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[svn-r11235] Purpose:

Browse Source 
Code cleanup

Description:
    Refactor, simplify and cleanup Kent's recent checking for collective
chunk I/O.  There's a bug that I need to talk to Kent about and some more
cleanups still, but this is reasonable for an interim point.

Platforms tested:
    FreeBSD 4.11 (sleipnir) w/parallel
    Too minor for h5committest
This commit is contained in:
Quincey Koziol 2005-08-12 10:53:55 -05:00
parent 1af1bd5fb3
commit 1ba06a8395
4 changed files with 421 additions and 516 deletions
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823
src/H5Dio.c
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File diff suppressed because it is too large Load Diff

28
src/H5Dmpio.c
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@ -40,7 +40,7 @@
static herr_t static herr_t
H5D_mpio_spaces_xfer(H5D_io_info_t *io_info, size_t elmt_size, H5D_mpio_spaces_xfer(H5D_io_info_t *io_info, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space, const H5S_t *file_space, const H5S_t *mem_space,
void *buf/*out*/, void *buf/*out*/,
hbool_t do_write); hbool_t do_write);
@ -60,7 +60,6 @@ H5D_mpio_spaces_xfer(H5D_io_info_t *io_info, size_t elmt_size,
* *
*------------------------------------------------------------------------- *-------------------------------------------------------------------------
*/ */
htri_t htri_t
H5D_mpio_opt_possible( const H5D_t *dset, const H5S_t *mem_space, const H5S_t *file_space, const unsigned flags) H5D_mpio_opt_possible( const H5D_t *dset, const H5S_t *mem_space, const H5S_t *file_space, const unsigned flags)
{ {
@ -88,16 +87,16 @@ H5D_mpio_opt_possible( const H5D_t *dset, const H5S_t *mem_space, const H5S_t *f
HGOTO_DONE(FALSE); HGOTO_DONE(FALSE);
/* Dataset storage must be contiguous or chunked */ /* Dataset storage must be contiguous or chunked */
if ((flags&H5S_CONV_STORAGE_MASK)!=H5S_CONV_STORAGE_CONTIGUOUS && if ((flags&H5S_CONV_STORAGE_MASK)!=H5S_CONV_STORAGE_CONTIGUOUS &&
(flags&H5S_CONV_STORAGE_MASK)!=H5S_CONV_STORAGE_CHUNKED) (flags&H5S_CONV_STORAGE_MASK)!=H5S_CONV_STORAGE_CHUNKED)
HGOTO_DONE(FALSE); HGOTO_DONE(FALSE);
/*The handling of memory space is different for chunking /*The handling of memory space is different for chunking
and contiguous storage, and contiguous storage,
For contigous storage, mem_space and file_space won't For contigous storage, mem_space and file_space won't
change when it it is doing disk IO. change when it it is doing disk IO.
For chunking storage, mem_space will change for different For chunking storage, mem_space will change for different
chunks. So for chunking storage, whether we can use chunks. So for chunking storage, whether we can use
collective IO will defer until the each chunk IO is reached. collective IO will defer until the each chunk IO is reached.
