[svn-r1494] Lots of various bug-fixes on VL datatypes. VL datatype fields in compound

datatypes aren't yet working, but other ways of using them (vlen atomic, vlen
compound and vlen vlen atomic, etc.) are working.

6 files changed, 115 insertions, 104 deletions

diff --git a/src/H5D.c b/src/H5D.c
index af4a188..5c366ba 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -987,7 +987,7 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type,
     }
 
     /* Create (open for write access) an object header */
-    if (H5O_create(f, 96, &(new_dset->ent)) < 0) {
+    if (H5O_create(f, 256, &(new_dset->ent)) < 0) {
 	HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
 		    "unable to create dataset object header");
     }
diff --git a/src/H5Sall.c b/src/H5Sall.c
index db27b00..ff08fbc 100644
--- a/src/H5Sall.c
+++ b/src/H5Sall.c
@@ -991,15 +991,15 @@ H5S_all_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t op
 
         ret_value=(*operator)(tmp_buf,type_id,rank,mem_offset,operator_data);
 
+        /* Decrement the number of elements to iterate through */
+        nelemts--;
+
         /* Advance the coordinate (currently in C memory order) */
         index=rank-1; /* Leave the byte offset in the element alone */
-        while(++mem_offset[index]==mem_size[index] && index>=0) {
+        while(index>=0 && ++mem_offset[index]==mem_size[index]) {
             mem_offset[index]=0;
             index--;
           } /* end while */
-
-        /* Decrement the number of elements to iterate through */
-        nelemts--;
       } /* end while */
 
     FUNC_LEAVE (ret_value);
diff --git a/src/H5T.c b/src/H5T.c
index 51c4fff..4b7184f 100644
--- a/src/H5T.c
+++ b/src/H5T.c
@@ -4696,6 +4696,35 @@ H5T_open_oid (H5G_entry_t *ent)
     FUNC_LEAVE (dt);
 }
 
+
+/*-------------------------------------------------------------------------
+ * Function:	H5T_cmp_field_off
+ *
+ * Purpose:	Compares field offsets for qsort
+ *
+ * Return:	<0, 0, or >0 if field1's offset is less than, equal to, or greater
+ *          than field2's offset
+ *
+ * Programmer:	Quincey Koziol
+ *		Thursday, July 15th, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+H5T_cmp_field_off(const void *_field1, const void *_field2)
+{
+    const H5T_cmemb_t *field1=(const H5T_cmemb_t *)_field1,
+        *field2=(const H5T_cmemb_t *)_field2;
+    
+    if(field1->offset < field2->offset)
+        return(-1);
+    else if(field1->offset > field2->offset)
+        return(1);
+    else
+        return(0);
+}
 
 
 /*-------------------------------------------------------------------------
@@ -4794,27 +4823,42 @@ H5T_copy(const H5T_t *old_dt, H5T_copy_t method)
     }
     
     if (H5T_COMPOUND == new_dt->type) {
-	/*
-	 * Copy all member fields to new type, then overwrite the
-	 * name and type fields of each new member with copied values.
-	 * That is, H5T_copy() is a deep copy.
-	 */
-	new_dt->u.compnd.memb = H5MM_malloc(new_dt->u.compnd.nalloc *
-					    sizeof(H5T_cmemb_t));
-	if (NULL==new_dt->u.compnd.memb) {
-	    HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL,
-			   "memory allocation failed");
-	}
-	HDmemcpy(new_dt->u.compnd.memb, old_dt->u.compnd.memb,
-		 new_dt->u.compnd.nmembs * sizeof(H5T_cmemb_t));
-	
-	for (i=0; i<new_dt->u.compnd.nmembs; i++) {
-	    s = new_dt->u.compnd.memb[i].name;
-	    new_dt->u.compnd.memb[i].name = H5MM_xstrdup(s);
-	    tmp = H5T_copy (old_dt->u.compnd.memb[i].type, method);
-	    new_dt->u.compnd.memb[i].type = tmp;
-	}
+        intn accum_change=0;    /* Amount of change in the offset of the fields */
+
+        /*
+         * Copy all member fields to new type, then overwrite the
+         * name and type fields of each new member with copied values.
+         * That is, H5T_copy() is a deep copy.
+         */
+        new_dt->u.compnd.memb = H5MM_malloc(new_dt->u.compnd.nalloc *
+                            sizeof(H5T_cmemb_t));
+        if (NULL==new_dt->u.compnd.memb) {
+            HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL,
+                   "memory allocation failed");
+        }
+        HDmemcpy(new_dt->u.compnd.memb, old_dt->u.compnd.memb,
+             new_dt->u.compnd.nmembs * sizeof(H5T_cmemb_t));
+
+        /* Sort the fields based on offsets */
+        qsort(new_dt->u.compnd.memb, new_dt->u.compnd.nmembs, sizeof(H5T_cmemb_t), H5T_cmp_field_off);
 	
