diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/H5Dchunk.c | 37 | ||||
| -rw-r--r-- | src/H5Dmpio.c | 149 | ||||
| -rw-r--r-- | src/H5Ocache.c | 28 | ||||
| -rw-r--r-- | src/H5Ofill.c | 20 | ||||
| -rw-r--r-- | src/H5Olayout.c | 4 | ||||
| -rw-r--r-- | src/H5Sselect.c | 2 | ||||
| -rw-r--r-- | src/H5detect.c | 16 |
7 files changed, 181 insertions, 75 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index f03ee8b..4906f3c 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -2935,8 +2935,41 @@ H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled, H5F_set_coll_md_read(idx_info.f, temp_cmr); #endif /* H5_HAVE_PARALLEL */ - /* Cache the information retrieved */ - H5D__chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, udata); + /* + * Cache the information retrieved. + * + * Note that if we are writing to the dataset in parallel and filters + * are involved, we skip caching this information as it is highly likely + * that the chunk information will be invalidated as a result of the + * filter operation (e.g. the chunk gets re-allocated to a different + * address in the file and/or gets re-allocated with a different size). + * If we were to cache this information, subsequent reads/writes would + * retrieve the invalid information and cause a variety of issues. + * + * It has been verified that in the serial library, when writing to chunks + * with the real chunk cache disabled and with filters involved, the + * functions within this file are correctly called in such a manner that + * this single chunk cache is always updated correctly. Therefore, this + * check is not needed for the serial library. + * + * This is an ugly and potentially frail check, but the + * H5D__chunk_cinfo_cache_reset() function is not currently available + * to functions outside of this file, so outside functions can not + * invalidate this single chunk cache. Even if the function were available, + * this check prevents us from doing the work of going through and caching + * each chunk in the write operation, when we're only going to invalidate + * the cache at the end of a parallel write anyway. + * + * - JTH (7/13/2018) + */ +#ifdef H5_HAVE_PARALLEL + if ( !( (H5F_HAS_FEATURE(idx_info.f, H5FD_FEAT_HAS_MPI)) + && (H5F_INTENT(dset->oloc.file) & H5F_ACC_RDWR) + && dset->shared->dcpl_cache.pline.nused + ) + ) +#endif + H5D__chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, udata); } /* end if */ } /* end else */ diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c index bc37840..d721ae6 100644 --- a/src/H5Dmpio.c +++ b/src/H5Dmpio.c @@ -234,7 +234,7 @@ static herr_t H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info H5D_filtered_collective_io_info_t *local_chunk_array, size_t *local_chunk_array_num_entries); static herr_t H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries, size_t array_entry_size, void **gathered_array, size_t *gathered_array_num_entries, - int nprocs, hbool_t allgather, int root, MPI_Comm comm, int (*sort_func)(const void *, const void *)); + hbool_t allgather, int root, MPI_Comm comm, int (*sort_func)(const void *, const void *)); static herr_t H5D__mpio_filtered_collective_write_type( H5D_filtered_collective_io_info_t *chunk_list, size_t num_entries, MPI_Datatype *new_mem_type, hbool_t *mem_type_derived, @@ -418,19 +418,16 @@ done: * Function: H5D__mpio_array_gatherv * * Purpose: Given an array, specified in local_array, by each processor - * calling this function, gathers each array into a single + * calling this function, collects each array into a single * array which is then either gathered to the processor * specified by root, when allgather is false, or is * distributed back to all processors when allgather is true. * - * The size of each entry and number of entries in the array - * contributed by an individual processor should be specified - * in array_entry_size and local_array_num_entries, + * The number of entries in the array contributed by an + * individual processor and the size of