For contiguous storage, if we find the MPI-IO cannot For contiguous storage, if we find the MPI-IO cannot
support complicated MPI derived data type, we will support complicated MPI derived data type, we will
@ -111,16 +110,13 @@ H5D_mpio_opt_possible( const H5D_t *dset, const H5S_t *mem_space, const H5S_t *f
HGOTO_DONE(FALSE); HGOTO_DONE(FALSE);
#endif #endif
} }
if(dset->shared->layout.type == H5D_CHUNKED)
if(dset->shared->dcpl_cache.pline.nused>0)
HGOTO_DONE(FALSE); /* Perform the independent write operation */
if(dset->shared->layout.type == H5D_CHUNKED)
if(dset->shared->dcpl_cache.pline.nused>0)
HGOTO_DONE(FALSE); /* Perform the independent write operation */
done: done:
FUNC_LEAVE_NOAPI(ret_value); FUNC_LEAVE_NOAPI(ret_value);
} /* H5D_mpio_opt_possible() */ } /* H5D_mpio_opt_possible() */
@ -219,7 +215,7 @@ H5D_mpio_spaces_xfer(H5D_io_info_t *io_info, size_t elmt_size,
else { else {
haddr_t chunk_addr; /* for collective chunk IO */ haddr_t chunk_addr; /* for collective chunk IO */
assert(io_info->dset->shared->layout.type == H5D_CHUNKED); assert(io_info->dset->shared->layout.type == H5D_CHUNKED);
chunk_addr=H5D_istore_get_addr(io_info,NULL); chunk_addr=H5D_istore_get_addr(io_info,NULL);
addr = H5F_BASE_ADDR(io_info->dset->ent.file) + chunk_addr + mpi_file_offset; addr = H5F_BASE_ADDR(io_info->dset->ent.file) + chunk_addr + mpi_file_offset;
} }
@ -288,8 +284,7 @@ H5D_mpio_select_read(H5D_io_info_t *io_info,
FUNC_ENTER_NOAPI_NOFUNC(H5D_mpio_select_read); FUNC_ENTER_NOAPI_NOFUNC(H5D_mpio_select_read);
ret_value = H5D_mpio_spaces_xfer(io_info, elmt_size, file_space,
ret_value = H5D_mpio_spaces_xfer(io_info, elmt_size, file_space,
mem_space, buf, 0/*read*/); mem_space, buf, 0/*read*/);
FUNC_LEAVE_NOAPI(ret_value); FUNC_LEAVE_NOAPI(ret_value);
@ -321,11 +316,10 @@ H5D_mpio_select_write(H5D_io_info_t *io_info,
FUNC_ENTER_NOAPI_NOFUNC(H5D_mpio_select_write); FUNC_ENTER_NOAPI_NOFUNC(H5D_mpio_select_write);
/*OKAY: CAST DISCARDS CONST QUALIFIER*/ /*OKAY: CAST DISCARDS CONST QUALIFIER*/
ret_value = H5D_mpio_spaces_xfer(io_info, elmt_size, file_space, ret_value = H5D_mpio_spaces_xfer(io_info, elmt_size, file_space,
mem_space, (void*)buf, 1/*write*/); mem_space, (void*)buf, 1/*write*/);
FUNC_LEAVE_NOAPI(ret_value); FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_mpio_spaces_write() */ } /* end H5D_mpio_spaces_write() */
#endif /* H5_HAVE_PARALLEL */ #endif /* H5_HAVE_PARALLEL */

8
src/H5Dpkg.h
View File

@ -233,12 +233,12 @@ H5_DLL ssize_t H5D_contig_writevv(const H5D_io_info_t *io_info,
/* Functions that operate on compact dataset storage */ /* Functions that operate on compact dataset storage */
H5_DLL ssize_t H5D_compact_readvv(const H5D_io_info_t *io_info, H5_DLL ssize_t H5D_compact_readvv(const H5D_io_info_t *io_info,
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_size_arr[], hsize_t dset_offset_arr[], size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_size_arr[], hsize_t dset_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[], size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[],
void *buf); void *buf);
H5_DLL ssize_t H5D_compact_writevv(const H5D_io_info_t *io_info, H5_DLL ssize_t H5D_compact_writevv(const H5D_io_info_t *io_info,
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_size_arr[], hsize_t dset_offset_arr[], size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_size_arr[], hsize_t dset_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[], size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[],
const void *buf); const void *buf);
/* Functions that operate on indexed storage */ /* Functions that operate on indexed storage */

78
src/H5Smpio.c
View File

@ -66,7 +66,7 @@ H5S_mpio_span_hyper_type( const H5S_t *space, size_t elmt_size,
hsize_t *extra_offset, hsize_t *extra_offset,
hbool_t *is_derived_type ); hbool_t *is_derived_type );
static herr_t H5S_obtain_datatype(const hsize_t size[], static herr_t H5S_obtain_datatype(const hsize_t size[],
H5S_hyper_span_t* span,MPI_Datatype *span_type, H5S_hyper_span_t* span,MPI_Datatype *span_type,
size_t elmt_size,int dimindex); size_t elmt_size,int dimindex);
@ -314,10 +314,10 @@ H5S_mpio_hyper_type( const H5S_t *space, size_t elmt_size,
goto empty; goto empty;
} }
} /* end else */ } /* end else */
/********************************************************************** /**********************************************************************
Compute array "offset[rank]" which gives the offsets for a multi- Compute array "offset[rank]" which gives the offsets for a multi-
dimensional array with dimensions "d[i].xtent" (i=0,1,...,rank-1). dimensional array with dimensions "d[i].xtent" (i=0,1,...,rank-1).
