Renamed 'index' variables into 'vindex' to suppress gcc warnings about

hiding global routine index(3).

Removed old code to convert output data into single-precision if requested
(IO::out3D_single = "yes"). Now the Hyperslab interface is used to do that,
where it also works in combination with downsampling.
This is quite handy especially for visualizing streamed HDF5 output.

NOTE: I'm using the new hyperslab interface from CactusPUGH/PUGHSlab now
      so you need to update this thorn as well.


git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@10 7842ec3a-9562-4be5-9c5b-06ba18f2b668

1 files changed, 98 insertions, 138 deletions

diff --git a/src/DumpVar.c b/src/DumpVar.c
index b12b5d4..adfad6b 100644
--- a/src/DumpVar.c
+++ b/src/DumpVar.c
@@ -14,7 +14,7 @@
 #include "cctk.h"
 #include "cctk_Parameters.h"
 #include "CactusPUGH/PUGH/src/include/pugh.h"
-#include "CactusPUGH/PUGHSlab/src/PUGHSlab.h" 
+#include "CactusPUGH/PUGHSlab/src/NewPUGHSlab.h" 
 #include "CactusBase/IOUtil/src/ioGH.h"
 #include "ioHDF5UtilGH.h"
 
@@ -37,28 +37,27 @@ typedef struct
 
 /* local function prototypes */
 static int IOHDF5Util_DumpGS (cGH *GH,
-                              int index,
+                              int vindex,
                               int timelevel,
                               int iohdf5_type,
                               int check_exisiting_objects,
                               hid_t file);
 static int IOHDF5Util_DumpGA (cGH *GH,
-                              int index,
+                              int vindex,
                               int timelevel,
                               ioHDF5Geo_t *slab,  
                               dumpInfo *info,
                               int check_exisiting_objects,
                               hid_t file);
 static int IOHDF5Util_getDumpData (cGH *GH,
-                                   int index,
+                                   int vindex,
                                    int timelevel,
                                    ioHDF5Geo_t *slab, 
                                    void **outme,
                                    int *free_outme, 
-                                   CCTK_INT *geom,
-                                   int element_size);
+                                   CCTK_INT *geom);
 static void IOHDF5Util_procDump (cGH *GH,
-                                 int index,
+                                 int vindex,
                                  int timelevel,
                                  ioHDF5Geo_t *slab, 
                                  void *outme,
@@ -70,7 +69,7 @@ static void IOHDF5Util_procDump (cGH *GH,
 #ifdef CCTK_MPI
 #ifdef HAVE_PARALLEL
 static void IOHDF5Util_collectiveDump (cGH *GH,
-                                       int index,
+                                       int vindex,
                                        int timelevel,
                                        ioHDF5Geo_t *slab,
                                        void *outme,
@@ -98,7 +97,7 @@ static void IOHDF5Util_collectiveDump (cGH *GH,
    @vtype      cGH *
    @vio        in
    @endvar
-   @var        index
+   @var        vindex
    @vdesc      index of the variable to be dumped
    @vtype      int
    @vio        in
@@ -135,7 +134,7 @@ static void IOHDF5Util_collectiveDump (cGH *GH,
    @endreturndesc
 @@*/
 int IOHDF5Util_DumpVar (cGH *GH,
-                        int index,
+                        int vindex,
                         int timelevel,
                         ioHDF5Geo_t *slab,
                         hid_t file,
@@ -154,7 +153,7 @@ int IOHDF5Util_DumpVar (cGH *GH,
   ioUtilGH = (ioGH *) CCTK_GHExtension (GH, "IO");
   myGH = (ioHDF5UtilGH *) CCTK_GHExtension (GH, "IOHDF5Util");
 
-  switch (CCTK_VarTypeI (index))
+  switch (CCTK_VarTypeI (vindex))
   {
     case CCTK_VARIABLE_CHAR:
       info.iohdf5_type = IOHDF5_CHAR;
@@ -192,20 +191,20 @@ int IOHDF5Util_DumpVar (cGH *GH,
     default:
       CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
                   "Unsupported variable datatype '%s'",
-                  CCTK_VarTypeName (CCTK_VarTypeI (index)));
+                  CCTK_VarTypeName (CCTK_VarTypeI (vindex)));
       return (-1);
   }
 
