Merge branch 'develop' into windows_open

1 files changed, 438 insertions, 447 deletions

diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c
index d047612..bc8527b 100644
--- a/tools/src/h5repack/h5repack.c
+++ b/tools/src/h5repack/h5repack.c
@@ -51,19 +51,19 @@ static int have_request(pack_opt_t *options);
  *-------------------------------------------------------------------------
  */
 int h5repack(const char* infile, const char* outfile, pack_opt_t *options) {
-	/* check input */
-	if (check_options(options) < 0)
-		return -1;
+    /* check input */
+    if (check_options(options) < 0)
+        return -1;
 
-	/* check for objects in input that are in the file */
-	if (check_objects(infile, options) < 0)
-		return -1;
+    /* check for objects in input that are in the file */
+    if (check_objects(infile, options) < 0)
+        return -1;
 
-	/* copy the objects  */
-	if (copy_objects(infile, outfile, options) < 0)
-		return -1;
+    /* copy the objects  */
+    if (copy_objects(infile, outfile, options) < 0)
+        return -1;
 
-	return 0;
+    return 0;
 }
 
 /*-------------------------------------------------------------------------
@@ -105,7 +105,7 @@ h5repack_init(pack_opt_t *options, int verbose, hbool_t latest)
  */
 
 int h5repack_end(pack_opt_t *options) {
-	return options_table_free(options->op_tbl);
+    return options_table_free(options->op_tbl);
 }
 
 /*-------------------------------------------------------------------------
@@ -121,10 +121,10 @@ int h5repack_end(pack_opt_t *options) {
 int
 h5repack_addfilter(const char* str, pack_opt_t *options)
 {
-    obj_list_t *obj_list = NULL; /* one object list for the -f and -l option entry */
-    filter_info_t filter;       /* filter info for the current -f option entry */
-    unsigned n_objs;    /* number of objects in the current -f or -l option entry */
-    int is_glb;         /* is the filter global */
+    obj_list_t   *obj_list = NULL; /* one object list for the -f and -l option entry */
+    filter_info_t filter;          /* filter info for the current -f option entry */
+    unsigned      n_objs;          /* number of objects in the current -f or -l option entry */
+    int           is_glb;          /* is the filter global */
 
     /* parse the -f option */
     if (NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb)))
@@ -163,10 +163,10 @@ int
 h5repack_addlayout(const char* str, pack_opt_t *options)
 {
     obj_list_t *obj_list = NULL; /*one object list for the -t and -c option entry */
-    unsigned n_objs; /*number of objects in the current -t or -c option entry */
-    pack_info_t pack; /*info about layout to extract from parse */
-    int j;
-    int ret_value = -1;
+    unsigned    n_objs;          /*number of objects in the current -t or -c option entry */
+    pack_info_t pack;            /*info about layout to extract from parse */
+    int         j;
+    int         ret_value = -1;
 
     init_packobject(&pack);
 