**********************************************************************/ **********************************************************************/
offset[rank-1] = 1; offset[rank-1] = 1;
max_xtent[rank-1] = d[rank-1].xtent; max_xtent[rank-1] = d[rank-1].xtent;
@ -397,9 +397,9 @@ H5S_mpio_hyper_type( const H5S_t *space, size_t elmt_size,
block_length[0] = 1; block_length[0] = 1;
block_length[1] = 1; block_length[1] = 1;
block_length[2] = 1; block_length[2] = 1;
displacement[0] = 0; displacement[0] = 0;
old_types[0] = MPI_LB; old_types[0] = MPI_LB;
old_types[1] = outer_type; old_types[1] = outer_type;
old_types[2] = MPI_UB; old_types[2] = MPI_UB;
@ -414,7 +414,7 @@ H5S_mpio_hyper_type( const H5S_t *space, size_t elmt_size,
displacement, /* displacements */ displacement, /* displacements */
old_types, /* old types */ old_types, /* old types */
&inner_type); /* new type */ &inner_type); /* new type */
MPI_Type_free (&outer_type); MPI_Type_free (&outer_type);
if (mpi_code!=MPI_SUCCESS) if (mpi_code!=MPI_SUCCESS)
HMPI_GOTO_ERROR(FAIL, "couldn't resize MPI vector type", mpi_code); HMPI_GOTO_ERROR(FAIL, "couldn't resize MPI vector type", mpi_code);
@ -424,7 +424,7 @@ H5S_mpio_hyper_type( const H5S_t *space, size_t elmt_size,
} }
} /* end for */ } /* end for */
/*************************** /***************************
* End of loop, walking * End of loop, walking
* thru dimensions. * thru dimensions.
***************************/ ***************************/
@ -469,7 +469,7 @@ done:
/*------------------------------------------------------------------------- /*-------------------------------------------------------------------------
* Function: H5S_mpio_span_hyper_type * Function: H5S_mpio_span_hyper_type
* *
* Purpose: Translate an HDF5 irregular hyperslab selection into an * Purpose: Translate an HDF5 irregular hyperslab selection into an
MPI type. MPI type.
* *
* Return: non-negative on success, negative on failure. * Return: non-negative on success, negative on failure.
