Made IOHDF5 compiling again.

Put in all the recent (mostly name) changes from IOUtil and the flesh.


git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5/trunk@19 4825ed28-b72c-4eae-9704-e50c059e567d

11 files changed, 159 insertions, 66 deletions

diff --git a/param.ccl b/param.ccl
index fa2e7ff..e7aae7c 100644
--- a/param.ccl
+++ b/param.ccl
@@ -139,7 +139,10 @@ STRING length "Default length of the hyperslab to stream"
 #########################
 # Checkpointing requested
 #########################
-BOOLEAN checkpoint "Do checkpointing with HDF5"
+BOOLEAN checkpoint "Do checkpointing with HDF5" STEERABLE = ALWAYS
+{
+} "no"
+BOOLEAN checkpoint_next "Checkpoint at next iteration" STEERABLE = ALWAYS
 {
 } "no"
 
diff --git a/schedule.ccl b/schedule.ccl
index 7d9ed82..54ce214 100644
--- a/schedule.ccl
+++ b/schedule.ccl
@@ -17,29 +17,20 @@ schedule SliceCenterSetup at BASEGRID after IOASCII_Choose1D
 ########################################################################
 ### register checkpointing routines
 ########################################################################
-if (checkpoint && checkpoint_ID)
+schedule IOHDF5_InitialDataDumpGH at CCTK_CPINITIAL
 {
-  schedule IOHDF5_InitialDataDumpGH at CCTK_CPINITIAL
-  {
-    LANG:C
-  } "Initial data checkpoint routine"
-}
+  LANG:C
+} "Initial data checkpoint routine"
 
-if (checkpoint && checkpoint_every > 0)
+schedule IOHDF5_ConditionallyDumpGH at CCTK_CHECKPOINT
 {
-  schedule IOHDF5_ConditionallyDumpGH at CCTK_CHECKPOINT
-  {
-    LANG:C
-  } "Regular checkpoint routine"
-}
+  LANG:C
+} "Regular checkpoint routine"
 
-#if (checkpoint)
+#schedule IOHDF5_TerminationDumpGH at CCTK_TERMINATE BEFORE Driver_Terminate
 #{
-#  schedule IOHDF5_TerminationDumpGH at CCTK_TERMINATE BEFORE Driver_Terminate
-#  {
-#    LANG:C
-#  } "Termination checkpoint routine"
-#}
+#  LANG:C
+#} "Termination checkpoint routine"
 
 if (! CCTK_Equals (recover, "no") && *recover_file)
 {
diff --git a/src/DumpGH.c b/src/DumpGH.c
index 74d7729..803bb8f 100644
--- a/src/DumpGH.c
+++ b/src/DumpGH.c
@@ -18,6 +18,7 @@
 #include "cctk.h"
 #include "cctk_Parameters.h"
 #include "CactusBase/IOUtil/src/ioGH.h"
+#include "CactusBase/IOUtil/src/ioutil_CheckpointRecovery.h"
 #include "ioHDF5GH.h"
 
 /* the rcs ID and its dummy funtion to use it */
@@ -52,13 +53,24 @@ void IOHDF5_ConditionallyDumpGH (cGH *GH)
 {
   DECLARE_CCTK_PARAMETERS
 
-  if (checkpoint_every > 0 && GH->cctk_iteration % checkpoint_every == 0) {
-    if (verbose) {
+
+  if (checkpoint &&
+      ((checkpoint_every > 0 && GH->cctk_iteration % checkpoint_every == 0) ||
+       checkpoint_next))
+  {
+    if (verbose)
+    {
       CCTK_INFO("------------------------------------------------------------");
       CCTK_VInfo (CCTK_THORNSTRING, "Dumping periodic checkpoint file at "
                   "iteration %d", GH->cctk_iteration);
     }
     IOHDF5_DumpGH (GH, CP_EVOLUTION_DATA);
+
+    /* reset the 'checkpoint_next' parameter */
+    if (checkpoint_next)
+    {
+      CCTK_ParameterSet ("checkpoint_next", CCTK_THORNSTRING, "no");
+    }
   }
 }
 
