Fixed a bug for chunked I/O when outputting hyperslabs with boundaries cropped off.

git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@51 7842ec3a-9562-4be5-9c5b-06ba18f2b668

1 files changed, 71 insertions, 52 deletions

diff --git a/src/DumpVar.c b/src/DumpVar.c
index 96b441d..fdca24a 100644
--- a/src/DumpVar.c
+++ b/src/DumpVar.c
@@ -478,9 +478,15 @@ static int IOHDF5Util_DumpGA (const cGH *GH,
         CACTUS_MPI_ERROR (MPI_Recv (tmpd, incoming, info->mpi_type, i,
                                     2*i + IOTAGBASE, pughGH->PUGH_COMM_WORLD,
                                     &ms));
-
-        IOHDF5Util_procDump (GH, vindex, timelevel, request, tmpd, geom, i,
-                             info->iohdf5_type, check_exisiting_objects, file);
+      }
+      else
+      {
+        tmpd = NULL;
+      }
+      IOHDF5Util_procDump (GH, vindex, timelevel, request, tmpd, geom, i,
+                           info->iohdf5_type, check_exisiting_objects, file);
+      if (tmpd)
+      {
         free (tmpd);
       }
 
@@ -714,7 +720,6 @@ static void IOHDF5Util_procDump (const cGH *GH,
   hssize_t *chunk_origin;
   hsize_t *chunk_dims, *file_dims;
   hsize_t buffersize;
-  int locpoints;
   DECLARE_CCTK_PARAMETERS
 
 
@@ -724,17 +729,6 @@ static void IOHDF5Util_procDump (const cGH *GH,
   sdim = request->sdim;
   myproc = CCTK_MyProc (GH);
 
-  /* Check if there are points to output */
-  locpoints = geom[sdim];
-  for (i = 1; i < sdim; i++)
-  {
-    locpoints *= geom[sdim + i];
-  }
-  if (locpoints <= 0)
-  {
-    return;
-  }
-
   chunk_origin = (hssize_t *) malloc (sdim * sizeof (hssize_t));
   chunk_dims   = (hsize_t *)  malloc (2*sdim * sizeof (hsize_t));
   file_dims    = chunk_dims + sdim;
@@ -754,9 +748,6 @@ static void IOHDF5Util_procDump (const cGH *GH,
   sprintf (datasetname, "%s timelevel %d at iteration %d",
            fullname, timelevel, GH->cctk_iteration);
 
-  /* create the memspace according to chunk dims */
-  IOHDF5_ERROR (memspace = H5Screate_simple (sdim, chunk_dims, NULL));
- 
   /* if restart from recovery delete an already existing dataset
       so that it can be created as anew */
   if (proc == myproc && check_exisiting_objects)
@@ -766,6 +757,16 @@ static void IOHDF5Util_procDump (const cGH *GH,
     IOHDF5_ERROR (H5Eset_auto (myGH->print_error_fn, myGH->print_error_fn_arg));
   }
 
+  if (outme)
+  {
+    /* create the memspace according to chunk dims */
+    IOHDF5_ERROR (memspace = H5Screate_simple (sdim, chunk_dims, NULL));
+  }
+  else
+  {
+    memspace = -1;
+  }
+
   if (ioUtilGH->unchunked)
   {
     /* create the (global) filespace and set the hyperslab for the chunk */
@@ -786,6 +787,7 @@ static void IOHDF5Util_procDump (const cGH *GH,
       }
       IOHDF5_ERROR (dataset = H5Dcreate (file, datasetname,
                                          iohdf5_type, filespace, plist));
+      IOHDF5_ERROR (H5Pclose (plist));
       IOHDF5Util_DumpCommonAttributes (GH, vindex, timelevel, &geom[2*sdim],
                                        request, dataset);
     }
@@ -794,20 +796,24 @@ static void IOHDF5Util_procDump (const cGH *GH,
       IOHDF5_ERROR (dataset = H5Dopen (file, datasetname));
     }
 
