Bringing IOPanda to a more up-to-date state.

Still developmental.


git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOPanda/trunk@7 38c3d835-c875-442e-b0fe-21c19ce1d001

9 files changed, 225 insertions, 214 deletions

diff --git a/src/DumpVar.c b/src/DumpVar.c
index f17a8a1..726eb0a 100644
--- a/src/DumpVar.c
+++ b/src/DumpVar.c
@@ -11,16 +11,10 @@
 
 #include <stdio.h>
 #include <stdlib.h>
-#ifdef SGI
-#include <time.h>
-#endif
 
 #include "cctk.h"
-#include "cctk_DefineThorn.h"
 #include "cctk_Parameters.h"
-#ifdef CACTUSPUGH_PUGH
 #include "CactusPUGH/PUGH/src/include/pugh.h"
-#endif
 #include "CactusBase/IOUtil/src/ioGH.h"
 #include "ioPandaGH.h"
 
@@ -32,17 +26,16 @@ static char *char_time_date = NULL;
 
 
 void IOPanda_getDumpData (cGH *GH, int index, int timelevel, void **outme,
-                         int *free_outme, CCTK_INT4 bnd [9], int element_size) 
+                         int *free_outme, CCTK_INT4 *geom, int element_size) 
 {
   DECLARE_CCTK_PARAMETERS
-  int i;
-  int myproc;
+  int i, myproc, do_downsample, dim;
   ioGH *ioUtilGH;
-  pGH *pughGH;
   CCTK_REAL4 *single_ptr;
   CCTK_REAL *real_ptr;
   CCTK_CHAR *char_ptr;
   CCTK_INT *int_ptr;
+  pGExtras *extras;
   void *data = CCTK_VarDataPtrI (GH, timelevel, index);
 
   /* to make the compiler happy */
@@ -51,19 +44,39 @@ void IOPanda_getDumpData (cGH *GH, int index, int timelevel, void **outme,
   char_ptr = NULL;
   int_ptr = NULL;
 
+  /* get the handle for IOUtil GH extensions */
   ioUtilGH = (ioGH *) GH->extensions [CCTK_GHExtensionHandle ("IO")];
-  pughGH = (pGH *) GH->extensions [CCTK_GHExtensionHandle ("PUGH")];
 
-  myproc = CCTK_MyProc (GH);
+  /* get the pGExtras pointer as a shortcut */
+  extras = ((pGA ***) PUGH_pGH (GH)->variables) [index][timelevel]->extras;
+
+  /* get the dimension of the variable */
+  dim = CCTK_GroupDimI (CCTK_GroupIndexFromVarI (index));
+
+  do_downsample = 0;
+  for (i = 0; i < dim; i++)
+    do_downsample |= ioUtilGH->downsample [i] > 1;
+
+  /* All the downsampling code is hard-coded for 3D data.
+     For other-dimensional variables we print a warning
+     and return the non-downsampled data. */
+  if (do_downsample && dim != 3) {
+    char *fullname = CCTK_FullName (index);
 
-  if (ioUtilGH->downsample_x == 1 &&
-      ioUtilGH->downsample_y == 1 &&
-      ioUtilGH->downsample_z == 1) {
+    CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
+                "No downsampling for %dD variable '%s' ! Downsampling is only "
+                "supported for 3D variables.", dim, fullname);
+    free (fullname);
+    do_downsample = 0;
+  }
+
+  /* Simple case if no downsampling */
+  if (! do_downsample) {
 
     if (ioUtilGH->out_single) {
-      single_ptr = (CCTK_REAL4 *) malloc (pughGH->npoints*sizeof (CCTK_REAL4));
+      single_ptr = (CCTK_REAL4 *) malloc (extras->npoints*sizeof (CCTK_REAL4));
 
-      for (i = 0; i < pughGH->npoints; i++)
+      for (i = 0; i < extras->npoints; i++)
         single_ptr [i] = (CCTK_REAL4) ((CCTK_REAL *) data) [i];
 
       *outme = single_ptr;
@@ -73,74 +86,65 @@ void IOPanda_getDumpData (cGH *GH, int index, int timelevel, void **outme,
       *free_outme = 0;
     }
 
-    for (i = 0; i < 3; i++) {
-      bnd [i] = GH->cctk_lbnd[i];     /* the bounds */
-      bnd [i+3] = GH->cctk_lsh[i];   /* the sizes */
-      bnd [i+6] = GH->cctk_gsh[i];  /* the global space */
+    /* set the bounds, the sizes, and the global shape */
+    for (i = 0; i < dim; i++) {
+      geom [i + 0*dim] = extras->lb [myproc][i];
+      geom [i + 1*dim] = extras->lnsize [i];
+      geom [i + 2*dim] = extras->nsize [i];
     }
 
