Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into bugfix/repack_external_storage

7 files changed, 33 insertions, 63 deletions

diff --git a/tools/src/h5dump/h5dump_xml.c b/tools/src/h5dump/h5dump_xml.c
index ec76511..2fa9fd0 100644
--- a/tools/src/h5dump/h5dump_xml.c
+++ b/tools/src/h5dump/h5dump_xml.c
@@ -2881,7 +2881,7 @@ xml_print_refs(hid_t did, int source)
             goto error;
     }
 
-    refbuf = (hobj_ref_t *) buf;
+    refbuf = (hobj_ref_t *)((void *)buf);
 
     /* setup */
     HDmemset(&buffer, 0, sizeof(h5tools_str_t));
@@ -3057,7 +3057,7 @@ xml_print_strs(hid_t did, int source)
 
     for (i = 0; i < (hsize_t)ssiz; i++) {
         if (is_vlstr) {
-            onestring = *(char **) bp;
+            onestring = *(char **)((void *)bp);
             if (onestring)
                 str_size = HDstrlen(onestring);
         }
diff --git a/tools/src/h5format_convert/h5format_convert.c b/tools/src/h5format_convert/h5format_convert.c
index b9ed9ce..257a047 100644
--- a/tools/src/h5format_convert/h5format_convert.c
+++ b/tools/src/h5format_convert/h5format_convert.c
@@ -259,7 +259,7 @@ convert(hid_t fid, const char *dname)
             error_msg("unable to get the chunk indexing type for \"%s\"\n", dname);
             h5tools_setstatus(EXIT_FAILURE);
             goto error;
-	    }
+        }
         else if(verbose_g)
             HDfprintf(stdout, "Retrieve the dataset's chunk indexing type\n");
 
@@ -268,11 +268,11 @@ convert(hid_t fid, const char *dname)
                 HDfprintf(stdout, "Dataset's chunk indexing type is already version 1 B-tree: no further action\n");
             h5tools_setstatus(EXIT_SUCCESS);
             goto done;
-	    }
+        }
         else if (verbose_g)
             HDfprintf(stdout, "Dataset's chunk indexing type is not version 1 B-tree\n");
 
-	    break;
+        break;
 
     case H5D_CONTIGUOUS:
         if(verbose_g)
@@ -302,8 +302,8 @@ convert(hid_t fid, const char *dname)
     if(noop_g) {
         if(verbose_g)
             HDfprintf(stdout, "Not converting the dataset\n");
-            h5tools_setstatus(EXIT_SUCCESS);
-            goto done;
+        h5tools_setstatus(EXIT_SUCCESS);
+        goto done;
     }
 
     if(verbose_g)
diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c
index c9cc020..d49a16b 100644
--- a/tools/src/h5repack/h5repack.c
+++ b/tools/src/h5repack/h5repack.c
@@ -752,7 +752,7 @@ check_objects(const char* fname, pack_opt_t *options)
     hid_t         did = -1;
     hid_t         sid = -1;
     unsigned int  i;
-    unsigned int  uf;
+    int  ifil;
     trav_table_t *travt = NULL;
     int           ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
 
@@ -787,12 +787,13 @@ check_objects(const char* fname, pack_opt_t *options)
      */
 
     if (options->verbose)
-        printf("Opening file. Searching %lu objects to modify ...\n",
+        printf("Opening file. Searching %zu objects to modify ...\n",
                 travt->nobjs);
 
     for (i = 0; i < options->op_tbl->nelems; i++) {
         pack_info_t obj = options->op_tbl->objs[i];
         char* name = obj.path;
+
         if (options->verbose)
             printf(" <%s>", name);
 
@@ -804,17 +805,17 @@ check_objects(const char* fname, pack_opt_t *options)
         if (options->verbose)
             printf("...Found\n");
 
-        for (uf = 0; uf < obj.nfilters; uf++) {
-            if (obj.filter[uf].filtn < 0)
+        for (ifil = 0; ifil < obj.nfilters; ifil++) {
+            if (obj.filter[ifil].filtn < 0)
                 HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid filter");
             /* check for extra filter conditions */
-            switch (obj.filter[uf].filtn) {
+            switch (obj.filter[ifil].filtn) {
             /* chunk size must be smaller than pixels per block */
             case H5Z_FILTER_SZIP:
                 {
                     int j;
                     hsize_t csize = 1;
-                    unsigned ppb = obj.filter[uf].cd_values[0];
+                    unsigned ppb = obj.filter[ifil].cd_values[0];
                     hsize_t dims[H5S_MAX_RANK];
                     int rank;
 
