hunting for memory erros

adding make targets to call mrmc and mrmc-tests with valgrind
fixing some memory errors in SSM, SSMTest, BitVector
adding an additional check to readLabFile

CMakeLists.txt

@@ -171,3 +171,6 @@ configure_file (
   "${PROJECT_SOURCE_DIR}/mrmc-config.h.in"
   "${PROJECT_BINARY_DIR}/mrmc-config.h"
 )
+
+add_custom_target(memcheck valgrind --leak-check=full --show-reachable=yes ./mrmc examples/dtmc/crowds/crowds5_5.tra examples/dtmc/crowds/crowds5_5.lab)
+add_custom_target(memcheck-tests valgrind --leak-check=full --show-reachable=yes ./mrmc-tests)

src/parser/readLabFile.cpp

@@ -124,7 +124,15 @@ LabParser::LabParser(uint_fast64_t node_count, const char * filename)
 		{
 			buf += cnt;
 			cnt = strcspn(buf, separator); // position of next separator
-			if (cnt > 0)
+			if (cnt >= sizeof(proposition))
+			{
+				/*
+				 *	if token is longer than our buffer, the following strncpy code might get risky...
+				 */
+				LOG4CPLUS_ERROR(logger, "Wrong file format in (" << filename << "). Atomic proposition with length > " << (sizeof(proposition)-1) << " was found.");
+				throw mrmc::exceptions::wrong_file_format();
+			}
+			else if (cnt > 0)
 			{
 				/*
 				 *	next token is: #DECLARATION: just skip it

src/storage/BitVector.h

@@ -113,17 +113,17 @@ public:
 
 		if (initTrue) {
 			// Finally, create the full bucket array.
-			bucketArray = new uint64_t[bucketCount];
+			this->bucketArray = new uint64_t[bucketCount];
 
 			// Now initialize the values.
 			for (uint_fast64_t i = 0; i < bucketCount; ++i) {
-				bucketArray[i] = -1ll;
+				this->bucketArray[i] = -1ll;
 			}
 
 			truncateLastBucket();
 		} else {
 			// Finally, create the full bucket array.
-			bucketArray = new uint64_t[bucketCount]();
+			this->bucketArray = new uint64_t[bucketCount]();
 		}
 	}
 
@@ -135,7 +135,7 @@ public:
 	BitVector(const BitVector &bv) : bucketCount(bv.bucketCount), bitCount(bv.bitCount), endIterator(*this, bitCount, bitCount, false) {
 		LOG4CPLUS_WARN(logger, "Invoking copy constructor.");
 		bucketArray = new uint64_t[bucketCount];
-		std::copy(bv.bucketArray, bv.bucketArray + bucketCount, bucketArray);
+		std::copy(bv.bucketArray, bv.bucketArray + this->bucketCount, this->bucketArray);
 	}
 
 	//! Destructor
@@ -143,8 +143,8 @@ public:
 	 * Destructor. Frees the underlying bucket array.
 	 */
 	~BitVector() {
-		if (bucketArray != nullptr) {
-			delete[] bucketArray;
+		if (this->bucketArray != nullptr) {
+			delete[] this->bucketArray;
 		}
 	}
 
@@ -179,7 +179,7 @@ public:
 		}
 
 		// Reserve a temporary array for copying.
-		uint_fast64_t* tempArray = new uint_fast64_t[newBucketCount];
+		uint64_t* tempArray = new uint64_t[newBucketCount];
 
 		// Copy over the elements from the old bit vector.
 		uint_fast64_t copySize = (newBucketCount <= bucketCount) ? newBucketCount : bucketCount;
@@ -506,9 +506,9 @@ private:
 	 * from (bitCount + 1).
 	 */
 	void truncateLastBucket() {
-		if ((bitCount & mod64mask) != 0) {
-			uint64_t mask = ((1ll << (bitCount & mod64mask)) - 1ll);
-			bucketArray[bucketCount - 1] = bucketArray[bucketCount - 1] & mask;
+		if ((this->bitCount & mod64mask) != 0) {
+			uint64_t mask = ((1ll << (this->bitCount & mod64mask)) - 1ll);
+			this->bucketArray[this->bucketCount - 1] = this->bucketArray[this->bucketCount - 1] & mask;
 		}
 	}
 

