[svn-r15656] Purpose: fix bug 1286

Description: Added configure test to see if pointer alignment restrictions are enforced (as in dereferencing an unaligned pointer causes an error).  Added code in H5Tvlen.c to avoid dereferencing unaligned pointers, conditionally compiled based on the configure test.  Added test case in dtypes.c which would previously cause such machines to fail.

Tested: kagiso, smirom, linew (h5committest); linew64

2 files changed, 157 insertions, 49 deletions

diff --git a/src/H5Tvlen.c b/src/H5Tvlen.c
index d80bd94..27eb0f6 100644
--- a/src/H5Tvlen.c
+++ b/src/H5Tvlen.c
@@ -248,7 +248,7 @@ H5T_vlen_set_loc(const H5T_t *dt, H5F_t *f, H5T_loc_t loc)
                     dt->shared->u.vlen.write = H5T_vlen_str_mem_write;
                     dt->shared->u.vlen.setnull = H5T_vlen_str_mem_setnull;
                 } else {
-                    assert(0 && "Invalid VL type");
+                    HDassert(0 && "Invalid VL type");
                 }
 
                 /* Reset file ID (since this VL is in memory) */
@@ -304,21 +304,35 @@ done:
  * Programmer:	Quincey Koziol
  *		Wednesday, June 2, 1999
  *
- * Modifications:
+ * Modifications:   Neil Fortner
+ *      Friday, August 22, 2008
+ *      Changed function to be tolerant of an hvl_t that is not aligned
+ *      properly in _vl.
  *
  *-------------------------------------------------------------------------
  */
 static ssize_t
 H5T_vlen_seq_mem_getlen(const void *_vl)
 {
+#ifdef H5_NO_ALIGNMENT_RESTRICTIONS
     const hvl_t *vl=(const hvl_t *)_vl;   /* Pointer to the user's hvl_t information */
+#else
+    hvl_t vl;             /* User's hvl_t information */
+#endif
 
     FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5T_vlen_seq_mem_getlen)
 
-    /* check parameters */
-    assert(vl);
+    /* check parameters, return result */
+#ifdef H5_NO_ALIGNMENT_RESTRICTIONS
+    HDassert(vl);
 
     FUNC_LEAVE_NOAPI((ssize_t)vl->len)
+#else
+    HDassert(_vl);
+    HDmemcpy(&vl, _vl, sizeof(hvl_t));
+
+    FUNC_LEAVE_NOAPI((ssize_t)vl.len)
+#endif
 }   /* end H5T_vlen_seq_mem_getlen() */
 
 
@@ -332,21 +346,35 @@ H5T_vlen_seq_mem_getlen(const void *_vl)
  * Programmer:	Quincey Koziol
  *		Saturday, June 12, 2004
  *
- * Modifications:
+ * Modifications:   Neil Fortner
+ *      Friday, August 22, 2008
+ *      Changed function to be tolerant of an hvl_t that is not aligned
+ *      properly in _vl.
  *
  *-------------------------------------------------------------------------
  */
 static void *
 H5T_vlen_seq_mem_getptr(void *_vl)
 {
-    hvl_t *vl=(hvl_t *)_vl;   /* Pointer to the user's hvl_t information */
+#ifdef H5_NO_ALIGNMENT_RESTRICTIONS
+    const hvl_t *vl=(const hvl_t *)_vl;   /* Pointer to the user's hvl_t information */
+#else
+    hvl_t vl;             /* User's hvl_t information */
+#endif
 
     FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5T_vlen_seq_mem_getptr)
 
-    /* check parameters */
-    assert(vl);
+    /* check parameters, return result */
+#ifdef H5_NO_ALIGNMENT_RESTRICTIONS
+    HDassert(vl);
 
     FUNC_LEAVE_NOAPI(vl->p)
+#else
+    HDassert(_vl);
+    HDmemcpy(&vl, _vl, sizeof(hvl_t));
+
+    FUNC_LEAVE_NOAPI(vl.p)
+#endif
 }   /* end H5T_vlen_seq_mem_getptr() */
 
 
@@ -360,7 +388,10 @@ H5T_vlen_seq_mem_getptr(void *_vl)
  * Programmer:	Quincey Koziol
  *		Saturday, November 8, 2003
  *
- * Modifications:
+ * Modifications:   Neil Fortner
+ *      Friday, August 22, 2008
+ *      Changed function to be tolerant of an hvl_t that is not aligned
+ *      properly in _vl.
  *
  *-------------------------------------------------------------------------
  */
@@ -368,14 +399,25 @@ H5T_vlen_seq_mem_getptr(void *_vl)
 static htri_t
 H5T_vlen_seq_mem_isnull(const H5F_t UNUSED *f, void *_vl)
 {
-    hvl_t *vl=(hvl_t *)_vl;   /* Pointer to the user's hvl_t information */
+#ifdef H5_NO_ALIGNMENT_RESTRICTIONS
+    const hvl_t *vl=(const hvl_t *)_vl;   /* Pointer to the user's hvl_t information */
+#else
+    hvl_t vl;             /* User's hvl_t information */
+#endif
 
     FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5T_vlen_seq_mem_isnull)
 
-    /* check parameters */
-    assert(vl);
+    /* check parameters, return result */
+#ifdef H5_NO_ALIGNMENT_RESTRICTIONS
+    HDassert(vl);
 
     FUNC_LEAVE_NOAPI((vl->len==0 || vl->p==NULL) ? TRUE : FALSE)
+#else
+    HDassert(_vl);
+    HDmemcpy(&vl, _vl, sizeof(hvl_t));
+
+    FUNC_LEAVE_NOAPI((vl.len==0 || vl.p==NULL) ? TRUE : FALSE)
+#endif
 }   /* end H5T_vlen_seq_mem_isnull() */
 
 
@@ -389,7 +431,10 @@ H5T_vlen_seq_mem_isnull(const H5F_t UNUSED *f, void *_vl)
  * Programmer:	Quincey Koziol
  *		Wednesday, June 2, 1999
  *
- * Modifications:
+ * Modifications:   Neil Fortner
+ *      Friday, August 22, 2008
+ *      Changed function to be tolerant of an hvl_t that is not aligned
+ *      properly in _vl.
  *
  *-------------------------------------------------------------------------
  */
@@ -397,15 +442,27 @@ H5T_vlen_seq_mem_isnull(const H5F_t UNUSED *f, void *_vl)
 static herr_t
 H5T_vlen_seq_mem_read(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_vl, void *buf, size_t len)
 {
-    hvl_t *vl=(hvl_t *)_vl;   /* Pointer to the user's hvl_t information */
+#ifdef H5_NO_ALIGNMENT_RESTRICTIONS
+    const hvl_t *vl=(const hvl_t *)_vl;   /* Pointer to the user's hvl_t information */
+#else
+    hvl_t vl;             /* User's hvl_t information */
+#endif
 
     FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5T_vlen_seq_mem_read)
 
-    /* check parameters */
-    assert(vl && vl->p);
-    assert(buf);
+    /* check parameters, copy data */
+    HDassert(buf);
+#ifdef H5_NO_ALIGNMENT_RESTRICTIONS
+    HDassert(vl && vl->p);
 
     HDmemcpy(buf,vl->p,len);
+#else
+    HDassert(_vl);
+    HDmemcpy(&vl, _vl, sizeof(hvl_t));
+    HDassert(vl.p);
+
+    HDmemcpy(buf,vl.p,len);
+#endif
 
     FUNC_LEAVE_NOAPI(SUCCEED)
 }   /* end H5T_vlen_seq_mem_read() */
@@ -436,8 +493,8 @@ H5T_vlen_seq_mem_write(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const H5T_vlen_all
     FUNC_ENTER_NOAPI_NOINIT(H5T_vlen_seq_mem_write)
 
     /* check parameters */
-    assert(_vl);
-    assert(buf);
+    HDassert(_vl);
+    HDassert(buf);
 
     if(seq_len!=0) {
         len=seq_len*base_size;
@@ -493,7 +550,7 @@ H5T_vlen_seq_mem_setnull(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_vl, void
     FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5T_vlen_seq_mem_setnull)
 
     /* check parameters */
-    assert(_vl);
+    HDassert(_vl);
 
     /* Set the "nil" hvl_t */
     vl.len=0;
@@ -516,19 +573,31 @@ H5T_vlen_seq_mem_setnull(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_vl, void
  * Programmer:	Quincey Koziol
  *		Wednesday, June 2, 1999
  *
- * Modifications:
+ * Modifications:   Neil Fortner
+ *      Friday, August 22, 2008
+ *      Changed function to be tolerant of a char * that is not aligned
+ *      properly in _vl.
  *
  *-------------------------------------------------------------------------
  */
 static ssize_t
 H5T_vlen_str_mem_getlen(const void *_vl)
 {
+#ifdef H5_NO_ALIGNMENT_RESTRICTIONS
     const char *s=*(const char * const *)_vl;   /* Pointer to the user's string information */
+#else
+    const char *s;      /* Pointer to the user's string information */
+#endif
 
     FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5T_vlen_str_mem_getlen)
 
     /* check parameters */
-    assert(s);
+#ifdef H5_NO_ALIGNMENT_RESTRICTIONS
+    HDassert(s);
+#else
+    HDassert(_vl);
+    HDmemcpy(&s, _vl, sizeof(char *));
+#endif
 
