diff --git a/tools/cooja/config/contiki_template.c b/tools/cooja/config/contiki_template.c
index 1cfb833db..d7f75041c 100644
--- a/tools/cooja/config/contiki_template.c
+++ b/tools/cooja/config/contiki_template.c
@@ -26,7 +26,7 @@
  * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  * SUCH DAMAGE.
  *
- * $Id: contiki_template.c,v 1.7 2008/02/10 22:36:36 oliverschmidt Exp $
+ * $Id: contiki_template.c,v 1.8 2008/11/20 16:36:27 fros4943 Exp $
  */
 
 /**
@@ -96,7 +96,7 @@
  * referenceVar is used for comparing absolute and process relative memory.
  * (this must not be static due to memory locations)
  */
-int referenceVar;
+long referenceVar;
 
 /*
  * process_run() infinite loop.
@@ -118,10 +118,10 @@ start_process_run_loop(void *data)
 
     /* Initialize communication stack */
     init_net();
-  
+
     /* Start user applications */
     autostart_start(autostart_processes);
-  
+
     while(1)
 	{
 		/* Always pretend we have processes left while inside process_run() */
@@ -145,8 +145,6 @@ start_process_run_loop(void *data)
 	}
 }
 
-extern unsigned long _end;
-
 /*---------------------------------------------------------------------------*/
 /**
  * \brief      Initialize a mote by starting processes etc.
@@ -179,9 +177,15 @@ Java_se_sics_cooja_corecomm_[CLASS_NAME]_init(JNIEnv *env, jobject obj)
  *             responsible Java part (MoteType.java).
  */
 JNIEXPORT void JNICALL
-Java_se_sics_cooja_corecomm_[CLASS_NAME]_getMemory(JNIEnv *env, jobject obj, jint start, jint length, jbyteArray mem_arr)
+Java_se_sics_cooja_corecomm_[CLASS_NAME]_getMemory(JNIEnv *env, jobject obj, jint rel_addr, jint length, jbyteArray mem_arr)
 {
-  (*env)->SetByteArrayRegion(env, mem_arr, 0, (size_t) length, (jbyte *) start);
+  (*env)->SetByteArrayRegion(
+      env,
+      mem_arr,
+      0,
+      (size_t) length,
+      (jbyte *) (((long)rel_addr) + referenceVar)
+  );
 }
 /*---------------------------------------------------------------------------*/
 /**
@@ -198,10 +202,13 @@ Java_se_sics_cooja_corecomm_[CLASS_NAME]_getMemory(JNIEnv *env, jobject obj, jin
  *             responsible Java part (MoteType.java).
  */
 JNIEXPORT void JNICALL
-Java_se_sics_cooja_corecomm_[CLASS_NAME]_setMemory(JNIEnv *env, jobject obj, jint start, jint length, jbyteArray mem_arr)
+Java_se_sics_cooja_corecomm_[CLASS_NAME]_setMemory(JNIEnv *env, jobject obj, jint rel_addr, jint length, jbyteArray mem_arr)
 {
   jbyte *mem = (*env)->GetByteArrayElements(env, mem_arr, 0);
-  memcpy((void *) start, mem, length);
+  memcpy(
+      (char*) (((long)rel_addr) + referenceVar),
+      mem,
+      length);
   (*env)->ReleaseByteArrayElements(env, mem_arr, mem, 0);
 }
 /*---------------------------------------------------------------------------*/
@@ -272,9 +279,9 @@ Java_se_sics_cooja_corecomm_[CLASS_NAME]_tick(JNIEnv *env, jobject obj)
  *             responsible Java part (MoteType.java).
  */
 JNIEXPORT jint JNICALL
-Java_se_sics_cooja_corecomm_[CLASS_NAME]_getReferenceAbsAddr(JNIEnv *env, jobject obj)
+Java_se_sics_cooja_corecomm_[CLASS_NAME]_setReferenceAddress(JNIEnv *env, jobject obj, jint addr)
 {
-  return (jint) &referenceVar;
+  referenceVar = (((long)&referenceVar) - ((long)addr));
 }
 
