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

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

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
@@ -194,6 +195,68 @@ 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
 ==================================
 

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)

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

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)

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");
+}

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]);

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);