@@ -232,87 +232,84 @@ h5repack_addlayout(const char* str, pack_opt_t *options)
  *-------------------------------------------------------------------------
  */
 hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
-		named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) {
-	named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
-	named_dt_t *dt_ret = NULL; /* Datatype to return */
-	H5O_info_t oinfo; /* Object info of input dtype */
-	hid_t ret_value = -1; /* The identifier of the named dtype in the out file */
-
-	if (H5Oget_info(type_in, &oinfo) < 0)
-		goto done;
-
-	if (*named_dt_head_p) {
-		/* Stack already exists, search for the datatype */
-		while (dt && dt->addr_in != oinfo.addr)
-			dt = dt->next;
-
-		dt_ret = dt;
-	}
-	else {
-		/* Create the stack */
-		size_t i;
-
-		for (i = 0; i < travt->nobjs; i++) {
-			if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) {
-				/* Push onto the stack */
-				if (NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) {
-					goto done;
-				}
-				dt->next = *named_dt_head_p;
-				*named_dt_head_p = dt;
-
-				/* Update the address and id */
-				dt->addr_in = travt->objs[i].objno;
-				dt->id_out = -1;
-
-				/* Check if this type is the one requested */
-				if (oinfo.addr == dt->addr_in) {
-					HDassert(!dt_ret);
-					dt_ret = dt;
-				} /* end if */
-			} /* end if */
-		} /* end for */
-	} /* end else */
-
-	/* Handle the case that the requested datatype was not found.  This is
-	 * possible if the datatype was committed anonymously in the input file. */
-	if (!dt_ret) {
-		/* Push the new datatype onto the stack */
-		if (NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) {
-			goto done;
-		}
-		dt_ret->next = *named_dt_head_p;
-		*named_dt_head_p = dt_ret;
-
-		/* Update the address and id */
-		dt_ret->addr_in = oinfo.addr;
-		dt_ret->id_out = -1;
-	} /* end if */
-
-	/* If the requested datatype does not yet exist in the output file, copy it
-	 * anonymously */
-	if (dt_ret->id_out < 0) {
-		if (options->use_native == 1)
-			dt_ret->id_out = h5tools_get_native_type(type_in);
-		else
-			dt_ret->id_out = H5Tcopy(type_in);
-		if (dt_ret->id_out < 0)
-			goto done;
-		if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
-			goto done;
-	} /* end if */
-
-	/* Set return value */
-	ret_value = dt_ret->id_out;
-
-	/* Increment the ref count on id_out, because the calling function will try
-	 * to close it */
-	if(H5Iinc_ref(ret_value) < 0) {
-		ret_value = -1;
-	}
+        named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) {
+    named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
+    named_dt_t *dt_ret = NULL;         /* Datatype to return */
+    H5O_info_t  oinfo;                 /* Object info of input dtype */
+    hid_t       ret_value = -1;        /* The identifier of the named dtype in the out file */
+
+    if (H5Oget_info(type_in, &oinfo) < 0)
+        goto done;
+
+    if (*named_dt_head_p) {
+        /* Stack already exists, search for the datatype */
+        while (dt && dt->addr_in != oinfo.addr)
+            dt = dt->next;
+
+        dt_ret = dt;
+    }
+    else {
+        /* Create the stack */
+        size_t i;
+
+        for (i = 0; i < travt->nobjs; i++) {
+            if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) {
+                /* Push onto the stack */
+                if (NULL == (dt = (named_dt_t *)HDmalloc(sizeof(named_dt_t))))
+                    goto done;
+                dt->next = *named_dt_head_p;
+                *named_dt_head_p = dt;
+
+                /* Update the address and id */
+                dt->addr_in = travt->objs[i].objno;
+                dt->id_out = -1;
+
+                /* Check if this type is the one requested */
+                if (oinfo.addr == dt->addr_in) {
+                    HDassert(!dt_ret);
+                    dt_ret = dt;
+                } /* end if */
+            } /* end if */
+        } /* end for */
+    } /* end else */
+
+    /* Handle the case that the requested datatype was not found.  This is
+    * possible if the datatype was committed anonymously in the input file. */
+    if (!dt_ret) {
+        /* Push the new datatype onto the stack */
+        if (NULL == (dt_ret = (named_dt_t *)HDmalloc(sizeof(named_dt_t))))
+            goto done;
+        dt_ret->next = *named_dt_head_p;
+        *named_dt_head_p = dt_ret;
+
+        /* Update the address and id */
+        dt_ret->addr_in = oinfo.addr;
+        dt_ret->id_out = -1;
+    } /* end if */
+
+    /* If the requested datatype does not yet exist in the output file, copy it
+    * anonymously */
+    if (dt_ret->id_out < 0) {
+        if (options->use_native == 1)
+            dt_ret->id_out = H5Tget_native_type(type_in, H5T_DIR_DEFAULT);
+        else
+            dt_ret->id_out = H5Tcopy(type_in);
+        if (dt_ret->id_out < 0)
+            goto done;
+        if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
+            goto done;
+    } /* end if */
+
+    /* Set return value */
+    ret_value = dt_ret->id_out;
+
+    /* Increment the ref count on id_out, because the calling function will try
+    * to close it */
+    if(H5Iinc_ref(ret_value) < 0)
+        ret_value = -1;
 
 done:
-	return (ret_value);
+    return (ret_value);
 } /* end copy_named_datatype */
 
