Added utility program to convert SDF datafiles into HDF5 so that they can be

imported into Cactus (using the filereader).
Still a prototype version only, therefore no documentation yet.


git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5/trunk@205 4825ed28-b72c-4eae-9704-e50c059e567d

3 files changed, 244 insertions, 0 deletions

diff --git a/src/make.configuration.defn b/src/make.configuration.defn
index c52aca4..b44abf3 100644
--- a/src/make.configuration.defn
+++ b/src/make.configuration.defn
@@ -7,3 +7,7 @@ ifeq ($(findstring CactusExternal/FlexIO,$(THORNS)),CactusExternal/FlexIO)
 ALL_UTILS += hdf5_convert_from_ieeeio
 FLEXIO_INC_DIRS = $(CCTK_HOME)$(DIRSEP)arrangements/CactusExternal/FlexIO/src
 endif
+
+ifeq ($(findstring CactusIO/IOSDF,$(THORNS)),CactusIO/IOSDF)
+ALL_UTILS += hdf5_convert_from_sdf
+endif
diff --git a/src/make.configuration.deps b/src/make.configuration.deps
index 3f8f3f8..f9d61ae 100644
--- a/src/make.configuration.deps
+++ b/src/make.configuration.deps
@@ -31,3 +31,23 @@ $(BUILD_DIR)$(DIRSEP)IOHDF5$(DIRSEP)hdf5_convert_from_ieeeio.o: $(PACKAGE_DIR)$(
 	if [ ! -d $(BUILD_DIR)$(DIRSEP)IOHDF5 ]; then $(MKDIR) $(MKDIRFLAGS) $(BUILD_DIR)$(DIRSEP)IOHDF5 ; fi
 	cd $(BUILD_DIR)$(DIRSEP)IOHDF5
 	$(CC) $< -DCCODE $(CFLAGS) -DANSI -I$(CONFIG) -I$(BINDINGS_DIR)$(DIRSEP)include -I$(FLESH_DIR)$(DIRSEP)include -I$(CCTK_HOME)$(DIRSEP)arrangements $(HDF5_INC_DIRS:%=-I%) $(FLEXIO_INC_DIRS:%=-I%) $(SYS_INC_DIRS:%=-I%) $(CCOMPILEONLY)$(OPTIONSEP)$@
+
+
+# need to extract SDF includes and libs from the bindings makefiles
+# (those are not included when building utilities)
+SDF_INC_DIRS := $(shell grep INC_DIRS $(CONFIG)/../bindings/Configuration/IOSDF/make.configuration.defn | cut -f2 -d'=')
+SDF_LIB_DIRS := $(shell grep LIBDIRS $(CONFIG)/../bindings/Configuration/make.link | cut -f2 -d'=')
+SDF_LIBS := $(shell grep LIBS $(CONFIG)/../bindings/Configuration/make.link | cut -f2 -d'=')
+
+# linking rule for hdf5_convert_from_sdf
+$(UTIL_DIR)$(DIRSEP)hdf5_convert_from_sdf: $(BUILD_DIR)$(DIRSEP)IOHDF5$(DIRSEP)hdf5_convert_from_sdf.o
+	@echo Creating hdf5_convert_from_sdf in $(UTIL_DIR) from $<
+	if [ ! -d $(UTIL_DIR) ]; then $(MKDIR) $(MKDIRFLAGS) $(UTIL_DIR) ; fi
+	$(LD) $(CREATEEXE)$(OPTIONSEP)$@ $(DEBUG_LD) $(LDFLAGS) $(EXTRAFLAGS) $< -L$(CCTK_LIBDIR) $(SDF_LIB_DIRS:%=-L%) $(SDF_LIBS:%=-l%) $(HDF5_LIB_DIRS:%=-L%) $(HDF5_LIBS:%=-l%) -lm
+
+# compile rule for hdf5_convert_from_sdf
+$(BUILD_DIR)$(DIRSEP)IOHDF5$(DIRSEP)hdf5_convert_from_sdf.o: $(PACKAGE_DIR)$(DIRSEP)CactusPUGHIO$(DIRSEP)IOHDF5$(DIRSEP)src$(DIRSEP)util$(DIRSEP)hdf5_convert_from_sdf.c
+	@echo Compiling $<
+	if [ ! -d $(BUILD_DIR)$(DIRSEP)IOHDF5 ]; then $(MKDIR) $(MKDIRFLAGS) $(BUILD_DIR)$(DIRSEP)IOHDF5 ; fi
+	cd $(BUILD_DIR)$(DIRSEP)IOHDF5
