Added utility program. See ThornGuide for details.

git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5/trunk@77 4825ed28-b72c-4eae-9704-e50c059e567d

3 files changed, 270 insertions, 1 deletions

diff --git a/src/make.configuration.defn b/src/make.configuration.defn
index 4642d40..d51e272 100644
--- a/src/make.configuration.defn
+++ b/src/make.configuration.defn
@@ -1,4 +1,8 @@
 # make.configuration.defn for IOHDF5
 
-# add the recombiner to the Cactus utitlity tools
+# add the recombiner and the IEEEIO converter to the Cactus utitlity tools
 ALL_UTILS += hdf5_recombiner
+
+ifeq ($(findstring CactusExternal/FlexIO,$(THORNS)),CactusExternal/FlexIO)
+ALL_UTILS += hdf5_convert_from_ieeeio
+endif
diff --git a/src/make.configuration.deps b/src/make.configuration.deps
index db013a6..1c3ef59 100644
--- a/src/make.configuration.deps
+++ b/src/make.configuration.deps
@@ -1,10 +1,26 @@
+# linking rule for hdf5_recombiner
 $(UTIL_DIR)$(DIRSEP)hdf5_recombiner: $(BUILD_DIR)$(DIRSEP)IOHDF5$(DIRSEP)hdf5_recombiner.o
 	@echo Creating hdf5_recombiner in $(UTIL_DIR) from $<
 	if [ ! -d $(UTIL_DIR) ]; then $(MKDIR) $(MKDIRFLAGS) $(UTIL_DIR) ; fi
 	$(LD) $(CREATEEXE)$(OPTIONSEP)$@ $(DEBUG_LD) $(LDFLAGS) $(EXTRAFLAGS) $< -L$(HDF5_LIB_DIRS) $(addprefix -l, $(HDF5_LIBS)) -lm
 
