I have a large number of files to process. I have written a script that get, sort and plot the datas I want. So far, so good. I have tested it and it gives the desired result. Then I wanted to do this using multithreading. I have looked into the doc and examples on the internet, and using one thread in my program works fine. But when I use more, at some point I get random matplotlib error, and I suspect some conflict there, even though I use a function with names for the plots, and iI can't see where the problem could be. Here is the whole script should you need more comment, i'll add them. Thank you. #!/usr/bin/python import matplotlib matplotlib.use('GTKAgg') import numpy as np from scipy.interpolate import griddata import matplotlib.pyplot as plt import matplotlib.colors as mcl from matplotlib import rc #for latex import time as tm import sys import threading import Queue #queue in 3.2 and Queue in 2.7 ! import pdb #the debugger rc('text', usetex=True)#for latex map=0 #initialize the map index. It will be use to index the array like this: array[map,[x,y]] time=np.zeros(1) #an array to store the time middle_h=np.zeros((0,3)) #x phi c #for the middle of the box current_file=open("single_void_cyl_periodic_phi_c_middle_h_out",'r') for line in current_file: if line.startswith('# === time'): map+=1 np.append(time,[float(line.strip('# === time '))]) elif line.startswith('#'): pass else: v=np.fromstring(line,dtype=float,sep=' ') middle_h=np.vstack( (middle_h,v[[1,3,4]]) ) current_file.close() middle_h=middle_h.reshape((map,-1,3)) #3d array: map, x, phi,c ##### def load_and_plot(): #will load a map file, and plot it along with the corresponding profile loaded before while not exit_flag: print("fecthing work ...") #try: if not tasks_queue.empty(): map_index=tasks_queue.get() print("----> working on map: %s" %map_index) x,y,zp=np.loadtxt("single_void_cyl_growth_periodic_post_map_"+str(map_index),unpack=True, usecols=[1, 2,3]) for i,el in enumerate(zp): if el<0.: zp[i]=0. xv=np.unique(x) yv=np.unique(y) X,Y= np.meshgrid(xv,yv) Z = griddata((x, y), zp, (X, Y),method='nearest') figure=plt.figure(num=map_index,figsize=(14, 8)) ax1=plt.subplot2grid((2,2),(0,0)) ax1.plot(middle_h[map_index,:,0],middle_h[map_index,:,1],'*b') ax1.grid(True) ax1.axis([-15, 15, 0, 1]) ax1.set_title('Profiles') ax1.set_ylabel(r'$\phi$') ax1.set_xlabel('x') ax2=plt.subplot2grid((2,2),(1,0)) ax2.plot(middle_h[map_index,:,0],middle_h[map_index,:,2],'*r') ax2.grid(True) ax2.axis([-15, 15, 0, 1]) ax2.set_ylabel('c') ax2.set_xlabel('x') ax3=plt.subplot2grid((2,2),(0,1),rowspan=2,aspect='equal') sub_contour=ax3.contourf(X,Y,Z,np.linspace(0,1,11),vmin=0.) figure.colorbar(sub_contour,ax=ax3) figure.savefig('single_void_cyl_'+str(map_index)+'.png') plt.close(map_index) tasks_queue.task_done() else: print("nothing left to do, other threads finishing,sleeping 2 seconds...") tm.sleep(2) # except: # print("failed this time: %s" %map_index+". Sleeping 2 seconds") # tm.sleep(2) ##### exit_flag=0 nb_threads=2 tasks_queue=Queue.Queue() threads_list=[] jobs=list(range(map)) #each job is composed of a map print("inserting jobs in the queue...") for job in jobs: tasks_queue.put(job) print("done") #launch the threads for i in range(nb_threads): working_bee=threading.Thread(target=load_and_plot) working_bee.daemon=True print("starting thread "+str(i)+' ...') threads_list.append(working_bee) working_bee.start() #wait for all tasks to be treated tasks_queue.join() #flip the flag, so the threads know it's time to stop exit_flag=1 for t in threads_list: print("waiting for threads %s to stop..."%t) t.join() print("all threads stopped")