steerable Hyperslab capabilities for Streamed HDF5

git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOStreamedHDF5/trunk@11 0888f3d4-9f52-45d2-93bc-d00801ff5e46

6 files changed, 34 insertions, 25 deletions

diff --git a/src/DumpVar.c b/src/DumpVar.c
index 2c33110..e44f0d7 100644
--- a/src/DumpVar.c
+++ b/src/DumpVar.c
@@ -1,7 +1,7 @@
 /*@@
    @file      DumpVar.c
    @date      Fri May 21 1999
-   @author    Thomas Radke
+   @author    Thomas Radke / Gerd Lanfermann
    @desc 
    Do the actual writing of a variable.
    @enddesc 
@@ -37,6 +37,7 @@ static int GetHDF5type (StreamedHDF5GH *myGH, int vtype, hid_t *hdf5_type);
   @author     Thomas Radke
   @desc
               Generic dump routine, just calls the appropriate dump routine
+	      Extracts the data with Hyperslab.
   @enddesc
   @calledby   StreamedHDF5_DumpGH IOHDF5_Write3D
   @history
@@ -67,9 +68,10 @@ int StreamedHDF5_DumpVar (cGH *GH, int index, int timelevel, hid_t fid)
   DECLARE_CCTK_PARAMETERS
   int i, vdim;
   void *data;
-  int *origin, *directions, *lengths, *downsamples, *hsizes;
+  int *hsizes;
   hid_t hdf5_type;
   StreamedHDF5GH *myGH;
+  StreamGeo_t geo;
   int vtype;
 
 
@@ -83,26 +85,18 @@ int StreamedHDF5_DumpVar (cGH *GH, int index, int timelevel, hid_t fid)
                 "Unsupported variable type %d", vtype);
     return (-1);
   }
+  /* shortcut to the slab geometry */
+  geo = myGH->geo_output[index];
 
   /* get the dimension of the variable */
   vdim = CCTK_GroupDimI (CCTK_GroupIndexFromVarI (index));
 
-  origin      = (int *) malloc (5 * vdim * sizeof (int));
-  directions  = origin + 1*vdim;
-  lengths     = origin + 2*vdim;
-  downsamples = origin + 3*vdim;
-  hsizes      = origin + 4*vdim;
-
-  for (i = 0; i < vdim; i++)
-  {
-    origin [i]      = 0;
-    lengths [i]     = -1;
-    downsamples [i] = 1;
-  }
+  hsizes = (int*)malloc(geo.sdim*sizeof(int));
 
   data = NULL;
-  if (Hyperslab_GetHyperslab (GH, 0, index, timelevel, vdim, origin,
-                              directions, lengths, downsamples,
+
+  if (Hyperslab_GetHyperslab (GH, 0, index, timelevel, geo.sdim, geo.origin,
+                              geo.direction, geo.length, geo.downs,
                               &data, hsizes) < 0)
   {
     char *fullname = CCTK_FullName (index);
@@ -111,7 +105,6 @@ int StreamedHDF5_DumpVar (cGH *GH, int index, int timelevel, hid_t fid)
     CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
                 "Failed to extract hyperslab for variable '%s'", fullname);
     free (fullname);
-    free (origin);
     return (-1);
   }
 
@@ -122,7 +115,6 @@ int StreamedHDF5_DumpVar (cGH *GH, int index, int timelevel, hid_t fid)
 
   if (data)
     free (data);
-  free (origin);
 
   return (0);
 }
diff --git a/src/GHExtension.c b/src/GHExtension.c
index 9912b0f..b64386e 100644
--- a/src/GHExtension.c
+++ b/src/GHExtension.c
@@ -34,6 +34,7 @@ void *StreamedHDF5_SetupGH (tFleshConfig *config, int convergence_level, cGH *GH
 
   newGH = (StreamedHDF5GH *) malloc (sizeof (StreamedHDF5GH));
   newGH->do_output = (char *) malloc (numvars * sizeof (char));
+  newGH->geo_output = (StreamGeo_t*) malloc (numvars * sizeof (StreamGeo_t));
   newGH->out_last = (int *) malloc (numvars * sizeof (int));
 
