[svn-r30278] Merge revision 30270 to the 1.8 branch

Fix an issue that could occur when allocating a chunked dataset in parallel,
with an alignment threshold set to be larger than the chunk size but smaller
than the size of the small data aggregator.

Tested: h5committest, jelly, ummon (trunk); h5committest, jelly, ummon (1.8)

5 files changed, 117 insertions, 5 deletions

diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 2c716dd..ddbd169 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -279,7 +279,11 @@ Bug Fixes since HDF5-1.8.16
 
     Parallel Library
     ----------------
-    - None
+    - Fixed a bug that could occur when allocating a chunked dataset in parallel
+      with an alignment set and an alignment threshold greater than the chunk
+      size but less than or equal to the raw data aggregator size.
+
+      (NAF, 2016/08/11, HDFFV-9969)
 
     Performance
     -------------
diff --git a/src/H5MFaggr.c b/src/H5MFaggr.c
index 21d460e..663e266 100644
--- a/src/H5MFaggr.c
+++ b/src/H5MFaggr.c
@@ -295,10 +295,26 @@ HDfprintf(stderr, "%s: Allocating block\n", FUNC);
                         if(H5MF_xfree(f, alloc_type, dxpl_id, aggr->addr, aggr->size) < 0)
                             HGOTO_ERROR(H5E_RESOURCE, H5E_CANTFREE, HADDR_UNDEF, "can't free aggregation block")
 
-                    /* Point the aggregator at the newly allocated block */
-                    aggr->addr = new_space;
-                    aggr->size = aggr->alloc_size;
-                    aggr->tot_size = aggr->alloc_size;
+                    /* If the block is not to be aligned, fold the eoa fragment
+                     * into the newly allocated aggregator, as it could have
+                     * been allocated in an aligned manner if the aggregator
+                     * block is larger than the threshold */
+                    if(eoa_frag_size && !alignment) {
+                        HDassert(eoa_frag_addr + eoa_frag_size == new_space);
+                        aggr->addr = eoa_frag_addr;
+                        aggr->size = aggr->alloc_size + eoa_frag_size;
+                        aggr->tot_size = aggr->size;
+
+                        /* Reset EOA fragment */
+                        eoa_frag_addr = HADDR_UNDEF;
+                        eoa_frag_size = 0;
+                    } /* end if */
+                    else {
+                        /* Point the aggregator at the newly allocated block */
+                        aggr->addr = new_space;
+                        aggr->size = aggr->alloc_size;
+                        aggr->tot_size = aggr->alloc_size;
+                    }
                 } /* end else */
 
 		/* Allocate space out of the metadata block */
diff --git a/testpar/t_mdset.c b/testpar/t_mdset.c
index f294b93..b4fa936 100644
--- a/testpar/t_mdset.c
+++ b/testpar/t_mdset.c
@@ -2608,6 +2608,92 @@ void rr_obj_hdr_flush_confusion_reader(MPI_Comm comm)
 #undef Writer_Root
 #undef Reader_Root
 
