I work with ATsam3a4c.I have a 4.5 keil compiler and a Jlink Jtag ,when I run a simple program for example an I/O ,on/ off output ,That make a blinking LED and a separate Timer everything is okay .but after I disconnect the jtag only the I\O was continue to blinking and Timer section Do not work.(I check the timer with timer out put pin).How can I resolve this problem.
Figure out what you're not initializing properly (clock, GPIO, etc), the debugger is likely configuring aspects of the system it is using, and you're not.
Everything is okay I have just changed the sequence of registers initialization.for example in USART in last line CLK register assigned.