Merge pull request #811 in HDFFV/hdf5 from hdf5_1_8_20 to 1.8/masterhdf5-1_8_20

* commit '60f76980aab92f0e0730170b99a2363acd3c97fa': (108 commits)
  Update version numbers and remove empty sections in RELEASE.txt.
  Restore line 1154: C2Cppfunction_map.mht to HTML_EXTRA_FILES.
  Update version for 1.8.20 release.
  Fixed documentation warnings
  HDFFV-10329 Correct LINK INTERFACE and VS20013 compile
  Switch default build mode from development to production. Increment version string to pre2.
  Add RELEASE.txt note for HDFFV-10274. (cherry picked from commit f7a7d0a00613cba997212fa8032091629a678797)
  Initialize hid_t variables in test_Attr_bug9. (cherry picked from commit 97bc393449f3fe02c5992872ab2842e12f611ef0)
  Fix HDFFV-10274.  When deleting all (or almost all) of the messages in an object header chunk, where the total amount deleted was greater than 64K, an error would occur due to an off by one error in the code that handled that case.  Fixed this and added a test case. (cherry picked from commit 1b2c2ca9a6a7d7e1fcd5c3302e203f2e2dabf0af)
  Fix linking of libs
  Changed file path to relative.
  iAdd NAG to supported compilers in RELEASE.txt.
  Add description to RELEASE.txt for HDFFV-10323
  Correct issue number
  Set version to 1.8.20-pre1
  Update supported and tested platforms in RELEASE.txt.
  HDFFV-10321 Merge from 1.8
  Incremented lib file .so numbers: revision for all except c++ for code change; current incremented, revision and age set to 0 for c++ due to symbols added and removed.
  updated issues related to Fortran
  Incremented lib file .so numbers: revision for all except c++ for dcode change; current incremented, revision and age set to 0 for c++ due to symbols added and removed.
  ...

1 files changed, 183 insertions, 299 deletions

diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index b41f7be..63233b8 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -78,49 +78,37 @@ static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t
  *
  * Return:   0, ok,
  *          -1 no
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: October, 23, 2003
- *
  *-------------------------------------------------------------------------
  */
 
 int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
 {
-    int           ret_value = 0;          /* no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    hid_t         fidin;
+    int           ret_value = 0;
+    hid_t         fidin = -1;
     hid_t         fidout = -1;
-    trav_table_t  *travt = NULL;
-    hsize_t       ub_size = 0;            /* size of user block */
+    hid_t         fcpl_in = -1;  /* file creation property list ID for input file */
+    hid_t         grp_in = -1;   /* group ID */
+    hid_t         gcpl_in = -1;  /* group creation property list */
     hid_t         fcpl = H5P_DEFAULT;     /* file creation property list ID */
     hid_t         fapl = H5P_DEFAULT;     /* file access property list ID */
+    trav_table_t *travt = NULL;
+    hsize_t       ub_size = 0;            /* size of user block */
     unsigned      crt_order_flags;        /* group creation order flag */
 
     /*-------------------------------------------------------------------------
      * open input file
      *-------------------------------------------------------------------------
      */
-    if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t) 0)) < 0) {
-        error_msg("<%s>: %s\n", fnamein, H5FOPENERROR);
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-    }
+    if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t) 0)) < 0)
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fnamein, H5FOPENERROR);
 
     /* get user block size and file space strategy/threshold */
     {
-        hid_t fcpl_in; /* file creation property list ID for input file */
-        hid_t grp_in = -1;   /* group ID */
-        hid_t gcpl_in = -1;  /* group creation property list */
+        if ((fcpl_in = H5Fget_create_plist(fidin)) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list");
 
-        if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
-            error_msg("failed to retrieve file creation property list\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
-
-        if (H5Pget_userblock(fcpl_in, &ub_size) < 0) {
-            error_msg("failed to retrieve userblock size\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
+        if (H5Pget_userblock(fcpl_in, &ub_size) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_userblock failed to retrieve userblock size");
 
