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-rw-r--r--src/CMakeLists.txt2
-rw-r--r--src/H5D.c2
-rw-r--r--src/H5Dchunk.c51
-rw-r--r--src/H5Ochunk.c2
-rw-r--r--src/H5TS.c4
-rw-r--r--src/H5VLconnector.h1
-rw-r--r--src/H5VLnative.h1
-rw-r--r--src/H5VLnative_dataset.c48
-rw-r--r--src/H5private.h4
-rw-r--r--src/H5trace.c6
10 files changed, 71 insertions, 50 deletions
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 070cf62..f582056 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.10)
+cmake_minimum_required (VERSION 3.12)
project (HDF5_SRC C)
#-----------------------------------------------------------------------------
diff --git a/src/H5D.c b/src/H5D.c
index 178bb30..61a40df 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -598,7 +598,7 @@ H5Dget_offset(hid_t dset_id)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, HADDR_UNDEF, "invalid dataset identifier")
/* Get the offset */
- if(H5VL_dataset_get(vol_obj, H5VL_DATASET_GET_OFFSET, H5P_DATASET_XFER_DEFAULT, H5_REQUEST_NULL, &ret_value) < 0)
+ if(H5VL_dataset_optional(vol_obj, H5VL_NATIVE_DATASET_GET_OFFSET, H5P_DATASET_XFER_DEFAULT, H5_REQUEST_NULL, &ret_value) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, HADDR_UNDEF, "unable to get offset")
done:
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 556e367..e760f63 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -323,6 +323,7 @@ static herr_t H5D__chunk_prune_fill(H5D_chunk_it_ud1_t *udata, hbool_t new_unfil
#ifdef H5_HAVE_PARALLEL
static herr_t H5D__chunk_collective_fill(const H5D_t *dset,
H5D_chunk_coll_info_t *chunk_info, size_t chunk_size, const void *fill_buf);
+static int H5D__chunk_cmp_addr(const void *addr1, const void *addr2);
#endif /* H5_HAVE_PARALLEL */
static int
@@ -4958,6 +4959,7 @@ H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_info_t *chunk_info,
MPI_Datatype mem_type, file_type;
H5FD_mpio_xfer_t prev_xfer_mode; /* Previous data xfer mode */
hbool_t have_xfer_mode = FALSE; /* Whether the previous xffer mode has been retrieved */
+ hbool_t need_addr_sort = FALSE;
int i; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
@@ -5006,19 +5008,28 @@ H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_info_t *chunk_info,
/* make sure that the addresses in the datatype are
monotonically non decreasing */
- if(i)
- HDassert(chunk_disp_array[i] > chunk_disp_array[i - 1]);
- } /* end if */
+ if(i && (chunk_disp_array[i] < chunk_disp_array[i - 1]))
+ need_addr_sort = TRUE;
+ } /* end for */
/* calculate if there are any leftover blocks after evenly
distributing. If there are, then round robin the distribution
to processes 0 -> leftover. */
if(leftover && leftover > mpi_rank) {
chunk_disp_array[blocks] = (MPI_Aint)chunk_info->addr[blocks*mpi_size + mpi_rank];
+ if(blocks && (chunk_disp_array[blocks] < chunk_disp_array[blocks - 1]))
+ need_addr_sort = TRUE;
block_lens[blocks] = block_len;
blocks++;
}
+ /*
+ * Ensure that the blocks are sorted in monotonically non-decreasing
+ * order of offset in the file.
