efl->nused>0) {
addr = 0;
} else {
addr = layout->addr;
}
addr += file_offset;
buf += mem_offset;
/*
* Now begin to walk through the array, copying data from disk to
* memory.
*/
#ifdef H5_HAVE_PARALLEL
if (H5FD_MPIO_COLLECTIVE==xfer_mode) {
/*
* Currently supports same number of collective access. Need to
* be changed LATER to combine all reads into one collective MPIO
* call.
*/
unsigned long max, min, temp;
temp = seq_len;
assert(temp==seq_len); /* verify no overflow */
MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX,
H5FD_mpio_communicator(f->shared->lf));
MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN,
H5FD_mpio_communicator(f->shared->lf));
#ifdef AKC
printf("seq_len=%lu, min=%lu, max=%lu\n", temp, min, max);
#endif
if (max != min)
HRETURN_ERROR(H5E_DATASET, H5E_READERROR, FAIL,
"collective access with unequal number of blocks not supported yet");
}
#endif
/* Read directly from file if the dataset is in an external file */
/* Note: We can't use data sieve buffers for datasets in external files
* because the 'addr' of all external files is set to 0 (above) and
* all datasets in external files would alias to the same set of
* file offsets, totally mixing up the data sieve buffer information. -QAK
*/
if (efl && efl->nused>0) {
if (H5O_efl_read(f, efl, addr, seq_len, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
"external data read failed");
}
} else {
if (H5F_contig_read(f, addr, seq_len, dxpl_id, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
"block read failed");
}
} /* end else */
break;
case H5D_CHUNKED:
/*
* This method is unable to access external raw data files
*/
if (efl && efl->nused>0) {
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL,
"chunking and external files are mutually exclusive");
}
/* Compute the file offset coordinates and hyperslab size */
if((ndims=H5S_get_simple_extent_dims(file_space,dset_dims,NULL))<0)
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to retrieve dataspace dimensions");
#ifdef QAK
/* The library shouldn't be reading partial elements currently */
assert(seq_len%elmt_size!=0);
assert(addr%elmt_size!=0);
#endif /* QAK */
#ifdef QAK
/* Print out the file offsets & hyperslab sizes */
{
static int count=0;
if(count<10) {
printf("%s: elmt_size=%d, addr=%d, seq_len=%d\n",FUNC,(int)elmt_size,(int)addr,(int)seq_len);
printf("%s: file_offset=%d, mem_offset=%d\n",FUNC,(int)file_offset,(int)mem_offset);
count++;
}
}
#endif /* QAK */
/* Set location in dataset from the file_offset */
addr=file_offset;
/* Convert the bytes into elements */
seq_len/=elmt_size;
addr/=elmt_size;
/* Compute the hyperslab offset from the address given */
for(i=ndims-1; i>=0; i--) {
coords[i]=addr%dset_dims[i];
addr/=dset_dims[i];
} /* end for */
coords[ndims]=0; /* No offset for element info */
/* Compute the hyperslab size from the length given */
for(i=ndims-1; i>=0; i--) {
/* Check if the hyperslab is wider than the width of the dimension */
if(seq_len>dset_dims[i]) {
if (0!=coords[i])
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to copy into a proper hyperslab");
hslab_size[i]=dset_dims[i];
} /* end if */
else
hslab_size[i]=seq_len;
/* Fold the length into the length in the next highest dimension */
seq_len/=dset_dims[i];
/* Make certain the hyperslab sizes don't go less than 1 */
if(seq_len<1)
seq_len=1;
} /* end for */
hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */
#ifdef QAK
/* Print out the file offsets & hyperslab sizes */
{
static int count=0;
if(count<10) {
printf("%s: elmt_size=%d, addr=%d, seq_len=%d\n",FUNC,(int)elmt_size,(int)addr,(int)seq_len);
for(i=0; i<=ndims; i++)
printf("%s: dset_dims[%d]=%d\n",FUNC,i,(int)dset_dims[i]);
for(i=0; i<=ndims; i++)
printf("%s: coords[%d]=%d, hslab_size[%d]=%d\n",FUNC,i,(int)coords[i],(int)i,(int)hslab_size[i]);
count++;
}
}
#endif /* QAK */
if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords,
hslab_size, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed");
}
break;
default:
assert("not implemented yet" && 0);
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout");
} /* end switch() */
FUNC_LEAVE(SUCCEED);
} /* H5F_seq_read() */
/*-------------------------------------------------------------------------
* Function: H5F_seq_write
*
* Purpose: Writes a sequence of bytes to a file dataset from a buffer in
* in memory. The data is written to file F and the array's size and
* storage information is in LAYOUT. External files are described
* according to the external file list, EFL. The sequence offset is
* FILE_OFFSET in the file and MEM_OFFSET in memory (offsets are
* in terms of bytes) and the size of the hyperslab is SEQ_LEN. The
* total size of the file array is implied in the LAYOUT argument.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Monday, October 9, 2000
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5F_seq_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline, const H5O_fill_t *fill,
const struct H5O_efl_t *efl, const H5S_t *file_space, size_t elmt_size,
hsize_t seq_len, hssize_t mem_offset, hssize_t file_offset,
const void *_buf)
{
const uint8_t *buf = (const uint8_t*)_buf; /*cast for arithmetic */
hsize_t dset_dims[H5O_LAYOUT_NDIMS]; /* dataspace dimensions */
hssize_t coords[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in dataspace */
hsize_t hslab_size[H5O_LAYOUT_NDIMS]; /* hyperslab size in dataspace*/
intn ndims;
haddr_t addr; /*address in file */
intn i; /*counters */
#ifdef H5_HAVE_PARALLEL
H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
#endif
FUNC_ENTER(H5F_seq_write, FAIL);
/* Check args */
assert(f);
assert(layout);
assert(buf);
#ifdef H5_HAVE_PARALLEL
{
/* Get the transfer mode */
H5F_xfer_t *dxpl;
H5FD_mpio_dxpl_t *dx;
if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
H5FD_MPIO==dxpl->driver_id && (dx=dxpl->driver_info) &&
H5FD_MPIO_INDEPENDENT!=dx->xfer_mode) {
xfer_mode = dx->xfer_mode;
}
}
/* Collective MPIO access is unsupported for non-contiguous datasets */
if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) {
HRETURN_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL,
"collective access on non-contiguous datasets not supported yet");
}
#endif
switch (layout->type) {
case H5D_CONTIGUOUS:
/* Filters cannot be used for contiguous data. */
if (pline && pline->nfilters>0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"filters are not allowed for contiguous data");
}
/*
* Initialize loop variables. The loop is a multi-dimensional loop
* that counts from SIZE down to zero and IDX is the counter. Each
* element of IDX is treated as a digit with IDX[0] being the least
* significant digit.
*/
if (efl && efl->nused>0) {
addr = 0;
} else {
addr = layout->addr;
}
addr += file_offset;
buf += mem_offset;
/*
* Now begin to walk through the array, copying data from disk to
* memory.
*/
#ifdef H5_HAVE_PARALLEL
if (H5FD_MPIO_COLLECTIVE==xfer_mode) {
/*
* Currently supports same number of collective access. Need to
* be changed LATER to combine all reads into one collective MPIO
* call.
*/
unsigned long max, min, temp;
temp = seq_len;
assert(temp==seq_len); /* verify no overflow */
MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX,
H5FD_mpio_communicator(f->shared->lf));
MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN,
H5FD_mpio_communicator(f->shared->lf));
#ifdef AKC
printf("seq_len=%lu, min=%lu, max=%lu\n", temp, min, max);
#endif
if (max != min)
HRETURN_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL,
"collective access with unequal number of blocks not supported yet");
}
#endif
/* Write directly to file if the dataset is in an external file */
/* Note: We can't use data sieve buffers for datasets in external files
* because the 'addr' of all external files is set to 0 (above) and
* all datasets in external files would alias to the same set of
* file offsets, totally mixing up the data sieve buffer information. -QAK
*/
if (efl && efl->nused>0) {
if (H5O_efl_write(f, efl, addr, seq_len, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"external data write failed");
}
} else {
if (H5F_contig_write(f, H5FD_MEM_DRAW, addr, seq_len, dxpl_id, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"block write failed");
}
} /* end else */
break;
case H5D_CHUNKED:
/*
* This method is unable to access external raw data files
*/
if (efl && efl->nused>0) {
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL,
"chunking and external files are mutually exclusive");
}
/* Compute the file offset coordinates and hyperslab size */
if((ndims=H5S_get_simple_extent_dims(file_space,dset_dims,NULL))<0)
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to retrieve dataspace dimensions");
#ifdef QAK
/* Print out the file offsets & hyperslab sizes */
{
static int count=0;
if(count<10) {
printf("%s: elmt_size=%d, addr=%d, seq_len=%lu\n",FUNC,(int)elmt_size,(int)addr,(unsigned long)seq_len);
printf("%s: file_offset=%d, mem_offset=%d\n",FUNC,(int)file_offset,(int)mem_offset);
count++;
}
}
#endif /* QAK */
#ifdef QAK
/* The library shouldn't be reading partial elements currently */
assert((seq_len%elmt_size)!=0);
assert((addr%elmt_size)!=0);
#endif /* QAK */
/* Set location in dataset from the file_offset */
addr=file_offset;
/* Convert the bytes into elements */
seq_len/=elmt_size;
addr/=elmt_size;
/* Compute the hyperslab offset from the address given */
for(i=ndims-1; i>=0; i--) {
coords[i]=addr%dset_dims[i];
addr/=dset_dims[i];
} /* end for */
coords[ndims]=0; /* No offset for element info */
/* Compute the hyperslab size from the length given */
for(i=ndims-1; i>=0; i--) {
/* Check if the hyperslab is wider than the width of the dimension */
if(seq_len>dset_dims[i]) {
if (0!=coords[i])
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to copy into a proper hyperslab");
hslab_size[i]=dset_dims[i];
} /* end if */
else
hslab_size[i]=seq_len;
/* Fold the length into the length in the next highest dimension */
seq_len/=dset_dims[i];
/* Make certain the hyperslab sizes don't go less than 1 */
if(seq_len<1)
seq_len=1;
} /* end for */
hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */
#ifdef QAK
/* Print out the file offsets & hyperslab sizes */
{
static int count=0;
if(count<10) {
printf("%s: elmt_size=%d, addr=%d, seq_len=%d\n",FUNC,(int)elmt_size,(int)addr,(int)seq_len);
for(i=0; i<=ndims; i++)
printf("%s: dset_dims[%d]=%d\n",FUNC,i,(int)dset_dims[i]);
for(i=0; i<=ndims; i++)
printf("%s: coords[%d]=%d, hslab_size[%d]=%d\n",FUNC,i,(int)coords[i],(int)i,(int)hslab_size[i]);
count++;
}
}
#endif /* QAK */
if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords,
hslab_size, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed");
}
break;
default:
assert("not implemented yet" && 0);
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout");
} /* end switch() */
FUNC_LEAVE(SUCCEED);
} /* H5F_seq_write() */

111
src/H5F.c
View File

@ -20,6 +20,8 @@ static char RcsId[] = "@(#)$Revision$";
/* $Id$ */
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
/* Predefined file drivers */
#include <H5FDcore.h> /*temporary in-memory files */
#include <H5FDfamily.h> /*family of files */
@ -41,7 +43,7 @@ static char RcsId[] = "@(#)$Revision$";
#include <H5Iprivate.h> /*object IDs */
#include <H5ACprivate.h> /*cache */
#include <H5Eprivate.h> /*error handling */
#include <H5Fprivate.h> /*file access */
#include <H5Fpkg.h> /*file access */
#include <H5FDprivate.h> /*file driver */
#include <H5Gprivate.h> /*symbol tables */
#include <H5MMprivate.h> /*core memory management */
@ -80,32 +82,6 @@ const H5F_create_t H5F_create_dflt = {
*/
H5F_access_t H5F_access_dflt;
/* Default data transfer property list */
/* Not const anymore before some of the VFL drivers modify this struct - QAK */
H5F_xfer_t H5F_xfer_dflt = {
1024*1024, /*Temporary buffer size */
NULL, /*Type conversion buffer or NULL */
NULL, /*Background buffer or NULL */
H5T_BKG_NO, /*Type of background buffer needed */
{0.1, 0.5, 0.9}, /*B-tree node splitting ratios */
#ifndef H5_HAVE_PARALLEL
1, /*Cache the hyperslab blocks */
#else
0, /*Don't cache the hyperslab blocks */
#endif /* H5_HAVE_PARALLEL */
0, /*No limit on hyperslab block size to cache */
NULL, /*Use malloc() for VL data allocations */
NULL, /*No information needed for malloc() calls */
NULL, /*Use free() for VL data frees */
NULL, /*No information needed for free() calls */
-2, /*See H5Pget_driver() */
NULL, /*No file driver-specific information yet */
#ifdef COALESCE_READS
0, /*coalesce single reads into a read */
/*transaction */
#endif
};
/*
* Define the default mount property list.
*/
@ -2448,6 +2424,87 @@ H5Freopen(hid_t file_id)
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5F_get_intent
*
* Purpose: Quick and dirty routine to retrieve the file's 'intent' flags
* (Mainly added to stop non-file routines from poking about in the
* H5F_t data structure)
*
* Return: 'intent' on success/abort on failure (shouldn't fail)
*
* Programmer: Quincey Koziol <koziol@ncsa.uiuc.edu>
* September 29, 2000
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
uintn
H5F_get_intent(H5F_t *f)
{
FUNC_ENTER(H5F_get_intent, 0);
assert(f);
FUNC_LEAVE(f->intent);
}
/*-------------------------------------------------------------------------
* Function: H5F_sizeof_addr
*
* Purpose: Quick and dirty routine to retrieve the size of the file's size_t
* (Mainly added to stop non-file routines from poking about in the
* H5F_t data structure)
*
* Return: 'sizeof_addr' on success/abort on failure (shouldn't fail)
*
* Programmer: Quincey Koziol <koziol@ncsa.uiuc.edu>
* September 29, 2000
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
size_t
H5F_sizeof_addr(H5F_t *f)
{
FUNC_ENTER(H5F_sizeof_addr, 0);
assert(f);
FUNC_LEAVE((f)->shared->fcpl->sizeof_addr)
}
/*-------------------------------------------------------------------------
* Function: H5F_sizeof_size
*
* Purpose: Quick and dirty routine to retrieve the size of the file's off_t
* (Mainly added to stop non-file routines from poking about in the
* H5F_t data structure)
*
* Return: 'sizeof_size' on success/abort on failure (shouldn't fail)
*
* Programmer: Quincey Koziol <koziol@ncsa.uiuc.edu>
* September 29, 2000
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
size_t
H5F_sizeof_size(H5F_t *f)
{
FUNC_ENTER(H5F_sizeof_size, 0);
assert(f);
FUNC_LEAVE((f)->shared->fcpl->sizeof_addr)
}
/*-------------------------------------------------------------------------
* Function: H5F_block_read

6
src/H5FD.c
View File

@ -12,10 +12,12 @@
* layer.
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
/* Packages needed by this file */
#include <H5private.h> /*library functions */
#include <H5Eprivate.h> /*error handling */
#include <H5Fprivate.h> /*files */
#include <H5Fpkg.h> /*files */
#include <H5FDprivate.h> /*virtual file driver */
#include <H5FLprivate.h> /*Free Lists */
#include <H5Iprivate.h> /*interface abstraction layer */
@ -282,7 +284,7 @@ H5FD_get_class(hid_t id)
{
H5FD_class_t *ret_value=NULL;
H5F_access_t *fapl=NULL;
H5F_xfer_t *dxpl=NULL;
H5D_xfer_t *dxpl=NULL;
FUNC_ENTER(H5FD_get_class, NULL);

1
src/H5FDcore.c
View File

@ -12,6 +12,7 @@
#include <H5private.h> /*library functions */
#include <H5Eprivate.h> /*error handling */
#include <H5Fprivate.h> /*files */
#include <H5FDprivate.h> /*file driver */
#include <H5FDcore.h> /* Core file driver */
#include <H5MMprivate.h> /* Memory allocation */
#include <H5Pprivate.h> /*property lists */

5
src/H5FDdpss.c
View File

@ -11,11 +11,10 @@
#include <hdf5.h>
#include <H5Eprivate.h> /* error handling */
#include <H5FDprivate.h> /*file driver */
#include <H5FDdpss.h>
#include <H5MMprivate.h> /* memory management */
/*** FIXME: should this be included here or in <hdf5.h> ??? ***/
#include "H5FDdpss.h"
#ifdef COALESCE_READS
/* Packages needed by this file.*/
#include <H5Fprivate.h>

1
src/H5FDfamily.c
View File

@ -24,6 +24,7 @@
#include <H5private.h> /*library functions */
#include <H5Eprivate.h> /*error handling */
#include <H5Fprivate.h> /*files */
#include <H5FDprivate.h> /*file driver */
#include <H5FDfamily.h> /* Family file driver */
#include <H5MMprivate.h> /* Memory allocation */
#include <H5Pprivate.h> /*property lists */

1
src/H5FDgass.c
View File

@ -11,6 +11,7 @@
#include <H5private.h> /*library functions */
#include <H5Eprivate.h> /*error handling */
#include <H5Fprivate.h> /*files */
#include <H5FDprivate.h> /*file driver */
#include <H5FDgass.h> /* Core file driver */
#include <H5MMprivate.h> /* Memory allocation */
#include <H5Pprivate.h> /*property lists */

5
src/H5FDlog.c
View File

@ -17,6 +17,7 @@
#include <H5private.h> /*library functions */
#include <H5Eprivate.h> /*error handling */
#include <H5Fprivate.h> /*files */
#include <H5FDprivate.h> /*file driver */
#include <H5FDlog.h> /* logging file driver */
#include <H5FLprivate.h> /*Free Lists */
#include <H5MMprivate.h> /* Memory allocation */
@ -40,7 +41,7 @@ static hid_t H5FD_LOG_g = 0;
/* Driver-specific file access properties */
typedef struct H5FD_log_fapl_t {
const char *logfile; /* Allocated log file name */
char *logfile; /* Allocated log file name */
intn verbosity; /* Verbosity of logging information */
} H5FD_log_fapl_t;
@ -257,7 +258,7 @@ H5FD_log_init(void)
*-------------------------------------------------------------------------
*/
herr_t
H5Pset_fapl_log(hid_t fapl_id, const char *logfile, int verbosity)
H5Pset_fapl_log(hid_t fapl_id, char *logfile, int verbosity)
{
H5FD_log_fapl_t fa; /* File access property list information */
herr_t ret_value=FAIL;

2
src/H5FDlog.h
View File

@ -15,7 +15,7 @@
#define H5FD_LOG (H5FD_log_init())
__DLL__ hid_t H5FD_log_init(void);
__DLL__ herr_t H5Pset_fapl_log(hid_t fapl_id, const char *logfile, int verbosity);
__DLL__ herr_t H5Pset_fapl_log(hid_t fapl_id, char *logfile, int verbosity);
#endif