         /* open root group */
         if ((grp_in = H5Gopen2(fidin, "/", H5P_DEFAULT)) < 0)
@@ -134,26 +122,19 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
         if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");
 
-        if (H5Pclose(fcpl_in) < 0) {
-            error_msg("failed to close property list\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
+        if (H5Pclose(fcpl_in) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed to close property list");
     }
 
     /* Check if we need to create a non-default file creation property list */
     if (options->latest || ub_size > 0) {
         /* Create file creation property list */
-        if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
-            error_msg("fail to create a file creation property list\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
+        if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create a file creation property list");
 
-        if (ub_size > 0) {
-            if (H5Pset_userblock(fcpl, ub_size) < 0) {
-                error_msg("failed to set non-default userblock size\n");
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            }
-        }
+        if (ub_size > 0)
+            if (H5Pset_userblock(fcpl, ub_size) < 0)
+                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_userblock failed to set non-default userblock size");
 
         if (options->latest) {
             unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];
@@ -161,10 +142,8 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
             /* Adjust group creation parameters for root group */
             /* (So that it is created in "dense storage" form) */
             if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact,
-                        (unsigned) options->grp_indexed) < 0) {
-                error_msg("fail to adjust group creation parameters for root group\n");
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            }
+                        (unsigned) options->grp_indexed) < 0)
+                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed to adjust group creation parameters for root group");
 
             for (i = 0; i < 5; i++) {
                 if (options->msg_size[i] > 0) {
@@ -199,30 +178,21 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
             } /* end for */
 
             if (nindex > 0) {
-                if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) {
-                    error_msg("fail to set the number of shared object header message indexes\n");
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-                }
+                if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0)
+                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_shared_mesg_nindexes failed to set the number of shared object header message indexes");
 
                 /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */
-                for (i = 0; i < (nindex - 1); i++) {
-                    if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) {
-                        error_msg("fail to configure the specified shared object header message index\n");
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-                    } /* end if */
-                } /* end for */
+                for (i = 0; i < (nindex - 1); i++)
+                    if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0)
+                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_shared_mesg_index failed to configure the specified shared object header message index");
             } /* if (nindex>0) */
 
             /* Create file access property list */
-            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
-                error_msg("Could not create file access property list\n");
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            } /* end if */
-
-            if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
-                error_msg("Could not set property for using latest version of the format\n");
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            } /* end if */
+            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
+                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list");
+
+            if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
+                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_libver_bounds failed to set property for using latest version of the format");
         } /* end if */
     } /* end if */
 #if defined (H5REPACK_DEBUG_USER_BLOCK)
@@ -235,19 +205,14 @@ print_user_block(fnamein, fidin);
      */
     if (options->ublock_size > 0) {
         /* either use the FCPL already created or create a new one */
-        if (fcpl == H5P_DEFAULT) {
+        if (fcpl == H5P_DEFAULT)
             /* create a file creation property list */
-            if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
-                error_msg("fail to create a file creation property list\n");
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            }
-        }
+            if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
+                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create a file creation property list");
 
         /* set user block size */
-        if (H5Pset_userblock(fcpl, options->ublock_size) < 0) {
-            error_msg("failed to set userblock size\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
+        if (H5Pset_userblock(fcpl, options->ublock_size) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_userblock failed to set userblock size");
     }
 
     /*-------------------------------------------------------------------------
@@ -256,18 +221,13 @@ print_user_block(fnamein, fidin);
      */
     if (options->alignment > 0) {
         /* either use the FAPL already created or create a new one */
-        if (fapl == H5P_DEFAULT) {
+        if (fapl == H5P_DEFAULT)
             /* create a file access property list */
-            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
-                error_msg("Could not create file access property list\n");
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            }
-        }
+            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
+                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list");
 
-        if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) {
-            error_msg("failed to set alignment\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
+        if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_alignment failed to set alignment");
     }
 
