[svn-r23600] Bring revisions #23085 - #23341 from trunk to revise_chunks.

h5committested.

8 files changed, 294 insertions, 267 deletions

diff --git a/tools/lib/CMakeLists.txt b/tools/lib/CMakeLists.txt
index 7f7b451..f0d0d01 100644
--- a/tools/lib/CMakeLists.txt
+++ b/tools/lib/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 2.8.6)
+cmake_minimum_required (VERSION 2.8.10)
 PROJECT (HDF5_TOOLS_LIB)
 
 #-----------------------------------------------------------------------------
diff --git a/tools/lib/Makefile.in b/tools/lib/Makefile.in
index 6a76e1d..743e158 100644
--- a/tools/lib/Makefile.in
+++ b/tools/lib/Makefile.in
@@ -226,6 +226,7 @@ H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HAVE_DMALLOC = @HAVE_DMALLOC@
 HAVE_FORTRAN_2003 = @HAVE_FORTRAN_2003@
+HAVE_PTHREAD = @HAVE_PTHREAD@
 HDF5_HL = @HDF5_HL@
 HDF5_INTERFACES = @HDF5_INTERFACES@
 HDF_CXX = @HDF_CXX@
@@ -277,7 +278,6 @@ PACKAGE_VERSION = @PACKAGE_VERSION@
 PARALLEL = @PARALLEL@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 PERL = @PERL@
-PTHREAD = @PTHREAD@
 RANLIB = @RANLIB@
 ROOT = @ROOT@
 RUNPARALLEL = @RUNPARALLEL@
diff --git a/tools/lib/h5diff_attr.c b/tools/lib/h5diff_attr.c
index 130a0d8..4899200 100644
--- a/tools/lib/h5diff_attr.c
+++ b/tools/lib/h5diff_attr.c
@@ -350,6 +350,13 @@ hsize_t diff_attr(hid_t loc1_id,
     if( build_match_list_attrs(loc1_id, loc2_id, &match_list_attrs, options) < 0)
         goto error;
 
+    /* if detect any unique extra attr */
+    if(match_list_attrs->nattrs_only1 || match_list_attrs->nattrs_only2)
+    {
+        /* exit will be 1 */
+        options->contents = 0;
+    }
+
     for(u = 0; u < (unsigned)match_list_attrs->nattrs; u++)
     {
         if( (match_list_attrs->attrs[u].exist[0]) && (match_list_attrs->attrs[u].exist[1]) )
diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c
index 7b6098d..5f4227c 100644
--- a/tools/lib/h5tools.c
+++ b/tools/lib/h5tools.c
@@ -30,16 +30,13 @@
 #include "h5tools_utils.h"
 #include "H5private.h"
 
-#define SANITY_CHECK
-
-#define ALIGN(A,Z)  ((((A) + (Z) - 1) / (Z)) * (Z))
-
 /* global variables */
 hid_t H5tools_ERR_STACK_g = 0;
 hid_t H5tools_ERR_CLS_g = -1;
 hid_t H5E_tools_g = -1;
 hid_t H5E_tools_min_id_g = -1;
 int         compound_data;
+FILE       *rawattrstream;      /* should initialize to stdout but gcc moans about it */
 FILE       *rawdatastream;      /* should initialize to stdout but gcc moans about it */
 FILE       *rawoutstream;       /* should initialize to stdout but gcc moans about it */
 FILE       *rawerrorstream;     /* should initialize to stderr but gcc moans about it */
@@ -119,6 +116,8 @@ h5tools_init(void)
         H5tools_ERR_STACK_g = H5Ecreate_stack();
         H5TOOLS_INIT_ERROR()
 
+        if (!rawattrstream)
+            rawattrstream = stdout;
         if (!rawdatastream)
             rawdatastream = stdout;
         if (!rawoutstream)
@@ -154,9 +153,19 @@ h5tools_close(void)
     H5E_auto2_t         tools_func;
     void               *tools_edata;
     if (h5tools_init_g) {
+        /* special case where only data is output to stdout */
+        if((rawoutstream == NULL) && rawdatastream && (rawdatastream == stdout))
+            HDfprintf(rawdatastream, "\n");
+
         H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata);
         if(tools_func!=NULL)
             H5Eprint2(H5tools_ERR_STACK_g, rawerrorstream);
+        if (rawattrstream && rawattrstream != stdout) {
+            if (fclose(rawattrstream))
+                perror("closing rawattrstream");
+            else
+                rawattrstream = NULL;
+        }
         if (rawdatastream && rawdatastream != stdout) {
             if (fclose(rawdatastream))
                 perror("closing rawdatastream");
@@ -573,6 +582,9 @@ h5tools_simple_prefix(FILE *stream, const h5tool_format_t *info,
     size_t templength = 0;
     int i, indentlevel = 0;
 
+    if (stream == NULL)
+        return;
+
     if (!ctx->need_prefix)
         return;
 
@@ -581,9 +593,9 @@ h5tools_simple_prefix(FILE *stream, const h5tool_format_t *info,
 
     /* Terminate previous line, if any */
     if (ctx->cur_column) {
-        HDfputs(OPT(info->line_suf, ""), stream);
+        PUTSTREAM(OPT(info->line_suf, ""), stream);
         HDputc('\n', stream);
-        HDfputs(OPT(info->line_sep, ""), stream);
+        PUTSTREAM(OPT(info->line_sep, ""), stream);
     }
 
     /* Calculate new prefix */
@@ -607,23 +619,26 @@ h5tools_simple_prefix(FILE *stream, const h5tool_format_t *info,
        the prefix is printed one indentation level before */
     if (info->pindex) {
         for (i = 0; i < indentlevel - 1; i++) {
-            HDfputs(h5tools_str_fmt(&str, 0, info->line_indent), stream);
+            PUTSTREAM(h5tools_str_fmt(&str, 0, info->line_indent), stream);
         }
     }
 