1
src/H5FDmpio.c
View File

@ -23,6 +23,7 @@
#include <H5private.h> /*library functions */
#include <H5Eprivate.h> /*error handling */
#include <H5Fprivate.h> /*files */
#include <H5FDprivate.h> /*file driver */
#include <H5FDmpio.h> /* MPI I/O file driver */
#include <H5MMprivate.h> /* Memory allocation */
#include <H5Pprivate.h> /*property lists */

1
src/H5FDsec2.c
View File

@ -15,6 +15,7 @@
#include <H5private.h> /*library functions */
#include <H5Eprivate.h> /*error handling */
#include <H5Fprivate.h> /*files */
#include <H5FDprivate.h> /*file driver */
#include <H5FDsec2.h> /* Sec2 file driver */
#include <H5FLprivate.h> /*Free Lists */
#include <H5MMprivate.h> /* Memory allocation */

1
src/H5FDsrb.c
View File

@ -10,6 +10,7 @@
#include <H5private.h> /*library functions */
#include <H5Eprivate.h> /*error handling */
#include <H5Fprivate.h> /*files */
#include <H5FDprivate.h> /*file driver */
#include <H5FDsrb.h> /* Core file driver */
#include <H5MMprivate.h> /* Memory allocation */
#include <H5Pprivate.h> /*property lists */

13
src/H5Farray.c
View File

@ -1,8 +1,8 @@
/*
* Copyright (C) 1998 Spizella Software
* All rights reserved.
* Copyright (C) 1998 NCSA
* All rights reserved.
*
* Programmer: Robb Matzke <robb@arborea.spizella.com>
* Programmer: Robb Matzke <matzke@llnl.gov>
* Thursday, January 15, 1998
*
* Purpose: Provides I/O facilities for multi-dimensional arrays of bytes
@ -11,10 +11,13 @@
* dimension. For example, a 10x20 array of int would
* translate to a 10x20x4 array of bytes at this level.
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h>
#include <H5Dprivate.h>
#include <H5Eprivate.h>
#include <H5Fprivate.h>
#include <H5Fpkg.h>
#include <H5FDprivate.h> /*file driver */
#include <H5Iprivate.h>
#include <H5MFprivate.h>
@ -140,7 +143,6 @@ H5F_arr_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
size_t nelmts, z; /*number of elements */
intn ndims; /*stride dimensionality */
haddr_t addr; /*address in file */
haddr_t eof; /*end of file address */
intn i, j; /*counters */
hbool_t carray; /*carry for subtraction */
#ifdef H5_HAVE_PARALLEL
@ -409,7 +411,6 @@ H5F_arr_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
size_t nelmts, z; /*number of elements */
intn ndims; /*dimensionality */
haddr_t addr; /*address in file */
haddr_t eof; /*end of file address */
intn i, j; /*counters */
hbool_t carray; /*carry for subtraction */
#ifdef H5_HAVE_PARALLEL

13
src/H5Fcontig.c
View File

@ -11,9 +11,12 @@
* H5F_seg_read/write.
*
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5Fprivate.h>
#include <H5Fpkg.h>
#include <H5FDprivate.h> /*file driver */
#include <H5MMprivate.h>
@ -244,8 +247,8 @@ H5F_contig_write(H5F_t *f, H5FD_mem_t type, haddr_t addr, hsize_t size,
f->shared->sieve_size=0;
} /* end if */
/* Write directly from the user's buffer */
if (H5F_block_write(f, H5FD_MEM_DRAW, addr, size, dxpl_id, buf)<0) {
/* Write directly to the user's buffer */
if (H5F_block_write(f, type, addr, size, dxpl_id, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"block write failed");
}
@ -293,7 +296,7 @@ H5F_contig_write(H5F_t *f, H5FD_mem_t type, haddr_t addr, hsize_t size,
else {
/* Check if we can actually hold the I/O request in the sieve buffer */
if(size>f->shared->sieve_buf_size) {
if (H5F_block_write(f, H5FD_MEM_DRAW, addr, size, dxpl_id, buf)<0) {
if (H5F_block_write(f, type, addr, size, dxpl_id, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"block write failed");
}
@ -330,7 +333,7 @@ H5F_contig_write(H5F_t *f, H5FD_mem_t type, haddr_t addr, hsize_t size,
} /* end else */
} /* end if */
else {
if (H5F_block_write(f, H5FD_MEM_DRAW, addr, size, dxpl_id, buf)<0) {
if (H5F_block_write(f, type, addr, size, dxpl_id, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"block write failed");
}

13
src/H5Fistore.c
View File

@ -29,10 +29,13 @@
* entries near the front of the list to make room for the new
* entry which is added to the end of the list.
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h>
#include <H5Dprivate.h>
#include <H5Eprivate.h>
#include <H5Fprivate.h>
#include <H5Fpkg.h>
#include <H5FLprivate.h> /*Free Lists */
#include <H5Iprivate.h>
#include <H5MFprivate.h>
@ -1498,8 +1501,8 @@ H5F_istore_lock(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
ent->chunk = chunk;
{
H5F_xfer_t *dxpl;
dxpl = (H5P_DEFAULT==dxpl_id) ? &H5F_xfer_dflt : (H5F_xfer_t *)H5I_object(dxpl_id);
H5D_xfer_t *dxpl;
dxpl = (H5P_DEFAULT==dxpl_id) ? &H5D_xfer_dflt : (H5D_xfer_t *)H5I_object(dxpl_id);
ent->split_ratios[0] = dxpl->split_ratios[0];
ent->split_ratios[1] = dxpl->split_ratios[1];
ent->split_ratios[2] = dxpl->split_ratios[2];
@ -1640,8 +1643,8 @@ H5F_istore_unlock(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
x.alloc_size = x.chunk_size;
x.chunk = chunk;
{
H5F_xfer_t *dxpl;
dxpl = (H5P_DEFAULT==dxpl_id) ? &H5F_xfer_dflt : (H5F_xfer_t *)H5I_object(dxpl_id);
H5D_xfer_t *dxpl;
dxpl = (H5P_DEFAULT==dxpl_id) ? &H5D_xfer_dflt : (H5D_xfer_t *)H5I_object(dxpl_id);
x.split_ratios[0] = dxpl->split_ratios[0];
x.split_ratios[1] = dxpl->split_ratios[1];
x.split_ratios[2] = dxpl->split_ratios[2];

212
src/H5Fpkg.h Normal file
View File

@ -0,0 +1,212 @@
/*
* Copyright (C) 2000 NCSA
* All rights reserved.
*
* Programmer: Quincey Koziol <koziol@ncsa.uiuc.edu>
* Thursday, September 28, 2000
*
* Purpose: This file contains declarations which are visible only within
* the H5F package. Source files outside the H5F package should
* include H5Fprivate.h instead.
*/
#ifndef H5F_PACKAGE
#error "Do not include this file outside the H5F package!"
#endif
#ifndef _H5Fpkg_H
#define _H5Fpkg_H
#include <H5Fprivate.h>
/* This is a near top-level header! Try not to include much! */
#include <H5private.h>
/*
* Feature: Define this constant to be non-zero if you want to enable code
* that minimizes the number of calls to lseek(). This has a huge
* performance benefit on some systems. Set this constant to zero
* on the compiler command line to disable that optimization.
*/
#ifndef H5F_OPT_SEEK
# define H5F_OPT_SEEK 1
#endif
/*
* Feature: Define this constant on the compiler command-line if you want to
* see some debugging messages on the debug stream.
*/
#ifdef NDEBUG
# undef H5F_DEBUG
#endif
/* Maximum size of boot-block buffer */
#define H5F_BOOTBLOCK_SIZE 1024
/* Define the HDF5 file signature */
#define H5F_SIGNATURE "\211HDF\r\n\032\n"
#define H5F_SIGNATURE_LEN 8
/*
* Private file open flags.
*/
#define H5F_ACC_PUBLIC_FLAGS 0x00ffu
/*
* Macros that check for overflows. These are somewhat dangerous to fiddle
* with.
*/
#if (SIZEOF_SIZE_T >= SIZEOF_OFF_T)
# define H5F_OVERFLOW_SIZET2OFFT(X) \
((size_t)(X)>=(size_t)((size_t)1<<(8*sizeof(off_t)-1)))
#else
# define H5F_OVERFLOW_SIZET2OFFT(X) 0
#endif
/* The raw data chunk cache */
typedef struct H5F_rdcc_t {
uintn ninits; /* Number of chunk creations */
uintn nhits; /* Number of cache hits */
uintn nmisses;/* Number of cache misses */
uintn nflushes;/* Number of cache flushes */
size_t nbytes; /* Current cached raw data in bytes */
intn nslots; /* Number of chunk slots allocated */
struct H5F_rdcc_ent_t *head; /* Head of doubly linked list */
struct H5F_rdcc_ent_t *tail; /* Tail of doubly linked list */
intn nused; /* Number of chunk slots in use */
struct H5F_rdcc_ent_t **slot; /* Chunk slots, each points to a chunk*/
} H5F_rdcc_t;
/*
* Define the structure to store the file information for HDF5 files. One of
* these structures is allocated per file, not per H5Fopen(). That is, set of
* H5F_t structs can all point to the same H5F_file_t struct. The `nrefs'
* count in this struct indicates the number of H5F_t structs which are
* pointing to this struct.
*/
typedef struct H5F_file_t {
uintn flags; /* Access Permissions for file */
H5FD_t *lf; /* Lower level file handle for I/O */
uintn nrefs; /* Ref count for times file is opened */
uint32_t consist_flags; /* File Consistency Flags */
haddr_t boot_addr; /* Absolute address of boot block */
haddr_t base_addr; /* Absolute base address for rel.addrs. */
haddr_t freespace_addr; /* Relative address of free-space info */
haddr_t driver_addr; /* File driver information block address*/
struct H5AC_t *cache; /* The object cache */
H5F_create_t *fcpl; /* File-creation property list */
/* This actually ends up being a pointer to a */
/* H5P_t type, which is returned from H5P_copy */
/* But that's ok because we only access it like */
/* a H5F_create_t until we pass it back to */
/* H5P_close to release it - QAK */
intn mdc_nelmts; /* Size of meta data cache (elements) */
intn rdcc_nelmts; /* Size of raw data chunk cache (elmts) */
size_t rdcc_nbytes; /* Size of raw data chunk cache (bytes) */
double rdcc_w0; /* Preempt read chunks first? [0.0..1.0]*/
hsize_t threshold; /* Threshold for alignment */
hsize_t alignment; /* Alignment */
uintn gc_ref; /* Garbage-collect references? */
struct H5G_t *root_grp; /* Open root group */
intn ncwfs; /* Num entries on cwfs list */
struct H5HG_heap_t **cwfs; /* Global heap cache */
/* Data Sieve Buffering fields */
unsigned char *sieve_buf; /* Buffer to hold data sieve buffer */
haddr_t sieve_loc; /* File location (offset) of the data sieve buffer */
hsize_t sieve_size; /* Size of the data sieve buffer used (in bytes) */
hsize_t sieve_buf_size; /* Size of the data sieve buffer allocated (in bytes) */
unsigned sieve_dirty; /* Flag to indicate that the data sieve buffer is dirty */
H5F_rdcc_t rdcc; /* Raw data chunk cache */
} H5F_file_t;
/* A record of the mount table */
typedef struct H5F_mount_t {
struct H5G_t *group; /* Mount point group held open */
struct H5F_t *file; /* File mounted at that point */
} H5F_mount_t;
/*
* The mount table describes what files are attached to (mounted on) the file
* to which this table belongs.
*/
typedef struct H5F_mtab_t {
struct H5F_t *parent;/* Parent file */
uintn nmounts;/* Number of children which are mounted */
uintn nalloc; /* Number of mount slots allocated */
H5F_mount_t *child; /* An array of mount records */
} H5F_mtab_t;
/*
* This is the top-level file descriptor. One of these structures is
* allocated every time H5Fopen() is called although they may contain pointers
* to shared H5F_file_t structs. The reference count (nrefs) indicates the
* number of times the file has been opened (the application can only open a
* file once explicitly, but the library can open the file a second time to
* indicate that the file is mounted on some other file).
*/
struct H5F_t {
uintn nrefs; /* Reference count */
uintn intent; /* The flags passed to H5F_open()*/
char *name; /* Name used to open file */
H5F_file_t *shared; /* The shared file info */
uintn nopen_objs; /* Number of open object headers*/
hid_t closing; /* H5I_FILE_CLOSING ID or zero */
H5F_mtab_t mtab; /* File mount table */
};
#ifdef H5_HAVE_PARALLEL
__DLLVAR__ hbool_t H5_mpi_1_metawrite_g;
#endif /* H5_HAVE_PARALLEL */
/* Private functions, not part of the publicly documented API */
__DLL__ void H5F_encode_length_unusual(const H5F_t *f, uint8_t **p,
uint8_t *l);
__DLL__ H5F_t *H5F_open(const char *name, uintn flags, hid_t fcpl_id,
hid_t fapl_id);
__DLL__ herr_t H5F_close(H5F_t *f);
__DLL__ herr_t H5F_close_all(void);
__DLL__ herr_t H5F_flush_all(hbool_t invalidate);
__DLL__ herr_t H5F_debug(H5F_t *f, haddr_t addr, FILE * stream,
intn indent, intn fwidth);
__DLL__ herr_t H5F_istore_debug(H5F_t *f, haddr_t addr, FILE * stream,
intn indent, intn fwidth, int ndims);
__DLL__ herr_t H5F_mountpoint(struct H5G_entry_t *find/*in,out*/);
/* Functions that operate on indexed storage */
__DLL__ herr_t H5F_istore_init (H5F_t *f);
__DLL__ herr_t H5F_istore_flush (H5F_t *f, hbool_t preempt);
__DLL__ herr_t H5F_istore_dest (H5F_t *f);
__DLL__ herr_t H5F_istore_stats (H5F_t *f, hbool_t headers);
__DLL__ herr_t H5F_istore_create(H5F_t *f,
struct H5O_layout_t *layout/*in,out*/);
__DLL__ herr_t H5F_istore_read(H5F_t *f, hid_t dxpl_id,
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const hssize_t offset[], const hsize_t size[],
void *buf/*out*/);
__DLL__ herr_t H5F_istore_write(H5F_t *f, hid_t dxpl_id,
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const hssize_t offset[], const hsize_t size[],
const void *buf);
__DLL__ herr_t H5F_istore_allocate (H5F_t *f, hid_t dxpl_id,
const struct H5O_layout_t *layout,
const hsize_t *space_dim,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill);
/* Functions that operate on contiguous storage wrt boot block */
__DLL__ herr_t H5F_contig_read(H5F_t *f, haddr_t addr, hsize_t size,
hid_t dxpl_id, void *_buf/*out*/);
__DLL__ herr_t H5F_contig_write(H5F_t *f, H5FD_mem_t type, haddr_t addr,
hsize_t size, hid_t dxpl_id, const void *buf);
/* Functions for allocation/releasing chunks */
__DLL__ void * H5F_istore_chunk_alloc(size_t chunk_size);
__DLL__ void * H5F_istore_chunk_realloc(void *chunk, size_t new_size);
#endif

