[svn-r15825] Description:

	Fix various problems with a the core & sec2 VFDs.

	Improve the h5_get_file_size() routine to handle files created with
VFDs that use multiple files.

Tested on:
        Mac OS X/32 10.5.5 (amazon) in debug mode
        Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe,
                                in production mode
        FreeBSD/32 6.3 (duty) in debug mode
        FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
        Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
                                in debug mode
        Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
                                w/C++ & FORTRAN, in production mode
        Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
                                w/szip filter, in production mode
        Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
                                in production mode
        Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
        Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode

4 files changed, 139 insertions, 47 deletions

diff --git a/src/H5FDcore.c b/src/H5FDcore.c
index de49e9e..8840720 100644
--- a/src/H5FDcore.c
+++ b/src/H5FDcore.c
@@ -91,6 +91,7 @@ static H5FD_t *H5FD_core_open(const char *name, unsigned flags, hid_t fapl_id,
 			      haddr_t maxaddr);
 static herr_t H5FD_core_close(H5FD_t *_file);
 static int H5FD_core_cmp(const H5FD_t *_f1, const H5FD_t *_f2);
+static herr_t H5FD_core_query(const H5FD_t *_f1, unsigned long *flags);
 static haddr_t H5FD_core_get_eoa(const H5FD_t *_file, H5FD_mem_t type);
 static herr_t H5FD_core_set_eoa(H5FD_t *_file, H5FD_mem_t type, haddr_t addr);
 static haddr_t H5FD_core_get_eof(const H5FD_t *_file);
@@ -100,6 +101,7 @@ static herr_t H5FD_core_read(H5FD_t *_file, H5FD_mem_t type, hid_t fapl_id, hadd
 static herr_t H5FD_core_write(H5FD_t *_file, H5FD_mem_t type, hid_t fapl_id, haddr_t addr,
 			      size_t size, const void *buf);
 static herr_t H5FD_core_flush(H5FD_t *_file, hid_t dxpl_id, unsigned closing);
+static herr_t H5FD_core_truncate(H5FD_t *_file, hid_t dxpl_id, hbool_t closing);
 
 static const H5FD_class_t H5FD_core_g = {
     "core",					/*name			*/
@@ -118,7 +120,7 @@ static const H5FD_class_t H5FD_core_g = {
     H5FD_core_open,				/*open			*/
     H5FD_core_close,				/*close			*/
     H5FD_core_cmp,				/*cmp			*/
-    NULL,				        /*query			*/
+    H5FD_core_query,			        /*query			*/
     NULL,					/*alloc			*/
     NULL,					/*free			*/
     H5FD_core_get_eoa,				/*get_eoa		*/
@@ -128,7 +130,7 @@ static const H5FD_class_t H5FD_core_g = {
     H5FD_core_read,				/*read			*/
     H5FD_core_write,				/*write			*/
     H5FD_core_flush,				/*flush			*/
-    NULL,					/*truncate		*/
+    H5FD_core_truncate,				/*truncate		*/
     NULL,                                       /*lock                  */
     NULL,                                       /*unlock                */
     H5FD_FLMAP_SINGLE 				/*fl_map		*/
@@ -344,7 +346,7 @@ H5FD_core_fapl_get(H5FD_t *_file)
         HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
 
     fa->increment = file->increment;
-    fa->backing_store = (file->fd>=0);
+    fa->backing_store = (hbool_t)(file->fd >= 0);
 
     /* Set return value */
     ret_value=fa;
@@ -558,6 +560,42 @@ done:
 