     /*-------------------------------------------------------------------------
@@ -276,18 +236,13 @@ print_user_block(fnamein, fidin);
      */
     if (options->meta_block_size > 0) {
         /* either use the FAPL already created or create a new one */
-        if (fapl == H5P_DEFAULT) {
+        if (fapl == H5P_DEFAULT)
             /* create a file access property list */
-            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
-                error_msg("Could not create file access property list\n");
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            }
-        }
+            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
+                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list");
 
-        if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) {
-            error_msg("failed to set metadata block size\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
+        if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_meta_block_size failed to set metadata block size");
     }
 
     /*-------------------------------------------------------------------------
@@ -296,13 +251,10 @@ print_user_block(fnamein, fidin);
      */
 
     /* either use the FCPL already created or create a new one */
-    if (fcpl == H5P_DEFAULT) {
+    if (fcpl == H5P_DEFAULT)
         /* create a file creation property list */
-        if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
-            error_msg("fail to create a file creation property list\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
-    }
+        if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create a file creation property list");
 
     if(H5Pset_link_creation_order(fcpl, crt_order_flags ) < 0)
         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed");
@@ -312,23 +264,18 @@ print_user_block(fnamein, fidin);
      *-------------------------------------------------------------------------
      */
     if (options->verbose)
-        printf("Making file <%s>...\n", fnameout);
+        printf("Making new file ...\n");
 
-    if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) {
-        error_msg("<%s>: Could not create file\n", fnameout);
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-    }
+    if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0)
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fcreate could not create file <%s>:", fnameout);
 
     /*-------------------------------------------------------------------------
      * write a new user block if requested
      *-------------------------------------------------------------------------
      */
-    if (options->ublock_size > 0) {
-        if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0) {
-            error_msg("Could not copy user block. Exiting...\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
-    }
+    if (options->ublock_size > 0)
+        if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not copy user block. Exiting...");
 
     /*-------------------------------------------------------------------------
      * get list of objects
@@ -340,70 +287,45 @@ print_user_block(fnamein, fidin);
     /* init table */
     trav_table_init(&travt);
 
-    /* get the list of objects in the file */
-    if (h5trav_gettable(fidin, travt) < 0)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-
-    /*-------------------------------------------------------------------------
-     * do the copy
-     *-------------------------------------------------------------------------
-     */
-    if (do_copy_objects(fidin, fidout, travt, options) < 0) {
-        error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-    } /* end if */
-
-    /*-------------------------------------------------------------------------
-     * do the copy of referenced objects
-     * and create hard links
-     *-------------------------------------------------------------------------
-     */
-    if (do_copy_refobjs(fidin, fidout, travt, options) < 0) {
-        printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout);
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+    if (travt) {
+        /* get the list of objects in the file */
+        if (h5trav_gettable(fidin, travt) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed");
+
+        /*-------------------------------------------------------------------------
+        * do the copy
+        *-------------------------------------------------------------------------
+        */
+        if (do_copy_objects(fidin, fidout, travt, options) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "do_copy_objects from <%s> could not copy data to <%s>", fnamein, fnameout);
+
+        /*-------------------------------------------------------------------------
+        * do the copy of referenced objects
+        * and create hard links
+        *-------------------------------------------------------------------------
+        */
+        if (do_copy_refobjs(fidin, fidout, travt, options) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "do_copy_refobjs from <%s> could not copy data to <%s>", fnamein, fnameout);
     }
 
     /*-------------------------------------------------------------------------
-     * close
-     *-------------------------------------------------------------------------
-     */
-
-    if (fapl > 0)
-        H5Pclose(fapl);
-
-    if (fcpl > 0)
-        H5Pclose(fcpl);
-
-    H5Fclose(fidin);
-    H5Fclose(fidout);
-
-    /* free table */
-    trav_table_free(travt);
-    travt = NULL;
-
-    /*-------------------------------------------------------------------------
      * write only the input file user block if there is no user block file input
      *-------------------------------------------------------------------------
      */
 
