[svn-r12870] Add a new macro H5_HAVE_DIRECT_ALIGN in configure.in. Some systems like copper and sleipnir

doesn't require alignment for Direct I/O.  If this's true, write or read data just like sec2
does.

2 files changed, 84 insertions, 5 deletions

diff --git a/src/H5FDdirect.c b/src/H5FDdirect.c
index 8a6a27a..89bf099 100644
--- a/src/H5FDdirect.c
+++ b/src/H5FDdirect.c
@@ -861,6 +861,8 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, ha
 {
     H5FD_direct_t	*file = (H5FD_direct_t*)_file;
     ssize_t		nbytes;
+    herr_t      	ret_value=SUCCEED;       /* Return value */
+#ifdef H5_HAVE_DIRECT_ALIGN
     size_t		alloc_size;
     void		*copy_buf, *p2, *p3;
     size_t		_boundary;
@@ -868,7 +870,7 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, ha
     size_t		_cbsize;
     haddr_t		copy_addr = addr;
     size_t		copy_size = size;
-    herr_t      	ret_value=SUCCEED;       /* Return value */
+#endif /*H5_HAVE_DIRECT_ALIGN*/
 
     FUNC_ENTER_NOAPI(H5FD_direct_read, FAIL)
 
@@ -883,6 +885,7 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, ha
     if (addr+size>file->eoa)
         HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow")
 
+#ifdef H5_HAVE_DIRECT_ALIGN /* If the system requires data to be aligned */
     /* Get the memory boundary for alignment, file system block size, and maximal 
      * copy buffer size.
      */
@@ -928,7 +931,7 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, ha
 	    else
 	    	alloc_size = _cbsize;
 	    if (HDposix_memalign(&copy_buf, _boundary, alloc_size) != 0)
-		HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "posix_memalign failed")
+		HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "HDposix_memalign failed")
 
 	    /* look for the aligned position for reading the data */
 	    if(file_seek(file->fd, (file_offset_t)(copy_addr - copy_addr % _fbsize), SEEK_SET) < 0)
@@ -985,6 +988,42 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, ha
 	    	HDfree(copy_buf);
     }
 
+#else /*H5_HAVE_DIRECT_ALIGN*/
+    /* If the system doesn't require data to be aligned, read the data in 
+     * the same way as sec2 driver.
+     */
+
+    /* Seek to the correct location */
+    if ((addr!=file->pos || OP_READ!=file->op) &&
+            file_seek(file->fd, (file_offset_t)addr, SEEK_SET)<0)
+        HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position")
+
+    /*
+     * Read data, being careful of interrupted system calls, partial results,
+     * and the end of the file.
+     */
+    while (size>0) {
+        do {
+            nbytes = HDread(file->fd, buf, size);
+        } while (-1==nbytes && EINTR==errno);
+        if (-1==nbytes) /* error */
+            HSYS_GOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed")
+        if (0==nbytes) {
+            /* end of file but not end of format address space */
+            HDmemset(buf, 0, size);
+            break;
+        }
+        assert(nbytes>=0);
+        assert((size_t)nbytes<=size);
+        H5_CHECK_OVERFLOW(nbytes,ssize_t,size_t);
+        size -= (size_t)nbytes;
+        H5_CHECK_OVERFLOW(nbytes,ssize_t,haddr_t);
+        addr += (haddr_t)nbytes;
+        buf = (char*)buf + nbytes;
+    }
+
+#endif /*H5_HAVE_DIRECT_ALIGN*/
+
     /* Update current position */
     file->pos = addr;
     file->op = OP_READ;
@@ -1024,6 +1063,8 @@ H5FD_direct_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, h
 {
     H5FD_direct_t	*file = (H5FD_direct_t*)_file;
     ssize_t		nbytes;
+    herr_t      	ret_value=SUCCEED;       /* Return value */
+#ifdef H5_HAVE_DIRECT_ALIGN
     size_t		alloc_size;
     void		*copy_buf, *p1, *p3;
     size_t		_boundary;
@@ -1031,7 +1072,7 @@ H5FD_direct_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, h
     size_t		_cbsize;
     haddr_t             copy_addr = addr;
     size_t             	copy_size = size;
-    herr_t      	ret_value=SUCCEED;       /* Return value */
+#endif /*H5_HAVE_DIRECT_ALIGN*/
 