 /*-------------------------------------------------------------------------
@@ -327,22 +324,22 @@ done:
  *-------------------------------------------------------------------------
  */
 int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) {
-	named_dt_t *dt = *named_dt_head_p;
-	int ret_value = -1;
+    named_dt_t *dt = *named_dt_head_p;
+    int         ret_value = -1;
 
-	while (dt) {
-		/* Pop the datatype off the stack and free it */
-		if (H5Tclose(dt->id_out) < 0 && !ignore_err)
-			goto done;
-		dt = dt->next;
-		HDfree(*named_dt_head_p);
-		*named_dt_head_p = dt;
-	} /* end while */
+    while (dt) {
+        /* Pop the datatype off the stack and free it */
+        if (H5Tclose(dt->id_out) < 0 && !ignore_err)
+            goto done;
+        dt = dt->next;
+        HDfree(*named_dt_head_p);
+        *named_dt_head_p = dt;
+    } /* end while */
 
-	ret_value = 0;
+    ret_value = 0;
 
 done:
-	return (ret_value);
+    return (ret_value);
 } /* end named_datatype_free */
 
 /*-------------------------------------------------------------------------
@@ -363,25 +360,25 @@ done:
  */
 int
 copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
-		trav_table_t *travt, pack_opt_t *options)
+        trav_table_t *travt, pack_opt_t *options)
 {
-    int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    hid_t attr_id = -1; /* attr ID */
-    hid_t attr_out = -1; /* attr ID */
-    hid_t space_id = -1; /* space ID */
-    hid_t ftype_id = -1; /* file type ID */
-    hid_t wtype_id = -1; /* read/write type ID */
-    size_t msize; /* size of type */
-    void *buf = NULL; /* data buffer */
-    hsize_t nelmts; /* number of elements in dataset */
-    int rank; /* rank of dataset */
-    htri_t is_named; /* Whether the datatype is named */
-    hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
-    char name[255];
-    H5O_info_t oinfo; /* object info */
-    int j;
-    unsigned u;
-    hbool_t is_ref = 0;
+    int         ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+    hid_t       attr_id = -1;  /* attr ID */
+    hid_t       attr_out = -1; /* attr ID */
+    hid_t       space_id = -1; /* space ID */
+    hid_t       ftype_id = -1; /* file type ID */
+    hid_t       wtype_id = -1; /* read/write type ID */
+    size_t      msize;         /* size of type */
+    void       *buf = NULL;    /* data buffer */
+    hsize_t     nelmts;        /* number of elements in dataset */
+    int         rank;          /* rank of dataset */
+    htri_t      is_named;      /* Whether the datatype is named */
+    hsize_t     dims[H5S_MAX_RANK];/* dimensions of dataset */
+    char        name[255];
+    H5O_info_t  oinfo;         /* object info */
+    int         j;
+    unsigned    u;
+    hbool_t     is_ref = 0;
     H5T_class_t type_class = -1;
 
     if (H5Oget_info(loc_in, &oinfo) < 0)
@@ -425,7 +422,7 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
         } /* end if */
         else {
             if (options->use_native == 1)
-                wtype_id = h5tools_get_native_type(ftype_id);
+                wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT);
             else
                 wtype_id = H5Tcopy(ftype_id);
         } /* end else */
@@ -466,7 +463,7 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
             int nmembers = H5Tget_nmembers(wtype_id);
 
             for (j = 0; j < nmembers; j++) {
-                hid_t mtid = H5Tget_member_type(wtype_id, (unsigned) j);
+                hid_t mtid = H5Tget_member_type(wtype_id, (unsigned)j);
                 H5T_class_t mtclass = H5Tget_class(mtid);
                 H5Tclose(mtid);
 
@@ -477,16 +474,13 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
             } /* for (j=0; i<nmembers; j++) */
         } /* if (type_class == H5T_COMPOUND) */
 
-        if (is_ref) {
-            ; /* handled by copy_refs_attr() */
-        }
-        else {
+        if (!is_ref) {
             /*-------------------------------------------------------------------------
              * read to memory
              *-------------------------------------------------------------------------
              */
 
