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-rw-r--r--testpar/t_coll_md_read.c336
1 files changed, 322 insertions, 14 deletions
diff --git a/testpar/t_coll_md_read.c b/testpar/t_coll_md_read.c
index f945d2b..912388c 100644
--- a/testpar/t_coll_md_read.c
+++ b/testpar/t_coll_md_read.c
@@ -32,6 +32,14 @@
#define PARTIAL_NO_SELECTION_Y_DIM_SCALE 5
#define PARTIAL_NO_SELECTION_X_DIM_SCALE 5
+#define MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS 2
+
+#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_NO_SEL_PROCESS (mpi_rank == mpi_size - 1)
+#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DATASET_NAME "linked_chunk_io_sort_chunk_issue"
+#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_Y_DIM_SCALE 20000
+#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE 1
+#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS 1
+
/*
* A test for issue HDFFV-10501. A parallel hang was reported which occurred
* in linked-chunk I/O when collective metadata reads are enabled and some ranks
@@ -57,13 +65,13 @@ void test_partial_no_selection_coll_md_read(void)
hsize_t stride[PARTIAL_NO_SELECTION_DATASET_NDIMS];
hsize_t count[PARTIAL_NO_SELECTION_DATASET_NDIMS];
hsize_t block[PARTIAL_NO_SELECTION_DATASET_NDIMS];
- hid_t file_id = -1;
- hid_t fapl_id = -1;
- hid_t dset_id = -1;
- hid_t dcpl_id = -1;
- hid_t dxpl_id = -1;
- hid_t fspace_id = -1;
- hid_t mspace_id = -1;
+ hid_t file_id = H5I_INVALID_HID;
+ hid_t fapl_id = H5I_INVALID_HID;
+ hid_t dset_id = H5I_INVALID_HID;
+ hid_t dcpl_id = H5I_INVALID_HID;
+ hid_t dxpl_id = H5I_INVALID_HID;
+ hid_t fspace_id = H5I_INVALID_HID;
+ hid_t mspace_id = H5I_INVALID_HID;
int mpi_rank, mpi_size;
void *data = NULL;
void *read_buf = NULL;
@@ -86,7 +94,7 @@ void test_partial_no_selection_coll_md_read(void)
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
VRFY((file_id >= 0), "H5Fcreate succeeded");
- dataset_dims = malloc(PARTIAL_NO_SELECTION_DATASET_NDIMS * sizeof(*dataset_dims));
+ dataset_dims = HDmalloc(PARTIAL_NO_SELECTION_DATASET_NDIMS * sizeof(*dataset_dims));
VRFY((dataset_dims != NULL), "malloc succeeded");
dataset_dims[0] = PARTIAL_NO_SELECTION_Y_DIM_SCALE * mpi_size;
@@ -129,7 +137,7 @@ void test_partial_no_selection_coll_md_read(void)
mspace_id = H5Screate_simple(1, sel_dims, NULL);
VRFY((mspace_id >= 0), "H5Screate_simple succeeded");
- data = calloc(1, count[1] * (PARTIAL_NO_SELECTION_Y_DIM_SCALE * PARTIAL_NO_SELECTION_X_DIM_SCALE) * sizeof(int));
+ data = HDcalloc(1, count[1] * (PARTIAL_NO_SELECTION_Y_DIM_SCALE * PARTIAL_NO_SELECTION_X_DIM_SCALE) * sizeof(int));
VRFY((data != NULL), "calloc succeeded");
dxpl_id = H5Pcreate(H5P_DATASET_XFER);
@@ -151,7 +159,7 @@ void test_partial_no_selection_coll_md_read(void)
*/
VRFY((H5Pset_dxpl_mpio_chunk_opt(dxpl_id, H5FD_MPIO_CHUNK_ONE_IO) >= 0), "H5Pset_dxpl_mpio_chunk_opt succeeded");
- read_buf = malloc(count[1] * (PARTIAL_NO_SELECTION_Y_DIM_SCALE * PARTIAL_NO_SELECTION_X_DIM_SCALE) * sizeof(int));
+ read_buf = HDmalloc(count[1] * (PARTIAL_NO_SELECTION_Y_DIM_SCALE * PARTIAL_NO_SELECTION_X_DIM_SCALE) * sizeof(int));
VRFY((read_buf != NULL), "malloc succeeded");
/*
@@ -171,21 +179,321 @@ void test_partial_no_selection_coll_md_read(void)
* Check data integrity just to be sure.
