[svn-r12820] Added fragmental copy buffer to H5FD_direct_write. This buffer size is set through

H5Pset_fapl_direct.  It's been added to H5FD_direct_read in the previous checkin.  Still, a test is
needed at later checkin.

2 files changed, 136 insertions, 92 deletions

diff --git a/src/H5FDdirect.c b/src/H5FDdirect.c
index 93a64f5..bf826aa 100644
--- a/src/H5FDdirect.c
+++ b/src/H5FDdirect.c
@@ -50,9 +50,9 @@ static hid_t H5FD_DIRECT_g = 0;
 
 /* Driver-specific file access properties */
 typedef struct H5FD_direct_fapl_t {
-    hsize_t	mboundary;	/* Memory boundary for alignment		*/
-    hsize_t	fbsize;		/* File system block size			*/
-    hsize_t	cbsize;		/* Maximal buffer size for copying user data	*/
+    size_t	mboundary;	/* Memory boundary for alignment		*/
+    size_t	fbsize;		/* File system block size			*/
+    size_t	cbsize;		/* Maximal buffer size for copying user data	*/
 } H5FD_direct_fapl_t;
 
 /*
@@ -306,7 +306,7 @@ H5FD_direct_term(void)
  *-------------------------------------------------------------------------
  */
 herr_t
-H5Pset_fapl_direct(hid_t fapl_id, hsize_t boundary, hsize_t block_size, hsize_t cbuf_size)
+H5Pset_fapl_direct(hid_t fapl_id, size_t boundary, size_t block_size, size_t cbuf_size)
 {
     H5P_genplist_t    	*plist;      /* Property list pointer */
     H5FD_direct_fapl_t	fa;
@@ -360,8 +360,8 @@ done:
  *-------------------------------------------------------------------------
  */
 herr_t
-H5Pget_fapl_direct(hid_t fapl_id, hsize_t *boundary/*out*/, hsize_t *block_size/*out*/, 
-		hsize_t *cbuf_size/*out*/)
+H5Pget_fapl_direct(hid_t fapl_id, size_t *boundary/*out*/, size_t *block_size/*out*/, 
+		size_t *cbuf_size/*out*/)
 {
     H5FD_direct_fapl_t	*fa;
     H5P_genplist_t *plist;      /* Property list pointer */
@@ -861,13 +861,13 @@ 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;
-    size_t		alloc_size, tmp_size;
+    size_t		alloc_size, dup_size;
     void		*copy_buf, *p1, *p2, *p3;
-    hsize_t		_boundary;
-    hsize_t		_fbsize;
-    hsize_t		_cbsize;
+    size_t		_boundary;
+    size_t		_fbsize;
+    size_t		_cbsize;
     haddr_t		copy_addr = addr;
-    hsize_t		copy_size = size;
+    size_t		copy_size = size;
     herr_t      	ret_value=SUCCEED;       /* Return value */
 
     FUNC_ENTER_NOAPI(H5FD_direct_read, FAIL)
@@ -893,7 +893,7 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, ha
     /* if the data is aligned, read it directly from the file.  If not, read a bigger 
      * and aligned data first, then copy the data into memory buffer.
      */
-    if((addr%_fbsize==0) && (size%_fbsize==0) && ((haddr_t)buf%_boundary==0)) {
+    if((addr%_fbsize==0) && (size%_fbsize==0) && ((size_t)buf%_boundary==0)) {
 	    /* Seek to the correct location */
 	    if ((addr!=file->pos || OP_READ!=file->op) &&
 		    file_seek(file->fd, (file_offset_t)addr, SEEK_SET)<0)
@@ -945,10 +945,10 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, ha
 	    	 * partial results, and the end of the file. */
 	    	memset(copy_buf, 0, alloc_size);
 	    	p1 = copy_buf;
-	    	tmp_size = alloc_size;
-	    	while(tmp_size > 0) {
+	    	dup_size = alloc_size;
+	    	while(dup_size > 0) {
 		    do {
-		    	nbytes = HDread(file->fd, p1, tmp_size);
+		    	nbytes = HDread(file->fd, p1, dup_size);
 		    } while(-1==nbytes && EINTR==errno);
 
