[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.

6 files changed, 215 insertions, 7 deletions

diff --git a/configure b/configure
index d4377b5..91c8792 100755
--- a/configure
+++ b/configure
@@ -51071,6 +51071,89 @@ else
 fi
 
 
+
+if test ${hdf5_direct_io} = "yes"; then
+    echo "$as_me:$LINENO: checking for Direct VFD alignment requirement" >&5
+echo $ECHO_N "checking for Direct VFD alignment requirement... $ECHO_C" >&6
+
+    if test "${hdf5_direct_align+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test "$cross_compiling" = yes; then
+  { { echo "$as_me:$LINENO: error: cannot run test program while cross compiling
+See \`config.log' for more details." >&5
+echo "$as_me: error: cannot run test program while cross compiling
+See \`config.log' for more details." >&2;}
+   { (exit 1); exit 1; }; }
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+            #include <stdlib.h>
+	    #include <sys/types.h>
+	    #include <sys/stat.h>
+	    #include <fcntl.h>
+            int main(void)
+            {
+                 int *buf;
+                 int fid;
+                 fid=open("tst_file", O_CREAT | O_TRUNC | O_DIRECT | O_RDWR, 0755);
+                 buf = (int*)malloc(sizeof(int));
+                 if(write(fid, (void*)buf, sizeof(int))<0) {
+                     close(fid);
+                     free(buf);
+                     remove("tst_file");
+		     exit(1);
+                 }
+                 close(fid);
+                 remove("tst_file");
+                 free(buf);
+                 exit (0);
+             }
+_ACEOF
+rm -f conftest$ac_exeext
+if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
+  (eval $ac_link) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+  (eval $ac_try) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+  hdf5_direct_align=no
+else
+  echo "$as_me: program exited with status $ac_status" >&5
+echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+hdf5_direct_align=yes
+fi
+rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+fi
+
+
+    if test ${hdf5_direct_align} = "yes"; then
+        echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_DIRECT_ALIGN 1
+_ACEOF
+
+    else
+        echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+    fi
+fi
+
 echo "$as_me:$LINENO: checking whether exception handling functions is checked during data conversions" >&5
 echo $ECHO_N "checking whether exception handling functions is checked during data conversions... $ECHO_C" >&6
 # Check whether --enable-dconv-exception or --disable-dconv-exception was given.
diff --git a/configure.in b/configure.in
index fa13ecd..ff618c7 100644
--- a/configure.in
+++ b/configure.in
@@ -2572,7 +2572,7 @@ if test "$STREAM_VFD" = "yes"; then
 fi
 
 dnl ----------------------------------------------------------------------
-dnl Check if Direct I/O driver is wanted by --enable-direct-vfd
+dnl Check if Direct I/O driver is enabled by --enable-direct-vfd
 dnl
 
 AC_MSG_CHECKING([for Direct Virtual File Driver support])
@@ -2612,6 +2612,46 @@ else
 fi
 
 AM_CONDITIONAL([DIRECT_VFD_CONDITIONAL], [test "X$DIRECT_VFD" = "Xyes"])
+
+dnl ----------------------------------------------------------------------
+dnl Check if Direct I/O driver requires alignment.
+dnl
+
+if test ${hdf5_direct_io} = "yes"; then
+    AC_MSG_CHECKING([for Direct VFD alignment requirement])
+
+    AC_CACHE_VAL([hdf5_direct_align],
+        [AC_TRY_RUN([
+            #include <stdlib.h>
+	    #include <sys/types.h>
+	    #include <sys/stat.h>
+	    #include <fcntl.h>
+            int main(void)
+            {
+                 int *buf;
+                 int fid; 
+                 fid=open("tst_file", O_CREAT | O_TRUNC | O_DIRECT | O_RDWR, 0755);
+                 buf = (int*)malloc(sizeof(int));
+                 if(write(fid, (void*)buf, sizeof(int))<0) {
+                     close(fid);
+                     free(buf);
+                     remove("tst_file"); 
+		     exit(1);
+                 }
+                 close(fid);  
+                 remove("tst_file"); 
+                 free(buf);
+                 exit (0);
+             }], [hdf5_direct_align=no], [hdf5_direct_align=yes],)])
+
+    if test ${hdf5_direct_align} = "yes"; then
+        AC_MSG_RESULT([yes])
+        AC_DEFINE([HAVE_DIRECT_ALIGN], [1],
+                [Define if the direct I/O VFD requires alignment])
+    else
+        AC_MSG_RESULT([no])
+    fi
+fi
  
 dnl ----------------------------------------------------------------------
 dnl Decide whether the presence of user's exception handling functions is
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
 
diff --git a/test/h5test.c b/test/h5test.c
index 840e126..93f992e 100644
--- a/test/h5test.c
+++ b/test/h5test.c
@@ -581,7 +581,7 @@ h5_fileaccess(void)
 #ifdef H5_HAVE_DIRECT
 	/* Linux direct read() and write() system calls.  Set memory boundary, file block size,
 	 * and copy buffer size to the default values. */
-	if (H5Pset_fapl_direct(fapl, 1024, 4096, 7*4096)<0) return -1;
+	if (H5Pset_fapl_direct(fapl, 1024, 4096, 8*4096)<0) return -1;
 #endif
     } else {
 	/* Unknown driver */
diff --git a/test/vfd.c b/test/vfd.c
index fdd710d..c8b67f7 100644
--- a/test/vfd.c
+++ b/test/vfd.c
@@ -214,6 +214,7 @@ test_direct(void)
     if(file_size<1*KB || file_size>4*KB)
         TEST_ERROR;
 
+#ifdef H5_HAVE_DIRECT_ALIGN
     /* Allocate aligned memory for data set 1. For data set 1, everything is aligned including
      * memory address, size of data, and file address. */
     if(posix_memalign(&points, (size_t)FBSIZE, (size_t)(DSET1_DIM1*DSET1_DIM2*sizeof(int)))!=0)
@@ -221,6 +222,11 @@ test_direct(void)
 
     if(posix_memalign(&check, (size_t)FBSIZE, (size_t)(DSET1_DIM1*DSET1_DIM2*sizeof(int)))!=0)
         TEST_ERROR;
+#else
+    /* Allocate aligned memory for data set 1. No need for alignment. */
+    points=(int*)malloc(DSET1_DIM1*DSET1_DIM2*sizeof(int));
+    check=(int*)malloc(DSET1_DIM1*DSET1_DIM2*sizeof(int));
+#endif
 
     /* Initialize the dset1 */
     p1 = points;