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hdf5/src/H5Smpio.c
Albert Cheng a224c0b56d [svn-r2735] Purpose: 
Bug fix
Description:
    Recent changes to H5FD_read() added a new argument of type of
    data to be written but the MPIO file driver call to H5FD_read()
    was not updated.  Also, the prototype of H5FD_read() in H5Fprivate.h
    was "screened out", thus the compiler could not detect the inconsistency.
    With the mismatched arguments, MPIO failed badly.
Solution:
    Update the H5FD_read() call with the new parameter.  Since the
    call is used by H5Dread call so far, it is hardcoded to use
    H5FD_MEM_DRAW as the value.  If the call is used besides for
    H5Dread, this parameter needs to be better defined.
    (Still need to fix the prototype being blocked off.)
Platforms tested:
    O2K -64 parallel.
2000-10-25 00:54:05 -05:00

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/*
* Copyright (C) 1998 NCSA
* All rights reserved.
*
* Programmer: rky 980813
*
* Purpose: Functions to read/write directly between app buffer and file.
*
* Beware of the ifdef'ed print statements.
* I didn't make them portable.
*/
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
#define H5S_PACKAGE /*suppress error about including H5Spkg */
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5Fpkg.h> /* Ugly, but necessary for the MPIO I/O accesses */
#include <H5Spkg.h>
#include <H5FDmpio.h> /*the MPIO file driver */
#ifndef H5_HAVE_PARALLEL
/*
* The H5S_mpio_xxxx functions are for parallel I/O only and are
* valid only when H5_HAVE_PARALLEL is #defined. This empty #ifndef
* body is used to allow this source file be included in the serial
* distribution.
* Some compilers/linkers may complain about "empty" object file.
* If that happens, uncomment the following statement to pacify
* them.
*/
/* const hbool_t H5S_mpio_avail = FALSE; */
#else /* H5_HAVE_PARALLEL */
/* Interface initialization */
#define PABLO_MASK H5Sall_mask
#define INTERFACE_INIT NULL
static intn interface_initialize_g = 0;
static herr_t
H5S_mpio_all_type( const H5S_t *space, const size_t elmt_size,
/* out: */
MPI_Datatype *new_type,
hsize_t *count,
hbool_t *is_derived_type );
static herr_t
H5S_mpio_hyper_type( const H5S_t *space, const size_t elmt_size,
/* out: */
MPI_Datatype *new_type,
hsize_t *count,
hbool_t *is_derived_type );
static herr_t
H5S_mpio_space_type( const H5S_t *space, const size_t elmt_size,
/* out: */
MPI_Datatype *new_type,
hsize_t *count,
hbool_t *is_derived_type );
static herr_t
H5S_mpio_spaces_xfer(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t UNUSED *pline,
const struct H5O_efl_t UNUSED *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*/, const hbool_t do_write);
/*-------------------------------------------------------------------------
* Function: H5S_mpio_all_type
*
* Purpose: Translate an HDF5 "all" selection into an MPI type.
*
* Return: non-negative on success, negative on failure.
*
* Outputs: *new_type the MPI type corresponding to the selection
* *count how many objects of the new_type in selection
* (useful if this is the buffer type for xfer)
* *is_derived_type 0 if MPI primitive type, 1 if derived
*
* Programmer: rky 980813
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5S_mpio_all_type( const H5S_t *space, const size_t elmt_size,
/* out: */
MPI_Datatype *new_type,
hsize_t *count,
hbool_t *is_derived_type )
{
hsize_t total_bytes;
int i;
FUNC_ENTER (H5S_mpio_all_type, FAIL);
/* Check args */
assert (space);
/* Just treat the entire extent as a block of bytes */
total_bytes = (hsize_t)elmt_size;
for (i=0; i<space->extent.u.simple.rank; ++i) {
total_bytes *= space->extent.u.simple.size[i];
}
/* fill in the return values */
*new_type = MPI_BYTE;
*count = total_bytes;
*is_derived_type = 0;
#ifdef H5Smpi_DEBUG
fprintf(stdout, "Leave %s total_bytes=%Hu\n", FUNC, total_bytes );
#endif
FUNC_LEAVE (SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5S_mpio_hyper_type
*
* Purpose: Translate an HDF5 hyperslab selection into an MPI type.
*
* Return: non-negative on success, negative on failure.