+        for (i=0; i<new_dt->u.compnd.nmembs; i++) {
+            s = new_dt->u.compnd.memb[i].name;
+            new_dt->u.compnd.memb[i].name = H5MM_xstrdup(s);
+            tmp = H5T_copy (old_dt->u.compnd.memb[i].type, method);
+            new_dt->u.compnd.memb[i].type = tmp;
+
+            /* Apply the accumulated size change to the offset of the field */
+            new_dt->u.compnd.memb[i].offset += accum_change;
+
+            /* If the field changed size, add that change to the accumulated size change */
+            if(new_dt->u.compnd.memb[i].type->size != old_dt->u.compnd.memb[i].type->size)
+                accum_change += (new_dt->u.compnd.memb[i].type->size - old_dt->u.compnd.memb[i].type->size);
+        }
+
+        /* Apply the accumulated size change to the size of the compound struct */
+        new_dt->size += accum_change;
+
     } else if (H5T_ENUM == new_dt->type) {
 	/*
 	 * Copy all member fields to new type, then overwrite the name fields
@@ -4836,9 +4880,11 @@ H5T_copy(const H5T_t *old_dt, H5T_copy_t method)
 	    new_dt->u.enumer.name[i] = H5MM_xstrdup(s);
     } 
     } else if (H5T_VLEN == new_dt->type) {
-        /* H5T_copy converts any VL type into a memory VL type */
-	    if (H5T_vlen_mark(new_dt, NULL, H5T_VLEN_MEMORY)<0) {
-            HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "invalid VL location");
+        if(method==H5T_COPY_TRANSIENT || method==H5T_COPY_REOPEN) {
+            /* H5T_copy converts any VL type into a memory VL type */
+            if (H5T_vlen_mark(new_dt, NULL, H5T_VLEN_MEMORY)<0) {
+                HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "invalid VL location");
+            }
         }
     } else if (H5T_OPAQUE == new_dt->type) {
         /*
diff --git a/src/H5Tconv.c b/src/H5Tconv.c
index e34d980..eaf930d 100644
--- a/src/H5Tconv.c
+++ b/src/H5Tconv.c
@@ -1903,12 +1903,8 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts,
                 if (H5T_convert(tpath, tsrc_id, tdst_id, seq_len, 0, conv_buf_ptr, NULL, dset_xfer_plist)<0)
                     HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed");
 
-                /* Allocate new VL buffer */
-                if((*(dst->u.vlen.alloc))(xfer_parms,d,seq_len,dst_base_size)<0)
-                    HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "allocation failed for VL data");
-
                 /* Write sequence to destination location */
-                if((*(dst->u.vlen.write))(dst->u.vlen.f,d,conv_buf_ptr,dst_size)<0)
+                if((*(dst->u.vlen.write))(xfer_parms,dst->u.vlen.f,d,conv_buf_ptr,seq_len,dst_base_size)<0)
                     HRETURN_ERROR(H5E_DATATYPE, H5E_WRITEERROR, FAIL, "can't write VL data");
 