each entry should be + * specified in local_array_num_entries and array_entry_size, * respectively. * - * The number of processors participating in the gather - * operation should be specified for nprocs. - * * The MPI communicator to use should be specified for comm. * * If the sort_func argument is supplied, the array is sorted @@ -448,14 +445,13 @@ done: static herr_t H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries, size_t array_entry_size, void **_gathered_array, size_t *_gathered_array_num_entries, - int nprocs, hbool_t allgather, int root, MPI_Comm comm, int (*sort_func)(const void *, const void *)) + hbool_t allgather, int root, MPI_Comm comm, int (*sort_func)(const void *, const void *)) { size_t gathered_array_num_entries = 0; /* The size of the newly-constructed array */ - size_t i; void *gathered_array = NULL; /* The newly-constructed array returned to the caller */ - int *receive_counts_array = NULL; /* Array containing number of entries each process is contributing */ - int *displacements_array = NULL; /* Array of displacements where each process places its data in the final array */ - int mpi_code; + int *receive_counts_array = NULL; /* Array containing number of entries each processor is contributing */ + int *displacements_array = NULL; /* Array of displacements where each processor places its data in the final array */ + int mpi_code, mpi_rank, mpi_size; int sendcount; herr_t ret_value = SUCCEED; @@ -464,34 +460,62 @@ H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries, HDassert(_gathered_array); HDassert(_gathered_array_num_entries); - /* Determine the size of the end result array */ + MPI_Comm_size(comm, &mpi_size); + MPI_Comm_rank(comm, &mpi_rank); + + /* + * Determine the size of the end result array by collecting the number + * of entries contributed by each processor into a single total. + */ if (MPI_SUCCESS != (mpi_code = MPI_Allreduce(&local_array_num_entries, &gathered_array_num_entries, 1, MPI_INT, MPI_SUM, comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code) - /* If 0 entries resulted from the collective operation, no one is writing anything */ + /* If 0 entries resulted from the collective operation, no processor is contributing anything and there is nothing to do */ if (gathered_array_num_entries > 0) { - if (NULL == (gathered_array = H5MM_malloc(gathered_array_num_entries * array_entry_size))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate gathered array") + /* + * If gathering to all processors, all processors need to allocate space for the resulting array, as well as + * the receive counts and displacements arrays for the collective MPI_Allgatherv call. Otherwise, only the + * root processor needs to allocate the space for an MPI_Gatherv call. + */ + if (allgather || (mpi_rank == root)) { + if (NULL == (gathered_array = H5MM_malloc(gathered_array_num_entries * array_entry_size))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate gathered array") - if (NULL == (receive_counts_array = (int *) H5MM_malloc((size_t) nprocs * sizeof(int)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate receive counts array") + if (NULL == (receive_counts_array = (int *) H5MM_malloc((size_t) mpi_size * sizeof(int)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate receive counts array") - if (NULL == (displacements_array = (int *) H5MM_malloc((size_t) nprocs * sizeof(int)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate receive displacements array") + if (NULL == (displacements_array = (int *) H5MM_malloc((size_t) mpi_size * sizeof(int)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate receive displacements array") + } /* end if */ - /* Inform each process of how many entries each other process is contributing to the resulting array */ - if (MPI_SUCCESS != (mpi_code = MPI_Allgather(&local_array_num_entries, 1, MPI_INT, receive_counts_array, 1, MPI_INT, comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Allgather failed", mpi_code) + /* + * If gathering