@@ -119,6 +131,7 @@ void IOHDF5_TerminationDumpGH (cGH *GH)
 
 void IOHDF5_InitialDataDumpGH (cGH *GH)
 {
+  DECLARE_CCTK_PARAMETERS
 
 /*** FIXME ***/
 #if 0
@@ -145,7 +158,11 @@ void IOHDF5_InitialDataDumpGH (cGH *GH)
   }
 #endif
 #endif
-  IOHDF5_DumpGH (GH, CP_INITIAL_DATA);
+
+  if (checkpoint && checkpoint_ID)
+  {
+    IOHDF5_DumpGH (GH, CP_INITIAL_DATA);
+  }
 }
 
 
diff --git a/src/DumpVar.c b/src/DumpVar.c
index f000024..e82cffb 100644
--- a/src/DumpVar.c
+++ b/src/DumpVar.c
@@ -156,11 +156,11 @@ int IOHDF5_DumpVar (cGH *GH, int index, int timelevel, ioHDF5Geo_t *geo, hid_t i
   }
 
   switch (CCTK_GroupTypeFromVarI (index)) {
-    case GROUP_SCALAR:
+    case CCTK_SCALAR:
       IOHDF5_DumpGS (GH, index, timelevel, iof, info.iohdf5_type);
       break;
-    case GROUP_ARRAY:
-    case GROUP_GF:
+    case CCTK_ARRAY:
+    case CCTK_GF:
       retval = IOHDF5_DumpGA (GH, index, timelevel, geo, iof, &info);
       break;
     default:
@@ -300,7 +300,7 @@ static int IOHDF5_DumpGA (cGH *GH, int index, int timelevel, ioHDF5Geo_t *slab_g
   pGH *pughGH;
   int myproc;
   int nprocs;
-  int dim,sdim;
+  int sdim;
   CCTK_INT *geom; /* Lower bounds, sizes and global shape of data */
   void *outme;    /* The data pointer to dump ... */
   int free_outme; /* and whether it needs freeing */
diff --git a/src/GHExtension.c b/src/GHExtension.c
index 4246036..c6faa95 100644
--- a/src/GHExtension.c
+++ b/src/GHExtension.c
@@ -22,8 +22,6 @@
 #include "cctk_Parameters.h"
 #include "cctk_Arguments.h"
 
-#include "CactusPUGH/PUGH/src/include/pugh.h"
-#include "CactusBase/IOUtil/src/ioGH.h"
 #include "ioHDF5GH.h"
 
 void IOHDF5_DefaultGeo(cGH *GH, int sdim, ioHDF5Geo_t *geo);
@@ -75,84 +73,107 @@ void *IOHDF5_SetupGH (tFleshConfig *config, int convergence_level, cGH *GH)
 int IOHDF5_InitGH (cGH *GH)
 {
   DECLARE_CCTK_PARAMETERS
-  int inum,idim,i;
+  int i;
   ioHDF5GH *myGH;
-  const cParamData *paramdata;
-  ioHDF5Geo_t geo_default;
+
 
   myGH = (ioHDF5GH *) GH->extensions [CCTK_GHExtensionHandle ("IOHDF5")];
 
   /* How often to output */
   myGH->out1D_every = out_every > 0 ? out_every : -1;
   if (out1D_every > 0)
+  {
     myGH->out1D_every = out1D_every;
-  IOUtil_ParseVarsForOutput (out1D_vars, myGH->do_out1D);
+  }
 
   myGH->out2D_every = out_every > 0 ? out_every : -1;
   if (out2D_every > 0)
+  {
     myGH->out2D_every = out2D_every;
-  IOUtil_ParseVarsForOutput (out2D_vars, myGH->do_out2D);
+  }
 
   myGH->out3D_every = out_every > 0 ? out_every : -1;
   if (out3D_every > 0)
+  {
     myGH->out3D_every = out3D_every;
-  IOUtil_ParseVarsForOutput (out3D_vars, myGH->do_out3D);
+  }
 
   /* Check whether "outdir2D" and/or "outdir3D" was set.
      If so take these dirs otherwise default to "IO::outdir" */
-  paramdata = CCTK_ParameterData ("outdir1D", CCTK_THORNSTRING);
-  if (paramdata && paramdata->n_set > 0)
+  if (CCTK_ParameterQueryTimesSet ("outdir1D", CCTK_THORNSTRING) > 0)
+  {
     myGH->outdir1D = strdup (outdir1D);
+  }
   else
+  {
     myGH->outdir1D = strdup (outdir);
+  }
 
-  paramdata = CCTK_ParameterData ("outdir2D", CCTK_THORNSTRING);
-  if (paramdata && paramdata->n_set > 0)
+  if (CCTK_ParameterQueryTimesSet ("outdir2D", CCTK_THORNSTRING) > 0)
+  {
     myGH->outdir2D = strdup (outdir2D);
+  }
   else
+  {
     myGH->outdir2D = strdup (outdir);
+  }
 