   } else {
 
+    /* NOTE: the following downsampling code is hard-coded for 3D data */
+
     int start [3], end [3];
     int i, j, k, l;
 
-    /* Downsampling code ... */
-    bnd [6] = GH->cctk_gsh[0] / ioUtilGH->downsample_x;
-    if (GH->cctk_gsh[0] % ioUtilGH->downsample_x)
-      bnd [6]++;
-    bnd [7] = GH->cctk_gsh[1] / ioUtilGH->downsample_y;
-    if (GH->cctk_gsh[1] % ioUtilGH->downsample_y)
-      bnd [7]++;
-    bnd [8] = GH->cctk_gsh[2] / ioUtilGH->downsample_z;
-    if (GH->cctk_gsh[2] % ioUtilGH->downsample_z)
-      bnd [8]++;
-
-    if (verbose) 
-      printf ("Downsampled sizes (%d, %d, %d) -> (%d, %d, %d)\n",
-              GH->cctk_gsh[0], GH->cctk_gsh[1], GH->cctk_gsh[2],
-              (int) bnd [6], (int) bnd [7], (int) bnd [8]);
-    
-    /* Now figure out the local downsampling */
-    /* The local starts are the lb modded into the downsample */
+    /* downsampled global shape */
     for (i = 0; i < 3; i++) {
-      int downsample;
+      geom [i + 6] = extras->nsize [i] / ioUtilGH->downsample [i];
+      if (extras->nsize [i] % ioUtilGH->downsample [i])
+        geom [i + 6]++;
+    }
 
-      if (i == 0)
-        downsample = ioUtilGH->downsample_x;
-      else if (i == 1)
-        downsample = ioUtilGH->downsample_y;
-      else
-        downsample = ioUtilGH->downsample_z;
+    if (verbose)
+      CCTK_VInfo (CCTK_THORNSTRING, "Downsampled sizes (%d, %d, %d) -> "
+                  "(%d, %d, %d)",
+                  extras->nsize [0], extras->nsize [1], extras->nsize [2],
+                  (int) geom [6], (int) geom [7], (int) geom [8]);
 
-      bnd [i]   = GH->cctk_lbnd[i] / downsample;
-      start [i] = bnd [i] * downsample;
+    /* Now figure out the local downsampling */
+    /* The local starts are the lb modded into the downsample */
+    for (i = 0; i < 3; i++) {
+      geom [i]  = extras->lb [myproc][i] / ioUtilGH->downsample [i];
+      start [i] = geom [i] * ioUtilGH->downsample [i];
       if (start [i] <
-          GH->cctk_lbnd[i] + pughGH->ownership [PUGH_VERTEXCTR][i][0]) {
-        start [i] += downsample;
-        bnd [i] ++;
+          extras->lb [myproc][i] + extras->ownership [PUGH_NO_STAGGER][0][i]) {
+        start [i] += ioUtilGH->downsample [i];
+        geom [i] ++;
       }
-      end [i]   = ((GH->cctk_lbnd [i] +
-                   pughGH->ownership [PUGH_VERTEXCTR][i][1] - 1) / downsample)
-                   * downsample;
-      bnd [i+3] = (end [i] - start [i]) / downsample + 1;
+      end [i]   = ((extras->lb [myproc][i] +
+                    extras->ownership [PUGH_NO_STAGGER][1][i] - 1) /
+                   ioUtilGH->downsample [i]) * ioUtilGH->downsample [i];
+      geom [i+3] = (end [i] - start [i]) / ioUtilGH->downsample [i] + 1;
     }
 
     if (verbose) {
-      printf ("Downsample ranges (%d, %d, %d) -> (%d, %d, %d)\n",
-        start [0], start [1], start [2],
-        end [0], end [1], end [2]);
-      printf ("Local size/bound  (%d, %d, %d)  (%d, %d, %d)\n",
-        (int) bnd [3], (int) bnd [4], (int) bnd [5],
-        (int) bnd [0], (int) bnd [1], (int) bnd [2]);
+      CCTK_VInfo (CCTK_THORNSTRING, "Downsample ranges (%d, %d, %d) -> "
+                  "(%d, %d, %d)",
+                  start [0], start [1], start [2], end [0], end [1], end [2]);
+      CCTK_VInfo (CCTK_THORNSTRING, "Local size/bound  (%d, %d, %d)  "
+                  "(%d, %d, %d)", (int) geom [3], (int) geom [4], (int) geom[5],
+                  (int) geom [0], (int) geom [1], (int) geom [2]);
     }
 
