Code cleanup before moving into producion mode.

You must also update BetaThorns/IOHDF5Util now.


git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5/trunk@124 4825ed28-b72c-4eae-9704-e50c059e567d

6 files changed, 71 insertions, 103 deletions

diff --git a/src/DumpGH.c b/src/DumpGH.c
index 1fb342d..b9d5674 100644
--- a/src/DumpGH.c
+++ b/src/DumpGH.c
@@ -36,15 +36,15 @@ CCTK_FILEVERSION(AlphaThorns_IOHDF5_DumpGH_c)
 /********************************************************************
  ********************    External Routines   ************************
  ********************************************************************/
-void IOHDF5_InitialDataCheckpoint (cGH *GH);
-void IOHDF5_EvolutionCheckpoint (cGH *GH);
-void IOHDF5_TerminationCheckpoint (cGH *GH);
+void IOHDF5_InitialDataCheckpoint (const cGH *GH);
+void IOHDF5_EvolutionCheckpoint (const cGH *GH);
+void IOHDF5_TerminationCheckpoint (const cGH *GH);
 
 
 /********************************************************************
  ********************    Internal Routines   ************************
  ********************************************************************/
-static int Checkpoint (cGH *GH, int called_from);
+static int Checkpoint (const cGH *GH, int called_from);
 
 
  /*@@
@@ -60,11 +60,11 @@ static int Checkpoint (cGH *GH, int called_from);
  
    @var        GH
    @vdesc      Pointer to CCTK grid hierarchy
-   @vtype      cGH *
+   @vtype      const cGH *
    @vio        in
    @endvar
 @@*/
-void IOHDF5_InitialDataCheckpoint (cGH *GH)
+void IOHDF5_InitialDataCheckpoint (const cGH *GH)
 {
   DECLARE_CCTK_PARAMETERS
 
@@ -89,11 +89,11 @@ void IOHDF5_InitialDataCheckpoint (cGH *GH)
  
    @var        GH
    @vdesc      Pointer to CCTK grid hierarchy
-   @vtype      cGH *
+   @vtype      const cGH *
    @vio        in
    @endvar
 @@*/
-void IOHDF5_EvolutionCheckpoint (cGH *GH)
+void IOHDF5_EvolutionCheckpoint (const cGH *GH)
 {
   DECLARE_CCTK_PARAMETERS
 
@@ -132,11 +132,11 @@ void IOHDF5_EvolutionCheckpoint (cGH *GH)
 
    @var        GH
    @vdesc      Pointer to CCTK grid hierarchy
-   @vtype      cGH *
+   @vtype      const cGH *
    @vio        in
    @endvar
 @@*/
-void IOHDF5_TerminationCheckpoint (cGH *GH)
+void IOHDF5_TerminationCheckpoint (const cGH *GH)
 {
   DECLARE_CCTK_PARAMETERS
 
@@ -166,7 +166,7 @@ void IOHDF5_TerminationCheckpoint (cGH *GH)
 
    @var        GH
    @vdesc      Pointer to CCTK grid hierarchy
-   @vtype      cGH *
+   @vtype      const cGH *
    @vio        in
    @endvar
    @var        called_from
@@ -182,7 +182,7 @@ void IOHDF5_TerminationCheckpoint (cGH *GH)
                or returncode of @seeroutine IOUtilHDF5_DumpGH
    @endreturndesc
 @@*/
-static int Checkpoint (cGH *GH, int called_from)
+static int Checkpoint (const cGH *GH, int called_from)
 {
   hid_t file;
   int myproc;
@@ -204,14 +204,13 @@ static int Checkpoint (cGH *GH, int called_from)
   file = -1;
   myproc = CCTK_MyProc (GH);
 
-  /* Get the GH extensions for IOUtil and IOHDF5 */
   ioUtilGH = (ioGH *) CCTK_GHExtension (GH, "IO");
   myGH = (ioHDF5GH *) CCTK_GHExtension (GH, "IOHDF5");
 