 		    if (-1==nbytes) /* error */
@@ -958,10 +958,10 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, ha
 		    	break;
 		    } else {
 		    	assert(nbytes>0);
-		    	assert((size_t)nbytes<=tmp_size);
+		    	assert((size_t)nbytes<=dup_size);
 		    	H5_CHECK_OVERFLOW(nbytes,ssize_t,size_t);
 		    	H5_CHECK_OVERFLOW(nbytes,ssize_t,haddr_t);
-		    	tmp_size -= (size_t)nbytes;
+		    	dup_size -= (size_t)nbytes;
 		    	p1 = (unsigned char*)p1 + nbytes;
 		    }
 	    	}
@@ -970,29 +970,30 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, ha
 		 * Consider all possible situations here: file address is not aligned on 
 		 * file block size; the end of data address is not aligned; the end of data
 		 * address is aligned; data size is smaller or bigger than maximal copy size.*/
-	    	p2 = (unsigned char*)copy_buf + copy_addr % _fbsize;
+	    	p2 = (unsigned char*)copy_buf + (size_t)(copy_addr % _fbsize);
 	    	if(size < _cbsize)
 	    	    memcpy(p3, p2, size);
-	    	else if(size >= _cbsize && copy_size <= alloc_size)
+	    	else if(size >= _cbsize && copy_size <= (alloc_size-(size_t)(copy_addr%_fbsize)))
 	    	    memcpy(p3, p2, copy_size);
-	    	else if(size >= _cbsize && copy_size > alloc_size) {
-	    	    memcpy(p3, p2, (alloc_size - copy_addr % _fbsize));
-	    	   p3 = (unsigned char*)p3 + (alloc_size - copy_addr % _fbsize); 
+	    	else if(size >= _cbsize && copy_size > (alloc_size-(size_t)(copy_addr%_fbsize))) {
+	    	    memcpy(p3, p2, (alloc_size - (size_t)(copy_addr % _fbsize)));
+	    	    p3 = (unsigned char*)p3 + (alloc_size - (size_t)(copy_addr % _fbsize)); 
 	    	}
 
 		/* update the size and address of data being read. */
-	    	if(copy_size > (alloc_size - copy_addr % _fbsize))
-	    	    copy_size -= (alloc_size - copy_addr % _fbsize);
+	    	if(copy_size > (alloc_size - (size_t)(copy_addr % _fbsize)))
+	    	    copy_size -= (alloc_size - (size_t)(copy_addr % _fbsize));
 	    	else
 		    copy_size = 0;
-	    	copy_addr += (alloc_size - copy_addr % _fbsize);
+	    	copy_addr += (alloc_size - (size_t)(copy_addr % _fbsize));
 	    } while (copy_size > 0);
 
 	    /*Final step: update address and buffer*/
 	    addr += (haddr_t)size;
 	    buf = (unsigned char*)buf + size;
 
-	    HDfree(copy_buf);
+	    if(copy_buf)
+	    	HDfree(copy_buf);
     }
 
     /* Update current position */
@@ -1035,10 +1036,12 @@ 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;
     size_t		alloc_size, dup_size;
-    void		*copy_buf, *p1, *p2;
-    hsize_t		_boundary;
-    hsize_t		_fbsize;
-    hsize_t		_cbsize;
+    void		*copy_buf, *p1, *p2, *p3;
+    size_t		_boundary;
+    size_t		_fbsize;
+    size_t		_cbsize;
+    haddr_t             copy_addr = addr;
+    size_t             	copy_size = size;
     herr_t      	ret_value=SUCCEED;       /* Return value */
 
     FUNC_ENTER_NOAPI(H5FD_direct_write, FAIL)
@@ -1065,7 +1068,7 @@ H5FD_direct_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, h
      * the aligned data first, update buffer with user data, then write the
      * data out.
      */
-    if((addr%_fbsize==0) && (size%_fbsize==0) && ((haddr_t)buf%_boundary==0)) {
+    if((addr%_fbsize==0) && (size%_fbsize==0) && ((size_t)buf%_boundary==0)) {
 	    /* Seek to the correct location */
 	    if ((addr!=file->pos || OP_WRITE!=file->op) &&
 		    file_seek(file->fd, (file_offset_t)addr, SEEK_SET)<0)
@@ -1086,78 +1089,119 @@ H5FD_direct_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, h
 		buf = (const char*)buf + nbytes;
 	    }
     } else {
-	    /* allocate memory needed for the Direct IO option. Make a 
-	     * bigger buffer for aligned I/O 
+	    /* allocate memory needed for the Direct IO option up to the maximal
+	     * copy buffer size. Make a bigger buffer for aligned I/O if size is
+	     * smaller than maximal copy buffer.
 	     */
-	    alloc_size = (size / _fbsize + 1) * _fbsize + _fbsize;
+	    if(size < _cbsize) 
+	    	alloc_size = (size / _fbsize + 1) * _fbsize + _fbsize;
+	    else
+		alloc_size = _cbsize;
+/*printf("alloc_size=%ld, size=%ld, _fbsize=%ld, _cbsize=%ld\n", alloc_size, size, _fbsize,
+_cbsize);*/
 	    if (posix_memalign(&copy_buf, _boundary, alloc_size) != 0)
 		HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "posix_memalign failed")
-	    memset(copy_buf, 0, alloc_size);
 