-    if (elmtno == 0 && secnum == 0 && info->line_1st)
-        HDfputs(h5tools_str_fmt(&prefix, 0, info->line_1st), stream);
-    else if (secnum && info->line_cont)
-        HDfputs(h5tools_str_fmt(&prefix, 0, info->line_cont), stream);
-    else
-        HDfputs(h5tools_str_fmt(&prefix, 0, info->line_pre), stream);
+    if (elmtno == 0 && secnum == 0 && info->line_1st) {
+        PUTSTREAM(h5tools_str_fmt(&prefix, 0, info->line_1st), stream);
+    }
+    else if (secnum && info->line_cont) {
+        PUTSTREAM(h5tools_str_fmt(&prefix, 0, info->line_cont), stream);
+    }
+    else {
+        PUTSTREAM(h5tools_str_fmt(&prefix, 0, info->line_pre), stream);
+    }
 
     templength = h5tools_str_len(&prefix);
 
     for (i = 0; i < indentlevel; i++) {
         /*we already made the indent for the array indices case */
         if (!info->pindex) {
-            HDfputs(h5tools_str_fmt(&prefix, 0, info->line_indent), stream);
+            PUTSTREAM(h5tools_str_fmt(&prefix, 0, info->line_indent), stream);
             templength += h5tools_str_len(&prefix);
         }
         else {
@@ -662,6 +677,9 @@ h5tools_region_simple_prefix(FILE *stream, const h5tool_format_t *info,
     size_t templength = 0;
     int i, indentlevel = 0;
 
+    if (stream == NULL)
+        return;
+
     if (!ctx->need_prefix)
         return;
 
@@ -670,9 +688,9 @@ h5tools_region_simple_prefix(FILE *stream, const h5tool_format_t *info,
 
     /* Terminate previous line, if any */
     if (ctx->cur_column) {
-        HDfputs(OPT(info->line_suf, ""), stream);
+        PUTSTREAM(OPT(info->line_suf, ""), stream);
         HDputc('\n', stream);
-        HDfputs(OPT(info->line_sep, ""), stream);
+        PUTSTREAM(OPT(info->line_sep, ""), stream);
     }
 
     /* Calculate new prefix */
@@ -696,23 +714,26 @@ h5tools_region_simple_prefix(FILE *stream, const h5tool_format_t *info,
        the prefix is printed one indentation level before */
     if (info->pindex) {
         for (i = 0; i < indentlevel - 1; i++) {
-            HDfputs(h5tools_str_fmt(&str, 0, info->line_indent), stream);
+            PUTSTREAM(h5tools_str_fmt(&str, 0, info->line_indent), stream);
         }
     }
 
-    if (elmtno == 0 && secnum == 0 && info->line_1st)
-        HDfputs(h5tools_str_fmt(&prefix, 0, info->line_1st), stream);
-    else if (secnum && info->line_cont)
-        HDfputs(h5tools_str_fmt(&prefix, 0, info->line_cont), stream);
-    else
-        HDfputs(h5tools_str_fmt(&prefix, 0, info->line_pre), stream);
+    if (elmtno == 0 && secnum == 0 && info->line_1st) {
+        PUTSTREAM(h5tools_str_fmt(&prefix, 0, info->line_1st), stream);
+    }
+    else if (secnum && info->line_cont) {
+        PUTSTREAM(h5tools_str_fmt(&prefix, 0, info->line_cont), stream);
+    }
+    else {
+        PUTSTREAM(h5tools_str_fmt(&prefix, 0, info->line_pre), stream);
+    }
 
     templength = h5tools_str_len(&prefix);
 
     for (i = 0; i < indentlevel; i++) {
         /*we already made the indent for the array indices case */
         if (!info->pindex) {
-            HDfputs(h5tools_str_fmt(&prefix, 0, info->line_indent), stream);
+            PUTSTREAM(h5tools_str_fmt(&prefix, 0, info->line_indent), stream);
             templength += h5tools_str_len(&prefix);
         }
         else {
@@ -766,6 +787,9 @@ h5tools_render_element(FILE *stream, const h5tool_format_t *info,
     int      secnum; /*section sequence number */
     int      multiline; /*datum was multiline  */
 
+    if (stream == NULL)
+        return dimension_break;
+
     s = h5tools_str_fmt(buffer, 0, "%s");
 
     /*
@@ -870,12 +894,12 @@ h5tools_render_element(FILE *stream, const h5tool_format_t *info,
             h5tools_simple_prefix(stream, info, ctx, *curr_pos, secnum);
         }
         else if ((local_elmt_counter || ctx->continuation) && secnum == 0) {
-            HDfputs(OPT(info->elmt_suf2, " "), stream);
+            PUTSTREAM(OPT(info->elmt_suf2, " "), stream);
             ctx->cur_column += HDstrlen(OPT(info->elmt_suf2, " "));
         }
 
         /* Print the section */
-        HDfputs(section, stream);
+        PUTSTREAM(section, stream);
         ctx->cur_column += HDstrlen(section);
     }
 
@@ -1026,12 +1050,12 @@ h5tools_render_region_element(FILE *stream, const h5tool_format_t *info,
             h5tools_region_simple_prefix(stream, info, ctx, local_elmt_counter, ptdata, secnum);
         }
         else if ((local_elmt_counter || ctx->continuation) && secnum == 0) {
-            HDfputs(OPT(info->elmt_suf2, " "), stream);
+            PUTSTREAM(OPT(info->elmt_suf2, " "), stream);
             ctx->cur_column += HDstrlen(OPT(info->elmt_suf2, " "));
         }
 
         /* Print the section */
-        HDfputs(section, stream);
+        PUTSTREAM(section, stream);
         ctx->cur_column += HDstrlen(section);
     }
 