-  paramdata = CCTK_ParameterData ("outdir3D", CCTK_THORNSTRING);
-  if (paramdata && paramdata->n_set > 0)
+  if (CCTK_ParameterQueryTimesSet ("outdir3D", CCTK_THORNSTRING) > 0)
+  {
     myGH->outdir3D = strdup (outdir3D);
+  }
   else
+  {
     myGH->outdir3D = strdup (outdir);
+  }
 
   /* Create the output directories */
-  if (CCTK_MyProc (GH) == 0) {
+  if (CCTK_MyProc (GH) == 0)
+  {
     i = CCTK_CreateDirectory (0755, myGH->outdir1D);
     if (i < 0)
+    {
       CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
              "Problem creating HDF5 1D output directory '%s'", myGH->outdir1D);
+    }
     else if (i > 0)
+    {
       CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
              "HDF5 1D output directory '%s' already exists", myGH->outdir1D);
+    }
 
     i = CCTK_CreateDirectory (0755, myGH->outdir2D);
     if (i < 0)
+    {
       CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
              "Problem creating HDF5 2D output directory '%s'", myGH->outdir2D);
+    }
     else if (i > 0)
+    {
       CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
              "HDF5 2D output directory '%s' already exists", myGH->outdir2D);
+    }
 
     i = CCTK_CreateDirectory (0755, myGH->outdir3D);
     if (i < 0)
+    {
       CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
              "Problem creating HDF5 3D output directory '%s'", myGH->outdir3D);
+    }
     else if (i > 0)
+    {
       CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
              "HDF5 3D output directory '%s' already exists", myGH->outdir3D);
+    }
   }
 
-  for (inum=0; inum<CCTK_NumVars(); inum++) 
+  for (i = 0; i < CCTK_NumVars (); i++) 
   {
-    myGH->out2D_last [inum] = myGH->out3D_last [inum] = -1;
-    myGH->out1D_last [inum] = myGH->out3D_last [inum] = -1;
+    myGH->out2D_last [i] = myGH->out3D_last [i] = -1;
+    myGH->out1D_last [i] = myGH->out3D_last [i] = -1;
   }
 
-
-  /* FIX ME default geometry should be set ehre, but has to 
+  /* FIXME default geometry should be set ehre, but has to 
      be done outside currently, because it needs spxyz and 
      needs to scheduled  at BASEGRID */
 
@@ -165,7 +186,9 @@ int IOHDF5_InitGH (cGH *GH)
     for (i = 0; i < 4; i++)
     {
       if ((myGH->timers[i] = CCTK_TimerCreateI ()) < 0)
+      {
         break;
+      }
     }
     if (i != 4)
     {
@@ -187,6 +210,7 @@ int IOHDF5_InitGH (cGH *GH)
   return (0);
 }
 
+
 void SliceCenterSetup(CCTK_ARGUMENTS)
 {    
   DECLARE_CCTK_PARAMETERS
@@ -194,15 +218,16 @@ void SliceCenterSetup(CCTK_ARGUMENTS)
   ioHDF5Geo_t geo_default;
   ioHDF5GH *myGH;
   
+
   myGH = (ioHDF5GH *) cctkGH->extensions [CCTK_GHExtensionHandle ("IOHDF5")];
 
   /* Loop over all slab dimension */
-  for (idim=0;idim<IOHDF5_MAXDIM;idim++) {
+  for (idim=0;idim<IOHDF5_MAXDIM;idim++)
+  {
     IOHDF5_DefaultGeo(cctkGH, idim, &geo_default);
 
     /* Set the default HDF5 slab geometry for slab with dimension -idim-*/
     for (inum=0; inum<CCTK_NumVars(); inum++) 
       myGH->out_geo[inum][idim] = geo_default;
   }
-
 }
diff --git a/src/Output1D.c b/src/Output1D.c
index 70c3b97..f601ef3 100644
--- a/src/Output1D.c
+++ b/src/Output1D.c
@@ -18,7 +18,6 @@
 
 #include "cctk.h"
 #include "cctk_Parameters.h"
-#include "CactusBase/IOUtil/src/ioGH.h"
 #include "ioHDF5GH.h"
 
 
@@ -26,6 +25,7 @@
 int IOHDF5_TimeFor1D (cGH *GH, int index);
 int IOHDF5_Output1DVarAs (cGH *GH, const char *var, const char *alias);
 static void CheckSteerableParameters (ioHDF5GH *myGH);
+static void SetOutputFlag (int index, const char *optstring, void *arg);
 