   /* now branch to the appropriate dump routine */
-  gtype = CCTK_GroupTypeFromVarI (index);
+  gtype = CCTK_GroupTypeFromVarI (vindex);
   if (gtype == CCTK_SCALAR)
   {
-    retval = IOHDF5Util_DumpGS (GH, index, timelevel, info.iohdf5_type,
+    retval = IOHDF5Util_DumpGS (GH, vindex, timelevel, info.iohdf5_type,
                                 check_exisiting_objects, file);
   }
   else if (gtype == CCTK_ARRAY || gtype == CCTK_GF)
   {
-    retval = IOHDF5Util_DumpGA (GH, index, timelevel, slab, &info,
+    retval = IOHDF5Util_DumpGA (GH, vindex, timelevel, slab, &info,
                                 check_exisiting_objects, file);
   }
   else
@@ -231,7 +230,7 @@ int IOHDF5Util_DumpVar (cGH *GH,
    @vtype      cGH
    @vio        in
    @endvar
-   @var        index
+   @var        vindex
    @vdesc      index of the variable to be dumped
    @vtype      int
    @vio        in
@@ -265,7 +264,7 @@ int IOHDF5Util_DumpVar (cGH *GH,
    @endreturndesc
 @@*/
 static int IOHDF5Util_DumpGS (cGH *GH,
-                              int index,
+                              int vindex,
                               int timelevel,
                               int iohdf5_type,
                               int check_exisiting_objects,
@@ -276,7 +275,7 @@ static int IOHDF5Util_DumpGS (cGH *GH,
   hid_t dataset;
   char *fullname;
   char *datasetname;
-  CCTK_INT global_shape[1] = {0};
+  static CCTK_INT global_shape[1] = {0};
 
 
   /* Get the handles for IOHDF5Util and IOUtil extensions */
@@ -288,7 +287,7 @@ static int IOHDF5Util_DumpGS (cGH *GH,
     return (0);
   }
 
-  fullname = CCTK_FullName (index);
+  fullname = CCTK_FullName (vindex);
   datasetname = (char *) malloc (strlen (fullname) + 80);
   sprintf (datasetname, "%s timelevel %d at iteration %d",
            fullname, timelevel, GH->cctk_iteration);
@@ -305,9 +304,9 @@ static int IOHDF5Util_DumpGS (cGH *GH,
   IOHDF5_ERROR (dataset = H5Dcreate (file, datasetname, iohdf5_type,
                                      myGH->scalar_dataspace, H5P_DEFAULT));
   IOHDF5_ERROR (H5Dwrite (dataset, iohdf5_type, H5S_ALL, H5S_ALL, H5P_DEFAULT,
-                          CCTK_VarDataPtrI (GH, timelevel, index)));
+                          CCTK_VarDataPtrI (GH, timelevel, vindex)));
     
-  IOHDF5Util_DumpCommonAttributes (GH, index, timelevel, global_shape,
+  IOHDF5Util_DumpCommonAttributes (GH, vindex, timelevel, global_shape,
                                    NULL, dataset);
 
   IOHDF5_ERROR (H5Dclose (dataset));
@@ -336,7 +335,7 @@ static int IOHDF5Util_DumpGS (cGH *GH,
    @vtype      cGH
    @vio        in
    @endvar
-   @var        index
+   @var        vindex
    @vdesc      index of the variable to be dumped
    @vtype      int
    @vio        in
@@ -379,7 +378,7 @@ static int IOHDF5Util_DumpGS (cGH *GH,
    @endreturndesc
 @@*/
 static int IOHDF5Util_DumpGA (cGH *GH,
-                              int index,
+                              int vindex,
                               int timelevel,
                               ioHDF5Geo_t *slab,  
                               dumpInfo *info,
@@ -412,8 +411,8 @@ static int IOHDF5Util_DumpGA (cGH *GH,
   geom = (CCTK_INT *) malloc (3 * slab->sdim * sizeof (CCTK_INT));
   
