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-rw-r--r--src/util/hdf5_merge.c373
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diff --git a/src/util/hdf5_merge.c b/src/util/hdf5_merge.c
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+ /*@@
+ @file hdf5_merge.c
+ @date Thu 10 Jan 2002
+ @author Thomas Radke
+ @desc
+ This utility program takes a list of Cactus HDF5 datafiles,
+ merges them at the group hierarchy level and dumps the resulting
+ tree to a new HDF5 file.
+ @enddesc
+ @version $Id: hdf5_merge.c,v 1.3 2009/09/29 14:38:14 schnetter Exp $
+ @@*/
+
+#include "cctk.h"
+
+#define H5_USE_16_API 1
+#include <hdf5.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+/* the rcs ID and its dummy function to use it */
+static const char *rcsid = "$Header: /cactusdevcvs/CactusExternal/HDF5/src/util/hdf5_merge.c,v 1.3 2009/09/29 14:38:14 schnetter Exp $";
+CCTK_FILEVERSION(CactusExternal_HDF5_util_hdf5_merge_c)
+
+
+/*****************************************************************************/
+/* macro definitions */
+/*****************************************************************************/
+/* macro to do an HDF5 call, check its return code, and print a warning
+ in case of an error */
+#define CHECK_ERROR(hdf5_call) \
+ do \
+ { \
+ int _error_code = hdf5_call; \
+ \
+ \
+ if (_error_code < 0) \
+ { \
+ fprintf (stderr, "WARNING: line %d: HDF5 call '%s' returned " \
+ "error code %d\n", \
+ __LINE__, #hdf5_call, _error_code); \
+ nerrors++; \
+ } \
+ } while (0)
+
+
+/*****************************************************************************/
+/* global variables */
+/*****************************************************************************/
+/* NOTE: although it isn't good programming practice
+ we make these variables global for convenience
+ since they are accessed from recursively or
+ indirectly called routines which only get passed
+ a single user-supplied argument */
+static char *pathname = NULL; /* pathname of the current object */
+static unsigned int nerrors = 0; /* global error counter */
+
+/*****************************************************************************/
+/* local function prototypes */
+/*****************************************************************************/
+static herr_t CopyObject (hid_t copy_from, const char *objectname, void *arg);
+static herr_t CopyAttribute (hid_t src, const char *attr_name, void *arg);
+
+
+ /*@@
+ @routine main
+ @date Sat 24 Feb 2001
+ @author Thomas Radke
+ @desc
+ Main routine of the HDF5 file merger
+ @enddesc
+
+ @calls CopyObject
+
+ @var argc
+ @vdesc number of command line arguments
+ @vtype int
+ @vio in
+ @endvar
+ @var argv
+ @vdesc command line arguments
+ @vtype char *[]
+ @vio in
+ @endvar
+
+ @returntype int
+ @returndesc
+ 0 for success, negative return values indicate an error
+ @endreturndesc
+@@*/
+int main (int argc, char *argv[])
+{
+ int i;
+ hid_t *infiles, outfile;
+
+
+ /* give some help if called with incorrect number of parameters */
+ if (argc < 3)
+ {
+ fprintf (stderr, "Usage: %s <infile1> [<infile2> ...] <outfile>\n",argv[0]);
+ fprintf (stderr, " eg, %s alp.time*.h5 alp.h5"
+ "\n\n", argv[0]);
+ return (0);
+ }
+
+ H5E_BEGIN_TRY
+ {
+ /* open the input files */
+ infiles = (hid_t *) malloc ((argc - 2) * sizeof (hid_t));
+ for (i = 0; i < argc - 2; i++)
+ {
+ infiles[i] = H5Fopen (argv[i + 1], H5F_ACC_RDONLY, H5P_DEFAULT);
