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[svn-r224] Initial implementation of the upper levels of PHDF5. The

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MPIO lower interface layer (H5Fmpio.c) has been commited by Kim already.
All PHDF5 codes are "bracket'ed" by #ifdef HAVE_PARALLEL macro.
This commit is contained in:
Albert Cheng 1998-02-05 22:00:35 -05:00
parent 858b8fbfae
commit 238cccd5e8
9 changed files with 207 additions and 34 deletions
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73
src/H5C.c
View File

@ -141,13 +141,14 @@ H5Ccreate(H5C_class_t type)
/* Allocate a new template and initialize it with default values */
switch (type) {
case H5C_FILE_CREATE:
tmpl = H5MM_xmalloc(sizeof(H5F_create_t));
tmpl = H5MM_xmalloc(sizeof(H5F_create_t));
memcpy(tmpl, &H5F_create_dflt, sizeof(H5F_create_t));
break;
case H5C_FILE_ACCESS:
HRETURN_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL,
"not implemented yet");
tmpl = H5MM_xmalloc(sizeof(H5F_access_t));
memcpy(tmpl, &H5F_access_dflt, sizeof(H5F_access_t));
break;
case H5C_DATASET_CREATE:
tmpl = H5MM_xmalloc(sizeof(H5D_create_t));
@ -233,6 +234,9 @@ H5Cclose(hid_t tid)
if (NULL == (tmpl = H5A_remove(tid))) {
HRETURN_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "unable to remove atom");
}
#ifdef LATER
/* this is for file access template too. Need to free the COMM and INFO objects too. */
#endif
H5MM_xfree(tmpl);
FUNC_LEAVE(SUCCEED);
@ -853,6 +857,69 @@ H5Cget_chunk(hid_t tid, int max_ndims, size_t dim[] /*out */ )
FUNC_LEAVE(tmpl->chunk_ndims);
}
#ifdef HAVE_PARALLEL
/*-------------------------------------------------------------------------
* Function: H5Cset_mpi
*
* Purpose: Sets the access mode for MPIO call and store the user supplied
* communicator and info.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Albert Cheng
* Feb 3, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Cset_mpi (hid_t tid, MPI_Comm comm, MPI_Info info, uintn access_mode)
{
int i;
H5F_access_t *tmpl = NULL;
MPI_Comm lcomm;
int mrc; /* MPI return code */
FUNC_ENTER(H5Cset_mpi, FAIL);
/* Check arguments */
if (H5C_FILE_ACCESS != H5Cget_class(tid) ||
NULL == (tmpl = H5A_object(tid))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL,
"not a file access template");
}
switch (access_mode){
case H5ACC_INDEPENDENT:
/* fall through to next case */
case H5ACC_COLLECTIVE:
tmpl->access_mode = access_mode;
break;
default:
HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL,
"unknown access_mode");
}
/* store a duplicate copy of comm so that user may freely modify comm after this */
/* call. */
#ifdef LATER
/* need to verify comm and info contain sensible information */
/* need to duplicate info too but don't know a quick way to do it now. */
#endif
if ((mrc = MPI_Comm_dup(comm, &lcomm) != MPI_SUCCESS))
HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL,
"failure to duplicate communicator");
tmpl->comm = comm;
tmpl->info = info;
FUNC_LEAVE(SUCCEED);
}
#endif /*HAVE_PARALLEL*/
/*--------------------------------------------------------------------------
NAME

4
src/H5Cpublic.h
View File

@ -61,6 +61,10 @@ herr_t H5Cset_layout (hid_t tid, H5D_layout_t layout);
H5D_layout_t H5Cget_layout (hid_t tid);
herr_t H5Cset_chunk (hid_t tid, int ndims, const size_t dim[]);
int H5Cget_chunk (hid_t tid, int max_ndims, size_t dim[]/*out*/);
#ifdef HAVE_PARALLEL
herr_t H5Cset_mpi (hid_t tid, MPI_Comm comm, MPI_Info info, uintn access_mode);
/* herr_t H5Cget_mpi (hid_t tid, int *ik); */ /* not defined yet */
#endif
#ifdef __cplusplus
}