   /* Get the pointer to the data we want to output (includes downsampling) */
-  retval = IOHDF5Util_getDumpData (GH, index, timelevel, slab, &outme,
-                                   &free_outme, geom, info->element_size);
+  retval = IOHDF5Util_getDumpData (GH, vindex, timelevel, slab, &outme,
+                                   &free_outme, geom);
   if (retval < 0)
   {
     return (retval);
@@ -426,7 +425,7 @@ static int IOHDF5Util_DumpGA (cGH *GH,
 #ifdef HAVE_PARALLEL
   if (ioUtilGH->unchunked)
   {
-    IOHDF5Util_collectiveDump (GH, index, timelevel, slab, outme, geom,
+    IOHDF5Util_collectiveDump (GH, vindex, timelevel, slab, outme, geom,
                                info->iohdf5_type, file);
     if (free_outme)
     {
@@ -441,7 +440,7 @@ static int IOHDF5Util_DumpGA (cGH *GH,
   /* Dump data held on IO processor */
   if (myproc == ioUtilGH->ioproc)
   {
-    IOHDF5Util_procDump (GH, index, timelevel, slab, outme, geom,
+    IOHDF5Util_procDump (GH, vindex, timelevel, slab, outme, geom,
                          myproc, info->iohdf5_type, check_exisiting_objects,
                          file);
   }
@@ -470,7 +469,7 @@ static int IOHDF5Util_DumpGA (cGH *GH,
                                     2*i + IOTAGBASE, pughGH->PUGH_COMM_WORLD,
                                     &ms));
 
-        IOHDF5Util_procDump (GH, index, timelevel, slab, tmpd, geom, i,
+        IOHDF5Util_procDump (GH, vindex, timelevel, slab, tmpd, geom, i,
                              info->iohdf5_type, check_exisiting_objects, file);
         free (tmpd);
       }
@@ -525,25 +524,21 @@ static int IOHDF5Util_DumpGA (cGH *GH,
 /*                             local functions                            */
 /**************************************************************************/
 static int IOHDF5Util_getDumpData (cGH *GH,
-                                   int index,
+                                   int vindex,
                                    int timelevel,
                                    ioHDF5Geo_t *slab, 
                                    void **outme,
                                    int *free_outme, 
-                                   CCTK_INT *geom,
-                                   int element_size)
+                                   CCTK_INT *geom)
 {
   ioGH *ioUtilGH;
-  pGExtras *extras=NULL;
-  CCTK_REAL4 *single_ptr;
-  int myproc, do_downsample;
+  int myproc;
   int i, sdim, vdim;             /*iteration, slab dim, variable dim */
   int *hsizes,*hsizes_global,*hsizes_offset; /* geometry information */
   int sdir[3];                      /* slab direction FIXME */
   int locdowns[3];                  /* Holds the downsampling in the order 
                                        specified in slab->direction[] */
   int slabstart[3];                 /* global start index for slab to extract */
-  int ip;
   void *data;
   char *fullname;
   
@@ -553,10 +548,6 @@ static int IOHDF5Util_getDumpData (cGH *GH,
   /* get GH extension for IOUtil */
   ioUtilGH = (ioGH *) CCTK_GHExtension (GH, "IO");
 
-  /* get the pointer to PUGH specific structures */
-  extras = ((pGA***) PUGH_pGH(GH)->variables)[index][timelevel]->extras;
-  data = CCTK_VarDataPtrI (GH, timelevel, index);
-
   /* Shortcuts */
   vdim = slab->vdim;
   sdim = slab->sdim;
@@ -571,104 +562,73 @@ static int IOHDF5Util_getDumpData (cGH *GH,
   for (i=0;i<sdim;i++)
     locdowns[i]=slab->downsample[slab->direction[i]];
 
-  /* Set downsample flag */
-  do_downsample = 0;
-  for (i = 0; i < sdim; i++)
-    do_downsample |= locdowns[i] > 1;
+  /* allocate array to hold size information of slab */
+  hsizes        = (int *) malloc (3 * sdim * sizeof (int));
+  hsizes_global = hsizes + 1*sdim;
+  hsizes_offset = hsizes + 2*sdim;
 
