This solution reads both files in one pass, excludes blank lines, and prints common lines regardless of their position in the file:
with open('some_file_1.txt', 'r') as file1:
with open('some_file_2.txt', 'r') as file2:
same = set(file1).intersection(file2)
same.discard('\n')
with open('some_output_file.txt', 'w') as file_out:
for line in same:
file_out.write(line)
Link to solution here