 
 /*@@
@@ -254,7 +254,7 @@ static void CheckSteerableParameters (ioHDF5GH *myGH)
 {
   DECLARE_CCTK_PARAMETERS
   int out1D_vars_current_nset;
-  static int out1D_vars_lastset = 0;
+  static int out1D_vars_lastset = -1;
 
 
   /* How often to output */
@@ -262,14 +262,33 @@ static void CheckSteerableParameters (ioHDF5GH *myGH)
   if (out1D_every > 0)
     myGH->out1D_every = out1D_every;
 
-  /* re-parse the 'out1D_vars' parameter if it was changed */
+  /* re-parse the 'IOHDF5::out1D_vars' parameter if it was changed */
   out1D_vars_current_nset = CCTK_ParameterQueryTimesSet ("out1D_vars",
                                                          CCTK_THORNSTRING);
   if (out1D_vars_current_nset != out1D_vars_lastset)
   {
-    IOUtil_ParseVarsForOutput (out1D_vars, myGH->do_out1D);
+    memset (myGH->do_out1D, 0, CCTK_NumVars ());
+    CCTK_TraverseString (out1D_vars, SetOutputFlag, myGH->do_out1D,
+                         CCTK_GROUP_OR_VAR);
 
     /* Save the last setting of 'out1D_vars' parameter */
     out1D_vars_lastset = out1D_vars_current_nset;
   }
 }
+
+
+/* callback for CCTK_TraverseString() to set the output flag
+   for the given variable */
+static void SetOutputFlag (int index, const char *optstring, void *arg)
+{
+  char *flags = (char *) arg;
+
+
+  flags[index] = 1;
+
+  if (optstring)
+  {
+    CCTK_VWarn (5, __LINE__, __FILE__, CCTK_THORNSTRING,
+                "Optional string '%s' in variable name ignored", optstring);
+  }
+}
diff --git a/src/Output2D.c b/src/Output2D.c
index b07efc8..021b258 100644
--- a/src/Output2D.c
+++ b/src/Output2D.c
@@ -18,7 +18,6 @@
 
 #include "cctk.h"
 #include "cctk_Parameters.h"
-#include "CactusBase/IOUtil/src/ioGH.h"
 #include "ioHDF5GH.h"
 
 
@@ -26,6 +25,7 @@
 int IOHDF5_TimeFor2D (cGH *GH, int index);
 int IOHDF5_Output2DVarAs (cGH *GH, const char *var, const char *alias);
 static void CheckSteerableParameters (ioHDF5GH *myGH);
+static void SetOutputFlag (int index, const char *optstring, void *arg);
 
 
 /*@@
@@ -262,14 +262,33 @@ static void CheckSteerableParameters (ioHDF5GH *myGH)
   if (out2D_every > 0)
     myGH->out2D_every = out2D_every;
 
-  /* re-parse the 'out2D_vars' parameter if it was changed */
+  /* re-parse the 'IOHDF5::out2D_vars' parameter if it was changed */
   out2D_vars_current_nset = CCTK_ParameterQueryTimesSet ("out2D_vars",
                                                          CCTK_THORNSTRING);
   if (out2D_vars_current_nset != out2D_vars_lastset)
   {
-    IOUtil_ParseVarsForOutput (out2D_vars, myGH->do_out2D);
+    memset (myGH->do_out2D, 0, CCTK_NumVars ());
+    CCTK_TraverseString (out2D_vars, SetOutputFlag, myGH->do_out2D,
+                         CCTK_GROUP_OR_VAR);
 
     /* Save the last setting of 'out2D_vars' parameter */
     out2D_vars_lastset = out2D_vars_current_nset;
   }
 }
+
+
+/* callback for CCTK_TraverseString() to set the output flag
+   for the given variable */
+static void SetOutputFlag (int index, const char *optstring, void *arg)
+{
+  char *flags = (char *) arg;
+
+
+  flags[index] = 1;
+
+  if (optstring)
+  {
+    CCTK_VWarn (5, __LINE__, __FILE__, CCTK_THORNSTRING,
+                "Optional string '%s' in variable name ignored", optstring);
+  }
+}
diff --git a/src/Output3D.c b/src/Output3D.c
index caaca4a..5bfcfaf 100644
--- a/src/Output3D.c
+++ b/src/Output3D.c
@@ -18,7 +18,6 @@
 