85
src/H5F.c
View File

@ -77,8 +77,8 @@ const H5F_create_t H5F_create_dflt = {
0, /* unused */
0, /* unused */
},
sizeof(size_t), /* Default offset size */
sizeof(size_t), /* Default length size */
4, /* Default offset size */
4, /* Default length size */
HDF5_BOOTBLOCK_VERSION, /* Current Boot-Block version # */
HDF5_SMALLOBJECT_VERSION, /* Current Small-Object heap version # */
HDF5_FREESPACE_VERSION, /* Current Free-Space info version # */
@ -86,6 +86,18 @@ const H5F_create_t H5F_create_dflt = {
HDF5_SHAREDHEADER_VERSION, /* Current Shared-Header format version # */
};
/*
* Define the default file access template.
*/
const H5F_access_t H5F_access_dflt =
{
H5ACC_DEFAULT, /* Default file access mode */
#ifdef HAVE_PARALLEL
MPI_COMM_NULL, /* Default is not using MPIO */
MPI_INFO_NULL, /* Default no info */
#endif
};
/* Interface initialization */
static intn interface_initialize_g = FALSE;
#define INTERFACE_INIT H5F_init_interface
@ -557,7 +569,7 @@ H5F_dest(H5F_t *f)
*/
H5F_t *
H5F_open(const H5F_low_class_t *type, const char *name, uintn flags,
const H5F_create_t *create_parms)
const H5F_create_t *create_parms, const H5F_access_t *access_parms)
{
H5F_t *f = NULL; /*return value */
H5F_t *ret_value = NULL; /*a copy of `f' */
@ -623,7 +635,7 @@ H5F_open(const H5F_low_class_t *type, const char *name, uintn flags,
fprintf(stderr, "HDF5-DIAG: opening a split file\n");
#endif
fullname[s - name] = '\0';
f = H5F_open(H5F_LOW_SPLIT, fullname, flags, create_parms);
f = H5F_open(H5F_LOW_SPLIT, fullname, flags, create_parms, access_parms);
HRETURN(f);
}
}
@ -984,6 +996,11 @@ H5Fcreate(const char *filename, uintn flags, hid_t create_temp,
const H5F_create_t *create_parms; /* pointer to the parameters to
* use when creating the file
*/
const H5F_access_t *access_parms; /* pointer to the file access
* parameters to use when creating
* the file
*/
const H5F_low_class_t *type; /* File type */
hid_t ret_value = FAIL;
FUNC_ENTER(H5Fcreate, FAIL);
@ -1001,19 +1018,35 @@ H5Fcreate(const char *filename, uintn flags, hid_t create_temp,
} else if (NULL == (create_parms = H5A_object(create_temp))) {
HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't unatomize template");
}
#ifdef LATER
if (access_temp <= 0) {
access_parms = &H5F_access_dflt;
} else if (NULL == (access_parms = H5A_object(access_temp))) {
HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL); /*can't unatomize template */
HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't unatomize template");
}
/* figure out what kind of file I/O to use. */
/* Currently, MPIO is the only alternative than default I/O */
switch (access_parms->access_mode){
case H5ACC_DEFAULT:
type = H5F_LOW_DFLT;
break;
#ifdef HAVE_PARALLEL
case H5ACC_INDEPENDENT:
type = H5F_LOW_MPIO;
break;
case H5ACC_COLLECTIVE:
/* not implemented yet */
/* type = H5F_LOW_MPIO; */
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Invalid file access mode");
#endif
default:
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Invalid file access mode");
}
/*
* Create a new file or truncate an existing file.
*/
if (NULL == (new_file = H5F_open(H5F_LOW_DFLT, filename, flags,
create_parms))) {
if (NULL == (new_file = H5F_open(type, filename, flags,
create_parms, access_parms))) {
HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, FAIL, "can't create file");
}
/* Get an atom for the file */
@ -1076,6 +1109,11 @@ hid_t
H5Fopen(const char *filename, uintn flags, hid_t access_temp)
{
H5F_t *new_file = NULL; /* file struct for new file */
const H5F_access_t *access_parms; /* pointer to the file access
* parameters to use when creating
* the file
*/
const H5F_low_class_t *type; /* File type */
hid_t ret_value = FAIL;
FUNC_ENTER(H5Fopen, FAIL);
@ -1085,15 +1123,32 @@ H5Fopen(const char *filename, uintn flags, hid_t access_temp)
HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "invalid file name");
flags = flags & H5ACC_WRITE ? H5F_ACC_WRITE : 0;
#ifdef LATER
if (access_temp <= 0)
access_temp = H5CPget_default_atom(H5_TEMPLATE);
if (NULL == (f_access_parms = H5A_object(access_temp)))
HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL); /*can't unatomize template */
if (access_temp <= 0) {
access_parms = &H5F_access_dflt;
} else if (NULL == (access_parms = H5A_object(access_temp))) {
HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't unatomize template");
}
/* figure out what kind of file I/O to use. */
/* Currently, MPIO is the only alternative than default I/O */
switch (access_parms->access_mode){
case H5ACC_DEFAULT:
type = H5F_LOW_DFLT;
break;
#ifdef HAVE_PARALLEL
case H5ACC_INDEPENDENT:
type = H5F_LOW_MPIO;
break;
case H5ACC_COLLECTIVE:
/* not implemented yet */
/* type = H5F_LOW_MPIO; */
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Invalid file access mode");
#endif
default:
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Invalid file access mode");
}
/* Open the file */
if (NULL == (new_file = H5F_open(H5F_LOW_DFLT, filename, flags, NULL))) {
if (NULL == (new_file = H5F_open(type, filename, flags, NULL, access_parms))) {
HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, FAIL, "cant open file");
}
/* Get an atom for the file */

