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-rw-r--r--src/H5Cmpio.c205
1 files changed, 117 insertions, 88 deletions
diff --git a/src/H5Cmpio.c b/src/H5Cmpio.c
index e17aacd..4e88e44 100644
--- a/src/H5Cmpio.c
+++ b/src/H5Cmpio.c
@@ -43,13 +43,13 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5Fpkg.h" /* Files */
#include "H5FDprivate.h" /* File drivers */
+#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
#include "H5Pprivate.h" /* Property lists */
-#include "H5SLprivate.h" /* Skip lists */
-#ifdef H5_HAVE_PARALLEL
+#ifdef H5_HAVE_PARALLEL
/****************/
/* Local Macros */
/****************/
@@ -64,6 +64,9 @@
/********************/
/* Local Prototypes */
/********************/
+static herr_t H5C__collective_write(H5F_t *f, hid_t dxpl_id,
+ H5SL_t *collective_write_list);
+static herr_t H5C__collective_write_free(void *_item, void *key, void *op_data);
/*********************/
@@ -80,6 +83,9 @@
/* Local Variables */
/*******************/
+/* Declare a free list to manage the H5C_collective_write_t struct */
+H5FL_DEFINE(H5C_collective_write_t);
+
/*-------------------------------------------------------------------------
@@ -261,7 +267,7 @@ H5C_apply_candidate_list(H5F_t * f,
/* Create skip list of entries for collective write */
if(NULL == (collective_write_list = H5SL_create(H5SL_TYPE_HADDR, NULL)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create skip list for entries")
- }
+ } /* end if */
n = num_candidates / mpi_size;
m = num_candidates % mpi_size;
@@ -376,7 +382,7 @@ H5C_apply_candidate_list(H5F_t * f,
if(TRUE == entry_ptr->coll_access) {
entry_ptr->coll_access = FALSE;
H5C__REMOVE_FROM_COLL_LIST(cache_ptr, entry_ptr, FAIL)
- }
+ } /* end if */
} /* end else */
} /* end for */
@@ -453,10 +459,8 @@ H5C_apply_candidate_list(H5F_t * f,
* will not call either the pre_serialize or serialize callbacks.
*/
- if(H5C__flush_single_entry(f, dxpl_id, clear_ptr,
- H5C__FLUSH_CLEAR_ONLY_FLAG | H5C__DEL_FROM_SLIST_ON_DESTROY_FLAG,
- NULL, NULL) < 0)
- HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Can't clear entry.")
+ if(H5C__flush_single_entry(f, dxpl_id, clear_ptr, H5C__FLUSH_CLEAR_ONLY_FLAG | H5C__DEL_FROM_SLIST_ON_DESTROY_FLAG, NULL, NULL) < 0)
+ HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't clear entry.")
} /* end if */
/* Else, if this process needs to flush this entry. */
@@ -500,9 +504,9 @@ H5C_apply_candidate_list(H5F_t * f,
cache_ptr->entries_removed_counter = 0;
cache_ptr->last_entry_removed_ptr = NULL;
- if(H5C__flush_single_entry(f, dxpl_id, flush_ptr, H5C__DEL_FROM_SLIST_ON_DESTROY_FLAG,
- NULL, collective_write_list) < 0)
- HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Can't flush entry.")
+ /* Add this entry to the list of entries to collectively write */
+ if(H5C__flush_single_entry(f, dxpl_id, flush_ptr, H5C__DEL_FROM_SLIST_ON_DESTROY_FLAG, NULL, collective_write_list) < 0)
+ HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't flush entry.")
if ( ( cache_ptr->entries_removed_counter > 1 ) ||
( cache_ptr->last_entry_removed_ptr == entry_ptr ) )
@@ -655,14 +659,12 @@ H5C_apply_candidate_list(H5F_t * f,
entries_cleared++;
#if ( H5C_APPLY_CANDIDATE_LIST__DEBUG > 1 )
- HDfprintf(stdout, "%s:%d: clearing 0x%llx.\n", FUNC, mpi_rank,
- (long long)clear_ptr->addr);
+ HDfprintf(stdout, "%s:%d: clearing 0x%llx.\n", FUNC, mpi_rank,
+ (long long)clear_ptr->addr);
#endif /* H5C_APPLY_CANDIDATE_LIST__DEBUG */
- if(H5C__flush_single_entry(f, dxpl_id, clear_ptr,
- H5C__FLUSH_CLEAR_ONLY_FLAG | H5C__DEL_FROM_SLIST_ON_DESTROY_FLAG,
- NULL, NULL) < 0)
- HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Can't clear entry.")
