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-rw-r--r--src/H5FDmpio.c130
1 files changed, 111 insertions, 19 deletions
diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c
index 1db700a..9a99b45 100644
--- a/src/H5FDmpio.c
+++ b/src/H5FDmpio.c
@@ -1281,7 +1281,7 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
#endif
HMPI_GOTO_ERROR(FAIL, "MPI_Bcast failed", 0)
- /* Get the type's size */
+ /* Get the type's size */
#if MPI_VERSION >= 3
if (MPI_SUCCESS != (mpi_code = MPI_Type_size_x(buf_type, &type_size)))
#else
@@ -1592,6 +1592,17 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou
H5FD_mpio_xfer_t xfer_mode; /* I/O transfer mode */
H5FD_mpio_collective_opt_t coll_opt_mode; /* whether we are doing collective or independent I/O */
int size_i;
+#if MPI_VERSION >= 3
+ MPI_Count bytes_read = 0; /* Number of bytes read in */
+ MPI_Count type_size; /* MPI datatype used for I/O's size */
+ MPI_Count io_size; /* Actual number of bytes requested */
+ MPI_Count n;
+#else
+ int bytes_read = 0; /* Number of bytes read in */
+ int type_size; /* MPI datatype used for I/O's size */
+ int io_size; /* Actual number of bytes requested */
+ int n;
+#endif
herr_t ret_value = SUCCEED;
FUNC_ENTER_STATIC
@@ -1615,19 +1626,6 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou
HDassert((count == 0) || (sizes[0] != 0));
HDassert((count == 0) || (types[0] != H5FD_MEM_NOLIST));
- /* sort the vector I/O request into increasing address order if required
- *
- * If the vector is already sorted, the base addresses of types, addrs, sizes,
- * and bufs will be returned in s_types, s_addrs, s_sizes, and s_bufs respectively.
- *
- * If the vector was not already sorted, new, sorted versions of types, addrs, sizes, and bufs
- * are allocated, populated, and returned in s_types, s_addrs, s_sizes, and s_bufs respectively.
- * In this case, this function must free the memory allocated for the sorted vectors.
- */
- if (H5FD_sort_vector_io_req(&vector_was_sorted, count, types, addrs, sizes, bufs, &s_types, &s_addrs,
- &s_sizes, &s_bufs) < 0)
- HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "can't sort vector I/O request")
-
/* Get the transfer mode from the API context
*
* This flag is set to H5FD_MPIO_COLLECTIVE if the API call is
@@ -1643,6 +1641,19 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou
if (count > 0) { /* create MPI derived types describing the vector write */
+ /* sort the vector I/O request into increasing address order if required
+ *
+ * If the vector is already sorted, the base addresses of types, addrs, sizes,
+ * and bufs will be returned in s_types, s_addrs, s_sizes, and s_bufs respectively.
+ *
+ * If the vector was not already sorted, new, sorted versions of types, addrs, sizes, and bufs
+ * are allocated, populated, and returned in s_types, s_addrs, s_sizes, and s_bufs respectively.
+ * In this case, this function must free the memory allocated for the sorted vectors.
