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git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@3 7842ec3a-9562-4be5-9c5b-06ba18f2b668

1 files changed, 217 insertions, 0 deletions

diff --git a/src/ioHDF5UtilGH.h b/src/ioHDF5UtilGH.h
new file mode 100644
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--- /dev/null
+++ b/src/ioHDF5UtilGH.h
@@ -0,0 +1,217 @@
+ /*@@
+   @header    ioHDF5UtilGH.h
+   @date      Fri Oct 6 2000
+   @author    Thomas Radke
+   @desc 
+              The GH extensions structure for IOHDF5Util.
+   @version $Id$
+ @@*/
+
+#ifndef _IOUTILHDF5_IOUTILHDF5GH_H_
+#define _IOUTILHDF5_IOUTILHDF5GH_H_
+
+/* include the HDF5 header file */
+#include <hdf5.h>
+
+
+/*****************************************************************************/
+/* some useful macros                                                        */
+/*****************************************************************************/
+/* Check error flags from HDF5 calls */
+#define IOHDF5_ERROR(fn_call)                                                 \
+    do                                                                        \
+    {                                                                         \
+      int error_code = fn_call;                                               \
+                                                                              \
+                                                                              \
+      if (error_code < 0)                                                     \
+      {                                                                       \
+        CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,                  \
+                    "HDF5 call '%s' returned error code %d\n",                \
+                    #fn_call, error_code);                                    \
+      }                                                                       \
+    } while (0)
+
+/* macro for writing an attribute */
+#define WRITE_ATTRIBUTE(name, value, dataset, dataspace, dim, datatype)       \
+          do                                                                  \
+          {                                                                   \
+            int len;                                                          \
+            hid_t attr;                                                       \
+            void *val = value;                                                \
+            hsize_t arrayDim = dim;                                           \
+                                                                              \
+                                                                              \
+            if (H5Tget_class (datatype) == H5T_STRING)                        \
+            {                                                                 \
+              len = strlen ((char *) val);                                    \
+              if (len == 0)      /* HDF5 doesn't like zero-len strings */     \
+              {                                                               \
+                len++;                                                        \
+              }                                                               \
+              IOHDF5_ERROR (H5Tset_size (datatype, len));                     \
+            }                                                                 \
+            if (arrayDim > 0)                                                 \
+            {                                                                 \
+              IOHDF5_ERROR (H5Sset_extent_simple (dataspace, 1,               \
+                                   &arrayDim, NULL));                         \
+            }                                                                 \
+            IOHDF5_ERROR (attr = H5Acreate (dataset, name, datatype,          \
+                                 dataspace, H5P_DEFAULT));                    \
+            IOHDF5_ERROR (H5Awrite (attr, datatype, val));                    \
+            IOHDF5_ERROR (H5Aclose (attr));                                   \
+          } while (0);
+
+/* macro for reading an attribute */
+#define READ_ATTRIBUTE(dataset, attrname, requested_type, buffer)             \
+          do                                                                  \
+          {                                                                   \
+            hid_t attr, attrtype;                                             \
+            hsize_t asize = 0;                                                \
+                                                                              \
+                                                                              \
+            if ((attr = H5Aopen_name (dataset, attrname)) < 0)                \
+            {                                                                 \
+              CCTK_WARN (1, "Can't find " attrname " attribute");             \
+            }                                                                 \
+            if (requested_type == H5T_C_S1)                                   \
+            {                                                                 \
+              IOHDF5_ERROR (attrtype = H5Aget_type (attr));                   \
+              IOHDF5_ERROR (asize = H5Tget_size (attrtype));                  \
+              if (asize + 1 >= sizeof (buffer))                               \