381
src/H5Fprivate.h
View File

@ -18,46 +18,13 @@
#ifndef _H5Fprivate_H
#define _H5Fprivate_H
#include <H5Fpublic.h>
/* This is a near top-level header! Try not to include much! */
#include <H5private.h>
#include <H5FDpublic.h> /*file drivers */
#include <H5MMpublic.h> /*for H5MM_allocate_t and H5MM_free_t types */
/*
* Feature: Define this constant to be non-zero if you want to enable code
* that minimizes the number of calls to lseek(). This has a huge
* performance benefit on some systems. Set this constant to zero
* on the compiler command line to disable that optimization.
*/
#ifndef H5F_OPT_SEEK
# define H5F_OPT_SEEK 1
#endif
/*
* Feature: Define this constant on the compiler command-line if you want to
* see some debugging messages on the debug stream.
*/
#ifdef NDEBUG
# undef H5F_DEBUG
#endif
/* Maximum size of boot-block buffer */
#define H5F_BOOTBLOCK_SIZE 1024
/* Define the HDF5 file signature */
#define H5F_SIGNATURE "\211HDF\r\n\032\n"
#define H5F_SIGNATURE_LEN 8
/* size of size_t and off_t as they exist on disk */
#define H5F_SIZEOF_ADDR(F) ((F)->shared->fcpl->sizeof_addr)
#define H5F_SIZEOF_SIZE(F) ((F)->shared->fcpl->sizeof_size)
/*
* Private file open flags.
*/
#define H5F_ACC_PUBLIC_FLAGS 0x00ffu
typedef struct H5F_t H5F_t;
/*
* Encode and decode macros for file meta-data.
@ -218,16 +185,74 @@
*/
#define NBYTEDECODE(s, d, n) { HDmemcpy(d,s,n); p+=n }
/*
* Macros that check for overflows. These are somewhat dangerous to fiddle
* with.
*/
#if (SIZEOF_SIZE_T >= SIZEOF_OFF_T)
# define H5F_OVERFLOW_SIZET2OFFT(X) \
((size_t)(X)>=(size_t)((size_t)1<<(8*sizeof(off_t)-1)))
#else
# define H5F_OVERFLOW_SIZET2OFFT(X) 0
#endif
/* Address-related macros */
#define H5F_addr_overflow(X,Z) (HADDR_UNDEF==(X) || \
HADDR_UNDEF==(X)+(haddr_t)(Z) || \
(X)+(haddr_t)(Z)<(X))
#define H5F_addr_hash(X,M) ((unsigned)((X)%(M)))
#define H5F_addr_defined(X) (X!=HADDR_UNDEF)
#define H5F_addr_eq(X,Y) ((X)!=HADDR_UNDEF && \
(Y)!=HADDR_UNDEF && \
(X)==(Y))
#define H5F_addr_ne(X,Y) (!H5F_addr_eq((X),(Y)))
#define H5F_addr_lt(X,Y) ((X)!=HADDR_UNDEF && \
(Y)!=HADDR_UNDEF && \
(X)<(Y))
#define H5F_addr_le(X,Y) ((X)!=HADDR_UNDEF && \
(Y)!=HADDR_UNDEF && \
(X)<=(Y))
#define H5F_addr_gt(X,Y) ((X)!=HADDR_UNDEF && \
(Y)!=HADDR_UNDEF && \
(X)>(Y))
#define H5F_addr_ge(X,Y) ((X)!=HADDR_UNDEF && \
(Y)!=HADDR_UNDEF && \
(X)>=(Y))
#define H5F_addr_cmp(X,Y) (H5F_addr_eq(X,Y)?0: \
(H5F_addr_lt(X, Y)?-1:1))
#define H5F_addr_pow2(N) ((haddr_t)1<<(N))
/* size of size_t and off_t as they exist on disk */
#ifdef H5F_PACKAGE
#define H5F_SIZEOF_ADDR(F) ((F)->shared->fcpl->sizeof_addr)
#define H5F_SIZEOF_SIZE(F) ((F)->shared->fcpl->sizeof_size)
#else /* H5F_PACKAGE */
#define H5F_SIZEOF_ADDR(F) (H5F_sizeof_addr(F))
#define H5F_SIZEOF_SIZE(F) (H5F_sizeof_size(F))
#endif /* H5F_PACKAGE */
__DLL__ size_t H5F_sizeof_addr(H5F_t *f);
__DLL__ size_t H5F_sizeof_size(H5F_t *f);
/* Macros to encode/decode offset/length's for storing in the file */
#ifdef NOT_YET
#define H5F_ENCODE_OFFSET(f,p,o) (H5F_SIZEOF_ADDR(f)==4 ? UINT32ENCODE(p,o) \
: H5F_SIZEOF_ADDR(f)==8 ? UINT64ENCODE(p,o) \
: H5F_SIZEOF_ADDR(f)==2 ? UINT16ENCODE(p,o) \
: H5FPencode_unusual_offset(f,&(p),(uint8_t*)&(o)))
#else /* NOT_YET */
#define H5F_ENCODE_OFFSET(f,p,o) switch(H5F_SIZEOF_ADDR(f)) { \
case 4: UINT32ENCODE(p,o); break; \
case 8: UINT64ENCODE(p,o); break; \
case 2: UINT16ENCODE(p,o); break; \
}
#endif /* NOT_YET */
#define H5F_DECODE_OFFSET(f,p,o) switch (H5F_SIZEOF_ADDR (f)) { \
case 4: UINT32DECODE (p, o); break; \
case 8: UINT64DECODE (p, o); break; \
case 2: UINT16DECODE (p, o); break; \
}
#define H5F_ENCODE_LENGTH(f,p,l) switch(H5F_SIZEOF_SIZE(f)) { \
case 4: UINT32ENCODE(p,l); break; \
case 8: UINT64ENCODE(p,l); break; \
case 2: UINT16ENCODE(p,l); break; \
}
#define H5F_DECODE_LENGTH(f,p,l) switch(H5F_SIZEOF_SIZE(f)) { \
case 4: UINT32DECODE(p,l); break; \
case 8: UINT64DECODE(p,l); break; \
case 2: UINT16DECODE(p,l); break; \
}
/*
* File-creation property list.
@ -261,164 +286,15 @@ typedef struct H5F_access_t {
void *driver_info; /* File driver specific information */
} H5F_access_t;
/* Data transfer property list */
typedef struct H5F_xfer_t {
size_t buf_size; /*max temp buffer size */
void *tconv_buf; /*type conversion buffer or null */
void *bkg_buf; /*background buffer or null */
H5T_bkg_t need_bkg; /*type of background buffer needed */
double split_ratios[3];/*B-tree node splitting ratios */
uintn cache_hyper; /*cache hyperslab blocks during I/O? */
uintn block_limit; /*largest hyperslab block to cache */
H5MM_allocate_t vlen_alloc; /*VL datatype allocation function */
void *alloc_info; /*VL datatype allocation information */
H5MM_free_t vlen_free; /*VL datatype free function */
void *free_info; /*VL datatype free information */
hid_t driver_id; /*File driver ID */
void *driver_info; /*File driver specific information */
#ifdef COALESCE_READS
uintn gather_reads; /*coalesce single reads into a read */
/*transaction */
#endif
} H5F_xfer_t;
/* The raw data chunk cache */
typedef struct H5F_rdcc_t {
uintn ninits; /* Number of chunk creations */
uintn nhits; /* Number of cache hits */
uintn nmisses;/* Number of cache misses */
uintn nflushes;/* Number of cache flushes */
size_t nbytes; /* Current cached raw data in bytes */
intn nslots; /* Number of chunk slots allocated */
struct H5F_rdcc_ent_t *head; /* Head of doubly linked list */
struct H5F_rdcc_ent_t *tail; /* Tail of doubly linked list */
intn nused; /* Number of chunk slots in use */
struct H5F_rdcc_ent_t **slot; /* Chunk slots, each points to a chunk*/
} H5F_rdcc_t;
/*
* Define the structure to store the file information for HDF5 files. One of
* these structures is allocated per file, not per H5Fopen(). That is, set of
* H5F_t structs can all point to the same H5F_file_t struct. The `nrefs'
* count in this struct indicates the number of H5F_t structs which are
* pointing to this struct.
*/
typedef struct H5F_file_t {
uintn flags; /* Access Permissions for file */
H5FD_t *lf; /* Lower level file handle for I/O */
uintn nrefs; /* Ref count for times file is opened */
uint32_t consist_flags; /* File Consistency Flags */
haddr_t boot_addr; /* Absolute address of boot block */
haddr_t base_addr; /* Absolute base address for rel.addrs. */
haddr_t freespace_addr; /* Relative address of free-space info */
haddr_t driver_addr; /* File driver information block address*/
struct H5AC_t *cache; /* The object cache */
H5F_create_t *fcpl; /* File-creation property list */
/* This actually ends up being a pointer to a */
/* H5P_t type, which is returned from H5P_copy */
/* But that's ok because we only access it like */
/* a H5F_create_t until we pass it back to */
/* H5P_close to release it - QAK */
intn mdc_nelmts; /* Size of meta data cache (elements) */
intn rdcc_nelmts; /* Size of raw data chunk cache (elmts) */
size_t rdcc_nbytes; /* Size of raw data chunk cache (bytes) */
double rdcc_w0; /* Preempt read chunks first? [0.0..1.0]*/
hsize_t threshold; /* Threshold for alignment */
hsize_t alignment; /* Alignment */
uintn gc_ref; /* Garbage-collect references? */
struct H5G_t *root_grp; /* Open root group */
intn ncwfs; /* Num entries on cwfs list */
struct H5HG_heap_t **cwfs; /* Global heap cache */
/* Data Sieve Buffering fields */
unsigned char *sieve_buf; /* Buffer to hold data sieve buffer */
haddr_t sieve_loc; /* File location (offset) of the data sieve buffer */
hsize_t sieve_size; /* Size of the data sieve buffer used (in bytes) */
hsize_t sieve_buf_size; /* Size of the data sieve buffer allocated (in bytes) */
unsigned sieve_dirty; /* Flag to indicate that the data sieve buffer is dirty */
H5F_rdcc_t rdcc; /* Raw data chunk cache */
} H5F_file_t;
/* Mount property list */
typedef struct H5F_mprop_t {
hbool_t local; /* Are absolute symlinks local to file? */
} H5F_mprop_t;
/* A record of the mount table */
typedef struct H5F_mount_t {
struct H5G_t *group; /* Mount point group held open */
struct H5F_t *file; /* File mounted at that point */
} H5F_mount_t;
/*
* The mount table describes what files are attached to (mounted on) the file
* to which this table belongs.
*/
typedef struct H5F_mtab_t {
struct H5F_t *parent;/* Parent file */
uintn nmounts;/* Number of children which are mounted */
uintn nalloc; /* Number of mount slots allocated */
H5F_mount_t *child; /* An array of mount records */
} H5F_mtab_t;
/*
* This is the top-level file descriptor. One of these structures is
* allocated every time H5Fopen() is called although they may contain pointers
* to shared H5F_file_t structs. The reference count (nrefs) indicates the
* number of times the file has been opened (the application can only open a
* file once explicitly, but the library can open the file a second time to
* indicate that the file is mounted on some other file).
*/
typedef struct H5F_t {
uintn nrefs; /* Reference count */
uintn intent; /* The flags passed to H5F_open()*/
char *name; /* Name used to open file */
H5F_file_t *shared; /* The shared file info */
uintn nopen_objs; /* Number of open object headers*/
hid_t closing; /* H5I_FILE_CLOSING ID or zero */
H5F_mtab_t mtab; /* File mount table */
} H5F_t;
#ifdef NOT_YET
#define H5F_ENCODE_OFFSET(f,p,o) (H5F_SIZEOF_ADDR(f)==4 ? UINT32ENCODE(p,o) \
: H5F_SIZEOF_ADDR(f)==8 ? UINT64ENCODE(p,o) \
: H5F_SIZEOF_ADDR(f)==2 ? UINT16ENCODE(p,o) \
: H5FPencode_unusual_offset(f,&(p),(uint8_t*)&(o)))
#else /* NOT_YET */
#define H5F_ENCODE_OFFSET(f,p,o) switch(H5F_SIZEOF_ADDR(f)) { \
case 4: UINT32ENCODE(p,o); break; \
case 8: UINT64ENCODE(p,o); break; \
case 2: UINT16ENCODE(p,o); break; \
}
#endif /* NOT_YET */
#define H5F_DECODE_OFFSET(f,p,o) \
switch (H5F_SIZEOF_ADDR (f)) { \
case 4: \
UINT32DECODE (p, o); \
break; \
case 8: \
UINT64DECODE (p, o); \
break; \
case 2: \
UINT16DECODE (p, o); \
break; \
}
#define H5F_encode_length(f,p,l) \
switch(H5F_SIZEOF_SIZE(f)) { \
case 4: UINT32ENCODE(p,l); break; \
case 8: UINT64ENCODE(p,l); break; \
case 2: UINT16ENCODE(p,l); break; \
}
#define H5F_decode_length(f,p,l) \
switch(H5F_SIZEOF_SIZE(f)) { \
case 4: UINT32DECODE(p,l); break; \
case 8: UINT64DECODE(p,l); break; \
case 2: UINT16DECODE(p,l); break; \
}
/* library variables */
__DLLVAR__ const H5F_create_t H5F_create_dflt;
__DLLVAR__ H5F_access_t H5F_access_dflt;
__DLLVAR__ const H5F_mprop_t H5F_mount_dflt;
/* Forward declarations for prototypes arguments */
struct H5O_layout_t;
@ -426,31 +302,11 @@ struct H5O_efl_t;
struct H5O_pline_t;
struct H5O_fill_t;
struct H5G_entry_t;
/* library variables */
__DLLVAR__ const H5F_create_t H5F_create_dflt;
__DLLVAR__ H5F_access_t H5F_access_dflt;
__DLLVAR__ H5F_xfer_t H5F_xfer_dflt;
__DLLVAR__ const H5F_mprop_t H5F_mount_dflt;
#ifdef H5_HAVE_PARALLEL
__DLLVAR__ hbool_t H5_mpi_1_metawrite_g;
#endif /* H5_HAVE_PARALLEL */
struct H5S_t;
/* Private functions, not part of the publicly documented API */
__DLL__ herr_t H5F_init(void);
__DLL__ void H5F_encode_length_unusual(const H5F_t *f, uint8_t **p,
uint8_t *l);
__DLL__ H5F_t *H5F_open(const char *name, uintn flags, hid_t fcpl_id,
hid_t fapl_id);
__DLL__ herr_t H5F_close(H5F_t *f);
__DLL__ herr_t H5F_close_all(void);
__DLL__ herr_t H5F_flush_all(hbool_t invalidate);
__DLL__ herr_t H5F_debug(H5F_t *f, haddr_t addr, FILE * stream,
intn indent, intn fwidth);
__DLL__ herr_t H5F_istore_debug(H5F_t *f, haddr_t addr, FILE * stream,
intn indent, intn fwidth, int ndims);
__DLL__ herr_t H5F_mountpoint(struct H5G_entry_t *find/*in,out*/);
__DLL__ uintn H5F_get_intent(H5F_t *f);
/* Functions that operate on array storage */
__DLL__ herr_t H5F_arr_create(H5F_t *f,
@ -474,81 +330,38 @@ __DLL__ herr_t H5F_arr_write (H5F_t *f, hid_t dxpl_id,
const hssize_t mem_offset[],
const hssize_t file_offset[], const void *_buf);
/* Functions that operate on indexed storage */
__DLL__ herr_t H5F_istore_init (H5F_t *f);
__DLL__ herr_t H5F_istore_flush (H5F_t *f, hbool_t preempt);
__DLL__ herr_t H5F_istore_dest (H5F_t *f);
__DLL__ hsize_t H5F_istore_allocated(H5F_t *f, int ndims, haddr_t addr);
__DLL__ herr_t H5F_istore_stats (H5F_t *f, hbool_t headers);
__DLL__ herr_t H5F_istore_create(H5F_t *f,
struct H5O_layout_t *layout/*in,out*/);
__DLL__ herr_t H5F_istore_read(H5F_t *f, hid_t dxpl_id,
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const hssize_t offset[], const hsize_t size[],
void *buf/*out*/);
__DLL__ herr_t H5F_istore_write(H5F_t *f, hid_t dxpl_id,
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const hssize_t offset[], const hsize_t size[],
const void *buf);
__DLL__ herr_t H5F_istore_allocate (H5F_t *f, hid_t dxpl_id,
const struct H5O_layout_t *layout,
const hsize_t *space_dim,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill);
__DLL__ herr_t H5F_istore_dump_btree(H5F_t *f, FILE *stream, int ndims,
haddr_t addr);
/* Functions that operate on contiguous storage wrt boot block */
__DLL__ herr_t H5F_contig_read(H5F_t *f, haddr_t addr, hsize_t size,
hid_t dxpl_id, void *_buf/*out*/);
__DLL__ herr_t H5F_contig_write(H5F_t *f, H5FD_mem_t type, haddr_t addr,
hsize_t size, hid_t dxpl_id, const void *buf);
/* Functions that operate on blocks of bytes wrt boot block */
__DLL__ herr_t H5F_block_read(H5F_t *f, haddr_t addr, hsize_t size,
hid_t dxpl_id, void *buf/*out*/);
__DLL__ herr_t H5F_block_write(H5F_t *f, H5FD_mem_t type, haddr_t addr,
hsize_t size, hid_t dxpl_id, const void *buf);
/* Address-related macros and functions */
#define H5F_addr_overflow(X,Z) (HADDR_UNDEF==(X) || \
HADDR_UNDEF==(X)+(haddr_t)(Z) || \
(X)+(haddr_t)(Z)<(X))
#define H5F_addr_hash(X,M) ((unsigned)((X)%(M)))
#define H5F_addr_defined(X) (X!=HADDR_UNDEF)
#define H5F_addr_eq(X,Y) ((X)!=HADDR_UNDEF && \
(Y)!=HADDR_UNDEF && \
(X)==(Y))
#define H5F_addr_ne(X,Y) (!H5F_addr_eq((X),(Y)))
#define H5F_addr_lt(X,Y) ((X)!=HADDR_UNDEF && \
(Y)!=HADDR_UNDEF && \
(X)<(Y))
#define H5F_addr_le(X,Y) ((X)!=HADDR_UNDEF && \
(Y)!=HADDR_UNDEF && \
(X)<=(Y))
#define H5F_addr_gt(X,Y) ((X)!=HADDR_UNDEF && \
(Y)!=HADDR_UNDEF && \
(X)>(Y))
#define H5F_addr_ge(X,Y) ((X)!=HADDR_UNDEF && \
(Y)!=HADDR_UNDEF && \
(X)>=(Y))
#define H5F_addr_cmp(X,Y) (H5F_addr_eq(X,Y)?0: \
(H5F_addr_lt(X, Y)?-1:1))
#define H5F_addr_pow2(N) ((haddr_t)1<<(N))
/* Functions that operate on byte sequences */
__DLL__ herr_t H5F_seq_read(H5F_t *f, hid_t dxpl_id,
const struct H5O_layout_t *layout, const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill, const struct H5O_efl_t *efl,
const struct H5S_t *file_space, size_t elmt_size, hsize_t seq_len,
hssize_t mem_offset, hssize_t file_offset, void *_buf/*out*/);
__DLL__ herr_t H5F_seq_write (H5F_t *f, hid_t dxpl_id,
const struct H5O_layout_t *layout, const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill, const struct H5O_efl_t *efl,
const struct H5S_t *file_space, size_t elmt_size, hsize_t seq_len,
hssize_t mem_offset, hssize_t file_offset, const void *_buf);
/* Functions that operate on indexed storage */
__DLL__ hsize_t H5F_istore_allocated(H5F_t *f, int ndims, haddr_t addr);
__DLL__ herr_t H5F_istore_dump_btree(H5F_t *f, FILE *stream, int ndims,
haddr_t addr);
/* Functions for allocation/releasing chunks */
__DLL__ void * H5F_istore_chunk_free(void *chunk);
/* Address-related functions */
__DLL__ void H5F_addr_encode(H5F_t *, uint8_t**/*in,out*/, haddr_t);
__DLL__ void H5F_addr_decode(H5F_t *, const uint8_t**/*in,out*/,
haddr_t*/*out*/);
__DLL__ herr_t H5F_addr_pack(H5F_t UNUSED *f, haddr_t *addr_p/*out*/,
const unsigned long objno[2]);
/* Functions for allocation/releasing chunks */
__DLL__ void * H5F_istore_chunk_alloc(size_t chunk_size);
__DLL__ void * H5F_istore_chunk_free(void *chunk);
__DLL__ void * H5F_istore_chunk_realloc(void *chunk, size_t new_size);
#endif