-    if (ub_size > 0 && options->ublock_size == 0) {
-        if (copy_user_block(fnamein, fnameout, ub_size) < 0) {
-            error_msg("Could not copy user block. Exiting...\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
-    }
-
-    return 0;
-
-    /*-------------------------------------------------------------------------
-     * out
-     *-------------------------------------------------------------------------
-     */
+    if (ub_size > 0 && options->ublock_size == 0)
+        if (copy_user_block(fnamein, fnameout, ub_size) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not copy user block. Exiting...");
 
 done:
     H5E_BEGIN_TRY {
+        H5Pclose(fcpl_in);
+        H5Pclose(gcpl_in);
         H5Pclose(fapl);
         H5Pclose(fcpl);
+        H5Gclose(grp_in);
+        H5Fclose(fidin);
+        H5Fclose(fidout);
         H5Fclose(fidin);
         H5Fclose(fidout);
     } H5E_END_TRY;
@@ -420,7 +342,7 @@ done:
  *          The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
  *          Return the hyperslab dimentions and size in byte.
  *
- * Return: 0 - SUCCEED, -1 FAILED
+ * Return:  0 - SUCCEED, -1 FAILED
  *
  * Parameters:
  *   dcpl_id : [IN] dataset creation property.
@@ -430,8 +352,6 @@ done:
  *   dims_hslab[] : [OUT] calculated hyperslab dimentions
  *   * hslab_nbytes_p : [OUT] total byte of the hyperslab
  *
- * Programmer: Jonathan Kim
- * Date: Feburary, 2012
  * Update:
  *   The hyperslab calucation would be depend on if the dataset is chunked
  *   or not.
@@ -445,25 +365,23 @@ done:
  *      the boundary would be dataset's dims.
  *
  *   The calulation starts from the last dimention (h5dump dims output).
- *
- * Note:
- *   Added for JIRA HDFFV-7862.
  *-----------------------------------------*/
 
-int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
+int
+Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
         size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p)
 {
-    int     ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+    int     ret_value = 0;
     int     k;
     H5D_layout_t dset_layout;
     int     rank_chunk;
     hsize_t dims_chunk[H5S_MAX_RANK];
     hsize_t size_chunk = 1;
-    hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
-    hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
+    hsize_t nchunk_fit;                   /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
+    hsize_t ndatum_fit;                   /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
     hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */
-    hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */
-    hsize_t hslab_nbytes; /* size of hyperslab in byte */
+    hsize_t hs_dims_map[H5S_MAX_RANK];    /* mapped hyperslab dimentions */
+    hsize_t hslab_nbytes;                 /* size of hyperslab in byte */
 
     /* init to set as size of a data element */
     hslab_nbytes = size_datum;
@@ -476,7 +394,7 @@ int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
         /* get chunk dims */
         rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk);
         if (rank_chunk < 0)
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_chunk failed");
 
         for (k = rank_dset; k > 0; --k)
             size_chunk *= dims_chunk[k - 1];
@@ -538,7 +456,7 @@ int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
                 hslab_nbytes *= dims_hslab[k - 1];
 
                 if (hslab_nbytes <= 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "calculate total size for the hyperslab failed");
             }
         }
     }
@@ -562,7 +480,7 @@ int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
             hslab_nbytes *= dims_hslab[k - 1];
 
             if (hslab_nbytes <= 0)
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "calculate total size for the hyperslab failed");
         }
     }
 