+ */
+ if (H5FD_sort_vector_io_req(&vector_was_sorted, count, types, addrs, sizes, bufs, &s_types, &s_addrs,
+ &s_sizes, &s_bufs) < 0)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "can't sort vector I/O request")
+
if ((NULL == (mpi_block_lengths = (int *)HDmalloc((size_t)count * sizeof(int)))) ||
(NULL == (mpi_displacments = (MPI_Aint *)HDmalloc((size_t)count * sizeof(MPI_Aint)))) ||
(NULL == (mpi_bufs = (MPI_Aint *)HDmalloc((size_t)count * sizeof(MPI_Aint))))) {
@@ -1810,9 +1821,60 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou
if (MPI_SUCCESS != (mpi_code = MPI_File_set_view(file->f, (MPI_Offset)0, MPI_BYTE, MPI_BYTE,
H5FD_mpi_native_g, file->info)))
HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code)
+
+ /* How many bytes were actually read? */
+#if MPI_VERSION >= 3
+ if (MPI_SUCCESS != (mpi_code = MPI_Get_elements_x(&mpi_stat, buf_type, &bytes_read)))
+#else
+ if (MPI_SUCCESS != (mpi_code = MPI_Get_elements(&mpi_stat, MPI_BYTE, &bytes_read)))
+#endif
+ HMPI_GOTO_ERROR(FAIL, "MPI_Get_elements failed", mpi_code)
+
+ /* Get the type's size */
+#if MPI_VERSION >= 3
+ if (MPI_SUCCESS != (mpi_code = MPI_Type_size_x(buf_type, &type_size)))
+#else
+ if (MPI_SUCCESS != (mpi_code = MPI_Type_size(buf_type, &type_size)))
+#endif
+ HMPI_GOTO_ERROR(FAIL, "MPI_Type_size failed", mpi_code)
+
+ /* Compute the actual number of bytes requested */
+ io_size = type_size * size_i;
+
+ /* Check for read failure */
+ if (bytes_read < 0 || bytes_read > io_size)
+ HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed")
+
+ /* Check for incomplete read */
+ n = io_size - bytes_read;
+ if (n > 0) {
+ i = (int)count - 1;
+
+ /* Iterate over sorted array in reverse, filling in zeroes to
+ * sections of the buffers that were not read to */
+ do {
+ HDassert(i >= 0);
+
+#if MPI_VERSION >= 3
+ io_size = MIN(n, (MPI_Count)s_sizes[i]);
+ bytes_read = (MPI_Count)s_sizes[i] - io_size;
+#else
+ io_size = MIN(n, (int)s_sizes[i]);
+ bytes_read = (int)s_sizes[i] - io_size;
+#endif
+ HDassert(bytes_read >= 0);
+
+ HDmemset((char *)bufs[i] + bytes_read, 0, (size_t)io_size);
+
+ n -= io_size;
+ i--;
+ } while (n > 0);
+ }
}
else if (count > 0) {
+ haddr_t max_addr = HADDR_MAX;
+
/* The read is part of an independent operation. As a result,
* we can't use MPI_File_set_view() (since it it a collective operation),
* and thus there is no point in setting up an MPI derived type, as
@@ -1832,7 +1894,7 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou
for (i = 0; i < (int)count; i++) {
- if (H5FD_mpi_haddr_to_MPIOff(s_addrs[i], &mpi_off) < 0)
+ if (H5FD_mpi_haddr_to_MPIOff(addrs[i], &mpi_off) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't convert from haddr to MPI off")
@@ -1845,16 +1907,46 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou
}
else {
- size = s_sizes[i];
+ size = sizes[i];
}
}
size_i = (int)size; /* todo: fix potential for overflow */
- if (MPI_SUCCESS !=
- (mpi_code = MPI_File_read_at(file->f, mpi_off, s_bufs[i], size_i, MPI_BYTE, &mpi_stat)))
+ /* Check if we acutally need to do I/O */
+ if (addrs[i] < max_addr) {
+ /* Issue read */
+ if (MPI_SUCCESS !=
+ (mpi_code = MPI_File_read_at(file->f, mpi_off, bufs[i], size_i, MPI_BYTE, &mpi_stat)))
- HMPI_GOTO_ERROR(FAIL, "MPI_File_read_at failed", mpi_code)
+ HMPI_GOTO_ERROR(FAIL, "MPI_File_read_at failed", mpi_code)
+
+ /* How many bytes were actually read? */
+#if MPI_VERSION >= 3
+ if (MPI_SUCCESS != (mpi_code = MPI_Get_elements_x(&mpi_stat, MPI_BYTE, &bytes_read)))
+#else
+ if (MPI_SUCCESS != (mpi_code = MPI_Get_elements(&mpi_stat, MPI_BYTE, &bytes_read)))
+#endif
+ HMPI_GOTO_ERROR(FAIL, "MPI_Get_elements failed", mpi_code)
+
+ /* Check for read failure */
+ if (bytes_read < 0 || bytes_read > size_i)
+ HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed")
+
+ /*
+ * If we didn't read the entire I/O, fill in zeroes beyond end of
+ * the physical MPI file and don't issue any more reads at higher
+ * addresses.
+ */
+ if ((n = (size_i - bytes_read)) > 0) {
+ HDmemset((char *)bufs[i] + bytes_read, 0, (size_t)n);
+ max_addr = addrs[i] + (haddr_t)bytes_read;
+ }
+ }
+ else {
+ /* Read is past the max address, fill in zeroes */
+ HDmemset((char *)bufs[i], 0, size);
+ }
}
}
generated by cgit v0.12 at 2024-08-28 23:08:10 (GMT)