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authorLarry Knox <lrknox@hdfgroup.org>2018-08-27 21:24:20 (GMT)
committerLarry Knox <lrknox@hdfgroup.org>2018-08-28 13:25:38 (GMT)
commitf4f2e83d2233699aaf32f2e7f715504b43542d42 (patch)
tree90cd4aa54908ebf1beef5941cecac86238547809
parentebc3d3eda5b9e5c3090322e19898e47141efeadd (diff)
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Merge pull request #1224 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to develop
* commit '763b95c6b0f027025a5a5bfb203b77317ffa2368': Update RELEASE.txt with suggested changes Update MANIFEST file for new t_coll_md_read.c file Remove now-unused local variable Add fix for HDFFV-10501
-rw-r--r--MANIFEST1
-rw-r--r--release_docs/RELEASE.txt63
-rw-r--r--src/H5Dmpio.c18
-rw-r--r--testpar/CMakeLists.txt1
-rw-r--r--testpar/Makefile.am2
-rw-r--r--testpar/t_coll_md_read.c199
-rw-r--r--testpar/testphdf5.c3
-rw-r--r--testpar/testphdf5.h1
8 files changed, 270 insertions, 18 deletions
diff --git a/MANIFEST b/MANIFEST
index 257a7c7..3b92b1a 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1248,6 +1248,7 @@
./testpar/t_cache_image.c
./testpar/t_chunk_alloc.c
./testpar/t_coll_chunk.c
+./testpar/t_coll_md_read.c
./testpar/t_dset.c
./testpar/t_file.c
./testpar/t_file_image.c
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 872bced..c022d73 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -34,6 +34,7 @@ CONTENTS
- New Features
- Support for new platforms and languages
+- Bug Fixes since HDF5-1.10.3
- Bug Fixes since HDF5-1.10.2
- Supported Platforms
- Tested Configuration Features Summary
@@ -229,6 +230,68 @@ Support for new platforms, languages and compilers.
=======================================
-
+Bug Fixes since HDF5-1.10.3 release
+==================================
+
+ Library
+ -------
+ - A bug was discovered in the parallel library where an application
+ would hang if a collective read/write of a chunked dataset occurred
+ when collective metadata reads were enabled and some of the ranks
+ had no selection in the dataset's dataspace. The ranks which had no
+ selection in the dataset's dataspace called H5D__chunk_addrmap() to
+ retrieve the lowest chunk address in the dataset. This is because we
+ require reads/writes to be performed in strictly non-decreasing order
+ of chunk address in the file.
+
+ When the chunk index used was a version 1 or 2 B-tree, these
+ non-participating ranks would issue a collective MPI_Bcast() call
+ that the participating ranks would not issue, causing the hang. Since
+ the non-participating ranks are not actually reading/writing anything,
+ the H5D__chunk_addrmap() call can be safely removed and the address used
+ for the read/write can be set to an arbitrary number (0 was chosen).
+
+ (JTH - 2018/08/25, HDFFV-10501)
+
+ Configuration
+ -------------
+ -
+
+ Performance
+ -------------
+ -
+
+ Fortran
+ --------
+ -
+
+ Tools
+ -----
+ -
+
+ High-Level APIs:
+ ------
+ -
+
+ Fortran High-Level APIs:
+ ------
+ -
+
+ Documentation
+ -------------
+ -
+
+ F90 APIs
+ --------
+ -
+
+ C++ APIs
+ --------
+ -
+
+ Testing
+ -------
+
Bug Fixes since HDF5-1.10.2 release
==================================
diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c
index 9bffd8b..a669593 100644
--- a/src/H5Dmpio.c
+++ b/src/H5Dmpio.c
@@ -925,7 +925,6 @@ H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *typ
hbool_t chunk_final_ftype_is_derived = FALSE;
H5D_storage_t ctg_store; /* Storage info for "fake" contiguous dataset */
size_t total_chunks;
- haddr_t *total_chunk_addr_array = NULL;
MPI_Datatype *chunk_mtype = NULL;
MPI_Datatype *chunk_ftype = NULL;
MPI_Aint *chunk_disp_array = NULL;
@@ -1146,20 +1145,7 @@ if(H5DEBUG(D))
mpi_buf_count = (hsize_t)1;
} /* end if */
else { /* no selection at all for this process */