     /* compute local ranges */
     for (i = 0; i < 3; i++) {
-      start [i] -= GH->cctk_lbnd [i];
-      end [i] -= GH->cctk_lbnd [i];
+      start [i] -= extras->lb [myproc][i];
+      end [i] -= extras->lb [myproc][i];
     }
 
-    *outme = malloc (bnd [3] * bnd [4] * bnd [5] * element_size);
+    *outme = malloc (geom [3] * geom [4] * geom [5] * element_size);
     *free_outme = 1;
 
     /* I hate it to repeat the loops for each case label
@@ -149,18 +153,18 @@ void IOPanda_getDumpData (cGH *GH, int index, int timelevel, void **outme,
     switch (CCTK_VarTypeI (index)) {
       case CCTK_VARIABLE_CHAR:
         char_ptr = (CCTK_CHAR *) *outme;
-        for (k = start [2]; k <= end [2]; k += ioUtilGH->downsample_z)
-          for (j = start [1]; j <= end [1]; j += ioUtilGH->downsample_y)
-            for (i = start [0]; i <= end [0]; i += ioUtilGH->downsample_x)
-              char_ptr [l++] = ((CCTK_CHAR *) data) [DI (pughGH, i, j, k)];
+        for (k = start [2]; k <= end [2]; k += ioUtilGH->downsample [2])
+          for (j = start [1]; j <= end [1]; j += ioUtilGH->downsample [1])
+            for (i = start [0]; i <= end [0]; i += ioUtilGH->downsample [0])
+              char_ptr [l++] = ((CCTK_CHAR *) data) [DATINDEX (extras, i, j, k)];
         break;
 
       case CCTK_VARIABLE_INT:
         int_ptr = (CCTK_INT *) *outme;
-        for (k = start [2]; k <= end [2]; k += ioUtilGH->downsample_z)
-          for (j = start [1]; j <= end [1]; j += ioUtilGH->downsample_y)
-            for (i = start [0]; i <= end [0]; i += ioUtilGH->downsample_x)
-              int_ptr [l++] = ((CCTK_INT *) data) [DI (pughGH, i, j, k)];
+        for (k = start [2]; k <= end [2]; k += ioUtilGH->downsample [2])
+          for (j = start [1]; j <= end [1]; j += ioUtilGH->downsample [1])
+            for (i = start [0]; i <= end [0]; i += ioUtilGH->downsample [0])
+              int_ptr [l++] = ((CCTK_INT *) data) [DATINDEX (extras, i, j, k)];
         break;
 
       case CCTK_VARIABLE_REAL:
@@ -168,14 +172,14 @@ void IOPanda_getDumpData (cGH *GH, int index, int timelevel, void **outme,
           single_ptr = (CCTK_REAL4 *) *outme;
         else
           real_ptr = (CCTK_REAL *) *outme;
-        for (k = start [2]; k <= end [2]; k += ioUtilGH->downsample_z)
-          for (j = start [1]; j <= end [1]; j += ioUtilGH->downsample_y)
-            for (i = start [0]; i <= end [0]; i += ioUtilGH->downsample_x)
+        for (k = start [2]; k <= end [2]; k += ioUtilGH->downsample [2])
+          for (j = start [1]; j <= end [1]; j += ioUtilGH->downsample [1])
+            for (i = start [0]; i <= end [0]; i += ioUtilGH->downsample [0])
               if (ioUtilGH->out_single)
                 single_ptr [l++] = (CCTK_REAL4)
-                                  (((CCTK_REAL *) data) [DI (pughGH, i, j, k)]);
+                                  (((CCTK_REAL *) data) [DATINDEX (extras, i, j, k)]);
               else
-                real_ptr [l++] = ((CCTK_REAL *) data) [DI (pughGH, i, j, k)];
+                real_ptr [l++] = ((CCTK_REAL *) data) [DATINDEX (extras, i, j, k)];
         break;
 
       default:
@@ -184,14 +188,18 @@ void IOPanda_getDumpData (cGH *GH, int index, int timelevel, void **outme,
     }
   }
 