+	$(CC) $< -DCCODE $(CFLAGS) -DANSI -I$(CONFIG) -I$(BINDINGS_DIR)$(DIRSEP)include -I$(FLESH_DIR)$(DIRSEP)include -I$(SDF_INC_DIRS) $(HDF5_INC_DIRS:%=-I%) $(FLEXIO_INC_DIRS:%=-I%) $(SYS_INC_DIRS:%=-I%) $(CCOMPILEONLY)$(OPTIONSEP)$@
diff --git a/src/util/hdf5_convert_from_sdf.c b/src/util/hdf5_convert_from_sdf.c
new file mode 100644
index 0000000..ef0ca79
--- /dev/null
+++ b/src/util/hdf5_convert_from_sdf.c
@@ -0,0 +1,220 @@
+ /*@@
+   @file      hdf5_convert_from_sdf.c
+   @date      Tue 24 August 2004
+   @author    Thomas Radke
+   @desc
+              Utility program to convert SDF 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"
+
+/* SDF includes */
+#include <bbhutil.h>
+#include <sdf_priv.h>
+
+/* HDF5 include */
+#include <hdf5.h>
+
+#define GLOBAL_ATTRIBUTES_GROUP "Global Attributes"
+
+/* the rcs ID and its dummy function to use it */
+static const char *rcsid = "$Header$";
+CCTK_FILEVERSION(CactusPUGHIO_IOHDF5_util_hdf5_convert_from_sdf_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);           \
+              exit (-1);                                                      \
+            }                                                                 \
+          } while (0)
+
+
+ /*@@
+   @routine    main
+   @date       Tue 24 August 2004
+   @author     Thomas Radke
+   @desc
+               Main routine of the SDF-to-HDF5 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 version, rank, dsize, csize, grouptype;
+  int *dims;
+  double timestep;
+  char *varname, *groupname, *coordname, *tag;
+  gft_sdf_file_data *infile;
+  double *coords, *data, *bbox;
+  hid_t outfile, dataset, dataspace, attr, attrDataspace;
+  hid_t group, hdf5String;
+  hsize_t hdf5Dims[MAXDIM];
+  int iteration, timelevel, ntimelevels;
+  char hdf5DatasetName[2 * MAXNAMESIZE];
+
+
+  if (argc <= 2)
+  {
+    fprintf (stderr, "Usage: %s <inputfile> <outputfile>\n", argv[0]);
+    fprintf (stderr, "   eg. %s foo.sdf bar.h5\n", argv[0]);
+    return (0);
+  }
+
+  infile = gft_open_sdf_file (argv[1]);
+  if (! infile)
+  {
+    printf ("Could not open SDF input file '%s'\n", argv[1]);
+    return (-1);
+  }
+
+  outfile = H5Fcreate (argv[2], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+  if (outfile < 0)
+  {
+    fprintf (stderr, "Could not create HDF5 output file '%s'\n", argv[2]);
+    return (-1);
+  }
+
+  printf ("\n  ----------------------------\n"
+            "  Cactus SDF-to-HDF5 Converter\n"
+            "  ----------------------------\n");
+
+  /* add a dummy GLOBAL_ATTRIBUTES_GROUP so that the HDF5 file is recognized as
+     unchunked Cactus data */
+  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));
+  i = 1;
+  CHECK_ERROR (H5Awrite (attr, H5T_NATIVE_INT, &i));
+  CHECK_ERROR (H5Aclose (attr));
+
+  CHECK_ERROR (attr = H5Acreate (group, "ioproc_every", H5T_NATIVE_INT,
+                                      attrDataspace, H5P_DEFAULT));
+  i = 1;
+  CHECK_ERROR (H5Awrite (attr, H5T_NATIVE_INT, &i));
