added utility program to convert CarpetIOHDF5 output data into PUGH's IOHDF5

format


git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5/trunk@231 4825ed28-b72c-4eae-9704-e50c059e567d

2 files changed, 436 insertions, 1 deletions

diff --git a/src/make.configuration.defn b/src/make.configuration.defn
index aba91f8..7e9ca9d 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
+ALL_UTILS += hdf5_recombiner hdf5_merge hdf5_extract hdf5_double_to_single hdf5_convert_from_carpetiohdf5
 
 ifneq ($(strip $(HAVE_FLEXIO)), )
   ALL_UTILS += hdf5_convert_from_ieeeio
diff --git a/src/util/hdf5_convert_from_carpetiohdf5.c b/src/util/hdf5_convert_from_carpetiohdf5.c
new file mode 100644
index 0000000..74e7c7c
--- /dev/null
+++ b/src/util/hdf5_convert_from_carpetiohdf5.c
@@ -0,0 +1,435 @@
+ /*@@
+   @file      hdf5_convert_from_carpetiohdf5.c
+   @date      Tue 11 October 2005
+   @author    Thomas Radke
+   @desc
+              Utility program to convert CarpetIOHDF5 datafiles
+              into IOHDF5 datafiles.
+   @enddesc
+   @version   $Id$
+ @@*/
+
+#define  MAXDIM       3
+#define  MAXNAMESIZE  100
+
+#include <stdio.h>
+#include <stdlib.h>
+
+
+/* Cactus includes (defines CCTK_FILEVERSION) */
+#include "cctk.h"
+#include "cctk_Version.h"
+
+/* IOHDF5 includes */
+#include "../../../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_convert_from_carpetiohdf5_c)
+
+
+/*****************************************************************************/
+/*                           macro definitions                               */
+/*****************************************************************************/
+/* uncomment the following to get some debugging output */
+/* #define IOHDF5_DEBUG  1 */
+
+/* metadata group in CarpetIOHDF5 files */
+/* FIXME: should rather include the proper CarpetIOHDF5 header file */
+#define METADATA_GROUP "Parameters and Global Attributes"
+
+/* 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);           \
+              exit (-1);                                                      \
+            }                                                                 \
+          } while (0)
+
+/*****************************************************************************/
+/*                           global variables                                */
+/*****************************************************************************/
+static int   nprocs = 0;           /* number of processors for IOHDF5 chunked data */
+static int   unchunked = 0;        /* flag indicating chunked/unchunked data */
+static char *pathname = NULL;      /* pathname of the current object */
+static int ntimelevels = 1;        /* value of the timelevel attribute */
+static const char *groupname = NULL; /* value of the groupname attribute */
+
+/*****************************************************************************/
+/*                           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       Tue 11 October 2005
+   @author     Thomas Radke
+   @desc
+               Main routine of the CarpetIOHDF5-to-IOHDF5 converter
+   @enddesc
+
+   @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, j;
+  int rank;
+  int *dims;
+  double timestep;
+  char *varname, *coordname, *tag;
+  double *coords, *data, *bbox, *origin, *delta;
+  hid_t infile, outfile, dataset, dataspace, attr, attrDataspace;
+  hid_t group, hdf5String;
+  hsize_t hdf5Dims[MAXDIM];
+  int iteration, timelevel;
+  char hdf5DatasetName[2 * MAXNAMESIZE];
