Added new INTEGER parameter IOHDF5Util::compression_level (ranging from 0..9)

to set the compression rate of HDF5 datasets. 0 (which is the default) disables
compression, 1..9 set the level the same way as for gzip (higher levels compress
better but are more expensive to compute).


git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@48 7842ec3a-9562-4be5-9c5b-06ba18f2b668

2 files changed, 48 insertions, 16 deletions

diff --git a/param.ccl b/param.ccl
index 0d2e70b..b9e3052 100644
--- a/param.ccl
+++ b/param.ccl
@@ -1,6 +1,15 @@
 # Parameter definitions for thorn IOHDF5Util
 # $Header$
 
+#####################
+# Compression level
+#####################
+INT compression_level "Compression level to use for writing HDF5 data"
+{
+  0:9 :: "A value of zero disables compression"
+} 0
+
+
 ######################
 # Hyperslab parameters
 ######################
diff --git a/src/DumpVar.c b/src/DumpVar.c
index a2f9a21..b955599 100644
--- a/src/DumpVar.c
+++ b/src/DumpVar.c
@@ -709,7 +709,7 @@ static void IOHDF5Util_procDump (const cGH *GH,
   int myproc;
   ioGH *ioUtilGH;
   ioHDF5UtilGH *myGH;
-  hid_t group, dataset, memspace, filespace, xfer_plist;
+  hid_t group, dataset, memspace, filespace, plist;
   char *fullname, *datasetname, *chunkname;
   hssize_t *chunk_origin;
   hsize_t *chunk_dims, *file_dims;
@@ -776,8 +776,15 @@ static void IOHDF5Util_procDump (const cGH *GH,
        when writing its own data, otherwise the dataset is reopened */
     if (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));
+      }
       IOHDF5_ERROR (dataset = H5Dcreate (file, datasetname,
-                                         iohdf5_type, filespace, H5P_DEFAULT));
+                                         iohdf5_type, filespace, plist));
       IOHDF5Util_DumpCommonAttributes (GH, vindex, timelevel, &geom[2*sdim],
                                        request, dataset);
     }
@@ -787,19 +794,19 @@ static void IOHDF5Util_procDump (const cGH *GH,
     }
 
     /* increase the buffer size if the default isn't sufficient */
-    IOHDF5_ERROR (xfer_plist = H5Pcreate (H5P_DATASET_XFER));
+    IOHDF5_ERROR (plist = H5Pcreate (H5P_DATASET_XFER));
     buffersize = H5Dget_storage_size (dataset);
-    if (buffersize > H5Pget_buffer (xfer_plist, NULL, NULL))
+    if (buffersize > H5Pget_buffer (plist, NULL, NULL))
     {
-      IOHDF5_ERROR (H5Pset_buffer (xfer_plist, buffersize, NULL, NULL));
+      IOHDF5_ERROR (H5Pset_buffer (plist, buffersize, NULL, NULL));
     }
 
     /* write the data */
     IOHDF5_ERROR (H5Dwrite (dataset, iohdf5_type, memspace, filespace,
-                            xfer_plist, outme));
+                            plist, outme));
 
     /* and close the transfer property list and the file dataspace */
-    IOHDF5_ERROR (H5Pclose (xfer_plist));
+    IOHDF5_ERROR (H5Pclose (plist));
     IOHDF5_ERROR (H5Sclose (filespace));
   }
   else
@@ -816,9 +823,17 @@ static void IOHDF5Util_procDump (const cGH *GH,
     /* 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, H5P_DEFAULT));
+                                       iohdf5_type, memspace, plist));
+    IOHDF5_ERROR (H5Pclose (plist));
     IOHDF5_ERROR (H5Dwrite (dataset, iohdf5_type, H5S_ALL, H5S_ALL,
                             H5P_DEFAULT, outme));
 
@@ -916,7 +931,7 @@ static void IOHDF5Util_collectiveDump (const cGH *GH,
   DECLARE_CCTK_PARAMETERS
   int i, dim;
   ioHDF5GH *myGH;
-  hid_t dataset, memspace, filespace, xfer_plist;
+  hid_t dataset, memspace, filespace, plist;
   char *fullname, *datasetname;
   hssize_t *chunk_origin;
   hsize_t *chunk_dims, *file_dims;
@@ -964,8 +979,16 @@ static void IOHDF5Util_collectiveDump (const cGH *GH,
     H5Gunlink (file, datasetname);
     IOHDF5_ERROR (H5Eset_auto (myGH->print_error_fn, myGH->print_error_fn_arg));
   }
+  /* enable compression for chunked dataset if compression was requested */
+  IOHDF5_ERROR (plist = H5Pcreate (H5P_DATASET_CREATE));
+  if (compression_level)
+  {
+    IOHDF5_ERROR (H5Pset_chunk (plist, sdim, chunk_dims));
+    IOHDF5_ERROR (H5Pset_deflate (plist, compression_level));
+  }
   IOHDF5_ERROR (dataset = H5Dcreate (file, datasetname, hdf5io_type, filespace,
-                                     H5P_DEFAULT));
+                                     plist));
+  IOHDF5_ERROR (H5Pclose (plist));
   if (CCTK_MyProc (GH) == 0)
   {
     IOHDF5Util_DumpCommonAttributes (GH, vindex, timelevel, &geom[2*sdim],
@@ -973,19 +996,19 @@ static void IOHDF5Util_collectiveDump (const cGH *GH,
   }
 
   /* increase the buffer size if the default isn't sufficient */
-  IOHDF5_ERROR (xfer_plist = H5Pcreate (H5P_DATASET_XFER));
+  IOHDF5_ERROR (plist = H5Pcreate (H5P_DATASET_XFER));
   buffersize = H5Dget_storage_size (dataset);
-  if (buffersize > H5Pget_buffer (xfer_plist, NULL, NULL))
+  if (buffersize > H5Pget_buffer (plist, NULL, NULL))
   {
-    IOHDF5_ERROR (H5Pset_buffer (xfer_plist, buffersize, NULL, NULL));
+    IOHDF5_ERROR (H5Pset_buffer (plist, buffersize, NULL, NULL));
   }
 
   /* write the data */
-  IOHDF5_ERROR (H5Dwrite (dataset, hdf5io_type, memspace,
-                       filespace, xfer_plist, outme));
+  IOHDF5_ERROR (H5Dwrite (dataset, hdf5io_type, memspace, filespace, plist,
+                          outme));
 
   /* close resources */
-  IOHDF5_ERROR (H5Pclose (xfer_plist));
+  IOHDF5_ERROR (H5Pclose (plist));
   IOHDF5_ERROR (H5Sclose (filespace));
   IOHDF5_ERROR (H5Dclose (dataset));
   IOHDF5_ERROR (H5Sclose (memspace));