@@ -856,7 +857,7 @@ check_objects(const char* fname, pack_opt_t *options)
             default:
                 break;
             } /* end switch */
-        } /* for uf (each user-defined filter) */
+        } /* for ifil (each user-defined filter) */
     } /* for i (each object in options traversal table) */
 
 done:
diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
index 0d6a6c5..5939df4 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -33,20 +33,6 @@
 /* size of buffer/# of bytes to xfer at a time when copying userblock */
 #define USERBLOCK_XFER_SIZE     512
 
-/* check H5Dread()/H5Dwrite() error, e.g. memory allocation error inside the library. */
-#define CHECK_H5DRW_ERROR(_fun, _fail, _did, _mtid, _msid, _fsid, _pid, _buf)  {  \
-    H5E_BEGIN_TRY {  \
-        if(_fun(_did, _mtid, _msid, _fsid, _pid, _buf) < 0) {  \
-            hid_t _err_num = 0; \
-            char _msg[80]; \
-            H5Ewalk2(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &_err_num); \
-            H5Eget_msg(_err_num, NULL, _msg, (size_t)80); \
-            error_msg("%s %s -- %s\n", #_fun, "failed", _msg); \
-            HGOTO_DONE(_fail) \
-        } \
-    } H5E_END_TRY; \
-}
-
 /*-------------------------------------------------------------------------
  * local functions
  *-------------------------------------------------------------------------
@@ -61,15 +47,7 @@ static int copy_user_block(const char *infile, const char *outfile,
 #if defined (H5REPACK_DEBUG_USER_BLOCK)
 static void print_user_block(const char *filename, hid_t fid);
 #endif
-static herr_t walk_error_callback(unsigned n, const H5E_error2_t *err_desc, void *udata);
-
-/* get the major number from the error stack. */
-static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata) {
-    if (err_desc)
-        *((hid_t *) udata) = err_desc->maj_num;
 
-    return 0;
-}
 
 /*-------------------------------------------------------------------------
  * Function: copy_objects
@@ -635,7 +613,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
     unsigned crt_order_flags; /* group creation order flag */
     unsigned i;
     unsigned u;
-    unsigned uf;
+    int ifil;
     int is_ref = 0;
     htri_t is_named;
     hbool_t limit_maxdims;
@@ -745,8 +723,8 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                 if (options->op_tbl->objs) {
                     for (u = 0; u < options->op_tbl->nelems; u++) {
                         if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0)
-                            for (uf = 0; uf < options->op_tbl->objs[uf].nfilters; uf++) {
-                                if (options->op_tbl->objs[u].filter[uf].filtn > 0)
+                            for (ifil = 0; ifil < options->op_tbl->objs[ifil].nfilters; ifil++) {
+                                if (options->op_tbl->objs[u].filter[ifil].filtn > 0)
                                     req_filter = 1;
                             }
                     }
@@ -1424,7 +1402,7 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr)
     if (!pr)
         printf(FORMAT_OBJ, "dset", objname);
     else {
-        char str[255], temp[28];
+        char str[512], temp[512];
 
         HDstrcpy(str, "dset     ");
         HDstrcat(str, strfilter);
diff --git a/tools/src/h5repack/h5repack_filters.c b/tools/src/h5repack/h5repack_filters.c
index 3d9472a..7e32def 100644
--- a/tools/src/h5repack/h5repack_filters.c
+++ b/tools/src/h5repack/h5repack_filters.c
@@ -42,7 +42,8 @@ static int aux_copy_obj(hid_t dcpl_id, /* dataset creation property list */
     H5D_layout_t layout;
     int          rank;           /* rank of dataset */
     hsize_t      chsize[64];     /* chunk size in elements */
-    unsigned int i;
+    int i;
+    unsigned u;
 
     /* get information about input filters */
     if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
@@ -65,8 +66,8 @@ static int aux_copy_obj(hid_t dcpl_id, /* dataset creation property list */
         if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize/*out*/)) < 0)
             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_chunk failed");
         objout->chunk.rank = rank;
-        for (i = 0; i < rank; i++)
-            objout->chunk.chunk_lengths[i] = chsize[i];
+        for (u = 0; u < (unsigned)rank; u++)
+            objout->chunk.chunk_lengths[u] = chsize[u];
     }
 
 done:
@@ -85,8 +86,7 @@ static int aux_find_obj(const char* name, /* object name from traverse list */
         pack_info_t *obj                  /*OUT*/) /* info about object to filter */
 {
     char         *pdest = NULL;
-    char         *pname = NULL;
-    int          result;
+    const char   *pname = NULL;
     unsigned int i;
 