-            buf = (void *) HDmalloc((size_t)(nelmts * msize));
+            buf = (void *)HDmalloc((size_t)(nelmts * msize));
             if (buf == NULL) {
                 error_msg("h5repack", "cannot read into memory\n");
                 HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
@@ -568,193 +562,188 @@ done:
  * Programmer: pvn@ncsa.uiuc.edu
  *
  * Date: September, 22, 2003
- *
- * Modification:
- *   Peter Cao, July 9, 2007
- *   Add "-L, --latest" and other options to pack a file with the latest file format
- *
  *-------------------------------------------------------------------------
  */
 static int check_options(pack_opt_t *options) {
-	unsigned int i;
-	int k, j, has_cp = 0, has_ck = 0;
-	char slayout[30];
-
-	/*-------------------------------------------------------------------------
-	 * objects to layout
-	 *-------------------------------------------------------------------------
-	 */
-	if (options->verbose && have_request(options) /* only print if requested */) {
-		printf("Objects to modify layout are...\n");
-		if (options->all_layout == 1) {
-			switch (options->layout_g) {
-			case H5D_COMPACT:
-				strcpy(slayout, "compact");
-				break;
-			case H5D_CONTIGUOUS:
-				strcpy(slayout, "contiguous");
-				break;
-			case H5D_CHUNKED:
-				strcpy(slayout, "chunked");
-				break;
-			case H5D_VIRTUAL:
-				strcpy(slayout, "virtual");
-				break;
-			case H5D_LAYOUT_ERROR:
-			case H5D_NLAYOUTS:
-				error_msg("invalid layout\n");
-				return -1;
-			default:
-				strcpy(slayout, "invalid layout\n");
-				return -1;
-			}
-			printf(" Apply %s layout to all\n", slayout);
-			if (H5D_CHUNKED == options->layout_g) {
-				printf("with dimension [");
-				for (j = 0; j < options->chunk_g.rank; j++)
-					printf("%d ", (int) options->chunk_g.chunk_lengths[j]);
-				printf("]\n");
-			}
-		}
-	}/* verbose */
-
-	for (i = 0; i < options->op_tbl->nelems; i++) {
-		char* name = options->op_tbl->objs[i].path;
-
-		if (options->op_tbl->objs[i].chunk.rank > 0) {
-			if (options->verbose) {
-				printf(" <%s> with chunk size ", name);
-				for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
-					printf("%d ",
-							(int) options->op_tbl->objs[i].chunk.chunk_lengths[k]);
-				printf("\n");
-			}
-			has_ck = 1;
-		}
-		else if (options->op_tbl->objs[i].chunk.rank == -2) {
-			if (options->verbose)
-				printf(" <%s> %s\n", name, "NONE (contigous)");
-			has_ck = 1;
-		}
-	}
-
-	if (options->all_layout == 1 && has_ck) {
-		error_msg(
-				"invalid chunking input: 'all' option\
+    unsigned int i;
+    int          k, j, has_cp = 0, has_ck = 0;
+    char         slayout[30];
+
+    /*-------------------------------------------------------------------------
+    * objects to layout
+    *-------------------------------------------------------------------------
+    */
+    if (options->verbose && have_request(options) /* only print if requested */) {
+        printf("Objects to modify layout are...\n");
+        if (options->all_layout == 1) {
+            switch (options->layout_g) {
+            case H5D_COMPACT:
+                strcpy(slayout, "compact");
+                break;
+            case H5D_CONTIGUOUS:
+                strcpy(slayout, "contiguous");
+                break;
+            case H5D_CHUNKED:
+                strcpy(slayout, "chunked");
+                break;
+            case H5D_VIRTUAL:
+                strcpy(slayout, "virtual");
+                break;
+            case H5D_LAYOUT_ERROR:
+            case H5D_NLAYOUTS:
+                error_msg("invalid layout\n");
+                return -1;
+            default:
+                strcpy(slayout, "invalid layout\n");
+                return -1;
+            }
+            printf(" Apply %s layout to all\n", slayout);
+            if (H5D_CHUNKED == options->layout_g) {
+                printf("with dimension [");
+                for (j = 0; j < options->chunk_g.rank; j++)
+                    printf("%d ", (int) options->chunk_g.chunk_lengths[j]);
+                printf("]\n");
+            }
+        }
+    }/* verbose */
+
+    for (i = 0; i < options->op_tbl->nelems; i++) {