*
* Outputs: *new_type the MPI type corresponding to the selection
* *count how many objects of the new_type in selection
* (useful if this is the buffer type for xfer)
* *is_derived_type 0 if MPI primitive type, 1 if derived
*
* Programmer: rky 980813
*
* Modifications: ppw 990401
* rky, ppw 2000-09-26 Freed old type after creating struct type.
* rky 2000-10-05 Changed displacements to be MPI_Aint.
* rky 2000-10-06 Added code for cases of empty hyperslab.
*
*-------------------------------------------------------------------------
*/
herr_t
H5S_mpio_hyper_type( const H5S_t *space, const size_t elmt_size,
/* out: */
MPI_Datatype *new_type,
hsize_t *count,
hbool_t *is_derived_type )
{
struct dim { /* less hassle than malloc/free & ilk */
hssize_t start;
hsize_t strid;
hsize_t block;
hsize_t xtent;
hsize_t count;
} d[32];
int i, err, new_rank, num_to_collapse;
int offset[32], max_xtent[32], block_length[2];
H5S_hyper_dim_t *diminfo; /* [rank] */
intn rank;
MPI_Datatype inner_type, outer_type, old_type[32];
MPI_Aint extent_len, displacement[2];
FUNC_ENTER (H5S_mpio_hyper_type, FAIL);
/* Check and abbreviate args */
assert (space);
assert(sizeof(MPI_Aint) >= sizeof(elmt_size));
diminfo = space->select.sel_info.hslab.diminfo;
assert (diminfo);
rank = space->extent.u.simple.rank;
assert (rank >= 0);
if (0==rank) goto empty;
if (0==elmt_size) goto empty;
/* make a local copy of the dimension info so we can transform them */
assert(rank<=32); /* within array bounds */
for ( i=0; i<rank; ++i) {
d[i].start = diminfo[i].start;
d[i].strid = diminfo[i].stride;
d[i].block = diminfo[i].block;
d[i].count = diminfo[i].count;
d[i].xtent = space->extent.u.simple.size[i];
#ifdef H5Smpi_DEBUG
HDfprintf(stdout, "hyper_type: start=%Hd stride=%Hu count=%Hu "
"block=%Hu xtent=%Hu",
d[i].start, d[i].strid, d[i].count, d[i].block, d[i].xtent );
if (i==0) fprintf(stdout, " rank=%d\n", rank );
else fprintf(stdout, "\n" );
#endif
if (0==d[i].block) goto empty;
if (0==d[i].count) goto empty;
if (0==d[i].xtent) goto empty;
}
/**********************************************************************
Compute array "offset[rank]" which gives the offsets for a multi-
dimensional array with dimensions "d[i].xtent" (i=0,1,...,rank-1).
**********************************************************************/
offset[rank-1] = 1;
max_xtent[rank-1] = d[rank-1].xtent;
#ifdef H5Smpi_DEBUG
i=rank-1;
fprintf(stdout, " offset[%2d]=%d; max_xtent[%2d]=%d\n",
i, offset[i], i, max_xtent[i]);
#endif
for (i=rank-2; i>=0; --i) {
offset[i] = offset[i+1]*d[i+1].xtent;
max_xtent[i] = max_xtent[i+1]*d[i].xtent;
#ifdef H5Smpi_DEBUG
fprintf(stdout, " offset[%2d]=%d; max_xtent[%2d]=%d\n",
i, offset[i], i, max_xtent[i]);
#endif
}
/* Create a type covering the selected hyperslab.
* Multidimensional dataspaces are stored in row-major order.
* The type is built from the inside out, going from the
* fastest-changing (i.e., inner) dimension * to the slowest (outer). */
/* Optimization: check for contiguous inner dimensions.
* Supposing the dimensions were numbered from 1 to rank, we find that
*
* dim d=rank is contiguous if:
* stride[d] = block[d]
* and count[d] * block[d] = extent.u.simple.size[d]
*
* (i.e., there's no overlap or gaps and the entire extent is filled.)
*
* dim d (1<=d<rank) is contiguous if:
* dim d+1 is contiguous
* and stride[d] = block[d]
* and count[d] * block[d] = extent.u.simple.size[d]
*
* There is also a weak sense in which the first noncollapsible dim
* is contiguous if it consists of a single unbroken range,
* and we also take advantage of that.