494
src/H5Fseq.c Normal file
View File

@ -0,0 +1,494 @@
/*
* Copyright (C) 2000 NCSA
* All rights reserved.
*
* Programmer: Quincey Koziol <koziol@ncsa.uiuc.edu>
* Thursday, September 28, 2000
*
* Purpose: Provides I/O facilities for sequences of bytes stored with various
* layout policies. These routines are similar to the H5Farray.c routines,
* these deal in terms of byte offsets and lengths, not coordinates and
* hyperslab sizes.
*
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h>
#include <H5Dprivate.h>
#include <H5Eprivate.h>
#include <H5Fpkg.h>
#include <H5FDprivate.h> /*file driver */
#include <H5Iprivate.h>
#include <H5MFprivate.h>
#include <H5MMprivate.h> /*memory management */
#include <H5Oprivate.h>
#include <H5Pprivate.h>
#include <H5Vprivate.h>
/* MPIO driver functions are needed for some special checks */
#include <H5FDmpio.h>
/* Interface initialization */
#define PABLO_MASK H5Fseq_mask
#define INTERFACE_INIT NULL
static intn interface_initialize_g = 0;
/*-------------------------------------------------------------------------
* Function: H5F_seq_read
*
* Purpose: Reads a sequence of bytes from a file dataset into a buffer in
* in memory. The data is read from file F and the array's size and
* storage information is in LAYOUT. External files are described
* according to the external file list, EFL. The sequence offset is
* FILE_OFFSET in the file and MEM_OFFSET in memory (offsets are
* in terms of bytes) and the size of the hyperslab is SEQ_LEN. The
* total size of the file array is implied in the LAYOUT argument.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, September 28, 2000
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5F_seq_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline, const H5O_fill_t *fill,
const struct H5O_efl_t *efl, const H5S_t *file_space, size_t elmt_size,
hsize_t seq_len, hssize_t mem_offset, hssize_t file_offset,
void *_buf/*out*/)
{
uint8_t *buf = (uint8_t*)_buf; /*cast for arithmetic */
hsize_t dset_dims[H5O_LAYOUT_NDIMS]; /* dataspace dimensions */
hssize_t coords[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in dataspace */
hsize_t hslab_size[H5O_LAYOUT_NDIMS]; /* hyperslab size in dataspace*/
intn ndims;
haddr_t addr; /*address in file */
intn i; /*counters */
#ifdef H5_HAVE_PARALLEL
H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
#endif
FUNC_ENTER(H5F_seq_read, FAIL);
/* Check args */
assert(f);
assert(layout);
assert(buf);
#ifdef H5_HAVE_PARALLEL
{
/* Get the transfer mode */
H5F_xfer_t *dxpl;
H5FD_mpio_dxpl_t *dx;
if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
H5FD_MPIO==dxpl->driver_id && (dx=dxpl->driver_info) &&
H5FD_MPIO_INDEPENDENT!=dx->xfer_mode) {
xfer_mode = dx->xfer_mode;
}
}
/* Collective MPIO access is unsupported for non-contiguous datasets */
if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) {
HRETURN_ERROR (H5E_DATASET, H5E_READERROR, FAIL,
"collective access on non-contiguous datasets not supported yet");
}
#endif
switch (layout->type) {
case H5D_CONTIGUOUS:
/* Filters cannot be used for contiguous data. */
if (pline && pline->nfilters>0) {
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
"filters are not allowed for contiguous data");
}
/*
* Initialize loop variables. The loop is a multi-dimensional loop
* that counts from SIZE down to zero and IDX is the counter. Each
* element of IDX is treated as a digit with IDX[0] being the least
* significant digit.
*/
if (efl && efl->nused>0) {
addr = 0;
} else {
addr = layout->addr;
}
addr += file_offset;
buf += mem_offset;
/*
* Now begin to walk through the array, copying data from disk to
* memory.
*/
#ifdef H5_HAVE_PARALLEL
if (H5FD_MPIO_COLLECTIVE==xfer_mode) {
/*
* Currently supports same number of collective access. Need to
* be changed LATER to combine all reads into one collective MPIO
* call.
*/
unsigned long max, min, temp;
temp = seq_len;
assert(temp==seq_len); /* verify no overflow */
MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX,
H5FD_mpio_communicator(f->shared->lf));
MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN,
H5FD_mpio_communicator(f->shared->lf));
#ifdef AKC
printf("seq_len=%lu, min=%lu, max=%lu\n", temp, min, max);
#endif
if (max != min)
HRETURN_ERROR(H5E_DATASET, H5E_READERROR, FAIL,
"collective access with unequal number of blocks not supported yet");
}
#endif
/* Read directly from file if the dataset is in an external file */
/* Note: We can't use data sieve buffers for datasets in external files
* because the 'addr' of all external files is set to 0 (above) and
* all datasets in external files would alias to the same set of
* file offsets, totally mixing up the data sieve buffer information. -QAK
*/
if (efl && efl->nused>0) {
if (H5O_efl_read(f, efl, addr, seq_len, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
"external data read failed");
}
} else {
if (H5F_contig_read(f, addr, seq_len, dxpl_id, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
"block read failed");
}
} /* end else */
break;
case H5D_CHUNKED:
/*
* This method is unable to access external raw data files
*/
if (efl && efl->nused>0) {
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL,
"chunking and external files are mutually exclusive");
}
/* Compute the file offset coordinates and hyperslab size */
if((ndims=H5S_get_simple_extent_dims(file_space,dset_dims,NULL))<0)
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to retrieve dataspace dimensions");
#ifdef QAK
/* The library shouldn't be reading partial elements currently */
assert(seq_len%elmt_size!=0);
assert(addr%elmt_size!=0);
#endif /* QAK */
#ifdef QAK
/* Print out the file offsets & hyperslab sizes */
{
static int count=0;
if(count<10) {
printf("%s: elmt_size=%d, addr=%d, seq_len=%d\n",FUNC,(int)elmt_size,(int)addr,(int)seq_len);
printf("%s: file_offset=%d, mem_offset=%d\n",FUNC,(int)file_offset,(int)mem_offset);
count++;
}
}
#endif /* QAK */
/* Set location in dataset from the file_offset */
addr=file_offset;
/* Convert the bytes into elements */
seq_len/=elmt_size;
addr/=elmt_size;
/* Compute the hyperslab offset from the address given */
for(i=ndims-1; i>=0; i--) {
coords[i]=addr%dset_dims[i];
addr/=dset_dims[i];
} /* end for */
coords[ndims]=0; /* No offset for element info */
/* Compute the hyperslab size from the length given */
for(i=ndims-1; i>=0; i--) {
/* Check if the hyperslab is wider than the width of the dimension */
if(seq_len>dset_dims[i]) {
if (0!=coords[i])
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to copy into a proper hyperslab");
hslab_size[i]=dset_dims[i];
} /* end if */
else
hslab_size[i]=seq_len;
/* Fold the length into the length in the next highest dimension */
seq_len/=dset_dims[i];
/* Make certain the hyperslab sizes don't go less than 1 */
if(seq_len<1)
seq_len=1;
} /* end for */
hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */
#ifdef QAK
/* Print out the file offsets & hyperslab sizes */
{
static int count=0;
if(count<10) {
printf("%s: elmt_size=%d, addr=%d, seq_len=%d\n",FUNC,(int)elmt_size,(int)addr,(int)seq_len);
for(i=0; i<=ndims; i++)
printf("%s: dset_dims[%d]=%d\n",FUNC,i,(int)dset_dims[i]);
for(i=0; i<=ndims; i++)
printf("%s: coords[%d]=%d, hslab_size[%d]=%d\n",FUNC,i,(int)coords[i],(int)i,(int)hslab_size[i]);
count++;
}
}
#endif /* QAK */
if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords,
hslab_size, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed");
}
break;
default:
assert("not implemented yet" && 0);
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout");
} /* end switch() */
FUNC_LEAVE(SUCCEED);
} /* H5F_seq_read() */
/*-------------------------------------------------------------------------
* Function: H5F_seq_write
*
* Purpose: Writes a sequence of bytes to a file dataset from a buffer in
* in memory. The data is written to file F and the array's size and
* storage information is in LAYOUT. External files are described
* according to the external file list, EFL. The sequence offset is
* FILE_OFFSET in the file and MEM_OFFSET in memory (offsets are
* in terms of bytes) and the size of the hyperslab is SEQ_LEN. The
* total size of the file array is implied in the LAYOUT argument.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Monday, October 9, 2000
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5F_seq_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline, const H5O_fill_t *fill,
const struct H5O_efl_t *efl, const H5S_t *file_space, size_t elmt_size,
hsize_t seq_len, hssize_t mem_offset, hssize_t file_offset,
const void *_buf)
{
const uint8_t *buf = (const uint8_t*)_buf; /*cast for arithmetic */
hsize_t dset_dims[H5O_LAYOUT_NDIMS]; /* dataspace dimensions */
hssize_t coords[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in dataspace */
hsize_t hslab_size[H5O_LAYOUT_NDIMS]; /* hyperslab size in dataspace*/
intn ndims;
haddr_t addr; /*address in file */
intn i; /*counters */
#ifdef H5_HAVE_PARALLEL
H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
#endif
FUNC_ENTER(H5F_seq_write, FAIL);
/* Check args */
assert(f);
assert(layout);
assert(buf);
#ifdef H5_HAVE_PARALLEL
{
/* Get the transfer mode */
H5F_xfer_t *dxpl;
H5FD_mpio_dxpl_t *dx;
if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
H5FD_MPIO==dxpl->driver_id && (dx=dxpl->driver_info) &&
H5FD_MPIO_INDEPENDENT!=dx->xfer_mode) {
xfer_mode = dx->xfer_mode;
}
}
/* Collective MPIO access is unsupported for non-contiguous datasets */
if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) {
HRETURN_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL,
"collective access on non-contiguous datasets not supported yet");
}
#endif
switch (layout->type) {
case H5D_CONTIGUOUS:
/* Filters cannot be used for contiguous data. */
if (pline && pline->nfilters>0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"filters are not allowed for contiguous data");
}
/*
* Initialize loop variables. The loop is a multi-dimensional loop
* that counts from SIZE down to zero and IDX is the counter. Each
* element of IDX is treated as a digit with IDX[0] being the least
* significant digit.
*/
if (efl && efl->nused>0) {
addr = 0;
} else {
addr = layout->addr;
}
addr += file_offset;
buf += mem_offset;
/*
* Now begin to walk through the array, copying data from disk to
* memory.
*/
#ifdef H5_HAVE_PARALLEL
if (H5FD_MPIO_COLLECTIVE==xfer_mode) {
/*
* Currently supports same number of collective access. Need to
* be changed LATER to combine all reads into one collective MPIO
* call.
*/
unsigned long max, min, temp;
temp = seq_len;
assert(temp==seq_len); /* verify no overflow */
MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX,
H5FD_mpio_communicator(f->shared->lf));
MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN,
H5FD_mpio_communicator(f->shared->lf));
#ifdef AKC
printf("seq_len=%lu, min=%lu, max=%lu\n", temp, min, max);
#endif
if (max != min)
HRETURN_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL,
"collective access with unequal number of blocks not supported yet");
}
#endif
/* Write directly to file if the dataset is in an external file */
/* Note: We can't use data sieve buffers for datasets in external files
* because the 'addr' of all external files is set to 0 (above) and
* all datasets in external files would alias to the same set of
* file offsets, totally mixing up the data sieve buffer information. -QAK
*/
if (efl && efl->nused>0) {
if (H5O_efl_write(f, efl, addr, seq_len, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"external data write failed");
}
} else {
if (H5F_contig_write(f, H5FD_MEM_DRAW, addr, seq_len, dxpl_id, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"block write failed");
}
} /* end else */
break;
case H5D_CHUNKED:
/*
* This method is unable to access external raw data files
*/
if (efl && efl->nused>0) {
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL,
"chunking and external files are mutually exclusive");
}
/* Compute the file offset coordinates and hyperslab size */
if((ndims=H5S_get_simple_extent_dims(file_space,dset_dims,NULL))<0)
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to retrieve dataspace dimensions");
#ifdef QAK
/* Print out the file offsets & hyperslab sizes */
{
static int count=0;
if(count<10) {
printf("%s: elmt_size=%d, addr=%d, seq_len=%lu\n",FUNC,(int)elmt_size,(int)addr,(unsigned long)seq_len);
printf("%s: file_offset=%d, mem_offset=%d\n",FUNC,(int)file_offset,(int)mem_offset);
count++;
}
}
#endif /* QAK */
#ifdef QAK
/* The library shouldn't be reading partial elements currently */
assert((seq_len%elmt_size)!=0);
assert((addr%elmt_size)!=0);
#endif /* QAK */
/* Set location in dataset from the file_offset */
addr=file_offset;
/* Convert the bytes into elements */
seq_len/=elmt_size;
addr/=elmt_size;
/* Compute the hyperslab offset from the address given */
for(i=ndims-1; i>=0; i--) {
coords[i]=addr%dset_dims[i];
addr/=dset_dims[i];
} /* end for */
coords[ndims]=0; /* No offset for element info */
/* Compute the hyperslab size from the length given */
for(i=ndims-1; i>=0; i--) {
/* Check if the hyperslab is wider than the width of the dimension */
if(seq_len>dset_dims[i]) {
if (0!=coords[i])
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to copy into a proper hyperslab");
hslab_size[i]=dset_dims[i];
} /* end if */
else
hslab_size[i]=seq_len;
/* Fold the length into the length in the next highest dimension */
seq_len/=dset_dims[i];
/* Make certain the hyperslab sizes don't go less than 1 */
if(seq_len<1)
seq_len=1;
} /* end for */
hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */
#ifdef QAK
/* Print out the file offsets & hyperslab sizes */
{
static int count=0;
if(count<10) {
printf("%s: elmt_size=%d, addr=%d, seq_len=%d\n",FUNC,(int)elmt_size,(int)addr,(int)seq_len);
for(i=0; i<=ndims; i++)
printf("%s: dset_dims[%d]=%d\n",FUNC,i,(int)dset_dims[i]);
for(i=0; i<=ndims; i++)
printf("%s: coords[%d]=%d, hslab_size[%d]=%d\n",FUNC,i,(int)coords[i],(int)i,(int)hslab_size[i]);
count++;
}
}
#endif /* QAK */
if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords,
hslab_size, buf)<0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed");
}
break;
default:
assert("not implemented yet" && 0);
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout");
} /* end switch() */
FUNC_LEAVE(SUCCEED);
} /* H5F_seq_write() */

4
src/H5G.c
View File

@ -71,7 +71,10 @@
*
*-------------------------------------------------------------------------
*/
#define H5G_PACKAGE /*suppress error message about including H5Gpkg.h */
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
/* Packages needed by this file... */
#include <H5private.h>
@ -79,6 +82,7 @@
#include <H5Bprivate.h>
#include <H5Dprivate.h>
#include <H5Eprivate.h>
#include <H5Fpkg.h> /*file access */
#include <H5FLprivate.h> /*Free Lists */
#include <H5Gpkg.h>
#include <H5HLprivate.h>

8
src/H5Gent.c
View File

@ -6,9 +6,11 @@
* Friday, September 19, 1997
*/
#define H5G_PACKAGE
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5Fpkg.h>
#include <H5Gpkg.h>
#include <H5HLprivate.h>
#include <H5MMprivate.h>
@ -161,7 +163,7 @@ H5G_ent_decode(H5F_t *f, const uint8_t **pp, H5G_entry_t *ent)
ent->file = f;
/* decode header */
H5F_decode_length(f, *pp, ent->name_off);
H5F_DECODE_LENGTH(f, *pp, ent->name_off);
H5F_addr_decode(f, pp, &(ent->header));
UINT32DECODE(*pp, tmp);
*pp += 4; /*reserved*/
@ -273,7 +275,7 @@ H5G_ent_encode(H5F_t *f, uint8_t **pp, const H5G_entry_t *ent)
if (ent) {
/* encode header */
H5F_encode_length(f, *pp, ent->name_off);
H5F_ENCODE_LENGTH(f, *pp, ent->name_off);
H5F_addr_encode(f, pp, ent->header);
UINT32ENCODE(*pp, ent->type);
UINT32ENCODE(*pp, 0); /*reserved*/
@ -297,7 +299,7 @@ H5G_ent_encode(H5F_t *f, uint8_t **pp, const H5G_entry_t *ent)
HDabort();
}
} else {
H5F_encode_length(f, *pp, 0);
H5F_ENCODE_LENGTH(f, *pp, 0);
H5F_addr_encode(f, pp, HADDR_UNDEF);
UINT32ENCODE(*pp, H5G_NOTHING_CACHED);
UINT32ENCODE(*pp, 0); /*reserved*/

7
src/H5Gnode.c
View File

@ -18,13 +18,14 @@
*-------------------------------------------------------------------------
*/
#define H5G_PACKAGE /*suppress error message about including H5Gpkg.h */
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
/* Packages needed by this file... */
#include <H5private.h> /*library */
#include <H5ACprivate.h> /*cache */
#include <H5Bprivate.h> /*B-link trees */
#include <H5Eprivate.h> /*error handling */
#include <H5Fprivate.h> /*file access */
#include <H5Fpkg.h> /*file access */
#include <H5FLprivate.h> /*Free Lists */
#include <H5Gpkg.h> /*me */
#include <H5HLprivate.h> /*local heap */
@ -159,7 +160,7 @@ H5G_node_decode_key(H5F_t *f, H5B_t UNUSED *bt, uint8_t *raw, void *_key)
assert(raw);
assert(key);
H5F_decode_length(f, raw, key->offset);
H5F_DECODE_LENGTH(f, raw, key->offset);
FUNC_LEAVE(SUCCEED);
}
@ -191,7 +192,7 @@ H5G_node_encode_key(H5F_t *f, H5B_t UNUSED *bt, uint8_t *raw, void *_key)
assert(raw);
assert(key);
H5F_encode_length(f, raw, key->offset);
H5F_ENCODE_LENGTH(f, raw, key->offset);
FUNC_LEAVE(SUCCEED);
}

2
src/H5Gstab.c
View File

@ -7,9 +7,11 @@
*
*/
#define H5G_PACKAGE
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5Fpkg.h> /*file access */
#include <H5Gpkg.h>
#include <H5HLprivate.h>
#include <H5MMprivate.h>

17
src/H5HG.c
View File

@ -24,9 +24,12 @@
* for a new object based on object size, amount of free space
* in the collection, and temporal locality.
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h> /*library */
#include <H5ACprivate.h> /*caching */
#include <H5Eprivate.h> /*error handling */
#include <H5Fpkg.h> /*file access */
#include <H5FLprivate.h> /*Free Lists */
#include <H5HGprivate.h> /*global heaps */
#include <H5MFprivate.h> /*file memory management */
@ -150,7 +153,7 @@ printf("%s: size=%d\n",FUNC,(int)size);
*p++ = 0; /*reserved*/
*p++ = 0; /*reserved*/
*p++ = 0; /*reserved*/
H5F_encode_length (f, p, size);
H5F_ENCODE_LENGTH (f, p, size);
/*
* Padding so free space object is aligned. If malloc returned memory
@ -171,7 +174,7 @@ printf("%s: heap->obj[0].size=%d, size=%d\n",FUNC,(int)heap->obj[0].size,(int)si
UINT16ENCODE(p, 0); /*object ID*/
UINT16ENCODE(p, 0); /*reference count*/
UINT32ENCODE(p, 0); /*reserved*/
H5F_encode_length (f, p, heap->obj[0].size);
H5F_ENCODE_LENGTH (f, p, heap->obj[0].size);
HDmemset (p, 0, (size_t)((heap->chunk+heap->size) - p));
/* Add the heap to the cache */
@ -276,7 +279,7 @@ H5HG_load (H5F_t *f, haddr_t addr, const void UNUSED *udata1,
p += 3;
/* Size */
H5F_decode_length (f, p, heap->size);
H5F_DECODE_LENGTH (f, p, heap->size);
assert (heap->size>=H5HG_MINSIZE);
/*
@ -322,7 +325,7 @@ H5HG_load (H5F_t *f, haddr_t addr, const void UNUSED *udata1,
assert (NULL==heap->obj[idx].begin);
UINT16DECODE (p, heap->obj[idx].nrefs);
p += 4; /*reserved*/
H5F_decode_length (f, p, heap->obj[idx].size);
H5F_DECODE_LENGTH (f, p, heap->obj[idx].size);
heap->obj[idx].begin = begin;
/*
* The total storage size includes the size of the object header
@ -490,7 +493,7 @@ H5HG_alloc (H5F_t *f, H5HG_heap_t *heap, int cwfsno, size_t size)
UINT16ENCODE(p, idx);
UINT16ENCODE(p, 0); /*nrefs*/
UINT32ENCODE(p, 0); /*reserved*/
H5F_encode_length (f, p, size);
H5F_ENCODE_LENGTH (f, p, size);
/* Fix the free space object */
if (need==heap->obj[0].size) {
@ -517,7 +520,7 @@ H5HG_alloc (H5F_t *f, H5HG_heap_t *heap, int cwfsno, size_t size)
UINT16ENCODE(p, 0); /*id*/
UINT16ENCODE(p, 0); /*nrefs*/
UINT32ENCODE(p, 0); /*reserved*/
H5F_encode_length (f, p, heap->obj[0].size);
H5F_ENCODE_LENGTH (f, p, heap->obj[0].size);
assert(H5HG_ISALIGNED(heap->obj[0].size));
} else {
@ -884,7 +887,7 @@ H5HG_remove (H5F_t *f, H5HG_t *hobj)
UINT16ENCODE(p, 0); /*id*/
UINT16ENCODE(p, 0); /*nrefs*/
UINT32ENCODE(p, 0); /*reserved*/
H5F_encode_length (f, p, need);
H5F_ENCODE_LENGTH (f, p, need);
}
HDmemset (heap->obj+hobj->idx, 0, sizeof(H5HG_obj_t));
heap->dirty = 1;

