Merge pull request #150 from ComputationalRadiationPhysics/release-1.2.4

Release 1.2.4

Author: f-schmitt-zih

CHANGELOG.md

@@ -1,6 +1,18 @@
 Change Log for libSplash
 ================================================================
 
+Release 1.2.4
+-------------
+**Date:** 2015-01-25
+
+This release fixes a bug with parallel NULL reads.
+
+**Bug Fixes**
+
+ - Fix Null-Access Parallel Read Hang #148
+ - Fix compile error on Red Hat #147
+
+
 Release 1.2.3
 -------------
 **Date:** 2014-10-14

src/DCDataSet.cpp

@@ -453,7 +453,7 @@ namespace splash
         // dst buffer is allowed to be NULL
         // in this case, only the size of the dataset is returned
         // if the dataset is empty, return just its size as there is nothing to read
-        if ((dst != NULL) && (getNDims() > 0))
+        if (getNDims() > 0)
         {
             log_msg(3,
                     "\n ndims         = %llu\n"
@@ -480,18 +480,23 @@ namespace splash
             if (dst_dataspace < 0)
                 throw DCException(getExceptionString("read: Failed to create target dataspace"));
 
-            if (H5Sselect_hyperslab(dst_dataspace, H5S_SELECT_SET, dstOffset.getPointer(), NULL,
-                    srcSize.getPointer(), NULL) < 0 ||
-                    H5Sselect_valid(dst_dataspace) <= 0)
-                throw DCException(getExceptionString("read: Target dataspace hyperslab selection is not valid!"));
-
-            if (H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, srcOffset.getPointer(), NULL,
-                    srcSize.getPointer(), NULL) < 0 ||
-                    H5Sselect_valid(dataspace) <= 0)
-                throw DCException(getExceptionString("read: Source dataspace hyperslab selection is not valid!"));
+            if (!dst) {
+                H5Sselect_none(dst_dataspace);
+            } else {
+                if (H5Sselect_hyperslab(dst_dataspace, H5S_SELECT_SET, dstOffset.getPointer(), NULL,
+                        srcSize.getPointer(), NULL) < 0 ||
+                        H5Sselect_valid(dst_dataspace) <= 0)
+                    throw DCException(getExceptionString("read: Target dataspace hyperslab selection is not valid!"));
+            }
 
-            if (srcSize.getScalarSize() == 0)
+            if (!dst || srcSize.getScalarSize() == 0) {
                 H5Sselect_none(dataspace);
+            } else {
+                if (H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, srcOffset.getPointer(), NULL,
+                        srcSize.getPointer(), NULL) < 0 ||
+                        H5Sselect_valid(dataspace) <= 0)
+                    throw DCException(getExceptionString("read: Source dataspace hyperslab selection is not valid!"));
+            }
 
             if (H5Dread(dataset, this->datatype, dst_dataspace, dataspace, dsetReadProperties, dst) < 0)
                 throw DCException(getExceptionString("read: Failed to read dataset"));

src/include/splash/core/DCHelper.hpp

@@ -26,6 +26,7 @@
 
 #include <map>
 #include <cmath>
+#include <cstdlib>
 #include <sstream>
 #include <iostream>
 #include <hdf5.h>
@@ -147,7 +148,7 @@ namespace splash
             while (current_chunk_size < target_chunk_size)
             {
                 // test if increasing chunk size optimizes towards target chunk size
-                size_t chunk_diff = std::abs(target_chunk_size - (current_chunk_size * 2));
+                size_t chunk_diff = abs(target_chunk_size - (current_chunk_size * 2));
                 if (chunk_diff >= last_chunk_diff)
                     break;
 

src/include/splash/version.hpp

@@ -1,5 +1,5 @@
 /**
- * Copyright 2013-2014 Felix Schmitt, Axel Huebl
+ * Copyright 2013-2015 Felix Schmitt, Axel Huebl
  *
  * This file is part of libSplash. 
  *
@@ -26,7 +26,7 @@
 /** the splash version reflects the changes in API */
 #define SPLASH_VERSION_MAJOR 1
 #define SPLASH_VERSION_MINOR 2
-#define SPLASH_VERSION_PATCH 3
+#define SPLASH_VERSION_PATCH 4
 
 /** we can always handle files from the same major release
  *  changes in the minor number have to be backwards compatible

tests/Parallel_ZeroAccessTest.cpp

@@ -84,15 +84,19 @@ void Parallel_ZeroAccessTest::testZeroAccess()
     /* test loops */
     for (size_t loop = 0; loop < NUM_TEST_LOOPS; ++loop)
     {
+        int64_t *nullData = NULL;
+
         /* clear data buffer */
         for (size_t i = 0; i < dataSize; ++i)
             data[i] = -1;
 
         /* set and write number of data elements for this round */
         size_t elements = 0;
         size_t zeroAccess = rand() % 2;
-        if (!zeroAccess)
-         elements = (rand() % dataSize) + 1;
+        if (!zeroAccess) {
+            elements = (rand() % dataSize) + 1;
+            nullData = new int64_t[elements];
+        }
 
         size_t readElements = 100000;
         for (size_t i = 0; i < elements; ++i)
@@ -149,8 +153,19 @@ void Parallel_ZeroAccessTest::testZeroAccess()
         /* read data for comparison */
         pdc->read(10, Dimensions(readElements, 1, 1), Dimensions(myOffset, 0, 0),
                 "data", sizeRead, data);
-        
+
         CPPUNIT_ASSERT(sizeRead == Dimensions(elements, 1, 1));
+
+        /* read data, use NULL ptr if none elements to read */
+        pdc->read(10, Dimensions(readElements, 1, 1), Dimensions(myOffset, 0, 0),
+                "data", sizeRead, nullData);
+
+        CPPUNIT_ASSERT(sizeRead == Dimensions(elements, 1, 1));
+
+        if (nullData)
+        {
+            delete[] nullData;
+        }
 
         for (size_t i = 0; i < dataSize; ++i)
         {