+ if(H5C__flush_single_entry(f, dxpl_id, clear_ptr, H5C__FLUSH_CLEAR_ONLY_FLAG | H5C__DEL_FROM_SLIST_ON_DESTROY_FLAG, NULL, NULL) < 0)
+ HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't clear entry.")
} /* end else-if */
/* Else, if this process needs to independently flush this entry. */
@@ -677,9 +679,9 @@ H5C_apply_candidate_list(H5F_t * f,
(long long)flush_ptr->addr);
#endif /* H5C_APPLY_CANDIDATE_LIST__DEBUG */
- if(H5C__flush_single_entry(f, dxpl_id, flush_ptr, H5C__DEL_FROM_SLIST_ON_DESTROY_FLAG,
- NULL, collective_write_list) < 0)
- HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Can't clear entry.")
+ /* Add this entry to the list of entries to collectively write */
+ if(H5C__flush_single_entry(f, dxpl_id, flush_ptr, H5C__DEL_FROM_SLIST_ON_DESTROY_FLAG, NULL, collective_write_list) < 0)
+ HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't clear entry.")
} /* end else-if */
} /* end if */
@@ -712,16 +714,15 @@ H5C_apply_candidate_list(H5F_t * f,
if (delayed_ptr) {
if (delayed_ptr->clear_on_unprotect) {
- if(H5C__flush_single_entry(f, dxpl_id, delayed_ptr, H5C__FLUSH_CLEAR_ONLY_FLAG,
- NULL, NULL) < 0)
- HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Can't flush entry collectively.")
+ if(H5C__flush_single_entry(f, dxpl_id, delayed_ptr, H5C__FLUSH_CLEAR_ONLY_FLAG, NULL, NULL) < 0)
+ HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't flush entry.")
entry_ptr->clear_on_unprotect = FALSE;
entries_cleared++;
} else if (delayed_ptr->flush_immediately) {
- if(H5C__flush_single_entry(f, dxpl_id, delayed_ptr, H5C__DEL_FROM_SLIST_ON_DESTROY_FLAG,
- NULL, collective_write_list) < 0)
- HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Can't flush entry collectively.")
+ /* Add this entry to the list of entries to collectively write */
+ if(H5C__flush_single_entry(f, dxpl_id, delayed_ptr, H5C__DEL_FROM_SLIST_ON_DESTROY_FLAG, NULL, collective_write_list) < 0)
+ HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't flush entry collectively.")
entry_ptr->flush_immediately = FALSE;
entries_flushed++;
@@ -731,15 +732,15 @@ H5C_apply_candidate_list(H5F_t * f,
entries_flushed_or_cleared_last++;
} /* end if */
+ /* If we've deferred writing to do it collectively, take care of that now */
if(f->coll_md_write) {
HDassert(collective_write_list);
/* Write collective list */
- if(H5C_collective_write(f,
- dxpl_id,
- collective_write_list) < 0)
- HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Can't write metadata collectively")
- }
+ if(H5C__collective_write(f, dxpl_id, collective_write_list) < 0)
+ HGOTO_ERROR(H5E_CACHE, H5E_WRITEERROR, FAIL, "Can't write metadata collectively")
+ } /* end if */
+
/* ====================================================================== *
* Finished flushing everything. *
* ====================================================================== */
@@ -750,9 +751,9 @@ H5C_apply_candidate_list(H5F_t * f,
HDassert((entries_flushed_collectively == entries_to_flush_collectively));
if((entries_flushed != entries_to_flush) ||
- (entries_cleared != entries_to_clear) ||
- (entries_flushed_or_cleared_last != entries_to_flush_or_clear_last) ||
- (entries_flushed_collectively != entries_to_flush_collectively))
+ (entries_cleared != entries_to_clear) ||
+ (entries_flushed_or_cleared_last != entries_to_flush_or_clear_last) ||
+ (entries_flushed_collectively != entries_to_flush_collectively))
HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "entry count mismatch.")
