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Merge pull request in HDFFV/hdf5 from ~MAINZER/hdf5_jrm:develop to develop

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* commit 'eb75dc1bb02e13902d73a36caafe763eea585d02':
  Removed commeted out code from H5C_dump_coll_write_list()
  Checkin of fix for CGNS bug (https://jira.hdfgroup.org/browse/HDFFV-10055).
This commit is contained in:
John Mainzer 2017-04-07 13:20:11 -05:00
commit ccb4e9ed9a
8 changed files with 293 additions and 26 deletions

107
src/H5Cdbg.c

@ -30,12 +30,16 @@
#include "H5Cmodule.h" /* This source code file is part of the H5C module */
#define H5AC_FRIEND
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5ACprivate.h" /* Metadata Cache */
#include "H5ACpkg.h" /* Metadata Cache */
#include "H5Cpkg.h" /* Cache */
#include "H5Eprivate.h" /* Error Handling */
@ -338,6 +342,107 @@ H5C_dump_cache_skip_list(H5C_t * cache_ptr, char * calling_fcn)
} /* H5C_dump_cache_skip_list() */
#endif /* NDEBUG */
/*-------------------------------------------------------------------------
* Function: H5C_dump_coll_write_list
*
* Purpose: Debugging routine that prints a summary of the contents of
* the collective write skip list used by the metadata cache
* in the parallel case to maintain a list of entries to write
* collectively at a sync point.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: John Mainzer
* 4/1/17
*
*-------------------------------------------------------------------------
*/
#ifdef H5_HAVE_PARALLEL
#ifndef NDEBUG
herr_t
H5C_dump_coll_write_list(H5C_t * cache_ptr, char * calling_fcn)
{
herr_t ret_value = SUCCEED; /* Return value */
int i;
int list_len;
H5AC_aux_t * aux_ptr = NULL;
H5C_cache_entry_t * entry_ptr = NULL;
H5SL_node_t * node_ptr = NULL;
FUNC_ENTER_NOAPI_NOERR
HDassert(cache_ptr != NULL);
HDassert(cache_ptr->magic == H5C__H5C_T_MAGIC);
HDassert(cache_ptr->aux_ptr);
aux_ptr = (H5AC_aux_t *)cache_ptr->aux_ptr;
HDassert(aux_ptr->magic == H5AC__H5AC_AUX_T_MAGIC);
HDassert(calling_fcn != NULL);
list_len = (int)H5SL_count(cache_ptr->coll_write_list);
HDfprintf(stdout, "\n\nDumping MDC coll write list from %d:%s.\n",
aux_ptr->mpi_rank, calling_fcn);
HDfprintf(stdout, " slist len = %u.\n", cache_ptr->slist_len);
if ( list_len > 0 ) {
/* scan the collective write list generating the desired output */
HDfprintf(stdout,
"Num: Addr: Len: Prot/Pind: Dirty: Type:\n");
i = 0;
node_ptr = H5SL_first(cache_ptr->coll_write_list);
if ( node_ptr != NULL )
entry_ptr = (H5C_cache_entry_t *)H5SL_item(node_ptr);
else
entry_ptr = NULL;
while ( entry_ptr != NULL ) {
HDassert(entry_ptr->magic == H5C__H5C_CACHE_ENTRY_T_MAGIC);
HDfprintf(stdout,
"%s%d 0x%016llx %4lld %d/%d %d %s\n",
cache_ptr->prefix, i,
(long long)(entry_ptr->addr),
(long long)(entry_ptr->size),
(int)(entry_ptr->is_protected),
(int)(entry_ptr->is_pinned),
(int)(entry_ptr->is_dirty),
entry_ptr->type->name);
node_ptr = H5SL_next(node_ptr);
if ( node_ptr != NULL )
entry_ptr = (H5C_cache_entry_t *)H5SL_item(node_ptr);
else
entry_ptr = NULL;
i++;
} /* end while */
} /* end if */
HDfprintf(stdout, "\n\n");
FUNC_LEAVE_NOAPI(ret_value)
} /* H5C_dump_coll_write_list() */
#endif /* NDEBUG */
#endif /* H5_HAVE_PARALLEL */
/*-------------------------------------------------------------------------
* Function: H5C_set_prefix