- /* Allocate chunking information */
- if(NULL == (total_chunk_addr_array = (haddr_t *)H5MM_malloc(sizeof(haddr_t) * total_chunks)))
- HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate total chunk address arraybuffer")
-
- /* Retrieve chunk address map */
- if(H5D__chunk_addrmap(io_info, total_chunk_addr_array) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address")
-
- /* Get chunk with lowest address */
- ctg_store.contig.dset_addr = HADDR_MAX;
- for(u = 0; u < total_chunks; u++)
- if(total_chunk_addr_array[u] < ctg_store.contig.dset_addr)
- ctg_store.contig.dset_addr = total_chunk_addr_array[u];
- HDassert(ctg_store.contig.dset_addr != HADDR_MAX);
+ ctg_store.contig.dset_addr = 0;
/* Set the MPI datatype */
chunk_final_ftype = MPI_BYTE;
@@ -1187,8 +1173,6 @@ if(H5DEBUG(D))
HDfprintf(H5DEBUG(D),"before freeing memory inside H5D_link_collective_io ret_value = %d\n", ret_value);
#endif
/* Release resources */
- if(total_chunk_addr_array)
- H5MM_xfree(total_chunk_addr_array);
if(chunk_addr_info_array)
H5MM_xfree(chunk_addr_info_array);
if(chunk_mtype)
diff --git a/testpar/CMakeLists.txt b/testpar/CMakeLists.txt
index c08a69e..0b3cbe3 100644
--- a/testpar/CMakeLists.txt
+++ b/testpar/CMakeLists.txt
@@ -17,6 +17,7 @@ set (testphdf5_SOURCES
${HDF5_TEST_PAR_SOURCE_DIR}/t_chunk_alloc.c
${HDF5_TEST_PAR_SOURCE_DIR}/t_filter_read.c
${HDF5_TEST_PAR_SOURCE_DIR}/t_prop.c
+ ${HDF5_TEST_PAR_SOURCE_DIR}/t_coll_md_read.c
)
#-- Adding test for testhdf5
diff --git a/testpar/Makefile.am b/testpar/Makefile.am
index 5c7cb26..7262ca6 100644
--- a/testpar/Makefile.am
+++ b/testpar/Makefile.am
@@ -29,7 +29,7 @@ check_PROGRAMS = $(TEST_PROG_PARA)
testphdf5_SOURCES=testphdf5.c t_dset.c t_file.c t_file_image.c t_mdset.c \
t_ph5basic.c t_coll_chunk.c t_span_tree.c t_chunk_alloc.c t_filter_read.c \
- t_prop.c
+ t_prop.c t_coll_md_read.c
# The tests all depend on the hdf5 library and the test library
LDADD = $(LIBH5TEST) $(LIBHDF5)
diff --git a/testpar/t_coll_md_read.c b/testpar/t_coll_md_read.c
new file mode 100644
index 0000000..f945d2b
--- /dev/null
+++ b/testpar/t_coll_md_read.c
@@ -0,0 +1,199 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the COPYING file, which can be found at the root of the source code *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
+ * If you do not have access to either file, you may request a copy from *
+ * help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * A test suite to test HDF5's collective metadata read capabilities, as enabled
+ * by making a call to H5Pset_all_coll_metadata_ops().
+ */
+
+#include "testphdf5.h"
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+/*
+ * Define the non-participating process as the "last"
+ * rank to avoid any weirdness potentially caused by
+ * an if (mpi_rank == 0) check.
+ */
+#define PARTIAL_NO_SELECTION_NO_SEL_PROCESS (mpi_rank == mpi_size - 1)
+#define PARTIAL_NO_SELECTION_DATASET_NAME "partial_no_selection_dset"
+#define PARTIAL_NO_SELECTION_DATASET_NDIMS 2
+#define PARTIAL_NO_SELECTION_Y_DIM_SCALE 5
+#define PARTIAL_NO_SELECTION_X_DIM_SCALE 5
+
+/*
+ * 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
+ * do not have any selection in a dataset's dataspace, while others do. The ranks
+ * which have no selection during the read/write operation called H5D__chunk_addrmap()
+ * to retrieve the lowest chunk address, since we require that the read/write be done
+ * in strictly non-decreasing order of chunk address. For version 1 and 2 B-trees,
+ * this caused the non-participating ranks to issue a collective MPI_Bcast() call
+ * which the other ranks did not issue, thus causing a hang.
+ *
+ * However, since these ranks are not actually reading/writing anything, this call
+ * can simply be removed and the address used for the read/write can be set to an
+ * arbitrary number (0 was chosen).