                 /*
diff --git a/src/H5Tpkg.h b/src/H5Tpkg.h
index 5941e0a..bb41580 100644
--- a/src/H5Tpkg.h
+++ b/src/H5Tpkg.h
@@ -88,8 +88,7 @@ typedef struct H5T_enum_t {
 /* VL function pointers */
 typedef hsize_t (*H5T_vlen_getlenfunc_t)(H5F_t *f, void *vl_addr);
 typedef herr_t (*H5T_vlen_readfunc_t)(H5F_t *f, void *vl_addr, void *buf, size_t len);
-typedef herr_t (*H5T_vlen_allocfunc_t)(const H5F_xfer_t *xfer_parms, void *vl_addr, hsize_t seq_len, hsize_t base_size);
-typedef herr_t (*H5T_vlen_writefunc_t)(H5F_t *f, void *vl_addr, void *buf, size_t len);
+typedef herr_t (*H5T_vlen_writefunc_t)(const H5F_xfer_t *xfer_parms, H5F_t *f, void *vl_addr, void *buf, hsize_t seq_len, hsize_t base_size);
 
 /* A VL datatype */
 typedef struct H5T_vlen_t {
@@ -97,7 +96,6 @@ typedef struct H5T_vlen_t {
     H5F_t *f;                   /* File ID (if VL data is on disk) */
     H5T_vlen_getlenfunc_t getlen;   /* Function to get VL sequence size (in element units, not bytes) */
     H5T_vlen_readfunc_t read;   /* Function to read VL sequence into buffer */
-    H5T_vlen_allocfunc_t alloc; /* Function to allocate space for VL sequence */
     H5T_vlen_writefunc_t write; /* Function to write VL sequence from buffer */
 } H5T_vlen_t;
 
@@ -208,6 +206,9 @@ __DLLVAR__ size_t	H5T_NATIVE_UINT_LEAST64_ALIGN_g;
 __DLLVAR__ size_t	H5T_NATIVE_INT_FAST64_ALIGN_g;
 __DLLVAR__ size_t	H5T_NATIVE_UINT_FAST64_ALIGN_g;
 
+/* H5Tcopy support functions */
+__DLL__ int H5T_cmp_field_off(const void *_field1, const void *_field2);
+
 /* Conversion functions */
 __DLL__ herr_t H5T_conv_noop(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
 			     size_t nelmts, size_t stride, void *buf,
@@ -541,12 +542,10 @@ __DLL__ htri_t H5T_bit_inc(uint8_t *buf, size_t start, size_t size);
 /* VL functions */
 __DLL__ hsize_t H5T_vlen_mem_getlen(H5F_t *f, void *vl_addr);
 __DLL__ herr_t H5T_vlen_mem_read(H5F_t *f, void *vl_addr, void *_buf, size_t len);
-__DLL__ herr_t H5T_vlen_mem_alloc(const H5F_xfer_t *xfer_parms, void *vl_addr, hsize_t seq_len, hsize_t base_size);
-__DLL__ herr_t H5T_vlen_mem_write(H5F_t *f, void *vl_addr, void *_buf, size_t len);
+__DLL__ herr_t H5T_vlen_mem_write(const H5F_xfer_t *xfer_parms, H5F_t *f, void *vl_addr, void *_buf, hsize_t seq_len, hsize_t base_size);
 __DLL__ hsize_t H5T_vlen_disk_getlen(H5F_t *f, void *vl_addr);
 __DLL__ herr_t H5T_vlen_disk_read(H5F_t *f, void *vl_addr, void *_buf, size_t len);
-__DLL__ herr_t H5T_vlen_disk_alloc(const H5F_xfer_t *xfer_parms, void *vl_addr, hsize_t seq_len, hsize_t base_size);
-__DLL__ herr_t H5T_vlen_disk_write(H5F_t *f, void *vl_addr, void *_buf, size_t len);
+__DLL__ herr_t H5T_vlen_disk_write(const H5F_xfer_t *xfer_parms, H5F_t *f, void *vl_addr, void *_buf, hsize_t seq_len, hsize_t base_size);
 