+  const char *cactus_version = "Cactus Beta16"; /* CCTK_FullVersion (); */
+
+
+  if (argc != 6)
+  {
+    fprintf (stderr, "Usage: %s <groupname> <ntimelevels> <nprocs> <inputfile> <outputfile>\n", argv[0]);
+    fprintf (stderr, "   eg. %s grid::coordinates 1 4 gxx-CarpetIOHDF5.h5 gxx-IOHDF5.h5\n", argv[0]);
+    return (0);
+  }
+
+  groupname = argv[1];
+  ntimelevels = atoi (argv[2]);
+  nprocs = atoi (argv[3]);
+
+  infile = H5Fopen (argv[4], H5F_ACC_RDONLY, H5P_DEFAULT);
+  if (infile < 0)
+  {
+    fprintf (stderr, "Could not open CarpetIOHDF5 input file '%s'\n", argv[4]);
+    return (-1);
+  }
+
+  outfile = H5Fcreate (argv[5], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+  if (outfile < 0)
+  {
+    fprintf (stderr, "Could not create HDF5 output file '%s'\n", argv[5]);
+    return (-1);
+  }
+
+  printf ("\n  ---------------------------------------\n"
+            "  Cactus CarpetIOHDF5-to-IOHDF5 Converter\n"
+            "  ---------------------------------------\n");
+
+  CHECK_ERROR (hdf5String = H5Tcopy (H5T_C_S1));
+
+#if 0
+  /* read the metadata group from the CarpetIOHDF5 file */
+  CHECK_ERROR (group = H5Gopen (infile, METADATA_GROUP));
+
+  CHECK_ERROR (attr = H5Aopen_name (group, "nioprocs"));
+  CHECK_ERROR (H5Aread (attr, H5T_NATIVE_INT, &nprocs));
+  CHECK_ERROR (H5Aclose (attr));
+
+  CHECK_ERROR (H5Gclose (group));
+#endif
+
+  /* create the metadata group in the IOHDF5 file */
+  CHECK_ERROR (group = H5Gcreate (outfile, GLOBAL_ATTRIBUTES_GROUP, 0));
+  CHECK_ERROR (attrDataspace = H5Screate (H5S_SCALAR));
+
+  CHECK_ERROR (attr = H5Acreate (group, "nprocs", H5T_NATIVE_INT,
+                                 attrDataspace, H5P_DEFAULT));
+  CHECK_ERROR (H5Awrite (attr, H5T_NATIVE_INT, &nprocs));
+  CHECK_ERROR (H5Aclose (attr));
+
+  CHECK_ERROR (attr = H5Acreate (group, "ioproc_every", H5T_NATIVE_INT,
+                                 attrDataspace, H5P_DEFAULT));
+  CHECK_ERROR (H5Awrite (attr, H5T_NATIVE_INT, &nprocs));
+  CHECK_ERROR (H5Aclose (attr));
+
+  CHECK_ERROR (attr = H5Acreate (group, "unchunked", H5T_NATIVE_INT,
+                                 attrDataspace, H5P_DEFAULT));
+  unchunked = nprocs == 1;
+  CHECK_ERROR (H5Awrite (attr, H5T_NATIVE_INT, &unchunked));
+  CHECK_ERROR (H5Aclose (attr));
+
+  CHECK_ERROR (H5Tset_size (hdf5String, strlen (cactus_version)));
+  CHECK_ERROR (attr = H5Acreate (group, "Cactus version", hdf5String,
+                                 attrDataspace, H5P_DEFAULT));
+  CHECK_ERROR (H5Awrite (attr, hdf5String, cactus_version));
+  CHECK_ERROR (H5Aclose (attr));
+
+  CHECK_ERROR (H5Gclose (group));
+
+  /* copy datasets as we traverse through the input file */
+  pathname = "";
+  CHECK_ERROR (H5Giterate (infile, "/", NULL, CopyObject, &outfile));
+
+  CHECK_ERROR (H5Sclose (attrDataspace));
+  CHECK_ERROR (H5Tclose (hdf5String));
+  CHECK_ERROR (H5Fclose (outfile));
+  CHECK_ERROR (H5Fclose (infile));
+
+  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, attr, attr_dataspace, attr_datatype, datatype, dataspace, dataset;
+  H5G_stat_t objectinfo;
+  char *current_pathname, *name;
+  size_t objectsize;
+  int i, iteration, timelevel;
+  char *data;
+   
+ 
+  /* skip the CarpetIOHDF5 metadata group */
+  if (! strcmp (objectname, METADATA_GROUP))
+  {
+    return (0);
+  }
+
+  /* check the type of the current object */
+  CHECK_ERROR (H5Gget_objinfo (from, objectname, 0, &objectinfo));
+  if (objectinfo.type != H5G_DATASET)
+  {
+    fprintf (stderr, "WARNING: Found object '%s/%s' which is not a dataset ! "