22
src/H5HL.c
View File

@ -18,10 +18,12 @@
*
*-------------------------------------------------------------------------
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h> /*library */
#include <H5ACprivate.h> /*cache */
#include <H5Eprivate.h> /*error handling */
#include <H5Fprivate.h> /*file access */
#include <H5Fpkg.h> /*file access */
#include <H5FLprivate.h> /*Free Lists */
#include <H5HLprivate.h> /*self */
#include <H5MFprivate.h> /*file memory management */
@ -239,11 +241,11 @@ H5HL_load(H5F_t *f, haddr_t addr, const void UNUSED *udata1,
p += 4;
/* heap data size */
H5F_decode_length(f, p, heap->disk_alloc);
H5F_DECODE_LENGTH(f, p, heap->disk_alloc);
heap->mem_alloc = heap->disk_alloc;
/* free list head */
H5F_decode_length(f, p, free_block);
H5F_DECODE_LENGTH(f, p, free_block);
if (free_block != H5HL_FREE_NULL && free_block >= heap->disk_alloc) {
HGOTO_ERROR(H5E_HEAP, H5E_CANTLOAD, NULL,
"bad heap free list");
@ -281,8 +283,8 @@ H5HL_load(H5F_t *f, haddr_t addr, const void UNUSED *udata1,
if (!heap->freelist) heap->freelist = fl;
p = heap->chunk + H5HL_SIZEOF_HDR(f) + free_block;
H5F_decode_length(f, p, free_block);
H5F_decode_length(f, p, fl->size);
H5F_DECODE_LENGTH(f, p, free_block);
H5F_DECODE_LENGTH(f, p, fl->size);
if (fl->offset + fl->size > heap->disk_alloc) {
HGOTO_ERROR(H5E_HEAP, H5E_CANTLOAD, NULL,
@ -366,8 +368,8 @@ H5HL_flush(H5F_t *f, hbool_t destroy, haddr_t addr, H5HL_t *heap)
*p++ = 0; /*reserved*/
*p++ = 0; /*reserved*/
*p++ = 0; /*reserved*/
H5F_encode_length(f, p, heap->mem_alloc);
H5F_encode_length(f, p, fl ? fl->offset : H5HL_FREE_NULL);
H5F_ENCODE_LENGTH(f, p, heap->mem_alloc);
H5F_ENCODE_LENGTH(f, p, fl ? fl->offset : H5HL_FREE_NULL);
H5F_addr_encode(f, &p, heap->addr);
/*
@ -377,11 +379,11 @@ H5HL_flush(H5F_t *f, hbool_t destroy, haddr_t addr, H5HL_t *heap)
assert (fl->offset == H5HL_ALIGN (fl->offset));
p = heap->chunk + H5HL_SIZEOF_HDR(f) + fl->offset;
if (fl->next) {
H5F_encode_length(f, p, fl->next->offset);
H5F_ENCODE_LENGTH(f, p, fl->next->offset);
} else {
H5F_encode_length(f, p, H5HL_FREE_NULL);
H5F_ENCODE_LENGTH(f, p, H5HL_FREE_NULL);
}
H5F_encode_length(f, p, fl->size);
H5F_ENCODE_LENGTH(f, p, fl->size);
fl = fl->next;
}

4
src/H5MF.c
View File

@ -20,9 +20,11 @@
*
*-------------------------------------------------------------------------
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5Fprivate.h>
#include <H5Fpkg.h>
#include <H5FDprivate.h>
#include <H5MFprivate.h>

1
src/H5MFprivate.h
View File

@ -20,6 +20,7 @@
/* Private headers needed by this file */
#include <H5private.h>
#include <H5Fprivate.h>
#include <H5FDprivate.h> /*file driver */
/*
* Feature: Define H5MF_DEBUG on the compiler command line if you want to

4
src/H5O.c
View File

@ -14,10 +14,12 @@
*
*-------------------------------------------------------------------------
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h>
#include <H5ACprivate.h>
#include <H5Eprivate.h>
#include <H5Fprivate.h>
#include <H5Fpkg.h>
#include <H5FLprivate.h> /*Free Lists */
#include <H5Iprivate.h>
#include <H5MFprivate.h>

4
src/H5Oattr.c
View File

@ -16,7 +16,8 @@ static char RcsId[] = "@(#)$Revision$";
/* $Id$ */
#define H5A_PACKAGE /*prevent warning from including H5Tpkg.h */
#define H5A_PACKAGE /*prevent warning from including H5Tpkg.h */
#define H5S_PACKAGE /*suppress error about including H5Spkg */
#include <H5private.h>
#include <H5Eprivate.h>
@ -25,6 +26,7 @@ static char RcsId[] = "@(#)$Revision$";
#include <H5MMprivate.h>
#include <H5Oprivate.h>
#include <H5Apkg.h>
#include <H5Spkg.h> /* Data spaces */
#define PABLO_MASK H5O_attr_mask

5
src/H5Ocont.c
View File

@ -17,6 +17,7 @@
*
*-------------------------------------------------------------------------
*/
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5MMprivate.h>
@ -85,7 +86,7 @@ H5O_cont_decode(H5F_t *f, const uint8_t *p, H5O_shared_t UNUSED *sh)
"memory allocation failed");
}
H5F_addr_decode(f, &p, &(cont->addr));
H5F_decode_length(f, p, cont->size);
H5F_DECODE_LENGTH(f, p, cont->size);
FUNC_LEAVE((void *) cont);
}
@ -119,7 +120,7 @@ H5O_cont_encode(H5F_t *f, uint8_t *p, const void *_mesg)
/* encode */
H5F_addr_encode(f, &p, cont->addr);
H5F_encode_length(f, p, cont->size);
H5F_ENCODE_LENGTH(f, p, cont->size);
FUNC_LEAVE(SUCCEED);
}

15
src/H5Oefl.c
View File

@ -5,8 +5,11 @@
* Programmer: Robb Matzke <matzke@llnl.gov>
* Tuesday, November 25, 1997
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5Fpkg.h>
#include <H5HLprivate.h>
#include <H5MMprivate.h>
#include <H5Oprivate.h>
@ -116,16 +119,16 @@ H5O_efl_decode(H5F_t *f, const uint8_t *p, H5O_shared_t UNUSED *sh)
}
for (i=0; i<mesg->nused; i++) {
/* Name */
H5F_decode_length (f, p, mesg->slot[i].name_offset);
H5F_DECODE_LENGTH (f, p, mesg->slot[i].name_offset);
s = H5HL_peek(f, mesg->heap_addr, mesg->slot[i].name_offset);
assert (s && *s);
mesg->slot[i].name = H5MM_xstrdup (s);
/* File offset */
H5F_decode_length (f, p, mesg->slot[i].offset);
H5F_DECODE_LENGTH (f, p, mesg->slot[i].offset);
/* Size */
H5F_decode_length (f, p, mesg->slot[i].size);
H5F_DECODE_LENGTH (f, p, mesg->slot[i].size);
assert (mesg->slot[i].size>0);
}
@ -191,9 +194,9 @@ H5O_efl_encode(H5F_t *f, uint8_t *p, const void *_mesg)
* created.
*/
assert(mesg->slot[i].name_offset);
H5F_encode_length (f, p, mesg->slot[i].name_offset);
H5F_encode_length (f, p, mesg->slot[i].offset);
H5F_encode_length (f, p, mesg->slot[i].size);
H5F_ENCODE_LENGTH (f, p, mesg->slot[i].name_offset);
H5F_ENCODE_LENGTH (f, p, mesg->slot[i].offset);
H5F_ENCODE_LENGTH (f, p, mesg->slot[i].size);
}
FUNC_LEAVE(SUCCEED);

4
src/H5Oprivate.h
View File

@ -25,7 +25,7 @@
#include <H5Gprivate.h>
#include <H5HGprivate.h>
#include <H5Tprivate.h>
#include <H5Sprivate.h>
#include <H5Spublic.h>
#include <H5Zprivate.h>
/*
@ -125,7 +125,7 @@ __DLLVAR__ const H5O_class_t H5O_NULL[1];
#define H5O_SDSPACE_ID 0x0001
__DLLVAR__ const H5O_class_t H5O_SDSPACE[1];
/* operates on an H5S_simple_t struct */
/* operates on an H5S_t struct */
/*
* Data Type Message.

19
src/H5Osdspace.c
View File

@ -16,12 +16,15 @@ static char RcsId[] = "@(#)$Revision$";
/* $Id$ */
#define H5S_PACKAGE /*prevent warning from including H5Spkg.h */
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5FLprivate.h> /*Free Lists */
#include <H5Gprivate.h>
#include <H5MMprivate.h>
#include <H5Oprivate.h>
#include <H5Spkg.h>
#define PABLO_MASK H5O_sdspace_mask
@ -125,7 +128,7 @@ H5O_sdspace_decode(H5F_t *f, const uint8_t *p, H5O_shared_t UNUSED *sh)
"memory allocation failed");
}
for (u = 0; u < sdim->rank; u++) {
H5F_decode_length (f, p, sdim->size[u]);
H5F_DECODE_LENGTH (f, p, sdim->size[u]);
}
if (flags & H5S_VALID_MAX) {
if (NULL==(sdim->max=H5FL_ARR_ALLOC(hsize_t,sdim->rank,0))) {
@ -133,7 +136,7 @@ H5O_sdspace_decode(H5F_t *f, const uint8_t *p, H5O_shared_t UNUSED *sh)
"memory allocation failed");
}
for (u = 0; u < sdim->rank; u++) {
H5F_decode_length (f, p, sdim->max[u]);
H5F_DECODE_LENGTH (f, p, sdim->max[u]);
}
}
#ifdef LATER
@ -212,11 +215,11 @@ H5O_sdspace_encode(H5F_t *f, uint8_t *p, const void *mesg)
if (sdim->rank > 0) {
for (u = 0; u < sdim->rank; u++) {
H5F_encode_length (f, p, sdim->size[u]);
H5F_ENCODE_LENGTH (f, p, sdim->size[u]);
}
if (flags & H5S_VALID_MAX) {
for (u = 0; u < sdim->rank; u++) {
H5F_encode_length (f, p, sdim->max[u]);
H5F_ENCODE_LENGTH (f, p, sdim->max[u]);
}
}
#ifdef LATER
@ -313,7 +316,7 @@ H5O_sdspace_copy(const void *mesg, void *dest)
static size_t
H5O_sdspace_size(H5F_t *f, const void *mesg)
{
const H5S_simple_t *sdim = (const H5S_simple_t *) mesg;
const H5S_simple_t *space = (const H5S_simple_t *) mesg;
/*
* All dimensionality messages are at least 8 bytes long.
@ -323,14 +326,14 @@ H5O_sdspace_size(H5F_t *f, const void *mesg)
FUNC_ENTER(H5O_sdspace_size, 0);
/* add in the dimension sizes */
ret_value += sdim->rank * H5F_SIZEOF_SIZE (f);
ret_value += space->rank * H5F_SIZEOF_SIZE (f);
/* add in the space for the maximum dimensions, if they are present */
ret_value += sdim->max ? sdim->rank * H5F_SIZEOF_SIZE (f) : 0;
ret_value += space->max ? space->rank * H5F_SIZEOF_SIZE (f) : 0;
#ifdef LATER
/* add in the space for the dimension permutations, if they are present */
ret_value += sdim->perm ? sdim->rank * 4 : 0;
ret_value += space->perm ? space->rank * 4 : 0;
#endif
FUNC_LEAVE(ret_value);

1
src/H5Oshared.c
View File

@ -13,6 +13,7 @@
* pointed-to message and the pointed-to message is stored in
* the global heap.
*/
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5MMprivate.h>

37
src/H5P.c
View File

@ -22,6 +22,7 @@ static char RcsId[] = "@(#)$Revision$";
#include <H5Bprivate.h> /* B-tree subclass names */
#include <H5Dprivate.h> /* Datasets */
#include <H5Eprivate.h> /* Error handling */
#include <H5Fprivate.h> /* Files */
#include <H5FDprivate.h> /* File drivers */
#include <H5FLprivate.h> /* Free Lists */
#include <H5MMprivate.h> /* Memory management */
@ -317,7 +318,7 @@ H5Pcreate(H5P_class_t type)
src = &H5D_create_dflt;
break;
case H5P_DATA_XFER:
src = &H5F_xfer_dflt;
src = &H5D_xfer_dflt;
break;
case H5P_MOUNT:
src = &H5F_mount_dflt;
@ -442,7 +443,7 @@ H5P_close(void *_plist)
{
H5P_t *plist=(H5P_t *)_plist;
H5F_access_t *fa_list = &(plist->u.faccess);
H5F_xfer_t *dx_list = &(plist->u.dxfer);
H5D_xfer_t *dx_list = &(plist->u.dxfer);
H5D_create_t *dc_list = &(plist->u.dcreate);
FUNC_ENTER (H5P_close, FAIL);
@ -657,7 +658,7 @@ H5P_copy (H5P_class_t type, const void *src)
const H5D_create_t *dc_src = NULL;
H5D_create_t *dc_dst = NULL;
H5F_access_t *fa_dst = NULL;
H5F_xfer_t *dx_dst = NULL;
H5D_xfer_t *dx_dst = NULL;
FUNC_ENTER (H5P_copy, NULL);
@ -676,7 +677,7 @@ H5P_copy (H5P_class_t type, const void *src)
break;
case H5P_DATA_XFER:
size = sizeof(H5F_xfer_t);
size = sizeof(H5D_xfer_t);
break;
case H5P_MOUNT:
@ -740,7 +741,7 @@ H5P_copy (H5P_class_t type, const void *src)
break;
case H5P_DATA_XFER:
dx_dst = (H5F_xfer_t*)dst;
dx_dst = (H5D_xfer_t*)dst;
if (dx_dst->driver_id>=0) {
H5I_inc_ref(dx_dst->driver_id);
@ -1662,7 +1663,7 @@ herr_t
H5Pset_driver(hid_t plist_id, hid_t driver_id, const void *driver_info)
{
H5F_access_t *fapl=NULL;
H5F_xfer_t *dxpl=NULL;
H5D_xfer_t *dxpl=NULL;
FUNC_ENTER(H5Pset_driver, FAIL);
H5TRACE3("e","iix",plist_id,driver_id,driver_info);
@ -1741,7 +1742,7 @@ hid_t
H5Pget_driver(hid_t plist_id)
{
H5F_access_t *fapl=NULL;
H5F_xfer_t *dxpl=NULL;
H5D_xfer_t *dxpl=NULL;
hid_t ret_value=-1;
FUNC_ENTER (H5Pget_driver, FAIL);
@ -1792,7 +1793,7 @@ void *
H5Pget_driver_info(hid_t plist_id)
{
H5F_access_t *fapl=NULL;
H5F_xfer_t *dxpl=NULL;
H5D_xfer_t *dxpl=NULL;
void *ret_value=NULL;
FUNC_ENTER(H5Pget_driver_info, NULL);
@ -1953,7 +1954,7 @@ H5Pget_cache(hid_t plist_id, int *mdc_nelmts,
herr_t
H5Pset_buffer(hid_t plist_id, size_t size, void *tconv, void *bkg)
{
H5F_xfer_t *plist = NULL;
H5D_xfer_t *plist = NULL;
FUNC_ENTER (H5Pset_buffer, FAIL);
H5TRACE4("e","izxx",plist_id,size,tconv,bkg);
@ -1997,7 +1998,7 @@ H5Pset_buffer(hid_t plist_id, size_t size, void *tconv, void *bkg)
size_t
H5Pget_buffer(hid_t plist_id, void **tconv/*out*/, void **bkg/*out*/)
{
H5F_xfer_t *plist = NULL;
H5D_xfer_t *plist = NULL;
FUNC_ENTER (H5Pget_buffer, 0);
H5TRACE3("z","ixx",plist_id,tconv,bkg);
@ -2045,7 +2046,7 @@ H5Pget_buffer(hid_t plist_id, void **tconv/*out*/, void **bkg/*out*/)
herr_t
H5Pset_hyper_cache(hid_t plist_id, unsigned cache, unsigned limit)
{
H5F_xfer_t *plist = NULL;
H5D_xfer_t *plist = NULL;
FUNC_ENTER (H5Pset_hyper_cache, FAIL);
H5TRACE3("e","iIuIu",plist_id,cache,limit);
@ -2083,7 +2084,7 @@ herr_t
H5Pget_hyper_cache(hid_t plist_id, unsigned *cache/*out*/,
unsigned *limit/*out*/)
{
H5F_xfer_t *plist = NULL;
H5D_xfer_t *plist = NULL;
FUNC_ENTER (H5Pget_hyper_cache, FAIL);
H5TRACE3("e","ixx",plist_id,cache,limit);
@ -2126,7 +2127,7 @@ H5Pget_hyper_cache(hid_t plist_id, unsigned *cache/*out*/,
herr_t
H5Pset_preserve(hid_t plist_id, hbool_t status)
{
H5F_xfer_t *plist = NULL;
H5D_xfer_t *plist = NULL;
FUNC_ENTER (H5Pset_preserve, FAIL);
H5TRACE2("e","ib",plist_id,status);
@ -2164,7 +2165,7 @@ H5Pset_preserve(hid_t plist_id, hbool_t status)
int
H5Pget_preserve(hid_t plist_id)
{
H5F_xfer_t *plist = NULL;
H5D_xfer_t *plist = NULL;
FUNC_ENTER (H5Pget_preserve, FAIL);
H5TRACE1("Is","i",plist_id);
@ -2483,7 +2484,7 @@ herr_t
H5Pget_btree_ratios(hid_t plist_id, double *left/*out*/, double *middle/*out*/,
double *right/*out*/)
{
H5F_xfer_t *plist = NULL;
H5D_xfer_t *plist = NULL;
FUNC_ENTER(H5Pget_btree_ratios, FAIL);
H5TRACE4("e","ixxx",plist_id,left,middle,right);
@ -2533,7 +2534,7 @@ herr_t
H5Pset_btree_ratios(hid_t plist_id, double left, double middle,
double right)
{
H5F_xfer_t *plist = NULL;
H5D_xfer_t *plist = NULL;
FUNC_ENTER(H5Pget_btree_ratios, FAIL);
H5TRACE4("e","iddd",plist_id,left,middle,right);
@ -2840,7 +2841,7 @@ herr_t
H5Pset_vlen_mem_manager(hid_t plist_id, H5MM_allocate_t alloc_func,
void *alloc_info, H5MM_free_t free_func, void *free_info)
{
H5F_xfer_t *plist = NULL;
H5D_xfer_t *plist = NULL;
FUNC_ENTER(H5Pset_vlen_mem_manager, FAIL);
H5TRACE5("e","ixxxx",plist_id,alloc_func,alloc_info,free_func,free_info);
@ -2882,7 +2883,7 @@ H5Pget_vlen_mem_manager(hid_t plist_id, H5MM_allocate_t *alloc_func/*out*/,
H5MM_free_t *free_func/*out*/,
void **free_info/*out*/)
{
H5F_xfer_t *plist = NULL;
H5D_xfer_t *plist = NULL;
FUNC_ENTER(H5Pget_vlen_mem_manager, FAIL);
H5TRACE5("e","ixxxx",plist_id,alloc_func,alloc_info,free_func,free_info);

