Add functions for safe memory allocation

8 files changed, 137 insertions, 7 deletions

diff --git a/Makefile b/Makefile
index be37846..8cc4277 100644
--- a/Makefile
+++ b/Makefile
@@ -36,6 +36,7 @@ lib/libgensvm.a: \
 	src/gensvm_kernel.o \
 	src/gensvm_lapack.o \
 	src/gensvm_matrix.o \
+	src/gensvm_memory.o \
 	src/gensvm_pred.o \
 	src/gensvm_strutil.o \
 	src/gensvm_sv.o \
@@ -49,6 +50,7 @@ lib/libgensvm.a: \
 		src/gensvm_init.o \
 		src/gensvm_io.o \
 		src/gensvm_matrix.o \
+		src/gensvm_memory.o \
 		src/gensvm_kernel.o \
 		src/gensvm_lapack.o \
 		src/gensvm_pred.o \
diff --git a/include/gensvm_memory.h b/include/gensvm_memory.h
new file mode 100644
index 0000000..bc4aae9
--- /dev/null
+++ b/include/gensvm_memory.h
@@ -0,0 +1,26 @@
+/**
+ * @file gensvm_memory.h
+ * @author Gertjan van den Burg
+ * @date May, 2016
+ * @brief Global definitions
+ *
+ */
+
+#ifndef GENSVM_MEMORY_H
+#define GENSVM_MEMORY_H
+
+#define Calloc(type, size) \
+	mycalloc(__FILE__, __LINE__, size, sizeof(type))
+#define Malloc(type, size) \
+	mymalloc(__FILE__, __LINE__, (size)*sizeof(type))
+#define Realloc(var, type, size) \
+	myrealloc(__FILE__, __LINE__, (size)*sizeof(type), var)
+#define Memset(var, type, size) \
+	memset(var, 0, (size)*sizeof(type))
+
+void *mycalloc(const char *file, int line, unsigned long size,
+	size_t typesize);
+void *mymalloc(const char *file, int line, unsigned long size);
+void *myrealloc(const char *file, int line, unsigned long size, void *var);
+
+#endif
diff --git a/include/globals.h b/include/globals.h
index eab1d9f..becde35 100644
--- a/include/globals.h
+++ b/include/globals.h
@@ -6,9 +6,8 @@
  *
  * @details
  * This header file contains defines and includes which are used in many
- * parts of the program. Most notable are the Calloc, Malloc and Memset
- * defines, which are commonly used to allocate memory. These functions
- * are shorthands for their lowercase counterparts.
+ * parts of the program. Most notably, it includes the gensvm_memory.h header
+ * which defines functions for safe memory allocation.
  *
  * Furthermore, a maximum and minimum function are defined here. These
  * functions have their own include guards, to ensure potential linked
@@ -24,11 +23,9 @@
 #include <stdbool.h>
 #include <string.h>
 
-#define MAX_LINE_LENGTH 1024
+#include "gensvm_memory.h"
 
-#define Calloc(type, n) (type *)calloc((n), sizeof(type))
-#define Malloc(type, n) (type *)malloc((n)*sizeof(type))
-#define Memset(var, type, n) memset(var, 0, (n)*sizeof(type))
+#define MAX_LINE_LENGTH 1024
 
 #ifndef MIN_MAX_DEFINE
 #define MIN_MAX_DEFINE
diff --git a/src/GenSVMtrain.c b/src/GenSVMtrain.c
index b9dc250..3bb9c09 100644
--- a/src/GenSVMtrain.c
+++ b/src/GenSVMtrain.c
@@ -14,6 +14,7 @@
 #include <time.h>
 #include <math.h>
 
+#include "globals.h"
 #include "libGenSVM.h"
 #include "gensvm.h"
 #include "gensvm_io.h"
diff --git a/src/gensvm_init.c b/src/gensvm_init.c
index 228e9fe..3b3f130 100644
--- a/src/gensvm_init.c
+++ b/src/gensvm_init.c
@@ -15,6 +15,7 @@
 
 #include <math.h>
 
+#include "globals.h"
 #include "gensvm.h"
 #include "gensvm_init.h"
 
diff --git a/src/gensvm_io.c b/src/gensvm_io.c
index d81f19b..c4798d8 100644
--- a/src/gensvm_io.c
+++ b/src/gensvm_io.c
@@ -10,6 +10,7 @@
  *
  */
 