@@ -1095,7 +1119,6 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem,  hsize_t
             while(block_index > 0) {
                 size_t bytes_in        = 0;    /* # of bytes to write  */
                 size_t bytes_wrote     = 0;    /* # of bytes written   */
-                size_t item_size       = size;    /* size of items in bytes */
 
                 if(block_index > sizeof(size_t))
                     bytes_in = sizeof(size_t);
@@ -1133,7 +1156,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem,  hsize_t
                     }
                     for (i = 0; i < size && (s[i] || pad != H5T_STR_NULLTERM); i++) {
                         HDmemcpy(&tempuchar, &s[i], sizeof(unsigned char));
-                        if (1 != HDfwrite(&tempuchar, size, 1, stream))
+                        if (1 != HDfwrite(&tempuchar, sizeof(unsigned char), 1, stream))
                             H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed");
                     } /* i */
                 } /* for (block_index = 0; block_index < block_nelmts; block_index++) */
@@ -1141,16 +1164,21 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem,  hsize_t
             break;
         case H5T_COMPOUND:
             {
-                unsigned j;
-                hid_t    memb;
+                int snmembs;
                 unsigned nmembs;
-                size_t   offset;
 
-                nmembs = H5Tget_nmembers(tid);
+                if((snmembs = H5Tget_nmembers(tid)) < 0)
+                    H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers of compound failed");
+                nmembs = (unsigned)snmembs;
 
                 for (block_index = 0; block_index < block_nelmts; block_index++) {
+                    unsigned j;
+
                     mem = ((unsigned char*)_mem) + block_index * size;
                     for (j = 0; j < nmembs; j++) {
+                        hid_t    memb;
+                        size_t   offset;
+
                         offset = H5Tget_member_offset(tid, j);
                         memb   = H5Tget_member_type(tid, j);
 
@@ -1165,7 +1193,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem,  hsize_t
         case H5T_ARRAY:
             {
                 int     k, ndims;
-                hsize_t i, dims[H5S_MAX_RANK], temp_nelmts, nelmts;
+                hsize_t dims[H5S_MAX_RANK], temp_nelmts, nelmts;
                 hid_t   memb;
 
                 /* get the array's base datatype for each element */
@@ -1192,7 +1220,6 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem,  hsize_t
             break;
         case H5T_VLEN:
             {
-                unsigned int i;
                 hsize_t      nelmts;
                 hid_t        memb;
 
@@ -1213,7 +1240,8 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem,  hsize_t
             break;
         case H5T_REFERENCE:
             {
-                if (H5Tequal(tid, H5T_STD_REF_DSETREG)) {
+                if (size == H5R_DSET_REG_REF_BUF_SIZE) {
+                    /* if (H5Tequal(tid, H5T_STD_REF_DSETREG)) */
                     if (region_output) {
                         /* region data */
                         hid_t   region_id, region_space;
@@ -1237,7 +1265,8 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem,  hsize_t
                         }
                     } /* end if (region_output... */
                 }
-                else if (H5Tequal(tid, H5T_STD_REF_OBJ)) {
+                else if (size == H5R_OBJ_REF_BUF_SIZE) {
+                    /* if (H5Tequal(tid, H5T_STD_REF_OBJ)) */
                     ;
                 }
             }
@@ -1276,10 +1305,9 @@ render_bin_output_region_data_blocks(hid_t region_id, FILE *stream,
     hsize_t     *start = NULL;
     hsize_t     *count = NULL;
     hsize_t      numelem;
-    hsize_t      numindex;
     hsize_t      total_size[H5S_MAX_RANK];
     int          jndx;
-    int          type_size;
+    size_t       type_size;
     hid_t        mem_space = -1;
     void        *region_buf = NULL;
     int          blkndx;
@@ -1370,15 +1398,17 @@ render_bin_output_region_blocks(hid_t region_space, hid_t region_id,
         FILE *stream, hid_t container)
 {
     HERR_INIT(hbool_t, TRUE)
-    hssize_t     nblocks;
+    hssize_t     snblocks;
+    hsize_t      nblocks;
     hsize_t      alloc_size;
-    hsize_t     *ptdata = NULL;
+    hsize_t     *ptdata;
     int          ndims;
     hid_t        dtype;
     hid_t        type_id;
 
-    if((nblocks = H5Sget_select_hyper_nblocks(region_space)) <= 0)
+    if((snblocks = H5Sget_select_hyper_nblocks(region_space)) <= 0)
         H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_hyper_nblocks failed");
+    nblocks = (hsize_t)snblocks;
 
     /* Print block information */
     if((ndims = H5Sget_simple_extent_ndims(region_space)) < 0)
@@ -1434,13 +1464,12 @@ render_bin_output_region_blocks(hid_t region_space, hid_t region_id,
  *      hssize_t npoints is the number of points in the region
  *-------------------------------------------------------------------------
  */
-int
+static int
 render_bin_output_region_data_points(hid_t region_space, hid_t region_id,
         FILE *stream, hid_t container,
-        int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata)
+        int ndims, hid_t type_id, hssize_t npoints)
 {
     hsize_t *dims1 = NULL;
-    int      jndx;
     int      type_size;
     hid_t    mem_space = -1;
     void    *region_buf = NULL;
@@ -1496,8 +1525,6 @@ render_bin_output_region_points(hid_t region_space, hid_t region_id,
 {
     HERR_INIT(hbool_t, TRUE)
     hssize_t npoints;
-    hsize_t  alloc_size;
-    hsize_t *ptdata;
     int      ndims;
     hid_t    dtype;
     hid_t    type_id;
@@ -1509,15 +1536,6 @@ render_bin_output_region_points(hid_t region_space, hid_t region_id,
     if((ndims = H5Sget_simple_extent_ndims(region_space)) < 0)
         H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
 