2
src/H5Pprivate.h
View File

@ -89,7 +89,7 @@ typedef struct {
H5F_create_t fcreate; /* File creation properties */
H5F_access_t faccess; /* File access properties */
H5D_create_t dcreate; /* Dataset creation properties */
H5F_xfer_t dxfer; /* Data transfer properties */
H5D_xfer_t dxfer; /* Data transfer properties */
H5F_mprop_t mount; /* Mounting properties */
} u;
H5P_class_t class; /* Property list class */

1
src/H5Ppublic.h
View File

@ -25,6 +25,7 @@
#include <H5Ipublic.h>
#include <H5Dpublic.h>
#include <H5Fpublic.h>
#include <H5MMpublic.h>
#include <H5Zpublic.h>
/* Property list classes */

4
src/H5R.c
View File

@ -16,11 +16,13 @@ static char RcsId[] = "@(#)$Revision$";
/* $Id$ */
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#include <H5private.h> /* Generic Functions */
#include <H5Iprivate.h> /* ID Functions */
#include <H5Dprivate.h> /* Datasets */
#include <H5Eprivate.h> /* Error handling */
#include <H5Fprivate.h> /* Files */
#include <H5Fpkg.h> /* Files */
#include <H5Gprivate.h> /* Groups */
#include <H5HGprivate.h> /* Global Heaps */
#include <H5MMprivate.h> /* Memory Management */

40
src/H5S.c
View File

@ -16,6 +16,8 @@ static char RcsId[] = "@(#)$Revision$";
/* $Id$ */
#define H5S_PACKAGE /*suppress error about including H5Spkg */
#define _H5S_IN_H5S_C
#include <H5private.h> /* Generic Functions */
#include <H5Iprivate.h> /* ID Functions */
@ -23,7 +25,7 @@ static char RcsId[] = "@(#)$Revision$";
#include <H5FLprivate.h> /* Free Lists */
#include <H5MMprivate.h> /* Memory Management functions */
#include <H5Oprivate.h> /* object headers */
#include <H5Sprivate.h> /* Data-space functions */
#include <H5Spkg.h> /* Data-space functions */
/* Interface initialization */
#define PABLO_MASK H5S_mask
@ -1722,6 +1724,40 @@ H5Screate_simple(int rank, const hsize_t dims[/*rank*/],
if (ret_value<0 && space) H5S_close(space);
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5S_get_simple_extent_type
*
* Purpose: Internal function for retrieving the type of extent for a dataspace object
*
* Return: Success: The class of the dataspace object
*
* Failure: N5S_NO_CLASS
*
* Errors:
*
* Programmer: Quincey Koziol
* Thursday, September 28, 2000
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
H5S_class_t
H5S_get_simple_extent_type(const H5S_t *space)
{
H5S_class_t ret_value = H5S_NO_CLASS;
FUNC_ENTER(H5S_get_simple_extent_type, H5S_NO_CLASS);
assert(space);
ret_value=space->extent.type;
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5Sget_simple_extent_type
@ -1755,7 +1791,7 @@ H5Sget_simple_extent_type(hid_t sid)
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, H5S_NO_CLASS, "not a dataspace");
}
ret_value=space->extent.type;
ret_value=H5S_get_simple_extent_type(space);
FUNC_LEAVE(ret_value);
}

5
src/H5Sall.c
View File

@ -7,10 +7,13 @@
*
* Purpose: "All" selection data space I/O functions.
*/
#define H5S_PACKAGE /*suppress error about including H5Spkg */
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5Iprivate.h>
#include <H5Sprivate.h>
#include <H5Spkg.h>
#include <H5Vprivate.h>
#include <H5Dprivate.h>

144
src/H5Shyper.c
View File

@ -7,14 +7,18 @@
*
* Purpose: Hyperslab selection data space I/O functions.
*/
#define H5S_PACKAGE /*suppress error about including H5Spkg */
#include <H5private.h>
#include <H5Dprivate.h>
#include <H5Eprivate.h>
#include <H5Fprivate.h>
#include <H5FLprivate.h> /*Free Lists */
#include <H5Iprivate.h>
#include <H5MMprivate.h>
#include <H5Pprivate.h>
#include <H5Sprivate.h>
#include <H5Spkg.h>
#include <H5Vprivate.h>
/* Interface initialization */
@ -585,13 +589,13 @@ H5S_hyper_fread (intn dim, H5S_hyper_io_info_t *io_info)
size_t i; /* Counters */
intn j;
size_t num_read=0; /* Number of elements read */
const H5F_xfer_t *xfer_parms;/* Data transfer property list */
const H5D_xfer_t *xfer_parms;/* Data transfer property list */
FUNC_ENTER (H5S_hyper_fread, 0);
assert(io_info);
if (H5P_DEFAULT==io_info->dxpl_id) {
xfer_parms = &H5F_xfer_dflt;
xfer_parms = &H5D_xfer_dflt;
} else {
xfer_parms = H5I_object(io_info->dxpl_id);
assert(xfer_parms);
@ -934,17 +938,19 @@ H5S_hyper_fread_opt (H5F_t *f, const struct H5O_layout_t *layout,
const H5S_t *file_space, H5S_sel_iter_t *file_iter,
size_t nelmts, hid_t dxpl_id, void *_buf/*out*/)
{
hsize_t hsize[H5O_LAYOUT_NDIMS]; /* Hyperslab size */
hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */
hssize_t offset[H5O_LAYOUT_NDIMS]; /* Offset on disk */
hsize_t slab[H5O_LAYOUT_NDIMS]; /* Hyperslab size */
hsize_t tmp_count[H5O_LAYOUT_NDIMS]; /* Temporary block count */
hsize_t tmp_block[H5O_LAYOUT_NDIMS]; /* Temporary block offset */
uint8_t *buf=(uint8_t *)_buf; /* Alias for pointer arithmetic */
intn fast_dim; /* Rank of the fastest changing dimension for the dataspace */
intn temp_dim; /* Temporary rank holder */
hsize_t acc; /* Accumulator */
size_t buf_off; /* Buffer offset for copying memory */
intn i; /* Counters */
intn ndims; /* Number of dimensions of dataset */
uintn actual_read; /* The actual number of elements to read in */
uintn actual_bytes; /* The actual number of bytes to copy */
size_t num_read=0; /* Number of elements read */
FUNC_ENTER (H5S_hyper_fread_opt, 0);
@ -965,15 +971,13 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
/* Set the rank of the fastest changing dimension */
fast_dim=file_space->extent.u.simple.rank-1;
/* Set up the hyperslab and 'zero' arrays */
ndims=file_space->extent.u.simple.rank;
/* initialize hyperslab size and offset in memory buffer */
for(i=0; i<(ndims+1); i++) {
hsize[i]=1; /* hyperslab size is 1, except for last element */
zero[i]=0; /* memory offset is 0 */
/* initialize row sizes for each dimension */
for(i=(ndims-1),acc=1; i>=0; i--) {
slab[i]=acc*elmt_size;
acc*=file_space->extent.u.simple.size[i];
} /* end for */
hsize[ndims] = elmt_size;
/* Check if we stopped in the middle of a sequence of elements */
if((file_iter->hyp.pos[fast_dim]-file_space->select.sel_info.hslab.diminfo[fast_dim].start)%file_space->select.sel_info.hslab.diminfo[fast_dim].stride!=0) {
@ -987,9 +991,7 @@ printf("%s: Check 1.0\n",FUNC);
/* Make certain that we don't read too many */
actual_read=MIN(leftover,nelmts);
/* Set the hyperslab size in the fastest changing dimension to read in */
hsize[fast_dim]=actual_read;
actual_bytes=actual_read*elmt_size;
/* Copy the location of the point to get */
HDmemcpy(offset, file_iter->hyp.pos,ndims*sizeof(hssize_t));
@ -999,9 +1001,13 @@ printf("%s: Check 1.0\n",FUNC);
for(i=0; i<ndims; i++)
offset[i] += file_space->select.offset[i];
/* Read in the rest of the sequence, if possible */
if (H5F_arr_read(f, dxpl_id, layout, pline, fill, efl, hsize,
hsize, zero, offset, buf/*out*/)<0) {
/* Compute the initial buffer offset */
for(i=0,buf_off=0; i<ndims; i++)
buf_off+=offset[i]*slab[i];
/* Read in the rest of the sequence */
if (H5F_seq_read(f, dxpl_id, layout, pline, fill, efl, file_space,
elmt_size, actual_bytes, 0, buf_off, buf/*out*/)<0) {
HRETURN_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error");
}
@ -1053,9 +1059,15 @@ printf("%s: Check 2.0\n",FUNC);
tmp_block[i] = (file_iter->hyp.pos[i]-file_space->select.sel_info.hslab.diminfo[i].start)/file_space->select.sel_info.hslab.diminfo[i].stride;
} /* end for */
/* Compute the initial buffer offset */
for(i=0,buf_off=0; i<ndims; i++)
buf_off+=offset[i]*slab[i];
/* Set the number of elements to read each time */
actual_read=file_space->select.sel_info.hslab.diminfo[fast_dim].block;
hsize[fast_dim]=actual_read;
/* Set the number of actual bytes */
actual_bytes=actual_read*elmt_size;
#ifdef QAK
printf("%s: actual_read=%d\n",FUNC,(int)actual_read);
for(i=0; i<file_space->extent.u.simple.rank; i++)
@ -1071,7 +1083,7 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
/* Check if we are running out of room in the buffer */
if((actual_read+num_read)>nelmts) {
actual_read=nelmts-num_read;
hsize[fast_dim]=actual_read;
actual_bytes=actual_read*elmt_size;
} /* end if */
#ifdef QAK
@ -1080,9 +1092,9 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
printf("%s: tmp_count[%d]=%d, offset[%d]=%d\n",FUNC,(int)i,(int)tmp_count[i],(int)i,(int)offset[i]);
#endif /* QAK */
/* Read in the sequence, if possible */
if (H5F_arr_read(f, dxpl_id, layout, pline, fill, efl, hsize,
hsize, zero, offset, buf/*out*/)<0) {
/* Read in the sequence */
if (H5F_seq_read(f, dxpl_id, layout, pline, fill, efl, file_space,
elmt_size, actual_bytes, 0, buf_off, buf/*out*/)<0) {
HRETURN_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error");
}
@ -1103,10 +1115,12 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
/* Check for partial block read! */
if(actual_read<file_space->select.sel_info.hslab.diminfo[fast_dim].block) {
offset[temp_dim]+=actual_read;
buf_off+=actual_bytes;
break;
} /* end if */
else {
offset[temp_dim]+=file_space->select.sel_info.hslab.diminfo[temp_dim].stride; /* reset the offset in the fastest dimension */
buf_off+=slab[temp_dim]*file_space->select.sel_info.hslab.diminfo[temp_dim].stride;
tmp_count[temp_dim]++;
} /* end else */
@ -1116,11 +1130,16 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
else {
tmp_count[temp_dim]=0; /* reset back to the beginning of the line */
offset[temp_dim]=file_space->select.sel_info.hslab.diminfo[temp_dim].start+file_space->select.offset[temp_dim];
/* Re-compute the initial buffer offset */
for(i=0,buf_off=0; i<ndims; i++)
buf_off+=offset[i]*slab[i];
} /* end else */
} /* end if */
else {
/* Move to the next row in the curent dimension */
offset[temp_dim]++;
buf_off+=slab[temp_dim];
tmp_block[temp_dim]++;
/* If this block is still in the range of blocks to output for the dimension, break out of loop */
@ -1129,6 +1148,7 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
else {
/* Move to the next block in the current dimension */
offset[temp_dim]+=(file_space->select.sel_info.hslab.diminfo[temp_dim].stride-file_space->select.sel_info.hslab.diminfo[temp_dim].block);
buf_off+=(file_space->select.sel_info.hslab.diminfo[temp_dim].stride-file_space->select.sel_info.hslab.diminfo[temp_dim].block)*slab[temp_dim];
tmp_block[temp_dim]=0;
tmp_count[temp_dim]++;
@ -1139,6 +1159,10 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
tmp_count[temp_dim]=0; /* reset back to the beginning of the line */
tmp_block[temp_dim]=0;
offset[temp_dim]=file_space->select.sel_info.hslab.diminfo[temp_dim].start+file_space->select.offset[temp_dim];
/* Re-compute the initial buffer offset */
for(i=0,buf_off=0; i<ndims; i++)
buf_off+=offset[i]*slab[i];
}
} /* end else */
} /* end else */
@ -1273,13 +1297,13 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_io_info_t *io_info)
size_t i; /* Counters */
intn j;
size_t num_written=0; /* Number of elements read */
const H5F_xfer_t *xfer_parms; /* Data transfer properties */
const H5D_xfer_t *xfer_parms; /* Data transfer properties */
FUNC_ENTER (H5S_hyper_fwrite, 0);
assert(io_info);
if (H5P_DEFAULT==io_info->dxpl_id) {
xfer_parms = &H5F_xfer_dflt;
xfer_parms = &H5D_xfer_dflt;
} else {
xfer_parms = H5I_object(io_info->dxpl_id);
assert(xfer_parms);
@ -1434,18 +1458,20 @@ H5S_hyper_fwrite_opt (H5F_t *f, const struct H5O_layout_t *layout,
const H5S_t *file_space, H5S_sel_iter_t *file_iter,
size_t nelmts, hid_t dxpl_id, const void *_buf)
{
hsize_t hsize[H5O_LAYOUT_NDIMS]; /* Hyperslab size */
hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */
hssize_t offset[H5O_LAYOUT_NDIMS]; /* Offset on disk */
hsize_t slab[H5O_LAYOUT_NDIMS]; /* Hyperslab size */
hsize_t tmp_count[H5O_LAYOUT_NDIMS]; /* Temporary block count */
hsize_t tmp_block[H5O_LAYOUT_NDIMS]; /* Temporary block offset */
const uint8_t *buf=(const uint8_t *)_buf; /* Alias for pointer arithmetic */
intn fast_dim; /* Rank of the fastest changing dimension for the dataspace */
intn temp_dim; /* Temporary rank holder */
hsize_t acc; /* Accumulator */
size_t buf_off; /* Buffer offset for copying memory */
intn i; /* Counters */
intn ndims; /* Number of dimensions of dataset */
uintn actual_write; /* The actual number of elements to read in */
size_t num_write=0; /* Number of elements read */
uintn actual_write; /* The actual number of elements to read in */
uintn actual_bytes; /* The actual number of bytes to copy */
size_t num_write=0; /* Number of elements read */
FUNC_ENTER (H5S_hyper_fwrite_opt, 0);
@ -1465,15 +1491,13 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
/* Set the rank of the fastest changing dimension */
fast_dim=file_space->extent.u.simple.rank-1;
/* Set up the hyperslab and 'zero' arrays */
ndims=file_space->extent.u.simple.rank;
/* initialize hyperslab size and offset in memory buffer */
for(i=0; i<(int)(ndims+1); i++) {
hsize[i]=1; /* hyperslab size is 1, except for last element */
zero[i]=0; /* memory offset is 0 */
/* initialize row sizes for each dimension */
for(i=(ndims-1),acc=1; i>=0; i--) {
slab[i]=acc*elmt_size;
acc*=file_space->extent.u.simple.size[i];
} /* end for */
hsize[ndims] = elmt_size;
/* Check if we stopped in the middle of a sequence of elements */
if((file_iter->hyp.pos[fast_dim]-file_space->select.sel_info.hslab.diminfo[fast_dim].start)%file_space->select.sel_info.hslab.diminfo[fast_dim].stride!=0) {
@ -1487,9 +1511,7 @@ printf("%s: Check 1.0\n",FUNC);
/* Make certain that we don't write too many */
actual_write=MIN(leftover,nelmts);
/* Set the hyperslab size in the fastest changing dimension to write in */
hsize[fast_dim]=actual_write;
actual_bytes=actual_write*elmt_size;
/* Copy the location of the point to get */
HDmemcpy(offset, file_iter->hyp.pos,ndims*sizeof(hssize_t));
@ -1499,10 +1521,14 @@ printf("%s: Check 1.0\n",FUNC);
for(i=0; i<ndims; i++)
offset[i] += file_space->select.offset[i];
/* Read in the rest of the sequence, if possible */
if (H5F_arr_write(f, dxpl_id, layout, pline, fill, efl, hsize,
hsize, zero, offset, buf)<0) {
HRETURN_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "write error");
/* Compute the initial buffer offset */
for(i=0,buf_off=0; i<ndims; i++)
buf_off+=offset[i]*slab[i];
/* Read in the rest of the sequence */
if (H5F_seq_write(f, dxpl_id, layout, pline, fill, efl, file_space,
elmt_size, actual_bytes, 0, buf_off, buf)<0) {
HRETURN_ERROR(H5E_DATASPACE, H5E_WRITEERROR, 0, "write error");
}
/* Increment the offset of the buffer */
@ -1553,9 +1579,15 @@ printf("%s: Check 2.0\n",FUNC);
tmp_block[i] = (file_iter->hyp.pos[i]-file_space->select.sel_info.hslab.diminfo[i].start)/file_space->select.sel_info.hslab.diminfo[i].stride;
} /* end for */
/* Compute the initial buffer offset */
for(i=0,buf_off=0; i<ndims; i++)
buf_off+=offset[i]*slab[i];
/* Set the number of elements to write each time */
actual_write=file_space->select.sel_info.hslab.diminfo[fast_dim].block;
hsize[fast_dim]=actual_write;
/* Set the number of actual bytes */
actual_bytes=actual_write*elmt_size;
#ifdef QAK
printf("%s: actual_write=%d\n",FUNC,(int)actual_write);
for(i=0; i<file_space->extent.u.simple.rank; i++)
@ -1571,7 +1603,7 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
/* Check if we are running out of room in the buffer */
if((actual_write+num_write)>nelmts) {
actual_write=nelmts-num_write;
hsize[fast_dim]=actual_write;
actual_bytes=actual_write*elmt_size;
} /* end if */
#ifdef QAK
@ -1580,10 +1612,10 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
printf("%s: tmp_count[%d]=%d, offset[%d]=%d\n",FUNC,(int)i,(int)tmp_count[i],(int)i,(int)offset[i]);
#endif /* QAK */
/* Read in the sequence, if possible */
if (H5F_arr_write(f, dxpl_id, layout, pline, fill, efl, hsize,
hsize, zero, offset, buf)<0) {
HRETURN_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "write error");
/* Read in the sequence */
if (H5F_seq_write(f, dxpl_id, layout, pline, fill, efl, file_space,
elmt_size, actual_bytes, 0, buf_off, buf)<0) {
HRETURN_ERROR(H5E_DATASPACE, H5E_WRITEERROR, 0, "write error");
}
/* Increment the offset of the buffer */
@ -1603,10 +1635,12 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
/* Check for partial block write! */
if(actual_write<file_space->select.sel_info.hslab.diminfo[fast_dim].block) {
offset[temp_dim]+=actual_write;
buf_off+=actual_bytes;
break;
} /* end if */
else {
offset[temp_dim]+=file_space->select.sel_info.hslab.diminfo[temp_dim].stride; /* reset the offset in the fastest dimension */
buf_off+=slab[temp_dim]*file_space->select.sel_info.hslab.diminfo[temp_dim].stride;
tmp_count[temp_dim]++;
} /* end else */
@ -1616,11 +1650,16 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
else {
tmp_count[temp_dim]=0; /* reset back to the beginning of the line */
offset[temp_dim]=file_space->select.sel_info.hslab.diminfo[temp_dim].start+file_space->select.offset[temp_dim];
/* Re-compute the initial buffer offset */
for(i=0,buf_off=0; i<ndims; i++)
buf_off+=offset[i]*slab[i];
} /* end else */
} /* end if */
else {
/* Move to the next row in the curent dimension */
offset[temp_dim]++;
buf_off+=slab[temp_dim];
tmp_block[temp_dim]++;
/* If this block is still in the range of blocks to output for the dimension, break out of loop */
@ -1629,6 +1668,7 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
else {
/* Move to the next block in the current dimension */
offset[temp_dim]+=(file_space->select.sel_info.hslab.diminfo[temp_dim].stride-file_space->select.sel_info.hslab.diminfo[temp_dim].block);
buf_off+=(file_space->select.sel_info.hslab.diminfo[temp_dim].stride-file_space->select.sel_info.hslab.diminfo[temp_dim].block)*slab[temp_dim];
tmp_block[temp_dim]=0;
tmp_count[temp_dim]++;
@ -1639,6 +1679,10 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
tmp_count[temp_dim]=0; /* reset back to the beginning of the line */
tmp_block[temp_dim]=0;
offset[temp_dim]=file_space->select.sel_info.hslab.diminfo[temp_dim].start+file_space->select.offset[temp_dim];
/* Re-compute the initial buffer offset */
for(i=0,buf_off=0; i<ndims; i++)
buf_off+=offset[i]*slab[i];
}
} /* end else */
} /* end else */
@ -1922,7 +1966,7 @@ H5S_hyper_mread_opt (const void *_buf, size_t elmt_size,
uintn actual_bytes; /* The actual number of bytes to copy */
size_t num_read=0; /* Number of elements read */
FUNC_ENTER (H5S_hyper_fread_opt, 0);
FUNC_ENTER (H5S_hyper_mread_opt, 0);
#ifdef QAK
printf("%s: Called!\n",FUNC);