 
 /*-------------------------------------------------------------------------
+ * Function:	H5FD_core_query
+ *
+ * Purpose:	Set the flags that this VFL driver is capable of supporting.
+ *              (listed in H5FDpublic.h)
+ *
+ * Return:	Success:	non-negative
+ *		Failure:	negative
+ *
+ * Programmer:	Quincey Koziol
+ *              Tuesday, October  7, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+/* ARGSUSED */
+static herr_t
+H5FD_core_query(const H5FD_t UNUSED * _f, unsigned long *flags /* out */)
+{
+    herr_t ret_value = SUCCEED;         /* Return value */
+
+    FUNC_ENTER_NOAPI(H5FD_core_query, FAIL)
+
+    /* Set the VFL feature flags that this driver supports */
+    if(flags) {
+        *flags = 0;
+        *flags |= H5FD_FEAT_AGGREGATE_METADATA; /* OK to aggregate metadata allocations */
+        *flags |= H5FD_FEAT_ACCUMULATE_METADATA; /* OK to accumulate metadata for faster writes */
+        *flags |= H5FD_FEAT_DATA_SIEVE;       /* OK to perform data sieving for faster raw data reads & writes */
+        *flags |= H5FD_FEAT_AGGREGATE_SMALLDATA; /* OK to aggregate "small" raw data allocations */
+    } /* end if */
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5FD_core_query() */
+
+
+/*-------------------------------------------------------------------------
  * Function:	H5FD_core_get_eoa
  *
  * Purpose:	Gets the end-of-address marker for the file. The EOA marker
@@ -620,18 +658,18 @@ static herr_t
 H5FD_core_set_eoa(H5FD_t *_file, H5FD_mem_t UNUSED type, haddr_t addr)
 {
     H5FD_core_t	*file = (H5FD_core_t*)_file;
-    herr_t      ret_value=SUCCEED;       /* Return value */
+    herr_t ret_value = SUCCEED;       /* Return value */
 
     FUNC_ENTER_NOAPI(H5FD_core_set_eoa, FAIL)
 
-    if (ADDR_OVERFLOW(addr))
+    if(ADDR_OVERFLOW(addr))
         HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "address overflow")
 
     file->eoa = addr;
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
-}
+} /* end H5FD_core_set_eoa() */
 
 
 /*-------------------------------------------------------------------------
@@ -795,18 +833,18 @@ static herr_t
 H5FD_core_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, haddr_t addr,
 		size_t size, const void *buf)
 {
-    H5FD_core_t		*file = (H5FD_core_t*)_file;
-    herr_t      ret_value=SUCCEED;       /* Return value */
+    H5FD_core_t *file = (H5FD_core_t*)_file;
+    herr_t ret_value = SUCCEED;       /* Return value */
 
     FUNC_ENTER_NOAPI(H5FD_core_write, FAIL)
 
-    assert(file && file->pub.cls);
-    assert(buf);
+    HDassert(file && file->pub.cls);
+    HDassert(buf);
 
     /* Check for overflow conditions */
-    if (REGION_OVERFLOW(addr, size))
+    if(REGION_OVERFLOW(addr, size))
         HGOTO_ERROR(H5E_IO, H5E_OVERFLOW, FAIL, "file address overflowed")
-    if (addr+size>file->eoa)
+    if(addr + size > file->eoa)
         HGOTO_ERROR(H5E_IO, H5E_OVERFLOW, FAIL, "file address overflowed")
 
     /*
@@ -815,34 +853,33 @@ H5FD_core_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, had
      * careful of non-Posix realloc() that doesn't understand what to do when
      * the first argument is null.
      */
-    if (addr+size>file->eof) {
+    if(addr + size > file->eof) {
         unsigned char *x;
         size_t new_eof;
 
-        H5_ASSIGN_OVERFLOW(new_eof,file->increment*((addr+size)/file->increment),hsize_t,size_t);
-
+        /* Determine new size of memory buffer */
+        H5_ASSIGN_OVERFLOW(new_eof, file->increment * ((addr + size) / file->increment), hsize_t, size_t);
         if((addr + size) % file->increment)
             new_eof += file->increment;
-        if(NULL == file->mem)
-            x = (unsigned char *)H5MM_malloc(new_eof);
-        else
-            x = (unsigned char *)H5MM_realloc(file->mem, new_eof);
+
+        /* (Re)allocate memory for the file buffer */
+        if(NULL == (x = (unsigned char *)H5MM_realloc(file->mem, new_eof)))
+            HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate memory block")
 #ifdef H5_CLEAR_MEMORY
 HDmemset(x + file->eof, 0, (size_t)(new_eof - file->eof));
 #endif /* H5_CLEAR_MEMORY */
-        if (!x)
-            HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate memory block")
         file->mem = x;
+
         file->eof = new_eof;
-    }
+    } /* end if */
 