+ */
+ if(need_addr_sort)
+ HDqsort(chunk_disp_array, blocks, sizeof(MPI_Aint), H5D__chunk_cmp_addr);
+
/* MSC - should use this if MPI_type_create_hindexed block is working:
* mpi_code = MPI_Type_create_hindexed_block(blocks, block_len, chunk_disp_array, MPI_BYTE, &file_type);
*/
@@ -5073,6 +5084,36 @@ done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__chunk_collective_fill() */
+
+
+static int
+H5D__chunk_cmp_addr(const void *addr1, const void *addr2)
+{
+ MPI_Aint _addr1 = (MPI_Aint)0, _addr2 = (MPI_Aint)0;
+ int ret_value = 0;
+
+ FUNC_ENTER_STATIC_NOERR
+
+ _addr1 = *((const MPI_Aint *) addr1);
+ _addr2 = *((const MPI_Aint *) addr2);
+
+#if MPI_VERSION >= 3 && MPI_SUBVERSION >= 1
+ {
+ MPI_Aint diff = MPI_Aint_diff(_addr1, _addr2);
+
+ if(diff < (MPI_Aint)0)
+ ret_value = -1;
+ else if(diff > (MPI_Aint)0)
+ ret_value = 1;
+ else
+ ret_value = 0;
+ }
+#else
+ ret_value = (_addr1 > _addr2) - (_addr1 < _addr2);
+#endif
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__chunk_cmp_addr() */
#endif /* H5_HAVE_PARALLEL */
@@ -7162,7 +7203,7 @@ H5D__get_num_chunks(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_
} /* end else */
done:
- FUNC_LEAVE_NOAPI(ret_value)
+ FUNC_LEAVE_NOAPI_TAG(ret_value)
} /* end H5D__get_num_chunks() */
@@ -7300,7 +7341,7 @@ H5D__get_chunk_info(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_
} /* end if H5F_addr_defined */
done:
- FUNC_LEAVE_NOAPI(ret_value)
+ FUNC_LEAVE_NOAPI_TAG(ret_value)
} /* end H5D__get_chunk_info() */
diff --git a/src/H5Ochunk.c b/src/H5Ochunk.c
index 9ce5a46..72402e4 100644
--- a/src/H5Ochunk.c
+++ b/src/H5Ochunk.c
@@ -358,7 +358,7 @@ H5O__chunk_update_idx(H5F_t *f, H5O_t *oh, unsigned idx)
HGOTO_ERROR(H5E_OHDR, H5E_CANTUNPROTECT, FAIL, "unable to release object header chunk")
done:
- FUNC_LEAVE_NOAPI(ret_value)
+ FUNC_LEAVE_NOAPI_TAG(ret_value)
} /* end H5O__chunk_update_idx() */
diff --git a/src/H5TS.c b/src/H5TS.c
index 9503e05..b0cef7f 100644
--- a/src/H5TS.c
+++ b/src/H5TS.c
@@ -262,7 +262,7 @@ H5TS_mutex_lock(H5TS_mutex_t *mutex)
if (ret_value)
return ret_value;
- if(mutex->lock_count && pthread_equal(HDpthread_self(), mutex->owner_thread)) {
+ if(mutex->lock_count && pthread_equal(pthread_self(), mutex->owner_thread)) {
/* already owned by self - increment count */
mutex->lock_count++;
} else {
@@ -271,7 +271,7 @@ H5TS_mutex_lock(H5TS_mutex_t *mutex)
pthread_cond_wait(&mutex->cond_var, &mutex->atomic_lock);
/* After we've received the signal, take ownership of the mutex */
- mutex->owner_thread = HDpthread_self();
+ mutex->owner_thread = pthread_self();
mutex->lock_count = 1;
}
diff --git a/src/H5VLconnector.h b/src/H5VLconnector.h
index baa4cca..39d9b14 100644
--- a/src/H5VLconnector.h
+++ b/src/H5VLconnector.h
@@ -91,7 +91,6 @@ typedef int H5VL_attr_optional_t;
typedef enum H5VL_dataset_get_t {
H5VL_DATASET_GET_DAPL, /* access property list */
H5VL_DATASET_GET_DCPL, /* creation property list */
- H5VL_DATASET_GET_OFFSET, /* offset */
H5VL_DATASET_GET_SPACE, /* dataspace */
H5VL_DATASET_GET_SPACE_STATUS, /* space status */