   /* save the original error printing routine and its argument */
diff --git a/src/Output.c b/src/Output.c
index 199db92..7309065 100644
--- a/src/Output.c
+++ b/src/Output.c
@@ -261,7 +261,7 @@ static void CheckSteerableParameters (StreamedHDF5GH *myGH)
 
   /* re-parse the 'out_vars' parameter if it was changed */
   if (paramdata->n_set != out_vars_lastset) {
-    IOUtil_ParseVarsForOutput (out_vars, myGH->do_output);
+    ParseVarsForOutput (myGH, out_vars);
 
     /* Save the last setting of 'out_vars' parameter */
     out_vars_lastset = paramdata->n_set;
diff --git a/src/Startup.c b/src/Startup.c
index 650570f..bd1cdb9 100644
--- a/src/Startup.c
+++ b/src/Startup.c
@@ -151,9 +151,10 @@ static void *StreamedHDF5_SetupGH (tFleshConfig *config, int convergence_level,
   numvars = CCTK_NumVars ();
 
   newGH = (StreamedHDF5GH *) malloc (sizeof (StreamedHDF5GH));
-  newGH->do_output = (char *) malloc (numvars * sizeof (char));
-  newGH->out_last = (int *) malloc (numvars * sizeof (int));
-  newGH->socket = socket;
+  newGH->do_output  = (char *) malloc (numvars * sizeof (char));
+  newGH->geo_output = (StreamGeo_t*) malloc (numvars * sizeof (StreamGeo_t));
+  newGH->out_last   = (int *) malloc (numvars * sizeof (int));
+  newGH->socket     = socket;
 
   /* save the original error printing routine and its argument */
   CACTUS_IOHDF5_ERROR (H5Eget_auto (&newGH->printErrorFn,
@@ -197,7 +198,7 @@ static int StreamedHDF5_InitGH (cGH *GH)
   myGH->out_every = out_every > 0 ? out_every : -1;
   if (outHDF5_every > 0)
     myGH->out_every = outHDF5_every;
-  IOUtil_ParseVarsForOutput (out_vars, myGH->do_output);
+  ParseVarsForOutput(myGH, out_vars);
 
   for (i = 0; i < CCTK_NumVars (); i++)
     myGH->out_last [i] = -1;
diff --git a/src/StreamedHDF5GH.h b/src/StreamedHDF5GH.h
index f0433a7..020bd27 100644
--- a/src/StreamedHDF5GH.h
+++ b/src/StreamedHDF5GH.h
@@ -105,6 +105,19 @@ extern "C" {
                         H5T_NATIVE_INT : H5T_NATIVE_SHORT)
 #define IOHDF5_CHAR    H5T_NATIVE_CHAR
 
+#define STREAM_MAXDIM 5
+
+/* Geometry information structure for output variable */
+typedef struct 
+{
+  int vdim;
+  int sdim;
+  int direction[STREAM_MAXDIM];
+  int origin[STREAM_MAXDIM];
+  int length[STREAM_MAXDIM];
+  int downs[STREAM_MAXDIM];
+} StreamGeo_t;
+
 
 /* StreamedHDF5 GH extension structure */
 typedef struct StreamedHDF5GH
@@ -113,7 +126,8 @@ typedef struct StreamedHDF5GH
   int  out_every;
 
   /* flags indicating output for var [i] */
-  char   *do_output;
+  char        *do_output;
+  StreamGeo_t *geo_output;
 
   /* the last iteration output */
   int   *out_last;
diff --git a/src/make.code.defn b/src/make.code.defn
index bab18b5..6cdc182 100644
--- a/src/make.code.defn
+++ b/src/make.code.defn
@@ -2,4 +2,5 @@
 # $Header$
 
 # Source files in this directory
-SRCS = Startup.c GHExtension.c Output.c Write.c DumpVar.c
+SRCS = Startup.c GHExtension.c Output.c Write.c DumpVar.c ParseGeometry.c ParseVars.c
+