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/*
* 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 */
H5D_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, H5FD_MEM_DRAW, 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 */
H5D_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() */
|