102
src/H5Cmpio.c

@ -950,12 +950,15 @@ H5C__collective_write(H5F_t *f, hid_t dxpl_id)
/* Get original transfer mode */
if(NULL == (plist = (H5P_genplist_t *)H5I_object(dxpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data transfer property list")
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, \
"not a data transfer property list")
if(H5P_get(plist, H5D_XFER_IO_XFER_MODE_NAME, &orig_xfer_mode) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set MPI-I/O property")
/* Get number of entries in collective write list */
count = (int)H5SL_count(cache_ptr->coll_write_list);
if(count > 0) {
H5FD_mpio_xfer_t xfer_mode = H5FD_MPIO_COLLECTIVE;
H5SL_node_t *node;
@ -964,21 +967,34 @@ H5C__collective_write(H5F_t *f, hid_t dxpl_id)
int i;
if(H5P_set(plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set MPI-I/O property")
HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, \
"can't set MPI-I/O property")
/* Allocate arrays */
if(NULL == (length_array = (int *)H5MM_malloc((size_t)count * sizeof(int))))
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "memory allocation failed for collective write table length array")
if(NULL == (buf_array = (MPI_Aint *)H5MM_malloc((size_t)count * sizeof(MPI_Aint))))
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "memory allocation failed for collective buf table length array")
if(NULL == (offset_array = (MPI_Aint *)H5MM_malloc((size_t)count * sizeof(MPI_Aint))))
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "memory allocation failed for collective offset table length array")
if ( NULL == (length_array =
(int *)H5MM_malloc((size_t)count * sizeof(int))) )
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, \
"memory allocation failed for collective write table length array")
if ( NULL == (buf_array =
(MPI_Aint *)H5MM_malloc((size_t)count * sizeof(MPI_Aint))) )
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, \
"memory allocation failed for collective buf table length array")
if(NULL == (offset_array =
(MPI_Aint *)H5MM_malloc((size_t)count * sizeof(MPI_Aint))) )
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, \
"memory allocation failed for collective offset table length array")
/* Fill arrays */
node = H5SL_first(cache_ptr->coll_write_list);
HDassert(node);
if(NULL == (entry_ptr = (H5C_cache_entry_t *)H5SL_item(node)))
HGOTO_ERROR(H5E_CACHE, H5E_NOTFOUND, FAIL, "can't retrieve skip list item")
HGOTO_ERROR(H5E_CACHE, H5E_NOTFOUND, FAIL, \
"can't retrieve skip list item")
/* Set up initial array position & buffer base address */
length_array[0] = (int)entry_ptr->size;
@ -989,8 +1005,10 @@ H5C__collective_write(H5F_t *f, hid_t dxpl_id)
node = H5SL_next(node);
i = 1;
while(node) {
if(NULL == (entry_ptr = (H5C_cache_entry_t *)H5SL_item(node)))
HGOTO_ERROR(H5E_CACHE, H5E_NOTFOUND, FAIL, "can't retrieve skip list item")
HGOTO_ERROR(H5E_CACHE, H5E_NOTFOUND, FAIL, \
"can't retrieve skip list item")
/* Set up array position */
length_array[i] = (int)entry_ptr->size;
@ -1003,48 +1021,85 @@ H5C__collective_write(H5F_t *f, hid_t dxpl_id)
} /* end while */
/* Create memory MPI type */
if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed(count, length_array, buf_array, MPI_BYTE, &btype)))
if(MPI_SUCCESS != (mpi_code =
MPI_Type_create_hindexed(count, length_array,
buf_array, MPI_BYTE,
&btype)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
btype_created = TRUE;
if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(&btype)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
/* Create file MPI type */
if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed(count, length_array, offset_array, MPI_BYTE, &ftype)))
if(MPI_SUCCESS != (mpi_code =
MPI_Type_create_hindexed(count, length_array,
offset_array, MPI_BYTE,
&ftype)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
ftype_created = TRUE;
if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(&ftype)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
/* Pass buf type, file type to the file driver */
if(H5FD_mpi_setup_collective(dxpl_id, &btype, &ftype) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set MPI-I/O properties")
HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, \
"can't set MPI-I/O properties")
/* Write data */
if(H5F_block_write(f, H5FD_MEM_DEFAULT, (haddr_t)0, (size_t)1, dxpl_id, base_buf) < 0)
HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to write entries collectively")
if(H5F_block_write(f, H5FD_MEM_DEFAULT, (haddr_t)0,
(size_t)1, dxpl_id, base_buf) < 0)
HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, \
"unable to write entries collectively")
} /* end if */
else {
MPI_Status mpi_stat;
MPI_File mpi_fh_p;
MPI_File *mpi_fh_p;
MPI_File mpi_fh;
MPI_Info *info_p;
MPI_Info info;
if(H5F_get_mpi_handle(f, (MPI_File **)&mpi_fh_p) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "can't get mpi file handle")
HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, \
"can't get mpi file handle")
mpi_fh = *(MPI_File*)mpi_fh_p;
/* just to match up with the 1st MPI_File_set_view from H5FD_mpio_write() */
if(MPI_SUCCESS != (mpi_code = MPI_File_set_view(mpi_fh, (MPI_Offset)0, MPI_BYTE, MPI_BYTE, "native", MPI_INFO_NULL)))
if (H5F_get_mpi_info(f, &info_p) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, \
"can't get mpi file info")
info = *info_p;
/* just to match up with the 1st MPI_File_set_view from
* H5FD_mpio_write()
*/
if(MPI_SUCCESS != (mpi_code =
MPI_File_set_view(mpi_fh, (MPI_Offset)0, MPI_BYTE,
MPI_BYTE, "native",
info)))
HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code)
/* just to match up with MPI_File_write_at_all from H5FD_mpio_write() */
HDmemset(&mpi_stat, 0, sizeof(MPI_Status));
if(MPI_SUCCESS != (mpi_code = MPI_File_write_at_all(mpi_fh, (MPI_Offset)0, NULL, 0, MPI_BYTE, &mpi_stat)))
if(MPI_SUCCESS != (mpi_code =
MPI_File_write_at_all(mpi_fh, (MPI_Offset)0,
NULL, 0, MPI_BYTE, &mpi_stat)))
HMPI_GOTO_ERROR(FAIL, "MPI_File_write_at_all failed", mpi_code)
/* just to match up with the 2nd MPI_File_set_view (reset) in H5FD_mpio_write() */
if(MPI_SUCCESS != (mpi_code = MPI_File_set_view(mpi_fh, (MPI_Offset)0, MPI_BYTE, MPI_BYTE, "native", MPI_INFO_NULL)))
/* just to match up with the 2nd MPI_File_set_view (reset) in
* H5FD_mpio_write()
*/
if(MPI_SUCCESS != (mpi_code =
MPI_File_set_view(mpi_fh, (MPI_Offset)0, MPI_BYTE,
MPI_BYTE, "native",
info)))
HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code)
} /* end else */
done:
@ -1063,7 +1118,8 @@ done:
if(orig_xfer_mode != H5FD_MPIO_COLLECTIVE) {
HDassert(plist);
if(H5P_set(plist, H5D_XFER_IO_XFER_MODE_NAME, &orig_xfer_mode) < 0)
HDONE_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set MPI-I/O property")
HDONE_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, \
"can't set MPI-I/O property")
} /* end if */
FUNC_LEAVE_NOAPI(ret_value);