done:
@@ -760,7 +761,7 @@ done:
candidate_assignment_table = (int *)H5MM_xfree((void *)candidate_assignment_table);
if(collective_write_list)
- if(H5SL_destroy(collective_write_list, H5C_collective_write_free, NULL) < 0)
+ if(H5SL_destroy(collective_write_list, H5C__collective_write_free, NULL) < 0)
HDONE_ERROR(H5E_CACHE, H5E_CANTFREE, FAIL, "failed to destroy skip list")
FUNC_LEAVE_NOAPI(ret_value)
@@ -1132,7 +1133,7 @@ H5C_mark_entries_as_clean(H5F_t * f,
if(TRUE == entry_ptr->coll_access) {
entry_ptr->coll_access = FALSE;
H5C__REMOVE_FROM_COLL_LIST(cache_ptr, entry_ptr, FAIL)
- }
+ } /* end if */
entry_ptr->clear_on_unprotect = TRUE;
#if H5C_DO_SANITY_CHECKS
@@ -1194,10 +1195,8 @@ H5C_mark_entries_as_clean(H5F_t * f,
entry_ptr = entry_ptr->prev;
entries_cleared++;
- if(H5C__flush_single_entry(f, dxpl_id, clear_ptr,
- H5C__FLUSH_CLEAR_ONLY_FLAG | H5C__DEL_FROM_SLIST_ON_DESTROY_FLAG,
- NULL, NULL) < 0)
- HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Can't clear entry.")
+ if(H5C__flush_single_entry(f, dxpl_id, clear_ptr, H5C__FLUSH_CLEAR_ONLY_FLAG | H5C__DEL_FROM_SLIST_ON_DESTROY_FLAG, NULL, NULL) < 0)
+ HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't clear entry.")
} else {
entry_ptr = entry_ptr->prev;
@@ -1224,10 +1223,8 @@ H5C_mark_entries_as_clean(H5F_t * f,
entry_ptr = entry_ptr->next;
entries_cleared++;
- if(H5C__flush_single_entry(f, dxpl_id, clear_ptr,
- H5C__FLUSH_CLEAR_ONLY_FLAG | H5C__DEL_FROM_SLIST_ON_DESTROY_FLAG,
- NULL, NULL) < 0 )
- HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Can't clear entry.")
+ if(H5C__flush_single_entry(f, dxpl_id, clear_ptr, H5C__FLUSH_CLEAR_ONLY_FLAG | H5C__DEL_FROM_SLIST_ON_DESTROY_FLAG, NULL, NULL) < 0 )
+ HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't clear entry.")
} else {
entry_ptr = entry_ptr->next;
@@ -1288,78 +1285,95 @@ done:
*-------------------------------------------------------------------------
*/
herr_t
-H5C_clear_coll_entries(H5C_t * cache_ptr, hbool_t partial)
+H5C_clear_coll_entries(H5C_t *cache_ptr, hbool_t partial)
{
- int32_t list_len, coll_entries_cleared = 0;
+ int32_t clear_cnt;
H5C_cache_entry_t * entry_ptr = NULL;
- H5C_cache_entry_t * prev_ptr;
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI_NOINIT
entry_ptr = cache_ptr->coll_tail_ptr;
- list_len = cache_ptr->coll_list_len;
-
- while(entry_ptr && (coll_entries_cleared < (partial ? list_len/2 : list_len))) {
- prev_ptr = entry_ptr->coll_prev;
+ clear_cnt = (partial ? cache_ptr->coll_list_len / 2 : cache_ptr->coll_list_len);
+ while(entry_ptr && clear_cnt > 0) {
+ H5C_cache_entry_t *prev_ptr = entry_ptr->coll_prev;
+ /* Sanity check */
HDassert(entry_ptr->coll_access);
+ /* Mark entry as independent */
entry_ptr->coll_access = FALSE;
H5C__REMOVE_FROM_COLL_LIST(cache_ptr, entry_ptr, FAIL)
- coll_entries_cleared ++;
+ /* Decrement entry count */
+ clear_cnt--;
+
+ /* Advance to next entry */
entry_ptr = prev_ptr;
- }
+ } /* end while */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5C_clear_coll_entries */
-herr_t
-H5C_collective_write(H5F_t *f,
- hid_t dxpl_id,
- H5SL_t *collective_write_list)
+
+/*-------------------------------------------------------------------------
+ *
+ * Function: H5C__collective_write
+ *
+ * Purpose: Perform a collective write of a list of metadata entries.
+ *
+ * Return: FAIL if error is detected, SUCCEED otherwise.
