[svn-r7984] Purpose: bug fix

Description: VL datatype fails in certain way(hard to describe)


Platforms tested: h5committest

8 files changed, 28 insertions, 17 deletions

diff --git a/src/H5FLprivate.h b/src/H5FLprivate.h
index 4f3d938..59e9ac2 100644
--- a/src/H5FLprivate.h
+++ b/src/H5FLprivate.h
@@ -35,7 +35,7 @@
 /* Private headers needed by this file */
 
 /* Macros for turning off free lists in the library */
-/* #define H5_NO_FREE_LISTS */
+#define H5_NO_FREE_LISTS
 #ifdef H5_NO_FREE_LISTS
 #define H5_NO_REG_FREE_LISTS
 #define H5_NO_ARR_FREE_LISTS
diff --git a/src/H5Gprivate.h b/src/H5Gprivate.h
index 2bf2c3f..b2bff6c 100644
--- a/src/H5Gprivate.h
+++ b/src/H5Gprivate.h
@@ -38,6 +38,7 @@
 #include "H5private.h"		/* Generic Functions			*/
 #include "H5Bprivate.h"		/* B-trees				*/
 #include "H5Fprivate.h"		/* File access				*/
+#include "H5Gprivate.h"		/* Group				*/
 #include "H5RSprivate.h"        /* Reference-counted strings            */
 
 /*
diff --git a/src/H5HG.c b/src/H5HG.c
index b4b7f17..b6045af 100644
--- a/src/H5HG.c
+++ b/src/H5HG.c
@@ -970,6 +970,9 @@ H5HG_remove (H5F_t *f, hid_t dxpl_id, H5HG_t *hobj)
         HGOTO_ERROR(H5E_HEAP, H5E_CANTLOAD, FAIL, "unable to load heap");
 
     assert (hobj->idx>0 && hobj->idx<heap->nalloc);
+if(!(heap->obj[hobj->idx].begin)) {
+    HDfprintf(stderr,"%s: hobj->idx=%d, heap=%p, heap->obj[hobj->idx].begin=%p\n",FUNC,hobj->idx,heap,heap->obj[hobj->idx].begin);
+}
     assert (heap->obj[hobj->idx].begin);
     obj_start = heap->obj[hobj->idx].begin;
     /* Include object header size */
diff --git a/src/H5I.c b/src/H5I.c
index ad2f450..a965ec2 100644
--- a/src/H5I.c
+++ b/src/H5I.c
@@ -117,8 +117,6 @@ H5FL_DEFINE_STATIC(H5I_id_info_t);
 /*--------------------- Local function prototypes ---------------------------*/
 static herr_t H5I_init_interface(void);
 static H5I_id_info_t *H5I_find_id(hid_t id);
-static hid_t H5I_get_file_id(hid_t obj_id);
-static int H5I_get_ref(hid_t id);
 #ifdef H5I_DEBUG_OUTPUT
 static herr_t H5I_debug(H5I_type_t grp);
 #endif /* H5I_DEBUG_OUTPUT */
@@ -844,7 +842,7 @@ done:
  *
  *-------------------------------------------------------------------------
  */
-static hid_t
+hid_t
 H5I_get_file_id(hid_t obj_id)
 {
     H5G_entry_t         *ent;
@@ -1345,8 +1343,11 @@ H5I_find_id(hid_t id)
 
     /* Check arguments */
     grp = H5I_GRP(id);
-    if (grp <= H5I_BADID || grp >= H5I_NGROUPS)
+
+    if (grp <= H5I_BADID || grp >= H5I_NGROUPS) {
 	HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, NULL, "invalid group number");
+    }
+
     grp_ptr = H5I_id_group_list_g[grp];
     if (grp_ptr == NULL || grp_ptr->count <= 0)
 	HGOTO_ERROR(H5E_ATOM, H5E_BADGROUP, NULL, "invalid group");
diff --git a/src/H5Iprivate.h b/src/H5Iprivate.h
index 79819a5..42369e3 100644
--- a/src/H5Iprivate.h
+++ b/src/H5Iprivate.h
@@ -67,6 +67,7 @@ H5_DLL hid_t H5I_register(H5I_type_t grp, void *object);
 H5_DLL void *H5I_object(hid_t id);
 H5_DLL void *H5I_object_verify(hid_t id, H5I_type_t id_type);
 H5_DLL H5I_type_t H5I_get_type(hid_t id);
+H5_DLL hid_t H5I_get_file_id(hid_t obj_id);
 H5_DLL void *H5I_remove(hid_t id);
 H5_DLL void *H5I_search(H5I_type_t grp, H5I_search_func_t func, void *key);
 H5_DLL int H5I_inc_ref(hid_t id);
diff --git a/src/H5Tbit.c b/src/H5Tbit.c
index f6e36c7..fae953a 100644
--- a/src/H5Tbit.c
+++ b/src/H5Tbit.c
@@ -183,12 +183,14 @@ H5T_bit_get_d (uint8_t *buf, size_t offset, size_t size)
     hsize_t	val=0;
     size_t	i, hs;
     hsize_t	ret_value;      /* Return value */
+    void        *pt;
     
