Why is ctypes so slow to convert a Python list to a C array?

Question

The bottleneck of my code is currently a conversion from a Python list to a C array using ctypes, as described in this question.

A small experiment shows that it is indeed very slow, in comparison of other Python instructions:

import timeit
setup="from array import array; import ctypes; t = [i for i in range(1000000)];"
print(timeit.timeit(stmt='(ctypes.c_uint32 * len(t))(*t)',setup=setup,number=10))
print(timeit.timeit(stmt='array("I",t)',setup=setup,number=10))
print(timeit.timeit(stmt='set(t)',setup=setup,number=10))

Gives:

1.790962941000089
0.0911122129996329
0.3200237319997541

I obtained these results with CPython 3.4.2. I get similar times with CPython 2.7.9 and Pypy 2.4.0.

I tried runing the above code with perf, commenting the timeit instructions to run only one at a time. I get these results:

ctypes

 Performance counter stats for 'python3 perf.py':

       1807,891637      task-clock (msec)         #    1,000 CPUs utilized          
                 8      context-switches          #    0,004 K/sec                  
                 0      cpu-migrations            #    0,000 K/sec                  
            59 523      page-faults               #    0,033 M/sec                  
     5 755 704 178      cycles                    #    3,184 GHz                    
    13 552 506 138      instructions              #    2,35  insn per cycle         
     3 217 289 822      branches                  # 1779,581 M/sec                  
           748 614      branch-misses             #    0,02% of all branches        

       1,808349671 seconds time elapsed

array

 Performance counter stats for 'python3 perf.py':

        144,678718      task-clock (msec)         #    0,998 CPUs utilized          
                 0      context-switches          #    0,000 K/sec                  
                 0      cpu-migrations            #    0,000 K/sec                  
            12 913      page-faults               #    0,089 M/sec                  
       458 284 661      cycles                    #    3,168 GHz                    
     1 253 747 066      instructions              #    2,74  insn per cycle         
       325 528 639      branches                  # 2250,011 M/sec                  
           708 280      branch-misses             #    0,22% of all branches        

       0,144966969 seconds time elapsed

set

 Performance counter stats for 'python3 perf.py':

        369,786395      task-clock (msec)         #    0,999 CPUs utilized          
                 0      context-switches          #    0,000 K/sec                  
                 0      cpu-migrations            #    0,000 K/sec                  
           108 584      page-faults               #    0,294 M/sec                  
     1 175 946 161      cycles                    #    3,180 GHz                    
     2 086 554 968      instructions              #    1,77  insn per cycle         
       422 531 402      branches                  # 1142,636 M/sec                  
           768 338      branch-misses             #    0,18% of all branches        

       0,370103043 seconds time elapsed

The code with ctypes has less page-faults than the code with set and the same number of branch-misses than the two others. The only thing I see is that there are more instructions and branches (but I still don't know why) and more context switches (but it is certainly a consequence of the longer run time rather than a cause).

I therefore have two questions:

1. Why is ctypes so slow ?
2. Is there a way to improve performances, either with ctype or with another library?

Answer 1

The solution is to use the array module and cast the address or use the from_buffer method...

import timeit
setup="from array import array; import ctypes; t = [i for i in range(1000000)];"
print(timeit.timeit(stmt="v = array('I',t);assert v.itemsize == 4; addr, count = v.buffer_info();p = ctypes.cast(addr,ctypes.POINTER(ctypes.c_uint32))",setup=setup,number=10))
print(timeit.timeit(stmt="v = array('I',t);a = (ctypes.c_uint32 * len(v)).from_buffer(v)",setup=setup,number=10))
print(timeit.timeit(stmt='(ctypes.c_uint32 * len(t))(*t)',setup=setup,number=10))
print(timeit.timeit(stmt='set(t)',setup=setup,number=10))

It is then many times faster when using Python 3:

$ python3 convert.py
0.08303386811167002
0.08139665238559246
1.5630637975409627
0.3013848252594471

Answer 2

While this is not a definitive answer, the problem seems to be the constructor call with *t. Doing the following instead, decreases the overhead significantly:

array =  (ctypes.c_uint32 * len(t))()
array[:] = t

Test:

import timeit
setup="from array import array; import ctypes; t = [i for i in range(1000000)];"
print(timeit.timeit(stmt='(ctypes.c_uint32 * len(t))(*t)',setup=setup,number=10))
print(timeit.timeit(stmt='a = (ctypes.c_uint32 * len(t))(); a[:] = t',setup=setup,number=10))
print(timeit.timeit(stmt='array("I",t)',setup=setup,number=10))
print(timeit.timeit(stmt='set(t)',setup=setup,number=10))

Output:

1.7090932869978133
0.3084979929990368
0.08278547400186653
0.2775516299989249