@@ -576,24 +494,9 @@ done:
 /*-------------------------------------------------------------------------
  * Function: do_copy_objects
  *
- * Purpose: duplicate all HDF5 objects in the file
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: October, 23, 2003
- *
- * Modifications:
- *
- *  July 2004:     Introduced the extra EC or NN option for SZIP
- *
- *  December 2004: Added a check for H5Dcreate; if the dataset cannot be created
- *                  with the requested filter, use the input one
- *
- *  October 2006:  Read/write using the file type by default.
+ * Purpose:  duplicate all HDF5 objects in the file
  *
- *  October 2006:  Read by hyperslabs for big datasets.
+ * Return:   0, ok, -1 no
  *
  *  A threshold of H5TOOLS_MALLOCSIZE (128 MB) is the limit upon which I/O hyperslab is done
  *  i.e., if the memory needed to read a dataset is greater than this limit,
@@ -634,31 +537,6 @@ done:
  *  in (2) is that, when using the strip mine size, it assures that the "remaining" part
  *  of the dataset that does not fill an entire strip mine is processed.
  *
- *  November 2006:  Use H5Ocopy in the copy of objects. The logic for using
- *   H5Ocopy or not is if a change of filters or layout is requested by the user
- *   then use read/write else use H5Ocopy.
- *
- * May, 1, 2008: Add a printing of the compression ratio of old size / new size
- *
- * Feburary 2012:  improve Read/Write by hyperslabs for big datasets.
- * Programmer: Jonathan Kim
- *
- *  A threshold of H5TOOLS_MALLOCSIZE is the limit upon which I/O hyperslab is done
- *  i.e., if the memory needed to read a dataset is greater than this limit,
- *  then hyperslab I/O is done instead of one operation I/O
- *  For each dataset, the memory needed is calculated according to
- *
- *  memory needed = number of elements * size of each element
- *
- *  if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
- *  are done
- *
- *  H5Dread( input_dataset )
- *  H5Dwrite( output_dataset )
- *
- *  with all elements in the datasets selected. If the memory needed is greater than
- *  H5TOOLS_MALLOCSIZE, then the following operations are done instead:
- *
  *  1. figure out a hyperslab (dimentions) and size  (refer to Get_hyperslab()).
  *  2. Calculate the hyperslab selections as the selection is moving forward.
  *     Selection would be same as the hyperslab except for the remaining edge portion
@@ -670,7 +548,7 @@ done:
 int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
         pack_opt_t *options) /* repack options */
 {
-    int   ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+    int   ret_value = 0;
     hid_t grp_in = -1;   /* group ID */
     hid_t grp_out = -1;  /* group ID */
     hid_t dset_in = -1;  /* read dataset ID */
@@ -702,13 +580,14 @@ int 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 is_ref = 0;
     htri_t is_named;
     hbool_t limit_maxdims;
     hsize_t size_dset;
 
     /*-------------------------------------------------------------------------
-     * copy the suppplied object list
+     * copy the supplied object list
      *-------------------------------------------------------------------------
      */
 
@@ -718,14 +597,14 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
         printf("-----------------------------------------\n");
     }
 
-    for (i = 0; i < travt->nobjs; i++) {
-        /* init variables per obj */
-        buf = NULL;
-        limit_maxdims = FALSE;
+    if (travt->objs) {
+        for (i = 0; i < travt->nobjs; i++) {
+            /* init variables per obj */
+            buf = NULL;
+            limit_maxdims = FALSE;
 
-        switch (travt->objs[i].type) {
+            switch (travt->objs[i].type) {
             case H5TRAV_TYPE_UNKNOWN:
-                HDassert(0);
                 break;
 
                 /*-------------------------------------------------------------------------
@@ -804,10 +683,15 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                     req_filter = 1;
 
                 /* check if filters were requested for individual objects */
-                for (u = 0; u < options->op_tbl->nelems; u++)
-                    if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0)
-                        if (options->op_tbl->objs[u].filter->filtn > 0)
-                            req_filter = 1;
+                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)
+                                    req_filter = 1;
+                            }
+                    }
+                }
 
                 /* check if layout change requested individual object */
                 if (options->layout_g != H5D_LAYOUT_ERROR) {
@@ -983,16 +867,22 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                                     buf = HDmalloc(need);
 
                                 if (buf != NULL) {
-                                    /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
-                                    CHECK_H5DRW_ERROR(H5Dread, FAIL, dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
-                                    CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+                                    if(H5Dread(dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
+                                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
+                                    if(H5Dwrite(dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
+                                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed");
 