-  /* check if IOHDF5 was registered as IO method */
+  /* check if IOHDF5 was registered as I/O method */
   if (myGH == NULL)
   {
-    CCTK_WARN (2, "No IOHDF5 IO methods registered");
+    CCTK_WARN (2, "No IOHDF5 I/O methods registered");
     return (-1);
   }
 
@@ -279,7 +278,7 @@ static int Checkpoint (cGH *GH, int called_from)
 
     if (file >= 0)
     {
-      IOHDF5_ERROR (H5Fclose (file));
+      HDF5_ERROR (H5Fclose (file));
     }
 
     /* delete the oldest checkpoint file if checkpoint_keep_all isn't set
diff --git a/src/Output.c b/src/Output.c
index 6b6ef2c..d66dc55 100644
--- a/src/Output.c
+++ b/src/Output.c
@@ -2,9 +2,9 @@
    @file      Output.c
    @date      Tue Jan 9 1999
    @author    Gabrielle Allen
-   @desc 
+   @desc
               Functions to deal with output of variables in HDF5 file format
-   @enddesc 
+   @enddesc
    @version   $Id$
  @@*/
 
@@ -23,7 +23,7 @@ CCTK_FILEVERSION(AlphaThorns_IOHDF5_Output_c)
 /********************************************************************
  ********************    Internal Routines   ************************
  ********************************************************************/
-static void CheckSteerableParameters (ioHDF5GH *myGH);
+static void CheckSteerableParameters (const cGH *GH);
 
 
 /*@@
@@ -58,10 +58,9 @@ int IOHDF5_OutputGH (const cGH *GH)
   DECLARE_CCTK_PARAMETERS
 
 
-  /* Get the GH extension for IOHDF5 */
   myGH = (ioHDF5GH *) CCTK_GHExtension (GH, "IOHDF5");
 
-  CheckSteerableParameters (myGH);
+  CheckSteerableParameters (GH);
 
   if (myGH->out_every <= 0)
   {
@@ -71,7 +70,6 @@ int IOHDF5_OutputGH (const cGH *GH)
   /* loop over all variables */
   for (vindex = retval = 0; vindex < CCTK_NumVars (); vindex++)
   {
-
     if (IOHDF5_TimeFor (GH, vindex))
     {
       name     = CCTK_VarName (vindex);
@@ -85,7 +83,7 @@ int IOHDF5_OutputGH (const cGH *GH)
 
       if (IOHDF5_OutputVarAs (GH, fullname, name) == 0)
       {
-        /* Register variable as having output this iteration */
+        /* register variable as having output this iteration */
         myGH->out_last[vindex] = GH->cctk_iteration;
         retval++;
       }
@@ -142,24 +140,24 @@ int IOHDF5_OutputVarAs (const cGH *GH, const char *fullname, const char *alias)
   if (verbose)
   {
     CCTK_VInfo (CCTK_THORNSTRING, "IOHDF5_OutputVarAs: fullname, alias, "
-                "index = (%s, %s, %d)", fullname, alias, vindex); 
+                "index = (%s, %s, %d)", fullname, alias, vindex);
   }
 
   /* check whether the variable already has an I/O request entry */
   myGH = (ioHDF5GH *) CCTK_GHExtension (GH, "IOHDF5");
-  oneshot = myGH->out_geo[vindex] == NULL;
+  oneshot = myGH->slablist[vindex] == NULL;
   if (oneshot)
   {
-    IOHDF5Util_ParseVarsForOutput (fullname, myGH->out_geo);
+    IOHDF5Util_ParseVarsForOutput (GH, fullname, myGH->slablist);
   }
 
   /* do the output */
   retval = IOHDF5_Write (GH, vindex, alias);
 