     FUNC_LEAVE_NOAPI((ssize_t)HDstrlen(s))
 }   /* end H5T_vlen_str_mem_getlen() */
@@ -544,19 +613,32 @@ H5T_vlen_str_mem_getlen(const void *_vl)
  * Programmer:	Quincey Koziol
  *		Saturday, June 12, 2004
  *
- * Modifications:
+ * Modifications:   Neil Fortner
+ *      Friday, August 22, 2008
+ *      Changed function to be tolerant of a char * that is not aligned
+ *      properly in _vl.
+ *      Added assertion on _vl.
  *
  *-------------------------------------------------------------------------
  */
 static void *
 H5T_vlen_str_mem_getptr(void *_vl)
 {
+#ifdef H5_NO_ALIGNMENT_RESTRICTIONS
     char *s=*(char **)_vl;   /* Pointer to the user's string information */
+#else
+    char *s;      /* Pointer to the user's string information */
+#endif
 
     FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5T_vlen_str_mem_getptr)
 
     /* check parameters */
-    assert(s);
+#ifdef H5_NO_ALIGNMENT_RESTRICTIONS
+    HDassert(s);
+#else
+    HDassert(_vl);
+    HDmemcpy(&s, _vl, sizeof(char *));
+#endif
 
     FUNC_LEAVE_NOAPI(s)
 }   /* end H5T_vlen_str_mem_getptr() */
@@ -572,7 +654,10 @@ H5T_vlen_str_mem_getptr(void *_vl)
  * Programmer:	Quincey Koziol
  *		Saturday, November 8, 2003
  *
- * Modifications:
+ * Modifications:   Neil Fortner
+ *      Friday, August 22, 2008
+ *      Changed function to be tolerant of a char * that is not aligned
+ *      properly in _vl.
  *
  *-------------------------------------------------------------------------
  */
@@ -580,10 +665,18 @@ H5T_vlen_str_mem_getptr(void *_vl)
 static htri_t
 H5T_vlen_str_mem_isnull(const H5F_t UNUSED *f, void *_vl)
 {
+#ifdef H5_NO_ALIGNMENT_RESTRICTIONS
     char *s=*(char **)_vl;   /* Pointer to the user's string information */
+#else
+    char *s;      /* Pointer to the user's string information */
+#endif
 
     FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5T_vlen_str_mem_isnull)
 
+#ifndef H5_NO_ALIGNMENT_RESTRICTIONS
+    HDmemcpy(&s, _vl, sizeof(char *));
+#endif
+
     FUNC_LEAVE_NOAPI(s==NULL ? TRUE : FALSE)
 }   /* end H5T_vlen_str_mem_isnull() */
 
@@ -598,7 +691,10 @@ H5T_vlen_str_mem_isnull(const H5F_t UNUSED *f, void *_vl)
  * Programmer:	Quincey Koziol
  *		Wednesday, June 2, 1999
  *
- * Modifications:
+ * Modifications:   Neil Fortner
+ *      Friday, August 22, 2008
+ *      Changed function to be tolerant of a char * that is not aligned
+ *      properly in _vl.
  *
  *-------------------------------------------------------------------------
  */
@@ -606,14 +702,23 @@ H5T_vlen_str_mem_isnull(const H5F_t UNUSED *f, void *_vl)
 static herr_t
 H5T_vlen_str_mem_read(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_vl, void *buf, size_t len)
 {
-    char *s=*(char **)_vl;   /* Pointer to the user's hvl_t information */
+#ifdef H5_NO_ALIGNMENT_RESTRICTIONS
+    char *s=*(char **)_vl;   /* Pointer to the user's string information */
+#else
+    char *s;      /* Pointer to the user's string information */
+#endif
 
     FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5T_vlen_str_mem_read)
 
     if(len>0) {
         /* check parameters */
-        assert(s);
-        assert(buf);
+        HDassert(buf);
+#ifdef H5_NO_ALIGNMENT_RESTRICTIONS
+        HDassert(s);
+#else
+        HDassert(_vl);
+        HDmemcpy(&s, _vl, sizeof(char *));
+#endif
 
         HDmemcpy(buf,s,len);
     } /* end if */
@@ -647,7 +752,7 @@ H5T_vlen_str_mem_write(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const H5T_vlen_all
     FUNC_ENTER_NOAPI_NOINIT(H5T_vlen_str_mem_write)
 
     /* check parameters */
-    assert(buf);
+    HDassert(buf);
 
     /* Use the user's memory allocation routine if one is defined */
     if(vl_alloc_info->alloc_func!=NULL) {
@@ -723,7 +828,7 @@ H5T_vlen_disk_getlen(const void *_vl)
     FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5T_vlen_disk_getlen)
 
     /* check parameters */
-    assert(vl);
+    HDassert(vl);
 
     UINT32DECODE(vl, seq_len);
 
@@ -752,7 +857,7 @@ H5T_vlen_disk_getptr(void UNUSED *vl)
     FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5T_vlen_disk_getptr)
 