-  if (verbose) {
-    printf ("Global size: %d %d %d\n",
-            (int) bnd [6], (int) bnd [7], (int) bnd [8]);
-    printf ("Lower bound: %d %d %d\n",
-            (int) bnd [0], (int) bnd [1], (int) bnd [2]);
-    printf ("Chunk size : %d %d %d\n",
-            (int) bnd [3], (int) bnd [4], (int) bnd [5]);
-  }
+#ifdef IOPANDA_DEBUG
+  printf ("Lower bound: %d", (int) geom [0]);
+  for (i = 1; i < dim; i++)
+    printf (" %d", (int) geom [i]);
+  printf ("\n");
+  printf ("Chunk size : %d", (int) geom [1*dim + 0]);
+  for (i = 1; i < dim; i++)
+    printf (" %d", (int) geom [1*dim + i]);
+  printf ("\n");
+  printf ("Global size: %d", (int) geom [2*dim + 0]);
+  for (i = 1; i < dim; i++)
+    printf (" %d", (int) geom [2*dim + i]);
+  printf ("\n");
+#endif
 }
-
-
diff --git a/src/GHExtension.c b/src/GHExtension.c
index 02aa021..b68459e 100644
--- a/src/GHExtension.c
+++ b/src/GHExtension.c
@@ -17,10 +17,8 @@
 #include "cctk.h"
 #include "cctk_DefineThorn.h"
 #include "cctk_Parameters.h"
-#ifdef	CACTUSPUGH_PUGH
-#include "CactusPUGH/PUGH/src/include/pugh.h"
-#endif
 #include "CactusBase/IOUtil/src/ioGH.h"
+#include "CactusPUGH/PUGH/src/include/pugh.h"
 #include "ioPandaGH.h"
 
 void Panda_Create(int, int);
@@ -33,8 +31,8 @@ void *IOPanda_SetupGH (tFleshConfig *config, int convergence_level, cGH *GH)
   numvars = CCTK_NumVars ();
 
   newGH = (pandaGH *) malloc (sizeof (pandaGH));
-  newGH->IO_3Dnum = (int *) malloc (numvars * sizeof (int));
-  newGH->IO_3Dlast = (int *) malloc (numvars * sizeof (int));
+  newGH->do_out3D = (char *) malloc (numvars * sizeof (char));
+  newGH->out3D_last = (int *) malloc (numvars * sizeof (int));
 
   return (newGH);
 }
@@ -45,42 +43,49 @@ int IOPanda_InitGH (cGH *GH)
   int i;
   ioGH *ioUtilGH;
   pandaGH *myGH; 
+  const cParamData *paramdata;
+
 
   /* get the handles for IOUtil and IOPanda extensions */
   ioUtilGH = (ioGH *) GH->extensions [CCTK_GHExtensionHandle ("IO")];
   myGH = (pandaGH *) GH->extensions [CCTK_GHExtensionHandle ("IOPanda")];
   
   /* How often to output */
-  myGH->IO_3Devery = out_every;
+  myGH->out3D_every = out_every > 0 ? out_every : -1;
   if (out3D_every > 0)
-    myGH->IO_3Devery = out3D_every;
+    myGH->out3D_every = out3D_every;
 
-  InitIONum (myGH->IO_3Dnum, out3D_vars);
+  ParseVarsForOutput (out3D_vars, myGH->do_out3D);
 
   /* Deal with the output directories */
-  myGH->outpfx_3D = outdir;
-  if (!CCTK_Equals(outdir3D,"outdir"))
-    myGH->outpfx_3D = outdir3D;
-
-  /* Create the output directories */
-  if (myGH->IO_3Devery > 0) {
-    if (CCTK_MyProc (GH) == 0) {
-      FILE *fp;
-
-      if (CCTK_mkdir (myGH->outpfx_3D) != 0)
-        CCTK_WARN (2,"Problem creating IO 3D directory");
-      fp = fopen("FILEPREFIX", "w");
-      fprintf(fp, "%s", myGH->outpfx_3D);
-      fclose(fp);
-    }
+  /* Check whether "outdir3D" was set.
+     If so take this dir otherwise default to "IO::outdir" */
+  paramdata = CCTK_ParameterData ("outdir3D", CCTK_THORNSTRING);
+  if (paramdata && paramdata->n_set > 0)
+    myGH->outdir3D = strdup (outdir3D);
+  else
+    myGH->outdir3D = strdup (outdir);
+
+  /* create the output dir */
+  if (CCTK_MyProc (GH) == 0) {
+    FILE *fp;
+
+    i = CCTK_mkdir (myGH->outdir3D);
+    if (i < 0)
+      CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
+          "Problem creating IOPanda 3D output directory '%s'", myGH->outdir3D);
+    else if (i > 0)
+      CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
+            "IOPanda 3D output directory '%s' already exists", myGH->outdir3D);
+    fp = fopen ("FILEPREFIX", "w");
+    fprintf (fp, "%s", myGH->outdir3D);
+    fclose (fp);
   }
 