+# compile rule for hdf5_recombiner
 $(BUILD_DIR)$(DIRSEP)IOHDF5$(DIRSEP)hdf5_recombiner.o: $(PACKAGE_DIR)$(DIRSEP)AlphaThorns$(DIRSEP)IOHDF5$(DIRSEP)src$(DIRSEP)util$(DIRSEP)hdf5_recombiner.c
 	@echo Compiling $<
 	if [ ! -d $(BUILD_DIR)$(DIRSEP)IOHDF5 ]; then $(MKDIR) $(MKDIRFLAGS) $(BUILD_DIR)$(DIRSEP)IOHDF5 ; fi
 	cd $(BUILD_DIR)$(DIRSEP)IOHDF5
 	$(CC) $< -DCCODE $(CFLAGS) -I$(CONFIG) -I$(BINDINGS_DIR)$(DIRSEP)include -I$(FLESH_DIR)$(DIRSEP)include -I$(CCTK_HOME)$(DIRSEP)arrangements -I$(HDF5_INC_DIRS) $(CCOMPILEONLY)$(OPTIONSEP)$@
+
+
+# linking rule for hdf5_convert_from_ieeeio
+$(UTIL_DIR)$(DIRSEP)hdf5_convert_from_ieeeio: $(BUILD_DIR)$(DIRSEP)IOHDF5$(DIRSEP)hdf5_convert_from_ieeeio.o
+	@echo Creating hdf5_convert_from_ieeeio in $(UTIL_DIR) from $<
+	if [ ! -d $(UTIL_DIR) ]; then $(MKDIR) $(MKDIRFLAGS) $(UTIL_DIR) ; fi
+	$(LD) $(CREATEEXE)$(OPTIONSEP)$@ $(DEBUG_LD) $(LDFLAGS) $(EXTRAFLAGS) $< -L$(CCTK_LIBDIR) -lFlexIO -L$(HDF5_LIB_DIRS) $(addprefix -l, $(HDF5_LIBS)) -lm
+
+# compile rule for hdf5_convert_from_ieeeio
+$(BUILD_DIR)$(DIRSEP)IOHDF5$(DIRSEP)hdf5_convert_from_ieeeio.o: $(PACKAGE_DIR)$(DIRSEP)AlphaThorns$(DIRSEP)IOHDF5$(DIRSEP)src$(DIRSEP)util$(DIRSEP)hdf5_convert_from_ieeeio.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$(CCTK_HOME)$(DIRSEP)arrangements -I$(HDF5_INC_DIRS) -I$(FLEXIO_INC_DIRS) $(CCOMPILEONLY)$(OPTIONSEP)$@
diff --git a/src/util/hdf5_convert_from_ieeeio.c b/src/util/hdf5_convert_from_ieeeio.c
new file mode 100644
index 0000000..d1b1f46
--- /dev/null
+++ b/src/util/hdf5_convert_from_ieeeio.c
@@ -0,0 +1,249 @@
+ /*@@
+   @file      hdf5_convert_from_ieeeio.c
+   @date      Fri 14 Dec 2001
+   @author    Thomas Radke
+   @desc
+              Utility program to convert IOFlexIO datafiles into IOHDF5
+              datafiles.
+   @enddesc
+   @version   $Id$
+ @@*/
+
+#define  MAXDIM       3
+#define  MAXNAMESIZE  100
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <assert.h>
+
+/* FlexIO includes */
+#include "IOProtos.h"
+#include "IEEEIO.h"
+
+/* HDF5 include */
+#include <hdf5.h>
+
+int main (int argc, char **argv)
+{
+  int i, j;
+  IOFile infile;
+  int nDatasets, nAttributes;
+  int ieeeDatatype, rank, dims [MAXDIM];
+  int attrNumberType;
+  Long attrLen;
+  char attrName [MAXNAMESIZE];
+  void *data, *attrData;
+  hid_t outfile, dataset, dataspace, attribute, attrDataspace, hdf5Datatype;
+  hid_t hdf5String;
+  hsize_t hdf5Dims [MAXDIM];
+  herr_t (*old_func) (void *);
+  void *old_client_data;
+  int iteration, timelevel;
+  char ieeeDatasetName [MAXNAMESIZE], hdf5DatasetName [2 * MAXNAMESIZE];
+
+
+  if (argc <= 2) {
+    printf ("Usage: %s <inputfile> <outputfile>\n", argv [0]);
+    printf ("   eg. %s foo.ieee bar.hdf5\n", argv [0]);
+    return (0);
+  }
+
+  infile = IEEEopen (argv [1], "r");
+  if (! IOisValid (infile)) {
+    printf ("Could not open 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 output file '%s'\n", argv [2]);
+    return (-1);
+  }
+
+  hdf5String = H5Tcopy (H5T_C_S1);
+
+  nDatasets = IOnDatasets (infile);
+  printf ("Input file contains %d datasets\n", nDatasets);
+
+  for (i = 0; i < nDatasets; i++)
+  {
+    if (IOreadInfo (infile, &ieeeDatatype, &rank, dims, MAXDIM) <= 0)
+    {
+      fprintf (stderr, "Cannot read info of datatset %d, skipping ...\n", i);
+      continue;
+    }
+
+    /* retrieve name and iteration attribute of dataset */
+    strcpy (attrName, "name");
+    j = IOreadAttributeInfo (infile, attrName, &attrNumberType, &attrLen);
+    if (j < 0)
+    {
+      fprintf (stderr,
+               "Cannot find name attribute of dataset %d, skipping ...\n", i);
+      continue;
+    }
+    if (IOreadAttribute (infile, j, ieeeDatasetName) < 0)
+    {
+      fprintf (stderr,
+               "Cannot read name attribute of dataset %d, skipping ...\n", i);
+      continue;
+    }
+    strcpy (attrName, "iteration");
+    j = IOreadAttributeInfo (infile, attrName, &attrNumberType, &attrLen);
+    if (j < 0)
+    {
+      fprintf (stderr, "Cannot find iteration attribute of dataset %d, "
+               "skipping ...\n", i);
+      continue;
+    }
+    if (IOreadAttribute (infile, j, &iteration) < 0)
+    {
+      fprintf (stderr, "Cannot read iteration attribute of dataset %d, "
+               "skipping ...\n", i);
+      continue;
+    }
+    strcpy (attrName, "timelevel");