-    /* increase the buffer size if the default isn't sufficient */
-    IOHDF5_ERROR (plist = H5Pcreate (H5P_DATASET_XFER));
-    buffersize = H5Dget_storage_size (dataset);
-    if (buffersize > H5Pget_buffer (plist, NULL, NULL))
+    if (memspace >= 0)
     {
-      IOHDF5_ERROR (H5Pset_buffer (plist, buffersize, NULL, NULL));
-    }
+      /* increase the buffer size if the default isn't sufficient */
+      IOHDF5_ERROR (plist = H5Pcreate (H5P_DATASET_XFER));
+      buffersize = H5Dget_storage_size (dataset);
+      if (buffersize > H5Pget_buffer (plist, NULL, NULL))
+      {
+        IOHDF5_ERROR (H5Pset_buffer (plist, buffersize, NULL, NULL));
+      }
 
-    /* write the data */
-    IOHDF5_ERROR (H5Dwrite (dataset, iohdf5_type, memspace, filespace,
-                            plist, outme));
+      /* write the data */
+      IOHDF5_ERROR (H5Dwrite (dataset, iohdf5_type, memspace, filespace,
+                              plist, outme));
 
-    /* and close the transfer property list and the file dataspace */
-    IOHDF5_ERROR (H5Pclose (plist));
+      /* close the transfer property list */
+      IOHDF5_ERROR (H5Pclose (plist));
+    }
+    /* close the file dataspace */
     IOHDF5_ERROR (H5Sclose (filespace));
   }
   else
@@ -821,33 +827,46 @@ static void IOHDF5Util_procDump (const cGH *GH,
       IOHDF5_ERROR (H5Gclose (group));
     }
 
-    /* now the chunk dataset for each processor is created within the group */
-    chunkname = (char *) malloc (strlen (datasetname) + 20);
-    sprintf (chunkname, "%s/chunk%d", datasetname, proc - myproc);
-    IOHDF5_ERROR (plist = H5Pcreate (H5P_DATASET_CREATE));
-    /* enable compression for chunked dataset if compression was requested */
-    if (compression_level)
+    if (memspace >= 0)
+    {
+      /* now the chunk dataset for each processor is created within the group */
+      chunkname = (char *) malloc (strlen (datasetname) + 20);
+      sprintf (chunkname, "%s/chunk%d", datasetname, proc - myproc);
+      IOHDF5_ERROR (plist = H5Pcreate (H5P_DATASET_CREATE));
+      /* enable compression for chunked dataset if compression was requested */
+      if (compression_level)
+      {
+        IOHDF5_ERROR (H5Pset_chunk (plist, sdim, chunk_dims));
+        IOHDF5_ERROR (H5Pset_deflate (plist, compression_level));
+      } 
+      /* create the chunk dataset and dump the chunk data */
+      IOHDF5_ERROR (dataset = H5Dcreate (file, chunkname,
+                                         iohdf5_type, memspace, plist));
+      IOHDF5_ERROR (H5Pclose (plist));
+      IOHDF5_ERROR (H5Dwrite (dataset, iohdf5_type, H5S_ALL, H5S_ALL,
+                              H5P_DEFAULT, outme));
+
+      /* add the "origin" attribute for the chunk */
+      WRITE_ATTRIBUTE ("chunk_origin", geom, dataset, myGH->array_dataspace,
+                       sdim, IOHDF5_INT);
+
+      free (chunkname);
+    }
+    else
     {
-      IOHDF5_ERROR (H5Pset_chunk (plist, sdim, chunk_dims));
-      IOHDF5_ERROR (H5Pset_deflate (plist, compression_level));
-    } 
-    /* create the chunk dataset and dump the chunk data */
-    IOHDF5_ERROR (dataset = H5Dcreate (file, chunkname,
-                                       iohdf5_type, memspace, plist));
-    IOHDF5_ERROR (H5Pclose (plist));
-    IOHDF5_ERROR (H5Dwrite (dataset, iohdf5_type, H5S_ALL, H5S_ALL,
-                            H5P_DEFAULT, outme));
-
-    /* add the "origin" attribute for the chunk */
-    WRITE_ATTRIBUTE ("chunk_origin", geom, dataset, myGH->array_dataspace, sdim,
-                     IOHDF5_INT);
-
-    free (chunkname);
+      dataset = -1;
+    }
   }
 
   /* close the dataset and the memspace */
-  IOHDF5_ERROR (H5Dclose (dataset));
-  IOHDF5_ERROR (H5Sclose (memspace));
+  if (dataset >= 0)
+  {
+    IOHDF5_ERROR (H5Dclose (dataset));
+  }
+  if (memspace >= 0)
+  {
+    IOHDF5_ERROR (H5Sclose (memspace));
+  }
 
   /* free allocated resources */
   free (datasetname);