H5VL_DATASET_GET_STORAGE_SIZE, /* storage size */
diff --git a/src/H5VLnative.h b/src/H5VLnative.h
index e1f3f93..b607abc 100644
--- a/src/H5VLnative.h
+++ b/src/H5VLnative.h
@@ -48,6 +48,7 @@
#define H5VL_NATIVE_DATASET_CHUNK_READ 6 /* H5Dchunk_read */
#define H5VL_NATIVE_DATASET_CHUNK_WRITE 7 /* H5Dchunk_write */
#define H5VL_NATIVE_DATASET_GET_VLEN_BUF_SIZE 8 /* H5Dvlen_get_buf_size */
+#define H5VL_NATIVE_DATASET_GET_OFFSET 9 /* H5Dget_offset */
/* Values for native VOL connector file optional VOL operations */
#define H5VL_NATIVE_FILE_CLEAR_ELINK_CACHE 0 /* H5Fclear_elink_file_cache */
diff --git a/src/H5VLnative_dataset.c b/src/H5VLnative_dataset.c
index bea2c50..8660e80 100644
--- a/src/H5VLnative_dataset.c
+++ b/src/H5VLnative_dataset.c
@@ -297,18 +297,6 @@ H5VL__native_dataset_get(void *obj, H5VL_dataset_get_t get_type,
break;
}
- /* H5Dget_offset */
- case H5VL_DATASET_GET_OFFSET:
- {
- haddr_t *ret = HDva_arg(arguments, haddr_t *);
-
- /* Set return value */
- *ret = H5D__get_offset(dset);
- if(!H5F_addr_defined(*ret))
- *ret = HADDR_UNDEF;
- break;
- }
-
default:
HGOTO_ERROR(H5E_VOL, H5E_CANTGET, FAIL, "can't get this type of information from dataset")
} /* end switch */
@@ -391,16 +379,17 @@ herr_t
H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
hid_t H5_ATTR_UNUSED dxpl_id, void H5_ATTR_UNUSED **req, va_list arguments)
{
- H5D_t *dset = NULL; /* Dataset */
- herr_t ret_value = SUCCEED; /* Return value */
+ H5D_t *dset = (H5D_t *)obj; /* Dataset */
+ herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
+ /* Sanity checks */
+ HDassert(dset);
+
switch(optional_type) {
case H5VL_NATIVE_DATASET_FORMAT_CONVERT:
{ /* H5Dformat_convert */
- dset = (H5D_t *)obj;
-
switch(dset->shared->layout.type) {
case H5D_CHUNKED:
/* Convert the chunk indexing type to version 1 B-tree if not */
@@ -436,8 +425,6 @@ H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
{ /* H5Dget_chunk_index_type */
H5D_chunk_index_t *idx_type = HDva_arg(arguments, H5D_chunk_index_t *);
- dset = (H5D_t *)obj;
-
/* Make sure the dataset is chunked */
if(H5D_CHUNKED != dset->shared->layout.type)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
@@ -453,8 +440,6 @@ H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
hsize_t *offset = HDva_arg(arguments, hsize_t *);
hsize_t *chunk_nbytes = HDva_arg(arguments, hsize_t *);
- dset = (H5D_t *)obj;
-
/* Make sure the dataset is chunked */
if(H5D_CHUNKED != dset->shared->layout.type)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
@@ -472,8 +457,6 @@ H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
hid_t space_id = HDva_arg(arguments, hid_t);
hsize_t *nchunks = HDva_arg(arguments, hsize_t *);
- dset = (H5D_t *)obj;
- HDassert(dset);
HDassert(dset->shared);
HDassert(dset->shared->space);
@@ -505,8 +488,6 @@ H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
haddr_t *addr = HDva_arg(arguments, haddr_t *);
hsize_t *size = HDva_arg(arguments, hsize_t *);
- dset = (H5D_t *)obj;
- HDassert(dset);
HDassert(dset->shared);