5
src/H5Cprivate.h

@ -2340,9 +2340,12 @@ H5_DLL herr_t H5C_dump_cache_LRU(H5C_t *cache_ptr, const char *cache_name);
H5_DLL hbool_t H5C_get_serialization_in_progress(const H5C_t *cache_ptr);
H5_DLL hbool_t H5C_cache_is_clean(const H5C_t *cache_ptr, H5C_ring_t inner_ring);
H5_DLL herr_t H5C_dump_cache_skip_list(H5C_t *cache_ptr, char *calling_fcn);
#ifdef H5_HAVE_PARALLEL
H5_DLL herr_t H5C_dump_coll_write_list(H5C_t * cache_ptr, char * calling_fcn);
#endif /* H5_HAVE_PARALLEL */
H5_DLL herr_t H5C_get_entry_ptr_from_addr(H5C_t *cache_ptr, haddr_t addr,
void **entry_ptr_ptr);
H5_DLL herr_t H5C_flush_dependency_exists(H5C_t *cache_ptr, haddr_t parent_addr,
H5_DLL herr_t H5C_flush_dependency_exists(H5C_t *cache_ptr, haddr_t parent_addr,
haddr_t child_addr, hbool_t *fd_exists_ptr);
H5_DLL herr_t H5C_verify_entry_type(H5C_t *cache_ptr, haddr_t addr,
const H5C_class_t *expected_type, hbool_t *in_cache_ptr,

39
src/H5FDmpi.c

@ -146,6 +146,45 @@ done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpi_get_comm() */
/*-------------------------------------------------------------------------
* Function: H5FD_get_mpi_info
*
* Purpose: Retrieves the file's mpi info
*
* Return: Success: SUCCEED
*
* Failure: Negative
*
* Programmer: John Mainzer
* 4/4/17
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5FD_get_mpi_info(H5FD_t *file, void** mpi_info)
{
const H5FD_class_mpi_t *cls;
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI_NOINIT
HDassert(file);
cls = (const H5FD_class_mpi_t *)(file->cls);
HDassert(cls);
HDassert(cls->get_mpi_info); /* All MPI drivers must implement this */
/* Dispatch to driver */
if ((ret_value=(cls->get_mpi_info)(file, mpi_info)) < 0)
HGOTO_ERROR(H5E_VFL, H5E_CANTGET, MPI_COMM_NULL, \
"driver get_mpi_info request failed")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_get_mpi_info() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpi_MPIOff_to_haddr