+        char* name = options->op_tbl->objs[i].path;
+
+        if (options->op_tbl->objs[i].chunk.rank > 0) {
+            if (options->verbose) {
+                printf(" <%s> with chunk size ", name);
+                for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
+                    printf("%d ",
+                            (int) options->op_tbl->objs[i].chunk.chunk_lengths[k]);
+                printf("\n");
+            }
+            has_ck = 1;
+        }
+        else if (options->op_tbl->objs[i].chunk.rank == -2) {
+            if (options->verbose)
+                printf(" <%s> %s\n", name, "NONE (contigous)");
+            has_ck = 1;
+        }
+    }
+
+    if (options->all_layout == 1 && has_ck) {
+        error_msg(
+                "invalid chunking input: 'all' option\
                             is present with other objects\n");
-		return -1;
-	}
-
-	/*-------------------------------------------------------------------------
-	 * objects to filter
-	 *-------------------------------------------------------------------------
-	 */
-
-	if (options->verbose && have_request(options) /* only print if requested */) {
-		printf("Objects to apply filter are...\n");
-		if (options->all_filter == 1) {
-			for (k = 0; k < options->n_filter_g; k++) {
-				H5Z_filter_t filtn = options->filter_g[k].filtn;
-				switch (filtn) {
-				case H5Z_FILTER_NONE:
-					printf(" Uncompress all\n");
-					break;
-				case H5Z_FILTER_SHUFFLE:
-				case H5Z_FILTER_FLETCHER32:
-					printf(" All with %s\n", get_sfilter(filtn));
-					break;
-				case H5Z_FILTER_SZIP:
-				case H5Z_FILTER_DEFLATE:
-					printf(" All with %s, parameter %d\n", get_sfilter(filtn),
-							options->filter_g[k].cd_values[0]);
-					break;
-				default:
-					printf(" User Defined %d\n", filtn);
-					break;
-				} /* k */
-			};
-		}
-	} /* verbose */
-
-	for (i = 0; i < options->op_tbl->nelems; i++) {
-		pack_info_t pack = options->op_tbl->objs[i];
-		char* name = pack.path;
-
-		for (j = 0; j < pack.nfilters; j++) {
-			if (options->verbose) {
-				printf(" <%s> with %s filter\n", name,
-						get_sfilter(pack.filter[j].filtn));
-			}
-
-			has_cp = 1;
-
-		} /* j */
-	} /* i */
-
-	if (options->all_filter == 1 && has_cp) {
-		error_msg(
-				"invalid compression input: 'all' option\
+        return -1;
+    }
+
+    /*-------------------------------------------------------------------------
+    * objects to filter
+    *-------------------------------------------------------------------------
+    */
+
+    if (options->verbose && have_request(options) /* only print if requested */) {
+        printf("Objects to apply filter are...\n");
+        if (options->all_filter == 1) {
+            for (k = 0; k < options->n_filter_g; k++) {
+                H5Z_filter_t filtn = options->filter_g[k].filtn;
+                switch (filtn) {
+                case H5Z_FILTER_NONE:
+                    printf(" Uncompress all\n");
+                    break;
+                case H5Z_FILTER_SHUFFLE:
+                case H5Z_FILTER_FLETCHER32:
+                    printf(" All with %s\n", get_sfilter(filtn));
+                    break;
+                case H5Z_FILTER_SZIP:
+                case H5Z_FILTER_DEFLATE:
+                    printf(" All with %s, parameter %d\n", get_sfilter(filtn),
+                            options->filter_g[k].cd_values[0]);
+                    break;
+                default:
+                    printf(" User Defined %d\n", filtn);
+                    break;
+                } /* k */
+            };
+        }
+    } /* verbose */
+
+    for (i = 0; i < options->op_tbl->nelems; i++) {
+        pack_info_t pack = options->op_tbl->objs[i];
+        char* name = pack.path;
+
+        for (j = 0; j < pack.nfilters; j++) {
+            if (options->verbose) {
+                printf(" <%s> with %s filter\n", name,
+                        get_sfilter(pack.filter[j].filtn));
+            }
+
+            has_cp = 1;
+
+        } /* j */
+    } /* i */
+
+    if (options->all_filter == 1 && has_cp) {
+        error_msg(
+                "invalid compression input: 'all' option\