+              {                                                               \
+                CCTK_WARN (1, "Can't read " attrname " attribute (too long)");\
+              }                                                               \
+            }                                                                 \
+            else                                                              \
+            {                                                                 \
+              attrtype = requested_type;                                      \
+            }                                                                 \
+            if (H5Aread (attr, attrtype, buffer) < 0)                         \
+            {                                                                 \
+              CCTK_WARN (1, "Can't read " attrname " attribute");             \
+            }                                                                 \
+            if (requested_type == H5T_C_S1)                                   \
+            {                                                                 \
+              ((char *) buffer)[asize] = 0;                                   \
+              IOHDF5_ERROR (H5Tclose (attrtype));                             \
+            }                                                                 \
+            IOHDF5_ERROR (H5Aclose (attr));                                   \
+          } while (0)
+
+
+/* Mapping off CCTK datatypes to HDF5 datatypes */
+#define IOHDF5_REAL4   H5T_NATIVE_FLOAT
+
+#ifdef  CCTK_REAL_PRECISION_16
+#define IOHDF5_REAL    H5T_NATIVE_LDOUBLE
+#elif   CCTK_REAL_PRECISION_8
+#define IOHDF5_REAL    H5T_NATIVE_DOUBLE
+#elif   CCTK_REAL_PRECISION_4
+#define IOHDF5_REAL    H5T_NATIVE_FLOAT
+#endif
+
+#define IOHDF5_INT     (sizeof (CCTK_INT) == sizeof (int) ?                   \
+                        H5T_NATIVE_INT : H5T_NATIVE_SHORT)
+#define IOHDF5_INT4    (sizeof (int) == 4 ?                                   \
+                        H5T_NATIVE_INT : H5T_NATIVE_SHORT)
+#define IOHDF5_CHAR    H5T_NATIVE_CHAR
+
+
+/* Constants to index timers within the timers array */
+#define CP_PARAMETERS_TIMER   0
+#define CP_VARIABLES_TIMER    1
+#define CP_TOTAL_TIMER        2
+#define RECOVERY_TIMER        3
+#define IOHDF5_NUM_TIMERS     4
+
+/* names of the groups that hold global attributes and parameters */
+#define GLOBAL_ATTRIBUTES_GROUP "Global Attributes"
+#define CACTUS_PARAMETERS_GROUP "Cactus Parameters"
+#define ALL_PARAMETERS          "All Parameters"
+
+
+/* Geometry information structure for output variable */
+/* FIXME: allocate arrays dynamically */
+#define IOHDF5_MAXDIM 5
+typedef struct
+{
+  int vdim;
+  int sdim;
+  int direction[IOHDF5_MAXDIM];
+  int origin[IOHDF5_MAXDIM];
+  int length[IOHDF5_MAXDIM];
+  int downsample[IOHDF5_MAXDIM];
+  int actlen[IOHDF5_MAXDIM];       /* actual index slab length (by PUGHSlab)*/
+} ioHDF5Geo_t;
+
+
+/* Structure describing a given recovery file */
+typedef struct
+{
+  int is_HDF5_file;         /* flag indicating valid file info */
+  hid_t file;               /* HDF5 file handle */
+  char *filename;           /* complete file name for recovery */
+  int nprocs;               /* number of total processors */
+  int ioproc;               /* the associated IO processor */
+  int ioproc_every;         /* how many IO processors there are */
+  int unchunked;            /* whether data was written chunked or unchunked */
+} fileinfo_t;
+
+
+/* IOHDF5Util GH extension structure */
+typedef struct
+{
+  /* while HDF5 error output is disabled
+     we keep the original error printing routine and its argument in here */
+  H5E_auto_t print_error_fn;
+  void      *print_error_fn_arg;
+
+  /* predefined dataspaces for writing scalar and array attributes */
+  hid_t scalar_dataspace, array_dataspace;
+
+  /* predefined datatype for writing CCTK_COMPLEX types */
+  hid_t IOHDF5_COMPLEX;
+
+  /* predefined datatype for writing C string string attributes */
+  hid_t IOHDF5_STRING;
+
+} ioHDF5UtilGH;
+
+
+#ifdef __cplusplus
+extern "C"
+{
+#endif
+
+/* exported functions */
+int IOHDF5Util_ParseVarsForOutput (const char *var_list, 
+                                   char do_output[], 
+                                   ioHDF5Geo_t geo_output[]);
+void IOHDF5Util_DefaultGeo (ioHDF5Geo_t *slab);
+void IOHDF5Util_DumpParameters (cGH *GH, hid_t group);
+void IOHDF5Util_DumpGHExtensions (cGH *GH, hid_t group);
+int  IOHDF5Util_DumpGH (cGH *GH, int timers[], hid_t file);
+void IOHDF5Util_DumpCommonAttributes (cGH *GH,
+                                      int index,
+                                      int timelevel,
+                                      CCTK_INT global_shape[],
+                                      ioHDF5Geo_t *slab,
+                                      hid_t dataset);
+int IOHDF5Util_DumpVar (cGH *GH,
+                        int index,
+                        int timelevel,
+                        ioHDF5Geo_t *slab,
+                        hid_t file,
+                        int check_exisiting_objects);
+int IOHDF5Util_RecoverParameters (fileinfo_t *filenfo);
+int IOHDF5Util_RecoverGHextensions (cGH *GH,
+                                    fileinfo_t *filenfo);
+int IOHDF5Util_RecoverVariables (cGH *GH,
+                                 fileinfo_t *filenfo);
+
+#ifdef __cplusplus
+} // extern "C"
+#endif
+
+#endif  /* _IOUTILHDF5_IOUTILHDF5GH_H_ */