-  for (i=0; i<CCTK_NumVars(); i++)
-    myGH->IO_3Dlast [i] = -1;
-
-  myGH->fileList_3D = NULL;
+  for (i = 0; i < CCTK_NumVars (); i++)
+    myGH->out3D_last [i] = -1;
 
-  Panda_Create(ioUtilGH->ioproc_every, 1);
+  Panda_Create (ioUtilGH->ioproc_every, 1);
 
   return (0);
 }
diff --git a/src/Output3D.c b/src/Output3D.c
index ea97b62..c7ef26a 100644
--- a/src/Output3D.c
+++ b/src/Output3D.c
@@ -9,24 +9,17 @@
  @@*/
 
 #include <stdio.h>
-#include <assert.h>
 #include <stdlib.h>
 #include <string.h>
 
 #include "cctk.h"
 #include "cctk_Parameters.h"
-#include "cctk_DefineThorn.h"
-#include "ioPandaGH.h"
-#include "Panda/c_interface.h"
 #include "CactusBase/IOUtil/src/ioGH.h"
-#ifdef CACTUSPUGH_PUGH
 #include "CactusPUGH/PUGH/src/include/pugh.h"
-#endif
-#ifdef SGI
-#include <time.h>
-#endif
-
 #include "external/IEEEIO/src/IOProtos.h"
+#include "ioPandaGH.h"
+#include "Panda/c_interface.h"
+
 
 int IOPanda_Output3DVarAs (cGH *GH, const char *var, const char *alias);
 int IOPanda_TimeFor3D (cGH *GH, int index);
@@ -43,10 +36,9 @@ void IOPanda_IEEEIOStructDump (cGH *GH, char *fname);
    @enddesc
    @calls    CCTK_GHExtensionHandle
              CCTK_NumVars
-             CCTK_ImplementationFromVar
              CCTK_VarName
              IOPanda_TimeFor3D
-             IOPanda_Output3DVarAs
+             IOPanda_Timestep
    @calledby
    @history
 
@@ -63,41 +55,30 @@ int IOPanda_Output3DGH (cGH *GH)
 {
   int i;
   pandaGH *myGH;
-  char *implementation;
-  char *name;
-  char *fullname;
   DECLARE_CCTK_PARAMETERS
 
   /* Get the GH extension for IOPanda */
   myGH = (pandaGH *) GH->extensions [CCTK_GHExtensionHandle ("IOPanda")];
 
-  if (myGH->IO_3Devery <= 0)
-    return;
+  if (myGH->out3D_every <= 0)
+    return (0);
 
   /* Loop over all variables */
   for (i = 0; i < CCTK_NumVars (); i++) {
     if (IOPanda_TimeFor3D (GH, i)) {
-      implementation = CCTK_ImpFromVarI (i);
-      name           = CCTK_VarName (i);
-      fullname       = (char *) malloc (strlen (implementation) +
-                                        strlen (name) + 3);
-      assert (fullname);
-      sprintf (fullname, "%s::%s", implementation, name);
-
       if (verbose) {
+        char *fullname = CCTK_FullName (i);
+
         printf ("IOPanda Output3DGH : \n");
-        printf ("  fullname/name = %s/%s\n", fullname, name);
+        printf ("  index/fullname = %d/%s\n", i, fullname);
+        free (fullname);
       }
 
-      IOPanda_Output3DVarAs (GH, fullname, name);
-
-      free (fullname);
+      /* Do the 3D output */
+      IOPanda_Timestep (GH, i, CCTK_VarName (i));
 
-      /* Register another 3D output for this GF */
-      myGH->IO_3Dnum [i]++;
-
-      /* Register GF as having 3D output this iteration */
-      myGH->IO_3Dlast [i] = GH->cctk_iteration;
+      /* Register variable as having 3D output this iteration */
+      myGH->out3D_last [i] = GH->cctk_iteration;
     }
   }
 
@@ -144,18 +125,12 @@ int IOPanda_Output3DVarAs (cGH *GH, const char *fullname, const char *alias)
 {
   DECLARE_CCTK_PARAMETERS
   int index;
-  pandaGH *myGH;
 
   index = CCTK_VarIndex(fullname);
 
-  /* Get the GH extension for IOPanda */
-  myGH = (pandaGH *) GH->extensions [CCTK_GHExtensionHandle ("IOPanda")];
-
   if (verbose) {
     printf ("\nIn IOPanda Output3DVarAs\n-------------------\n");
-    printf ("  Fullname = -%s-\n", fullname);
-    printf ("  Alias = -%s-\n", alias);
-    printf ("  Index = %d\n", index);
+    printf ("  index/fullname/alias = %d/%s/%s\n", index, fullname, alias);
   }
 
