[svn-r12928] code revision

12 files changed, 110 insertions, 70 deletions

diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c
index 3469704..2c220c3 100644
--- a/tools/h5repack/h5repack.c
+++ b/tools/h5repack/h5repack.c
@@ -247,8 +247,9 @@ int h5repack_addlayout(const char* str,
  */
 static int check_options(pack_opt_t *options)
 {
- int   i, k, j, has_cp=0, has_ck=0;
- char  slayout[30];
+ unsigned int   i;
+ int            k, j, has_cp=0, has_ck=0;
+ char           slayout[30];
 
 /*-------------------------------------------------------------------------
  * objects to layout
diff --git a/tools/h5repack/h5repack.h b/tools/h5repack/h5repack.h
index 0f5ccfe..9b1d911 100644
--- a/tools/h5repack/h5repack.h
+++ b/tools/h5repack/h5repack.h
@@ -80,9 +80,9 @@ typedef struct {
 
 /* store a table of all objects */
 typedef struct {
- int         size;
- int         nelems;
- pack_info_t *objs;
+ unsigned int size;
+ unsigned int nelems;
+ pack_info_t  *objs;
 } pack_opttbl_t;
 
 
@@ -102,7 +102,6 @@ typedef struct {
  int             verbose;     /*verbose mode */
  hsize_t         threshold;   /*minimum size to compress, in bytes */
  int             use_native;  /*use a native type in write */  
- int             have_fc_f;   /*has input to use filter/chunking flag */
 } pack_opt_t;
 
 
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 03da178..f6b738c 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -24,7 +24,6 @@ extern char  *progname;
 static int do_create_refs;
 
 
-
 #define PER(A,B) { per = 0;                                       \
                    if (A!=0)                                      \
                     per = (float)fabs( ((float)B - (float)A) / (float) A  ); \
@@ -317,9 +316,12 @@ int do_copy_objects(hid_t fidin,
  float    per;            /* percent utilization of storage */
  void     *buf=NULL;      /* buffer for raw data */
  void     *sm_buf=NULL;   /* buffer for raw data */
- int      i, j;
+ unsigned i;
  int      nfilters;       /* number of filters in DCPL */
  H5D_layout_t layout;
+#if defined(H5REPACK_GETTIME)
+ time_t start_time, finish_time, time_secs;
+#endif
 
 /*-------------------------------------------------------------------------
  * copy the suppplied object list
@@ -411,6 +413,11 @@ int do_copy_objects(hid_t fidin,
        options->all_filter==1 || options->all_layout==1
        )
    {
+    int j;
+
+#if defined(H5REPACK_GETTIME)
+    time( &start_time );  
+#endif
     if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
      goto error;
     if ((f_space_id=H5Dget_space(dset_in))<0)
@@ -540,6 +547,7 @@ int do_copy_objects(hid_t fidin,
         hsize_t       hs_size[H5S_MAX_RANK];  /*size this pass */
         hsize_t       hs_nelmts;              /*elements in request */
         hsize_t       zero[8];                /*vector of zeros */
+        int           k;          
         
         /* check if we have VL data in the dataset's datatype */
         if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
@@ -551,9 +559,9 @@ int do_copy_objects(hid_t fidin,
          */
         sm_nbytes = p_type_nbytes;
         
-        for (i = rank; i > 0; --i) {
-         sm_size[i - 1] = MIN(dims[i - 1], H5TOOLS_BUFSIZE / sm_nbytes);
-         sm_nbytes *= sm_size[i - 1];
+        for (k = rank; k > 0; --k) {
+         sm_size[k - 1] = MIN(dims[k - 1], H5TOOLS_BUFSIZE / sm_nbytes);
+         sm_nbytes *= sm_size[k - 1];
          assert(sm_nbytes > 0);
         }
         sm_buf = HDmalloc((size_t)sm_nbytes);
@@ -570,10 +578,10 @@ int do_copy_objects(hid_t fidin,
          /* calculate the hyperslab size */
          if (rank > 0) 
          {
-          for (i = 0, hs_nelmts = 1; i < rank; i++) 
+          for (k = 0, hs_nelmts = 1; k < rank; k++) 
           {
-           hs_size[i] = MIN(dims[i] - hs_offset[i], sm_size[i]);
-           hs_nelmts *= hs_size[i];
+           hs_size[k] = MIN(dims[k] - hs_offset[k], sm_size[k]);
+           hs_nelmts *= hs_size[k];
           }
           
           if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL)<0)
@@ -599,14 +607,14 @@ int do_copy_objects(hid_t fidin,
           H5Dvlen_reclaim(wtype_id, sm_space, H5P_DEFAULT, sm_buf);
          
