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refactoring

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This commit is contained in:
gsell
2008-06-19 15:28:44 +00:00
parent d0f262e755
commit 0547eb1817
14 changed files with 13 additions and 533 deletions
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.gitattributes
-2
View File
@@ -379,8 +379,6 @@ src/h5/errorhandling.c -text
src/h5/errorhandling.h -text
src/h5/errorhandling_private.h -text
src/h5/general.c -text
src/h5/h5.c -text
src/h5/h5.h -text
src/h5/h5_core.h -text
src/h5/h5_private.h -text
src/h5/h5_types.h -text
src/H5Block.c
+1 -1
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@@ -45,7 +45,7 @@
#include <hdf5.h>
#include "h5/h5.h"
#include "h5/h5_core.h"
#include "h5/h5_private.h"
#include "H5Part.h"
#include "H5Block.h"
src/H5Part.c
+1 -1
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@@ -90,7 +90,7 @@ Last modified on April 19, 2007.
#define close _close
#endif /* WIN32 */
#include "h5/h5.h"
#include "h5/h5_core.h"
#include "h5/h5_private.h"
#include "H5Part.h"
src/H5Part.h
+1 -1
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@@ -4,7 +4,7 @@
#include <stdlib.h>
#include <stdarg.h>
#include <hdf5.h>
#include "h5.h"
#include "h5/h5_core.h"
#ifdef PARALLEL_IO
#include <mpi.h>
#endif
src/h5/Makefile.am
+3 -3
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@@ -43,7 +43,7 @@ EXTRA_LIBRARIES = libH5.a
# Header files that I wish to install in $(prefix)/include
include_HEADERS = \
h5.h \
h5_core.h \
h5_types.h \
attribs.h \
errorhandling.h \
@@ -57,7 +57,7 @@ EXTRA_HEADERS =
# Listing of sources
libH5_a_SOURCES = \
h5.c \
general.c \
attribs.c \
errorhandling.c \
t_openclose.c \
@@ -74,7 +74,7 @@ libH5.a: $(libH5_a_OBJECTS)
%.o : %.c
$(CC) $(CFLAGS) $(INC) -c $<
$(libH5_a_OBJECTS): h5.h
$(libH5_a_OBJECTS): h5_core.h
errorhandling.o: errorhandling.c
src/h5/attribs.c
+1 -1
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@@ -6,7 +6,7 @@
#include <fcntl.h>
#include <hdf5.h>
#include "h5.h"
#include "h5_core.h"
#include "h5_private.h"
#include "H5Part.h"
#include "H5Block.h"
src/h5/errorhandling.c
+1 -1
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@@ -6,7 +6,7 @@
#include <fcntl.h>
#include <hdf5.h>
#include "h5.h"
#include "h5_core.h"
#include "h5_private.h"
#include "H5Part.h"
src/h5/general.c
+1 -1
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@@ -7,7 +7,7 @@
#include <fcntl.h>
#include <hdf5.h>
#include "h5.h"
#include "h5_core.h"
#include "h5_private.h"
#include "H5Part.h"
#include "H5Block.h"
src/h5/h5.c
-470
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@@ -1,470 +0,0 @@
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <stdarg.h> /* va_arg - System dependent ?! */
#include <string.h>
#include <errno.h>
#include <fcntl.h>
#include <hdf5.h>
#include "h5.h"
#include "h5_private.h"
#include "H5Part.h"
#include "H5Block.h"
extern h5part_error_handler _err_handler;
extern h5part_int64_t _h5part_errno;
extern unsigned _debug;
/*!
\ingroup h5block_private
\internal
Check whether \c f points to a valid file handle.
\return H5PART_SUCCESS or error code
*/
h5part_int64_t
h5_check_filehandle (
const h5_file *f /*!< filehandle to check validity of */
) {
if ( f == NULL )
return HANDLE_H5_BADFD_ERR;
if ( f->file == 0 )
return HANDLE_H5_BADFD_ERR;
if ( f->block == NULL )
return HANDLE_H5_BADFD_ERR;
return H5PART_SUCCESS;
}
/*!
Initialize H5Part
*/
static herr_t
_h5_error_handler ( void* unused ) {
if ( _debug >= 5 ) {
H5Eprint (stderr);
}
return 0;
}
static h5part_int64_t
_init ( void ) {
static int __init = 0;
herr_t r5;
if ( ! __init ) {
r5 = H5Eset_auto ( _h5_error_handler, NULL );
if ( r5 < 0 ) return H5PART_ERR_INIT;
}
__init = 1;
return H5PART_SUCCESS;
}
/*!
