Write all the Cactus parameters into a dataset rather than a single string

attribute. This fixes a problem with very many parameters to dump as HDF5
has a 16k size limit on attributes.


git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@106 7842ec3a-9562-4be5-9c5b-06ba18f2b668

2 files changed, 48 insertions, 18 deletions

diff --git a/src/DumpUtils.c b/src/DumpUtils.c
index a37bb93..fd9c389 100644
--- a/src/DumpUtils.c
+++ b/src/DumpUtils.c
@@ -286,8 +286,13 @@ void IOHDF5Util_DumpCommonAttributes (const cGH *GH, const ioRequest *request,
    @author     Thomas Radke
    @desc
                Collects the parameters of all active implementations
-               into a single string and writes it as an attribute
-               attached to the CACTUS_PARAMETERS_GROUP group in the HDF5 file.
+               into a single string and writes it as a single dataset
+               into the CACTUS_PARAMETERS_GROUP group in the HDF5 file.
+
+               Note that we used to write the parameters string as a single
+               attribute attached to the CACTUS_PARAMETERS_GROUP group.
+               This caused problems with very long strings (HDF5 has a 16k-limit
+               on the total size of attributes).
    @enddesc
    @var        GH
    @vdesc      pointer to CCTK grid hierarchy
@@ -310,7 +315,8 @@ void IOHDF5Util_DumpParameters (const cGH *GH, int all, hid_t file)
 {
   ioHDF5UtilGH *myGH;
   char *parameters;
-  hid_t group;
+  hid_t group, dataspace, dataset;
+  hsize_t size;
   DECLARE_CCTK_PARAMETERS
 
 
@@ -325,9 +331,15 @@ void IOHDF5Util_DumpParameters (const cGH *GH, int all, hid_t file)
   if (parameters)
   {
     myGH = CCTK_GHExtension (GH, "IOHDF5Util");
+    size = strlen (parameters) + 1;
     HDF5_ERROR (group = H5Gcreate (file, CACTUS_PARAMETERS_GROUP, 0));
-    WRITE_ATTRIBUTE (ALL_PARAMETERS, parameters, group, myGH, 0,
-                     myGH->HDF5_STRING);
+    HDF5_ERROR (dataspace = H5Screate_simple (1, &size, NULL));
+    HDF5_ERROR (dataset = H5Dcreate (group, ALL_PARAMETERS, H5T_NATIVE_UCHAR,
+                                     dataspace, H5P_DEFAULT));
+    HDF5_ERROR (H5Dwrite (dataset, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL,
+                          H5P_DEFAULT, parameters));
+    HDF5_ERROR (H5Dclose (dataset));
+    HDF5_ERROR (H5Sclose (dataspace));
     HDF5_ERROR (H5Gclose (group));
 
     free (parameters);
diff --git a/src/RecoverVar.c b/src/RecoverVar.c
index 8724f7b..f8e63da 100644
--- a/src/RecoverVar.c
+++ b/src/RecoverVar.c
@@ -247,14 +247,14 @@ int IOHDF5Util_RecoverGHextensions (cGH *GH, const fileinfo_t *fileinfo)
          (don't have subcommunicators yet) */
 int IOHDF5Util_RecoverParameters (const fileinfo_t *fileinfo)
 {
-  hid_t group, attr, atype;
+  hid_t group, attr, dataset, atype;
   char *parameters;
   CCTK_INT4 parameterSize;
   DECLARE_CCTK_PARAMETERS
 
 
   /* To make the compiler happy */
-  group = attr = 0;
+  group = attr = dataset = -1;
   parameters = NULL;
   parameterSize = 0;
 
@@ -267,21 +267,35 @@ int IOHDF5Util_RecoverParameters (const fileinfo_t *fileinfo)
     }
 
     /* the parameters are stored in the CACTUS_PARAMETERS_GROUP group
-       in the attribute ALL_PARAMETERS */
+       in the attribute (old style) or dataset (new style) ALL_PARAMETERS */
     group = H5Gopen (fileinfo->file, CACTUS_PARAMETERS_GROUP);
     if (group > 0)
     {
-      attr = H5Aopen_name (group, ALL_PARAMETERS);
+      H5E_BEGIN_TRY
+      {
+        attr = H5Aopen_name (group, ALL_PARAMETERS);
+        dataset = H5Dopen (group, ALL_PARAMETERS);
+      } H5E_END_TRY
     }
 
-    if (group > 0 && attr > 0)
+    if (group >= 0 && (attr >= 0 || dataset >= 0))
     {
-      HDF5_ERROR (atype = H5Aget_type (attr));
-      parameterSize = H5Tget_size (atype);
-      parameters = malloc (parameterSize + 1);
-      HDF5_ERROR (H5Aread (attr, atype, parameters));
-      parameters[parameterSize] = 0;
-      HDF5_ERROR (H5Tclose (atype));
+      if (attr >= 0)
+      {
+        HDF5_ERROR (atype = H5Aget_type (attr));
+        parameterSize = H5Tget_size (atype);
+        parameters = malloc (parameterSize + 1);
+        HDF5_ERROR (H5Aread (attr, atype, parameters));
+        parameters[parameterSize] = 0;
+        HDF5_ERROR (H5Tclose (atype));
+      }
+      else
+      {
+        parameterSize = H5Dget_storage_size (dataset);
+        parameters = malloc (parameterSize);
+        HDF5_ERROR (H5Dread (dataset, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL,
+                             H5P_DEFAULT, parameters));
+      }
     }
     else
     {
@@ -289,11 +303,15 @@ int IOHDF5Util_RecoverParameters (const fileinfo_t *fileinfo)
                     "Is this really a Cactus HDF5 checkpoint file ?");
     }
 
-    if (attr > 0)
+    if (attr >= 0)
     {
       HDF5_ERROR (H5Aclose (attr));
     }
-    if (group > 0)
+    if (dataset >= 0)
+    {
+      HDF5_ERROR (H5Dclose (dataset));
+    }
+    if (group >= 0)
     {
       HDF5_ERROR (H5Gclose (group));
     }