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-rw-r--r--src/util/hdf5_merge.c375
1 files changed, 0 insertions, 375 deletions
diff --git a/src/util/hdf5_merge.c b/src/util/hdf5_merge.c
deleted file mode 100644
index 12cd0ec..0000000
--- a/src/util/hdf5_merge.c
+++ /dev/null
@@ -1,375 +0,0 @@
- /*@@
- @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 $Id$
- @@*/
-
-#include "cctk.h"
-
-#include <hdf5.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include "CactusPUGHIO/IOHDF5Util/src/ioHDF5UtilGH.h"
-
-/* the rcs ID and its dummy function to use it */
-static const char *rcsid = "$Header$";
-CCTK_FILEVERSION(CactusPUGHIO_IOHDF5_util_hdf5_merge_c)
-
-
-/*****************************************************************************/
-/* macro definitions */
-/*****************************************************************************/
-/* uncomment the following to get some debugging output */
-/* #define IOHDF5_DEBUG 1 */
-
-/* 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: %d 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",
- 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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