   /* Do the 3D output */
@@ -173,11 +148,6 @@ int IOPanda_Output3DVarAs (cGH *GH, const char *fullname, const char *alias)
    Decides if it is time to output a variable using the IOPanda 3D output
    method
    @enddesc
-   @calls    CCTK_GHExtensionHandle
-             CCTK_GroupTypeFromVarI
-             CCTK_WARN
-             CCTK_QueryGroupStorageI
-             CCTK_GroupNameFromVarI
    @calledby IOPanda_Output3DGH
    @history
 
@@ -203,28 +173,18 @@ int IOPanda_TimeFor3D (cGH *GH, int index)
   /* Get the GH extension for IOPanda */
   myGH = (pandaGH *) GH->extensions [CCTK_GHExtensionHandle ("IOPanda")];
 
-  /* Check this GF should be output */
-  if (! (myGH->IO_3Dnum [index] != 0 &&
-         GH->cctk_iteration % myGH->IO_3Devery == 0))
+  /* Check this variable should be output */
+  if (! (myGH->do_out3D [index] && GH->cctk_iteration % myGH->out3D_every == 0))
     return (0);
 
-  /* Check GF not already output this iteration */
-  if (myGH->IO_3Dlast [index] == GH->cctk_iteration) {
-      CCTK_WARN (2, "Already done 3D output in IOPanda");
-      return (0);
-  }
-
-  /* Check GF has storage */
-  if (! CCTK_QueryGroupStorageI (GH,
-            CCTK_GroupIndexFromVarI(index))) {
-    char *fullname = CCTK_FullName (index);
-    char *msg = (char *) malloc (80 + strlen (fullname));
+  /* Check variable not already output this iteration */
+  if (myGH->out3D_last [index] == GH->cctk_iteration) {
+      char *fullname = CCTK_FullName (index);
 
-    sprintf (msg, "No IOPandaIO 3D output for '%s' (no storage)", fullname);
-    CCTK_WARN (2, msg);
-    free (fullname);
-    free (msg);
-    return (0);
+      CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
+                  "Already done IOPanda 3D output for '%s'", fullname);
+      free (fullname);
+      return (0);
   }
 
   return (1);
@@ -264,7 +224,7 @@ int IOPanda_TriggerOutput3D (cGH *GH, int index)
 {
   DECLARE_CCTK_PARAMETERS
   pandaGH *myGH;
-  char *varname;
+  const char *varname;
 
   varname = CCTK_VarName (index);
 
@@ -273,23 +233,19 @@ int IOPanda_TriggerOutput3D (cGH *GH, int index)
 
   if (verbose) {
     printf("\nIn IOPanda TriggerOutput3D\n---------------------\n");
-    printf("  Index = %d\n", index);
-    printf("  Variable = -%s-\n", varname);
+    printf("  index/name = %d/%s\n", index, varname);
   }
 
   /* Do the 3D output */
   IOPanda_Timestep (GH, index, varname);
 
-  /* Register another 3D output for this GF */
-  myGH->IO_3Dnum [index]++;
-
-  /* Register GF as having 3D output this iteration */
-  myGH->IO_3Dlast [index] = GH->cctk_iteration;
+  /* Register variable as having 3D output this iteration */
+  myGH->out3D_last [index] = GH->cctk_iteration;
 
   return (0);
 }
 
-void IOPanda_Timestep(cGH *GH, int index, const char *alias)
+void IOPanda_Timestep (cGH *GH, int index, const char *alias)
 {
   DECLARE_CCTK_PARAMETERS
   void *data;
@@ -307,8 +263,19 @@ void IOPanda_Timestep(cGH *GH, int index, const char *alias)
     return;
   } 
   
+  /* check if variable has storage assigned */
+  if (! CCTK_QueryGroupStorageI (GH, CCTK_GroupIndexFromVarI (index))) {
+    char *fullname = CCTK_FullName (index);
+
+    CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
+                "No IOPanda 3D output for '%s' (no storage)", fullname);
+    free (fullname);
+    return;
+  }
+
+  /* get the handles for PUGH and IOUtil GH extensions */
+  pughGH = PUGH_pGH (GH);
   ioUtilGH = (ioGH *) GH->extensions [CCTK_GHExtensionHandle ("IO")];
-  pughGH = (pGH *) GH->extensions [CCTK_GHExtensionHandle ("PUGH")];
   
   ainfo.name_ = (char *)alias;
   
