diff options
| -rw-r--r-- | release_docs/RELEASE.txt | 42 | ||||
| -rw-r--r-- | src/H5Dcompact.c | 106 | ||||
| -rw-r--r-- | src/H5FDpublic.h | 24 | ||||
| -rw-r--r-- | src/H5Fprivate.h | 5 | ||||
| -rw-r--r-- | src/H5Fquery.c | 23 |
5 files changed, 187 insertions, 13 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 0c3a398..ec558c6 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -469,6 +469,48 @@ New Features Library: -------- + - Adds new file driver-level memory copy operation for + "ctl" callback and updates compact dataset I/O routines + to utilize it + + When accessing an HDF5 file with a file driver that uses + memory allocated in special ways (e.g., without standard + library's `malloc`), a crash could be observed when HDF5 + tries to perform `memcpy` operations on such a memory + region. + + These changes add a new H5FD_FEAT_MEMMANAGE VFD feature + flag, which, if specified as supported by a VFD, will + inform HDF5 that the VFD either uses special memory + management routines or wishes to perform memory management + in a specific way. Therefore, this flag instructs HDF5 to + ask the file driver to perform memory management for + certain operations. + + These changes also introduce a new "ctl" callback + operation identified by the H5FD_CTL__MEM_COPY op code. + This operation simply asks a VFD to perform a memory copy. + The arguments to this operation are passed to the "ctl" + callback's "input" parameter as a pointer to a struct + defined as: + + struct H5FD_ctl_memcpy_args_t { + void * dstbuf; /**< Destination buffer */ + hsize_t dst_off; /**< Offset within destination buffer */ + const void *srcbuf; /**< Source buffer */ + hsize_t src_off; /**< Offset within source buffer */ + size_t len; /**< Length of data to copy from source buffer */ + } H5FD_ctl_memcpy_args_t; + + Further, HDF5's compact dataset I/O routines were + identified as a problematic area that could cause a crash + for VFDs that make use of special memory management. Those + I/O routines were therefore updated to make use of this new + "ctl" callback operation in order to ask the underlying + file driver to correctly handle memory copies. + + (JTH - 2021/09/28) + - Adds new "ctl" callback to VFD H5FD_class_t structure with the following prototype: diff --git a/src/H5Dcompact.c b/src/H5Dcompact.c index fe41298..88926c2 100644 --- a/src/H5Dcompact.c +++ b/src/H5Dcompact.c @@ -47,6 +47,15 @@ /* Local Typedefs */ /******************/ +/* Callback info for I/O operation when file driver + * wishes to do its own memory management + */ +typedef struct H5D_compact_iovv_memmanage_ud_t { + H5F_shared_t *f_sh; /* Shared file for dataset */ + void * dstbuf; /* Pointer to buffer to be read into/written into */ + const void * srcbuf; /* Pointer to buffer to be read from/written from */ +} H5D_compact_iovv_memmanage_ud_t; + /********************/ /* Local Prototypes */ /********************/ @@ -57,6 +66,7 @@ static hbool_t H5D__compact_is_space_alloc(const H5O_storage_t *storage); static herr_t H5D__compact_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space, H5D_chunk_map_t *cm); +static herr_t H5D__compact_iovv_memmanage_cb(hsize_t dst_off, hsize_t src_off, size_t len, void *_udata); static ssize_t H5D__compact_readvv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_size_arr[], hsize_t dset_offset_arr[], size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[]); @@ -240,6 +250,48 @@ H5D__compact_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t H5_ATTR } /* end H5D__compact_io_init() */ /*------------------------------------------------------------------------- + * Function: H5D__compact_iovv_memmanage_cb + * + * Purpose: Callback operator for H5D__compact_readvv()/_writevv() to + * send a memory copy request to the underlying file driver. + * + * Return: Non-negative on success/Negative on failure + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__compact_iovv_memmanage_cb(hsize_t dst_off, hsize_t src_off, size_t len, void *_udata) +{ + H5D_compact_iovv_memmanage_ud_t *udata = (H5D_compact_iovv_memmanage_ud_t *)_udata; + H5FD_ctl_memcpy_args_t op_args; + uint64_t op_flags; + H5FD_t * file_handle = NULL; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_STATIC + + /* Retrieve pointer to file driver structure for ctl call */ + if (H5F_shared_get_file_driver(udata->f_sh, &file_handle) < 0) + HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "can't get file handle") + + /* Setup operation flags and arguments */ + op_flags = H5FD_CTL__ROUTE_TO_TERMINAL_VFD_FLAG | H5FD_CTL__FAIL_IF_UNKNOWN_FLAG; + + op_args.dstbuf = udata->dstbuf; + op_args.dst_off = dst_off; + op_args.srcbuf = udata->srcbuf; + op_args.src_off = src_off; + op_args.len = len; + + /* Make request to file driver */ + if (H5FD_ctl(file_handle, H5FD_CTL__MEM_COPY, op_flags, &op_args, NULL) < 0) + HGOTO_ERROR(H5E_IO, H5E_FCNTL, FAIL, "VFD memcpy request failed") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__compact_iovv_memmanage_cb() */ + +/*------------------------------------------------------------------------- * Function: H5D__compact_readvv * * Purpose: Reads some data vectors from a dataset into a buffer. @@ -268,11 +320,28 @@ H5D__compact_readvv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t * HDassert(io_info); - /* Use the vectorized memory copy routine to do actual work */ - if ((ret_value = H5VM_memcpyvv(io_info->u.rbuf, mem_max_nseq, mem_curr_seq, mem_size_arr, mem_offset_arr, - io_info->store->compact.buf, dset_max_nseq, dset_curr_seq, dset_size_arr, - dset_offset_arr)) < 0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed") + /* Check if file driver wishes to do its own memory management */ + if (H5F_SHARED_HAS_FEATURE(io_info->f_sh, H5FD_FEAT_MEMMANAGE)) { + H5D_compact_iovv_memmanage_ud_t udata; + + /* Set up udata for memory copy operation */ + udata.f_sh = io_info->f_sh; + udata.dstbuf = io_info->u.rbuf; + udata.srcbuf = io_info->store->compact.buf; + + /* Request that file driver does the memory copy */ + if ((ret_value = H5VM_opvv(mem_max_nseq, mem_curr_seq, mem_size_arr, mem_offset_arr, dset_max_nseq, + dset_curr_seq, dset_size_arr, dset_offset_arr, + H5D__compact_iovv_memmanage_cb, &udata)) < 0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed") + } + else { + /* Use the vectorized memory copy routine to do actual work */ + if ((ret_value = H5VM_memcpyvv(io_info->u.rbuf, mem_max_nseq, mem_curr_seq, mem_size_arr, + mem_offset_arr, io_info->store->compact.buf, dset_max_nseq, + dset_curr_seq, dset_size_arr, dset_offset_arr)) < 0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed") + } done: FUNC_LEAVE_NOAPI(ret_value) @@ -310,11 +379,28 @@ H5D__compact_writevv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t HDassert(io_info); - /* Use the vectorized memory copy routine to do actual work */ - if ((ret_value = H5VM_memcpyvv(io_info->store->compact.buf, dset_max_nseq, dset_curr_seq, dset_size_arr, - dset_offset_arr, io_info->u.wbuf, mem_max_nseq, mem_curr_seq, mem_size_arr, - mem_offset_arr)) < 0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed") + /* Check if file driver wishes to do its own memory management */ + if (H5F_SHARED_HAS_FEATURE(io_info->f_sh, H5FD_FEAT_MEMMANAGE)) { + H5D_compact_iovv_memmanage_ud_t udata; + + /* Set up udata for memory copy operation */ + udata.f_sh = io_info->f_sh; + udata.dstbuf = io_info->store->compact.buf; + udata.srcbuf = io_info->u.wbuf; + + /* Request that file driver does the memory copy */ + if ((ret_value = H5VM_opvv(dset_max_nseq, dset_curr_seq, dset_size_arr, dset_offset_arr, mem_max_nseq, + mem_curr_seq, mem_size_arr, mem_offset_arr, H5D__compact_iovv_memmanage_cb, + &udata)) < 0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed") + } + else { + /* Use the vectorized memory copy routine to do actual work */ + if ((ret_value = H5VM_memcpyvv(io_info->store->compact.buf, dset_max_nseq, dset_curr_seq, + dset_size_arr, dset_offset_arr, io_info->u.wbuf, mem_max_nseq, + mem_curr_seq, mem_size_arr, mem_offset_arr)) < 