+ */
+void test_partial_no_selection_coll_md_read(void)
+{
+ const char *filename;
+ hsize_t *dataset_dims = NULL;
+ hsize_t max_dataset_dims[PARTIAL_NO_SELECTION_DATASET_NDIMS];
+ hsize_t sel_dims[1];
+ hsize_t chunk_dims[PARTIAL_NO_SELECTION_DATASET_NDIMS] = { PARTIAL_NO_SELECTION_Y_DIM_SCALE, PARTIAL_NO_SELECTION_X_DIM_SCALE };
+ hsize_t start[PARTIAL_NO_SELECTION_DATASET_NDIMS];
+ 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;
+ 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 = malloc(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;
+ dataset_dims[1] = PARTIAL_NO_SELECTION_X_DIM_SCALE * mpi_size;
+ max_dataset_dims[0] = H5S_UNLIMITED;
+ max_dataset_dims[1] = H5S_UNLIMITED;
+
+ fspace_id = H5Screate_simple(PARTIAL_NO_SELECTION_DATASET_NDIMS, 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, PARTIAL_NO_SELECTION_DATASET_NDIMS, chunk_dims) >= 0), "H5Pset_chunk succeeded");
+
+ dset_id = H5Dcreate2(file_id, PARTIAL_NO_SELECTION_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.
+ */
+ start[0] = PARTIAL_NO_SELECTION_Y_DIM_SCALE * mpi_rank;
+ start[1] = 0;
+ stride[0] = PARTIAL_NO_SELECTION_Y_DIM_SCALE;
+ stride[1] = PARTIAL_NO_SELECTION_X_DIM_SCALE;
+ count[0] = 1;
+ count[1] = mpi_size;
+ block[0] = PARTIAL_NO_SELECTION_Y_DIM_SCALE;
+ block[1] = PARTIAL_NO_SELECTION_X_DIM_SCALE;
+
+ VRFY((H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, start, stride, count, block) >= 0), "H5Sselect_hyperslab succeeded");
+
+ sel_dims[0] = count[1] * (PARTIAL_NO_SELECTION_Y_DIM_SCALE * PARTIAL_NO_SELECTION_X_DIM_SCALE);
+
+ 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));
+ 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 = malloc(count[1] * (PARTIAL_NO_SELECTION_Y_DIM_SCALE * PARTIAL_NO_SELECTION_X_DIM_SCALE) * sizeof(int));
+ VRFY((read_buf != NULL), "malloc succeeded");
+
+ /*
+ * Make sure to call H5Sselect_none() on the non-participating process.
+ */
+ if (PARTIAL_NO_SELECTION_NO_SEL_PROCESS) {
+ VRFY((H5Sselect_none(fspace_id) >= 0), "H5Sselect_none succeeded");
+ VRFY((H5Sselect_none(mspace_id) >= 0), "H5Sselect_none 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");
+
+ /*
+ * 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");
+ }
+
+ if (dataset_dims) {
+ free(dataset_dims);
+ dataset_dims = NULL;
+ }
+
+ if (data) {
+ free(data);
+ data = NULL;
+ }
+
+ if (read_buf) {
+ free(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");
+}
diff --git a/testpar/testphdf5.c b/testpar/testphdf5.c
index 87d9056..69b66ae 100644
--- a/testpar/testphdf5.c
+++ b/testpar/testphdf5.c
@@ -547,6 +547,9 @@ int main(int argc, char **argv)
AddTest("denseattr", test_dense_attr, NULL,
"Store Dense Attributes", PARATESTFILE);
+ AddTest("noselcollmdread", test_partial_no_selection_coll_md_read, NULL,
+ "Collective Metadata read with some ranks having no selection", PARATESTFILE);
+
/* Display testing information */
TestInfo(argv[0]);
diff --git a/testpar/testphdf5.h b/testpar/testphdf5.h
index 322cb9b..176574e 100644
--- a/testpar/testphdf5.h
+++ b/testpar/testphdf5.h
@@ -294,6 +294,7 @@ void file_image_daisy_chain_test(void);
void compress_readAll(void);
#endif /* H5_HAVE_FILTER_DEFLATE */
void test_dense_attr(void);
+void test_partial_no_selection_coll_md_read(void);
/* commonly used prototypes */
hid_t create_faccess_plist(MPI_Comm comm, MPI_Info info, int l_facc_type);