          /* calculate the next hyperslab offset */
-         for (i = rank, carry = 1; i > 0 && carry; --i) 
+         for (k = rank, carry = 1; k > 0 && carry; --k) 
          {
-          hs_offset[i - 1] += hs_size[i - 1];
-          if (hs_offset[i - 1] == dims[i - 1])
-           hs_offset[i - 1] = 0;
+          hs_offset[k - 1] += hs_size[k - 1];
+          if (hs_offset[k - 1] == dims[k - 1])
+           hs_offset[k - 1] = 0;
           else
            carry = 0;
-         } /* i */
+         } /* k */
         } /* elmtno */
         
         H5Sclose(sm_space);
@@ -677,6 +685,12 @@ int do_copy_objects(hid_t fidin,
     if (H5Dclose(dset_in)<0)
      goto error;
 
+#if defined(H5REPACK_GETTIME)
+    time( &finish_time ); 
+    time_secs = finish_time-start_time;
+    printf("time1=%d secs\n",time_secs);
+#endif
+
     }
   /*-------------------------------------------------------------------------
    * we do not have request for filter/chunking use H5Ocopy instead
@@ -686,6 +700,10 @@ int do_copy_objects(hid_t fidin,
     {
      hid_t        pid;
      
+#if defined(H5REPACK_GETTIME)
+     time( &start_time );  
+#endif
+     
      /* create property to pass copy options */
      if ( (pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) 
       goto error;
@@ -707,6 +725,13 @@ int do_copy_objects(hid_t fidin,
      if (H5Pclose(pid)<0)
       goto error;
      
+#if defined(H5REPACK_GETTIME)
+     time( &finish_time ); 
+     time_secs = finish_time-start_time;
+     printf("time2=%d secs\n",time_secs);
+#endif
+
+     
     } /* end do we have request for filter/chunking */
 
 
@@ -1003,7 +1028,7 @@ error:
 static
 int do_hardlinks(hid_t fidout,trav_table_t *travt)
 {
- int i, j;
+ unsigned int i, j;
 
  for ( i = 0; i < travt->nobjs; i++)
  {
@@ -1093,7 +1118,8 @@ int do_copy_refobjs(hid_t fidin,
  int       rank;              /* rank of dataset */
  hsize_t   dims[H5S_MAX_RANK];/* dimensions of dataset */
  int       next;              /* external files */
- int       i, j;
+ unsigned  i;
+ int j;
 
 /*-------------------------------------------------------------------------
  * browse
@@ -1739,7 +1765,7 @@ static const char* MapIdToName(hid_t refobj_id,
  hid_t fid;
  H5G_stat_t refstat;    /* Stat for the refobj id */
  H5G_stat_t objstat;    /* Stat for objects in the file */
- int   i;
+ unsigned int   i;
 
  /* obtain information to identify the referenced object uniquely */
  if(H5Gget_objinfo(refobj_id, ".", 0, &refstat) <0)
diff --git a/tools/h5repack/h5repack_filters.c b/tools/h5repack/h5repack_filters.c
index 60a0336..a525e0d 100644
--- a/tools/h5repack/h5repack_filters.c
+++ b/tools/h5repack/h5repack_filters.c
@@ -32,7 +32,7 @@ int aux_find_obj(const char* name,          /* object name from traverse list */
 {
  char *pdest;
  int  result;
-	int  i;
+	unsigned int  i;
 
  for ( i=0; i<options->op_tbl->nelems; i++)
  {
diff --git a/tools/h5repack/h5repack_list.c b/tools/h5repack/h5repack_list.c
index 9912732..cb9cad9 100644
--- a/tools/h5repack/h5repack_list.c
+++ b/tools/h5repack/h5repack_list.c
@@ -39,7 +39,7 @@ int check_objects(const char* fname,
                   pack_opt_t *options)
 {
  hid_t         fid;
- int           i;
+ unsigned int  i;
  trav_table_t  *travt=NULL;
 