+    j = IOreadAttributeInfo (infile, attrName, &attrNumberType, &attrLen);
+    if (j < 0)
+    {
+      fprintf (stderr, "Cannot find timelevel attribute of dataset %d,\n"
+               "assuming Cactus 3.x dataset with implicite timelevel 0 "
+               "...\n", i);
+      timelevel = 0;
+    }
+    else if (IOreadAttribute (infile, j, &timelevel) < 0)
+    {
+      fprintf (stderr, "Cannot read timelevel attribute of dataset %d, "
+               "skipping ...\n", i);
+      continue;
+    }
+
+    switch (ieeeDatatype)
+    {
+      case BYTE:
+      case CHAR:
+        hdf5Datatype = H5T_NATIVE_CHAR; break;
+
+      case FLOAT32:
+        hdf5Datatype = H5T_NATIVE_FLOAT; break;
+
+      case FLOAT64:
+        hdf5Datatype = H5T_NATIVE_DOUBLE; break;
+
+      case INT32:
+        hdf5Datatype = H5T_NATIVE_INT; break;
+
+      default:
+        fprintf (stderr, "Unknown datatype %d for dataset %d, skipping ...\n",
+                 ieeeDatatype, i);
+        continue;
+    }
+
+    /* convert ordering (FlexIO uses fortran order, HDF5 uses C order) */
+    for (j = 0; j < rank; j++)
+    {
+      hdf5Dims [j] = dims [rank - j - 1];
+    }
+    dataspace = H5Screate_simple (rank, hdf5Dims, NULL);
+    assert (dataspace >= 0);
+
+    sprintf (hdf5DatasetName, "/%s@%d@%d", ieeeDatasetName, iteration, timelevel);
+    dataset = H5Dcreate (outfile, hdf5DatasetName, hdf5Datatype, dataspace,
+                         H5P_DEFAULT);
+    assert (dataset >= 0);
+
+    data = malloc (IOnBytes (ieeeDatatype, rank, dims));
+    IOread (infile, data);
+    assert (H5Dwrite (dataset, hdf5Datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+                      data) >= 0);
+
+    nAttributes = IOnAttributes (infile);
+    printf ("Processing dataset '%s' with %d attributes\n",
+            ieeeDatasetName, nAttributes);
+
+    for (j = 0; j < nAttributes; j++)
+    {
+      int len;
+
+      if (IOreadIndexedAttributeInfo (infile, j, attrName, &attrNumberType,
+                                      &attrLen, MAXNAMESIZE) < 0)
+      {
+#if  0
+        /* it's only a bug if IOreadIndexedAttributeInfo() returns -1 */
+        printf ("Cannot read info of attribute %d, skipping ...\n", j);
+        continue;
+#endif
+      }
+
+      len = (int) attrLen;
+      /* I don't know why but I have to add one byte - otherwise
+         it crashes sometimes when freeing this memory */
+      attrData = malloc (1 + IOnBytes (attrNumberType, 1, &len));
+      if (IOreadAttribute (infile, j, attrData) < 0)
+      {
+        fprintf (stderr, "Cannot read value of attribute %d, skipping ...\n",j);
+        continue;
+      }
+
+      switch (attrNumberType)
+      {
+        case BYTE:
+        case CHAR:
+          hdf5Datatype = hdf5String;
+          if (len > 1)
+          {
+            len--;              /* cut trailing '\0' */
+          }
+          H5Tset_size (hdf5Datatype, len);
+          attrDataspace = H5Screate (H5S_SCALAR);
+          break;
+
+        case FLOAT64:
+          hdf5Datatype = H5T_NATIVE_DOUBLE;
+          hdf5Dims [0] = len;
+          attrDataspace = H5Screate_simple (1, hdf5Dims, NULL);
+          break;
+
+        case INT32:
+          hdf5Datatype = H5T_NATIVE_INT;
+          hdf5Dims [0] = len;
+          attrDataspace = H5Screate_simple (1, hdf5Dims, NULL);
+          break;
+
+        default:
+          fprintf (stderr, "Unknown datatype %d for attribute %s, skipping "
+                   "...\n", attrNumberType, attrName);
+          continue;
+      }
+
+      assert (attrDataspace >= 0);
+
+      /* turn off error handling during check
+               for an already existing attribute */
+      H5Eget_auto (&old_func, &old_client_data);
+      H5Eset_auto (NULL, NULL);
+      H5Adelete (dataset, attrName);
+      H5Eset_auto (old_func, old_client_data);
+
+      attribute = H5Acreate (dataset, attrName, hdf5Datatype,
+                             attrDataspace, H5P_DEFAULT);
+      assert (attribute >= 0);
+      assert (H5Awrite (attribute, hdf5Datatype, attrData) >= 0);
+      H5Sclose (attrDataspace);
+      H5Aclose (attribute);
+
+      free (attrData);
+    }
+
+    H5Dclose (dataset);
+    H5Sclose (dataspace);
+    free (data);
+  }
+
+  H5Tclose (hdf5String);
+  H5Fclose (outfile);
+  IOclose (infile);
+
+  return (0);
+}