moved driver-independent HDF5 utilities from here to CactusExternal/HDF5

git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5/trunk@232 4825ed28-b72c-4eae-9704-e50c059e567d

5 files changed, 1 insertions, 1147 deletions

diff --git a/doc/documentation.tex b/doc/documentation.tex
index 55ea7d2..645a098 100644
--- a/doc/documentation.tex
+++ b/doc/documentation.tex
@@ -308,15 +308,6 @@ Thorn \ThisThorn\ provides the following utility programs:
   \item {\tt hdf5\_convert\_from\_sdf}\\
     Converts a datafile created by thorn {\bf CactusIO/IOSDF} or other Cactus-external programs into an HDF5 datafile. Your thornlist must include this thorn
     in its thornlist in order to build the SDF-to-HDF5 utility program.
-  \item {\tt hdf5\_merge}\\
-    Merges a list of HDF5 input files into a single HDF5 output file.
-    This can be used to concatenate HDF5 output data created as one file per
-    timestep.
-  \item {\tt hdf5\_extract}\\
-    Extracts a given list of named objects (groups or datasets) from an HDF5
-    input file and writes them into a new HDF5 output file.
-    This is the reverse operation to what {\tt hdf5\_merge.c} does. Useful eg.
-    for extracting individual timesteps from a time series HDF5 datafile.
 \end{itemize}
 %
 All utility programs are located in the {\tt src/util/} subdirectory of thorn
diff --git a/src/make.configuration.defn b/src/make.configuration.defn
index 7e9ca9d..764fd00 100644
--- a/src/make.configuration.defn
+++ b/src/make.configuration.defn
@@ -2,7 +2,7 @@
 # $Header$
 
 # add the recombiner and the IEEEIO converter to the Cactus utitlity tools
-ALL_UTILS += hdf5_recombiner hdf5_merge hdf5_extract hdf5_double_to_single hdf5_convert_from_carpetiohdf5
+ALL_UTILS += hdf5_recombiner hdf5_convert_from_carpetiohdf5
 
