diff -r 9b5c712f4488 -r 2e0fbdd152de targets/Xenomai/plc_Xenomai_main.c
--- a/targets/Xenomai/plc_Xenomai_main.c	Mon Apr 16 11:00:04 2018 +0200
+++ b/targets/Xenomai/plc_Xenomai_main.c	Mon Apr 16 16:11:18 2018 +0200
@@ -37,6 +37,15 @@
 #define PYTHON_PIPE_MINOR            3
 #define PIPE_SIZE                    1 
 
+// rt-pipes commands
+
+#define PYTHON_PENDING_COMMAND 1
+#define PYTHON_FINISH 2
+
+#define DEBUG_FINISH 2
+
+#define DEBUG_PENDING_DATA 1
+#define DEBUG_UNLOCK 1
 
 long AtomicCompareExchange(long* atomicvar,long compared, long exchange)
 {
@@ -82,6 +91,18 @@
         if (PLC_shutdown) break;
         rt_task_wait_period(NULL);
     }
+    /* since xenomai 3 it is not enough to close() 
+       file descriptor to unblock read()... */
+    {
+        /* explicitely finish python thread */
+        char msg = PYTHON_FINISH;
+        rt_pipe_write(&WaitPython_pipe, &msg, sizeof(msg), P_NORMAL);
+    }
+    {
+        /* explicitely finish debug thread */
+        char msg = DEBUG_FINISH;
+        rt_pipe_write(&WaitDebug_pipe, &msg, sizeof(msg), P_NORMAL);
+    }
 }
 
 static unsigned long __debug_tick;
@@ -256,7 +277,6 @@
     return 0;
 }
 
-#define DEBUG_UNLOCK 1
 void LeaveDebugSection(void)
 {
     if(AtomicCompareExchange( &debug_state, 
@@ -269,7 +289,6 @@
 
 extern unsigned long __tick;
 
-#define DEBUG_PENDING_DATA 1
 int WaitDebugData(unsigned long *tick)
 {
     char cmd;
@@ -319,8 +338,6 @@
     AtomicCompareExchange( &debug_state, DEBUG_BUSY, DEBUG_FREE);
 }
 
-#define PYTHON_PENDING_COMMAND 1
-
 #define PYTHON_FREE 0
 #define PYTHON_BUSY 1
 static long python_state = PYTHON_FREE;