Update compact dataset I/O routines to handle driver-level memory copy (#1054)

* Update compact dataset I/O routines to handle driver-level memory copy

* Combine compact I/O read/write struct into single I/O struct

Rename CTL memory copy flag and H5Fquery routine to get file driver
structure

* Add RELEASE.txt entry for new "ctl" memory copy operation

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