                             is present with other objects\n");
-		return -1;
-	}
-
-	/*-------------------------------------------------------------------------
-	 * check options for the latest format
-	 *-------------------------------------------------------------------------
-	 */
-
-	if (options->grp_compact < 0) {
-		error_msg(
-				"invalid maximum number of links to store as header messages\n");
-		return -1;
-	}
-	if (options->grp_indexed < 0) {
-		error_msg(
-				"invalid minimum number of links to store in the indexed format\n");
-		return -1;
-	}
-	if (options->grp_indexed > options->grp_compact) {
-		error_msg(
-				"minimum indexed size is greater than the maximum compact size\n");
-		return -1;
-	}
-	for (i = 0; i < 8; i++) {
-		if (options->msg_size[i] < 0) {
-			error_msg("invalid shared message size\n");
-			return -1;
-		}
-	}
-
-	/*--------------------------------------------------------------------------------
-	 * verify new user userblock options; file name must be present
-	 *---------------------------------------------------------------------------------
-	 */
-	if (options->ublock_filename != NULL && options->ublock_size == 0) {
-		if (options->verbose) {
-			printf(
-					"Warning: user block size missing for file %s. Assigning a default size of 1024...\n",
-					options->ublock_filename);
-			options->ublock_size = 1024;
-		}
-	}
-
-	if (options->ublock_filename == NULL && options->ublock_size != 0) {
-		error_msg("file name missing for user block\n",
-				options->ublock_filename);
-		return -1;
-	}
-
-	/*--------------------------------------------------------------------------------
-	 * verify alignment options; threshold is zero default but alignment not
-	 *---------------------------------------------------------------------------------
-	 */
-
-	if (options->alignment == 0 && options->threshold != 0) {
-		error_msg("alignment for H5Pset_alignment missing\n");
-		return -1;
-	}
-
-	return 0;
+        return -1;
+    }
+
+    /*-------------------------------------------------------------------------
+    * check options for the latest format
+    *-------------------------------------------------------------------------
+    */
+
+    if (options->grp_compact < 0) {
+        error_msg(
+                "invalid maximum number of links to store as header messages\n");
+        return -1;
+    }
+    if (options->grp_indexed < 0) {
+        error_msg(
+                "invalid minimum number of links to store in the indexed format\n");
+        return -1;
+    }
+    if (options->grp_indexed > options->grp_compact) {
+        error_msg(
+                "minimum indexed size is greater than the maximum compact size\n");
+        return -1;
+    }
+    for (i = 0; i < 8; i++) {
+        if (options->msg_size[i] < 0) {
+            error_msg("invalid shared message size\n");
+            return -1;
+        }
+    }
+
+    /*--------------------------------------------------------------------------------
+    * verify new user userblock options; file name must be present
+    *---------------------------------------------------------------------------------
+    */
+    if (options->ublock_filename != NULL && options->ublock_size == 0) {
+        if (options->verbose) {
+            printf(
+                    "Warning: user block size missing for file %s. Assigning a default size of 1024...\n",
+                    options->ublock_filename);
+            options->ublock_size = 1024;
+        }
+    }
+
+    if (options->ublock_filename == NULL && options->ublock_size != 0) {
+        error_msg("file name missing for user block\n",
+                options->ublock_filename);
+        return -1;
+    }
+
+    /*--------------------------------------------------------------------------------
+    * verify alignment options; threshold is zero default but alignment not
+    *---------------------------------------------------------------------------------
+    */
+
+    if (options->alignment == 0 && options->threshold != 0) {
+        error_msg("alignment for H5Pset_alignment missing\n");
+        return -1;
+    }
+
+    return 0;
 }
 