     FUNC_ENTER_NOAPI(H5T_bit_get_d, 0);
 
     assert (8*sizeof(val)>=size);
 
     H5T_bit_copy ((uint8_t*)&val, 0, buf, offset, size);
+
     switch (((H5T_t*)(H5I_object(H5T_NATIVE_INT_g)))->u.atomic.order) {
         case H5T_ORDER_LE:
             break;
diff --git a/src/H5Tconv.c b/src/H5Tconv.c
index daa37f5..2d043d7 100644
--- a/src/H5Tconv.c
+++ b/src/H5Tconv.c
@@ -2455,6 +2455,7 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
                     if(nested) {
                         uint8_t *tmp=bg_ptr;
                         UINT32DECODE(tmp, bg_seq_len);
+
                         if(bg_seq_len>0) {
                             H5_CHECK_OVERFLOW( bg_seq_len*MAX(src_base_size,dst_base_size) ,hsize_t,size_t);
                             if(tmp_buf_size<(size_t)(bg_seq_len*MAX(src_base_size, dst_base_size))) {
@@ -2478,12 +2479,12 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
 
                     /* Convert VL sequence */
                     H5_CHECK_OVERFLOW(seq_len,hssize_t,hsize_t);
-                    if (H5T_convert(tpath, tsrc_id, tdst_id, (hsize_t)seq_len, 0, bkg_stride, conv_buf, tmp_buf, dxpl_id)<0)
+
+                    if (H5T_convert(tpath, tsrc_id, tdst_id, (hsize_t)seq_len, 0, 0, conv_buf, tmp_buf, dxpl_id)<0)
                         HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed");
 
                     /* Write sequence to destination location */
                     if((*(dst->u.vlen.write))(dst->u.vlen.f,dxpl_id,d,conv_buf, bg_ptr, (hsize_t)seq_len,(hsize_t)dst_base_size)<0)
-                        HGOTO_ERROR(H5E_DATATYPE, H5E_WRITEERROR, FAIL, "can't write VL data");
 
                     /* For nested VL case, free leftover heap objects from the deeper level if the length of new data elements is shorted than the old data elements.*/
                     H5_CHECK_OVERFLOW(bg_seq_len,hsize_t,hssize_t);
diff --git a/src/H5Tvlen.c b/src/H5Tvlen.c
index 1a01458..057a309 100644
--- a/src/H5Tvlen.c
+++ b/src/H5Tvlen.c
@@ -818,16 +818,18 @@ H5T_vlen_disk_write(H5F_t *f, hid_t dxpl_id, void *_vl, void *buf, void *_bg, hs
 	HDmemset(&bg_hobjid,0,sizeof(H5HG_t));
         UINT32DECODE(bg, bg_seq_len);
 
-        /* Get heap information */
-        H5F_addr_decode(f, (const uint8_t **)&bg, &(bg_hobjid.addr));
-        INT32DECODE(bg, bg_hobjid.idx);
-
-        /* Free heap object for old data */
-        if(bg_hobjid.addr>0) {
-            /* Free heap object */
-            if(H5HG_remove(f, dxpl_id, &bg_hobjid)<0)
-                HGOTO_ERROR(H5E_DATATYPE, H5E_WRITEERROR, FAIL, "Unable to remove heap object")
-         } /* end if */
+        if(bg_seq_len > 0) {
+            /* Get heap information */
+            H5F_addr_decode(f, (const uint8_t **)&bg, &(bg_hobjid.addr));
+            INT32DECODE(bg, bg_hobjid.idx);
+
+            /* Free heap object for old data */
+            if(bg_hobjid.addr>0) {
+                /* Free heap object */
+                if(H5HG_remove(f, dxpl_id, &bg_hobjid)<0)
+                    HGOTO_ERROR(H5E_DATATYPE, H5E_WRITEERROR, FAIL, "Unable to remove heap object")
+            } /* end if */
+        } /* end if */
     } /* end if */
 
     /* Set the length of the sequence */