4
src/H5Smpio.c
View File

@ -10,10 +10,12 @@
* I didn't make them portable.
*/
#define H5S_PACKAGE /*suppress error about including H5Spkg */
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5FDprivate.h>
#include <H5Sprivate.h>
#include <H5Spkg.h>
#include <H5FDmpio.h> /*the MPIO file driver */

5
src/H5Snone.c
View File

@ -7,10 +7,13 @@
*
* Purpose: "None" selection data space I/O functions.
*/
#define H5S_PACKAGE /*suppress error about including H5Spkg */
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5Iprivate.h>
#include <H5Sprivate.h>
#include <H5Spkg.h>
#include <H5Vprivate.h>
#include <H5Dprivate.h>

234
src/H5Spkg.h Normal file
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@ -0,0 +1,234 @@
/*
* Copyright (C) 2000 NCSA
* All rights reserved.
*
* Programmer: Quincey Koziol <koziol@ncsa.uiuc.edu>
* Thursday, September 28, 2000
*
* Purpose: This file contains declarations which are visible only within
* the H5S package. Source files outside the H5S package should
* include H5Sprivate.h instead.
*/
#ifndef H5S_PACKAGE
#error "Do not include this file outside the H5S package!"
#endif
#ifndef _H5Spkg_H
#define _H5Spkg_H
#include <H5Sprivate.h>
/*
* Dataspace extent information
*/
/* Simple extent container */
typedef struct H5S_simple_t {
intn rank; /* Number of dimensions */
hsize_t *size; /* Current size of the dimensions */
hsize_t *max; /* Maximum size of the dimensions */
#ifdef LATER
hsize_t *perm; /* Dimension permutation array */
#endif /* LATER */
} H5S_simple_t;
/* Extent container */
typedef struct {
H5S_class_t type; /* Type of extent */
union {
H5S_simple_t simple; /* Simple dimensionality information */
} u;
} H5S_extent_t;
/*
* Dataspace selection information
*/
/* Node in point selection list (typedef'd in H5Sprivate.h) */
struct H5S_pnt_node_t {
hssize_t *pnt; /* Pointer to a selected point */
struct H5S_pnt_node_t *next; /* pointer to next point in list */
};
/* Information about point selection list */
typedef struct {
H5S_pnt_node_t *head; /* Pointer to head of point list */
} H5S_pnt_list_t;
/* Node in hyperslab selection list */
typedef struct H5S_hyper_node_tag {
hssize_t *start; /* Pointer to a corner of a hyperslab closest to the origin */
hssize_t *end; /* Pointer to a corner of a hyperslab furthest from the origin */
struct {
uintn cached; /* Flag to indicate that the block is cached (during I/O only) */
size_t size; /* Size of cached block (in elements) */
uintn rleft; /* Read elements left to access in block */
uintn wleft; /* Write elements left to access in block */
uint8_t *block; /* Pointer into buffer for cache */
uint8_t *rpos; /* Pointer to current read location within block */
uint8_t *wpos; /* Pointer to current write location within block */
} cinfo;
struct H5S_hyper_node_tag *next; /* pointer to next hyperslab in list */
} H5S_hyper_node_t;
/* Region in dimension */
typedef struct H5S_hyper_region_tag {
hssize_t start; /* The low bound of a region in a dimension */
hssize_t end; /* The high bound of a region in a dimension */
H5S_hyper_node_t *node; /* pointer to the node the region is in */
} H5S_hyper_region_t;
/* Information about hyperslab boundary and pointer to hyperslab node */
typedef struct {
hssize_t bound; /* Location of boundary */
H5S_hyper_node_t *node; /* Boundary's node */
} H5S_hyper_bound_t;
/* Information about hyperslab list */
typedef struct {
size_t count; /* Number of nodes in list */
H5S_hyper_node_t *head; /* Pointer to head of hyperslab list */
H5S_hyper_bound_t **lo_bounds; /* Lower (closest to the origin) bound array for each dimension */
} H5S_hyper_list_t;
/* Information about one dimension in a hyperslab selection */
typedef struct {
hssize_t start;
hsize_t stride;
hsize_t count;
hsize_t block;
} H5S_hyper_dim_t;
/* Information about hyperslab selection */
typedef struct {
H5S_hyper_dim_t *diminfo; /* ->[rank] of per-dim selection info */
/* diminfo only points to one array, which holds the information
* for one hyperslab selection. Perhaps this might need to be
* expanded into a list of arrays when the H5Sselect_hyperslab's
* restriction to H5S_SELECT_SET is removed. */
H5S_hyper_dim_t *app_diminfo;/* ->[rank] of per-dim selection info */
/* 'diminfo' points to a [potentially] optimized version of the user's
* hyperslab information. 'app_diminfo' points to the actual parameters
* that the application used for setting the hyperslab selection. These
* are only used for re-gurgitating the original values used to set the
* hyperslab to the application when it queries the hyperslab selection
* information. */
H5S_hyper_list_t *hyper_lst; /* List of selected hyperslabs (order is not important) */
} H5S_hyper_sel_t;
/* Selection information container */
typedef struct {
H5S_sel_type type; /* Type of selection (list of points or hyperslabs) */
hssize_t *offset; /* Offset within the extent (NULL means a 0 offset) */
hsize_t *order; /* Selection order. (NULL means a specific ordering of points) */
hsize_t num_elem; /* Number of elements in selection */
union {
H5S_pnt_list_t *pnt_lst; /* List of selected points (order is important) */
H5S_hyper_sel_t hslab; /* Info about hyperslab selections */
} sel_info;
} H5S_select_t;
/* Main dataspace structure (typedef'd in H5Sprivate.h) */
struct H5S_t {
H5S_extent_t extent; /* Dataspace extent */
H5S_select_t select; /* Dataspace selection */
};
__DLL__ herr_t H5S_close_simple(H5S_simple_t *simple);
__DLL__ herr_t H5S_release_simple(H5S_simple_t *simple);
__DLL__ herr_t H5S_extent_copy(H5S_extent_t *dst, const H5S_extent_t *src);
__DLL__ herr_t H5S_register(H5S_sel_type cls, const H5S_fconv_t *fconv,
const H5S_mconv_t *mconv);
/* Point select functions */
__DLL__ herr_t H5S_point_add(H5S_t *space, H5S_seloper_t op, size_t num_elem,
const hssize_t **coord);
__DLL__ herr_t H5S_point_release(H5S_t *space);
__DLL__ hsize_t H5S_point_npoints(const H5S_t *space);
__DLL__ herr_t H5S_point_copy(H5S_t *dst, const H5S_t *src);
__DLL__ htri_t H5S_point_select_valid(const H5S_t *space);
__DLL__ hssize_t H5S_point_select_serial_size(const H5S_t *space);
__DLL__ herr_t H5S_point_select_serialize(const H5S_t *space, uint8_t *buf);
__DLL__ herr_t H5S_point_select_deserialize(H5S_t *space, const uint8_t *buf);
__DLL__ herr_t H5S_point_bounds(H5S_t *space, hsize_t *start, hsize_t *end);
__DLL__ htri_t H5S_point_select_contiguous(const H5S_t *space);
__DLL__ herr_t H5S_point_select_iterate(void *buf, hid_t type_id, H5S_t *space,
H5D_operator_t op,
void *operator_data);
/* "All" select functions */
__DLL__ herr_t H5S_all_release(H5S_t *space);
__DLL__ hsize_t H5S_all_npoints(const H5S_t *space);
__DLL__ herr_t H5S_all_select_serialize(const H5S_t *space, uint8_t *buf);
__DLL__ herr_t H5S_all_select_deserialize(H5S_t *space, const uint8_t *buf);
__DLL__ herr_t H5S_all_bounds(H5S_t *space, hsize_t *start, hsize_t *end);
__DLL__ herr_t H5S_all_read(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, void *buf/*out*/,
hbool_t *must_convert/*out*/);
__DLL__ herr_t H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, const void *buf,
hbool_t *must_convert/*out*/);
__DLL__ herr_t H5S_all_select_iterate(void *buf, hid_t type_id, H5S_t *space,
H5D_operator_t op, void *operator_data);
/* Hyperslab selection functions */
__DLL__ herr_t H5S_hyper_release(H5S_t *space);
__DLL__ herr_t H5S_hyper_sel_iter_release(H5S_sel_iter_t *sel_iter);
__DLL__ hsize_t H5S_hyper_npoints(const H5S_t *space);
__DLL__ int H5S_hyper_compare_regions(const void *r1, const void *r2);
__DLL__ int H5S_hyper_compare_bounds(const void *r1, const void *r2);
__DLL__ herr_t H5S_hyper_copy(H5S_t *dst, const H5S_t *src);
__DLL__ htri_t H5S_hyper_select_valid(const H5S_t *space);
__DLL__ intn H5S_hyper_bound_comp(const void *_b1, const void *_b2);
__DLL__ herr_t H5S_hyper_node_add(H5S_hyper_node_t **head, intn endflag,
intn rank, const hssize_t *start,
const hsize_t *size);
__DLL__ herr_t H5S_hyper_clip(H5S_t *space, H5S_hyper_node_t *nodes,
H5S_hyper_node_t **uniq,
H5S_hyper_node_t **overlap);
__DLL__ hssize_t H5S_hyper_select_serial_size(const H5S_t *space);
__DLL__ herr_t H5S_hyper_select_serialize(const H5S_t *space, uint8_t *buf);
__DLL__ herr_t H5S_hyper_select_deserialize(H5S_t *space, const uint8_t *buf);
__DLL__ herr_t H5S_hyper_bounds(H5S_t *space, hsize_t *start, hsize_t *end);
__DLL__ htri_t H5S_hyper_select_contiguous(const H5S_t *space);
__DLL__ herr_t H5S_hyper_select_iterate(void *buf, hid_t type_id, H5S_t *space,
H5D_operator_t op, void *operator_data);
/* "None" selection functions */
__DLL__ herr_t H5S_none_select_serialize(const H5S_t *space, uint8_t *buf);
__DLL__ herr_t H5S_none_select_deserialize(H5S_t *space, const uint8_t *buf);
__DLL__ herr_t H5S_none_select_iterate(void *buf, hid_t type_id, H5S_t *space,
H5D_operator_t op, void *operator_data);
#ifdef H5_HAVE_PARALLEL
/* MPI-IO function to read directly from app buffer to file rky980813 */
__DLL__ herr_t H5S_mpio_spaces_read(H5F_t *f,
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, hid_t dxpl_id,
void *buf/*out*/,
hbool_t *must_convert /*out*/ );
/* MPI-IO function to write directly from app buffer to file rky980813 */
__DLL__ herr_t H5S_mpio_spaces_write(H5F_t *f,
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, hid_t dxpl_id,
const void *buf,
hbool_t *must_convert /*out*/ );
#ifndef _H5S_IN_H5S_C
/* Global var whose value comes from environment variable */
__DLLVAR__ hbool_t H5_mpi_opt_types_g;
#endif /* _H5S_IN_H5S_C */
#endif /* H5_HAVE_PARALLEL */
#endif

5
src/H5Spoint.c
View File

@ -7,11 +7,14 @@
*
* Purpose: Point selection data space I/O functions.
*/
#define H5S_PACKAGE /*suppress error about including H5Spkg */
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5Iprivate.h>
#include <H5MMprivate.h>
#include <H5Sprivate.h>
#include <H5Spkg.h>
#include <H5Vprivate.h>
#include <H5Dprivate.h>