+#include "globals.h"
 #include "gensvm.h"
 #include "gensvm_io.h"
 #include "gensvm_matrix.h"
diff --git a/src/gensvm_memory.c b/src/gensvm_memory.c
new file mode 100644
index 0000000..529ef79
--- /dev/null
+++ b/src/gensvm_memory.c
@@ -0,0 +1,101 @@
+/**
+ * @file gensvm_memory.c
+ * @author Gertjan van den Burg
+ * @date May, 2016
+ * @brief Utility functions for memory allocation
+ *
+ */
+
+#include "globals.h" // imports gensvm_memory.h
+#include "gensvm_util.h"
+
+/**
+ * @brief Wrapper for calloc() which warns when allocation fails
+ *
+ * @details
+ * This is a wrapper function around calloc from <stdlib.h>. It tries to
+ * allocate the requested memory and checks if the memory was correctly
+ * allocated. If not, an error is printed using err(), which describes the
+ * file and linenumber and size failed to allocate. After this, the program
+ * exits. See also the defines in gensvm_memory.h.
+ *
+ * @note
+ * This function should not be used directly. Calloc() should be used.
+ *
+ * @param[in] 	file 		filename used for error printing
+ * @param[in] 	line 		line number used for error printing
+ * @param[in] 	size 		the size to allocate
+ * @param[in] 	typesize 	the size of the type to allocate
+ * @return 			the pointer to the memory allocated
+ */
+void *mycalloc(const char *file, int line, unsigned long size,
+	       	size_t typesize)
+{
+	void *ptr = calloc(size, typesize);
+
+	if (!ptr) {
+		err("Could not allocate memory: %d bytes (%s:%d)\n",
+				size, file, line);
+		exit(EXIT_FAILURE);
+	}
+	return ptr;
+}
+
+/**
+ * @brief Wrapper for malloc() which warns when allocation fails
+ *
+ * @details
+ * This is a wrapper function around malloc from <stdlib.h>. It tries to
+ * allocate the requested memory and checks if the memory was correctly
+ * allocated. If not, an error is printed using err(), which describes the
+ * file and linenumber and size failed to allocate. After this, the program
+ * exits. See also the defines in gensvm_memory.h.
+ *
+ * @note
+ * This function should not be used directly. Malloc() should be used.
+ *
+ * @param[in] 	file 		filename used for error printing
+ * @param[in] 	line 		line number used for error printing
+ * @param[in] 	size 		the size to allocate
+ * @return 			the pointer to the memory allocated
+ */
+void *mymalloc(const char *file, int line, unsigned long size)
+{
+	void *ptr = malloc(size);
+	if (!ptr) {
+		err("Could not allocate memory: %d bytes (%s:%d)\n",
+				size, file, line);
+		exit(EXIT_FAILURE);
+	}
+	return ptr;
+}
+
+/**
+ * @brief Wrapper for realloc() which warns when allocation fails
+ *
+ * @details
+ * This is a wrapper function around realloc from <stdlib.h>. It tries to
+ * reallocate the requested memory and checks if the memory was correctly
+ * reallocated. If not, an error is printed using err(), which describes the
+ * file and linenumber and size failed to reallocate. After this, the program
+ * exits. See also the defines in gensvm_memory.h.
+ *
+ * @note
+ * This function should not be used directly. Realloc() should be used.
+ *
+ * @param[in] 	file 		filename used for error printing
+ * @param[in] 	line 		line number used for error printing
+ * @param[in] 	size 		the size to allocate
+ * @param[in] 	var 		the pointer to the memory to reallocate
+ * @return 			the pointer to the memory reallocated
+ */
+void *myrealloc(const char *file, int line, unsigned long size, void *var)
+{
+	void *ptr = realloc(var, size);
+	if (!ptr) {
+		err("Could not reallocate memory: %d bytes (%s:%d)\n",
+				size, file, line);
+		exit(EXIT_FAILURE);
+	}
+	return ptr;
+}
diff --git a/src/gensvm_train.c b/src/gensvm_train.c
index 8c32809..371970a 100644
--- a/src/gensvm_train.c
+++ b/src/gensvm_train.c
@@ -13,6 +13,7 @@
 #include <math.h>
 #include <cblas.h>
 
+#include "globals.h"
 #include "libGenSVM.h"
 #include "gensvm.h"
 #include "gensvm_lapack.h"