 /*-------------------------------------------------------------------------
diff --git a/tools/h5repack/h5repack_opttable.c b/tools/h5repack/h5repack_opttable.c
index a0b1698..c77837e 100644
--- a/tools/h5repack/h5repack_opttable.c
+++ b/tools/h5repack/h5repack_opttable.c
@@ -122,7 +122,7 @@ static void aux_tblinsert_layout(pack_opttbl_t *table,
 
 static int aux_inctable(pack_opttbl_t *table, int n_objs )
 {
- int i;
+ unsigned int i;
 
  table->size += n_objs;
  table->objs = (pack_info_t*)realloc(table->objs, table->size * sizeof(pack_info_t));
@@ -149,7 +149,7 @@ static int aux_inctable(pack_opttbl_t *table, int n_objs )
 
 int options_table_init( pack_opttbl_t **tbl )
 {
- int i;
+ unsigned int i;
  pack_opttbl_t* table = (pack_opttbl_t*) malloc(sizeof(pack_opttbl_t));
  if (table==NULL) {
   error_msg(progname, "not enough memory for options table\n");
@@ -206,7 +206,8 @@ int options_add_layout( obj_list_t *obj_list,
                         pack_info_t *pack,
                         pack_opttbl_t *table )
 {
- int i, j, I, added=0, found=0;
+ unsigned int i;
+ int          j, I, added=0, found=0;
 
  /* increase the size of the collection by N_OBJS if necessary */
  if (table->nelems+n_objs >= table->size)
@@ -304,7 +305,8 @@ int options_add_filter(obj_list_t *obj_list,
                        pack_opttbl_t *table )
 {
 
- int i, j, I, added=0, found=0;
+ unsigned int i;
+ int          j, I, added=0, found=0;
 
  /* increase the size of the collection by N_OBJS if necessary */
  if (table->nelems+n_objs >= table->size)
@@ -387,7 +389,7 @@ int options_add_filter(obj_list_t *obj_list,
 pack_info_t* options_get_object( const char *path,
                                  pack_opttbl_t *table )
 {
- int i;
+ unsigned int i;
 
  for ( i = 0; i < table->nelems; i++)
  {
diff --git a/tools/h5repack/h5repack_verify.c b/tools/h5repack/h5repack_verify.c
index a19f9f6..2247171 100644
--- a/tools/h5repack/h5repack_verify.c
+++ b/tools/h5repack/h5repack_verify.c
@@ -173,7 +173,9 @@ int h5repack_verify(const char *fname,
  hid_t  dset_id=-1;  /* dataset ID */
  hid_t  dcpl_id=-1;  /* dataset creation property list ID */
  hid_t  space_id=-1; /* space ID */
- int    ret=1, i, j;
+ int    ret=1;
+ unsigned int i;
+ int j;
  trav_table_t  *travt=NULL;
 
  /* open the file */
@@ -355,7 +357,8 @@ int h5repack_cmpdcpl(const char *fname1,
  hid_t         dcpl2=-1;      /* dataset creation property list ID */
  trav_table_t  *travt1=NULL;
  trav_table_t  *travt2=NULL;
- int           ret=1, i;
+ int           ret=1;
+ unsigned int  i;
 
 /*-------------------------------------------------------------------------
  * open the files first; if they are not valid, no point in continuing
diff --git a/tools/h5repack/h5repacktst.c b/tools/h5repack/h5repacktst.c
index 801ed5a..df231aa 100644
--- a/tools/h5repack/h5repacktst.c
+++ b/tools/h5repack/h5repacktst.c
@@ -98,7 +98,7 @@ int make_nbit(hid_t loc_id);
 int make_scaleoffset(hid_t loc_id);
 int make_all(hid_t loc_id);
 int make_fill(hid_t loc_id);
-int make_big(hid_t loc_id);
+int make_big(hid_t loc_id, int set_chunk);
 int make_testfiles(void);
 void write_dset_in(hid_t loc_id,const char* dset_name,hid_t file_id,int make_diffs );
 void write_attr_in(hid_t loc_id,const char* dset_name,hid_t fid,int make_diffs );
@@ -1448,12 +1448,12 @@ int make_testfiles(void)
   return -1;
 