-    alloc_size = npoints * ndims * sizeof(ptdata[0]);
-    HDassert(alloc_size == (hsize_t) ((size_t) alloc_size)); /*check for overflow*/
-    if(NULL == (ptdata = (hsize_t *)HDmalloc((size_t) alloc_size)))
-        HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "Could not allocate buffer for ptdata");
-
-    H5_CHECK_OVERFLOW(npoints, hssize_t, hsize_t);
-    if(H5Sget_select_elem_pointlist(region_space, (hsize_t) 0, (hsize_t) npoints, ptdata) < 0)
-        HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Sget_select_elem_pointlist failed");
-
     if((dtype = H5Dget_type(region_id)) < 0)
         HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Dget_type failed");
 
@@ -1525,11 +1543,9 @@ render_bin_output_region_points(hid_t region_space, hid_t region_id,
         HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Tget_native_type failed");
 
     render_bin_output_region_data_points(region_space, region_id,
-            stream, container, ndims, type_id, npoints, ptdata);
+            stream, container, ndims, type_id, npoints);
 
  done:
-    HDfree(ptdata);
-
     if(H5Tclose(type_id) < 0)
         HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
 
diff --git a/tools/lib/h5tools.h b/tools/lib/h5tools.h
index 1a2b81c..8e5b9c8 100644
--- a/tools/lib/h5tools.h
+++ b/tools/lib/h5tools.h
@@ -36,6 +36,12 @@
 
 #define H5TOOLS_DUMP_MAX_RANK     H5S_MAX_RANK
 
+/* Stream macros */
+#define FLUSHSTREAM(S)           if(S != NULL) HDfflush(S)
+#define PRINTSTREAM(S, F, ...)   if(S != NULL) HDfprintf(S, F, __VA_ARGS__)
+#define PRINTVALSTREAM(S, V)   if(S != NULL) HDfprintf(S, V)
+#define PUTSTREAM(X,S)          if(S != NULL) HDfputs(X, S);
+
 /*
  * Strings for output - these were duplicated from the h5dump.h
  * file in order to support region reference data display
@@ -533,6 +539,7 @@ H5TOOLS_DLLVAR int     packed_bits_num;     /* number of packed bits to display
 H5TOOLS_DLLVAR int     packed_data_offset;  /* offset of packed bits to display */
 H5TOOLS_DLLVAR int     packed_data_length; /* lengtht of packed bits to display */
 H5TOOLS_DLLVAR unsigned long long packed_data_mask;  /* mask in which packed bits to display */
+H5TOOLS_DLLVAR FILE   *rawattrstream;       /* output stream for raw attribute data */
 H5TOOLS_DLLVAR FILE   *rawdatastream;       /* output stream for raw data */
 H5TOOLS_DLLVAR FILE   *rawoutstream;        /* output stream for raw output */
 H5TOOLS_DLLVAR FILE   *rawerrorstream;      /* output stream for raw error */
diff --git a/tools/lib/h5tools_dump.c b/tools/lib/h5tools_dump.c
index 33fef3c..e1f71eb 100644
--- a/tools/lib/h5tools_dump.c
+++ b/tools/lib/h5tools_dump.c
@@ -284,9 +284,9 @@ h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, hid_t contai
                                      *to the ctx->size_last_dim.   */
 
     /* binary dump */
-    if (bin_output) {
+    if (bin_output && (rawdatastream != NULL)) {
         if (render_bin_output(rawdatastream, container, type, _mem, nelmts) < 0) {
-            HDfprintf(rawoutstream,"\nError in writing binary stream\n");
+            PRINTVALSTREAM(rawoutstream, "\nError in writing binary stream\n");
         }
     } /* end if */
     else {
@@ -303,7 +303,7 @@ h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, hid_t contai
          */
         curr_pos = ctx->sm_pos;
 
-        if (region_output && H5Tequal(type, H5T_STD_REF_DSETREG)) {
+        if (region_output && (size == H5R_DSET_REG_REF_BUF_SIZE)) {
             for (i = 0; i < nelmts; i++, ctx->cur_elmt++, elmt_counter++) {
                 void* memref = mem + i * size;
                 char ref_name[1024];
@@ -1838,7 +1838,7 @@ h5tools_dump_mem(FILE *stream, const h5tool_format_t *info, h5tools_context_t *c
     if (H5Sis_simple(space) <= 0)
         H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sis_simple failed")
 
-     H5_LEAVE(h5tools_dump_simple_mem(stream, info, ctx, obj_id, type, space, mem))
+     H5_LEAVE(h5tools_dump_simple_mem(rawattrstream, info, ctx, obj_id, type, space, mem))
 
 CATCH
     return ret_value;
diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c
index 11850f2..b46dc18 100644
--- a/tools/lib/h5tools_str.c
+++ b/tools/lib/h5tools_str.c
@@ -700,7 +700,8 @@ char *
 h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t container,
                    hid_t type, void *vp, h5tools_context_t *ctx)
 {
-    size_t         n, offset, size=0, nelmts, start;
+    size_t         nsize, offset, size=0, nelmts, start;
+    H5T_sign_t     nsign;
     char          *name;
     unsigned char *ucp_vp = (unsigned char *)vp;
     char          *cp_vp = (char *)vp;
@@ -730,15 +731,16 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai
     /* Append value depending on data type */
     start = h5tools_str_len(str);
 
+    nsize = H5Tget_size(type);
+    nsign = H5Tget_sign(type);
     if (info->raw) {
         size_t i;
 
-        n = H5Tget_size(type);
-        if (1 == n) {
+        if (1 == nsize) {
             h5tools_str_append(str, OPT(info->fmt_raw, "0x%02x"), ucp_vp[0]);
         }
         else {
-            for (i = 0; i < n; i++) {
+            for (i = 0; i < nsize; i++) {
                 if (i)
                     h5tools_str_append(str, ":");
                 h5tools_str_append(str, OPT(info->fmt_raw, "%02x"), ucp_vp[i]);
@@ -750,20 +752,23 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai
             return NULL;
         switch (type_class) {
             case H5T_FLOAT:
-                if (H5Tequal(type, H5T_NATIVE_FLOAT)) {
+                if (sizeof(float) == nsize) {
+                    /* if (H5Tequal(type, H5T_NATIVE_FLOAT)) */
                     float tempfloat;
 