-  if (oneshot && myGH->out_geo[vindex])
+  if (oneshot && myGH->slablist[vindex])
   {
-    free (myGH->out_geo[vindex]);
-    myGH->out_geo[vindex] = NULL;
+    free (myGH->slablist[vindex]);
+    myGH->slablist[vindex] = NULL;
   }
   return (retval);
 }
@@ -200,13 +198,11 @@ int IOHDF5_TimeFor (const cGH *GH, int vindex)
   char *fullname;
 
 
-  /* get the GH extension for IOHDF5 */
-  myGH = (ioHDF5GH *) CCTK_GHExtension (GH, "IOHDF5");
-
-  CheckSteerableParameters (myGH);
+  CheckSteerableParameters (GH);
 
   /* check if this variable should be output */
-  retval = myGH->out_every > 0 && myGH->out_geo[vindex] &&
+  myGH = (ioHDF5GH *) CCTK_GHExtension (GH, "IOHDF5");
+  retval = myGH->out_every > 0 && myGH->slablist[vindex] &&
            GH->cctk_iteration % myGH->out_every == 0;
   if (retval)
   {
@@ -301,20 +297,23 @@ int IOHDF5_TriggerOutput (const cGH *GH, int vindex)
 
    @calls      IOHDF5Util_ParseVarsForOutput
 
-   @var        myGH
-   @vdesc      Pointer to IOHDF5 GH
-   @vtype      ioHDF5GH *
+   @var        GH
+   @vdesc      Pointer to CCTK grid hierarchy
+   @vtype      const cGH *
    @vio        in
    @endvar
 @@*/
-static void CheckSteerableParameters (ioHDF5GH *myGH)
+static void CheckSteerableParameters (const cGH *GH)
 {
   int times_set;
+  ioHDF5GH *myGH;
   static int out_vars_lastset = -1, user_was_warned = 0;
   DECLARE_CCTK_PARAMETERS
 
 
-  /* How often to output */
+  myGH = (ioHDF5GH *) CCTK_GHExtension (GH, "IOHDF5");
+
+  /* how often to output */
   if (out_every >= 0 || outHDF5_every >= 0)
   {
     if (out_every < 0)
@@ -336,15 +335,14 @@ static void CheckSteerableParameters (ioHDF5GH *myGH)
   {
     myGH->out_every = *(const CCTK_INT *)
                       CCTK_ParameterGet ("out_every",
-                                         CCTK_ImplementationThorn ("IO"),
-                                         NULL);
+                                         CCTK_ImplementationThorn ("IO"), NULL);
   }
 
   /* re-parse the 'IOHDF5::out_vars' parameter if it was changed */
   times_set = CCTK_ParameterQueryTimesSet ("out_vars", CCTK_THORNSTRING);
   if (times_set != out_vars_lastset)
   {
-    IOHDF5Util_ParseVarsForOutput (out_vars, myGH->out_geo);
+    IOHDF5Util_ParseVarsForOutput (GH, out_vars, myGH->slablist);
 
     /* Save the last setting of 'out_vars' parameter */
     out_vars_lastset = times_set;
diff --git a/src/RecoverGH.c b/src/RecoverGH.c
index a6854bf..e8c4b8d 100644
--- a/src/RecoverGH.c
+++ b/src/RecoverGH.c
@@ -39,10 +39,8 @@ int IOHDF5_RecoverParameters (void);
 /********************************************************************
  ********************    Internal Routines   ************************
  ********************************************************************/
-static int IOHDF5_OpenFile (cGH *GH,
-                            const char *basefilename,
-                            int called_from,
-                            fileinfo_t *fileinfo);
+static int OpenFile (cGH *GH, const char *basefilename, int called_from,
+                     fileinfo_t *fileinfo);
 
 
  /*@@
@@ -72,7 +70,7 @@ static int IOHDF5_OpenFile (cGH *GH,
    @vio        in
    @endvar
 