 /** @} */
diff --git a/tools/cooja/config/corecomm_template.java b/tools/cooja/config/corecomm_template.java
index c1ef362f5..b9a34001a 100644
--- a/tools/cooja/config/corecomm_template.java
+++ b/tools/cooja/config/corecomm_template.java
@@ -52,7 +52,7 @@ public class [CLASSNAME] extends CoreComm {
 
   public native void tick();
   public native void init();
-  public native int getReferenceAbsAddr();
-  public native void getMemory(int start, int length, byte[] mem);
-  public native void setMemory(int start, int length, byte[] mem);
+  public native void setReferenceAddress(int addr);
+  public native void getMemory(int rel_addr, int length, byte[] mem);
+  public native void setMemory(int rel_addr, int length, byte[] mem);
 }
diff --git a/tools/cooja/java/se/sics/cooja/CoreComm.java b/tools/cooja/java/se/sics/cooja/CoreComm.java
index 153a007b7..374fd250e 100644
--- a/tools/cooja/java/se/sics/cooja/CoreComm.java
+++ b/tools/cooja/java/se/sics/cooja/CoreComm.java
@@ -24,7 +24,7 @@
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *
- * $Id: CoreComm.java,v 1.11 2008/02/12 15:03:02 fros4943 Exp $
+ * $Id: CoreComm.java,v 1.12 2008/11/20 16:34:45 fros4943 Exp $
  */
 
 package se.sics.cooja;
@@ -361,35 +361,29 @@ public abstract class CoreComm {
   protected abstract void init();
 
   /**
-   * Returns absolute memory location of the core variable referenceVar. Used to
-   * get offset between relative and absolute memory addresses.
+   * Sets the relative memory address of the reference variable.
+   * Is used by Contiki to map between absolute and relative memory addresses.
    *
-   * @return Absolute memory address
+   * @param addr Relative address
    */
-  public abstract int getReferenceAbsAddr();
+  public abstract void setReferenceAddress(int addr);
 
   /**
    * Fills an byte array with memory segment identified by start and length.
    *
-   * @param start
-   *          Start address of segment
-   * @param length
-   *          Length of segment
-   * @param mem
-   *          Array to fill with memory segment
+   * @param relAddr Relative memory start address
+   * @param length Length of segment
+   * @param mem Array to fill with memory segment
    */
-  public abstract void getMemory(int start, int length, byte[] mem);
+  public abstract void getMemory(int relAddr, int length, byte[] mem);
 
   /**
    * Overwrites a memory segment identified by start and length.
    *
-   * @param start
-   *          Start address of segment
-   * @param length
-   *          Length of segment
-   * @param mem
-   *          New memory segment data
+   * @param relAddr Relative memory start address
+   * @param length Length of segment
+   * @param mem New memory segment data
    */
-  public abstract void setMemory(int start, int length, byte[] mem);
+  public abstract void setMemory(int relAddr, int length, byte[] mem);
 
 }
diff --git a/tools/cooja/java/se/sics/cooja/contikimote/ContikiMoteType.java b/tools/cooja/java/se/sics/cooja/contikimote/ContikiMoteType.java
index b0e1a8c9f..b09601490 100644
--- a/tools/cooja/java/se/sics/cooja/contikimote/ContikiMoteType.java
+++ b/tools/cooja/java/se/sics/cooja/contikimote/ContikiMoteType.java
@@ -26,7 +26,7 @@
  * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  * SUCH DAMAGE.
  *
- * $Id: ContikiMoteType.java,v 1.27 2008/05/02 05:47:22 fros4943 Exp $
+ * $Id: ContikiMoteType.java,v 1.28 2008/11/20 16:35:44 fros4943 Exp $
  */
 
 package se.sics.cooja.contikimote;
@@ -172,7 +172,7 @@ public class ContikiMoteType implements MoteType {
   // Core communication variables
   private String libraryClassName = null;
 
-  private int offsetRelToAbs = 0;
+  private int relAddressOfRefenceVariable = 0;
 
   private CoreComm myCoreComm = null;
 