                     HDmemcpy(&tempfloat, vp, sizeof(float));
                     h5tools_str_append(str, OPT(info->fmt_float, "%g"), tempfloat);
                 }
-                else if (H5Tequal(type, H5T_NATIVE_DOUBLE)) {
+                else if (sizeof(double) == nsize) {
+                    /* if (H5Tequal(type, H5T_NATIVE_DOUBLE)) */
                     double tempdouble;
 
                     HDmemcpy(&tempdouble, vp, sizeof(double));
                     h5tools_str_append(str, OPT(info->fmt_double, "%g"), tempdouble);
 #if H5_SIZEOF_LONG_DOUBLE !=0
                 }
-                else if (H5Tequal(type, H5T_NATIVE_LDOUBLE)) {
+                else if (sizeof(long double) == nsize) {
+                    /* if (H5Tequal(type, H5T_NATIVE_LDOUBLE)) */
                     long double templdouble;
 
                     HDmemcpy(&templdouble, vp, sizeof(long double));
@@ -848,147 +853,140 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai
                 }
                 break;
             case H5T_INTEGER:
-                if (H5Tequal(type, H5T_NATIVE_INT)) {
-                    HDmemcpy(&tempint, vp, sizeof(int));
-                    if (packed_bits_num) {
-                        if (packed_data_offset >= 8 * sizeof(int))
-                            tempint = 0;
-                        else
-                            tempint = (tempint >> packed_data_offset) & packed_data_mask;
-                    }
-                    h5tools_str_append(str, OPT(info->fmt_int, "%d"), tempint);
-                }
-                else if (H5Tequal(type, H5T_NATIVE_UINT)) {
-                    HDmemcpy(&tempuint, vp, sizeof(unsigned int));
-                    if (packed_bits_num) {
-                        if (packed_data_offset >= 8 * sizeof(unsigned int))
-                            tempuint = 0;
-                        else
-                            tempuint = (tempuint >> packed_data_offset) & packed_data_mask;
-                    }
-                    h5tools_str_append(str, OPT(info->fmt_uint, "%u"), tempuint);
-                }
-                else if (info->ascii && (H5Tequal(type, H5T_NATIVE_SCHAR) || H5Tequal(type, H5T_NATIVE_UCHAR))) {
-                    h5tools_print_char(str, info, (char) (*ucp_vp));
-                }
-                else if (H5Tequal(type, H5T_NATIVE_SCHAR)) {
-                    signed char tempchar;
-                    HDmemcpy(&tempchar, cp_vp, sizeof(char));
-                    if (packed_bits_num) {
-                        if (packed_data_offset >= 8 * sizeof(char))
-                            tempchar = 0;
-                        else
-                            tempchar = (tempchar >> packed_data_offset) & packed_data_mask;
-                    }
-#ifdef H5_VMS
-                    h5tools_str_append(str, OPT(info->fmt_schar, "%hd"), tempchar);
-#else
-                    h5tools_str_append(str, OPT(info->fmt_schar, "%hhd"), tempchar);
-#endif      
-                }
-                else if (H5Tequal(type, H5T_NATIVE_UCHAR)) {
-                    unsigned char tempuchar;
-                    HDmemcpy(&tempuchar, ucp_vp, sizeof(unsigned char));
-                    if (packed_bits_num) {
-                        if (packed_data_offset >= 8 * sizeof(unsigned char))
-                            tempuchar = 0;
-                        else
-                            tempuchar = (tempuchar >> packed_data_offset) & packed_data_mask;
-                    }
-                    h5tools_str_append(str, OPT(info->fmt_uchar, "%u"), tempuchar);
-                }
-                else if (H5Tequal(type, H5T_NATIVE_SHORT)) {
-                    short tempshort;
-
-                    HDmemcpy(&tempshort, vp, sizeof(short));
-                    if (packed_bits_num) {
-                        if (packed_data_offset >= 8 * sizeof(short))
-                            tempshort = 0;
-                        else
-                            tempshort = (tempshort >> packed_data_offset) & packed_data_mask;
-                    }
-                    h5tools_str_append(str, OPT(info->fmt_short, "%d"), tempshort);
-                }
-                else if (H5Tequal(type, H5T_NATIVE_USHORT)) {
-                    unsigned short tempushort;
-
-                    HDmemcpy(&tempushort, vp, sizeof(unsigned short));
-                    if (packed_bits_num) {
-                        if (packed_data_offset >= 8 * sizeof(unsigned short))
-                            tempushort = 0;
-                        else
-                            tempushort = (tempushort >> packed_data_offset) & packed_data_mask;
-                    }
-                    h5tools_str_append(str, OPT(info->fmt_ushort, "%u"), tempushort);
-                }
-                else if (H5Tequal(type, H5T_NATIVE_LONG)) {
-                    HDmemcpy(&templong, vp, sizeof(long));
-                    if (packed_bits_num) {
-                        if (packed_data_offset >= 8 * sizeof(long))
-                            templong = 0;
-                        else
-                            templong = (templong >> packed_data_offset) & packed_data_mask;
+                if (sizeof(char) == nsize) {
+                    /* if ((H5Tequal(type, H5T_NATIVE_SCHAR) || H5Tequal(type, H5T_NATIVE_UCHAR))) */
+                    if (info->ascii) {
+                        h5tools_print_char(str, info, (char) (*ucp_vp));
                     }
-                    h5tools_str_append(str, OPT(info->fmt_long, "%ld"), templong);
-                }
-                else if (H5Tequal(type, H5T_NATIVE_ULONG)) {
-                    HDmemcpy(&tempulong, vp, sizeof(unsigned long));
-                    if (packed_bits_num) {
-                        if (packed_data_offset >= 8 * sizeof(unsigned long))
-                            tempulong = 0;
-                        else
-                            tempulong = (tempulong >> packed_data_offset) & packed_data_mask;
+                    else if(H5T_SGN_NONE == nsign) {
+                        /* if (H5Tequal(type, H5T_NATIVE_UCHAR)) */
+                        unsigned char tempuchar;
+                        HDmemcpy(&tempuchar, ucp_vp, sizeof(unsigned char));
+                        if (packed_bits_num) {
+                            if (packed_data_offset >= 8 * sizeof(unsigned char))
+                                tempuchar = 0;
+                            else
+                                tempuchar = (tempuchar >> packed_data_offset) & packed_data_mask;
+                        }
+                        h5tools_str_append(str, OPT(info->fmt_uchar, "%u"), tempuchar);
                     }
-                    h5tools_str_append(str, OPT(info->fmt_ulong, "%lu"), tempulong);
-                }
-                else if (H5Tequal(type, H5T_NATIVE_LLONG)) {
-                    HDmemcpy(&templlong, vp, sizeof(long long));
-                    if (packed_bits_num) {
-                        if (packed_data_offset >= 8 * sizeof(long long))
-                            templlong = 0;
-                        else
-                            templlong = (templlong >> packed_data_offset) & packed_data_mask;
+                    else {
+                        /* if (H5Tequal(type, H5T_NATIVE_SCHAR)) */
+                        signed char tempchar;
+                        HDmemcpy(&tempchar, cp_vp, sizeof(char));