-   @calls      IOHDF5_OpenFile
+   @calls      OpenFile
                IOHDF5Util_RecoverParameters
                IOHDF5Util_RecoverVariables
                IOHDF5Util_RecoverGHextensions
@@ -114,7 +112,7 @@ int IOHDF5_Recover (cGH *GH, const char *basefilename, int called_from)
       called_from == FILEREADER_DATA ||
       (GH && (GH->cctk_levfac[0] > 1 || GH->cctk_convlevel > 0)))
   {
-    if (IOHDF5_OpenFile (GH, basefilename, called_from, &fileinfo) < 0)
+    if (OpenFile (GH, basefilename, called_from, &fileinfo) < 0)
     {
       return (-1);
     }
@@ -175,7 +173,7 @@ int IOHDF5_Recover (cGH *GH, const char *basefilename, int called_from)
                     fileinfo.filename);
       }
     }
-    IOHDF5_ERROR (H5Fclose (fileinfo.file));
+    HDF5_ERROR (H5Fclose (fileinfo.file));
 
     if (called_from == CP_RECOVER_DATA && recover_and_remove)
     {
@@ -250,11 +248,11 @@ int IOHDF5_RecoverParameters (void)
 }
 
 
-/**************************************************************************/
-/*                            local routines                              */
-/**************************************************************************/
+/********************************************************************
+ ********************    Internal Routines   ************************
+ ********************************************************************/
  /*@@
-   @routine    IOHDF5_OpenFile
+   @routine    OpenFile
    @date       Tue Oct 10 2000
    @author     Thomas Radke
    @desc
@@ -295,10 +293,8 @@ int IOHDF5_RecoverParameters (void)
                0 for success, -1 if file could not be opened
    @endreturndesc
 @@*/
-static int IOHDF5_OpenFile (cGH *GH,
-                            const char *basefilename,
-                            int called_from,
-                            fileinfo_t *fileinfo)
+static int OpenFile (cGH *GH, const char *basefilename, int called_from,
+                     fileinfo_t *fileinfo)
 {
   int nprocs, myproc;
   hid_t group, version_attr;
@@ -409,10 +405,10 @@ static int IOHDF5_OpenFile (cGH *GH,
       fileinfo->has_version = version_attr >= 0;
       if (version_attr >= 0)
       {
-        IOHDF5_ERROR (H5Aclose (version_attr));
+        HDF5_ERROR (H5Aclose (version_attr));
       }
 
-      IOHDF5_ERROR (H5Gclose (group));
+      HDF5_ERROR (H5Gclose (group));
 
       /* If we recover from multiple files the number of
        * writing processors must match the number of reading 
@@ -512,6 +508,6 @@ static int IOHDF5_OpenFile (cGH *GH,
   /* set the filename in the info structure */
   fileinfo->filename = strdup (filename);
 
-  /* Return 0 for success otherwise negative */
+  /* return 0 for success otherwise negative */
   return (fileinfo->is_HDF5_file ? 0 : -1);
 }
diff --git a/src/Startup.c b/src/Startup.c
index b213adf..15dc785 100644
--- a/src/Startup.c
+++ b/src/Startup.c
@@ -33,9 +33,7 @@ void IOHDF5_Startup (void);
 /********************************************************************
  ********************    Internal Routines   ************************
  ********************************************************************/
-static void *IOHDF5_SetupGH (tFleshConfig *config,
-                             int convergence_level,
-                             cGH *GH);
+static void *SetupGH (tFleshConfig *config, int conv_level, cGH *GH);
 