 /*-------------------------------------------------------------------------
- * create a big file 
+ * create a big dataset
  *-------------------------------------------------------------------------
  */
  if((loc_id = H5Fcreate(FNAME14,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT))<0)
   return -1;
- if (make_big(loc_id)<0)
+ if (make_big(loc_id, 1)<0)
   goto out;
  if(H5Fclose(loc_id)<0)
   return -1;
@@ -2554,13 +2554,14 @@ out:
 /*-------------------------------------------------------------------------
  * Function: make_big 
  *
- * Purpose: used in test read by hyperslabs. create a dataset with 1GB dimensions
- *  by iterating trough 1MB hyperslabs 
+ * Purpose: used in test read by hyperslabs. Can create 1GB datasets, either with 
+ *  chunk layout or with contiguous layout, by iterating trough 1MB hyperslabs.
+ *  Only 1 hyperslab is written. Only the chunk case is called.
  *
  *-------------------------------------------------------------------------
  */
 
-int make_big(hid_t loc_id)
+int make_big(hid_t loc_id, int set_chunk)
 {
  hid_t   did=-1;
  hid_t   f_sid=-1;
@@ -2577,17 +2578,25 @@ int make_big(hid_t loc_id)
  char    *buf=NULL;
  int     i, j, s;
  char    c;
+ char    name[20];
+
+ strcpy(name,"conti");
 
  /* create */ 
  if ((dcpl = H5Pcreate(H5P_DATASET_CREATE))<0)
   goto out;
  if (H5Pset_fill_value(dcpl, H5T_NATIVE_CHAR, &fillvalue)<0)
   goto out;
- if(H5Pset_chunk(dcpl, 1, chunk_dims)<0)
-  goto out;
+
+ if (set_chunk)
+ {
+  strcpy(name,"chunk");
+  if(H5Pset_chunk(dcpl, 1, chunk_dims)<0)
+   goto out;
+ }
  if ((f_sid = H5Screate_simple(1,dims,NULL))<0)
   goto out;
- if ((did = H5Dcreate(loc_id,"big",H5T_NATIVE_CHAR,f_sid,dcpl))<0)
+ if ((did = H5Dcreate(loc_id,name,H5T_NATIVE_CHAR,f_sid,dcpl))<0)
   goto out;
  if ((m_sid = H5Screate_simple(1, hs_size, hs_size))<0) 
   goto out;
diff --git a/tools/lib/h5diff.c b/tools/lib/h5diff.c
index 7907d38..bc0f7cc 100644
--- a/tools/lib/h5diff.c
+++ b/tools/lib/h5diff.c
@@ -382,7 +382,7 @@ hsize_t diff_match (hid_t file1_id,
  unsigned infile[2];
  char c1, c2;
  hsize_t nfound = 0;
- int i;
+ unsigned i;
 
 /*-------------------------------------------------------------------------
  * build the list
diff --git a/tools/lib/h5trav.c b/tools/lib/h5trav.c
index dc145ec..4ef495d 100644
--- a/tools/lib/h5trav.c
+++ b/tools/lib/h5trav.c
@@ -146,15 +146,15 @@ int h5trav_getindex( const char *obj, int nobjs, trav_info_t *info )
 void h5trav_freeinfo( trav_info_t *info, int nobjs )
 {
  int i;
-	if ( info )
-	{
-		for ( i = 0; i < nobjs; i++)
-		{
-			if (info[i].name)
-		 	HDfree( info[i].name );
-		}
-		HDfree(info);
-	}
+    if ( info )
+    {
+        for ( i = 0; i < nobjs; i++)
+        {
+            if (info[i].name)
+            HDfree( info[i].name );
+        }
+        HDfree(info);
+    }
 }
 