HDassert(dset->shared->space);
@@ -534,8 +515,6 @@ H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
haddr_t *addr = HDva_arg(arguments, haddr_t *);
hsize_t *size = HDva_arg(arguments, hsize_t *);
- dset = (H5D_t *)obj;
- HDassert(dset);
HDassert(dset->shared);
/* Make sure the dataset is chunked */
@@ -556,8 +535,6 @@ H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
void *buf = HDva_arg(arguments, void *);
hsize_t offset_copy[H5O_LAYOUT_NDIMS]; /* Internal copy of chunk offset */
- dset = (H5D_t *)obj;
-
/* Check arguments */
if(NULL == dset->oloc.file)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not associated with a file")
@@ -585,8 +562,6 @@ H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
const void *buf = HDva_arg(arguments, const void *);
hsize_t offset_copy[H5O_LAYOUT_NDIMS]; /* Internal copy of chunk offset */
- dset = (H5D_t *)obj;
-
/* Check arguments */
if(NULL == dset->oloc.file)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not associated with a file")
@@ -612,13 +587,22 @@ H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
hid_t space_id = HDva_arg(arguments, hid_t);
hsize_t *size = HDva_arg(arguments, hsize_t *);
- dset = (H5D_t *)obj;
-
if(H5D__vlen_get_buf_size(dset, type_id, space_id, size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get size of vlen buf needed")
break;
}
+ /* H5Dget_offset */
+ case H5VL_NATIVE_DATASET_GET_OFFSET:
+ {
+ haddr_t *ret = HDva_arg(arguments, haddr_t *);
+
+ /* Set return value */
+ *ret = H5D__get_offset(dset);
+ if(!H5F_addr_defined(*ret))
+ *ret = HADDR_UNDEF;
+ break;
+ }
default:
HGOTO_ERROR(H5E_VOL, H5E_UNSUPPORTED, FAIL, "invalid optional operation")
diff --git a/src/H5private.h b/src/H5private.h
index 3759446..f570723 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -1570,10 +1570,6 @@ extern char *strdup(const char *s);
#define HDstrdup(S) strdup(S)
#endif /* HDstrdup */
-#ifndef HDpthread_self
- #define HDpthread_self() pthread_self()
-#endif /* HDpthread_self */
-
/* Macro for "stringizing" an integer in the C preprocessor (use H5_TOSTRING) */
/* (use H5_TOSTRING, H5_STRINGIZE is just part of the implementation) */
#define H5_STRINGIZE(x) #x
diff --git a/src/H5trace.c b/src/H5trace.c
index ec5c6a2..7168d5d 100644
--- a/src/H5trace.c
+++ b/src/H5trace.c
@@ -2746,9 +2746,6 @@ H5_trace(const double *returning, const char *func, const char *type, ...)
case H5VL_DATASET_GET_STORAGE_SIZE:
HDfprintf(out, "H5VL_DATASET_GET_STORAGE_SIZE");
break;
- case H5VL_DATASET_GET_OFFSET:
- HDfprintf(out, "H5VL_DATASET_GET_OFFSET");
- break;
default:
HDfprintf(out, "%ld", (long)get);
break;
@@ -3276,6 +3273,9 @@ H5_trace(const double *returning, const char *func, const char *type, ...)
case H5VL_NATIVE_DATASET_GET_VLEN_BUF_SIZE:
HDfprintf(out, "H5VL_NATIVE_DATASET_GET_VLEN_BUF_SIZE");
break;
+ case H5VL_NATIVE_DATASET_GET_OFFSET:
+ HDfprintf(out, "H5VL_NATIVE_DATASET_GET_OFFSET");
+ break;
default:
HDfprintf(out, "%ld", (long)optional);
break;
generated by cgit v0.12 at 2025-01-31 10:59:49 (GMT)