     FUNC_ENTER_NOAPI(H5FD_direct_write, FAIL)
 
@@ -1046,6 +1087,7 @@ H5FD_direct_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, h
     if (addr+size>file->eoa)
         HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow")
 
+#ifdef H5_HAVE_DIRECT_ALIGN /* If the system requires data to be aligned */
     /* Get the memory boundary for alignment, file system block size, and maximal 
      * copy buffer size.
      */
@@ -1088,7 +1130,7 @@ H5FD_direct_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, h
 		alloc_size = _cbsize;
 
 	    if (HDposix_memalign(&copy_buf, _boundary, alloc_size) != 0)
-		HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "posix_memalign failed")
+		HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "HDposix_memalign failed")
 
 	    /* look for the right position for reading the data */
 	    if(file_seek(file->fd, (file_offset_t)(copy_addr - copy_addr % _fbsize), SEEK_SET) < 0)
@@ -1162,6 +1204,37 @@ H5FD_direct_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, h
 	    HDfree(copy_buf);
     }
 
+#else /*H5_HAVE_DIRECT_ALIGN*/
+    /* If the system doesn't require data to be aligned, write the data in 
+     * the same way as sec2 driver.
+     */
+
+    /* Seek to the correct location */
+    if ((addr!=file->pos || OP_WRITE!=file->op) &&
+            file_seek(file->fd, (file_offset_t)addr, SEEK_SET)<0)
+        HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position")
+
+    /*
+     * Write the data, being careful of interrupted system calls and partial
+     * results
+     */
+    while (size>0) {
+        do {
+            nbytes = HDwrite(file->fd, buf, size);
+        } while (-1==nbytes && EINTR==errno);
+        if (-1==nbytes) /* error */
+            HSYS_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed")
+        assert(nbytes>0);
+        assert((size_t)nbytes<=size);
+        H5_CHECK_OVERFLOW(nbytes,ssize_t,size_t);
+        size -= (size_t)nbytes;
+        H5_CHECK_OVERFLOW(nbytes,ssize_t,haddr_t);
+        addr += (haddr_t)nbytes;
+        buf = (const char*)buf + nbytes;
+    }
+
+#endif /*H5_HAVE_DIRECT_ALIGN*/
+
     /* Update current position and eof */
     file->pos = addr;
     file->op = OP_WRITE;
@@ -1232,13 +1305,16 @@ H5FD_direct_flush(H5FD_t *_file, hid_t UNUSED dxpl_id, unsigned UNUSED closing)
         /* Reset last file I/O information */
         file->pos = HADDR_UNDEF;
         file->op = OP_UNKNOWN;
-    } else { 
+    } 
+#ifdef H5_HAVE_DIRECT_ALIGN
+    else { 
 	/*Even though eof is equal to eoa, file is still truncated because Direct I/O
 	 *write introduces some extra data for alignment.
 	 */
         if (-1==file_truncate(file->fd, (file_offset_t)file->eof))
             HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to extend file properly")
     }
+#endif /*H5_HAVE_DIRECT_ALIGN*/
     
 done:
     FUNC_LEAVE_NOAPI(ret_value)
diff --git a/src/H5config.h.in b/src/H5config.h.in
index 0853964..998a616 100644
--- a/src/H5config.h.in
+++ b/src/H5config.h.in
@@ -57,6 +57,9 @@
 /* Define if the direct I/O virtual file driver should be compiled */
 #undef HAVE_DIRECT
 
+/* Define if the direct I/O VFD requires alignment */
+#undef HAVE_DIRECT_ALIGN
+
 /* Define to 1 if you have the <dlfcn.h> header file. */
 #undef HAVE_DLFCN_H