+  CHECK_ERROR (H5Aclose (attr));
+
+  CHECK_ERROR (attr = H5Acreate (group, "unchunked", H5T_NATIVE_INT,
+                                      attrDataspace, H5P_DEFAULT));
+  i = 1;
+  CHECK_ERROR (H5Awrite (attr, H5T_NATIVE_INT, &i));
+  CHECK_ERROR (H5Aclose (attr));
+
+  CHECK_ERROR (H5Gclose (group));
+
+  CHECK_ERROR (hdf5String = H5Tcopy (H5T_C_S1));
+
+  /*** FIXME: get iteration number and timelevel information from user ***/
+  iteration = timelevel = 0;
+  ntimelevels = 1;
+  grouptype = CCTK_GF;
+  groupname = "grid::coordinates";
+
+  while (low_read_sdf_stream (1, infile->fp, &timestep, &version, &rank, &dsize,
+                              &csize, &varname, &coordname, &tag, &dims, &bbox,
+                              &coords, &data))
+  {
+    /*** FIXME: give the dataset a valid variable name ***/
+    varname = strdup ("grid::x");
+
+    printf ("Processing dataset '%s' (timestep %f)\n", varname, timestep);
+
+    /* convert from int to hsize_t */
+    for (j = 0; j < rank; j++)
+    {
+      hdf5Dims[j] = dims[j];
+    }
+    CHECK_ERROR (dataspace = H5Screate_simple (rank, hdf5Dims, NULL));
+
+    sprintf (hdf5DatasetName, "/%s timelevel %d at iteration %d",
+             varname, timelevel, iteration);
+    CHECK_ERROR (dataset = H5Dcreate (outfile, hdf5DatasetName,
+                                      H5T_NATIVE_DOUBLE,dataspace,H5P_DEFAULT));
+    CHECK_ERROR (H5Dwrite (dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
+                           H5P_DEFAULT, data));
+
+    /* attach necessary attributes */
+    CHECK_ERROR (H5Tset_size (hdf5String, strlen (groupname)));
+    CHECK_ERROR (attr = H5Acreate (dataset, "groupname", hdf5String,
+                                   attrDataspace, H5P_DEFAULT));
+    CHECK_ERROR (H5Awrite (attr, hdf5String, groupname));
+    CHECK_ERROR (H5Aclose (attr));
+
+    CHECK_ERROR (attr = H5Acreate (dataset, "grouptype", H5T_NATIVE_INT,
+                                   attrDataspace, H5P_DEFAULT));
+    CHECK_ERROR (H5Awrite (attr, H5T_NATIVE_INT, &grouptype));
+    CHECK_ERROR (H5Aclose (attr));
+
+    CHECK_ERROR (attr = H5Acreate (dataset, "ntimelevels", H5T_NATIVE_INT,
+                                   attrDataspace, H5P_DEFAULT));
+    CHECK_ERROR (H5Awrite (attr, H5T_NATIVE_INT, &ntimelevels));
+    CHECK_ERROR (H5Aclose (attr));
+
+    CHECK_ERROR (H5Dclose (dataset));
+
+    CHECK_ERROR (H5Sclose (dataspace));
+
+    free (varname);
+    free (coordname);
+    free (tag);
+    free (dims);
+    free (bbox);
+    free (coords);
+    free (data);
+
+    /*** FIXME: increment iteration number to distinguish datasets ***/
+    iteration++;
+  }
+
+  CHECK_ERROR (H5Sclose (attrDataspace));
+  CHECK_ERROR (H5Tclose (hdf5String));
+  CHECK_ERROR (H5Fclose (outfile));
+  gsfd_close (infile);
+
+  return (0);
+}