+                     "Object will not be copied.\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);
+  printf ("  copying dataset '%s'\n", pathname);
+
+  /* get the output object identifier */
+  to = *(hid_t *) _to;
+
+  CHECK_ERROR (from = H5Dopen (from, objectname));
+  CHECK_ERROR (attr = H5Aopen_name (from, "name"));
+  CHECK_ERROR (datatype = H5Aget_type (attr));
+  CHECK_ERROR (objectsize = H5Tget_size (datatype));
+  data = malloc (objectsize + 1);
+  CHECK_ERROR (H5Aread (attr, datatype, data));
+  data[objectsize] = 0;
+  CHECK_ERROR (H5Tclose (datatype));
+  CHECK_ERROR (H5Aclose (attr));
+
+  CHECK_ERROR (attr = H5Aopen_name (from, "timestep"));
+  CHECK_ERROR (H5Aread (attr, H5T_NATIVE_INT, &iteration));
+  CHECK_ERROR (H5Aclose (attr));
+
+  CHECK_ERROR (attr = H5Aopen_name (from, "group_timelevel"));
+  CHECK_ERROR (H5Aread (attr, H5T_NATIVE_INT, &timelevel));
+  CHECK_ERROR (H5Aclose (attr));
+
+  /* build the new name for the PUGH dataset */
+  name = malloc (objectsize + 100);
+  sprintf (name, "%s timelevel %d at iteration %d", data, timelevel, iteration);
+  free (data);
+
+  CHECK_ERROR (dataspace = H5Dget_space (from));
+  CHECK_ERROR (datatype = H5Dget_type (from));
+  objectsize = H5Tget_size (datatype); 
+  if (H5Sis_simple (dataspace)) {
+    objectsize *= H5Sget_simple_extent_npoints (dataspace);
+  }
+
+  data = malloc (objectsize);
+  CHECK_ERROR (H5Dread (from, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, data));
+
+  if (! unchunked) {
+    CHECK_ERROR (to = H5Gcreate (to, name, 0));
+  }
+  for (i = 0; i < nprocs; i++) {
+    char chunkname[20];
+    sprintf (chunkname, "chunk%d", i);
+    CHECK_ERROR (dataset = H5Dcreate (to, unchunked ? name : chunkname,
+                                      datatype, dataspace, H5P_DEFAULT));
+    CHECK_ERROR (H5Dwrite (dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+                           data));
+    if (i + 1 < nprocs) {
+      CHECK_ERROR (H5Dclose (dataset));
+    }
+  }
+  free (name);
+  free (data);
+  CHECK_ERROR (H5Sclose (dataspace));
+  CHECK_ERROR (H5Tclose (datatype));
+
+  to = unchunked ? dataset : to;
+
+  /* copy Carpet attributes */
+  CHECK_ERROR (H5Aiterate (from, NULL, CopyAttribute, &to));
+  CHECK_ERROR (H5Dclose (from));
+
+  /* add attributes which aren't stored by Carpet but needed by PUGH */
+  CHECK_ERROR (dataspace = H5Screate (H5S_SCALAR));
+
+  const int grouptype = 403; /* CCTK_ARRAY */
+  CHECK_ERROR (attr = H5Acreate (to, "grouptype", H5T_NATIVE_INT,
+                                 dataspace, H5P_DEFAULT));
+  CHECK_ERROR (H5Awrite (attr, H5T_NATIVE_INT, &grouptype));
+  CHECK_ERROR (H5Aclose (attr));
+
+  CHECK_ERROR (attr = H5Acreate (to, "ntimelevels", H5T_NATIVE_INT,
+                                 dataspace, H5P_DEFAULT));
+  CHECK_ERROR (H5Awrite (attr, H5T_NATIVE_INT, &ntimelevels));
+  CHECK_ERROR (H5Aclose (attr));
+
+  CHECK_ERROR (datatype = H5Tcopy (H5T_C_S1));
+  CHECK_ERROR (H5Tset_size (datatype, strlen (groupname)));
+  CHECK_ERROR (attr = H5Acreate (to, "groupname", datatype,
+                                 dataspace, H5P_DEFAULT));
+  CHECK_ERROR (H5Awrite (attr, datatype, groupname));
+  CHECK_ERROR (H5Aclose (attr));
+  CHECK_ERROR (H5Tclose (datatype));
+
+  CHECK_ERROR (H5Sclose (dataspace));
+
+  if (unchunked) {
+    CHECK_ERROR (H5Dclose (to));
+  } else {
+    CHECK_ERROR (H5Gclose (to));
+  }
+
+  /* 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);
+}