+ *
+ * Programmer: Mohamad Chaarawi
+ * February, 2016
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5C__collective_write(H5F_t *f, hid_t dxpl_id, H5SL_t *collective_write_list)
{
H5P_genplist_t *plist = NULL;
- H5FD_mpio_xfer_t xfer_mode = H5FD_MPIO_COLLECTIVE;
- H5FD_mpio_xfer_t orig_xfer_mode;
- H5SL_node_t *node;
- H5C_collective_write_t *item;
+ H5FD_mpio_xfer_t orig_xfer_mode = H5FD_MPIO_COLLECTIVE;
int count;
- void *base_buf;
int *length_array = NULL;
MPI_Aint *buf_array = NULL;
MPI_Aint *offset_array = NULL;
MPI_Datatype btype;
- MPI_Datatype ftype;
hbool_t btype_created = FALSE;
+ MPI_Datatype ftype;
hbool_t ftype_created = FALSE;
int mpi_code;
- int i;
herr_t ret_value = SUCCEED;
- FUNC_ENTER_NOAPI_NOINIT
-
- count = (int)H5SL_count(collective_write_list);
+ FUNC_ENTER_STATIC
+ /* 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")
-
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(collective_write_list);
+
if(count > 0) {
+ H5FD_mpio_xfer_t xfer_mode = H5FD_MPIO_COLLECTIVE;
+ H5SL_node_t *node;
+ H5C_collective_write_t *item;
+ void *base_buf;
+ 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")
/* Allocate arrays */
if(NULL == (length_array = (int *)H5MM_malloc((size_t)count * sizeof(int))))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for collective write table length array")
+ 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_NOSPACE, FAIL, "memory allocation failed for collective buf table length array")
+ 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_NOSPACE, FAIL, "memory allocation failed for collective offset table length array")
+ HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "memory allocation failed for collective offset table length array")
/* Fill arrays */
node = H5SL_first(collective_write_list);
@@ -1367,6 +1381,7 @@ H5C_collective_write(H5F_t *f,
if(NULL == (item = (H5C_collective_write_t *)H5SL_item(node)))
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)item->length;
base_buf = item->buf;
buf_array[0] = (MPI_Aint)0;
@@ -1378,28 +1393,31 @@ H5C_collective_write(H5F_t *f,
if(NULL == (item = (H5C_collective_write_t *)H5SL_item(node)))
HGOTO_ERROR(H5E_CACHE, H5E_NOTFOUND, FAIL, "can't retrieve skip list item")
+ /* Set up array position */
length_array[i] = (int)item->length;
buf_array[i] = (MPI_Aint)item->buf - (MPI_Aint)base_buf;
offset_array[i] = (MPI_Aint)item->offset;
+
+ /* Advance to next node & array location */
node = H5SL_next(node);
i++;
} /* end while */
- /* Create memory mpi type */
+ /* Create memory MPI type */
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 */
+ /* Create file MPI type */
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. */
+ /* 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")
@@ -1417,19 +1435,16 @@ H5C_collective_write(H5F_t *f,
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(MPI_SUCCESS != (mpi_code = MPI_File_set_view(mpi_fh, (MPI_Offset)0, MPI_BYTE, MPI_BYTE, "native", MPI_INFO_NULL)))
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)))
+ if(MPI_SUCCESS != (mpi_code = MPI_File_set_view(mpi_fh, (MPI_Offset)0, MPI_BYTE, MPI_BYTE, "native", MPI_INFO_NULL)))
HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code)
} /* end else */
@@ -1453,23 +1468,37 @@ done:
} /* end if */
FUNC_LEAVE_NOAPI(ret_value);
-} /* end H5C_collective_write() */
+} /* end H5C__collective_write() */
-herr_t
-H5C_collective_write_free(void *_item, void H5_ATTR_UNUSED *key, void H5_ATTR_UNUSED *op_data)
+
+/*-------------------------------------------------------------------------
+ *
+ * Function: H5C__collective_write_free
+ *
+ * Purpose: Release node on collective write skiplist
+ *
+ * Return: FAIL if error is detected, SUCCEED otherwise.
+ *
+ * Programmer: Mohamad Chaarawi
+ * February, 2016
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5C__collective_write_free(void *_item, void H5_ATTR_UNUSED *key, void H5_ATTR_UNUSED *op_data)
{
H5C_collective_write_t *item = (H5C_collective_write_t *)_item;
- FUNC_ENTER_NOAPI_NOINIT_NOERR
+ FUNC_ENTER_STATIC_NOERR
- HDassert(item);
+ /* Sanity check */
+ HDassert(item);
if(item->free_buf)
item->buf = H5MM_xfree(item->buf);
- /*!FIXME change to use free list for items */
- H5MM_free(item);
+ H5FL_FREE(H5C_collective_write_t, item);
FUNC_LEAVE_NOAPI(SUCCEED)
-} /* end H5C_collective_write_free() */
+} /* end H5C__collective_write_free() */
#endif /* H5_HAVE_PARALLEL */
generated by cgit v0.12 at 2024-10-30 05:43:13 (GMT)