Moved a lot of code into IOHDF5Util and inherit from this thorn.

git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5/trunk@25 4825ed28-b72c-4eae-9704-e50c059e567d

1 files changed, 35 insertions, 162 deletions

diff --git a/src/ioHDF5GH.h b/src/ioHDF5GH.h
index c7134c0..5aa5926 100644
--- a/src/ioHDF5GH.h
+++ b/src/ioHDF5GH.h
@@ -1,199 +1,70 @@
  /*@@
    @header    ioHDF5GH.h
-   @date      Fri May 21 1999
+   @date      Jun 20 2000
    @author    Thomas Radke
    @desc 
-   The extensions to the GH structure from IOHDF5.
-   @history
-   @hauthor Thomas Radke @hdate May 21 1999
-   @hdesc Just copied from thorn FlexIO.
-   @endhistory
+              The extensions to the GH structure from IOHDF5.
+   @version $Id$
  @@*/
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#include <string.h>
-#include <hdf5.h>
+#ifndef _IOHDF5_IOHDF5GH_H_
+#define _IOHDF5_IOHDF5GH_H_
 
+#include "BetaThorns/IOHDF5Util/src/ioHDF5UtilGH.h"
 #include "StoreNamedData.h"
 
-
-/* names of the (empty) groups that hold GH extensions or global parameters */
-#define GHEXTENSIONS_GROUP      "GHextensions_group"
-#define GLOBAL_PARAMETERS_GROUP "global_parameters_group"
-#define GLOBAL_PARAMETERS       "global_parameters"
-
-/*****************************************************************************/
-/* some useful macros                                                        */
-/*****************************************************************************/
-/* Check error flags from HDF5 calls */
-#define CACTUS_IOHDF5_ERROR(fn_call)                                          \
-    do {                                                                      \
-      /*size_t strlen(const char *str);*/                                     \
-                                                                              \
-      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 {                                                                \
-            hid_t attr;                                                       \
-            void *val = value;                                                \
-            hsize_t arrayDim = dim;                                           \
-                                                                              \
-            if (H5Tget_class (datatype) == H5T_STRING) {                      \
-              int len = strlen ((char *) val);                                \
-                                                                              \
-              if (len == 0)      /* HDF5 doesn't like zero-len strings */     \
-                len++;                                                        \
-              CACTUS_IOHDF5_ERROR (H5Tset_size (datatype, len));              \
-            }                                                                 \
-            if (arrayDim > 0)                                                 \
-              CACTUS_IOHDF5_ERROR (H5Sset_extent_simple (dataspace, 1,        \
-                                   &arrayDim, NULL));                         \
-            CACTUS_IOHDF5_ERROR (attr = H5Acreate (dataset, name, datatype,   \
-                                 dataspace, H5P_DEFAULT));                    \
-            CACTUS_IOHDF5_ERROR (H5Awrite (attr, datatype, val));             \
-            CACTUS_IOHDF5_ERROR (H5Aclose (attr));                            \
-          } while (0);
-
-/* macro for reading an attribute */
-#define READ_ATTRIBUTE(dataset, attrname, requested_type, buffer)             \
-          { 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) {                                 \
-              CACTUS_IOHDF5_ERROR (attrtype = H5Aget_type (attr));            \
-              CACTUS_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;                                  \
-              CACTUS_IOHDF5_ERROR (H5Tclose (attrtype));                      \
-            }                                                                 \
-            CACTUS_IOHDF5_ERROR (H5Aclose (attr));                            \
-          }
-
-
-/* define the HDF5 datatypes according to CCTK_??? 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
-
-#define IOHDF5_MAXDIM 4
-
-/* structure holding necessary information about a recovery file */
-typedef struct {
-  int is_HDF5_file;         /* flag indicating valid file info */
-  hid_t fid;                /* HDF5 file handle */
-  char filename [1024];     /* 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;
-
-/* structure holding information on the output geometry */
-typedef struct ioHDF5Geo
-{
-  int vdim;                        /* dimension of the gridvariable (dynamic) */
-  int sdim;                        /* dimension of the slab (dynamic) */
-  int direction[IOHDF5_MAXDIM];    /* direction of slab (by parameter) */
-  int slab_start[IOHDF5_MAXDIM];   /* global start index  (by parameter) */
-  int length[IOHDF5_MAXDIM];       /* requested index slab length (by parameter) */
-  int actlen[IOHDF5_MAXDIM];       /* actual index slab length (by PUGHSlab)*/
-  int downs[IOHDF5_MAXDIM];        /* downsampling (by parameter) */
-} ioHDF5Geo_t;
-
 /* IOHDF5 GH extension structure */
-typedef struct IOHDF5GH {
+typedef struct
+{
 