 ifneq ($(strip $(HAVE_FLEXIO)), )
   ALL_UTILS += hdf5_convert_from_ieeeio
diff --git a/src/util/hdf5_double_to_single.c b/src/util/hdf5_double_to_single.c
deleted file mode 100644
index 67ce10f..0000000
--- a/src/util/hdf5_double_to_single.c
+++ /dev/null
@@ -1,342 +0,0 @@
- /*@@
-   @file      hdf5_double_to_single.c
-   @date      Thu 10 Jan 2002
-   @author    Thomas Radke
-   @desc
-              This utility program copies a Cactus HDF5 datafile reverting
-              double-precision datasets into single-precision.
-   @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_double_to_single_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       Thu 10 Jan 2002
-   @author     Thomas Radke
-   @desc
-               Main routine of the HDF5 double-to-single converter
-   @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[])
-{
-  hid_t infile, outfile;
-
-
-  /* give some help if called with incorrect number of parameters */
-  if (argc != 3)
-  {
-    fprintf (stderr, "Usage: %s <infile> <outfile>\n", argv[0]);
-    fprintf (stderr, "   eg, %s alp.h5 alp_single.h5\n\n", argv[0]);
-    return (0);
-  }
-
-  H5E_BEGIN_TRY
-  {
-    /* open the input file */
-    infile = H5Fopen (argv[1], H5F_ACC_RDONLY, H5P_DEFAULT);
-    if (infile < 0)
-    {
-      fprintf (stderr, "ERROR: Cannot open HDF5 input file '%s' !\n\n",argv[1]);
-      return (-1);
-    }
-
-    /* create output file */
-    outfile = H5Fcreate (argv[2], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
-    if (outfile < 0)
-    {
-      fprintf (stderr, "ERROR: Cannot create HDF5 output file '%s' !\n\n",
-               argv[2]);
-      return (-1);
-    }
-  } H5E_END_TRY
-
-  printf ("\n  --------------------------------------------------\n"
-            "  Cactus 4 HDF5 double-to-single precision Converter\n"
-            "  --------------------------------------------------\n");
-
-  /* do the copying by iterating over all objects */
-  pathname = "";
-  CHECK_ERROR (H5Giterate (infile, "/", NULL, CopyObject, &outfile));
-
-  /* finally, close all open files */
-  CHECK_ERROR (H5Fclose (infile));
-  CHECK_ERROR (H5Fclose (outfile));
-
-  /* report status */
-  if (nerrors == 0)
-  {
-    printf ("\n\n   *** All Cactus data successfully converted. ***\n\n");
-  }
-  else
-  {
-    fprintf (stderr, "\n\n   *** WARNING: %d errors occured during "
-                     "conversion. ***\n\n", nerrors);
-  }
-
-  return (0);
-}
-
-
-/*****************************************************************************/
-/*                           local routines                                  */
-/*****************************************************************************/
- /*@@
-   @routine    CopyObject
-   @date       Thu 10 Jan 2002
-   @author     Thomas Radke
-   @desc
-               Iterator recursively called by H5Giterate() for every object
-               in the input file
-   @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)
-{
-  hid_t to, datatype, dataspace;
-  H5G_stat_t objectinfo;
-  char *current_pathname;
-  size_t objectsize;
-  char *data;
-
-
-  /* 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);
-
-  /* get the output object identifier */
-  to = *(hid_t *) _to;
-
-  /* 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)
-  {
-    CHECK_ERROR (from = H5Dopen (from, objectname));
-    CHECK_ERROR (dataspace = H5Dget_space (from));
-    CHECK_ERROR (datatype = H5Dget_type (from));
-    if (H5Tget_class (datatype) == H5T_FLOAT)
-    {
-      CHECK_ERROR (H5Tclose (datatype));
-      CHECK_ERROR (datatype = H5Tcopy (H5T_NATIVE_FLOAT));
-      printf ("  converting dataset '%s'\n", pathname);
-    }
-    else
-    {
-      printf ("  copying dataset '%s'\n", pathname);
-    }
-    CHECK_ERROR (to = H5Dcreate (to, objectname, datatype, dataspace,
-                                 H5P_DEFAULT));
-    objectsize = H5Tget_size (datatype);
-    if (H5Sis_simple (dataspace))
-    {
-      objectsize *= H5Sget_simple_extent_npoints (dataspace);
-    }
-    if (objectsize > 0)
-    {
-      data = (char *) malloc (objectsize);
-      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 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       Thu 10 Jan 2002
-   @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);
-}
diff --git a/src/util/hdf5_extract.c b/src/util/hdf5_extract.c
deleted file mode 100644
index 4029472..0000000
--- a/src/util/hdf5_extract.c
+++ /dev/null
@@ -1,420 +0,0 @@
- /*@@
-   @file      hdf5_extract.c
-   @date      Thu 19 Feb 2002
-   @author    Thomas Radke
-   @desc
-              This utility program extracts objects from an HDF5 file and writes
-              them into a new one.
-   @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_extract_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 */
-static unsigned int check_parents = 0;   /* flag to check for parent groups */
-
-/*****************************************************************************/
-/*                           local function prototypes                       */
-/*****************************************************************************/
-static herr_t CopyObject (hid_t from, const char *objectname, void *_to);
-static herr_t CopyAttribute (hid_t src, const char *attr_name, void *arg);
-
-
- /*@@
-   @routine    main
-   @date       Thu 19 Feb 2002
-   @author     Thomas Radke
-   @desc
-               Main routine of the HDF5 file extractor
-   @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[])
-{
-  char objectname[256];
-  FILE *listfile;
-  hid_t infile, outfile;
-
-
-  /* give some help if called with incorrect number of parameters */
-  if (argc != 4)
-  {
-    fprintf (stderr, "Usage: %s <listfile> <infile> <outfile>\n", argv[0]);
-    fprintf (stderr, "       where <listfile> can be created from the output of the h5ls command\n\n");
