Merge pull request #137 from ComputationalRadiationPhysics/dev

Release 1.2.1: Non-Extensible Data Sets

Author: f-schmitt-zih

CHANGELOG.md

@@ -1,6 +1,22 @@
 Change Log for libSplash
 ================================================================
 
+Release 1.2.1
+-------------
+**Date:** 2014-06-20
+
+This release contains a minor improvement in the data format.
+The internal format was increased to version 2.1 (which is
+backwards compatible to all 2.x formated files).
+
+**Misc**
+
+ - parallel simple data test re-enabled #130
+ - data sets: use fixed size (non-extensible) by default,
+   use `H5F_UNLIMTED` only in append mode #135
+ - update install notes #134
+
+
 Release 1.2.0
 -------------
 **Date:** 2014-04-30

doc/INSTALL.md

@@ -8,9 +8,8 @@ Requirements
 using the command
 `$ git clone git@github.com:ComputationalRadiationPhysics/libSplash.git`
 
-Building libSplash **requires HDF5 in version 1.8.6** or higher with **shared library support**
-(`--enable-shared`).
-However, we recommend that you use HDF5 1.8.11 or newer for best support and results.
+Building libSplash **requires HDF5 in version 1.8.6** or higher.
+For **MPI based parallel output** configure HDF5 with `--enable-parallel`.
 
 To use the CMakeLists.txt file which comes with the source code, you must have
 **CMake version 2.8.5** or higher installed.

src/DCDataSet.cpp

@@ -194,7 +194,8 @@ namespace splash
     }
 
     void DCDataSet::create(const CollectionType& colType,
-            hid_t group, const Dimensions size, uint32_t ndims, bool compression)
+            hid_t group, const Dimensions size, uint32_t ndims,
+            bool compression, bool extensible)
     throw (DCException)
     {
         log_msg(2, "DCDataSet::create (%s, size %s)", name.c_str(), size.toString().c_str());
@@ -222,7 +223,12 @@ namespace splash
         {
             hsize_t *max_dims = new hsize_t[ndims];
             for (size_t i = 0; i < ndims; ++i)
-                max_dims[i] = H5F_UNLIMITED;
+            {
+                if (extensible)
+                    max_dims[i] = H5F_UNLIMITED;
+                else
+                    max_dims[i] = getPhysicalSize()[i];
+            }
 
             dataspace = H5Screate_simple(ndims, getPhysicalSize().getPointer(), max_dims);
 

src/ParallelDataCollector.cpp

@@ -917,7 +917,9 @@ namespace splash
 
         DCParallelDataSet dataset(name);
         // always create dataset but write data only if all dimensions > 0
-        dataset.create(datatype, group, globalSize, ndims, this->options.enableCompression);
+        // not extensible
+        dataset.create(datatype, group, globalSize, ndims,
+                this->options.enableCompression, false);
         dataset.write(srcSelect, globalOffset, data);
         dataset.close();
     }
@@ -1017,8 +1019,9 @@ namespace splash
         group.openCreate(handles.get(id), group_path);
 
         DCParallelDataSet dataset(dset_name.c_str());
-        // create the empty dataset
-        dataset.create(type, group.getHandle(), globalSize, ndims, this->options.enableCompression);
+        // create the empty extensible dataset
+        dataset.create(type, group.getHandle(), globalSize, ndims,
+                this->options.enableCompression, true);
         dataset.close();
     }
 

src/SerialDataCollector.cpp

@@ -807,7 +807,9 @@ namespace splash
 
         DCDataSet dataset(name);
         // always create dataset but write data only if all dimensions > 0 and data available
-        dataset.create(datatype, group, select.count, ndims, this->enableCompression);
+        // not extensible
+        dataset.create(datatype, group, select.count, ndims,
+                this->enableCompression, false);
         if (data && (select.count.getScalarSize() > 0))
             dataset.write(select, Dimensions(0, 0, 0), data);
         dataset.close();
@@ -824,7 +826,8 @@ namespace splash
         if (!dataset.open(group))
         {
             Dimensions data_size(count, 1, 1);
-            dataset.create(datatype, group, data_size, 1, this->enableCompression);
+            // create dataset extensible
+            dataset.create(datatype, group, data_size, 1, this->enableCompression, true);
 
             if (count > 0)
                 dataset.write(Selection(data_size,

src/include/splash/core/DCDataSet.hpp

@@ -89,9 +89,10 @@ namespace splash
          * @param size target size
          * @param ndims number of dimensions
          * @param compression enables transparent compression on the data
+         * @param extensible enable the dataset to be extensible
          */
         void create(const CollectionType& colType, hid_t group, const Dimensions size,
-                uint32_t ndims, bool compression) throw (DCException);
+                uint32_t ndims, bool compression, bool extensible) throw (DCException);
 
         /**
          * Create an object reference

src/include/splash/version.hpp

@@ -31,6 +31,6 @@
  *  changes in the minor number have to be backwards compatible
  */
 #define SPLASH_FILE_FORMAT_MAJOR 2
-#define SPLASH_FILE_FORMAT_MINOR 0
+#define SPLASH_FILE_FORMAT_MINOR 1
 
 #endif	/* VERSION_HPP */

tests/run_parallel_tests

@@ -25,7 +25,7 @@ function testMPI()
     fi
 }
 
-#testMPI ./Parallel_SimpleDataTest.cpp.out 8 "Testing simple data read/write (parallel)..."
+testMPI ./Parallel_SimpleDataTest.cpp.out 8 "Testing simple data read/write (parallel)..."
 
 testMPI ./Parallel_ListFilesTest.cpp.out 1 "Testing list files (parallel)..."