                                     /* Check if we have VL data in the dataset's
                                      * datatype that must be reclaimed */
                                     if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
                                         if (H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0)
                                             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dvlen_reclaim failed");
-                                }
+                                    /* free */
+                                    if (buf != NULL) {
+                                        HDfree(buf);
+                                        buf = NULL;
+                                    }
+                                 }
                                 else { /* possibly not enough memory, read/write by hyperslabs */
                                     size_t p_type_nbytes = msize; /*size of memory type */
                                     hsize_t p_nelmts = nelmts; /*total elements */
@@ -1068,9 +958,10 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                                             hs_select_nelmts = 1;
                                         } /* rank */
 
-                                        /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
-                                        CHECK_H5DRW_ERROR(H5Dread, FAIL, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
-                                        CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
+                                        if(H5Dread(dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0)
+                                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
+                                        if(H5Dwrite(dset_out, wtype_id,  hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0)
+                                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed");
 
                                         /* reclaim any VL memory, if necessary */
                                         if (vl_data)
@@ -1161,7 +1052,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                  *-------------------------------------------------------------------------
                  */
                 else {
-                    hid_t pid;
+                    hid_t pid = -1;
 
                     /* create property to pass copy options */
                     if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
@@ -1239,6 +1130,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
                 if (H5Tclose(type_out) < 0)
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+                type_out = -1; /* named datatypes stack, named_dt_head, manages allocation */
 
                 break;
 
@@ -1264,21 +1156,23 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
 
             default:
                 HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Object type not found");
-        } /* switch */
-
-        /* free */
-        if (buf != NULL) {
-            HDfree(buf);
-            buf = NULL;
-        }
-    } /* i */
+            } /* switch */
+        } /* end for */
+    } /* end if */
 
-    /* Finalize (link) the stack of named datatypes (if any) */
-    named_datatype_free(&named_dt_head, 0);
+done:
 
-    return ret_value;
+    /* Finalize (link) the stack of named datatypes (if any) first
+     * because of reference counting */
+    if (0 == ret_value && named_dt_head != NULL) {
+        if (named_datatype_free(&named_dt_head, 0) < 0)
+            H5TOOLS_INFO(H5E_tools_min_id_g, "named_datatype_free failed");
+    }
+    else
+        H5E_BEGIN_TRY {
+            named_datatype_free(&named_dt_head, 1);
+        } H5E_END_TRY;
 
-done:
     H5E_BEGIN_TRY
     {
         H5Gclose(grp_in);
@@ -1293,8 +1187,7 @@ done:
         H5Tclose(wtype_id);
         H5Tclose(type_in);
         H5Tclose(type_out);
-        named_datatype_free(&named_dt_head, 1);
-    }H5E_END_TRY;
+    } H5E_END_TRY;
 
     /* free */
     if (buf != NULL)
@@ -1309,10 +1202,10 @@ done:
  * Function: print_dataset_info
  *
  * Purpose: print name, filters, percentage compression of a dataset
- *
  *-------------------------------------------------------------------------
  */
-static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr)
+static void
+print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr)
 {
     char     strfilter[255];
 #if defined (PRINT_DEBUG )
@@ -1324,7 +1217,7 @@ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int p
     unsigned cd_values[20];  /* filter client data values */
     size_t   cd_nelmts;      /* filter client number of values */
     char     f_objname[256]; /* filter objname */
-    int     i;
+    int      i;
 
     HDstrcpy(strfilter, "\0");
 
@@ -1335,8 +1228,11 @@ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int p
     for (i = 0; i < nfilters; i++) {
         cd_nelmts = NELMTS(cd_values);
 
-        filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts,
-                        cd_values, sizeof(f_objname), f_objname, NULL);
+        if ((filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts,
+                        cd_values, sizeof(f_objname), f_objname, NULL)) < 0) {
+            HDstrcat(strfilter, "ERROR ");
+            continue;
+        }
 
         switch (filtn) {
             case H5Z_FILTER_NONE:
@@ -1413,29 +1309,24 @@ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int p
 /*-------------------------------------------------------------------------
  * Function: copy_user_block
  *
- * Purpose: copy user block from one file to another
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Peter Cao
- *
- * Date: October, 25, 2007
+ * Purpose:  copy user block from one file to another
  *
+ * Return:   0, ok, -1 no
  *-------------------------------------------------------------------------
  */
-static int copy_user_block(const char *infile, const char *outfile, hsize_t size)
+static int
+copy_user_block(const char *infile, const char *outfile, hsize_t size)
 {
-    int ret_value = 0;           /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+    int ret_value = 0;
     int infid = -1, outfid = -1; /* File descriptors */
 