*/
if (!PARTIAL_NO_SELECTION_NO_SEL_PROCESS) {
- VRFY((!memcmp(data, read_buf, count[1] * (PARTIAL_NO_SELECTION_Y_DIM_SCALE * PARTIAL_NO_SELECTION_X_DIM_SCALE) * sizeof(int))), "memcmp succeeded");
+ VRFY((!HDmemcmp(data, read_buf, count[1] * (PARTIAL_NO_SELECTION_Y_DIM_SCALE * PARTIAL_NO_SELECTION_X_DIM_SCALE) * sizeof(int))), "memcmp succeeded");
+ }
+
+ if (dataset_dims) {
+ HDfree(dataset_dims);
+ dataset_dims = NULL;
}
+ if (data) {
+ HDfree(data);
+ data = NULL;
+ }
+
+ if (read_buf) {
+ HDfree(read_buf);
+ read_buf = NULL;
+ }
+
+ VRFY((H5Sclose(fspace_id) >= 0), "H5Sclose succeeded");
+ VRFY((H5Sclose(mspace_id) >= 0), "H5Sclose succeeded");
+ VRFY((H5Pclose(dcpl_id) >= 0), "H5Pclose succeeded");
+ VRFY((H5Pclose(dxpl_id) >= 0), "H5Pclose succeeded");
+ VRFY((H5Dclose(dset_id) >= 0), "H5Dclose succeeded");
+ VRFY((H5Pclose(fapl_id) >= 0), "H5Pclose succeeded");
+ VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded");
+}
+
+/*
+ * A test for HDFFV-10562 which attempts to verify that using multi-chunk
+ * I/O with collective metadata reads enabled doesn't causes issues due to
+ * collective metadata reads being made only by process 0 in H5D__chunk_addrmap().
+ *
+ * Failure in this test may either cause a hang, or, due to how the MPI calls
+ * pertaining to this issue might mistakenly match up, may cause an MPI error
+ * message similar to:
+ *
+ * #008: H5Dmpio.c line 2546 in H5D__obtain_mpio_mode(): MPI_BCast failed
+ * major: Internal error (too specific to document in detail)
+ * minor: Some MPI function failed
+ * #009: H5Dmpio.c line 2546 in H5D__obtain_mpio_mode(): Message truncated, error stack:
+ *PMPI_Bcast(1600)..................: MPI_Bcast(buf=0x1df98e0, count=18, MPI_BYTE, root=0, comm=0x84000006) failed
+ *MPIR_Bcast_impl(1452).............:
+ *MPIR_Bcast(1476)..................:
+ *MPIR_Bcast_intra(1249)............:
+ *MPIR_SMP_Bcast(1088)..............:
+ *MPIR_Bcast_binomial(239)..........:
+ *MPIDI_CH3U_Receive_data_found(131): Message from rank 0 and tag 2 truncated; 2616 bytes received but buffer size is 18
+ * major: Internal error (too specific to document in detail)
+ * minor: MPI Error String
+ *
+ */
+void test_multi_chunk_io_addrmap_issue(void)
+{
+ const char *filename;
+ hsize_t start[MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS];
+ hsize_t stride[MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS];
+ hsize_t count[MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS];
+ hsize_t block[MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS];
+ hsize_t dims[MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS] = {10, 5};
+ hsize_t chunk_dims[MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS] = {5, 5};
+ hsize_t max_dims[MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS] = {H5S_UNLIMITED, H5S_UNLIMITED};
+ hid_t file_id = H5I_INVALID_HID;
+ hid_t fapl_id = H5I_INVALID_HID;
+ hid_t dset_id = H5I_INVALID_HID;
+ hid_t dcpl_id = H5I_INVALID_HID;
+ hid_t dxpl_id = H5I_INVALID_HID;
+ hid_t space_id = H5I_INVALID_HID;
+ void *read_buf = NULL;
+ int mpi_rank;
+ int data[5][5] = { {0, 1, 2, 3, 4},
+ {0, 1, 2, 3, 4},
+ {0, 1, 2, 3, 4},
+ {0, 1, 2, 3, 4},
+ {0, 1, 2, 3, 4} };
+
+ MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
+
+ filename = GetTestParameters();
+
+ fapl_id = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type);
+ VRFY((fapl_id >= 0), "create_faccess_plist succeeded");
+
+ /*
+ * Even though the testphdf5 framework currently sets collective metadata reads
+ * on the FAPL, we call it here just to be sure this is futureproof, since
+ * demonstrating this issue relies upon it.