@ -482,9 +482,9 @@ done:
* *
* Programmer: kyang * Programmer: kyang
* *
*/ */
static herr_t static herr_t
H5S_mpio_span_hyper_type( const H5S_t *space, H5S_mpio_span_hyper_type( const H5S_t *space,
size_t elmt_size, size_t elmt_size,
MPI_Datatype *new_type,/* out: */ MPI_Datatype *new_type,/* out: */
size_t *count, size_t *count,
@ -499,26 +499,26 @@ H5S_mpio_span_hyper_type( const H5S_t *space,
herr_t ret_value = SUCCEED; herr_t ret_value = SUCCEED;
MPI_Aint extent,lb; MPI_Aint extent,lb;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5S_mpio_span_hyper_type); FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5S_mpio_span_hyper_type);
/* Check args */ /* Check args */
assert (space); assert (space);
/* assert(sizeof(MPI_Aint) >= sizeof(elmt_size)); not sure the reason*/ /* assert(sizeof(MPI_Aint) >= sizeof(elmt_size)); not sure the reason*/
rank = space->extent.rank; rank = space->extent.rank;
/* size = HDcalloc((size_t)rank,sizeof(hsize_t)); */ /* size = HDcalloc((size_t)rank,sizeof(hsize_t)); */
if (0==elmt_size) if (0==elmt_size)
goto empty; goto empty;
size = space->extent.size; size = space->extent.size;
if(size == 0) if(size == 0)
goto empty; goto empty;
odown = space->select.sel_info.hslab->span_lst; odown = space->select.sel_info.hslab->span_lst;
if(odown == NULL) if(odown == NULL)
goto empty; goto empty;
ospan = odown->head; ospan = odown->head;
if(ospan == NULL) if(ospan == NULL)
@ -527,13 +527,13 @@ H5S_mpio_span_hyper_type( const H5S_t *space,
/* obtain derived data type */ /* obtain derived data type */
H5S_obtain_datatype(space->extent.size,ospan,&span_type,elmt_size,rank); H5S_obtain_datatype(space->extent.size,ospan,&span_type,elmt_size,rank);
MPI_Type_commit(&span_type); MPI_Type_commit(&span_type);
*new_type = span_type; *new_type = span_type;
/* fill in the remaining return values */ /* fill in the remaining return values */
*count = 1; *count = 1;
*extra_offset = 0; *extra_offset = 0;
*is_derived_type = 1; *is_derived_type = 1;
HGOTO_DONE(SUCCEED); HGOTO_DONE(SUCCEED);
empty: empty:
@ -551,8 +551,8 @@ done:
/*------------------------------------------------------------------------- /*-------------------------------------------------------------------------
* Function: obtain datatype * Function: obtain datatype
* *
* Purpose: Obtain an MPI derived datatype based on span-tree * Purpose: Obtain an MPI derived datatype based on span-tree
implementation implementation
* *
* Return: non-negative on success, negative on failure. * Return: non-negative on success, negative on failure.
* *
@ -560,13 +560,13 @@ done:
* *
* Programmer: kyang * Programmer: kyang
* *
*/ */
static herr_t H5S_obtain_datatype(const hsize_t size[], static herr_t H5S_obtain_datatype(const hsize_t size[],
H5S_hyper_span_t* span, H5S_hyper_span_t* span,
MPI_Datatype *span_type, MPI_Datatype *span_type,
size_t elmt_size, size_t elmt_size,
int dimindex) { int dimindex)
{
int innercount,outercount; int innercount,outercount;
MPI_Datatype bas_type; MPI_Datatype bas_type;
MPI_Datatype temp_type; MPI_Datatype temp_type;
@ -579,7 +579,7 @@ static herr_t H5S_obtain_datatype(const hsize_t size[],
H5S_hyper_span_info_t *down; H5S_hyper_span_info_t *down;
H5S_hyper_span_t *tspan; H5S_hyper_span_t *tspan;
int mpi_code; int mpi_code;
herr_t ret_value; herr_t ret_value = SUCCEED;
#ifdef H5_HAVE_MPI2 #ifdef H5_HAVE_MPI2
MPI_Aint sizeaint,sizedtype; MPI_Aint sizeaint,sizedtype;
@ -587,10 +587,10 @@ static herr_t H5S_obtain_datatype(const hsize_t size[],