+
+/*
+ * Test creating a chunked dataset in parallel in a file with an alignment set
+ * and an alignment threshold large enough to avoid aligning the chunks but
+ * small enough that the raw data aggregator will be aligned if it is treated as
+ * an object that must be aligned by the library
+ */
+#define CHUNK_SIZE 72
+#define NCHUNKS 32
+#define AGGR_SIZE 2048
+#define EXTRA_ALIGN 100
+
+ void chunk_align_bug_1(void)
+ {
+    int                 mpi_rank;
+    hid_t               file_id, dset_id, fapl_id, dcpl_id, space_id;
+    hsize_t             dims = CHUNK_SIZE * NCHUNKS, cdims = CHUNK_SIZE;
+    h5_stat_size_t      file_size;
+    hsize_t             align;
+    herr_t              ret;
+    const char          *filename;
+
+    MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
+
+    filename = (const char *)GetTestParameters();
+
+    /* Create file without alignment */
+    fapl_id = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type);
+    VRFY((fapl_id >= 0), "create_faccess_plist succeeded");
+    file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
+    VRFY((file_id >= 0), "H5Fcreate succeeded");
+
+    /* Close file */
+    ret = H5Fclose(file_id);
+    VRFY((ret >= 0), "H5Fclose succeeded");
+
+    /* Get file size */
+    file_size = h5_get_file_size(filename, fapl_id);
+    VRFY((file_size >= 0), "h5_get_file_size succeeded");
+
+    /* Calculate alignment value, set to allow a chunk to squeak in between the
+     * original EOF and the aligned location of the aggregator.  Add some space
+     * for the dataset metadata */
+    align = (hsize_t)file_size + CHUNK_SIZE + EXTRA_ALIGN;
+
+    /* Set aggregator size and alignment, disable metadata aggregator */
+    HDassert(AGGR_SIZE > CHUNK_SIZE);
+    ret = H5Pset_small_data_block_size(fapl_id, AGGR_SIZE);
+    VRFY((ret >= 0), "H5Pset_small_data_block_size succeeded");
+    ret = H5Pset_meta_block_size(fapl_id, 0);
+    VRFY((ret >= 0), "H5Pset_meta_block_size succeeded");
+    ret = H5Pset_alignment(fapl_id, CHUNK_SIZE + 1, align);
+    VRFY((ret >= 0), "H5Pset_small_data_block_size succeeded");
+
+    /* Reopen file with new settings */
+    file_id = H5Fopen(filename, H5F_ACC_RDWR, fapl_id);
+    VRFY((file_id >= 0), "H5Fopen succeeded");
+
+    /* Create dataset */
+    space_id = H5Screate_simple(1, &dims, NULL);
+    VRFY((space_id >= 0), "H5Screate_simple succeeded");
+    dcpl_id = H5Pcreate(H5P_DATASET_CREATE);
+    VRFY((dcpl_id >= 0), "H5Pcreate succeeded");
+    ret = H5Pset_chunk(dcpl_id, 1, &cdims);
+    VRFY((ret >= 0), "H5Pset_chunk succeeded");
+    dset_id = H5Dcreate2(file_id, "dset", H5T_NATIVE_CHAR, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
+    VRFY((dset_id >= 0), "H5Dcreate2 succeeded");
+
+    /* Close ids */
+    ret = H5Dclose(dset_id);
+    VRFY((dset_id >= 0), "H5Dclose succeeded");
+    ret = H5Sclose(space_id);
+    VRFY((space_id >= 0), "H5Sclose succeeded");
+    ret = H5Pclose(dcpl_id);
+    VRFY((dcpl_id >= 0), "H5Pclose succeeded");
+    ret = H5Pclose(fapl_id);
+    VRFY((fapl_id >= 0), "H5Pclose succeeded");
+
+    /* Close file */
+    ret = H5Fclose(file_id);
+    VRFY((ret >= 0), "H5Fclose succeeded");
+
+    return;
+} /* end chunk_align_bug_1() */
+
+
 /*=============================================================================
  *                         End of t_mdset.c
  *===========================================================================*/
diff --git a/testpar/testphdf5.c b/testpar/testphdf5.c
index 7992e80..eaa9eb1 100644
--- a/testpar/testphdf5.c
+++ b/testpar/testphdf5.c
@@ -489,6 +489,11 @@ int main(int argc, char **argv)
                 &rr_obj_flush_confusion_params);
     }
 
+    AddTest("alnbg1",
+            chunk_align_bug_1, NULL,
+            "Chunk allocation with alignment bug.",
+            PARATESTFILE);
+
     AddTest("tldsc",
             lower_dim_size_comp_test, NULL,
             "test lower dim size comp in span tree to mpi derived type", 
diff --git a/testpar/testphdf5.h b/testpar/testphdf5.h
index efd3424..4fb668e 100644
--- a/testpar/testphdf5.h
+++ b/testpar/testphdf5.h
@@ -283,6 +283,7 @@ void io_mode_confusion(void);
 void rr_obj_hdr_flush_confusion(void);
 void rr_obj_hdr_flush_confusion_reader(MPI_Comm comm);
 void rr_obj_hdr_flush_confusion_writer(MPI_Comm comm);
+void chunk_align_bug_1(void);
 void lower_dim_size_comp_test(void);
 void link_chunk_collective_io_test(void);
 void contig_hyperslab_dr_pio_test(ShapeSameTestMethods sstest_type);