+ */
+ VRFY((H5Pset_all_coll_metadata_ops(fapl_id, true) >= 0), "Set collective metadata reads succeeded");
+
+ file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
+ VRFY((file_id >= 0), "H5Fcreate succeeded");
+
+ space_id = H5Screate_simple(MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS, dims, max_dims);
+ VRFY((space_id >= 0), "H5Screate_simple succeeded");
+
+ dcpl_id = H5Pcreate(H5P_DATASET_CREATE);
+ VRFY((dcpl_id >= 0), "H5Pcreate succeeded");
+
+ VRFY((H5Pset_chunk(dcpl_id, MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS, chunk_dims) >= 0), "H5Pset_chunk succeeded");
+
+ dset_id = H5Dcreate2(file_id, "dset", H5T_NATIVE_INT, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
+ VRFY((dset_id >= 0), "H5Dcreate2 succeeded");
+
+ dxpl_id = H5Pcreate(H5P_DATASET_XFER);
+ VRFY((dxpl_id >= 0), "H5Pcreate succeeded");
+
+ VRFY((H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) >= 0), "H5Pset_dxpl_mpio succeeded");
+ VRFY((H5Pset_dxpl_mpio_chunk_opt(dxpl_id, H5FD_MPIO_CHUNK_MULTI_IO) >= 0), "H5Pset_dxpl_mpio_chunk_opt succeeded");
+
+ start[1] = 0;
+ stride[0] = stride[1] = 1;
+ count[0] = count[1] = 5;
+ block[0] = block[1] = 1;
+
+ if (mpi_rank == 0)
+ start[0] = 0;
+ else
+ start[0] = 5;
+
+ VRFY((H5Sselect_hyperslab(space_id, H5S_SELECT_SET, start, stride, count, block) >= 0), "H5Sselect_hyperslab succeeded");
+ if (mpi_rank != 0)
+ VRFY((H5Sselect_none(space_id) >= 0), "H5Sselect_none succeeded");
+
+ VRFY((H5Dwrite(dset_id, H5T_NATIVE_INT, H5S_ALL, space_id, dxpl_id, data) >= 0), "H5Dwrite succeeded");
+
+ VRFY((H5Fflush(file_id, H5F_SCOPE_GLOBAL) >= 0), "H5Fflush succeeded");
+
+ read_buf = HDmalloc(50 * sizeof(int));
+ VRFY((read_buf != NULL), "malloc succeeded");
+
+ VRFY((H5Dread(dset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "H5Dread succeeded");
+
+ if (read_buf) {
+ HDfree(read_buf);
+ read_buf = NULL;
+ }
+
+ VRFY((H5Sclose(space_id) >= 0), "H5Sclose succeeded");
+ VRFY((H5Pclose(dcpl_id) >= 0), "H5Pclose succeeded");
+ VRFY((H5Pclose(dxpl_id) >= 0), "H5Pclose succeeded");
+ VRFY((H5Dclose(dset_id) >= 0), "H5Dclose succeeded");
+ VRFY((H5Pclose(fapl_id) >= 0), "H5Pclose succeeded");
+ VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded");
+}
+
+/*
+ * A test for HDFFV-10562 which attempts to verify that using linked-chunk
+ * I/O with collective metadata reads enabled doesn't cause issues due to
+ * collective metadata reads being made only by process 0 in H5D__sort_chunk().