@@ -342,8 +309,11 @@ void IOPanda_Timestep(cGH *GH, int index, const char *alias)
     }
   }
   
+  /* FIXME: rank */
   ainfo.mem_rank_ = 3;
-  tmp2[0] = pughGH->nprocz; tmp2[1] = pughGH->nprocy; tmp2[2] = pughGH->nprocx;
+  tmp2[0] = pughGH->Connectivity [2]->nprocs [2];
+  tmp2[1] = pughGH->Connectivity [2]->nprocs [1];
+  tmp2[2] = pughGH->Connectivity [2]->nprocs [0];
   ainfo.mem_layout_ = tmp2;
   dist1[0] = dist1[1] = dist1[2] = BLOCK;
   ainfo.mem_dist_ = dist1;
@@ -361,12 +331,18 @@ void IOPanda_Timestep(cGH *GH, int index, const char *alias)
   IOPanda_getDumpData(GH, index, timelevel, &data, &free_flag, bnd, 
 		      ainfo.esize_);
   ainfo.data_ = (char *)data;
-  ainfo.stencil_width_ = pughGH->nghostzones;
 
+  /*** FIXME: asymmetric ghostzones */
+  ainfo.stencil_width_ = GH->cctk_nghostzones [0];
 
   PandaTimestep(&ainfo);
+  if (free_flag)
+    free (data);
+
   IOPanda_AddCommonAttributes(GH, index, timelevel, ainfo.size_, ainfo.name_);
-  if (PandaIsNewFile(ainfo.name_)) IOPanda_IEEEIOStructDump(GH, ainfo.name_);
+
+  if (PandaIsNewFile(ainfo.name_))
+    IOPanda_IEEEIOStructDump(GH, ainfo.name_);
 }
 
 void IOPanda_AddCommonAttributes (cGH *GH, int index, int timelevel,
@@ -425,14 +401,15 @@ void IOPanda_AddCommonAttributes (cGH *GH, int index, int timelevel,
   Panda_WriteAttribute (fname, "min_ext",FLOAT64,3,d3_to_IO);
   Panda_WriteAttribute (fname, "max_ext",FLOAT64, 3,d3_to_IO+3);
 
-  d3_to_IO [0] = GH->cctk_delta_space [0] * ioUtilGH->downsample_x;
-  d3_to_IO [1] = GH->cctk_delta_space [1] * ioUtilGH->downsample_y;
-  d3_to_IO [2] = GH->cctk_delta_space [2] * ioUtilGH->downsample_z;
+  /* FIXME: dimension */
+  d3_to_IO [0] = GH->cctk_delta_space [0] * ioUtilGH->downsample[0];
+  d3_to_IO [1] = GH->cctk_delta_space [1] * ioUtilGH->downsample[1];
+  d3_to_IO [2] = GH->cctk_delta_space [2] * ioUtilGH->downsample[2];
   Panda_WriteAttribute (fname, "delta", FLOAT64, 3,d3_to_IO);
 
-  if (ioUtilGH->downsample_x > 1 ||
-      ioUtilGH->downsample_y > 1 ||
-      ioUtilGH->downsample_z > 1) {
+  if (ioUtilGH->downsample[0] > 1 ||
+      ioUtilGH->downsample[1] > 1 ||
+      ioUtilGH->downsample[2] > 1) {
     d3_to_IO [0] = GH->cctk_delta_space [0];
     d3_to_IO [1] = GH->cctk_delta_space [1];
     d3_to_IO [2] = GH->cctk_delta_space [2];
diff --git a/src/Panda/c_interface.C b/src/Panda/c_interface.C
index b6085d6..571e166 100644
--- a/src/Panda/c_interface.C
+++ b/src/Panda/c_interface.C
@@ -106,7 +106,7 @@ void PandaTimestep(ArrayInfo *ptr)
 		    ptr->data_, ptr->stencil_width_);
 
   global_bear->app_barrier();
-  printf("---------------- Panda Timestep -------------------\n");
+//  printf("---------------- Panda Timestep -------------------\n");
   //printf("name %s rank %d size %d %d %d esize %d mem_layout %d %d %d disk_layout %d stencil_width_ %d\n", ptr->name_, ptr->rank_, ptr->size_[0], ptr->size_[1], ptr->size_[2], ptr->esize_, ptr->mem_layout_[0], ptr->mem_layout_[1], ptr->mem_layout_[2], ptr->disk_layout_[0], ptr->stencil_width_);
 
   array->timestep();
diff --git a/src/Panda/make.code.defn b/src/Panda/make.code.defn
index dd9edc3..0604ab6 100644
--- a/src/Panda/make.code.defn
+++ b/src/Panda/make.code.defn
@@ -2,6 +2,8 @@ SRCS = App_Info.C Array.C ArrayDistribution.C ArrayLayout.C Attribute.C Chunk.C
 