     /* Write from BUF to memory */
-    HDmemcpy(file->mem+addr, buf, size);
+    HDmemcpy(file->mem + addr, buf, size);
     file->dirty = TRUE;
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
-}
+} /* end H5FD_core_write() */
 
 
 /*-------------------------------------------------------------------------
@@ -900,3 +937,62 @@ done:
     FUNC_LEAVE_NOAPI(ret_value)
 }
 
+
+/*-------------------------------------------------------------------------
+ * Function:	H5FD_core_truncate
+ *
+ * Purpose:	Makes sure that the true file size is the same (or larger)
+ *		than the end-of-address.
+ *
+ * Return:	Success:	Non-negative
+ *		Failure:	Negative
+ *
+ * Programmer:	Quincey Koziol
+ *              Tuesday, October  7, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+/* ARGSUSED */
+static herr_t
+H5FD_core_truncate(H5FD_t *_file, hid_t UNUSED dxpl_id, hbool_t UNUSED closing)
+{
+    H5FD_core_t *file = (H5FD_core_t*)_file;
+    size_t new_eof;                             /* New size of memory buffer */
+    herr_t ret_value = SUCCEED;                 /* Return value */
+
+    FUNC_ENTER_NOAPI(H5FD_core_truncate, FAIL)
+
+    HDassert(file);
+
+    /* Determine new size of memory buffer */
+    H5_ASSIGN_OVERFLOW(new_eof, file->increment * (file->eoa / file->increment), hsize_t, size_t);
+    if(file->eoa % file->increment)
+        new_eof += file->increment;
+
+    /* Extend the file to make sure it's large enough */
+    if(!H5F_addr_eq((haddr_t)new_eof, file->eof)) {
+        unsigned char *x;       /* Pointer to new buffer for file data */
+
+        /* (Re)allocate memory for the file buffer */
+        if(NULL == (x = (unsigned char *)H5MM_realloc(file->mem, new_eof)))
+            HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate memory block")
+#ifdef H5_CLEAR_MEMORY
+if(file->eof < new_eof)
+    HDmemset(x + file->eof, 0, (size_t)(new_eof - file->eof));
+#endif /* H5_CLEAR_MEMORY */
+        file->mem = x;
+
+        /* Update backing store, if using it */
+        if(file->fd >= 0 && file->backing_store) {
+            if(-1 == HDftruncate(file->fd, (off_t)new_eof))
+                HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to extend file properly")
+        } /* end if */
+
+        /* Update the eof value */
+        file->eof = new_eof;
+    } /* end if */
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5FD_core_truncate() */
+
diff --git a/src/H5FDsec2.c b/src/H5FDsec2.c
index cace117..cd3419b 100644
--- a/src/H5FDsec2.c
+++ b/src/H5FDsec2.c
@@ -101,24 +101,16 @@ typedef struct H5FD_sec2_t {
  * file_offset_t:	The datatype for file offsets, the second argument of
  *			the lseek() or lseek64() call.
  *
- * file_seek:		The function which adjusts the current file position,
- *			either lseek() or lseek64().
  */
 /* adding for windows NT file system support. */
 
 #ifdef H5_HAVE_LSEEK64
 #   define file_offset_t	off64_t
-#   define file_seek		lseek64
-#   define file_truncate	ftruncate64
 #elif defined (_WIN32) && !defined(__MWERKS__)
 # /*MSVC*/
-#   define file_offset_t __int64
-#   define file_seek _lseeki64
-#   define file_truncate	_chsize
+#   define file_offset_t        __int64
 #else
 #   define file_offset_t	off_t
-#   define file_seek		lseek
-#   define file_truncate	HDftruncate
 #endif
 
 /*
@@ -517,36 +509,33 @@ done:
  *              (listed in H5FDpublic.h)
  *
  * Return:	Success:	non-negative
- *
  *		Failure:	negative
  *
  * Programmer:	Quincey Koziol
  *              Friday, August 25, 2000
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 /* ARGSUSED */
 static herr_t
 H5FD_sec2_query(const H5FD_t UNUSED * _f, unsigned long *flags /* out */)
 {
-    herr_t ret_value=SUCCEED;
+    herr_t ret_value = SUCCEED;         /* Return value */
 
     FUNC_ENTER_NOAPI(H5FD_sec2_query, FAIL)
 