+ *
+ * NOTE: Due to the way that the threshold value which pertains to this test
+ * is currently calculated within HDF5, there are several conditions that this
+ * test must maintain. Refer to the function H5D__sort_chunk in H5Dmpio.c for
+ * a better idea of why.
+ *
+ * Condition 1: We need to make sure that the test always selects every single
+ * chunk in the dataset. It is fine if the selection is split up among multiple
+ * ranks, but their combined selection must cover the whole dataset.
+ *
+ * Condition 2: The number of chunks in the dataset divided by the number of MPI
+ * ranks must exceed or equal 10000. In other words, each MPI rank must be
+ * responsible for 10000 or more unique chunks.
+ *
+ * Condition 3: This test will currently only be reliably reproducable for 2 or 3
+ * MPI ranks. The threshold value calculated reduces to a constant 100 / mpi_size,
+ * and is compared against a default value of 30%.
+ *
+ * Failure in this test may either cause a hang, or, due to how the MPI calls
+ * pertaining to this issue might mistakenly match up, may cause an MPI error
+ * message similar to:
+ *
+ * #008: H5Dmpio.c line 2338 in H5D__sort_chunk(): MPI_BCast failed
+ * major: Internal error (too specific to document in detail)
+ * minor: Some MPI function failed
+ * #009: H5Dmpio.c line 2338 in H5D__sort_chunk(): Other MPI error, error stack:
+ *PMPI_Bcast(1600)........: MPI_Bcast(buf=0x7eae610, count=320000, MPI_BYTE, root=0, comm=0x84000006) failed
+ *MPIR_Bcast_impl(1452)...:
+ *MPIR_Bcast(1476)........:
+ *MPIR_Bcast_intra(1249)..:
+ *MPIR_SMP_Bcast(1088)....:
+ *MPIR_Bcast_binomial(250): message sizes do not match across processes in the collective routine: Received 2096 but expected 320000
+ * major: Internal error (too specific to document in detail)
+ * minor: MPI Error String
+ */
+void test_link_chunk_io_sort_chunk_issue(void)
+{
+ const char *filename;
+ hsize_t *dataset_dims = NULL;
+ hsize_t max_dataset_dims[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS];
+ hsize_t sel_dims[1];
+ hsize_t chunk_dims[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS] = { LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS };
+ hsize_t start[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS];
+ hsize_t stride[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS];
+ hsize_t count[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS];
+ hsize_t block[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS];
+ hid_t file_id = H5I_INVALID_HID;
+ hid_t fapl_id = H5I_INVALID_HID;
+ hid_t dset_id = H5I_INVALID_HID;
+ hid_t dcpl_id = H5I_INVALID_HID;
+ hid_t dxpl_id = H5I_INVALID_HID;
+ hid_t fspace_id = H5I_INVALID_HID;
+ hid_t mspace_id = H5I_INVALID_HID;
+ int mpi_rank, mpi_size;
+ void *data = NULL;
+ void *read_buf = NULL;
+
+ MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
+ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
+
+ filename = GetTestParameters();
+
+ fapl_id = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type);
+ VRFY((fapl_id >= 0), "create_faccess_plist succeeded");
+
+ /*
+ * Even though the testphdf5 framework currently sets collective metadata reads
+ * on the FAPL, we call it here just to be sure this is futureproof, since
+ * demonstrating this issue relies upon it.
+ */
+ VRFY((H5Pset_all_coll_metadata_ops(fapl_id, true) >= 0), "Set collective metadata reads succeeded");
+
+ file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
+ VRFY((file_id >= 0), "H5Fcreate succeeded");
+
+ dataset_dims = HDmalloc(LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS * sizeof(*dataset_dims));
+ VRFY((dataset_dims != NULL), "malloc succeeded");
+
+ dataset_dims[0] = LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE * mpi_size * LINK_CHUNK_IO_SORT_CHUNK_ISSUE_Y_DIM_SCALE;
+ max_dataset_dims[0] = H5S_UNLIMITED;
+
+ fspace_id = H5Screate_simple(LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS, dataset_dims, max_dataset_dims);
+ VRFY((fspace_id >= 0), "H5Screate_simple succeeded");
+
+ /*
+ * Set up chunking on the dataset in order to reproduce the problem.