 SUBDIRS = 
 
+FILEPREFIX=\"bla\"
+
 # The 9000 names of the cygwin tools and T3E...
 TMPUN   := $(shell uname)
 ifeq ($(TMPUN), CYGWIN32_95)
@@ -21,7 +23,7 @@ endif
 # 64 Bit Irix
 ifeq ($(UNAME), IRIX64)
 
-CXXFLAGS += -DANSI -DFILEPREFIX -ptused 
+CXXFLAGS += -DANSI -DFILEPREFIX=${FILEPREFIX} -ptused 
 
 endif
 
@@ -49,7 +51,7 @@ endif
 # Linux
 ifeq ($(UNAME), Linux)
 
-CXXFLAGS += -DANSI 
+CXXFLAGS += -DANSI -DFILEPREFIX=${FILEPREFIX}
 
 endif
 
diff --git a/src/Panda/os-detected b/src/Panda/os-detected
index 4f378d7..8b13789 100644
--- a/src/Panda/os-detected
+++ b/src/Panda/os-detected
@@ -1 +1 @@
-irix
+
diff --git a/src/Startup.c b/src/Startup.c
index 2f9ada8..38ad63b 100644
--- a/src/Startup.c
+++ b/src/Startup.c
@@ -51,6 +51,20 @@ void IOPanda_Startup (void)
   int IO_GHExtension;
   int IOMethod;
 
+
+  if (CCTK_GHExtensionHandle ("IO") < 0)
+  {
+    CCTK_WARN (1, "Thorn IOUtil was not activated. "
+                  "No IOPanda IO methods will be enabled.");
+    return;
+  }
+  if (CCTK_GHExtensionHandle ("PUGH") < 0)
+  {
+    CCTK_WARN (1, "Thorn PUGH was not activated. "
+                  "No IOPanda IO methods will be enabled.");
+    return;
+  }
+
   IO_GHExtension = CCTK_RegisterGHExtension ("IOPanda");
   CCTK_RegisterGHExtensionSetupGH (IO_GHExtension, IOPanda_SetupGH);
   CCTK_RegisterGHExtensionInitGH (IO_GHExtension, IOPanda_InitGH);
diff --git a/src/ioPandaGH.h b/src/ioPandaGH.h
index f4da8d7..b4c20a8 100644
--- a/src/ioPandaGH.h
+++ b/src/ioPandaGH.h
@@ -14,19 +14,16 @@
 
 typedef struct IOPandaGH {
 
-  /* The number of times output */
-  int   *IO_3Dnum;
+  /* the number of times to output */
+  int  out3D_every;
 
-  /* How often to output */
-  int  IO_3Devery;
+  /* flags indicating output for var [i] */
+  char *do_out3D;
 
-  /* Directory in which to output */
-  char  *outpfx_3D;
+  /* directory in which to output */
+  char *outdir3D;
 
-  /* The last iteration output */
-  int   *IO_3Dlast;
-
-  /* filename database for opened files */
-  pNamedData *fileList_3D;
+  /* the last iteration output for var [i] */
+  int  *out3D_last;
 
 } pandaGH;
diff --git a/src/make.configuration.defn b/src/make.configuration.defn
index 448649e..b051521 100644
--- a/src/make.configuration.defn
+++ b/src/make.configuration.defn
@@ -1,6 +1,6 @@
 # make.configuration.defn for IOPanda
 
-# make sure that IOPanda was configured in with MPI and IEEEIO
+# make sure that IOPanda was configured in with MPI, PUGH, and IEEEIO
 
 ifeq ($(findstring external/IEEEIO,$(THORNS)),)
 .pseudo: MissingIEEEIOinIOPanda
@@ -10,6 +10,14 @@ MissingIEEEIOinIOPanda:
 	exit 2
 endif
 
+ifeq ($(findstring CactusPUGH/PUGH,$(THORNS)),)
+.pseudo: MissingPUGHinIOPanda
+MissingPUGHinIOPanda:
+	@echo "IOPanda: requires PUGH"
+	@echo "IOPanda: Please add CactusPUGH/PUGH or remove IOPanda from Thornlist !"
+	exit 2
+endif
+
 ifeq ($(strip $(MPI_LIBS)), )
 $(NAME): MissingMPIinIOPanda
 .pseudo: MissingMPIinIOPanda