-    fprintf (stderr, "   eg, h5ls alp.h5 > listfile\n"
-                     "       # now edit listfile to select all datasets to be extracted\n"
-                     "       # (don't forget to remove backslashes and the trailing 'Dataset {...}')\n"
-                     "       %s extract_list alp.h5 alp_extract.h5\n\n", argv[0]);
-
-    return (0);
-  }
-
-  /* open the list file */
-  listfile = fopen (argv[1], "r");
-  if (listfile == NULL)
-  {
-    fprintf (stderr, "ERROR: Cannot open list file '%s' !\n\n", argv[1]);
-    return (-1);
-  }
-
-  H5E_BEGIN_TRY
-  {
-    /* open the input file */
-    infile = H5Fopen (argv[2], H5F_ACC_RDONLY, H5P_DEFAULT);
-    if (infile < 0)
-    {
-      fprintf (stderr, "ERROR: Cannot open HDF5 input file '%s' !\n\n",argv[2]);
-      return (-1);
-    }
-
-    /* try to open an existing outfile file in append mode,
-       if this fails create it as a new file */
-    outfile = H5Fopen (argv[3], H5F_ACC_RDWR, H5P_DEFAULT);
-    if (outfile < 0)
-    {
-      outfile = H5Fcreate (argv[3], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
-    }
-    if (outfile < 0)
-    {
-      fprintf (stderr, "ERROR: Cannot create HDF5 output file '%s' !\n\n",
-               argv[3]);
-      return (-1);
-    }
-  } H5E_END_TRY
-
-  printf ("\n  ----------------------------\n"
-            "  Cactus 4 HDF5 File Extractor\n"
-            "  ----------------------------\n");
-
-  /* do the copying by iterating over all objects */
-  while (fgets (objectname, sizeof (objectname), listfile))
-  {
-    /* get rid of the trailing newline */
-    objectname[strlen (objectname) - 1] = 0;
-    pathname = "";
-
-    check_parents = 1;
-    CopyObject (infile, objectname, &outfile);
-  }
-
-  /* finally, close all open files */
-  CHECK_ERROR (H5Fclose (infile));
-  CHECK_ERROR (H5Fclose (outfile));
-  fclose (listfile);
-
-  /* report status */
-  if (nerrors == 0)
-  {
-    printf ("\n\n   *** All objects successfully extracted. ***\n\n");
-  }
-  else
-  {
-    fprintf (stderr, "\n\n   *** WARNING: %d errors occured during "
-                     "data extraction. ***\n\n", nerrors);
-  }
-
-  return (0);
-}
-
-
-/*****************************************************************************/
-/*                           local routines                                  */
-/*****************************************************************************/
- /*@@
-   @routine    CopyObject
-   @date       Thu 19 Feb 2002
-   @author     Thomas Radke
-   @desc
-               Copies an object with given name from the input file into the
-               output file.
-   @enddesc
-
-   @calls      CopyAttribute
-
-   @var        from
-   @vdesc      input group handle
-   @vtype      hid_t
-   @vio        in
-   @endvar
-   @var        objectname
-   @vdesc      name of the object to extract
-   @vtype      const char *
-   @vio        in
-   @endvar
-   @var        _to
-   @vdesc      output group handle
-   @vtype      void *
-   @vio        in
-   @endvar
-
-   @returntype herr_t
-   @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)
-{
-  hid_t to, datatype, dataspace, from_group, to_group;
-  H5G_stat_t objectinfo;
-  char *current_pathname;
-  size_t objectsize;
-  herr_t result;
-  char *data, *slash;
-
-
-  /* get the output object identifier */
-  to = *(hid_t *) _to;
-
-  /* check whether the requested object was already extracted */
-  H5E_BEGIN_TRY
-  {
-    result = H5Gget_objinfo (to, objectname, 0, &objectinfo);
-  } H5E_END_TRY
-  if (result >= 0)
-  {
-    fprintf (stderr, "WARNING: object '%s' was already extracted\n",objectname);
-    return (0);
-  }
-
-  /* check whether the requested object exists */
-  H5E_BEGIN_TRY
-  {
-    result = H5Gget_objinfo (from, objectname, 0, &objectinfo);
-  } H5E_END_TRY
-  if (result < 0)
-  {
-    fprintf (stderr, "WARNING: object '%s' will not be extracted (object "
-                     "doesn't exist)\n", objectname);
-    nerrors++;
-    return (0);
-  }
-
-  /* make sure that all parent groups exist */
-  if (check_parents)
-  {
-    slash = pathname;
-    /* skip leading slashes */
-    while (*slash == '/')
-    {
-      slash++;
-    }
-
-    /* now go through all groups (separated by slashes) */
-    while ((slash = strchr (slash, '/')) != NULL)
-    {
-      *slash = 0;
-
-      /* try to create the group */
-      H5E_BEGIN_TRY
-      {
-        to_group = H5Gcreate (to, pathname, 0);
-      } H5E_END_TRY
-      if (to_group >= 0)
-      {
-        /* copy all attributes */
-        CHECK_ERROR (from_group = H5Gopen (from, pathname));
-        CHECK_ERROR (H5Aiterate (from_group, NULL, CopyAttribute, &to_group));
-        CHECK_ERROR (H5Gclose (from_group));
-        CHECK_ERROR (H5Gclose (to_group));
-      }
-      *slash++ = '/';
-    }
-    check_parents = 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 */
-  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)
-  {
-    CHECK_ERROR (from = H5Dopen (from, objectname));
-    CHECK_ERROR (dataspace = H5Dget_space (from));
-    CHECK_ERROR (datatype = H5Dget_type (from));
-
-    printf ("  copying dataset '%s'\n", pathname);
-    CHECK_ERROR (to = H5Dcreate (to, objectname, datatype, dataspace,
-                                 H5P_DEFAULT));
-    objectsize = H5Tget_size (datatype);
-    if (H5Sis_simple (dataspace))
-    {
-      objectsize *= H5Sget_simple_extent_npoints (dataspace);
-    }
-    if (objectsize > 0)
-    {
-      data = (char *) malloc (objectsize);
-      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 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       Thu 19 Feb 2002
-   @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);
-}
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);
-}