+                        if (packed_bits_num) {
+                            if (packed_data_offset >= 8 * sizeof(char))
+                                tempchar = 0;
+                            else
+                                tempchar = (tempchar >> packed_data_offset) & packed_data_mask;
+                        }
+    #ifdef H5_VMS
+                        h5tools_str_append(str, OPT(info->fmt_schar, "%hd"), tempchar);
+    #else
+                        h5tools_str_append(str, OPT(info->fmt_schar, "%hhd"), tempchar);
+    #endif
                     }
-                    h5tools_str_append(str, OPT(info->fmt_llong, fmt_llong), templlong);
-                }
-                else if (H5Tequal(type, H5T_NATIVE_ULLONG)) {
-                    HDmemcpy(&tempullong, vp, sizeof(unsigned long long));
-                    if (packed_bits_num) {
-                        if (packed_data_offset >= 8 * sizeof(unsigned long long))
-                            tempullong = 0;
-                        else
-                            tempullong = (tempullong >> packed_data_offset) & packed_data_mask;
+                } /* end if (sizeof(char) == nsize) */
+                else if (sizeof(int) == nsize) {
+                    if(H5T_SGN_NONE == nsign) {
+                        /* if (H5Tequal(type, H5T_NATIVE_UINT)) */
+                        HDmemcpy(&tempuint, vp, sizeof(unsigned int));
+                        if (packed_bits_num) {
+                            if (packed_data_offset >= 8 * sizeof(unsigned int))
+                                tempuint = 0;
+                            else
+                                tempuint = (tempuint >> packed_data_offset) & packed_data_mask;
+                        }
+                        h5tools_str_append(str, OPT(info->fmt_uint, "%u"), tempuint);
                     }
-                    h5tools_str_append(str, OPT(info->fmt_ullong, fmt_ullong), tempullong);
-                }
-                else if (H5Tequal(type, H5T_NATIVE_HSSIZE)) {
-                    if (sizeof(hssize_t) == sizeof(int)) {
+                    else {
+                        /* if (H5Tequal(type, H5T_NATIVE_INT)) */
                         HDmemcpy(&tempint, vp, sizeof(int));
+                        if (packed_bits_num) {
+                            if (packed_data_offset >= 8 * sizeof(int))
+                                tempint = 0;
+                            else
+                                tempint = (tempint >> packed_data_offset) & packed_data_mask;
+                        }
                         h5tools_str_append(str, OPT(info->fmt_int, "%d"), tempint);
                     }
-                    else if (sizeof(hssize_t) == sizeof(long)) {
-                        HDmemcpy(&templong, vp, sizeof(long));
-                        h5tools_str_append(str, OPT(info->fmt_long, "%ld"), templong);
+                } /* end if (sizeof(int) == nsize) */
+                else if (sizeof(short) == nsize) {
+                    if(H5T_SGN_NONE == nsign) {
+                        /* if (H5Tequal(type, H5T_NATIVE_USHORT)) */
+                        unsigned short tempushort;
+
+                        HDmemcpy(&tempushort, vp, sizeof(unsigned short));
+                        if (packed_bits_num) {
+                            if (packed_data_offset >= 8 * sizeof(unsigned short))
+                                tempushort = 0;
+                            else
+                                tempushort = (tempushort >> packed_data_offset) & packed_data_mask;
+                        }
+                        h5tools_str_append(str, OPT(info->fmt_ushort, "%u"), tempushort);
                     }
                     else {
-                        HDmemcpy(&templlong, vp, sizeof(long long));
-                        h5tools_str_append(str, OPT(info->fmt_llong, fmt_llong), templlong);
-                    }
-                }
-                else if (H5Tequal(type, H5T_NATIVE_HSIZE)) {
-                    if (sizeof(hsize_t) == sizeof(int)) {
-                        HDmemcpy(&tempuint, vp, sizeof(unsigned int));
-                        h5tools_str_append(str, OPT(info->fmt_uint, "%u"), tempuint);
+                        /* if (H5Tequal(type, H5T_NATIVE_SHORT)) */
+                        short tempshort;
+
+                        HDmemcpy(&tempshort, vp, sizeof(short));
+                        if (packed_bits_num) {
+                            if (packed_data_offset >= 8 * sizeof(short))
+                                tempshort = 0;
+                            else
+                                tempshort = (tempshort >> packed_data_offset) & packed_data_mask;
+                        }
+                        h5tools_str_append(str, OPT(info->fmt_short, "%d"), tempshort);
                     }
-                    else if (sizeof(hsize_t) == sizeof(long)) {
-                        HDmemcpy(&tempulong, vp, sizeof(long));
+                } /* end if (sizeof(short) == nsize) */
+                else if (sizeof(long) == nsize) {
+                    if(H5T_SGN_NONE == nsign) {
+                        /* if (H5Tequal(type, H5T_NATIVE_ULONG)) */
+                        HDmemcpy(&tempulong, vp, sizeof(unsigned long));
+                        if (packed_bits_num) {
+                            if (packed_data_offset >= 8 * sizeof(unsigned long))
+                                tempulong = 0;
+                            else
+                                tempulong = (tempulong >> packed_data_offset) & packed_data_mask;
+                        }
                         h5tools_str_append(str, OPT(info->fmt_ulong, "%lu"), tempulong);
                     }
                     else {
+                        /* if (H5Tequal(type, H5T_NATIVE_LONG)) */
+                        HDmemcpy(&templong, vp, sizeof(long));
+                        if (packed_bits_num) {
+                            if (packed_data_offset >= 8 * sizeof(long))
+                                templong = 0;
+                            else
+                                templong = (templong >> packed_data_offset) & packed_data_mask;
+                        }
+                        h5tools_str_append(str, OPT(info->fmt_long, "%ld"), templong);
+                    }
+                } /* end if (sizeof(long) == nsize) */
+                else if (sizeof(long long) == nsize) {
+                    if(H5T_SGN_NONE == nsign) {
+                        /* if (H5Tequal(type, H5T_NATIVE_ULLONG)) */
                         HDmemcpy(&tempullong, vp, sizeof(unsigned long long));
+                        if (packed_bits_num) {
+                            if (packed_data_offset >= 8 * sizeof(unsigned long long))
+                                tempullong = 0;
+                            else
+                                tempullong = (tempullong >> packed_data_offset) & packed_data_mask;
+                        }
                         h5tools_str_append(str, OPT(info->fmt_ullong, fmt_ullong), tempullong);
                     }
-                }
+                    else {
+                        /* if (H5Tequal(type, H5T_NATIVE_LLONG)) */
+                        HDmemcpy(&templlong, vp, sizeof(long long));
+                        if (packed_bits_num) {
+                            if (packed_data_offset >= 8 * sizeof(long long))