\ingroup h5_private
\internal
Initialize unstructured data internal data structure.
\return H5_SUCCESS or error code
*/
static h5part_int64_t
_h5u_open_file (
h5_file *f /*!< IN: file handle */
) {
f->shape = 0;
f->diskshape = H5S_ALL;
f->memshape = H5S_ALL;
f->viewstart = -1;
f->viewend = -1;
f->pnparticles =
(h5part_int64_t*) malloc (f->nprocs * sizeof (h5part_int64_t));
if (f->pnparticles == NULL) {
return HANDLE_H5_NOMEM_ERR;
}
return H5_SUCCESS;
}
/*!
\ingroup h5_private
\internal
Initialize H5Block internal structure.
\return H5_SUCCESS or error code
*/
static h5part_int64_t
_h5b_open_file (
h5_file *f /*!< IN: file handle */
) {
struct h5b_fdata *b;
if ( (f == 0) || (f->file == 0) ) return HANDLE_H5_BADFD_ERR;
if ( f->block ) return H5_SUCCESS;
f->block = (struct h5b_fdata*) malloc( sizeof (*f->block) );
if ( f->block == NULL ) {
return HANDLE_H5_NOMEM_ERR;
}
b = f->block;
memset ( b, 0, sizeof (*b) );
b->user_layout = (struct H5BlockPartition*) malloc (
f->nprocs * sizeof (b->user_layout[0]) );
if ( b->user_layout == NULL ) {
return HANDLE_H5_NOMEM_ERR;
}
b->write_layout = (struct H5BlockPartition*) malloc (
f->nprocs * sizeof (b->write_layout[0]) );
if ( b->write_layout == NULL ) {
return HANDLE_H5_NOMEM_ERR;
}
b->step_idx = -1;
b->blockgroup = -1;
b->shape = -1;
b->diskshape = -1;
b->memshape = -1;
b->field_group_id = -1;
b->have_layout = 0;
return H5PART_SUCCESS;
}
h5_file*
h5_open_file (
const char *filename, /*!< [in] The name of the data file to open. */
unsigned flags, /*!< [in] The access mode for the file. */
MPI_Comm comm /*!< [in] MPI communicator */
) {
h5_info ( "Opening file %s.", filename );
if ( _init() < 0 ) {
HANDLE_H5_INIT_ERR;
return NULL;
}
_h5part_errno = H5PART_SUCCESS;
h5_file *f = NULL;
f = (h5_file*) malloc( sizeof (h5_file) );
if( f == NULL ) {
HANDLE_H5_NOMEM_ERR;
goto error_cleanup;
}
memset (f, 0, sizeof (h5_file));
f->prefix_step_name = strdup ( H5PART_GROUPNAME_STEP );
if( f->prefix_step_name == NULL ) {
HANDLE_H5_NOMEM_ERR;
goto error_cleanup;
}
f->width_step_idx = 0;
f->xfer_prop = f->create_prop = f->access_prop = H5P_DEFAULT;
f->comm = 0; /* init values for serial case */
f->nprocs = 1;
f->myproc = 0;
#ifdef PARALLEL_IO
f->comm = comm;
if (MPI_Comm_size (comm, &f->nprocs) != MPI_SUCCESS) {
HANDLE_MPI_COMM_SIZE_ERR;
goto error_cleanup;
}
if (MPI_Comm_rank (comm, &f->myproc) != MPI_SUCCESS) {
HANDLE_MPI_COMM_RANK_ERR;
goto error_cleanup;
}
/* for the SP2... perhaps different for linux */
MPI_Info info = MPI_INFO_NULL;
/* ks: IBM_large_block_io */
MPI_Info_create(&info);
MPI_Info_set(info, "IBM_largeblock_io", "true" );
if (H5Pset_fapl_mpio (f->access_prop, comm, info) < 0) {
HANDLE_H5P_SET_FAPL_MPIO_ERR;
goto error_cleanup;
}
MPI_Info_free(&info);