-  /* Simple case if no downsampling and sdim==vdim */
-  if (! do_downsample && sdim==vdim)
+  /* TEMPORARY FIX DUE TO INCONSISTENT DIR SPECIFICATION */
+  /* direction vector of 1d line in 3d volume */
+  if (sdim == 1)
   {
-    if (ioUtilGH->out_single) {
-      single_ptr = (CCTK_REAL4 *) malloc (extras->npoints*sizeof (CCTK_REAL4));
-      for (ip = 0; ip < extras->npoints; ip++)
-        single_ptr[ip] = (CCTK_REAL4) ((CCTK_REAL *) data)[ip];
-
-      *outme      = single_ptr;
-      *free_outme = 1;
-    } 
-    else 
-    {
-      *outme      = data;
-      *free_outme = 0;
-    }
-
-    for (i = 0; i < sdim; i++) {
-      geom[i + 0*sdim] = extras->lb[myproc][i];
-      geom[i + 1*sdim] = extras->lnsize[i];        
-      geom[i + 2*sdim] = extras->nsize[i];
-    }
+    sdir[0] = slab->direction[0] == 0;
+    sdir[1] = slab->direction[0] == 1;
+    sdir[2] = slab->direction[0] == 2;
   }
-  else  /* Call Hyperslab else */
-  {  
-
-    /* allocate array to hold size information of slab */
-    hsizes        = (int *) malloc (3 * sdim * sizeof (int));
-    hsizes_global = hsizes + 1*sdim;
-    hsizes_offset = hsizes + 2*sdim;
+  /* norm vector of 2d surface in 3d volume */
+  else if (sdim==2)
+  {
+    sdir[0] = slab->direction[0] == 1 && slab->direction[1] == 2;
+    sdir[1] = slab->direction[0] == 0 && slab->direction[1] == 2;
+    sdir[2] = slab->direction[0] == 0 && slab->direction[1] == 1;
+  }
+  /* spanning directions for 3d */
+  else if (sdim==3)
+  {
+    sdir[0] = slab->direction[0];
+    sdir[1] = slab->direction[1];
+    sdir[2] = slab->direction[2];
+  }
+  
+  /* Get the start indeces for the slab from origin. */
+  /* Slab_start from the geo structure is not a true start index,
+     it is currently used as the intersection point of three surfaces,
+     that's why two entries have to be set to zero in the case of a
+     surface (one entry for line)
+     FIXME */
+  for (i = 0; i < vdim; i++)
+  {
+    slabstart[i] = slab->origin[i];
+  }
+  for (i = 0; i < sdim; i++)
+  {
+    slabstart[slab->direction[i]] = 0;
+  }     
 
-    /* TEMPORARY FIX DUE TO INCONSISTENT DIR SPECIFICATION */
-    /* direction vector of 1d line in 3d volume */
-    if (sdim == 1)
-    {
-      sdir[0] = slab->direction[0] == 0;
-      sdir[1] = slab->direction[0] == 1;
-      sdir[2] = slab->direction[0] == 2;
-    }
-    /* norm vector of 2d surface in 3d volume */
-    else if (sdim==2)
-    {
-      sdir[0] = slab->direction[0] == 1 && slab->direction[1] == 2;
-      sdir[1] = slab->direction[0] == 0 && slab->direction[1] == 2;
-      sdir[2] = slab->direction[0] == 0 && slab->direction[1] == 1;
-    }
-    /* spanning directions for 3d */
-    else if (sdim==3)
-    {
-      sdir[0] = slab->direction[0];
-      sdir[1] = slab->direction[1];
-      sdir[2] = slab->direction[2];
-    }
-    
-    /* Get the start indeces for the slab from origin. */
-    /* Slab_start from the geo structure is not a true start index,
-       it is currently used as the intersection point of three surfaces,
-       that's why two entries have to be set to zero in the case of a
-       surface (one entry for line)
-       FIXME */
-    for (i = 0; i < vdim; i++)
-    {
-      slabstart[i] = slab->origin[i];
-    }
-    for (i = 0; i < sdim; i++)
-    {
-      slabstart[slab->direction[i]] = 0;
-    }     
+  if (NewHyperslab_GetLocalHyperslab (GH, vindex, timelevel, sdim, CCTK_VARIABLE_REAL4, NULL, slab->origin,
+                                   sdir, slab->length, locdowns, outme,
+                                   hsizes, hsizes_global, hsizes_offset) < 0)
+  {
+    fullname = CCTK_FullName (vindex);
+    CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
+                "Failed to extract hyperslab for variable '%s'", fullname);
+    free (fullname);
+    *free_outme = 0;
+    return (-1);
+  }
 
-    if (Hyperslab_GetLocalHyperslab (GH, index, timelevel, sdim, slab->origin,
-                                     sdir, slab->length, locdowns, outme,
-                                     hsizes, hsizes_global, hsizes_offset) < 0)
-    {
-      fullname = CCTK_FullName (index);
-      CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
-                  "Failed to extract hyperslab for variable '%s'", fullname);
-      free (fullname);
-      *free_outme = 0;
-      return (-1);
-    }
+  *free_outme = 1;
 