+ */
+ dcpl_id = H5Pcreate(H5P_DATASET_CREATE);
+ VRFY((dcpl_id >= 0), "H5Pcreate succeeded");
+
+ VRFY((H5Pset_chunk(dcpl_id, LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS, chunk_dims) >= 0), "H5Pset_chunk succeeded");
+
+ dset_id = H5Dcreate2(file_id, LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DATASET_NAME, H5T_NATIVE_INT, fspace_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
+ VRFY((dset_id >= 0), "H5Dcreate2 succeeded");
+
+ /*
+ * Setup hyperslab selection to split the dataset among the ranks.
+ *
+ * The ranks will write rows across the dataset.
+ */
+ stride[0] = LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE;
+ count[0] = (dataset_dims[0] / LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE) / mpi_size;
+ start[0] = count[0] * mpi_rank;
+ block[0] = LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE;
+
+ VRFY((H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, start, stride, count, block) >= 0), "H5Sselect_hyperslab succeeded");
+
+ sel_dims[0] = count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE);
+
+ mspace_id = H5Screate_simple(1, sel_dims, NULL);
+ VRFY((mspace_id >= 0), "H5Screate_simple succeeded");
+
+ data = HDcalloc(1, count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE) * sizeof(int));
+ VRFY((data != NULL), "calloc succeeded");
+
+ dxpl_id = H5Pcreate(H5P_DATASET_XFER);
+ VRFY((dxpl_id >= 0), "H5Pcreate succeeded");
+
+ /*
+ * Enable collective access for the data transfer.
+ */
+ VRFY((H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) >= 0), "H5Pset_dxpl_mpio succeeded");
+
+ VRFY((H5Dwrite(dset_id, H5T_NATIVE_INT, mspace_id, fspace_id, dxpl_id, data) >= 0), "H5Dwrite succeeded");
+
+ VRFY((H5Fflush(file_id, H5F_SCOPE_GLOBAL) >= 0), "H5Fflush succeeded");
+
+ /*
+ * Ensure that linked-chunk I/O is performed since this is
+ * the particular code path where the issue lies and we don't
+ * want the library doing multi-chunk I/O behind our backs.
+ */
+ VRFY((H5Pset_dxpl_mpio_chunk_opt(dxpl_id, H5FD_MPIO_CHUNK_ONE_IO) >= 0), "H5Pset_dxpl_mpio_chunk_opt succeeded");
+
+ read_buf = HDmalloc(count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE) * sizeof(int));
+ VRFY((read_buf != NULL), "malloc succeeded");
+
+ VRFY((H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, start, stride, count, block) >= 0), "H5Sselect_hyperslab succeeded");
+
+ sel_dims[0] = count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE);
+
+ VRFY((H5Sclose(mspace_id) >= 0), "H5Sclose succeeded");
+
+ mspace_id = H5Screate_simple(1, sel_dims, NULL);
+ VRFY((mspace_id >= 0), "H5Screate_simple succeeded");
+
+ read_buf = HDrealloc(read_buf, count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE) * sizeof(int));
+ VRFY((read_buf != NULL), "realloc succeeded");
+
+ /*
+ * Finally have each rank read their section of data back from the dataset.
+ */
+ VRFY((H5Dread(dset_id, H5T_NATIVE_INT, mspace_id, fspace_id, dxpl_id, read_buf) >= 0), "H5Dread succeeded");
+
if (dataset_dims) {
- free(dataset_dims);
+ HDfree(dataset_dims);
dataset_dims = NULL;
}
if (data) {
- free(data);
+ HDfree(data);
data = NULL;
}
if (read_buf) {
- free(read_buf);
+ HDfree(read_buf);
read_buf = NULL;
}
generated by cgit v0.12 at 2024-06-26 02:32:17 (GMT)