     for (i = 0; i < options->op_tbl->nelems; i++) {
diff --git a/tools/src/h5repack/h5repack_refs.c b/tools/src/h5repack/h5repack_refs.c
index a275443..f5846ba 100644
--- a/tools/src/h5repack/h5repack_refs.c
+++ b/tools/src/h5repack/h5repack_refs.c
@@ -22,7 +22,7 @@
  */
 
 static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt);
-static int copy_refs_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options,
+static int copy_refs_attr(hid_t loc_in, hid_t loc_out, 
                           trav_table_t *travt, hid_t fidout);
 static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
         hid_t fid_out, void *ref_out, trav_table_t *travt);
@@ -81,7 +81,7 @@ int do_copy_refobjs(hid_t fidin,
                 if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
 
-                if(copy_refs_attr(grp_in, grp_out, options, travt, fidout) < 0)
+                if(copy_refs_attr(grp_in, grp_out, travt, fidout) < 0)
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed");
 
                 if(H5Gclose(grp_out) < 0)
@@ -316,7 +316,7 @@ int do_copy_refobjs(hid_t fidin,
                      * copy referenced objects in attributes
                      *-------------------------------------------------------------------------
                      */
-                    if(copy_refs_attr(dset_in, dset_out, options, travt, fidout) < 0)
+                    if(copy_refs_attr(dset_in, dset_out, travt, fidout) < 0)
                         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed");
 
                     /*-------------------------------------------------------------------------
@@ -426,7 +426,6 @@ done:
 
 static int copy_refs_attr(hid_t loc_in,
                           hid_t loc_out,
-                          pack_opt_t *options,
                           trav_table_t *travt,
                           hid_t fidout)         /* for saving references */
 {
@@ -450,7 +449,6 @@ static int copy_refs_attr(hid_t loc_in,
                 is_ref_comp = 0;
     void       *refbuf = NULL;
     void       *buf = NULL;
-    const char *refname = NULL;
     unsigned   *ref_comp_index = NULL;
     size_t     *ref_comp_size = NULL;
     int         ref_comp_field_n = 0;
@@ -604,12 +602,9 @@ static int copy_refs_attr(hid_t loc_in,
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed");
                 } /* end if */
 
-                for(i = 0; i < (unsigned)nelmts; i++) {
-                    if (update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, &((hobj_ref_t *)refbuf)[i], travt)<0)
+                for(i = 0; i < (unsigned)nelmts; i++)
+                    if(update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, &((hobj_ref_t *)refbuf)[i], travt) < 0)
                         continue;
-                    if(options->verbose)
-                        printf("object <%s> reference created to <%s>\n", name, refname);
-                } /* i */
             } /* H5T_STD_REF_OBJ */
             /* handle region references */
             else if((is_ref || is_ref_array) && (H5R_DSET_REG_REF_BUF_SIZE == msize)) {
@@ -632,12 +627,9 @@ static int copy_refs_attr(hid_t loc_in,
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed");
                 } /* end if */
 
-                for(i = 0; i < (unsigned)nelmts; i++) {
-                    if (update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, &((hdset_reg_ref_t *)refbuf)[i], travt)<0)
+                for(i = 0; i < (unsigned)nelmts; i++)
+                    if(update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, &((hdset_reg_ref_t *)refbuf)[i], travt) < 0)
                         continue;
-                    if(options->verbose)
-                        printf("object <%s> region reference created to <%s>\n", name, refname);
-                }
             } /* H5T_STD_REF_DSETREG */
             else if (is_ref_vlen) {
                 /* handle VLEN of references */
@@ -700,7 +692,7 @@ static int copy_refs_attr(hid_t loc_in,
                             size_t idx = (i * msize) + H5Tget_member_offset(mtype_id, ref_comp_index[j]);
                             hobj_ref_t ref_out;
 
-                            if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
+                            if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)((void *)(((char *)buf)+idx)), fidout, &ref_out, travt) < 0) /* Extra (void *) cast to quiet "cast to create alignment" warning - 2019/07/05, QAK */
                                 continue;
                             HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
                         } /* if */
diff --git a/tools/src/h5stat/h5stat.c b/tools/src/h5stat/h5stat.c
index 8109b93..450f731 100644
--- a/tools/src/h5stat/h5stat.c
+++ b/tools/src/h5stat/h5stat.c
@@ -509,8 +509,7 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "attribute_stats() failed");
 
     /* Get storage info */
-    if((storage = H5Dget_storage_size(did)) < 0)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_storage_size() failed");
+    storage = H5Dget_storage_size(did);
 
     /* Gather layout statistics */
     if((dcpl = H5Dget_create_plist(did)) < 0)