f->access_prop = H5Pcreate (H5P_FILE_ACCESS);
if (f->access_prop < 0) {
HANDLE_H5P_CREATE_ERR;
goto error_cleanup;
}
/* f->create_prop = H5Pcreate(H5P_FILE_CREATE); */
f->create_prop = H5P_DEFAULT;
/* xfer_prop: also used for parallel I/O, during actual writes
rather than the access_prop which is for file creation. */
f->xfer_prop = H5Pcreate (H5P_DATASET_XFER);
if (f->xfer_prop < 0) {
HANDLE_H5P_CREATE_ERR;
goto error_cleanup;
}
#ifdef COLLECTIVE_IO
if (H5Pset_dxpl_mpio (f->xfer_prop,H5FD_MPIO_COLLECTIVE) < 0) {
HANDLE_H5P_SET_DXPL_MPIO_ERR;
goto error_cleanup;
}
#endif /* COLLECTIVE_IO */
#endif /* PARALLEL_IO */
if ( flags == H5_O_RDONLY ) {
f->file = H5Fopen (filename, H5F_ACC_RDONLY, f->access_prop);
}
else if ( flags == H5_O_WRONLY ){
f->file = H5Fcreate (filename, H5F_ACC_TRUNC, f->create_prop,
f->access_prop);
f->empty = 1;
}
else if ( flags == H5_O_APPEND || H5_O_RDWR ) {
int fd = open (filename, O_RDONLY, 0);
if ( (fd == -1) && (errno == ENOENT) ) {
f->file = H5Fcreate(filename, H5F_ACC_TRUNC,
f->create_prop, f->access_prop);
f->empty = 1;
}
else if (fd != -1) {
close (fd);
f->file = H5Fopen (filename, H5F_ACC_RDWR,
f->access_prop);
}
}
else {
HANDLE_H5_FILE_ACCESS_TYPE_ERR ( flags );
goto error_cleanup;
}
if (f->file < 0) {
HANDLE_H5F_OPEN_ERR ( filename, flags );
goto error_cleanup;
}
f->root_gid = H5Gopen( f->file, "/" );
if ( f->root_gid < 0 ) {
HANDLE_H5G_OPEN_ERR ( "/" );
goto error_cleanup;
}
f->mode = flags;
f->step_gid = -1;
sprintf (
f->step_name,
"%s#%0*lld",
f->prefix_step_name, f->width_step_idx, (long long) f->step_idx );
if ( _h5u_open_file ( f ) < 0 ) {
goto error_cleanup;
}
if ( _h5b_open_file ( f ) < 0 ) {
goto error_cleanup;
}
if ( _h5t_open_file ( f ) < 0 ) {
goto error_cleanup;
}
return f;
error_cleanup:
if (f != NULL ) {
if (f->prefix_step_name) {
free (f->prefix_step_name);
}
if (f->pnparticles != NULL) {
free (f->pnparticles);
}
free (f);
}
return NULL;
}
/*!
\ingroup h5_private
\internal
De-initialize H5Block internal structure. Open HDF5 objects are
closed and allocated memory freed.
\return H5PART_SUCCESS or error code
*/
static h5part_int64_t
_h5u_close_file (
h5_file *f /*!< IN: file handle */
) {
herr_t herr;
_h5part_errno = H5_SUCCESS;
if( f->shape > 0 ) {
herr = H5Sclose( f->shape );
if ( herr < 0 ) HANDLE_H5S_CLOSE_ERR;
f->shape = 0;
}
if( f->diskshape != H5S_ALL ) {
herr = H5Sclose( f->diskshape );
if ( herr < 0 ) HANDLE_H5S_CLOSE_ERR;
f->diskshape = 0;
}
if( f->memshape != H5S_ALL ) {
herr = H5Sclose( f->memshape );
if ( herr < 0 ) HANDLE_H5S_CLOSE_ERR;
f->memshape = 0;
}
if( f->pnparticles ) {
free( f->pnparticles );
}
return _h5part_errno;
}
/*!
\ingroup h5block_private
\internal
De-initialize H5Block internal structure. Open HDF5 objects are
closed and allocated memory freed.