18
src/H5Fmpio.c
View File

@ -127,7 +127,7 @@ ino_t mpio_inode_num = 0; /* fake "inode" number */
*-------------------------------------------------------------------------
*/
static hbool_t
H5F_mpio_access(char *name, int mode, H5F_search_t *key /*out */ )
H5F_mpio_access(const char *name, int mode, H5F_search_t *key /*out */ )
{
hbool_t ret_val = FALSE;
MPI_File fh;
@ -150,24 +150,25 @@ H5F_mpio_access(char *name, int mode, H5F_search_t *key /*out */ )
break;
case W_OK: mpi_mode = MPI_MODE_WRONLY;
break;
default: HRETURN_ERROR(H5E_IO, H5E_ARGS, FAIL,
default: HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL,
"invalid mode parameter");
}
mpierr = MPI_File_open( MPI_COMM_SELF, name, mpi_mode, MPI_INFO_NULL, &fh );
/* (char*) name is okay since MPI_File_open will not change it. */
mpierr = MPI_File_open( MPI_COMM_SELF, (char*) name, mpi_mode, MPI_INFO_NULL, &fh );
if (mpierr == MPI_SUCCESS) {
mpierr = MPI_File_close( &fh );
if (mpierr != MPI_SUCCESS)
HRETURN_ERROR(H5E_IO, H5E_ARGS, FAIL, "MPI_File_open failed");
HRETURN_ERROR(H5E_IO, H5E_CLOSEERROR, FAIL, "MPI_File_close failed");
ret_val = TRUE;
} else if (mode == F_OK) {
/* to see if it exists, this time try to open for write */
mpierr = MPI_File_open( MPI_COMM_SELF, name, MPI_MODE_WRONLY,
mpierr = MPI_File_open( MPI_COMM_SELF, (char*)name, MPI_MODE_WRONLY,
MPI_INFO_NULL, &fh );
if (mpierr == MPI_SUCCESS) {
mpierr = MPI_File_close( &fh );
if (mpierr != MPI_SUCCESS)
HRETURN_ERROR(H5E_IO, H5E_INTERNAL, FAIL, "MPI_File_close failed");
HRETURN_ERROR(H5E_IO, H5E_CLOSEERROR, FAIL, "MPI_File_close failed");
ret_val = TRUE;
}
}
@ -214,7 +215,7 @@ H5F_mpio_access(char *name, int mode, H5F_search_t *key /*out */ )
*-------------------------------------------------------------------------
*/
static H5F_low_t *
H5F_mpio_open(char *name, uintn flags, H5F_search_t *key /*out */ )
H5F_mpio_open(const char *name, uintn flags, H5F_search_t *key /*out */ )
{
H5F_low_t *lf = NULL;
MPI_File fh;
@ -234,7 +235,7 @@ H5F_mpio_open(char *name, uintn flags, H5F_search_t *key /*out */ )
if (flags&H5F_ACC_CREAT) mpi_amode |= MPI_MODE_CREATE;
if (flags&H5F_ACC_EXCL) mpi_amode |= MPI_MODE_EXCL;
mpierr = MPI_File_open(MPI_COMM_WORLD, name, mpi_amode, MPI_INFO_NULL, &fh);
mpierr = MPI_File_open(MPI_COMM_WORLD, (char*)name, mpi_amode, MPI_INFO_NULL, &fh);
if (mpierr != MPI_SUCCESS) {
MPI_Error_string( mpierr, mpierrmsg, &msglen );
HRETURN_ERROR(H5E_IO, H5E_CANTOPENFILE, NULL, mpierrmsg );
@ -391,6 +392,7 @@ H5F_mpio_read(H5F_low_t *lf, const haddr_t *addr, size_t size, uint8 *buf)