     /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
-    HDassert(size > 0);
 
     /* Open files */
     if ((infid = HDopen(infile, O_RDONLY, 0)) < 0)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed");
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed input file <%s>", infile);
     if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed");
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed output file <%s>", outfile);
 
     /* Copy the userblock from the input file to the output file */
     while (size > 0) {
@@ -1449,7 +1340,7 @@ static int copy_user_block(const char *infile, const char *outfile, hsize_t size
         else
             nread = HDread(infid, rbuf, (size_t)size);
         if (nread < 0)
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDread failed");
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDread failed to read userblock");
 
         /* Write buffer to destination file */
         /* (compensating for interrupted writes & checking for errors, etc.) */
@@ -1488,69 +1379,62 @@ done:
 /*-------------------------------------------------------------------------
  * Function: print_user_block
  *
- * Purpose: print user block
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Pedro Vicente
- *
- * Date: August, 20, 2008
+ * Purpose:  print user block
  *
+ * Return:   0, ok, -1 no
  *-------------------------------------------------------------------------
  */
 #if defined (H5REPACK_DEBUG_USER_BLOCK)
 static
-void print_user_block(const char *filename, hid_t fid)
+void
+print_user_block(const char *filename, hid_t fid)
 {
-    int     ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    int     fh;   /* file handle  */
-    hsize_t ub_size; /* user block size */
-    hsize_t size; /* size read */
-    hid_t   fcpl; /* file creation property list ID for HDF5 file */
+    int     ret_value = 0;
+    int     fh = -1;   /* file handle */
+    hsize_t ub_size;   /* user block size */
+    hsize_t size;      /* size read */
+    hid_t   fcpl = -1; /* file creation property list ID for HDF5 file */
     int     i;
 
     /* get user block size */
-    if(( fcpl = H5Fget_create_plist(fid)) < 0) {
-        error_msg("failed to retrieve file creation property list\n");
-        HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fget_create_plist failed");
+    if ((fcpl = H5Fget_create_plist(fid)) < 0) {
+        HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list");
     }
 
-    if(H5Pget_userblock(fcpl, &ub_size) < 0) {
-        error_msg("failed to retrieve userblock size\n");
-        HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_userblock failed");
+    if (H5Pget_userblock(fcpl, &ub_size) < 0) {
+        HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_userblock failed to retrieve userblock size");
     }
 
-    if(H5Pclose(fcpl) < 0) {
-        error_msg("failed to close property list\n");
-        HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+    if (H5Pclose(fcpl) < 0) {
+        HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed to close property list");
     }
 
     /* open file */
-    if((fh = HDopen(filename, O_RDONLY, 0)) < 0) {
-        HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed");
+    if ((fh = HDopen(filename, O_RDONLY)) < 0) {
+        HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed to open file <%s>", filename);
     }
 
     size = ub_size;
 
     /* read file */
-    while(size > 0) {
+    while (size > 0) {
         ssize_t nread; /* # of bytes read */
         char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */
 
         /* read buffer */
-        if(size > USERBLOCK_XFER_SIZE)
+        if (size > USERBLOCK_XFER_SIZE)
             nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
         else
             nread = HDread(fh, rbuf, (size_t)size);
 
-        for(i = 0; i < nread; i++) {
+        for (i = 0; i < nread; i++) {
 
             printf("%c ", rbuf[i]);
 
         }
         printf("\n");
 
-        if(nread < 0) {
+        if (nread < 0) {
             HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "nread < 0");
         }
 
@@ -1559,7 +1443,7 @@ void print_user_block(const char *filename, hid_t fid)
     }
 
 done:
-    if(fh > 0)
+    if (fh > 0)
         HDclose(fh);
 
     return;