 
@@ -625,7 +625,7 @@ void h5trav_printinfo(int nobjs, trav_info_t *travi)
  */
 void h5trav_printtable(trav_table_t *table)
 {
- int i, j;
+ unsigned int i, j;
 
  for ( i = 0; i < table->nobjs; i++)
  {
@@ -678,7 +678,7 @@ int h5trav_getindext(const char *name, trav_table_t *table)
 {
  char *pdest;
  int  result;
- int  i, j;
+ unsigned int  i, j;
 
  for ( i = 0; i < table->nobjs; i++)
  {
diff --git a/tools/lib/h5trav.h b/tools/lib/h5trav.h
index 40fa63d..4befcde 100644
--- a/tools/lib/h5trav.h
+++ b/tools/lib/h5trav.h
@@ -21,16 +21,16 @@
  * public struct to store name and type of an object
  * the TYPE can be:
  *    H5G_UNKNOWN = -1,
- *    H5G_GROUP,		    Object is a group
- *    H5G_DATASET,		    Object is a dataset
- *    H5G_TYPE,			    Object is a named data type
- *    H5G_LINK,		            Object is a symbolic link
+ *    H5G_GROUP,            Object is a group
+ *    H5G_DATASET,          Object is a dataset
+ *    H5G_TYPE,             Object is a named data type
+ *    H5G_LINK,             Object is a symbolic link
  *-------------------------------------------------------------------------
  */
 
 typedef struct trav_info_t {
-	char      *name;
-	H5G_obj_t type;
+    char      *name;
+    H5G_obj_t type;
 } trav_info_t;
 
 
@@ -39,7 +39,7 @@ typedef struct trav_info_t {
  *-------------------------------------------------------------------------
  */
 typedef struct trav_link_t {
-	char      *new_name;
+    char      *new_name;
 } trav_link_t;
 
 
@@ -56,7 +56,7 @@ typedef struct trav_obj_t {
     H5G_obj_t   type;      /* type of object */
     trav_link_t *links;    /* array of possible link names */
     int         sizelinks; /* size of links array */
-    int         nlinks;    /* number of links */
+    unsigned    nlinks;    /* number of links */
 } trav_obj_t;
 
 
@@ -66,9 +66,9 @@ typedef struct trav_obj_t {
  */
 
 typedef struct trav_table_t {
-	int        size;
-	int        nobjs;
-	trav_obj_t *objs;
+    unsigned        size;
+    unsigned        nobjs;
+    trav_obj_t *objs;
 } trav_table_t;
 
 
diff --git a/tools/lib/h5trav_table.c b/tools/lib/h5trav_table.c
index 2ebcd6b..5fb8c75 100644
--- a/tools/lib/h5trav_table.c
+++ b/tools/lib/h5trav_table.c
@@ -32,7 +32,7 @@
 
 int trav_table_search(haddr_t objno, trav_table_t *table )
 {
- int i;
+ unsigned int i;
 
  for (i = 0; i < table->nobjs; i++)
   if (table->objs[i].objno == objno)
@@ -61,7 +61,7 @@ void trav_table_add(haddr_t objno,
                     H5G_obj_t type,
                     trav_table_t *table)
 {
- int i;
+ unsigned int i;
 
  if (table->nobjs == table->size) {
   table->size *= 2;
@@ -110,7 +110,7 @@ void trav_table_addflags(unsigned *flags,
                          H5G_obj_t type,
                          trav_table_t *table)
 {
- int i;
+ unsigned int i;
 
  if (table->nobjs == table->size) {
   table->size *= 2;
@@ -157,7 +157,7 @@ void trav_table_addflags(unsigned *flags,
 
 void trav_table_init( trav_table_t **tbl )
 {
- int i;
+ unsigned int i;
  trav_table_t* table = (trav_table_t*) HDmalloc(sizeof(trav_table_t));
 
  table->size = 20;
@@ -197,7 +197,7 @@ void trav_table_init( trav_table_t **tbl )
 
 void trav_table_free( trav_table_t *table )
 {
- int i, j;
+ unsigned int i, j;
 
  for ( i = 0; i < table->nobjs; i++)
  {
@@ -234,14 +234,14 @@ void trav_table_addlink(trav_table_t *table,
                         int j /* the object index */,
                         char *path )
 {
- int k;
+ unsigned int k;
 
  /* already inserted */
  if (strcmp(table->objs[j].name,path)==0)
   return;
 
  /* allocate space if necessary */
- if (table->objs[j].nlinks == table->objs[j].sizelinks) {
+ if (table->objs[j].nlinks == (unsigned)table->objs[j].sizelinks) {
   table->objs[j].sizelinks += 2;
   table->objs[j].links =
    (trav_link_t*)HDrealloc(table->objs[j].links,