src/storage/SquareSparseMatrix.h

@@ -112,19 +112,19 @@ public:
 	 */
 	~SquareSparseMatrix() {
 		setState(MatrixStatus::UnInitialized);
-		if (valueStorage != NULL) {
+		if (valueStorage != nullptr) {
 			//free(value_storage);
 			delete[] valueStorage;
 		}
-		if (columnIndications != NULL) {
+		if (columnIndications != nullptr) {
 			//free(column_indications);
 			delete[] columnIndications;
 		}
-		if (rowIndications != NULL) {
+		if (rowIndications != nullptr) {
 			//free(row_indications);
 			delete[] rowIndications;
 		}
-		if (diagonalStorage != NULL) {
+		if (diagonalStorage != nullptr) {
 			//free(diagonal_storage);
 			delete[] diagonalStorage;
 		}
@@ -507,7 +507,7 @@ public:
 			uint_fast64_t rowStart;
 			uint_fast64_t rowEnd;
 			uint_fast64_t zeroCount = 0;
-			for (uint_fast64_t row = 0; row <= rowCount; ++row) {
+			for (uint_fast64_t row = 0; row < rowCount; ++row) {
 				rowStart = rowIndications[row];
 				rowEnd = rowIndications[row + 1];
 				while (rowStart < rowEnd) {
@@ -518,7 +518,7 @@ public:
 			}
 
 			// Then add the elements on the diagonal.
-			for (uint_fast64_t i = 0; i <= rowCount; ++i) {
+			for (uint_fast64_t i = 0; i < rowCount; ++i) {
 				if (diagonalStorage[i] == 0) zeroCount++;
 				// tripletList.push_back(IntTriplet(i, i, diagonalStorage[i]));
 			}

test/storage/SquareSparseMatrixTest.cpp

@@ -157,6 +157,8 @@ TEST(SquareSparseMatrixTest, ConversionFromDenseEigen_ColMajor_SparseMatrixTest)
 			ASSERT_EQ(target, row * 10 + col);
 		}
 	}
+	
+	delete ssm;
 }
 
 TEST(SquareSparseMatrixTest, ConversionFromDenseEigen_RowMajor_SparseMatrixTest) {
@@ -187,6 +189,8 @@ TEST(SquareSparseMatrixTest, ConversionFromDenseEigen_RowMajor_SparseMatrixTest)
 			ASSERT_EQ(target, row * 10 + col);
 		}
 	}
+	
+	delete ssm;
 }
 
 TEST(SquareSparseMatrixTest, ConversionFromSparseEigen_ColMajor_SparseMatrixTest) {
@@ -234,6 +238,8 @@ TEST(SquareSparseMatrixTest, ConversionFromSparseEigen_ColMajor_SparseMatrixTest
 		ASSERT_TRUE(ssm->getValue(coeff.row(), coeff.col(), &target));
 		ASSERT_EQ(target, coeff.value());
 	}
+	
+	delete ssm;
 }
 
 TEST(SquareSparseMatrixTest, ConversionFromSparseEigen_RowMajor_SparseMatrixTest) {
@@ -281,6 +287,8 @@ TEST(SquareSparseMatrixTest, ConversionFromSparseEigen_RowMajor_SparseMatrixTest
 		ASSERT_TRUE(ssm->getValue(coeff.row(), coeff.col(), &target));
 		ASSERT_EQ(target, coeff.value());
 	}
+	
+	delete ssm;
 }
 
 TEST(SquareSparseMatrixTest, ConversionToSparseEigen_RowMajor_SparseMatrixTest) {
@@ -311,4 +319,7 @@ TEST(SquareSparseMatrixTest, ConversionToSparseEigen_RowMajor_SparseMatrixTest)
 			ASSERT_EQ(values[row * 10 + col], esm->coeff(row, col));
 		}
 	}
+	
+	delete esm;
+	delete ssm;
 }