+ if (infiles[i] < 0)
+ {
+ fprintf (stderr, "ERROR: Cannot open HDF5 input file '%s' !\n\n",
+ argv[i + 1]);
+ return (-1);
+ }
+ }
+
+ /* try to open an existing outfile file in append mode,
+ if this fails create it as a new file */
+ outfile = H5Fopen (argv[argc-1], H5F_ACC_RDWR, H5P_DEFAULT);
+ if (outfile < 0)
+ {
+ outfile = H5Fcreate (argv[argc-1], H5F_ACC_TRUNC, H5P_DEFAULT,
+ H5P_DEFAULT);
+ }
+ if (outfile < 0)
+ {
+ fprintf (stderr, "ERROR: Cannot open HDF5 output file '%s' !\n\n",
+ argv[argc - 1]);
+ return (-1);
+ }
+ } H5E_END_TRY
+
+ printf ("\n -------------------------\n"
+ " Cactus 4 HDF5 File Merger\n"
+ " -------------------------\n");
+
+ /* do the copying by iterating over all objects */
+ for (i = 0; i < argc - 2; i++)
+ {
+ printf ("\n Merging objects from input file '%s' into output file '%s'\n",
+ argv[i + 1], argv[argc-1]);
+ pathname = "";
+ CHECK_ERROR (H5Giterate (infiles[i], "/", NULL, CopyObject, &outfile));
+ }
+
+ /* finally, close all open files */
+ for (i = 0; i < argc - 2; i++)
+ {
+ CHECK_ERROR (H5Fclose (infiles[i]));
+ }
+ CHECK_ERROR (H5Fclose (outfile));
+ free (infiles);
+
+ /* report status */
+ if (nerrors == 0)
+ {
+ printf ("\n\n *** All input files successfully merged. ***\n\n");
+ }
+ else
+ {
+ fprintf (stderr, "\n\n *** WARNING: %u errors occured during "
+ "file merging. ***\n\n", nerrors);
+ }
+
+ return (0);
+}
+
+
+/*****************************************************************************/
+/* local routines */
+/*****************************************************************************/
+ /*@@
+ @routine CopyObject
+ @date Sat 24 Feb 2001
+ @author Thomas Radke
+ @desc
+ Iterator recursively called by H5Giterate() for every object
+ in the input file
+ It copies the current object to the output file if it didn't
+ already exist there.
+ @enddesc
+
+ @calls CopyAttribute
+
+ @var from
+ @vdesc identifier for the group the current object belongs to
+ @vtype hid_t
+ @vio in
+ @endvar
+ @var objectname
+ @vdesc name of the current object
+ @vtype const char *
+ @vio in
+ @endvar
+ @var _to
+ @vdesc user-supplied argument indicating the output object identifier
+ @vtype hid_t
+ @vio in
+ @endvar
+
+ @returntype int
+ @returndesc
+ 0 - continue the iteration for following group objects
+ 1 - short-curcuit, no further iteration of this group
+ @endreturndesc
+@@*/
+static herr_t CopyObject (hid_t from,
+ const char *objectname,
+ void *_to)
+{
+ int i;
+ hid_t to, datatype, dataspace;
+ H5G_stat_t objectinfo;
+ char *current_pathname;
+ size_t objectsize;
+ void *data;
+
+
+ /* get the output object identifier */
+ to = *(hid_t *) _to;
+
+ /* check whether an object by that name already exists */
+ H5E_BEGIN_TRY
+ {
+ i = H5Gget_objinfo (to, objectname, 0, &objectinfo) >= 0;
+ } H5E_END_TRY
+ if (i)
+ {
+ printf (" object '%s/%s' will not be copied (already exists)\n",
+ pathname, objectname);
+ return (0);
+ }
+
+ /* build the full pathname for the current to object to process */
+ current_pathname = pathname;
+ pathname = (char *) malloc (strlen (current_pathname) +
+ strlen (objectname) + 2);
+ sprintf (pathname, "%s/%s", current_pathname, objectname);
+
+ /* check the type of the current object */
+ CHECK_ERROR (H5Gget_objinfo (from, objectname, 0, &objectinfo));
+ if (objectinfo.type == H5G_GROUP)
+ {
+ printf (" copying group '%s'\n", pathname);