\return H5PART_SUCCESS or error code
*/
static h5part_int64_t
_h5b_close_file (
h5_file *f /*!< IN: file handle */
) {
herr_t herr;
struct h5b_fdata *b = f->block;
if ( b->blockgroup >= 0 ) {
herr = H5Gclose ( b->blockgroup );
if ( herr < 0 ) return HANDLE_H5G_CLOSE_ERR;
b->blockgroup = -1;
}
if ( b->shape >= 0 ) {
herr = H5Sclose ( b->shape );
if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR;
b->shape = -1;
}
if ( b->diskshape >= 0 ) {
herr = H5Sclose ( b->diskshape );
if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR;
b->diskshape = -1;
}
if ( b->memshape >= 0 ) {
herr = H5Sclose ( b->memshape );
if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR;
b->memshape = -1;
}
free ( f->block );
f->block = NULL;
return H5PART_SUCCESS;
}
h5part_int64_t
h5_close_file (
h5_file *f
) {
herr_t r = 0;
_h5part_errno = H5PART_SUCCESS;
CHECK_FILEHANDLE ( f );
_h5_close_step ( f );
_h5u_close_file ( f );
_h5b_close_file ( f );
_h5t_close_file ( f );
if( f->step_gid >= 0 ) {
r = H5Gclose( f->step_gid );
if ( r < 0 ) HANDLE_H5G_CLOSE_ERR;
f->step_gid = -1;
}
if( f->xfer_prop != H5P_DEFAULT ) {
r = H5Pclose( f->xfer_prop );
if ( r < 0 ) HANDLE_H5P_CLOSE_ERR ( "f->xfer_prop" );
f->xfer_prop = H5P_DEFAULT;
}
if( f->access_prop != H5P_DEFAULT ) {
r = H5Pclose( f->access_prop );
if ( r < 0 ) HANDLE_H5P_CLOSE_ERR ( "f->access_prop" );
f->access_prop = H5P_DEFAULT;
}
if( f->create_prop != H5P_DEFAULT ) {
r = H5Pclose( f->create_prop );
if ( r < 0 ) HANDLE_H5P_CLOSE_ERR ( "f->create_prop" );
f->create_prop = H5P_DEFAULT;
}
if ( f->root_gid >= 0 ) {
r = H5Gclose ( f->root_gid );
if ( r < 0 ) HANDLE_H5G_CLOSE_ERR;
f->root_gid = 0;
}
if ( f->file ) {
r = H5Fclose( f->file );
if ( r < 0 ) HANDLE_H5F_CLOSE_ERR;
f->file = 0;
}
if (f->prefix_step_name) {
free (f->prefix_step_name);
}
free( f );
return _h5part_errno;
}
h5_int64_t
h5_define_stepname_fmt (
h5_file *f,
const char *name,
const h5part_int64_t width
) {
f->prefix_step_name = strdup ( name );
if( f->prefix_step_name == NULL ) {
return HANDLE_H5_NOMEM_ERR;
}
f->width_step_idx = (int)width;
return H5PART_SUCCESS;
}
h5_err_t
h5_get_stepname_fmt (
h5_file * f,
char *name,
h5_int64_t *width
) {
return -1;
}
h5_int64_t
h5_get_step (
h5_file * f
) {
return -1;
}
h5_int64_t
h5_has_step (
h5_file * f,
h5_int64_t step
) {
char name[128];
sprintf ( name, "%s#%0*lld", f->prefix_step_name, f->width_step_idx, (long long) step );
return ( H5Gget_objinfo( f->file, name, 1, NULL ) >= 0 );
}
src/h5/h5.h
-48
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@@ -1,48 +0,0 @@
#ifndef __H5_H
#define __H5_H
#include "h5_types.h"
h5_file*
h5_open_file (
const char *filename,
unsigned flags,
MPI_Comm comm
);
h5part_int64_t
h5_check_filehandle (
const h5_file *f
);
h5part_int64_t
h5_close_file (
h5_file *f
);
h5part_int64_t
h5_define_stepname_fmt (
h5_file *f,
const char *name,
const h5part_int64_t width
);
h5_err_t
_h5_close_step (
h5_file *f
);
h5_int64_t
h5_has_step (
h5_file * f,
h5_int64_t step
);
#include "attribs.h"
#include "errorhandling.h"
#include "readwrite.h"
#include "t_openclose.h"
#include "t_readwrite.h"
#include "u_readwrite.h"
#endif
src/h5/readwrite.c
+1 -1
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@@ -6,7 +6,7 @@
#include <fcntl.h>
#include <hdf5.h>
#include "h5.h"
#include "h5_core.h"
#include "h5_private.h"
#include "H5Part.h"
#include "H5Block.h"
src/h5/t_openclose.c
+1 -1
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@@ -7,7 +7,7 @@
#include <fcntl.h>
#include <hdf5.h>
#include "h5/h5.h"
#include "h5/h5_core.h"
#include "h5/h5_private.h"
#include "H5Part.h"
src/h5/t_readwrite.c
+1 -1
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@@ -6,7 +6,7 @@
#include <fcntl.h>
#include <hdf5.h>
#include "h5.h"
#include "h5_core.h"
#include "h5_private.h"
#include "H5Part.h"
#include "H5Block.h"
src/h5/u_readwrite.c
+1 -1
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@@ -6,7 +6,7 @@
#include <fcntl.h>
#include <hdf5.h>
#include "h5.h"
#include "h5_core.h"
#include "h5_private.h"
#include "H5Part.h"