Split tools into src and test - add folders

1 files changed, 942 insertions, 0 deletions

diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c
new file mode 100644
index 0000000..ef2085c
--- /dev/null
+++ b/tools/src/h5repack/h5repack.c
@@ -0,0 +1,942 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+ * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+
+#include "H5private.h"
+#include "h5repack.h"
+#include "h5tools.h"
+#include "h5tools_utils.h"
+
+/*-------------------------------------------------------------------------
+ * File: h5repack.c
+ * Purpose: Public API functions
+ *-------------------------------------------------------------------------
+ */
+
+static int check_options(pack_opt_t *options);
+static int check_objects(const char* fname, pack_opt_t *options);
+static const char* get_sfilter(H5Z_filter_t filtn);
+static int have_request(pack_opt_t *options);
+
+/*-------------------------------------------------------------------------
+ * Function: h5repack
+ *
+ * Purpose: locate all high-level HDF5 objects in the file
+ *  and compress/chunk them using options
+ *
+ * Algorithm: 2 traversals are made to the file; the 1st builds a list of
+ *  the objects, the 2nd makes a copy of them, using the options;
+ *  the reason for the 1st traversal is to check for invalid
+ *  object name requests
+ *
+ * Return: 0, ok, -1, fail
+ *
+ * Programmer: pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 22, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+int h5repack(const char* infile, const char* outfile, pack_opt_t *options) {
+	/* 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;
+
+	/* copy the objects  */
+	if (copy_objects(infile, outfile, options) < 0)
+		return -1;
+
+	return 0;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: h5repack_init
+ *
+ * Purpose: initialize options
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+int h5repack_init(pack_opt_t *options, int verbose, hbool_t latest,
+		H5F_file_space_type_t strategy, hsize_t threshold) {
+	int k, n;
+
+	HDmemset(options, 0, sizeof(pack_opt_t));
+	options->min_comp = 0;
+	options->verbose = verbose;
+    	options->latest = latest;
+	options->layout_g = H5D_LAYOUT_ERROR;
+
+	for (n = 0; n < H5_REPACK_MAX_NFILTERS; n++) {
+		options->filter_g[n].filtn = -1;
+		options->filter_g[n].cd_nelmts = 0;
+		for (k = 0; k < CD_VALUES; k++)
+			options->filter_g[n].cd_values[k] = 0;
+	}
+
+	options->fs_strategy = strategy;
+	options->fs_threshold = threshold;
+
+	return (options_table_init(&(options->op_tbl)));
+}
+
+/*-------------------------------------------------------------------------
+ * Function: h5repack_end
+ *
+ * Purpose: free options table
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int h5repack_end(pack_opt_t *options) {
+	return options_table_free(options->op_tbl);
+}
+
+/*-------------------------------------------------------------------------
+ * Function: h5repack_addfilter
+ *
+ * Purpose: add a compression -f option to table
+ *   Example: -f dset:GZIP=6
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+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 */
+
+    /* parse the -f option */
+    if (NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb)))
+        return -1;
+
+    /* if it applies to all objects */
+    if (is_glb) {
+        int n;
+
+        n = options->n_filter_g++; /* increase # of global filters */
+        if (options->n_filter_g > H5_REPACK_MAX_NFILTERS) {
+            error_msg("maximum number of filters exceeded for <%s>\n", str);
+            HDfree(obj_list);
+            return -1;
+        }
+
+        options->filter_g[n] = filter;
+    }
+    else
+        options_add_filter(obj_list, n_objs, filter, options->op_tbl);
+
+    HDfree(obj_list);
+    return 0;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: h5repack_addlayout
+ *
+ * Purpose: add a layout option
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+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;
+
+    init_packobject(&pack);
+
+    if (options->all_layout == 1) {
+        error_msg( "invalid layout input: 'all' option is present with other objects <%s>\n", str);
+        return ret_value;
+    }
+
+    /* parse the layout option */
+    obj_list = parse_layout(str, &n_objs, &pack, options);
+    if (obj_list) {
+        /* set layout option */
+        options->layout_g = pack.layout;
+
+        /* no individual dataset specified */
+        if (options->all_layout == 1) {
+            if (pack.layout == H5D_CHUNKED) {
+                /* -2 means the NONE option, remove chunking
+                 and set the global layout to contiguous */
+                if (pack.chunk.rank == -2)
+                    options->layout_g = H5D_CONTIGUOUS;
+                /* otherwise set the global chunking type */
+                else {
+                    options->chunk_g.rank = pack.chunk.rank;
+                    for (j = 0; j < pack.chunk.rank; j++)
+                        options->chunk_g.chunk_lengths[j] = pack.chunk.chunk_lengths[j];
+                }
+            }
+        }
+
+        /* individual dataset specified */
+        if (options->all_layout == 0)
+            ret_value = options_add_layout(obj_list, n_objs, &pack, options->op_tbl);
+
+        HDfree(obj_list);
+        ret_value = 0;
+    }
+
+    return ret_value;
+}
+
+/* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr()
+ * were located in h5repack_copy.c as static prior to bugfix1726.