+
+ CHECK_ERROR (from = H5Gopen (from, objectname));
+ CHECK_ERROR (to = H5Gcreate (to, objectname, 0));
+ /* iterate over all objects in the (first) input file */
+ CHECK_ERROR (H5Giterate (from, ".", NULL, CopyObject, &to));
+ CHECK_ERROR (H5Aiterate (from, NULL, CopyAttribute, &to));
+ CHECK_ERROR (H5Gclose (to));
+ CHECK_ERROR (H5Gclose (from));
+ }
+ else if (objectinfo.type == H5G_DATASET)
+ {
+ printf (" copying dataset '%s'\n", pathname);
+
+ CHECK_ERROR (from = H5Dopen (from, objectname));
+ CHECK_ERROR (datatype = H5Dget_type (from));
+ CHECK_ERROR (dataspace = H5Dget_space (from));
+ CHECK_ERROR (to = H5Dcreate (to, objectname, datatype, dataspace,
+ H5P_DEFAULT));
+ objectsize = H5Sget_select_npoints (dataspace) * H5Tget_size (datatype);
+ if (objectsize > 0)
+ {
+ data = malloc (objectsize);
+ if (data == NULL)
+ {
+ fprintf (stderr, "failled to allocate %d bytes of memory, giving up\n",
+ (int) objectsize);
+ exit (-1);
+ }
+ CHECK_ERROR (H5Dread (from, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+ data));
+ CHECK_ERROR (H5Dwrite (to, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT,data));
+ free (data);
+ }
+ CHECK_ERROR (H5Aiterate (from, NULL, CopyAttribute, &to));
+ CHECK_ERROR (H5Dclose (to));
+ CHECK_ERROR (H5Dclose (from));
+ CHECK_ERROR (H5Sclose (dataspace));
+ CHECK_ERROR (H5Tclose (datatype));
+ }
+ else
+ {
+ fprintf (stderr, "WARNING: Found object '%s' which is not neither a "
+ "group nor a dataset ! Object will not be copied.\n",
+ pathname);
+ nerrors++;
+ }
+
+ /* reset the pathname */
+ free (pathname);
+ pathname = current_pathname;
+
+ return (0);
+}
+
+
+ /*@@
+ @routine CopyAttribute
+ @date Sat 24 Feb 2001
+ @author Thomas Radke
+ @desc
+ Iterator recursively called by H5Aiterate() for every attribute
+ of an object (dataset or group)
+ @enddesc
+
+ @var from
+ @vdesc identifier for the group or dataset to read the attribute from
+ @vtype hid_t
+ @vio in
+ @endvar
+ @var attrname
+ @vdesc name of the current attribute
+ @vtype const char *
+ @vio in
+ @endvar
+ @var _to
+ @vdesc user-supplied argument indicating the group or dataset
+ to copy the attribute to
+ @vtype hid_t
+ @vio in
+ @endvar
+
+ @returntype int
+ @returndesc
+ 0 - continue the iteration for following attributes
+ @endreturndesc
+@@*/
+static herr_t CopyAttribute (hid_t from,
+ const char *attrname,
+ void *_to)
+{
+ hid_t attr, datatype, dataspace, to;
+ size_t attrsize;
+ void *value;
+
+
+ /* get the target group/dataset identifier */
+ to = *(hid_t *) _to;
+
+ /* open the attribute given by its name, get type, dataspace, and value
+ and just copy it */
+ CHECK_ERROR (attr = H5Aopen_name (from, attrname));
+ CHECK_ERROR (datatype = H5Aget_type (attr));
+ CHECK_ERROR (dataspace = H5Aget_space (attr));
+ attrsize = H5Tget_size (datatype);
+ if (H5Sis_simple (dataspace) > 0)
+ {
+ attrsize *= H5Sget_simple_extent_npoints (dataspace);
+ }
+ if (attrsize > 0)
+ {
+ value = malloc (attrsize);
+ CHECK_ERROR (H5Aread (attr, datatype, value));
+ CHECK_ERROR (H5Aclose (attr));
+ CHECK_ERROR (attr = H5Acreate (to, attrname, datatype, dataspace,
+ H5P_DEFAULT));
+ CHECK_ERROR (H5Awrite (attr, datatype, value));
+ free (value);
+ }
+ CHECK_ERROR (H5Aclose (attr));
+ CHECK_ERROR (H5Sclose (dataspace));
+ CHECK_ERROR (H5Tclose (datatype));
+
+ return (0);
+}
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