hsize_t total_lowd,total_lowd1; hsize_t total_lowd,total_lowd1;
int i; int i;
int ret; int ret;
FUNC_ENTER_NOAPI_NOINIT(H5S_obtain_datatype); FUNC_ENTER_NOAPI_NOINIT(H5S_obtain_datatype);
ret_value = SUCCEED;
assert(span); assert(span);
inner_type = NULL; inner_type = NULL;
down = NULL; down = NULL;
tspan = NULL; tspan = NULL;
@ -625,8 +625,8 @@ static herr_t H5S_obtain_datatype(const hsize_t size[],
inner_type = (MPI_Datatype *)HDcalloc((size_t)outercount,sizeof(int)); inner_type = (MPI_Datatype *)HDcalloc((size_t)outercount,sizeof(int));
#endif #endif
tspan = span; tspan = span;
outercount = 0; outercount = 0;
@ -650,7 +650,7 @@ static herr_t H5S_obtain_datatype(const hsize_t size[],
if(MPI_SUCCESS != (mpi_code = MPI_Type_hindexed(outercount,blocklen, if(MPI_SUCCESS != (mpi_code = MPI_Type_hindexed(outercount,blocklen,
disp,bas_type,span_type))) disp,bas_type,span_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_hindexed failed", mpi_code); HMPI_GOTO_ERROR(FAIL, "MPI_Type_hindexed failed", mpi_code);
} }
else {/* dimindex is the rank of the dimension */ else {/* dimindex is the rank of the dimension */
@ -664,9 +664,9 @@ static herr_t H5S_obtain_datatype(const hsize_t size[],
for ( i = dimindex-1; i > 1; i--) for ( i = dimindex-1; i > 1; i--)
total_lowd1 = total_lowd1 * size[i]; total_lowd1 = total_lowd1 * size[i];
while(tspan){ while(tspan){
/* Displacement should be in byte and should have dimension information */ /* Displacement should be in byte and should have dimension information */
/* First using MPI Type vector to build derived data type for this span only */ /* First using MPI Type vector to build derived data type for this span only */
/* Need to calculate the disp in byte for this dimension. */ /* Need to calculate the disp in byte for this dimension. */
@ -676,7 +676,7 @@ static herr_t H5S_obtain_datatype(const hsize_t size[],
blocklen[outercount] = 1; blocklen[outercount] = 1;
/* generating inner derived datatype by using MPI_Type_hvector */ /* generating inner derived datatype by using MPI_Type_hvector */
if(FAIL == H5S_obtain_datatype(size,tspan->down->head,&temp_type,elmt_size,dimindex-1)) if(FAIL == H5S_obtain_datatype(size,tspan->down->head,&temp_type,elmt_size,dimindex-1))
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't obtain MPI derived data type"); HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't obtain MPI derived data type");
if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(&temp_type))) if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(&temp_type)))
@ -698,20 +698,18 @@ static herr_t H5S_obtain_datatype(const hsize_t size[],
tspan = tspan->next; tspan = tspan->next;
} }
/* building the whole vector datatype */ /* building the whole vector datatype */
if(MPI_SUCCESS != (mpi_code =
if(MPI_SUCCESS != (mpi_code =
MPI_Type_struct(outercount,blocklen,disp,inner_type,span_type))) MPI_Type_struct(outercount,blocklen,disp,inner_type,span_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_struct failed", mpi_code); HMPI_GOTO_ERROR(FAIL, "MPI_Type_struct failed", mpi_code);
} }
if(inner_type != NULL){ if(inner_type != NULL){
if(down != NULL) { if(down != NULL) {
for(i=0;i<outercount;i++) for(i=0;i<outercount;i++)
MPI_Type_free(&inner_type[i]); MPI_Type_free(&inner_type[i]);
} }
} }
@ -721,7 +719,7 @@ static herr_t H5S_obtain_datatype(const hsize_t size[],
HDfree(blocklen); HDfree(blocklen);
if(disp != NULL) if(disp != NULL)
HDfree(disp); HDfree(disp);
done: done:
FUNC_LEAVE_NOAPI(ret_value); FUNC_LEAVE_NOAPI(ret_value);
} }