 /* Reference specific functions */
 __DLL__ H5R_type_t H5T_get_ref_type(H5T_t *dt);
diff --git a/src/H5Tvlen.c b/src/H5Tvlen.c
index 1a70aa8..c9d0e35 100644
--- a/src/H5Tvlen.c
+++ b/src/H5Tvlen.c
@@ -71,7 +71,6 @@ H5T_vlen_set_loc(H5T_t *dt, H5F_t *f, H5T_vlen_type_t loc)
             /* Set up the function pointers to access the VL information (in memory) */
             dt->u.vlen.getlen=H5T_vlen_mem_getlen;
             dt->u.vlen.read=H5T_vlen_mem_read;
-            dt->u.vlen.alloc=H5T_vlen_mem_alloc;
             dt->u.vlen.write=H5T_vlen_mem_write;
 
             /* Reset file ID (since this VL is in memory) */
@@ -86,14 +85,14 @@ H5T_vlen_set_loc(H5T_t *dt, H5F_t *f, H5T_vlen_type_t loc)
 
             /* 
              * Size of element on disk is 4 bytes for the length, plus the size
-             * of an address in this file.  Memory size is different
+             * of an address in this file, plus 4 bytes for the size of a heap
+             * ID.  Memory size is different
              */
-            dt->size = H5F_SIZEOF_ADDR(f)+4;
+            dt->size = 4 + H5F_SIZEOF_ADDR(f) + 4;
 
             /* Set up the function pointers to access the VL information (in memory) */
             dt->u.vlen.getlen=H5T_vlen_disk_getlen;
             dt->u.vlen.read=H5T_vlen_disk_read;
-            dt->u.vlen.alloc=H5T_vlen_disk_alloc;
             dt->u.vlen.write=H5T_vlen_disk_write;
 
             /* Set file ID (since this VL is on disk) */
@@ -169,9 +168,9 @@ herr_t H5T_vlen_mem_read(H5F_t UNUSED *f, void *vl_addr, void *buf, size_t len)
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5T_vlen_mem_alloc
+ * Function:	H5T_vlen_mem_write
  *
- * Purpose:	Allocates a memory based VL sequence
+ * Purpose:	"Writes" the memory based VL sequence from a buffer
  *
  * Return:	Non-negative on success/Negative on failure
  *
@@ -182,14 +181,16 @@ herr_t H5T_vlen_mem_read(H5F_t UNUSED *f, void *vl_addr, void *buf, size_t len)
  *
  *-------------------------------------------------------------------------
  */
-herr_t H5T_vlen_mem_alloc(const H5F_xfer_t *xfer_parms, void *vl_addr, hsize_t seq_len, hsize_t base_size)
+herr_t H5T_vlen_mem_write(const H5F_xfer_t *xfer_parms, H5F_t UNUSED *f, void *vl_addr, void *buf, hsize_t seq_len, hsize_t base_size)
 {
     hvl_t *vl=(hvl_t *)vl_addr;   /* Pointer to the user's hvl_t information */
+    size_t len=seq_len*base_size;
 
-    FUNC_ENTER (H5T_vlen_mem_alloc, FAIL);
+    FUNC_ENTER (H5T_vlen_mem_write, FAIL);
 
     /* check parameters */
     assert(vl);
+    assert(buf);
 
     /* Use the user's memory allocation routine is one is defined */
     if(xfer_parms->vlen_alloc!=NULL) {
@@ -202,34 +203,6 @@ herr_t H5T_vlen_mem_alloc(const H5F_xfer_t *xfer_parms, void *vl_addr, hsize_t s
       } /* end else */
     vl->len=seq_len;
 
-    FUNC_LEAVE (SUCCEED);
-}   /* end H5T_vlen_mem_alloc() */
-
-
-/*-------------------------------------------------------------------------
- * Function:	H5T_vlen_mem_write
- *
- * Purpose:	"Writes" the memory based VL sequence from a buffer
- *
- * Return:	Non-negative on success/Negative on failure
- *
- * Programmer:	Quincey Koziol
- *		Wednesday, June 2, 1999
- *
- * Modifications:
- *
- *-------------------------------------------------------------------------
- */
-herr_t H5T_vlen_mem_write(H5F_t UNUSED *f, void *vl_addr, void *buf, size_t len)
-{
-    hvl_t *vl=(hvl_t *)vl_addr;   /* Pointer to the user's hvl_t information */
-
-    FUNC_ENTER (H5T_vlen_mem_write, FAIL);
-
-    /* check parameters */
-    assert(vl && vl->p);
-    assert(buf);
-
     HDmemcpy(vl->p,buf,len);
 