*/
/* figure out how many dimensions we can eliminate */
/* This loop examines contiguity from the inside out. */
for ( i=0; i<rank; ++i) {
if ((d[rank-i-1].strid != d[rank-i-1].block)
||
(d[rank-i-1].count*d[rank-i-1].block) != space->extent.u.simple.size[rank-i-1]) {
break;
}
} /* end for */
num_to_collapse = i;
if (num_to_collapse == rank) num_to_collapse--;
assert(0<=num_to_collapse && num_to_collapse<rank);
new_rank = rank - num_to_collapse;
#ifdef H5Smpi_DEBUG
fprintf(stdout, "num_to_collapse=%d\n", num_to_collapse);
fprintf(stdout, "hyper_type: new_rank=%d\n", new_rank );
#endif
/* To collapse dims, just transform dimension info (from inner to outer) */
/* must multiply r.h.s. by "count" --- ppw 03/11/99 */
for (i=rank-1; i>=new_rank; --i) {
d[i-1].block *= d[i].count * d[i].block;
d[i-1].strid *= d[i].count * d[i].block;
d[i-1].xtent *= d[i].count * d[i].block;
assert( d[i].start == 0 );
/* d[i-1].start stays unchanged */
/* d[i-1].count stays unchanged */
}
/* check for possibility to coalesce blocks of the uncoalesced dimensions */
for (i=0; i<new_rank; ++i) {
if (d[i].strid == d[i].block) {
/* transform smaller blocks to 1 larger block of combined size */
d[i].strid = d[i].block *= d[i].count;
d[i].count = 1;
}
}
/*******************************************************
* Construct contig type for inner contig dims:
*******************************************************/
#ifdef H5Smpi_DEBUG
fprintf(stdout, "hyper_type: Making contig type %d MPI_BYTEs\n", elmt_size );
for (i=new_rank-1; i>=0; --i) {
HDfprintf(stdout, "d[%d].xtent=%Hu \n", i, d[i].xtent);
}
#endif
err = MPI_Type_contiguous( (int)elmt_size, MPI_BYTE, &inner_type );
if (err) {
HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL,"couldn't create MPI contiguous type");
}
/*******************************************************
* Construct the type by walking the hyperslab dims
* from the inside out:
*******************************************************/
for ( i=new_rank-1; i>=0; --i) {
#ifdef H5Smpi_DEBUG
HDfprintf(stdout, "hyper_type: Dimension i=%d \n"
"count=%Hu block=%Hu stride=%Hu\n",
i, d[i].count, d[i].block, d[i].strid );
#endif
#ifdef H5Smpi_DEBUG
HDfprintf(stdout, "hyper_type: i=%d Making vector-type \n", i);
#endif
/****************************************
* Build vector in current dimension:
****************************************/
err = MPI_Type_vector ( (int)(d[i].count), /* count */
(int)(d[i].block), /* blocklength */
(MPI_Aint)(d[i].strid), /* stride */
inner_type, /* old type */
&outer_type ); /* new type */
MPI_Type_free( &inner_type );
if (err) {
HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL,"couldn't create MPI vector type");
}
displacement[1] = elmt_size * max_xtent[i];
err = MPI_Type_extent(outer_type, &extent_len);
/*************************************************
* Restructure this datatype ("outer_type")
* so that it still starts at 0, but its extent
* is the full extent in this dimension.
*************************************************/
if ((int)extent_len < displacement[1]) {
#ifdef H5Smpi_DEBUG
HDfprintf(stdout, "hyper_type: i=%d Extending struct type\n"
"***displacements: 0, %d\n", i, displacement[1]);
#endif
#ifdef HAVE_MPI2 /* have MPI-2 */
err = MPI_Type_create_resized
( outer_type, /* old type */
0, /* blocklengths */
displacement[1], /* displacements */
&inner_type); /* new type */
#else /* do not have MPI-2 */
block_length[0] = 1;
block_length[1] = 1;
displacement[0] = 0;
old_type[0] = outer_type;
old_type[1] = MPI_UB;
#ifdef H5Smpi_DEBUG
HDfprintf(stdout, "hyper_type: i=%d Extending struct type\n"
"***displacements: 0, %d\n", i, displacement[1]);
#endif
err = MPI_Type_struct ( 2, /* count */
block_length, /* blocklengths */
displacement, /* displacements */
old_type, /* old types */
&inner_type); /* new type */
#endif
MPI_Type_free (&outer_type);
if (err) {
HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL,"couldn't resize MPI vector type");
}
}
else {
inner_type = outer_type;
}
} /* end for */
/***************************
* End of loop, walking
* thru dimensions.