 	    /* look for the right position for reading the data */
-	    if(file_seek(file->fd, (file_offset_t)(addr - addr % _fbsize), SEEK_SET) < 0)	
+	    if(file_seek(file->fd, (file_offset_t)(copy_addr - copy_addr % _fbsize), SEEK_SET) < 0)
 		HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position")
 
-	    /*
-	     * Read the aligned data first, being careful of interrupted system calls, 
-	     * partial results, and the end of the file.
-	     */
-	    p2 = copy_buf;
-	    dup_size = alloc_size;
-	    while(dup_size > 0) {
-		do {
-		    nbytes = read(file->fd, p2, dup_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 */
-		    break;
-		} else {
-		    assert(nbytes>0);
-		    assert((size_t)nbytes<=dup_size);
-		    H5_CHECK_OVERFLOW(nbytes,ssize_t,size_t);
-		    H5_CHECK_OVERFLOW(nbytes,ssize_t,haddr_t);
-		    dup_size -= (size_t)nbytes;
-		    p2 = (unsigned char*)p2 + nbytes;
+	    p3 = buf;
+	    do {
+	    	/*
+	     	 * Read the aligned data first if the aligned region doesn't fall entirely in 
+	    	 * the range to be writen.  Be careful of interrupted system calls, partial 
+	    	 * results, and the end of the file.
+	    	 */
+	    	memset(copy_buf, 0, alloc_size);
+	    	p2 = copy_buf;
+	    	dup_size = alloc_size;
+		if(copy_addr <= addr || (copy_addr + alloc_size) >= (addr + size)) {
+		    while(dup_size > 0) {
+			do {
+			    nbytes = read(file->fd, p2, dup_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 */
+			    break;
+			} else {
+			    assert(nbytes>0);
+			    assert((size_t)nbytes<=dup_size);
+			    H5_CHECK_OVERFLOW(nbytes,ssize_t,size_t);
+			    H5_CHECK_OVERFLOW(nbytes,ssize_t,haddr_t);
+			    dup_size -= (size_t)nbytes;
+			    p2 = (unsigned char*)p2 + nbytes;
+			}
+		    }
 		}
-	    }
 
-	    /*append or copy the data to be written to the aligned buffer.*/
-	    p1 = (unsigned char*)copy_buf + addr % _fbsize;
-	    memcpy(p1, buf, size);
+	    	/* look for the right position and append or copy the data to be written to 
+	     	 * the aligned buffer.
+            	 * Consider all possible situations here: file address is not aligned on
+            	 * file block size; the end of data address is not aligned; the end of data
+            	 * address is aligned; data size is smaller or bigger than maximal copy size.
+	    	 */
+	    	p1 = (unsigned char*)copy_buf + (size_t)(copy_addr % _fbsize);
+	    	if(size < _cbsize)
+	    	    memcpy(p1, p3, size);
+	    	else if(size >= _cbsize && copy_size <= (alloc_size-(size_t)(copy_addr%_fbsize))) {
+/*printf("copy_size=%d, alloc_size=%d, size=%d, copy_addr%_fbsize=%ld\n", copy_size, alloc_size,
+size, copy_addr%_fbsize);*/
+		    memcpy(p1, p3, copy_size);
+	    	}else if(size >= _cbsize && copy_size > (alloc_size-(size_t)(copy_addr%_fbsize))) {
+		    memcpy(p1, p3, (alloc_size - (size_t)(copy_addr % _fbsize)));
+		    p3 = (unsigned char*)p3 + (alloc_size - (size_t)(copy_addr % _fbsize));
+	    	}
+ 
+	    	/*look for the aligned position for writing the data*/
+	    	if(file_seek(file->fd, (file_offset_t)(copy_addr - copy_addr % _fbsize), 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 write.  
+	    	 * It doesn't truncate the extra data introduced by alignment because that step 
+	    	 * is done in H5FD_direct_flush.
+	    	 */
+	    	p2 = copy_buf;
+	    	dup_size = alloc_size;
+	    	while (dup_size>0) {
+		    do {
+		    	nbytes = HDwrite(file->fd, p2, dup_size);
+		    } while (-1==nbytes && EINTR==errno);
 