 /*-------------------------------------------------------------------------
@@ -772,119 +761,121 @@ static int check_options(pack_opt_t *options) {
  *-------------------------------------------------------------------------
  */
 static int check_objects(const char* fname, pack_opt_t *options) {
-	hid_t fid;
-	unsigned int i;
-	trav_table_t *travt = NULL;
-
-	/* nothing to do */
-	if (options->op_tbl->nelems == 0)
-		return 0;
-
-	/*-------------------------------------------------------------------------
-	 * open the file
-	 *-------------------------------------------------------------------------
-	 */
-	if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0))
-			< 0) {
-		printf("<%s>: %s\n", fname, H5FOPENERROR);
-		return -1;
-	}
-
-	/*-------------------------------------------------------------------------
-	 * get the list of objects in the file
-	 *-------------------------------------------------------------------------
-	 */
-
-	/* init table */
-	trav_table_init(&travt);
-
-	/* get the list of objects in the file */
-	if (h5trav_gettable(fid, travt) < 0)
-		goto out;
-
-	/*-------------------------------------------------------------------------
-	 * compare with user supplied list
-	 *-------------------------------------------------------------------------
-	 */
-
-	if (options->verbose)
-		printf("Opening file <%s>. Searching for objects to modify...\n",
-				fname);
-
-	for (i = 0; i < options->op_tbl->nelems; i++) {
-		char* name = options->op_tbl->objs[i].path;
-		if (options->verbose)
-			printf(" <%s>", name);
-
-		/* the input object names are present in the file and are valid */
-		if (h5trav_getindext(name, travt) < 0) {
-			error_msg("%s Could not find <%s> in file <%s>. Exiting...\n",
-					(options->verbose ? "\n" : ""), name, fname);
-			goto out;
-		}
-		if (options->verbose)
-			printf("...Found\n");
-
-		/* check for extra filter conditions */
-		switch (options->op_tbl->objs[i].filter->filtn) {
-		/* chunk size must be smaller than pixels per block */
-		case H5Z_FILTER_SZIP:
-			{
-				int j;
-				hsize_t csize = 1;
-				unsigned ppb = options->op_tbl->objs[i].filter->cd_values[0];
-				hsize_t dims[H5S_MAX_RANK];
-				int rank;
-				hid_t did;
-				hid_t sid;
-
-				if (options->op_tbl->objs[i].chunk.rank > 0) {
-					rank = options->op_tbl->objs[i].chunk.rank;
-					for (j = 0; j < rank; j++)
-						csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j];
-				}
-				else {
-					if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
-						goto out;
-					if ((sid = H5Dget_space(did)) < 0)
-						goto out;
-					if ((rank = H5Sget_simple_extent_ndims(sid)) < 0)
-						goto out;
-					HDmemset(dims, 0, sizeof dims);
-					if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
-						goto out;
-					for (j = 0; j < rank; j++)
-						csize *= dims[j];
-					if (H5Sclose(sid) < 0)
-						goto out;
-					if (H5Dclose(did) < 0)
-						goto out;
-				}
-
-				if (csize < ppb) {
-					printf(
-							" <warning: SZIP settins, chunk size is smaller than pixels per block>\n");
-					goto out;
-				}
-			}
-			break;
-		default:
-			break;
-		}
-	} /* i */
-
-	/*-------------------------------------------------------------------------
-	 * close
-	 *-------------------------------------------------------------------------
-	 */
-	H5Fclose(fid);
-	trav_table_free(travt);
-	return 0;
+    hid_t         fid;
+    unsigned int  i;
+    trav_table_t *travt = NULL;
+
+    /* nothing to do */
+    if (options->op_tbl->nelems == 0)
+        return 0;
+
+    /*-------------------------------------------------------------------------
+    * open the file
+    *-------------------------------------------------------------------------
+    */
+    if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0))
+            < 0) {
+        printf("<%s>: %s\n", fname, H5FOPENERROR);
+        return -1;
+    }
+
+    /*-------------------------------------------------------------------------
+    * get the list of objects in the file
+    *-------------------------------------------------------------------------
+    */
+
+    /* Initialize indexing options */
+    h5trav_set_index(sort_by, sort_order);
+    /* init table */
+    trav_table_init(&travt);
+
+    /* get the list of objects in the file */
+    if (h5trav_gettable(fid, travt) < 0)
+        goto out;
+
+    /*-------------------------------------------------------------------------
+    * compare with user supplied list
+    *-------------------------------------------------------------------------
+    */
+
+    if (options->verbose)
+        printf("Opening file <%s>. Searching for objects to modify...\n",
+                fname);
+
+    for (i = 0; i < options->op_tbl->nelems; i++) {
+        char* name = options->op_tbl->objs[i].path;
+        if (options->verbose)
+            printf(" <%s>", name);
+
+        /* the input object names are present in the file and are valid */
+        if (h5trav_getindext(name, travt) < 0) {
+            error_msg("%s Could not find <%s> in file <%s>. Exiting...\n",
+                    (options->verbose ? "\n" : ""), name, fname);
+            goto out;
+        }
+        if (options->verbose)
+            printf("...Found\n");
+
+        /* check for extra filter conditions */
+        switch (options->op_tbl->objs[i].filter->filtn) {
+        /* chunk size must be smaller than pixels per block */
+        case H5Z_FILTER_SZIP:
+            {
+                int j;
+                hsize_t csize = 1;
+                unsigned ppb = options->op_tbl->objs[i].filter->cd_values[0];
+                hsize_t dims[H5S_MAX_RANK];
+                int rank;
+                hid_t did;
+                hid_t sid;
+
+                if (options->op_tbl->objs[i].chunk.rank > 0) {
+                    rank = options->op_tbl->objs[i].chunk.rank;
+                    for (j = 0; j < rank; j++)
+                        csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j];
+                }
+                else {
+                    if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
+                        goto out;
+                    if ((sid = H5Dget_space(did)) < 0)
+                        goto out;
+                    if ((rank = H5Sget_simple_extent_ndims(sid)) < 0)
+                        goto out;
+                    HDmemset(dims, 0, sizeof dims);
+                    if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
+                        goto out;
+                    for (j = 0; j < rank; j++)
+                        csize *= dims[j];
+                    if (H5Sclose(sid) < 0)
+                        goto out;
+                    if (H5Dclose(did) < 0)
+                        goto out;
+                }
+
+                if (csize < ppb) {
+                    printf(
+                            " <warning: SZIP settins, chunk size is smaller than pixels per block>\n");
+                    goto out;
+                }
+            }
+            break;
+        default:
+            break;
+        }
+    } /* i */
+
+    /*-------------------------------------------------------------------------
+    * close
+    *-------------------------------------------------------------------------
+    */
+    H5Fclose(fid);
+    trav_table_free(travt);
+    return 0;
 
