from Tkinter import *
import tkFileDialog
import tkMessageBox
import os
import ttkimport serial
import timeit
import time######################################################################################
class MyApp:def __init__(self, parent):
########################################################
#Setup Framesself.MiddleFrame = Frame(parent) #Middle Frameself.MiddleFrame.pack()#GLOBAL VARIABLESself.chip_number = 0 #number of chip testing
############################################Middle Frame setup  Label(self.MiddleFrame, text='Done').grid(row=8, column=1, sticky = E)self.Done = Canvas(self.MiddleFrame, bg="yellow", width=10, height=10)self.Done.grid(row=8, column=2)         Label(self.MiddleFrame, text='Chip Number:').grid(row=9, column=1, sticky = E)#start buttonself.button1 = Button(self.MiddleFrame,state=NORMAL, command= self.start_pre)self.button1["text"]= "START"self.button1.grid(row=1, column=2, sticky = E)
########################################### 
#Action of Start Buttondef start_pre(self):x = 0while x<10000:         self.start_button()x=x+1#Talking to Boarddef start_button(self):#increase chip count number and updateself.chip_number += 1Label(self.MiddleFrame, text=str(self.chip_number)).grid(row=9, column=2, sticky = E)#reset-yellowself.reset_color()          print "Still Working", self.chip_numberself.Done.configure(background="green")self.Done.update_idletasks()                 ###############################################################
#Color Boxes
#Resetdef reset_color(self):self.Done.configure(background="yellow")self.Done.update_idletasks() 
###############################################################################################################
#Start Programs
root = Tk() #makes window
root.title("Interface")
myapp = MyApp(root) #this really runs program
root.mainloop() #keep window open                                                                           

With my program, i first push the start button. I will print "still working" and the GUi will update chip number and blink done light over and over. The start button go to function that will execute 10000 times. However after 3000 iterations, the gui freeze, but the program is still print "still working". How do I keep the gui from crashing?

There are many problems with your code. For one, this is fundamentally flawed:

while self.stop == True:         self.start_button()time.sleep(0.5)

You simply can't expect a GUI to behave properly with code like that. As a general rule of thumb you should never have the main thread of a GUI call sleep. Causing sleep prevents the event loop from processing any events, including low level events such as requests to refresh the screen.

The use of sleep has been asked and answered many times on stackoverflow. You might find some of those questions useful. For example,

• windows thinks tkinter is not responding
• Python Tkinter coords function not moving canvas objects inside loop
• How do widgets update in Tkinter?
• Tkinter multiple operations
• Python Tkinter Stopwatch Error

You have another problem that falls into the category of a memory leak. From that while loop, you call self.start_button() indefinitely. This happens about once a second, due to sleep being called for half a second in the loop, and another half a second in start_button.

Each time you call start_button, you create another label widget that you stack on top of all previous widgets in row 9, column 2. Eventually this will cause your program to crash. I'm surprised that it causes your program to fail so quickly, but that's beside the point.

My recommendation is to start over with a simple example that does nothing but update a label every second. Get that working so that you understand the basic mechanism. Then, once it's working, you can add in your code that reads from the serial port.