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, mpierrmsg );
}
#define MPI_KLUGE0202
#ifdef MPI_KLUGE0202
/* KLUGE rky 980202 MPI_Get_count incorrectly returns negative count;
fake a complete read */

26
src/H5Fprivate.h
View File

@ -22,7 +22,7 @@
/* This is a near top-level header! Try not to include much! */
#include <H5private.h>
#ifdef PHDF5
#ifdef HAVE_PARALLEL
#ifndef MPI_SUCCESS
#include <mpi.h>
#include <mpio.h>
@ -230,6 +230,17 @@ typedef struct H5F_create_t {
intn sharedheader_ver;/* Version # of the shared header format */
} H5F_create_t;
/*
* File-access template.
*/
typedef struct H5F_access_t {
uintn access_mode; /* file access mode */
#ifdef HAVE_PARALLEL
MPI_Comm comm; /* communicator for file access */
MPI_Info info; /* optional info for MPI-IO */
#endif /*HAVE_PARALLEL*/
} H5F_access_t;
/*
* These things make a file unique.
*/
@ -304,7 +315,7 @@ typedef struct H5F_low_t {
size_t alloc; /* Current size of MEM buffer */
} core;
#ifdef PHDF5
#ifdef HAVE_PARALLEL
/* MPI-IO */
struct {
MPI_File f; /* MPI-IO file handle */
@ -323,10 +334,8 @@ extern const H5F_low_class_t H5F_LOW_STDIO[]; /* Posix stdio */
extern const H5F_low_class_t H5F_LOW_CORE[]; /* In-core temp file */
extern const H5F_low_class_t H5F_LOW_FAM[]; /* File family */
extern const H5F_low_class_t H5F_LOW_SPLIT[]; /* Split meta/raw data */
#ifdef PHDF5
#ifdef HAVE_PARALLEL
extern const H5F_low_class_t H5F_LOW_MPIO[]; /* MPI-IO */
# undef H5F_LOW_DFLT
# define H5F_LOW_DFLT H5F_LOW_MPIO /* The default type */
#endif
/*
@ -346,8 +355,8 @@ typedef struct H5F_file_t {
haddr_t hdf5_eof; /* Relative addr of end of all hdf5 data*/
struct H5AC_t *cache; /* The object cache */
H5F_create_t create_parms; /* File-creation template */
#ifdef LATER
file_access_temp_t file_access_parms; /* File-access template */
#ifdef HAVE_PARALLEL
H5F_access_t access_parms; /* File-access template */
#endif
struct H5G_entry_t *root_ent; /* Root symbol table entry */
} H5F_file_t;
@ -414,11 +423,12 @@ struct H5O_layout_t; /*forward decl for prototype arguments */
/* library variables */
extern const H5F_create_t H5F_create_dflt;
extern const H5F_access_t H5F_access_dflt;
/* Private functions, not part of the publicly documented API */
void H5F_encode_length_unusual(const H5F_t *f, uint8 **p, uint8 *l);
H5F_t *H5F_open(const H5F_low_class_t *type, const char *name, uintn flags,
const H5F_create_t *create_parms);
const H5F_create_t *create_parms, const H5F_access_t *access_parms);
herr_t H5F_close(H5F_t *f);
herr_t H5F_debug(H5F_t *f, const haddr_t *addr, FILE * stream, intn indent,
intn fwidth);

