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[svn-r30270] Fix an issue that could occur when allocating a chunked dataset in parallel,

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with an alignment threshold set to be larger than the chunk size but smaller
than the size of the small data aggregator.

Tested: koala, ostrich (h5committest); jelly, ummon
This commit is contained in:
Neil Fortner 2016-08-08 16:56:50 -05:00
parent 36c595e5ea
commit 7de719287a
4 changed files with 112 additions and 4 deletions
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24
src/H5MFaggr.c
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@ -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 */

86
testpar/t_mdset.c
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@ -2610,6 +2610,92 @@ 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
*===========================================================================*/

5
testpar/testphdf5.c
View File

@ -496,6 +496,11 @@ 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",

1
testpar/testphdf5.h
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@ -285,6 +285,7 @@ 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);