     /* Set the VFL feature flags that this driver supports */
     if(flags) {
         *flags = 0;
-        *flags|=H5FD_FEAT_AGGREGATE_METADATA; /* OK to aggregate metadata allocations */
-        *flags|=H5FD_FEAT_ACCUMULATE_METADATA; /* OK to accumulate metadata for faster writes */
-        *flags|=H5FD_FEAT_DATA_SIEVE;       /* OK to perform data sieving for faster raw data reads & writes */
-        *flags|=H5FD_FEAT_AGGREGATE_SMALLDATA; /* OK to aggregate "small" raw data allocations */
-    }
+        *flags |= H5FD_FEAT_AGGREGATE_METADATA; /* OK to aggregate metadata allocations */
+        *flags |= H5FD_FEAT_ACCUMULATE_METADATA; /* OK to accumulate metadata for faster writes */
+        *flags |= H5FD_FEAT_DATA_SIEVE;       /* OK to perform data sieving for faster raw data reads & writes */
+        *flags |= H5FD_FEAT_AGGREGATE_SMALLDATA; /* OK to aggregate "small" raw data allocations */
+    } /* end if */
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
-}
+} /* end H5FD_sec2_query() */
 
 
 /*-------------------------------------------------------------------------
@@ -733,7 +722,7 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, hadd
 
     /* Seek to the correct location */
     if ((addr!=file->pos || OP_READ!=file->op) &&
-            file_seek(file->fd, (file_offset_t)addr, SEEK_SET)<0)
+            HDlseek(file->fd, (file_offset_t)addr, SEEK_SET)<0)
         HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position")
 
     /*
@@ -817,7 +806,7 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, had
 
     /* Seek to the correct location */
     if ((addr!=file->pos || OP_WRITE!=file->op) &&
-            file_seek(file->fd, (file_offset_t)addr, SEEK_SET)<0)
+            HDlseek(file->fd, (file_offset_t)addr, SEEK_SET)<0)
         HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position")
 
     /*
@@ -901,7 +890,7 @@ HDfprintf(stderr, "%s: file->eof = %a, file->eoa = %a\n", FUNC, file->eof, file-
         if(SetEndOfFile((HANDLE)filehandle) == 0)
             HGOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to extend file properly")
 #else /* _WIN32 */
-        if(-1 == file_truncate(file->fd, (file_offset_t)file->eoa))
+        if(-1 == HDftruncate(file->fd, (file_offset_t)file->eoa))
             HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to extend file properly")
 #endif /* _WIN32 */
 
diff --git a/src/H5config.h.in b/src/H5config.h.in
index efa3469..c4606c9 100644
--- a/src/H5config.h.in
+++ b/src/H5config.h.in
@@ -122,6 +122,9 @@
 /* Define to 1 if you have the `ftello' function. */
 #undef HAVE_FTELLO
 
+/* Define to 1 if you have the `ftruncate64' function. */
+#undef HAVE_FTRUNCATE64
+
 /* Define if the compiler understand the __FUNCTION__ keyword */
 #undef HAVE_FUNCTION
 
diff --git a/src/H5private.h b/src/H5private.h
index cc9274f..63bbcf4 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -779,7 +779,11 @@ H5_DLL int HDfprintf (FILE *stream, const char *fmt, ...);
     #define HDftell(F)		ftell(F)
 #endif /* HDftell */
 #ifndef HDftruncate
+  #ifdef H5_HAVE_FTRUNCATE64
+    #define HDftruncate(F,L)        ftruncate64(F,L)
+  #else
     #define HDftruncate(F,L)        ftruncate(F,L)
+  #endif
 #endif /* HDftruncate */
 #ifndef HDfwrite
     #define HDfwrite(M,Z,N,F)	fwrite(M,Z,N,F)
@@ -920,7 +924,7 @@ H5_DLL int HDfprintf (FILE *stream, const char *fmt, ...);
     #define HDlongjmp(J,N)		longjmp(J,N)
 #endif /* HDlongjmp */
 #ifndef HDlseek
-    #ifdef H5_HAVE_FSEEK64
+    #ifdef H5_HAVE_LSEEK64
        #define HDlseek(F,O,W)	lseek64(F,O,W)
     #else
        #define HDlseek(F,O,W)	lseek(F,O,W)