37
src/H5FDmpio.c

@ -95,6 +95,7 @@ static herr_t H5FD_mpio_truncate(H5FD_t *_file, hid_t dxpl_id, hbool_t closing);
static int H5FD_mpio_mpi_rank(const H5FD_t *_file);
static int H5FD_mpio_mpi_size(const H5FD_t *_file);
static MPI_Comm H5FD_mpio_communicator(const H5FD_t *_file);
static herr_t H5FD_mpio_get_info(H5FD_t *_file, void** mpi_info);
/* The MPIO file driver information */
static const H5FD_class_mpi_t H5FD_mpio_g = {
@ -134,7 +135,8 @@ static const H5FD_class_mpi_t H5FD_mpio_g = {
}, /* End of superclass information */
H5FD_mpio_mpi_rank, /*get_rank */
H5FD_mpio_mpi_size, /*get_size */
H5FD_mpio_communicator /*get_comm */
H5FD_mpio_communicator, /*get_comm */
H5FD_mpio_get_info /*get_info */
};
#ifdef H5FDmpio_DEBUG
@ -1306,6 +1308,39 @@ done:
FUNC_LEAVE_NOAPI(ret_value)
}
/*-------------------------------------------------------------------------
* Function: H5FD_mpio_get_info
*
* Purpose: Returns the file info of MPIO file driver.
*
* Returns: Non-negative if succeed or negative if fails.
*
* Programmer: John Mainzer
* April 4, 2017
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5FD_mpio_get_info(H5FD_t *_file, void** mpi_info)
{
H5FD_mpio_t *file = (H5FD_mpio_t *)_file;
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI_NOINIT
if(!mpi_info)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "mpi info not valid")
*mpi_info = &(file->info);
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5FD_mpio_get_info() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpio_read

2
src/H5FDprivate.h

@ -53,6 +53,7 @@ typedef struct H5FD_class_mpi_t {
int (*get_rank)(const H5FD_t *file); /* Get the MPI rank of a process */
int (*get_size)(const H5FD_t *file); /* Get the MPI size of a communicator */
MPI_Comm (*get_comm)(const H5FD_t *file); /* Get the communicator for a file */
herr_t (*get_mpi_info)(H5FD_t *file, void** mpi_info); /* get MPI_Info for a file */
} H5FD_class_mpi_t;
#endif
@ -202,6 +203,7 @@ H5_DLL herr_t H5FD_get_mpio_atomicity(H5FD_t *file, hbool_t *flag);
H5_DLL int H5FD_mpi_get_rank(const H5FD_t *file);
H5_DLL int H5FD_mpi_get_size(const H5FD_t *file);
H5_DLL MPI_Comm H5FD_mpi_get_comm(const H5FD_t *_file);
H5_DLL herr_t H5FD_get_mpi_info(H5FD_t *file, void** file_info);
#endif /* H5_HAVE_PARALLEL */
#endif /* !_H5FDprivate_H */

26
src/H5Fmpi.c

@ -356,5 +356,31 @@ done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5F_mpi_retrieve_comm */
/*-------------------------------------------------------------------------
* Function: H5F_get_mpi_info
*
* Purpose: Retrieves MPI File info.
*
* Return: Success: The size (positive)
* Failure: Negative
*
*-------------------------------------------------------------------------
*/
herr_t
H5F_get_mpi_info(const H5F_t *f, MPI_Info **f_info)
{
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(FAIL)
HDassert(f && f->shared);
/* Dispatch to driver */
if ((ret_value = H5FD_get_mpi_info(f->shared->lf, (void **)f_info)) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "can't get mpi file info")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5F_get_mpi_info() */
#endif /* H5_HAVE_PARALLEL */

1
src/H5Fprivate.h

@ -852,6 +852,7 @@ H5_DLL int H5F_mpi_get_rank(const H5F_t *f);
H5_DLL MPI_Comm H5F_mpi_get_comm(const H5F_t *f);
H5_DLL int H5F_mpi_get_size(const H5F_t *f);
H5_DLL herr_t H5F_mpi_retrieve_comm(hid_t loc_id, hid_t acspl_id, MPI_Comm *mpi_comm);
H5_DLL herr_t H5F_get_mpi_info(const H5F_t *f, MPI_Info **f_info);
#endif /* H5_HAVE_PARALLEL */
/* External file cache routines */