 out:
-	H5Fclose(fid);
-	trav_table_free(travt);
-	return -1;
+    H5Fclose(fid);
+    trav_table_free(travt);
+    return -1;
 }
 
 /*-------------------------------------------------------------------------
@@ -900,10 +891,10 @@ out:
  */
 static int have_request(pack_opt_t *options) {
 
-	if (options->all_filter || options->all_layout || options->op_tbl->nelems)
-		return 1;
+    if (options->all_filter || options->all_layout || options->op_tbl->nelems)
+        return 1;
 
-	return 0;
+    return 0;
 
 }
 
@@ -918,21 +909,21 @@ static int have_request(pack_opt_t *options) {
  */
 
 static const char* get_sfilter(H5Z_filter_t filtn) {
-	if (filtn == H5Z_FILTER_NONE)
-		return "NONE";
-	else if (filtn == H5Z_FILTER_DEFLATE)
-		return "GZIP";
-	else if (filtn == H5Z_FILTER_SZIP)
-		return "SZIP";
-	else if (filtn == H5Z_FILTER_SHUFFLE)
-		return "SHUFFLE";
-	else if (filtn == H5Z_FILTER_FLETCHER32)
-		return "FLETCHER32";
-	else if (filtn == H5Z_FILTER_NBIT)
-		return "NBIT";
-	else if (filtn == H5Z_FILTER_SCALEOFFSET)
-		return "SOFF";
-	else
-		return "UD";
+    if (filtn == H5Z_FILTER_NONE)
+        return "NONE";
+    else if (filtn == H5Z_FILTER_DEFLATE)
+        return "GZIP";
+    else if (filtn == H5Z_FILTER_SZIP)
+        return "SZIP";
+    else if (filtn == H5Z_FILTER_SHUFFLE)
+        return "SHUFFLE";
+    else if (filtn == H5Z_FILTER_FLETCHER32)
+        return "FLETCHER32";
+    else if (filtn == H5Z_FILTER_NBIT)
+        return "NBIT";
+    else if (filtn == H5Z_FILTER_SCALEOFFSET)
+        return "SOFF";
+    else
+        return "UD";
 }