229
src/H5Sprivate.h
View File

@ -22,7 +22,6 @@
#include <H5private.h>
#include <H5Dpublic.h>
#include <H5Fprivate.h>
#include <H5Gprivate.h> /*for H5G_entry_t */
#include <H5Oprivate.h>
#define H5S_RESERVED_ATOMS 2
@ -31,30 +30,10 @@
#define H5S_VALID_MAX 0x01
#define H5S_VALID_PERM 0x02
/*
* Dataspace extent information
*/
/* Simple extent container */
typedef struct H5S_simple_t {
intn rank; /* Number of dimensions */
hsize_t *size; /* Current size of the dimensions */
hsize_t *max; /* Maximum size of the dimensions */
#ifdef LATER
hsize_t *perm; /* Dimension permutation array */
#endif /* LATER */
} H5S_simple_t;
/* Forward references of common typedefs */
typedef struct H5S_t H5S_t;
typedef struct H5S_pnt_node_t H5S_pnt_node_t;
/* Extent container */
typedef struct {
H5S_class_t type; /* Type of extent */
union {
H5S_simple_t simple; /* Simple dimensionality information */
} u;
} H5S_extent_t;
/*
* Dataspace selection information
*/
/* Enumerated type for the type of selection */
typedef enum {
H5S_SEL_ERROR = -1, /* Error */
@ -65,90 +44,6 @@ typedef enum {
H5S_SEL_N = 4 /*THIS MUST BE LAST */
}H5S_sel_type;
/* Node in point selection list */
typedef struct H5S_pnt_node_tag {
hssize_t *pnt; /* Pointer to a selected point */
struct H5S_pnt_node_tag *next; /* pointer to next point in list */
} H5S_pnt_node_t;
/* Information about point selection list */
typedef struct {
H5S_pnt_node_t *head; /* Pointer to head of point list */
} H5S_pnt_list_t;
/* Node in hyperslab selection list */
typedef struct H5S_hyper_node_tag {
hssize_t *start; /* Pointer to a corner of a hyperslab closest to the origin */
hssize_t *end; /* Pointer to a corner of a hyperslab furthest from the origin */
struct {
uintn cached; /* Flag to indicate that the block is cached (during I/O only) */
size_t size; /* Size of cached block (in elements) */
uintn rleft; /* Read elements left to access in block */
uintn wleft; /* Write elements left to access in block */
uint8_t *block; /* Pointer into buffer for cache */
uint8_t *rpos; /* Pointer to current read location within block */
uint8_t *wpos; /* Pointer to current write location within block */
} cinfo;
struct H5S_hyper_node_tag *next; /* pointer to next hyperslab in list */
} H5S_hyper_node_t;
/* Region in dimension */
typedef struct H5S_hyper_region_tag {
hssize_t start; /* The low bound of a region in a dimension */
hssize_t end; /* The high bound of a region in a dimension */
H5S_hyper_node_t *node; /* pointer to the node the region is in */
} H5S_hyper_region_t;
/* Information about hyperslab boundary and pointer to hyperslab node */
typedef struct {
hssize_t bound; /* Location of boundary */
H5S_hyper_node_t *node; /* Boundary's node */
} H5S_hyper_bound_t;
/* Information about hyperslab list */
typedef struct {
size_t count; /* Number of nodes in list */
H5S_hyper_node_t *head; /* Pointer to head of hyperslab list */
H5S_hyper_bound_t **lo_bounds; /* Lower (closest to the origin) bound array for each dimension */
} H5S_hyper_list_t;
/* Information about one dimension in a hyperslab selection */
typedef struct {
hssize_t start;
hsize_t stride;
hsize_t count;
hsize_t block;
} H5S_hyper_dim_t;
/* Information about hyperslab selection */
typedef struct {
H5S_hyper_dim_t *diminfo; /* ->[rank] of per-dim selection info */
/* diminfo only points to one array, which holds the information
* for one hyperslab selection. Perhaps this might need to be
* expanded into a list of arrays when the H5Sselect_hyperslab's
* restriction to H5S_SELECT_SET is removed. */
H5S_hyper_dim_t *app_diminfo;/* ->[rank] of per-dim selection info */
/* 'diminfo' points to a [potentially] optimized version of the user's
* hyperslab information. 'app_diminfo' points to the actual parameters
* that the application used for setting the hyperslab selection. These
* are only used for re-gurgitating the original values used to set the
* hyperslab to the application when it queries the hyperslab selection
* information. */
H5S_hyper_list_t *hyper_lst; /* List of selected hyperslabs (order is not important) */
} H5S_hyper_sel_t;
/* Selection information container */
typedef struct {
H5S_sel_type type; /* Type of selection (list of points or hyperslabs) */
hssize_t *offset; /* Offset within the extent (NULL means a 0 offset) */
hsize_t *order; /* Selection order. (NULL means a specific ordering of points) */
hsize_t num_elem; /* Number of elements in selection */
union {
H5S_pnt_list_t *pnt_lst; /* List of selected points (order is important) */
H5S_hyper_sel_t hslab; /* Info about hyperslab selections */
} sel_info;
} H5S_select_t;
/* Point selection iteration container */
typedef struct {
hsize_t elmt_left; /* Number of elements left to iterate over */
@ -174,12 +69,6 @@ typedef union {
H5S_all_iter_t all; /* "All" selection iteration information */
} H5S_sel_iter_t;
/* Main dataspace structure */
typedef struct H5S_t {
H5S_extent_t extent; /* Dataspace extent */
H5S_select_t select; /* Dataspace selection */
} H5S_t;
/*
* Data space conversions usually take place in two halves. One half
* transfers data points between memory and a data type conversion array
@ -303,21 +192,24 @@ __DLLVAR__ const H5S_mconv_t H5S_ALL_MCONV[];
__DLLVAR__ const H5S_fconv_t H5S_HYPER_FCONV[];
__DLLVAR__ const H5S_mconv_t H5S_HYPER_MCONV[];
/* Forward declarations for prototypes arguments */
struct H5G_entry_t;
__DLL__ H5S_t *H5S_create(H5S_class_t type);
__DLL__ H5S_t *H5S_copy(const H5S_t *src);
__DLL__ herr_t H5S_close_simple(H5S_simple_t *simple);
__DLL__ herr_t H5S_close(H5S_t *ds);
__DLL__ H5S_conv_t *H5S_find(const H5S_t *mem_space, const H5S_t *file_space);
__DLL__ H5S_class_t H5S_get_simple_extent_type(const H5S_t *ds);
__DLL__ hsize_t H5S_get_simple_extent_npoints(const H5S_t *ds);
__DLL__ hsize_t H5S_get_npoints_max(const H5S_t *ds);
__DLL__ intn H5S_get_simple_extent_ndims(const H5S_t *ds);
__DLL__ intn H5S_get_simple_extent_dims(const H5S_t *ds, hsize_t dims[]/*out*/,
hsize_t max_dims[]/*out*/);
__DLL__ herr_t H5S_modify(H5G_entry_t *ent, const H5S_t *space);
__DLL__ H5S_t *H5S_read(H5G_entry_t *ent);
__DLL__ herr_t H5S_modify(struct H5G_entry_t *ent, const H5S_t *space);
__DLL__ H5S_t *H5S_read(struct H5G_entry_t *ent);
__DLL__ intn H5S_cmp(const H5S_t *ds1, const H5S_t *ds2);
__DLL__ htri_t H5S_is_simple(const H5S_t *sdim);
__DLL__ uintn H5S_nelem(const H5S_t *space);
__DLL__ H5S_conv_t *H5S_find(const H5S_t *mem_space, const H5S_t *file_space);
__DLL__ herr_t H5S_select_hyperslab(H5S_t *space, H5S_seloper_t op,
const hssize_t start[],
const hsize_t _stride[],
@ -325,13 +217,9 @@ __DLL__ herr_t H5S_select_hyperslab(H5S_t *space, H5S_seloper_t op,
const hsize_t _block[]);
__DLL__ intn H5S_get_hyperslab(const H5S_t *ds, hssize_t offset[]/*out*/,
hsize_t size[]/*out*/, hsize_t stride[]/*out*/);
__DLL__ herr_t H5S_release_simple(H5S_simple_t *simple);
__DLL__ herr_t H5S_extent_copy(H5S_extent_t *dst, const H5S_extent_t *src);
__DLL__ herr_t H5S_select_copy(H5S_t *dst, const H5S_t *src);
__DLL__ herr_t H5S_extent_release(H5S_t *space);
__DLL__ herr_t H5S_select_release(H5S_t *space);
__DLL__ herr_t H5S_sel_iter_release(const H5S_t *space,
H5S_sel_iter_t *sel_iter);
__DLL__ hssize_t H5S_get_select_npoints(const H5S_t *space);
__DLL__ intn H5S_extend(H5S_t *space, const hsize_t *size);
__DLL__ herr_t H5S_set_extent_simple(H5S_t *space, int rank,
@ -339,106 +227,13 @@ __DLL__ herr_t H5S_set_extent_simple(H5S_t *space, int rank,
__DLL__ htri_t H5S_select_valid(const H5S_t *space);
__DLL__ herr_t H5S_debug(H5F_t *f, const void *_mesg, FILE *stream,
intn indent, intn fwidth);
__DLL__ herr_t H5S_register(H5S_sel_type cls, const H5S_fconv_t *fconv,
const H5S_mconv_t *mconv);
__DLL__ hssize_t H5S_select_serial_size(const H5S_t *space);
__DLL__ herr_t H5S_select_serialize(const H5S_t *space, uint8_t *buf);
__DLL__ herr_t H5S_select_deserialize(H5S_t *space, const uint8_t *buf);
__DLL__ htri_t H5S_select_contiguous(const H5S_t *space);
__DLL__ herr_t H5S_select_iterate(void *buf, hid_t type_id, H5S_t *space,
H5D_operator_t op, void *operator_data);
/* Point select functions */
__DLL__ herr_t H5S_point_add(H5S_t *space, H5S_seloper_t op, size_t num_elem,
const hssize_t **coord);
__DLL__ herr_t H5S_point_release(H5S_t *space);
__DLL__ hsize_t H5S_point_npoints(const H5S_t *space);
__DLL__ herr_t H5S_point_copy(H5S_t *dst, const H5S_t *src);
__DLL__ htri_t H5S_point_select_valid(const H5S_t *space);
__DLL__ hssize_t H5S_point_select_serial_size(const H5S_t *space);
__DLL__ herr_t H5S_point_select_serialize(const H5S_t *space, uint8_t *buf);
__DLL__ herr_t H5S_point_select_deserialize(H5S_t *space, const uint8_t *buf);
__DLL__ herr_t H5S_point_bounds(H5S_t *space, hsize_t *start, hsize_t *end);
__DLL__ htri_t H5S_point_select_contiguous(const H5S_t *space);
__DLL__ herr_t H5S_point_select_iterate(void *buf, hid_t type_id, H5S_t *space,
H5D_operator_t op,
void *operator_data);
/* "All" select functions */
__DLL__ herr_t H5S_all_release(H5S_t *space);
__DLL__ hsize_t H5S_all_npoints(const H5S_t *space);
__DLL__ herr_t H5S_all_select_serialize(const H5S_t *space, uint8_t *buf);
__DLL__ herr_t H5S_all_select_deserialize(H5S_t *space, const uint8_t *buf);
__DLL__ herr_t H5S_all_bounds(H5S_t *space, hsize_t *start, hsize_t *end);
__DLL__ herr_t H5S_all_read(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, void *buf/*out*/,
hbool_t *must_convert/*out*/);
__DLL__ herr_t H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, const void *buf,
hbool_t *must_convert/*out*/);
__DLL__ herr_t H5S_all_select_iterate(void *buf, hid_t type_id, H5S_t *space,
H5D_operator_t op, void *operator_data);
/* Hyperslab selection functions */
__DLL__ herr_t H5S_hyper_release(H5S_t *space);
__DLL__ herr_t H5S_hyper_sel_iter_release(H5S_sel_iter_t *sel_iter);
__DLL__ hsize_t H5S_hyper_npoints(const H5S_t *space);
__DLL__ int H5S_hyper_compare_regions(const void *r1, const void *r2);
__DLL__ int H5S_hyper_compare_bounds(const void *r1, const void *r2);
__DLL__ herr_t H5S_hyper_copy(H5S_t *dst, const H5S_t *src);
__DLL__ htri_t H5S_hyper_select_valid(const H5S_t *space);
__DLL__ intn H5S_hyper_bound_comp(const void *_b1, const void *_b2);
__DLL__ herr_t H5S_hyper_node_add(H5S_hyper_node_t **head, intn endflag,
intn rank, const hssize_t *start,
const hsize_t *size);
__DLL__ herr_t H5S_hyper_clip(H5S_t *space, H5S_hyper_node_t *nodes,
H5S_hyper_node_t **uniq,
H5S_hyper_node_t **overlap);
__DLL__ hssize_t H5S_hyper_select_serial_size(const H5S_t *space);
__DLL__ herr_t H5S_hyper_select_serialize(const H5S_t *space, uint8_t *buf);
__DLL__ herr_t H5S_hyper_select_deserialize(H5S_t *space, const uint8_t *buf);
__DLL__ herr_t H5S_hyper_bounds(H5S_t *space, hsize_t *start, hsize_t *end);
__DLL__ htri_t H5S_hyper_select_contiguous(const H5S_t *space);
__DLL__ herr_t H5S_hyper_select_iterate(void *buf, hid_t type_id, H5S_t *space,
H5D_operator_t op, void *operator_data);
/* "None" selection functions */
__DLL__ herr_t H5S_none_select_serialize(const H5S_t *space, uint8_t *buf);
__DLL__ herr_t H5S_none_select_deserialize(H5S_t *space, const uint8_t *buf);
__DLL__ herr_t H5S_none_select_iterate(void *buf, hid_t type_id, H5S_t *space,
H5D_operator_t op, void *operator_data);
#ifdef H5_HAVE_PARALLEL
/* MPI-IO function to read directly from app buffer to file rky980813 */
__DLL__ herr_t H5S_mpio_spaces_read(H5F_t *f,
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, hid_t dxpl_id,
void *buf/*out*/,
hbool_t *must_convert /*out*/ );
/* MPI-IO function to write directly from app buffer to file rky980813 */
__DLL__ herr_t H5S_mpio_spaces_write(H5F_t *f,
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, hid_t dxpl_id,
const void *buf,
hbool_t *must_convert /*out*/ );
#ifndef _H5S_IN_H5S_C
/* Global var whose value comes from environment variable */
__DLLVAR__ hbool_t H5_mpi_opt_types_g;
#endif /* _H5S_IN_H5S_C */
#endif /* H5_HAVE_PARALLEL */
__DLL__ herr_t H5S_sel_iter_release(const H5S_t *space,
H5S_sel_iter_t *sel_iter);
#endif /* _H5Sprivate_H */

4
src/H5Sselect.c
View File

@ -8,12 +8,14 @@
* Purpose: Dataspace functions.
*/
#define H5S_PACKAGE /*suppress error about including H5Spkg */
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5FLprivate.h> /*Free Lists */
#include <H5Iprivate.h>
#include <H5MMprivate.h>
#include <H5Sprivate.h>
#include <H5Spkg.h>
#include <H5Vprivate.h>
/* Interface initialization */

4
src/H5Tconv.c
View File

@ -1813,7 +1813,7 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts,
size_t buf_stride, size_t UNUSED bkg_stride, void *_buf,
void UNUSED *_bkg, hid_t dset_xfer_plist)
{
const H5F_xfer_t *xfer_parms = NULL;
const H5D_xfer_t *xfer_parms = NULL;
H5T_path_t *tpath; /* Type conversion path */
hid_t tsrc_id = -1, tdst_id = -1;/*temporary type atoms */
H5T_t *src = NULL; /*source data type */
@ -1877,7 +1877,7 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts,
/* Get the dataset transfer property list */
if (H5P_DEFAULT == dset_xfer_plist) {
xfer_parms = &H5F_xfer_dflt;
xfer_parms = &H5D_xfer_dflt;
} else if (H5P_DATA_XFER != H5P_get_class(dset_xfer_plist) ||
NULL == (xfer_parms = H5I_object(dset_xfer_plist))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms");

11
src/H5Tpkg.h
View File

@ -24,8 +24,9 @@
#endif
#include <H5HGprivate.h>
#include <H5Dprivate.h>
#include <H5Fprivate.h>
#include <H5Rprivate.h>
#include <H5Rpublic.h> /* Publicly accessible reference information needed also */
#include <H5Tprivate.h>
typedef struct H5T_atomic_t {
@ -88,7 +89,7 @@ typedef struct H5T_enum_t {
/* VL function pointers */
typedef hssize_t (*H5T_vlen_getlenfunc_t)(H5F_t *f, void *vl_addr);
typedef herr_t (*H5T_vlen_readfunc_t)(H5F_t *f, void *vl_addr, void *buf, size_t len);
typedef herr_t (*H5T_vlen_writefunc_t)(const H5F_xfer_t *xfer_parms, H5F_t *f, void *vl_addr, void *buf, hsize_t seq_len, hsize_t base_size);
typedef herr_t (*H5T_vlen_writefunc_t)(const H5D_xfer_t *xfer_parms, H5F_t *f, void *vl_addr, void *buf, hsize_t seq_len, hsize_t base_size);
/* A VL datatype */
typedef struct H5T_vlen_t {
@ -737,13 +738,13 @@ __DLL__ htri_t H5T_bit_inc(uint8_t *buf, size_t start, size_t size);
/* VL functions */
__DLL__ hssize_t H5T_vlen_seq_mem_getlen(H5F_t *f, void *vl_addr);
__DLL__ herr_t H5T_vlen_seq_mem_read(H5F_t *f, void *vl_addr, void *_buf, size_t len);
__DLL__ herr_t H5T_vlen_seq_mem_write(const H5F_xfer_t *xfer_parms, H5F_t *f, void *vl_addr, void *_buf, hsize_t seq_len, hsize_t base_size);
__DLL__ herr_t H5T_vlen_seq_mem_write(const H5D_xfer_t *xfer_parms, H5F_t *f, void *vl_addr, void *_buf, hsize_t seq_len, hsize_t base_size);
__DLL__ hssize_t H5T_vlen_str_mem_getlen(H5F_t *f, void *vl_addr);
__DLL__ herr_t H5T_vlen_str_mem_read(H5F_t *f, void *vl_addr, void *_buf, size_t len);
__DLL__ herr_t H5T_vlen_str_mem_write(const H5F_xfer_t *xfer_parms, H5F_t *f, void *vl_addr, void *_buf, hsize_t seq_len, hsize_t base_size);
__DLL__ herr_t H5T_vlen_str_mem_write(const H5D_xfer_t *xfer_parms, H5F_t *f, void *vl_addr, void *_buf, hsize_t seq_len, hsize_t base_size);
__DLL__ hssize_t H5T_vlen_disk_getlen(H5F_t *f, void *vl_addr);
__DLL__ herr_t H5T_vlen_disk_read(H5F_t *f, void *vl_addr, void *_buf, size_t len);
__DLL__ herr_t H5T_vlen_disk_write(const H5F_xfer_t *xfer_parms, H5F_t *f, void *vl_addr, void *_buf, hsize_t seq_len, hsize_t base_size);
__DLL__ herr_t H5T_vlen_disk_write(const H5D_xfer_t *xfer_parms, H5F_t *f, void *vl_addr, void *_buf, hsize_t seq_len, hsize_t base_size);
/* Reference specific functions */
__DLL__ H5R_type_t H5T_get_ref_type(const H5T_t *dt);

8
src/H5Tvlen.c
View File

@ -206,7 +206,7 @@ herr_t H5T_vlen_seq_mem_read(H5F_t UNUSED *f, void *vl_addr, void *buf, size_t l
*
*-------------------------------------------------------------------------
*/
herr_t H5T_vlen_seq_mem_write(const H5F_xfer_t *xfer_parms, H5F_t UNUSED *f, void *vl_addr, void *buf, hsize_t seq_len, hsize_t base_size)
herr_t H5T_vlen_seq_mem_write(const H5D_xfer_t *xfer_parms, H5F_t UNUSED *f, void *vl_addr, void *buf, hsize_t seq_len, hsize_t base_size)
{
hvl_t *vl=(hvl_t *)vl_addr; /* Pointer to the user's hvl_t information */
size_t len=seq_len*base_size;
@ -308,7 +308,7 @@ herr_t H5T_vlen_str_mem_read(H5F_t UNUSED *f, void *vl_addr, void *buf, size_t l
*
*-------------------------------------------------------------------------
*/
herr_t H5T_vlen_str_mem_write(const H5F_xfer_t *xfer_parms, H5F_t UNUSED *f, void *vl_addr, void *buf, hsize_t seq_len, hsize_t base_size)
herr_t H5T_vlen_str_mem_write(const H5D_xfer_t *xfer_parms, H5F_t UNUSED *f, void *vl_addr, void *buf, hsize_t seq_len, hsize_t base_size)
{
char **s=(char **)vl_addr; /* Pointer to the user's hvl_t information */
size_t len=seq_len*base_size;
@ -421,7 +421,7 @@ herr_t H5T_vlen_disk_read(H5F_t *f, void *vl_addr, void *buf, size_t UNUSED len)
*
*-------------------------------------------------------------------------
*/
herr_t H5T_vlen_disk_write(const H5F_xfer_t UNUSED *xfer_parms, H5F_t *f, void *vl_addr, void *buf, hsize_t seq_len, hsize_t base_size)
herr_t H5T_vlen_disk_write(const H5D_xfer_t UNUSED *xfer_parms, H5F_t *f, void *vl_addr, void *buf, hsize_t seq_len, hsize_t base_size)
{
uint8_t *vl=(uint8_t *)vl_addr; /* Pointer to the user's hvl_t information */
H5HG_t hobjid;
@ -576,7 +576,7 @@ done:
herr_t
H5T_vlen_reclaim(void *elem, hid_t type_id, hsize_t UNUSED ndim, hssize_t UNUSED *point, void *op_data)
{
H5F_xfer_t *xfer_parms = (H5F_xfer_t *)op_data; /* Dataset transfer plist from iterator */
H5D_xfer_t *xfer_parms = (H5D_xfer_t *)op_data; /* Dataset transfer plist from iterator */
H5T_t *dt = NULL;
herr_t ret_value = FAIL;

16
src/Makefile.in
View File

@ -20,14 +20,14 @@ CLEAN=libhdf5.settings
## Source and object files for the library (lexicographically)...
LIB_SRC=H5.c H5A.c H5AC.c H5B.c H5D.c H5E.c H5F.c H5Farray.c H5Fcontig.c \
H5Fistore.c H5FD.c H5FDsec2.c H5FDfamily.c H5FDmpio.c H5FDcore.c H5FDdpss.c \
H5FDmulti.c H5FDgass.c H5FDlog.c H5FDsrb.c H5FDstdio.c H5FDstream.c H5FL.c \
H5G.c H5Gent.c H5Gnode.c H5Gstab.c H5HG.c H5HL.c H5I.c H5MF.c H5MM.c H5O.c \
H5Oattr.c H5Ocomp.c H5Ocont.c H5Odtype.c H5Oefl.c H5Ofill.c H5Olayout.c \
H5Omtime.c H5Oname.c H5Onull.c H5Osdspace.c H5Oshared.c H5Ostab.c H5P.c \
H5R.c H5RA.c H5S.c H5Sall.c H5Shyper.c H5Smpio.c H5Snone.c H5Spoint.c \
H5Sselect.c H5T.c H5Tbit.c H5Tconv.c H5Tinit.c H5Tvlen.c H5TB.c H5TS.c \
H5V.c H5Z.c H5Zdeflate.c
H5Fistore.c H5Fseq.c H5FD.c H5FDsec2.c H5FDfamily.c H5FDmpio.c H5FDcore.c \
H5FDdpss.c H5FDmulti.c H5FDgass.c H5FDlog.c H5FDsrb.c H5FDstdio.c \
H5FDstream.c H5FL.c H5G.c H5Gent.c H5Gnode.c H5Gstab.c H5HG.c H5HL.c H5I.c \
H5MF.c H5MM.c H5O.c H5Oattr.c H5Ocomp.c H5Ocont.c H5Odtype.c H5Oefl.c \
H5Ofill.c H5Olayout.c H5Omtime.c H5Oname.c H5Onull.c H5Osdspace.c \
H5Oshared.c H5Ostab.c H5P.c H5R.c H5RA.c H5S.c H5Sall.c H5Shyper.c \
H5Smpio.c H5Snone.c H5Spoint.c H5Sselect.c H5T.c H5Tbit.c H5Tconv.c \
H5Tinit.c H5Tvlen.c H5TB.c H5TS.c H5V.c H5Z.c H5Zdeflate.c
LIB_OBJ=$(LIB_SRC:.c=.lo)