***************************/
/* At this point inner_type is actually the outermost type, even for 0-trip loop */
/***************************************************************
* Final task: create a struct which is a "clone" of the
* current struct, but displaced according to the d[i].start
* values given in the hyperslab description:
***************************************************************/
displacement[0] = 0;
for (i=new_rank-1; i>=0; i--)
displacement[0] += d[i].start * offset[i];
if (displacement[0] > 0) {
displacement[0] *= elmt_size;
block_length[0] = 1;
old_type[0] = inner_type;
#ifdef H5Smpi_DEBUG
HDfprintf(stdout, "hyper_type: Making final struct\n"
"***count=1:\n");
HDfprintf(stdout, "\tblocklength[0]=%d; displacement[0]=%d\n",
block_length[0], displacement[0]);
#endif
err = MPI_Type_struct( 1, /* count */
block_length, /* blocklengths */
displacement, /* displacements */
old_type, /* old type */
new_type ); /* new type */
if (err) {
HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL,"couldn't create MPI struct type");
}
MPI_Type_free (&old_type[0]);
if (err) {
HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL,"couldn't resize MPI vector type");
}
}
else {
*new_type = inner_type;
}
err = MPI_Type_commit( new_type );
if (err) {
HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL,"couldn't commit MPI vector type");
}
/* fill in the remaining return values */
*count = 1; /* only have to move one of these suckers! */
*is_derived_type = 1;
goto done;
empty:
/* special case: empty hyperslab */
*new_type = MPI_BYTE;
*count = 0;
*is_derived_type = 0;
done:
#ifdef H5Smpi_DEBUG
HDfprintf(stdout, "Leave %s, count=%Hu is_derived_type=%d\n",
FUNC, *count, *is_derived_type );
#endif
FUNC_LEAVE (SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5S_mpio_space_type
*
* Purpose: Translate an HDF5 dataspace selection into an MPI type.
* Currently handle only hyperslab and "all" selections.
*
* Return: non-negative on success, negative on failure.
*
* Outputs: *new_type the MPI type corresponding to the selection
* *count how many objects of the new_type in selection
* (useful if this is the buffer type for xfer)
* *is_derived_type 0 if MPI primitive type, 1 if derived
*
* Programmer: rky 980813
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5S_mpio_space_type( const H5S_t *space, const size_t elmt_size,
/* out: */
MPI_Datatype *new_type,
hsize_t *count,
hbool_t *is_derived_type )
{
int err;
herr_t ret_value = SUCCEED;
FUNC_ENTER (H5S_mpio_space_type, FAIL);
/* Check args */
assert (space);
/* Creat MPI type based on the kind of selection */
switch (space->extent.type) {
case H5S_SCALAR:
/* not yet implemented */
ret_value = FAIL;
break;
case H5S_SIMPLE:
switch(space->select.type) {
case H5S_SEL_NONE:
case H5S_SEL_ALL:
err = H5S_mpio_all_type( space, elmt_size,
/* out: */ new_type, count, is_derived_type );
if (err<0) {
HRETURN_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type");
}
break;
case H5S_SEL_POINTS:
/* not yet implemented */
ret_value = FAIL;
break;
case H5S_SEL_HYPERSLABS:
err = H5S_mpio_hyper_type( space, elmt_size,
/* out: */ new_type, count, is_derived_type );
if (err) {
HRETURN_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type");
}
break;
default:
assert("unknown selection type" && 0);
break;
} /* end switch */
break;
case H5S_COMPLEX:
/* not yet implemented */
ret_value = FAIL;
break;
default:
assert("unknown data space type" && 0);
break;
}
FUNC_LEAVE (ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5S_mpio_spaces_xfer
*
* Purpose: Use MPI-IO to transfer data efficiently
* directly between app buffer and file.
*
* Return: non-negative on success, negative on failure.
*
* Programmer: rky 980813
*
* Modifications:
*
* rky 980918
* Added must_convert parameter to let caller know we can't optimize the xfer.