5
src/H5Fpublic.h
View File

@ -24,6 +24,11 @@
#define H5ACC_DEFAULT 0x0000/*use in H5Fopen & H5Fcreate to open a file with default access*/
#define H5ACC_WRITE 0x0001/*use in H5Fopen to open a file with write access*/
#define H5ACC_OVERWRITE 0x0002/*use in H5Fcreate truncate an existing file*/
#ifdef HAVE_PARALLEL
#define H5ACC_INDEPENDENT 0x0010/*use in H5Cset_mpi for MPI independent access*/
#define H5ACC_COLLECTIVE 0x0011/*use in H5Cset_mpi for MPI collective access*/
#endif
#ifdef __cplusplus
extern "C" {

17
src/H5M.c
View File

@ -76,6 +76,23 @@ static meta_func_t meta_func_arr[] =
NULL, /* File-Creation Template GetFile */
H5Cclose /* File-Creation Template Release */
},
{ /* Template object meta-functions (defined in H5C.c) */
H5_TEMPLATE_1, /* File-Access Template Type ID */
NULL, /* File-Access Template Create */
NULL, /* File-Access Template Access */
H5Ccopy, /* File-Access Template Copy */
NULL, /* File-Access Template FindName */
NULL, /* File-Access Template NameLen */
NULL, /* File-Access Template GetName */
NULL, /* File-Access Template SetName */
NULL, /* File-Access Template Search */
NULL, /* File-Access Template Index */
NULL, /* File-Access Template Flush */
NULL, /* File-Access Template Delete */
NULL, /* File-Access Template GetParent */
NULL, /* File-Access Template GetFile */
H5Cclose /* File-Access Template Release */
},
{ /* Datatype object meta-functions (defined in H5T.c) */
H5_DATATYPE, /* Datatype Type ID */
NULL, /* Datatype Create */

9
src/H5private.h
View File

@ -46,6 +46,15 @@
# include <unistd.h>
#endif
#ifdef HAVE_PARALLEL
/*
* MPIO headers
*/
# include <mpi.h>
# include <mpio.h>
#endif
/*
* Pablo support files.
*/

4
src/H5public.h
View File

@ -18,6 +18,10 @@
#include <H5config.h> /*from configure */
#include <sys/types.h>
#ifdef HAVE_PARALLEL
#include <mpi.h>
#include <mpio.h>
#endif
/*
* Data types