-	    /*look for the aligned position for writing the data*/
-	    if(file_seek(file->fd, (file_offset_t)(addr - addr % _fbsize), SEEK_SET) < 0)
-		HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position")
+		    if (-1==nbytes) { /* error */
+		    	HSYS_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed")
+		    }
+		    if (0==nbytes) {
+		    	/* end of file but not end of format address space */
+		    	break;
+		    } else {
+		    	assert(nbytes>0);
+		    	assert((size_t)nbytes<=dup_size);
+		    	H5_CHECK_OVERFLOW(nbytes,ssize_t,size_t);
+		    	H5_CHECK_OVERFLOW(nbytes,ssize_t,haddr_t);
+		    	dup_size -= (size_t)nbytes;
+		    	p2 = (unsigned char*)p2 + nbytes;
+		    }
+	    	}
 
-	    /*
-	     * Write the data, being careful of interrupted system calls and partial write.  
-	     * It doesn't truncate the extra data introduced by alignment because that step 
-	     * is done in H5FD_direct_flush.
-	     */
-	    p2 = copy_buf;
-	    while (alloc_size>0) {
-		do {
-		    nbytes = HDwrite(file->fd, p2, alloc_size);
-		} while (-1==nbytes && EINTR==errno);
+            	/* update the size and address of data being read. */
+            	if(copy_size > (alloc_size - (size_t)(copy_addr % _fbsize)))
+                    copy_size -= (alloc_size - (size_t)(copy_addr % _fbsize));
+            	else
+                    copy_size = 0;
 
-		if (-1==nbytes) { /* error */
-		    HSYS_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed")
-		}
-		assert(nbytes>0);
-		assert((size_t)nbytes<=alloc_size);
-		H5_CHECK_OVERFLOW(nbytes,ssize_t,size_t);
-		H5_CHECK_OVERFLOW(nbytes,ssize_t,haddr_t);
-		alloc_size -= (size_t)nbytes;
-		p2 = (unsigned char*)p2 + nbytes;
-	    }
+            	copy_addr += (alloc_size - (size_t)(copy_addr % _fbsize));
+	} while (copy_size > 0);
 
 	    /*Update the address and size*/
 	    addr += (haddr_t)size;
 	    buf = (const char*)buf + size;
-
-	    HDfree(copy_buf);
+	
+	    if(copy_buf)
+	    	HDfree(copy_buf);
     }
 
     /* Update current position and eof */
diff --git a/src/H5FDdirect.h b/src/H5FDdirect.h
index 754cd3b..e4cdc32 100644
--- a/src/H5FDdirect.h
+++ b/src/H5FDdirect.h
@@ -38,14 +38,14 @@ extern "C" {
  * Application can set these values through the function H5Pset_fapl_direct. */
 #define MBOUNDARY_DEF		4096
 #define FBSIZE_DEF		4096
-#define CBSIZE_DEF		128*1024*1024
+#define CBSIZE_DEF		16*1024*1024
 
 H5_DLL hid_t H5FD_direct_init(void);
 H5_DLL void H5FD_direct_term(void);
-H5_DLL herr_t H5Pset_fapl_direct(hid_t fapl_id, hsize_t alignment, hsize_t block_size, 
-			hsize_t cbuf_size);
-H5_DLL herr_t H5Pget_fapl_direct(hid_t fapl_id, hsize_t *boundary/*out*/, 
-			hsize_t *block_size/*out*/, hsize_t *cbuf_size/*out*/);
+H5_DLL herr_t H5Pset_fapl_direct(hid_t fapl_id, size_t alignment, size_t block_size, 
+			size_t cbuf_size);
+H5_DLL herr_t H5Pget_fapl_direct(hid_t fapl_id, size_t *boundary/*out*/, 
+			size_t *block_size/*out*/, size_t *cbuf_size/*out*/);
 
 #ifdef __cplusplus
 }