+                                templlong = 0;
+                            else
+                                templlong = (templlong >> packed_data_offset) & packed_data_mask;
+                        }
+                        h5tools_str_append(str, OPT(info->fmt_llong, fmt_llong), templlong);
+                    }
+                } /* end if (sizeof(long long) == nsize) */
                 break;
             case H5T_COMPOUND:
                 if(ctx->cmpd_listv) { /* there is <list_of_fields> */
@@ -1089,75 +1087,71 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai
                     }
                     else {
                         size_t i;
-                        n = H5Tget_size(type);
-                        if (1 == n) {
+                        if (1 == nsize) {
                             h5tools_str_append(str, "0x%02x", ucp_vp[0]);
                         }
                         else {
-                            for (i = 0; i < n; i++)
+                            for (i = 0; i < nsize; i++)
                                 h5tools_str_append(str, "%s%02x", i ? ":" : "", ucp_vp[i]);
                         }
                     }
                 }
                 break;
             case H5T_REFERENCE:
-                if (H5Tequal(type, H5T_STD_REF_DSETREG)) {
-                    if (h5tools_str_is_zero(vp, H5Tget_size(type))) {
-                        h5tools_str_append(str, "NULL");
-                    }
-                    else {
-                        h5tools_str_sprint_region(str, info, container, vp);
-                    }
+                if (h5tools_str_is_zero(vp, nsize)) {
+                    h5tools_str_append(str, "NULL");
                 }
-                else if (H5Tequal(type, H5T_STD_REF_OBJ)) {
-                    /*
-                     * Object references -- show the type and OID of the referenced
-                     * object.
-                     */
-                    if (h5tools_str_is_zero(vp, H5Tget_size(type))) {
-                        h5tools_str_append(str, "NULL");
+                else {
+                    if (nsize == H5R_DSET_REG_REF_BUF_SIZE) {
+                        /* if (H5Tequal(type, H5T_STD_REF_DSETREG)) */
+                        h5tools_str_sprint_region(str, info, container, vp);
                     }
-                    else {
-                        H5O_info_t oi;
-                        const char *path;
-
-                        obj = H5Rdereference2(container, H5P_DEFAULT, H5R_OBJECT, vp);
-                        H5Oget_info(obj, &oi);
-
-                        /* Print object type and close object */
-                        switch (oi.type) {
-                            case H5O_TYPE_GROUP:
-                                h5tools_str_append(str, H5_TOOLS_GROUP);
-                                break;
-
-                            case H5O_TYPE_DATASET:
-                                h5tools_str_append(str, H5_TOOLS_DATASET);
-                                break;
-
-                            case H5O_TYPE_NAMED_DATATYPE:
-                                h5tools_str_append(str, H5_TOOLS_DATATYPE);
-                                break;
-
-                            default:
-                                h5tools_str_append(str, "%u-", (unsigned) oi.type);
-                                break;
-                        } /* end switch */
-                        H5Oclose(obj);
-
-                        /* Print OID */
-                        if (info->obj_hidefileno)
-                            h5tools_str_append(str, info->obj_format, oi.addr);
-                        else
-                            h5tools_str_append(str, info->obj_format, oi.fileno, oi.addr);
-
-                        /* Print name */
-                        path = lookup_ref_path(*(haddr_t *) vp);
-                        if (path) {
-                            h5tools_str_append(str, " ");
-                            h5tools_str_append(str, path);
-                            h5tools_str_append(str, " ");
-                        } /* end if */
-                    } /* end else */
+                    else if (nsize == H5R_OBJ_REF_BUF_SIZE) {
+                        /* if (H5Tequal(type, H5T_STD_REF_OBJ)) */
+                            /*
+                             * Object references -- show the type and OID of the referenced
+                             * object.
+                             */
+                            H5O_info_t oi;
+                            const char *path;
+
+                            obj = H5Rdereference2(container, H5P_DEFAULT, H5R_OBJECT, vp);
+                            H5Oget_info(obj, &oi);
+
+                            /* Print object type and close object */
+                            switch (oi.type) {
+                                case H5O_TYPE_GROUP:
+                                    h5tools_str_append(str, H5_TOOLS_GROUP);
+                                    break;
+
+                                case H5O_TYPE_DATASET:
+                                    h5tools_str_append(str, H5_TOOLS_DATASET);
+                                    break;
+
+                                case H5O_TYPE_NAMED_DATATYPE:
+                                    h5tools_str_append(str, H5_TOOLS_DATATYPE);
+                                    break;
+
+                                default:
+                                    h5tools_str_append(str, "%u-", (unsigned) oi.type);
+                                    break;
+                            } /* end switch */
+                            H5Oclose(obj);
+
+                            /* Print OID */
+                            if (info->obj_hidefileno)
+                                h5tools_str_append(str, info->obj_format, oi.addr);
+                            else
+                                h5tools_str_append(str, info->obj_format, oi.fileno, oi.addr);
+
+                            /* Print name */
+                            path = lookup_ref_path(*(haddr_t *) vp);
+                            if (path) {
+                                h5tools_str_append(str, " ");
+                                h5tools_str_append(str, path);
+                                h5tools_str_append(str, " ");
+                            } /* end if */
+                    } /* end else if (H5Tequal(type, H5T_STD_REF_OBJ)) */
                 }
                 break;
             case H5T_ARRAY:
@@ -1271,12 +1265,11 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai
                 {
                     /* All other types get printed as hexadecimal */
                     size_t i;
-                    n = H5Tget_size(type);
-                    if (1 == n) {
+                    if (1 == nsize) {
                         h5tools_str_append(str, "0x%02x", ucp_vp[0]);
                     }
                     else {
-                        for (i = 0; i < n; i++)
+                        for (i = 0; i < nsize; i++)
                             h5tools_str_append(str, "%s%02x", i ? ":" : "", ucp_vp[i]);
                     }
                 }
diff --git a/tools/lib/h5tools_utils.c b/tools/lib/h5tools_utils.c
index 79322bc..d7c5adb 100644
--- a/tools/lib/h5tools_utils.c
+++ b/tools/lib/h5tools_utils.c
@@ -152,8 +152,9 @@ error_msg(const char *fmt, ...)
     va_list ap;
 