+ * Made shared functions as copy_attr() was needed in h5repack_refs.c.
+ * However copy_attr() may be obsoleted when H5Acopy is available and put back
+ * others to static in h5repack_copy.c.
+ */
+/*-------------------------------------------------------------------------
+ * Function: copy_named_datatype
+ *
+ * Purpose: Copies the specified datatype anonymously, and returns an open
+ *          id for that datatype in the output file.  The first time this
+ *          is called it scans every named datatype in travt into a
+ *          private stack, afterwards it simply scans that stack.  The id
+ *          returned must be closed after it is no longer needed.
+ *          named_datatype_free must be called before the program exits
+ *          to free the stack.
+ *
+ * Programmer: Neil Fortner
+ *
+ * Date: April 14, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+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;
+	}
+
+done:
+	return (ret_value);
+} /* end copy_named_datatype */
+
+/*-------------------------------------------------------------------------
+ * Function: named_datatype_free
+ *
+ * Purpose: Frees the stack of named datatypes.
+ *
+ * Programmer: Neil Fortner
+ *
+ * Date: April 14, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+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;
+
+	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;
+
+done:
+	return (ret_value);
+} /* end named_datatype_free */
+
+/*-------------------------------------------------------------------------
+ * Function: copy_attr
+ *
+ * Purpose: copy attributes located in LOC_IN, which is obtained either from
+ * loc_id = H5Gopen2( fid, name);
+ * loc_id = H5Dopen2( fid, name);
+ * loc_id = H5Topen2( fid, name);
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 28, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+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)
+{
+    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)
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Oget_info failed");
+
+    /*-------------------------------------------------------------------------
+     * copy all attributes
+     *-------------------------------------------------------------------------
+     */
+    for (u = 0; u < (unsigned) oinfo.num_attrs; u++) {
+        /* open attribute */
+        if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed");
+
+        /* get name */
+        if (H5Aget_name(attr_id, (size_t) 255, name) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+
+        /* get the file datatype  */
+        if ((ftype_id = H5Aget_type(attr_id)) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_type failed");
+
+        /* Check if the datatype is committed */
+        if ((is_named = H5Tcommitted(ftype_id)) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommitted failed");
+        if (is_named && travt) {
+            hid_t fidout;
+
+            /* Create out file id */
+            if ((fidout = H5Iget_file_id(loc_out)) < 0)
+                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Iget_file_id failed");
+
+            /* Copy named dt */
+            if ((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p, travt, options)) < 0) {
+                H5Fclose(fidout);
+                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed");
+            } /* end if */
+
+            if (H5Fclose(fidout) < 0)
+                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed");
+        } /* end if */
+        else {
+            if (options->use_native == 1)
+                wtype_id = h5tools_get_native_type(ftype_id);
+            else
+                wtype_id = H5Tcopy(ftype_id);
+        } /* end else */
+
+        /* get the dataspace handle  */
+        if ((space_id = H5Aget_space(attr_id)) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_space failed");
+
+        /* get dimensions  */
+        if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
+
+        nelmts = 1;
+        for (j = 0; j < rank; j++)
+            nelmts *= dims[j];
+
+        if ((msize = H5Tget_size(wtype_id)) == 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
+
+        /*-------------------------------------------------------------------------
+         * object references are a special case. We cannot just copy the buffers,
+         * but instead we recreate the reference.