-    *free_outme = 1;
+  for (i = 0; i < sdim; i++)
+  {
+    geom[i + 0*sdim] = hsizes_offset[i];
+    geom[i + 1*sdim] = hsizes[i];        
+    geom[i + 2*sdim] = hsizes_global[i];
+    slab->actlen[i]  = hsizes_global[i];
+  }
 
-    for (i = 0; i < sdim; i++)
-    {
-      geom[i + 0*sdim] = hsizes_offset[i];
-      geom[i + 1*sdim] = hsizes[i];        
-      geom[i + 2*sdim] = hsizes_global[i];
-      slab->actlen[i]  = hsizes_global[i];
-    }
+  free (hsizes);
 
-    free (hsizes);
-  }
 #ifdef DEBUG_ME
   printf ("***** %dD \n",sdim);
   printf ("Lower bound: %d", (int) geom[0]);
@@ -726,7 +686,7 @@ static int IOHDF5Util_getDumpData (cGH *GH,
    @vtype      cGH *
    @vio        in
    @endvar
-   @var        index
+   @var        vindex
    @vdesc      global index of the variable to be dumped
    @vtype      int
    @vio        in
@@ -766,7 +726,7 @@ static int IOHDF5Util_getDumpData (cGH *GH,
    @endvar
 @@*/
 static void IOHDF5Util_procDump (cGH *GH,
-                                 int index,
+                                 int vindex,
                                  int timelevel,
                                  ioHDF5Geo_t *slab,
                                  void *outme,
@@ -820,7 +780,7 @@ static void IOHDF5Util_procDump (cGH *GH,
 
   /* build the unique dataset name from the variable's full name,
      the timelevel and the current iteration number */
-  fullname = CCTK_FullName (index);
+  fullname = CCTK_FullName (vindex);
   datasetname = (char *) malloc (strlen (fullname) + 80);
   sprintf (datasetname, "%s timelevel %d at iteration %d",
            fullname, timelevel, GH->cctk_iteration);
@@ -850,7 +810,7 @@ static void IOHDF5Util_procDump (cGH *GH,
     {
       IOHDF5_ERROR (dataset = H5Dcreate (file, datasetname,
                                          iohdf5_type, filespace, H5P_DEFAULT));
-      IOHDF5Util_DumpCommonAttributes (GH, index, timelevel, &geom[2*sdim],
+      IOHDF5Util_DumpCommonAttributes (GH, vindex, timelevel, &geom[2*sdim],
                                        slab, dataset);
     }
     else
@@ -880,7 +840,7 @@ static void IOHDF5Util_procDump (cGH *GH,
     if (proc == myproc)
     {
       IOHDF5_ERROR (group = H5Gcreate (file, datasetname, 0));
-      IOHDF5Util_DumpCommonAttributes (GH, index, timelevel, &geom[2*sdim],
+      IOHDF5Util_DumpCommonAttributes (GH, vindex, timelevel, &geom[2*sdim],
                                        slab, group);
       IOHDF5_ERROR (H5Gclose (group));
     }
@@ -930,7 +890,7 @@ static void IOHDF5Util_procDump (cGH *GH,
    @vtype      cGH *
    @vio        in
    @endvar
-   @var        index
+   @var        vindex
    @vdesc      global index of the variable to be dumped
    @vtype      int
    @vio        in
@@ -965,7 +925,7 @@ static void IOHDF5Util_procDump (cGH *GH,
    @endvar
 @@*/
 static void IOHDF5Util_collectiveDump (cGH *GH,
-                                       int index,
+                                       int vindex,
                                        int timelevel,
                                        ioHDF5Geo_t *slab,  
                                        void *outme,
@@ -1001,7 +961,7 @@ static void IOHDF5Util_collectiveDump (cGH *GH,
   }
 
   /* build the unique dataset name */
-  fullname = CCTK_FullName (index);
+  fullname = CCTK_FullName (vindex);
   datasetname = (char *) malloc (strlen (fullname) + 80);
   sprintf (datasetname, "%s timelevel %d at iteration %d",
            fullname, timelevel, GH->cctk_iteration);
@@ -1028,7 +988,7 @@ static void IOHDF5Util_collectiveDump (cGH *GH,
                                      H5P_DEFAULT));
   if (CCTK_MyProc (GH) == 0)
   {
-    IOHDF5Util_DumpCommonAttributes (GH, index, timelevel, &geom[2*sdim],
+    IOHDF5Util_DumpCommonAttributes (GH, vindex, timelevel, &geom[2*sdim],
                                      slab, dataset);
   }