     HDva_start(ap, fmt);
-    HDfflush(rawdatastream);
-    HDfflush(rawoutstream);
+    FLUSHSTREAM(rawattrstream);
+    FLUSHSTREAM(rawdatastream);
+    FLUSHSTREAM(rawoutstream);
     HDfprintf(rawerrorstream, "%s error: ", h5tools_getprogname());
     HDvfprintf(rawerrorstream, fmt, ap);
 
@@ -182,8 +183,9 @@ warn_msg(const char *fmt, ...)
     va_list ap;
 
     HDva_start(ap, fmt);
-    HDfflush(rawdatastream);
-    HDfflush(rawoutstream);
+    FLUSHSTREAM(rawattrstream);
+    FLUSHSTREAM(rawdatastream);
+    FLUSHSTREAM(rawoutstream);
     HDfprintf(rawerrorstream, "%s warning: ", h5tools_getprogname());
     HDvfprintf(rawerrorstream, fmt, ap);
     HDva_end(ap);
@@ -275,6 +277,8 @@ get_option(int argc, const char **argv, const char *opts, const struct long_opti
 
                         opt_opt = '?';
                     }
+                    else
+                        opt_arg = NULL;
                 } 
                 else {
                     if (arg[len] == '=') {
@@ -388,7 +392,7 @@ indentation(int x)
 {
     if (x < h5tools_nCols) {
         while (x-- > 0)
-            HDfprintf(rawoutstream, " ");
+            PRINTVALSTREAM(rawoutstream, " ");
     } 
     else {
         HDfprintf(rawerrorstream, "error: the indentation exceeds the number of cols.\n");
@@ -414,7 +418,7 @@ indentation(int x)
 void
 print_version(const char *progname)
 {
-    HDfprintf(rawoutstream, "%s: Version %u.%u.%u%s%s\n",
+    PRINTSTREAM(rawoutstream, "%s: Version %u.%u.%u%s%s\n",
            progname, H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE,
            ((char *)H5_VERS_SUBRELEASE)[0] ? "-" : "", H5_VERS_SUBRELEASE);
 }
@@ -494,9 +498,9 @@ dump_table(char* tablename, table_t *table)
 {
     unsigned u;
 
-    HDfprintf(rawoutstream,"%s: # of entries = %d\n", tablename,table->nobjs);
+    PRINTSTREAM(rawoutstream,"%s: # of entries = %d\n", tablename,table->nobjs);
     for (u = 0; u < table->nobjs; u++)
-    HDfprintf(rawoutstream,"%a %s %d %d\n", table->objs[u].objno,
+        PRINTSTREAM(rawoutstream,"%a %s %d %d\n", table->objs[u].objno,
            table->objs[u].objname,
            table->objs[u].displayed, table->objs[u].recorded);
 }