0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed") + } /* Mark the compact dataset's buffer as dirty */ *io_info->store->compact.dirty = TRUE; diff --git a/src/H5FDpublic.h b/src/H5FDpublic.h index a72dc80..d774210 100644 --- a/src/H5FDpublic.h +++ b/src/H5FDpublic.h @@ -170,6 +170,14 @@ * enabled may be used as the Write-Only (W/O) channel driver. */ #define H5FD_FEAT_DEFAULT_VFD_COMPATIBLE 0x00008000 +/* + * Defining H5FD_FEAT_MEMMANAGE for a VFL driver means that + * the driver uses special memory management routines or wishes + * to do memory management in a specific manner. Therefore, HDF5 + * should request that the driver handle any memory management + * operations when appropriate. + */ +#define H5FD_FEAT_MEMMANAGE 0x00010000 /* ctl function definitions: */ #define H5FD_CTL_OPC_RESERVED 512 /* Opcodes below this value are reserved for library use */ @@ -185,6 +193,9 @@ #define H5FD_CTL__GET_MPI_COMMUNICATOR_OPCODE 2 #define H5FD_CTL__GET_MPI_RANK_OPCODE 3 #define H5FD_CTL__GET_MPI_SIZE_OPCODE 4 +#define H5FD_CTL__MEM_ALLOC 5 +#define H5FD_CTL__MEM_FREE 6 +#define H5FD_CTL__MEM_COPY 7 /* ctl function flags: */ @@ -367,6 +378,19 @@ typedef struct { } H5FD_file_image_callbacks_t; //! <!-- [H5FD_file_image_callbacks_t_snip] --> +/** + * Define structure to hold "ctl memory copy" parameters + */ +//! <!-- [H5FD_ctl_memcpy_args_t_snip] --> +typedef struct H5FD_ctl_memcpy_args_t { + void * dstbuf; /**< Destination buffer */ + hsize_t dst_off; /**< Offset within destination buffer */ + const void *srcbuf; /**< Source buffer */ + hsize_t src_off; /**< Offset within source buffer */ + size_t len; /**< Length of data to copy from source buffer */ +} H5FD_ctl_memcpy_args_t; +//! <!-- [H5FD_ctl_memcpy_args_t_snip] --> + /********************/ /* Public Variables */ /********************/ diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h index 051abd9..a5ccbab 100644 --- a/src/H5Fprivate.h +++ b/src/H5Fprivate.h @@ -24,11 +24,9 @@ typedef struct H5F_t H5F_t; /* Include package's public header */ #include "H5Fpublic.h" -/* Public headers needed by this file */ -#include "H5FDpublic.h" /* File drivers */ - /* Private headers needed by this file */ #include "H5MMprivate.h" /* Memory management */ +#include "H5FDprivate.h" /* File drivers */ #ifdef H5_HAVE_PARALLEL #include "H5Pprivate.h" /* Property lists */ #endif /* H5_HAVE_PARALLEL */ @@ -906,6 +904,7 @@ H5_DLL hbool_t H5F_shared_has_feature(const H5F_shared_t *f, unsigned feature); H5_DLL hbool_t H5F_has_feature(const H5F_t *f, unsigned feature); H5_DLL haddr_t H5F_shared_get_eoa(const H5F_shared_t *f_sh, H5FD_mem_t type); H5_DLL haddr_t H5F_get_eoa(const H5F_t *f, H5FD_mem_t type); +H5_DLL herr_t H5F_shared_get_file_driver(const H5F_shared_t *f_sh, H5FD_t **file_handle); H5_DLL herr_t H5F_get_vfd_handle(const H5F_t *file, hid_t fapl, void **file_handle); /* File mounting routines */ diff --git a/src/H5Fquery.c b/src/H5Fquery.c index 04792b4..a625897 100644 --- a/src/H5Fquery.c +++ b/src/H5Fquery.c @@ -950,6 +950,29 @@ done: } /* end H5F_get_eoa() */ /*------------------------------------------------------------------------- + * Function: H5F_shared_get_file_driver + * + * Purpose: Returns a pointer to the file driver structure of the + * file's 'shared' structure. + * + * Return: file handle on success/abort on failure (shouldn't fail) + *------------------------------------------------------------------------- + */ +herr_t +H5F_shared_get_file_driver(const H5F_shared_t *f_sh, H5FD_t **file_handle) +{ + /* Use FUNC_ENTER_NOAPI_NOINIT_NOERR here to avoid performance issues */ + FUNC_ENTER_NOAPI_NOINIT_NOERR + + HDassert(f_sh); + HDassert(file_handle); + + *file_handle = f_sh->lf; + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* end H5F_shared_get_file_driver() */ + +/*------------------------------------------------------------------------- * Function: H5F_get_vfd_handle * * Purpose: Returns a pointer to the file handle of the low-level file |