@@ -385,7 +385,7 @@ public class ContikiMoteType implements MoteType {
 
     try {
       // Get offset between relative and absolute addresses
-      offsetRelToAbs = getReferenceAbsAddr() - (Integer) varAddresses.get("referenceVar");
+      relAddressOfRefenceVariable = (Integer) varAddresses.get("referenceVar");
     } catch (Exception e) {
       throw (MoteTypeCreationException) new MoteTypeCreationException(
           "JNI call error: " + e.getMessage()).initCause(e);
@@ -397,12 +397,14 @@ public class ContikiMoteType implements MoteType {
           "Could not parse section addresses correctly");
     }
 
+    myCoreComm.setReferenceAddress(relAddressOfRefenceVariable);
+
     // Create initial memory
     byte[] initialDataSection = new byte[dataSectionSize];
-    getCoreMemory(relDataSectionAddr + offsetRelToAbs, dataSectionSize,
+    getCoreMemory(relDataSectionAddr, dataSectionSize,
         initialDataSection);
     byte[] initialBssSection = new byte[bssSectionSize];
-    getCoreMemory(relBssSectionAddr + offsetRelToAbs, bssSectionSize,
+    getCoreMemory(relBssSectionAddr, bssSectionSize,
         initialBssSection);
     initialMemory = new SectionMoteMemory(varAddresses);
     initialMemory.setMemorySegment(relDataSectionAddr, initialDataSection);
@@ -437,8 +439,9 @@ public class ContikiMoteType implements MoteType {
    */
   public void setCoreMemory(SectionMoteMemory mem) {
     for (int i = 0; i < mem.getNumberOfSections(); i++) {
-      setCoreMemory(mem.getStartAddrOfSection(i) + offsetRelToAbs, mem
-          .getSizeOfSection(i), mem.getDataOfSection(i));
+      setCoreMemory(
+          mem.getStartAddrOfSection(i),
+          mem.getSizeOfSection(i), mem.getDataOfSection(i));
     }
   }
 
@@ -501,8 +504,8 @@ public class ContikiMoteType implements MoteType {
         } else {
           int oldAddress = (Integer) varAddresses.get(varName);
           if (oldAddress != varAddress) {
-            logger.warn("Warning, command response not matching previous entry of: "
-                + varName);
+            /*logger.warn("Warning, command response not matching previous entry of: "
+                + varName);*/
             nrMismatch++;
           }
 
@@ -514,7 +517,7 @@ public class ContikiMoteType implements MoteType {
     if (nrMismatch > 0) {
       logger.debug("Command response parsing summary: Added " + nrNew
           + " variables. Found " + nrOld
-          + " old variables. MISMATCHING ADDRESSES: " + nrMismatch);
+          + " old variables. Mismatching addresses: " + nrMismatch);
     } else {
       logger.debug("Command response parsing summary: Added " + nrNew
           + " variables. Found " + nrOld + " old variables");
@@ -536,7 +539,7 @@ public class ContikiMoteType implements MoteType {
       int size = mem.getSizeOfSection(i);
       byte[] data = mem.getDataOfSection(i);
 
-      getCoreMemory(startAddr + offsetRelToAbs, size, data);
+      getCoreMemory(startAddr, size, data);
     }
   }
 
@@ -613,16 +616,12 @@ public class ContikiMoteType implements MoteType {
     }
   }
 
-  private int getReferenceAbsAddr() {
-    return myCoreComm.getReferenceAbsAddr();
+  private void getCoreMemory(int relAddr, int length, byte[] data) {
+    myCoreComm.getMemory(relAddr, length, data);
   }
 
-  private void getCoreMemory(int start, int length, byte[] data) {
-    myCoreComm.getMemory(start, length, data);
-  }
-
-  private void setCoreMemory(int start, int length, byte[] mem) {
-    myCoreComm.setMemory(start, length, mem);
+  private void setCoreMemory(int relAddr, int length, byte[] mem) {
+    myCoreComm.setMemory(relAddr, length, mem);
   }
 
   private static String getFirstMatchGroup(Vector<String> lines, String regexp,