+         * This is done on a second sweep of the file that just copies the referenced
+         * objects at copy_refs_attr()
+         *-------------------------------------------------------------------------
+         */
+        type_class = H5Tget_class(wtype_id);
+        is_ref = (type_class == H5T_REFERENCE);
+        if (type_class == H5T_VLEN || type_class == H5T_ARRAY) {
+            hid_t base_type = -1;
+
+            base_type = H5Tget_super(ftype_id);
+            is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE));
+            H5Tclose(base_type);
+        }
+
+        if (type_class == H5T_COMPOUND) {
+            int nmembers = H5Tget_nmembers(wtype_id);
+
+            for (j = 0; j < nmembers; j++) {
+                hid_t mtid = H5Tget_member_type(wtype_id, (unsigned) j);
+                H5T_class_t mtclass = H5Tget_class(mtid);
+                H5Tclose(mtid);
+
+                if (mtclass == H5T_REFERENCE) {
+                    is_ref = 1;
+                    break;
+                }
+            } /* for (j=0; i<nmembers; j++) */
+        } /* if (type_class == H5T_COMPOUND) */
+
+        if (is_ref) {
+            ; /* handled by copy_refs_attr() */
+        }
+        else {
+            /*-------------------------------------------------------------------------
+             * read to memory
+             *-------------------------------------------------------------------------
+             */
+
+            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");
+            } /* end if */
+            if (H5Aread(attr_id, wtype_id, buf) < 0)
+                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");
+
+            /*-------------------------------------------------------------------------
+             * copy
+             *-------------------------------------------------------------------------
+             */
+
+            if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Acreate2 failed");
+            if (H5Awrite(attr_out, wtype_id, buf) < 0)
+                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Awrite failed");
+
+            /*close*/
+            if (H5Aclose(attr_out) < 0)
+                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
+
+            /* Check if we have VL data and string in the attribute's  datatype that must
+             * be reclaimed */
+            if (TRUE == h5tools_detect_vlen(wtype_id))
+                H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
+            HDfree(buf);
+            buf = NULL;
+        } /*H5T_REFERENCE*/
+
+        if (options->verbose)
+            printf(FORMAT_OBJ_ATTR, "attr", name);
+
+        /*-------------------------------------------------------------------------
+         * close
+         *-------------------------------------------------------------------------
+         */
+
+        if (H5Tclose(ftype_id) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+        if (H5Tclose(wtype_id) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+        if (H5Sclose(space_id) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
+        if (H5Aclose(attr_id) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
+    } /* u */
+
+    return 0;
+
+done:
+    H5E_BEGIN_TRY {
+        if (buf) {
+            /* Check if we have VL data and string in the attribute's  datatype that must
+            * be reclaimed */
+            if (TRUE == h5tools_detect_vlen(wtype_id))
+                H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
+
+            /* Free buf */
+            HDfree(buf);
+        } /* end if */
+
+        H5Tclose(ftype_id);
+        H5Tclose(wtype_id);
+        H5Sclose(space_id);
+        H5Aclose(attr_id);
+        H5Aclose(attr_out);
+    } H5E_END_TRY;
+
+    return ret_value;
+} /* end copy_attr() */
+
+/*-------------------------------------------------------------------------
+ * Function: check_options
+ *
+ * Purpose: print options, checks for invalid options
+ *
+ * Return: void, return -1 on error
+ *
+ * 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\
+                            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\
+                            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;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: check_objects
+ *
+ * Purpose: locate all HDF5 objects in the file and compare with user
+ *  supplied list
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 23, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+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;
+
+out:
+	H5Fclose(fid);
+	trav_table_free(travt);
+	return -1;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: have_request
+ *
+ * Purpose: check if a filter or layout was requested
+ *
+ * Return: 1 yes, 0 no
+ *
+ * Date: May, 24, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+static int have_request(pack_opt_t *options) {
+
+	if (options->all_filter || options->all_layout || options->op_tbl->nelems)
+		return 1;
+
+	return 0;
+
+}
+
+/*-------------------------------------------------------------------------
+ * Function: get_sfilter
+ *
+ * Purpose: return the filter as a string name
+ *
+ * Return: name of filter, exit on error
+ *
+ *-------------------------------------------------------------------------
+ */
+
+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";
+}
+