to all processors, inform each processor of how many entries each other processor is + * contributing to the resulting array by collecting the counts into each processor's "receive counts" + * array. Otherwise, inform only the root processor of how many entries each other processor is contributing. + */ + if (allgather) { + if (MPI_SUCCESS != (mpi_code = MPI_Allgather(&local_array_num_entries, 1, MPI_INT, receive_counts_array, 1, MPI_INT, comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Allgather failed", mpi_code) + } /* end if */ + else { + if (MPI_SUCCESS != (mpi_code = MPI_Gather(&local_array_num_entries, 1, MPI_INT, receive_counts_array, 1, MPI_INT, root, comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Gather failed", mpi_code) + } /* end else */ - /* Multiply each receive count by the size of the array entry, since the data is sent as bytes */ - for (i = 0; i < (size_t) nprocs; i++) - H5_CHECKED_ASSIGN(receive_counts_array[i], int, (size_t) receive_counts_array[i] * array_entry_size, size_t); + if (allgather || (mpi_rank == root)) { + size_t i; - /* Set receive buffer offsets for MPI_Allgatherv */ - displacements_array[0] = 0; - for (i = 1; i < (size_t) nprocs; i++) - displacements_array[i] = displacements_array[i - 1] + receive_counts_array[i - 1]; + /* Multiply each receive count by the size of the array entry, since the data is sent as bytes. */ + for (i = 0; i < (size_t) mpi_size; i++) + H5_CHECKED_ASSIGN(receive_counts_array[i], int, (size_t) receive_counts_array[i] * array_entry_size, size_t); + /* Set receive buffer offsets for the collective MPI_Allgatherv/MPI_Gatherv call. */ + displacements_array[0] = 0; + for (i = 1; i < (size_t) mpi_size; i++) + displacements_array[i] = displacements_array[i - 1] + receive_counts_array[i - 1]; + } /* end if */ + + /* As the data is sent as bytes, calculate the true sendcount for the data. */ H5_CHECKED_ASSIGN(sendcount, int, local_array_num_entries * array_entry_size, size_t); if (allgather) { @@ -502,10 +526,11 @@ H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries, else { if (MPI_SUCCESS != (mpi_code = MPI_Gatherv(local_array, sendcount, MPI_BYTE, gathered_array, receive_counts_array, displacements_array, MPI_BYTE, root, comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Allgatherv failed", mpi_code) + HMPI_GOTO_ERROR(FAIL, "MPI_Gatherv failed", mpi_code) } /* end else */ - if (sort_func) HDqsort(gathered_array, gathered_array_num_entries, array_entry_size, sort_func); + if (sort_func && (allgather || (mpi_rank == root))) + HDqsort(gathered_array, gathered_array_num_entries, array_entry_size, sort_func); } /* end if */ *_gathered_array = gathered_array; @@ -1295,8 +1320,7 @@ H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_in * of the chunks in the file. */ if (H5D__mpio_array_gatherv(chunk_list, chunk_list_num_entries, sizeof(H5D_filtered_collective_io_info_t), - (void **) &collective_chunk_list, &collective_chunk_list_num_entries, mpi_size, - true, 0, io_info->comm, NULL) < 0) + (void **) &collective_chunk_list, &collective_chunk_list_num_entries, true, 0, io_info->comm, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, "couldn't gather new chunk sizes") /* Collectively re-allocate the modified chunks (from each process) in the file */ @@ -1768,8 +1792,7 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i * of the chunks in the file */ if (H5D__mpio_array_gatherv(&chunk_list[i], have_chunk_to_process ? 