 
  /*@@
@@ -53,17 +51,7 @@ static void *IOHDF5_SetupGH (tFleshConfig *config,
 @@*/
 void IOHDF5_Startup (void)
 {
-  /* check that thorn IOHDF5Util was activated */
-  if (CCTK_GHExtensionHandle ("IOHDF5Util") >= 0)
-  {
-    CCTK_RegisterGHExtensionSetupGH (CCTK_RegisterGHExtension ("IOHDF5"),
-                                     IOHDF5_SetupGH);
-  }
-  else
-  {
-    CCTK_WARN (1, "Thorn IOHDF5Util was not activated. "
-                  "No IOHDF5 IO methods will be registered.");
-  }
+  CCTK_RegisterGHExtensionSetupGH (CCTK_RegisterGHExtension ("IOHDF5"),SetupGH);
 }
 
 
@@ -71,7 +59,7 @@ void IOHDF5_Startup (void)
  ********************    Internal Routines   ************************
  ********************************************************************/
  /*@@
-   @routine    IOHDF5_SetupGH
+   @routine    SetupGH
    @date       Mon Jun 19 2000
    @author     Thomas Radke
    @desc
@@ -93,7 +81,7 @@ void IOHDF5_Startup (void)
    @vtype      tFleshConfig *
    @vio        usused
    @endvar
-   @var        convergence_level
+   @var        conv_level
    @vdesc      the convergence level
    @vtype      int
    @vio        unused
@@ -109,9 +97,7 @@ void IOHDF5_Startup (void)
                pointer to the new GH extension structure
    @endreturndesc
 @@*/
-static void *IOHDF5_SetupGH (tFleshConfig *config,
-                             int convergence_level,
-                             cGH *GH)
+static void *SetupGH (tFleshConfig *config, int conv_level, cGH *GH)
 {
   int i, numvars;
   ioHDF5GH *myGH;
@@ -125,16 +111,16 @@ static void *IOHDF5_SetupGH (tFleshConfig *config,
 
   /* suppress compiler warnings about unused variables */
   (void) (config + 0);
-  (void) (convergence_level + 0);
+  (void) (conv_level + 0);
 
-  /* Register the IOHDF5 routines as a new IO method */
+  /* register the IOHDF5 routines as a new I/O method */
   i = CCTK_RegisterIOMethod ("IOHDF5");
   CCTK_RegisterIOMethodOutputGH (i, IOHDF5_OutputGH);
   CCTK_RegisterIOMethodOutputVarAs (i, IOHDF5_OutputVarAs);
   CCTK_RegisterIOMethodTimeToOutput (i, IOHDF5_TimeFor);
   CCTK_RegisterIOMethodTriggerOutput (i, IOHDF5_TriggerOutput);
 
-  /* Register the IOHDF5 recovery routine with thorn IOUtil */
+  /* register the IOHDF5 recovery routine with thorn IOUtil */
   if (IOUtil_RegisterRecover ("IOHDF5 recovery", IOHDF5_Recover) < 0)
   {
     CCTK_WARN (1, "Failed to register IOHDF5 recovery routine");
@@ -144,8 +130,7 @@ static void *IOHDF5_SetupGH (tFleshConfig *config,
   numvars = CCTK_NumVars ();
   myGH            = (ioHDF5GH *) malloc (sizeof (ioHDF5GH));
   myGH->out_last  = (int *) malloc (numvars * sizeof (int));
-  myGH->out_geo   = (ioHDF5Geo_t **) calloc (numvars, sizeof (ioHDF5Geo_t *));
-  myGH->check_exisiting_objects = (char *) calloc (numvars, 1);
+  myGH->slablist  = (ioSlab **) calloc (numvars, sizeof (ioSlab *));
   myGH->cp_filename_list = (char **) calloc (checkpoint_keep, sizeof (char *));
   myGH->cp_filename_index = 0;
 
diff --git a/src/Write.c b/src/Write.c
index a390385..b1e8f20 100644
--- a/src/Write.c
+++ b/src/Write.c
@@ -78,7 +78,6 @@ int IOHDF5_Write (const cGH *GH, int vindex, const char *alias)
   DECLARE_CCTK_PARAMETERS
 