     FUNC_LEAVE (SUCCEED);
@@ -309,32 +282,6 @@ herr_t H5T_vlen_disk_read(H5F_t *f, void *vl_addr, void *buf, size_t UNUSED len)
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5T_vlen_disk_alloc
- *
- * Purpose:	Allocates a disk based VL sequence
- *      NOTE: This function is currently a NOOP, allocation of the heap block
- *          is done when the block is written out.
- *
- * Return:	Non-negative on success/Negative on failure
- *
- * Programmer:	Quincey Koziol
- *		Wednesday, June 2, 1999
- *
- * Modifications:
- *
- *-------------------------------------------------------------------------
- */
-herr_t H5T_vlen_disk_alloc(const H5F_xfer_t UNUSED *f, void UNUSED *vl_addr, hsize_t UNUSED seq_len, hsize_t UNUSED base_size)
-{
-    FUNC_ENTER (H5T_vlen_disk_alloc, FAIL);
-
-    /* check parameters */
-
-    FUNC_LEAVE (SUCCEED);
-}   /* end H5T_vlen_disk_alloc() */
-
-
-/*-------------------------------------------------------------------------
  * Function:	H5T_vlen_disk_write
  *
  * Purpose:	Writes the disk based VL sequence from a buffer
@@ -348,11 +295,11 @@ herr_t H5T_vlen_disk_alloc(const H5F_xfer_t UNUSED *f, void UNUSED *vl_addr, hsi
  *
  *-------------------------------------------------------------------------
  */
-herr_t H5T_vlen_disk_write(H5F_t *f, void *vl_addr, void *buf, size_t len)
+herr_t H5T_vlen_disk_write(const H5F_xfer_t UNUSED *xfer_parms, H5F_t *f, void *vl_addr, void *buf, hsize_t seq_len, hsize_t base_size)
 {
     uint8_t *vl=(uint8_t *)vl_addr;   /* Pointer to the user's hvl_t information */
     H5HG_t hobjid;
-    uint32_t seq_len;
+    size_t len=seq_len*base_size;
 
     FUNC_ENTER (H5T_vlen_disk_write, FAIL);
 
@@ -554,13 +501,36 @@ H5T_vlen_mark(H5T_t *dt, H5F_t *f, H5T_vlen_type_t loc)
     switch(dt->type) {
         /* Check each field and recurse on VL and compound ones */
         case H5T_COMPOUND:
+        {
+            intn accum_change=0;    /* Amount of change in the offset of the fields */
+            size_t old_size;        /* Preview size of a field */
+
+            /* Sort the fields based on offsets */
+            qsort(dt->u.compnd.memb, dt->u.compnd.nmembs, sizeof(H5T_cmemb_t), H5T_cmp_field_off);
+	
             for (i=0; i<dt->u.compnd.nmembs; i++) {
+                /* Apply the accumulated size change to the offset of the field */
+                dt->u.compnd.memb[i].offset += accum_change;
+
                 /* Recurse if it's VL or compound */
                 if(dt->u.compnd.memb[i].type->type==H5T_COMPOUND || dt->u.compnd.memb[i].type->type==H5T_VLEN) {
+                    /* Keep the old field size for later */
+                    old_size=dt->u.compnd.memb[i].type->size;
+
+                    /* Mark the VL or compound type */
                     if(H5T_vlen_mark(dt->u.compnd.memb[i].type,f,loc)<0)
                         HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "Unable to set VL location");
+                    
+                    /* If the field changed size, add that change to the accumulated size change */
+                    if(old_size != dt->u.compnd.memb[i].type->size)
+                        accum_change += (dt->u.compnd.memb[i].type->size - (int)old_size);
                 } /* end if */
             } /* end for */
+
+            /* Apply the accumulated size change to the datatype */
+            dt->size += accum_change;
+	
+        } /* end case */
             break;
 
         /* Recurse on the VL information if it's VL or compound, then free VL sequence */