   /* how often to output */
-  int  out1D_every;
-  int  out2D_every;
-  int  out3D_every;
+  int  out_every;
 
   /* flags indicating output for var [i] */
-  char   *do_out1D;
-  char   *do_out2D;
-  char   *do_out3D;
+  char   *do_output;
 
   /* directories in which to output */
-  char  *outdir1D;
-  char  *outdir2D;
-  char  *outdir3D;
+  char  *outdir;
 
   /* the last iteration output */
-  int   *out1D_last;
-  int   *out2D_last;
-  int   *out3D_last;
+  int   *out_last;
 
   /* filename database for opened files */
-  pNamedData *filenameList;
+  pNamedData *open_output_files;
 
   /* for restart from recovery: flags indicating whether to check for already
      existing groups/datasets to delete before creating them anew */
-  char  *checkForExistingObjects;
-
-  /* variables holding the original error printing routine and its argument */
-  H5E_auto_t printErrorFn;
-  void      *printErrorFnArg;
-
-  /* predefined dataspaces for writing scalar and array attributes */
-  hid_t scalarDataspace, arrayDataspace;
-
-  /* predefined datatype for writing CCTK_COMPLEX types */
-  hid_t IOHDF5_COMPLEX;
-
-  /* predefined datatype for writing C string string attributes */
-  hid_t IOHDF5_STRING;
+  char  *check_exisiting_objects;
 
   /* timer array for checkpointing/recovery */
-  int timers[4];
+  int timers[IOHDF5_NUM_TIMERS];
 
   /* flag to indicate request for timer output */
   int print_timing_info;
 
   /* geometry information (downsampling, zooming, etc.) */
-  ioHDF5Geo_t **out_geo; 
+  ioHDF5Geo_t *out_geo; 
+
+  /* ring buffer for list of successfully created cp files */
+  int    cp_filename_index;
+  char **cp_filename_list;
 
 } ioHDF5GH;
 
-/* function prototypes */
-int IOHDF5_Write3D (cGH *GH, int index, const char *alias);
-int IOHDF5_Write2D (cGH *GH, int index, const char *alias);
-int IOHDF5_Write1D (cGH *GH, int index, const char *alias);
+#ifdef __cplusplus
+extern "C"
+{
+#endif
 
-void IOHDF5_DumpParams (cGH *GH, hid_t group);
-void IOHDF5_DumpGHExtensions (cGH *GH, hid_t group);
-int  IOHDF5_DumpVar (cGH *GH, int index, int timelevel, ioHDF5Geo_t *geo, hid_t iof);
-void IOHDF5_DumpGH (cGH *GH, int called_from);
+/* prototypes of functions to be registered as IOHDF5's IO method */
+int IOHDF5_OutputGH (cGH *GH);
+int IOHDF5_TriggerOutput (cGH *GH, int);
+int IOHDF5_TimeFor (cGH *GH, int);
+int IOHDF5_OutputVarAs (cGH *GH, const char *var, const char *alias);
+int IOHDF5_Recover (cGH *GH, const char *basename, int called_from);
 
+/* other function prototypes */
+void IOHDF5_Write (cGH *GH, int index, const char *alias);
 int IOHDF5_WriteIsosurface (cGH *GH,
                             const char *filename,
                             const char *GVname,
@@ -208,5 +79,7 @@ int IOHDF5_WriteIsosurface (cGH *GH,
                             CCTK_REAL4 *vertices);
 
 #ifdef __cplusplus
-} // extern "C" {
+} // extern "C"
 #endif
+
+#endif  /* _IOHDF5_IOHDF5GH_H_ */