1 : 0, sizeof(H5D_filtered_collective_io_info_t), - (void **) &collective_chunk_list, &collective_chunk_list_num_entries, mpi_size, - true, 0, io_info->comm, NULL) < 0) + (void **) &collective_chunk_list, &collective_chunk_list_num_entries, true, 0, io_info->comm, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, "couldn't gather new chunk sizes") /* Participate in the collective re-allocation of all chunks modified @@ -2655,8 +2678,8 @@ H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info, const H5D_ty * call, the gathered list will initially be sorted in increasing order of chunk offset in the file. */ if (H5D__mpio_array_gatherv(local_chunk_array, *local_chunk_array_num_entries, sizeof(H5D_filtered_collective_io_info_t), - (void **) &shared_chunks_info_array, &shared_chunks_info_array_num_entries, mpi_size, - false, 0, io_info->comm, H5D__cmp_filtered_collective_io_info_entry) < 0) + (void **) &shared_chunks_info_array, &shared_chunks_info_array_num_entries, false, 0, + io_info->comm, H5D__cmp_filtered_collective_io_info_entry) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, "couldn't gather array") /* Rank 0 redistributes any shared chunks to new owners as necessary */ @@ -2981,7 +3004,7 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk { H5D_chunk_info_t *chunk_info = NULL; H5S_sel_iter_t *mem_iter = NULL; /* Memory iterator for H5D__scatter_mem/H5D__gather_mem */ - unsigned char *mod_data = NULL; /* Chunk modification data sent by a process to a chunk's owner */ + H5S_sel_iter_t *file_iter = NULL; H5Z_EDC_t err_detect; /* Error detection info */ H5Z_cb_t filter_cb; /* I/O filter callback function */ unsigned filter_mask = 0; @@ -2989,11 +3012,13 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk hssize_t extent_npoints; hsize_t true_chunk_size; hbool_t mem_iter_init = FALSE; + hbool_t file_iter_init = FALSE; size_t buf_size; size_t i; H5S_t *dataspace = NULL; /* Other process' dataspace for the chunk */ - void *tmp_gath_buf = NULL; /* Temporary gather buffer for owner of the chunk to gather into from - application write buffer before scattering out to the chunk data buffer */ + void *tmp_gath_buf = NULL; /* Temporary gather buffer to gather into from application buffer + before scattering out to the chunk data buffer (when writing data), + or vice versa (when reading data) */ int mpi_code; herr_t ret_value = SUCCEED; @@ -3073,9 +3098,6 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information") mem_iter_init = TRUE; - if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid") - /* If this is a read operation, scatter the read chunk data to the user's buffer. * * If this is a write operation, update the chunk data buffer with the modifications @@ -3084,16 +3106,39 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk */ switch (io_info->op_type) { case H5D_IO_OP_READ: - if (H5D__scatter_mem(chunk_entry->buf, chunk_info->mspace, mem_iter, (size_t)iter_nelmts, io_info->u.rbuf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't scatter to read buffer") + if (NULL == (file_iter = (H5S_sel_iter_t *) H5MM_malloc(sizeof(H5S_sel_iter_t)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate file iterator") + + if (H5S_select_iter_init(file_iter, chunk_info->fspace, type_info->src_type_size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information") + file_iter_init = TRUE; + + if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->fspace)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid") + + if (NULL == (tmp_gath_buf = H5MM_malloc((hsize_t) iter_nelmts * type_info->src_type_size))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate temporary gather buffer") + + if (!H5D__gather_mem(chunk_entry->buf, chunk_info->fspace, file_iter, (size_t) iter_nelmts, tmp_gath_buf)) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "couldn't gather from chunk buffer") + + if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid") + + if (H5D__scatter_mem(tmp_gath_buf, chunk_info->mspace, mem_iter, (size_t) iter_nelmts, io_info->u.rbuf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't scatter to read buffer") + break; case H5D_IO_OP_WRITE: + if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid") + if (NULL == (tmp_gath_buf = H5MM_malloc((hsize_t) iter_nelmts * type_info->src_type_size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate temporary gather buffer") /* Gather modification data from the application write buffer into a temporary buffer */ - if(!H5D__gather_mem(io_info->u.wbuf, chunk_info->mspace, mem_iter, (size_t)iter_nelmts, tmp_gath_buf)) + if(!H5D__gather_mem(io_info->u.wbuf, chunk_info->mspace, mem_iter, (size_t) iter_nelmts, tmp_gath_buf)) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "couldn't gather from write buffer") if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0) @@ -3111,7 +3156,7 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk /* Scatter the owner's modification data into the chunk data buffer according to * the file space. */ - if(H5D__scatter_mem(tmp_gath_buf, chunk_info->fspace, mem_iter, (size_t)iter_nelmts, chunk_entry->buf) < 0) + if(H5D__scatter_mem(tmp_gath_buf, chunk_info->fspace, mem_iter, (size_t) iter_nelmts, chunk_entry->buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't scatter to chunk data buffer") if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0) @@ -3177,10 +3222,12 @@ done: H5MM_free(chunk_entry->async_info.receive_buffer_array); if (chunk_entry->async_info.receive_requests_array) H5MM_free(chunk_entry->async_info.receive_requests_array); - if (mod_data) - H5MM_free(mod_data); if (tmp_gath_buf) H5MM_free(tmp_gath_buf); + if (file_iter_init && H5S_SELECT_ITER_RELEASE(file_iter) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator") + if (file_iter) + H5MM_free(file_iter); if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator") if (mem_iter) diff --git a/src/H5Ocache.c b/src/H5Ocache.c index 3607839..d65942b 100644 --- a/src/H5Ocache.c +++ b/src/H5Ocache.c @@ -1430,9 +1430,10 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image /* Check for combining two adjacent 'null' messages */ if((udata->file_intent & H5F_ACC_RDWR) && - H5O_NULL_ID == id && oh->nmesgs > 0 && - H5O_NULL_ID == oh->mesg[oh->nmesgs - 1].type->id && - oh->mesg[oh->nmesgs - 1].chunkno == chunkno) { + H5O_NULL_ID == id && oh->nmesgs > 0 && + H5O_NULL_ID == oh->mesg[oh->nmesgs - 1].type->id && + oh->mesg[oh->nmesgs - 1].chunkno == chunkno) { + size_t mesgno; /* Current message to operate on */ /* Combine adjacent null messages */ @@ -1467,13 +1468,13 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image /* Point unknown messages at 'unknown' message class */ /* (Usually from future versions of the library) */ - if(id >= H5O_UNKNOWN_ID || + if(id >= H5O_UNKNOWN_ID || #ifdef H5O_ENABLE_BOGUS - id == H5O_BOGUS_VALID_ID || + id == H5O_BOGUS_VALID_ID || #endif - NULL == H5O_msg_class_g[id]) { + NULL == H5O_msg_class_g[id]) { - H5O_unknown_t *unknown; /* Pointer to "unknown" message info */ + H5O_unknown_t *unknown; /* Pointer to "unknown" message info */ /* Allocate "unknown" message info */ if(NULL == (unknown = H5FL_MALLOC(H5O_unknown_t))) @@ -1490,9 +1491,9 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image /* Check for "fail if unknown" message flags */ if(((udata->file_intent & H5F_ACC_RDWR) && - (flags & H5O_MSG_FLAG_FAIL_IF_UNKNOWN_AND_OPEN_FOR_WRITE)) - || (flags & H5O_MSG_FLAG_FAIL_IF_UNKNOWN_ALWAYS)) - HGOTO_ERROR(H5E_OHDR, H5E_BADMESG, FAIL, "unknown message with 'fail if unknown' flag found") + (flags & H5O_MSG_FLAG_FAIL_IF_UNKNOWN_AND_OPEN_FOR_WRITE)) + || (flags & H5O_MSG_FLAG_FAIL_IF_UNKNOWN_ALWAYS)) + HGOTO_ERROR(H5E_OHDR, H5E_BADMESG, FAIL, "unknown message with 'fail if unknown' flag found") /* Check for "mark if unknown" message flag, etc. */ else if((flags & H5O_MSG_FLAG_MARK_IF_UNKNOWN) && !(flags & H5O_MSG_FLAG_WAS_UNKNOWN) && @@ -1543,7 +1544,8 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image H5O_refcount_t *refcount; /* Decode ref. count message */ - HDassert(oh->version > H5O_VERSION_1); + if(oh->version <= H5O_VERSION_1) + HGOTO_ERROR(H5E_OHDR, H5E_VERSION, FAIL, "object header version does not support reference count message") refcount = (H5O_refcount_t *)(H5O_MSG_REFCOUNT->decode)(udata->f, NULL, 0, &ioflags, mesg->raw_size, mesg->raw); /* Save 'native' form of ref. count message */ @@ -1614,6 +1616,10 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image } /* end if */ done: + if(ret_value < 0 && udata->cont_msg_info->msgs) { + udata->cont_msg_info->msgs = (H5O_chunk_t *)H5FL_SEQ_FREE(H5O_cont_t, udata->cont_msg_info->msgs); + udata->cont_msg_info->alloc_nmsgs = 0; + } FUNC_LEAVE_NOAPI(ret_value) } /* H5O__chunk_deserialize() */ diff --git a/src/H5Ofill.c b/src/H5Ofill.c index 932241f..da9829b 100644 --- a/src/H5Ofill.c +++ b/src/H5Ofill.c @@ -307,11 +307,13 @@ done: *------------------------------------------------------------------------- */ static void * -H5O_fill_old_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh, +H5O_fill_old_decode(H5F_t *f, H5O_t *open_oh, unsigned H5_ATTR_UNUSED mesg_flags, unsigned H5_ATTR_UNUSED *ioflags, size_t H5_ATTR_UNUSED p_size, const uint8_t *p) { H5O_fill_t *fill = NULL; /* Decoded fill value message */ + htri_t exists = FALSE; + H5T_t *dt = NULL; void *ret_value = NULL; /* Return value */ FUNC_ENTER_NOAPI_NOINIT @@ -332,6 +334,19 @@ H5O_fill_old_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh, /* Only decode the fill value itself if there is one */ if(fill->size > 0) { + H5_CHECK_OVERFLOW(fill->size, ssize_t, size_t); + + /* Get the datatype message */ + if((exists = H5O_msg_exists_oh(open_oh, H5O_DTYPE_ID)) < 0) + HGOTO_ERROR(H5E_SYM, H5E_NOTFOUND, NULL, "unable to read object header") + if(exists) { + if((dt = H5O_msg_read_oh(f, open_oh, H5O_DTYPE_ID, NULL)) < 0) + HGOTO_ERROR(H5E_SYM, H5E_CANTGET, NULL, "can't read DTYPE message") + /* Verify size */ + if(fill->size != H5T_GET_SIZE(dt)) + HGOTO_ERROR(H5E_SYM, H5E_CANTGET, NULL, "inconsistent fill value size") + } + if(NULL == (fill->buf = H5MM_malloc((size_t)fill->size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for fill value") HDmemcpy(fill->buf, p, (size_t)fill->size); @@ -344,6 +359,9 @@ H5O_fill_old_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh, ret_value = (void*)fill; done: + if(dt) + H5O_msg_free(H5O_DTYPE_ID, dt); + if(!ret_value && fill) { if(fill->buf) H5MM_xfree(fill->buf); diff --git a/src/H5Olayout.c b/src/H5Olayout.c index d8f05f0..5f16837 100644 --- a/src/H5Olayout.c +++ b/src/H5Olayout.c @@ -125,8 +125,8 @@ H5O__layout_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, /* Dimensionality */ ndims = *p++; - if(ndims > H5O_LAYOUT_NDIMS) - HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "dimensionality is too large") + if(!ndims || ndims > H5O_LAYOUT_NDIMS) + HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "dimensionality is out of range") /* Layout class */ mesg->type = (H5D_layout_t)*p++; diff --git a/src/H5Sselect.c b/src/H5Sselect.c index 08ac255..ec74523 100644 --- a/src/H5Sselect.c +++ b/src/H5Sselect.c @@ -160,7 +160,7 @@ H5S_select_release(H5S_t *ds) HDassert(ds); /* Call the selection type's release function */ - if((ret_value = (*ds->select.type->release)(ds)) < 0) + if((ds->select.type) && ((ret_value = (*ds->select.type->release)(ds)) < 0)) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection") done: diff --git a/src/H5detect.c b/src/H5detect.c index 6ad45aa..2d33a3d 100644 --- a/src/H5detect.c +++ b/src/H5detect.c @@ -55,13 +55,13 @@ static const char *FileHeader = "\n\ #include "H5Rpublic.h" #if defined(__has_attribute) -#if __has_attribute(no_sanitize) -#define HDF_NO_UBSAN __attribute__((no_sanitize("undefined"))) +# if __has_attribute(no_sanitize_address) +# define HDF_NO_UBSAN __attribute__((no_sanitize_address)) +# else +# define HDF_NO_UBSAN +# endif #else -#define HDF_NO_UBSAN -#endif -#else -#define HDF_NO_UBSAN +# define HDF_NO_UBSAN #endif #define MAXDETECT 64 @@ -1675,11 +1675,13 @@ detect_alignments(void) */ static int verify_signal_handlers(int signum, void (*handler)(int)) { -#if defined(__has_feature) +#if defined(__has_feature) /* Clang */ #if __has_feature(address_sanitizer) || __has_feature(thread_sanitizer) /* Under the address and thread sanitizers, don't raise any signals. */ return 0; #endif +#elif defined(__SANITIZE_ADDRESS__) || defined(__SANITIZE_THREAD__) /* GCC */ + return 0; #endif void (*save_handler)(int) = HDsignal(signum, handler); volatile int i, val; |