     /* check parameters */
-    assert(vl);
+    HDassert(vl);
 
     FUNC_LEAVE_NOAPI(NULL)
 }   /* end H5T_vlen_disk_getptr() */
@@ -781,7 +886,7 @@ H5T_vlen_disk_isnull(const H5F_t *f, void *_vl)
     FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5T_vlen_disk_isnull)
 
     /* check parameters */
-    assert(vl);
+    HDassert(vl);
 
     /* Skip the sequence's length */
     vl+=4;
@@ -818,9 +923,9 @@ H5T_vlen_disk_read(H5F_t *f, hid_t dxpl_id, void *_vl, void *buf, size_t UNUSED
     FUNC_ENTER_NOAPI_NOINIT(H5T_vlen_disk_read)
 
     /* check parameters */
-    assert(vl);
-    assert(buf);
-    assert(f);
+    HDassert(vl);
+    HDassert(buf);
+    HDassert(f);
 
     /* Skip the length of the sequence */
     vl += 4;
@@ -872,9 +977,9 @@ H5T_vlen_disk_write(H5F_t *f, hid_t dxpl_id, const H5T_vlen_alloc_info_t UNUSED
     FUNC_ENTER_NOAPI_NOINIT(H5T_vlen_disk_write)
 
     /* check parameters */
-    assert(vl);
-    assert(seq_len==0 || buf);
-    assert(f);
+    HDassert(vl);
+    HDassert(seq_len==0 || buf);
+    HDassert(f);
 
     /* Free heap object for old data.  */
     if(bg!=NULL) {
@@ -937,8 +1042,8 @@ H5T_vlen_disk_setnull(H5F_t *f, hid_t dxpl_id, void *_vl, void *_bg)
     FUNC_ENTER_NOAPI_NOINIT(H5T_vlen_disk_setnull)
 
     /* check parameters */
-    assert(f);
-    assert(vl);
+    HDassert(f);
+    HDassert(vl);
 
     /* Free heap object for old data.  */
     if(bg!=NULL) {
@@ -1000,8 +1105,8 @@ H5T_vlen_reclaim_recurse(void *elem, const H5T_t *dt, H5MM_free_t free_func, voi
 
     FUNC_ENTER_NOAPI_NOINIT(H5T_vlen_reclaim_recurse)
 
-    assert(elem);
-    assert(dt);
+    HDassert(elem);
+    HDassert(dt);
 
     /* Check the datatype of this element */
     switch(dt->shared->type) {
@@ -1067,7 +1172,7 @@ H5T_vlen_reclaim_recurse(void *elem, const H5T_t *dt, H5MM_free_t free_func, voi
                 else
                     H5MM_xfree(*(char **)elem);
             } else {
-                assert(0 && "Invalid VL type");
+                HDassert(0 && "Invalid VL type");
             } /* end else */
             break;
 
@@ -1114,9 +1219,9 @@ H5T_vlen_reclaim(void *elem, hid_t type_id, unsigned UNUSED ndim, const hsize_t
 
     FUNC_ENTER_NOAPI(H5T_vlen_reclaim, FAIL)
 
-    assert(elem);
-    assert(vl_alloc_info);
-    assert(H5I_DATATYPE == H5I_get_type(type_id));
+    HDassert(elem);
+    HDassert(vl_alloc_info);
+    HDassert(H5I_DATATYPE == H5I_get_type(type_id));
 
     /* Check args */
     if (NULL==(dt=H5I_object_verify(type_id,H5I_DATATYPE)))
@@ -1161,8 +1266,8 @@ H5T_vlen_get_alloc_info(hid_t dxpl_id, H5T_vlen_alloc_info_t **vl_alloc_info)
 
     FUNC_ENTER_NOAPI(H5T_vlen_get_alloc_info, FAIL)
 
-    assert(H5I_GENPROP_LST == H5I_get_type(dxpl_id));
-    assert(vl_alloc_info);
+    HDassert(H5I_GENPROP_LST == H5I_get_type(dxpl_id));
+    HDassert(vl_alloc_info);
 
     /* Check for the default DXPL */
     if(dxpl_id==H5P_DATASET_XFER_DEFAULT)
diff --git a/src/H5config.h.in b/src/H5config.h.in
index a12f3bc..efa3469 100644
--- a/src/H5config.h.in
+++ b/src/H5config.h.in
@@ -436,6 +436,9 @@
 /* Define if your system can handle special collective IO properly. */
 #undef MPI_SPECIAL_COLLECTIVE_IO_WORKS
 
+/* Define if we can violate pointer alignment restrictions */
+#undef NO_ALIGNMENT_RESTRICTIONS
+
 /* Define if deprecated public API symbols are disabled */
 #undef NO_DEPRECATED_SYMBOLS