 
-  /* Get the handles for IO and IOHDF5 extensions */
   ioUtilGH = (ioGH *) CCTK_GHExtension (GH, "IO");
   myGH     = (ioHDF5GH *) CCTK_GHExtension (GH, "IOHDF5");
 
@@ -121,12 +120,12 @@ int IOHDF5_Write (const cGH *GH, int vindex, const char *alias)
                   is_new_file ? "Opening" : "Appending", filename);
     }
 
-    IOHDF5_ERROR (plist = H5Pcreate (H5P_FILE_ACCESS));
+    HDF5_ERROR (plist = H5Pcreate (H5P_FILE_ACCESS));
 #ifdef CCTK_MPI
 #ifdef H5_HAVE_PARALLEL
     if (ioUtilGH->unchunked)
     {
-      IOHDF5_ERROR (H5Pset_fapl_mpio (plist, PUGH_pGH (GH)->PUGH_COMM_WORLD,
+      HDF5_ERROR (H5Pset_fapl_mpio (plist, PUGH_pGH (GH)->PUGH_COMM_WORLD,
                                       MPI_INFO_NULL));
     }
 #endif
@@ -134,12 +133,12 @@ int IOHDF5_Write (const cGH *GH, int vindex, const char *alias)
 
     if (is_new_file)
     {
-      IOHDF5_ERROR (file = H5Fcreate (filename, H5F_ACC_TRUNC, H5P_DEFAULT,
+      HDF5_ERROR (file = H5Fcreate (filename, H5F_ACC_TRUNC, H5P_DEFAULT,
                                       plist));
     }
     else
     {
-      IOHDF5_ERROR (file = H5Fopen (filename, H5F_ACC_RDWR, plist));
+      HDF5_ERROR (file = H5Fopen (filename, H5F_ACC_RDWR, plist));
     }
     if (file < 0)
     {
@@ -148,7 +147,7 @@ int IOHDF5_Write (const cGH *GH, int vindex, const char *alias)
                   is_new_file ? "create" : "open", filename);
     }
 
-    IOHDF5_ERROR (H5Pclose (plist));
+    HDF5_ERROR (H5Pclose (plist));
   }
 
   /* output global attributes */
@@ -165,8 +164,7 @@ int IOHDF5_Write (const cGH *GH, int vindex, const char *alias)
   }
 
   /* output the data */
-  retval = IOHDF5Util_DumpVar (GH, vindex, 0, myGH->out_geo[vindex], file,
-                               myGH->check_exisiting_objects[vindex]);
+  retval = IOHDF5Util_DumpVar (GH, myGH->slablist[vindex], file);
 
   /* close the file */
   if (file >= 0)
@@ -175,7 +173,7 @@ int IOHDF5_Write (const cGH *GH, int vindex, const char *alias)
     {
       CCTK_INFO ("Closing HDF5 output file from this iteration");
     }
-    IOHDF5_ERROR (H5Fclose (file));
+    HDF5_ERROR (H5Fclose (file));
   }
 
   /* free the filename if it was not registered for re-opening
@@ -356,10 +354,6 @@ static char *IOHDF5_GetFilename (const cGH *GH,
         {
           *is_new_file = H5Fis_hdf5 (filename) <= 0;
         } H5E_END_TRY;
-        if (! *is_new_file)
-        {
-          myGH->check_exisiting_objects[vindex] = 1;
-        }
       }
       else
       {
diff --git a/src/ioHDF5GH.h b/src/ioHDF5GH.h
index 087926c..4af80f4 100644
--- a/src/ioHDF5GH.h
+++ b/src/ioHDF5GH.h
@@ -29,18 +29,14 @@ typedef struct
   /* filename database for opened files */
   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  *check_exisiting_objects;
-
   /* timer array for checkpointing/recovery */
   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; 
+  /* hyperslab description list (for all variables) */
+  ioSlab **slablist; 
 
   /* ring buffer for list of successfully created cp files */
   int    cp_filename_index;