*
*-------------------------------------------------------------------------
*/
herr_t
H5S_mpio_spaces_xfer(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t UNUSED *pline,
const struct H5O_efl_t UNUSED *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*/,
const hbool_t do_write )
{
herr_t ret_value = SUCCEED;
int err;
haddr_t disp, addr;
size_t mpi_count;
hsize_t mpi_buf_count, mpi_unused_count;
MPI_Datatype mpi_buf_type, mpi_file_type;
hbool_t mbt_is_derived, mft_is_derived;
FUNC_ENTER (H5S_mpio_spaces_xfer, FAIL);
*must_convert = 0; /* means we at least tried to do optimized xfer */
/* Check args */
assert (f);
assert (layout);
assert (file_space);
assert (mem_space);
assert (buf);
assert (IS_H5FD_MPIO(f));
/* INCOMPLETE!!! rky 980816 */
/* Currently can only handle H5D_CONTIGUOUS layout */
if (layout->type != H5D_CONTIGUOUS) {
#ifdef H5S_DEBUG
if (H5DEBUG(S)) {
fprintf (H5DEBUG(S), "H5S: can only create MPI datatype for hyperslab when layout is contiguous.\n" );
}
#endif
*must_convert = 1; /* can't do optimized xfer; do the old way */
goto done;
}
/* create the MPI buffer type */
err = H5S_mpio_space_type( mem_space, elmt_size,
/* out: */
&mpi_buf_type,
&mpi_buf_count,
&mbt_is_derived );
if (MPI_SUCCESS != err)
HRETURN_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't create MPI buf type");
/* create the MPI file type */
err = H5S_mpio_space_type( file_space, elmt_size,
/* out: */
&mpi_file_type,
&mpi_unused_count,
&mft_is_derived );
if (MPI_SUCCESS != err)
HRETURN_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't create MPI file type");
/* calculate the absolute base addr (i.e., the file view disp) */
disp = f->shared->base_addr + layout->addr;
#ifdef H5Smpi_DEBUG
HDfprintf(stdout, "spaces_xfer: disp=%Hu\n", disp );
#endif
/* Effective address determined by base addr and the MPI file type */
addr = 0;
/*
* Pass buf type, file type, and absolute base address (i.e., the file
* view disp) to the file driver. Request a dataspace transfer (instead
* of an elementary byteblock transfer).
*/
H5FD_mpio_setup(f->shared->lf, mpi_buf_type, mpi_file_type, disp, 1);
/* transfer the data */
mpi_count = (size_t)mpi_buf_count;
if (mpi_count != mpi_buf_count) {
HRETURN_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,
"transfer size overflows size_t");
}
if (do_write) {
err = H5FD_write(f->shared->lf, H5FD_MEM_DRAW, dxpl_id, addr, mpi_count, buf);
if (err) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,"MPI write failed");
}
} else {
err = H5FD_read (f->shared->lf, H5FD_MEM_DRAW, dxpl_id, addr, mpi_count, buf);
if (err) {
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,"MPI read failed");
}
}
/* free the MPI buf and file types */
if (mbt_is_derived) {
err = MPI_Type_free( &mpi_buf_type );
if (MPI_SUCCESS != err) {
HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL,
"unable to free MPI file type");
}
}
if (mft_is_derived) {
err = MPI_Type_free( &mpi_file_type );
if (MPI_SUCCESS != err) {
HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL,
"unable to free MPI file type");
}
}
done:
FUNC_LEAVE (ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5S_mpio_spaces_read
*
* Purpose: MPI-IO function to read directly from app buffer to file.
*
* Return: non-negative on success, negative on failure.
*
* Programmer: rky 980813
*
* Modifications:
*
* rky 980918
* Added must_convert parameter to let caller know we can't optimize the xfer.
*
*-------------------------------------------------------------------------
*/
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*/)
{
herr_t ret_value = FAIL;
FUNC_ENTER (H5S_mpio_spaces_read, FAIL);
ret_value = H5S_mpio_spaces_xfer(f, layout, pline, efl, elmt_size,
file_space, mem_space, dxpl_id,
buf, must_convert/*out*/, 0/*read*/);
FUNC_LEAVE (ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5S_mpio_spaces_write
*
* Purpose: MPI-IO function to write directly from app buffer to file.
*
* Return: non-negative on success, negative on failure.
*
* Programmer: rky 980813
*
* Modifications:
*
* rky 980918
* Added must_convert parameter to let caller know we can't optimize the xfer.
*
*-------------------------------------------------------------------------
*/
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*/)
{
herr_t ret_value = FAIL;
FUNC_ENTER (H5S_mpio_spaces_write, FAIL);
ret_value = H5S_mpio_spaces_xfer(f, layout, pline, efl, elmt_size,
file_space, mem_space, dxpl_id,
(void*)buf, must_convert/*out*/,
1/*write*/);
FUNC_LEAVE (ret_value);
}
#endif /* H5_HAVE_PARALLEL */
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