 #include "cctk.h"
 #include "cctk_Parameters.h"
-#include "CactusBase/IOUtil/src/ioGH.h"
 #include "ioHDF5GH.h"
 
 
@@ -26,6 +25,7 @@
 int IOHDF5_TimeFor3D (cGH *GH, int index);
 int IOHDF5_Output3DVarAs (cGH *GH, const char *var, const char *alias);
 static void CheckSteerableParameters (ioHDF5GH *myGH);
+static void SetOutputFlag (int index, const char *optstring, void *arg);
 
 
 /*@@
@@ -253,14 +253,33 @@ static void CheckSteerableParameters (ioHDF5GH *myGH)
   if (out3D_every > 0)
     myGH->out3D_every = out3D_every;
 
-  /* re-parse the 'out3D_vars' parameter if it was changed */
+  /* re-parse the 'IOHDF5::out3D_vars' parameter if it was changed */
   out3D_vars_current_nset = CCTK_ParameterQueryTimesSet ("out3D_vars",
                                                          CCTK_THORNSTRING);
   if (out3D_vars_current_nset != out3D_vars_lastset)
   {
-    IOUtil_ParseVarsForOutput (out3D_vars, myGH->do_out3D);
+    memset (myGH->do_out3D, 0, CCTK_NumVars ());
+    CCTK_TraverseString (out3D_vars, SetOutputFlag, myGH->do_out3D,
+                         CCTK_GROUP_OR_VAR);
 
     /* Save the last setting of 'out3D_vars' parameter */
     out3D_vars_lastset = out3D_vars_current_nset;
   }
 }
+
+
+/* callback for CCTK_TraverseString() to set the output flag
+   for the given variable */
+static void SetOutputFlag (int index, const char *optstring, void *arg)
+{
+  char *flags = (char *) arg;
+
+
+  flags[index] = 1;
+
+  if (optstring)
+  {
+    CCTK_VWarn (5, __LINE__, __FILE__, CCTK_THORNSTRING,
+                "Optional string '%s' in variable name ignored", optstring);
+  }
+}
diff --git a/src/RecoverGH.c b/src/RecoverGH.c
index e97e86f..29249bc 100644
--- a/src/RecoverGH.c
+++ b/src/RecoverGH.c
@@ -26,7 +26,7 @@
 #include "cctk.h"
 #include "cctk_Parameters.h"
 #include "CactusPUGH/PUGH/src/include/pugh.h"
-#include "CactusBase/IOUtil/src/ioGH.h"
+#include "CactusBase/IOUtil/src/ioutil_CheckpointRecovery.h"
 #include "ioHDF5GH.h"
 
 
diff --git a/src/RestoreFile.c b/src/RestoreFile.c
index 78eaa78..ef9db7b 100644
--- a/src/RestoreFile.c
+++ b/src/RestoreFile.c
@@ -272,10 +272,10 @@ static int GetCommonAttributes (cGH *GH, hid_t dataset, const char *datasetname,
   if (groupdata.dim != rank_stored)
     flag = 1;
   switch (groupdata.grouptype) {
-    case GROUP_SCALAR:
+    case CCTK_SCALAR:
       break;
-    case GROUP_ARRAY:
-    case GROUP_GF:
+    case CCTK_ARRAY:
+    case CCTK_GF:
       extras = ((pGA ***) PUGH_pGH (GH)->variables)[*index][*timelevel]->extras;
       dims = unchunked ? extras->nsize : extras->lnsize;
       for (i = 0; i < groupdata.dim; i++)
@@ -558,11 +558,11 @@ static herr_t processDataset (hid_t group, const char *datasetname, void *arg)
 
   /* Read in the data */
   switch (gtype) {
-    case GROUP_SCALAR:
+    case CCTK_SCALAR:
       IOHDF5_RestoreGS (dataset, index, timelevel, &rec_info);
       break;
-    case GROUP_GF:
-    case GROUP_ARRAY:
+    case CCTK_GF:
+    case CCTK_ARRAY:
       IOHDF5_RestoreGA (dataset, index, timelevel, &rec_info);
       break;
     default:
diff --git a/src/Startup.c b/src/Startup.c
index 2ec6c14..a2e6690 100644
--- a/src/Startup.c
+++ b/src/Startup.c
@@ -15,7 +15,7 @@
 
 #include "cctk.h"
 #include "cctk_Parameters.h"
-#include "CactusBase/IOUtil/src/ioGH.h"
+#include "CactusBase/IOUtil/src/ioutil_CheckpointRecovery.h"
 
 
 /* prototypes of functions to be registered */