[IPython-dev] Performance sanity check: 7.21s to scatter 5000X1000 float array to 7 engines

Anand Patil anand.prabhakar.patil@gmail....
Thu Jan 10 21:28:29 CST 2008


On Jan 10, 2008 2:25 PM, Anand Patil <anand.prabhakar.patil@gmail.com>
wrote:

> Hi all,
>
> Just trying to figure out whether something is wrong with my installation:
> I'm using mpi4py with mpich, on a machine with two quad-core 3.0Ghz intel
> processors. The following script takes 7.21s (wall time) with seven
> IPEngines, with almost all of the time spent in the scatterAll() operation:
>
>
> from numpy import *
> from ipython1 import *
> import ipython1.kernel.api as kernel
> rc = kernel.RemoteController(('127.0.0.1',10105))
>
> C=ones((5000,1000),dtype=float)
> rc.scatterAll('C',C)
>
> rc.resetAll()
>
>
> Is this fairly typical, and if not is there anything I can do to speed up
> the pushing and pulling?
>
> Thanks,
> Anand Patil
>


I got similar results with OpenMPI. Here are the profiler results:

In [11]: run -p test
         2809230 function calls in 9.891 CPU seconds

   Ordered by: internal time

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
      618    6.075    0.010    6.075    0.010 {method 'recv' of
'_socket.socket' objects}
        6    1.484    0.247    1.484    0.247 <string>:1(sendall)
        1    0.980    0.980    1.855    1.855 base64.py:285(encode)
   701757    0.371    0.000    0.371    0.000 {binascii.b2a_base64}
        1    0.216    0.216    0.216    0.216 {cPickle.dumps}
   701759    0.205    0.000    0.205    0.000 {method 'read' of '
cStringIO.StringI' objects}
       60    0.183    0.003    0.183    0.003 {method 'join' of 'str'
objects}
   702494    0.173    0.000    0.173    0.000 {method 'append' of 'list'
objects}
   701798    0.125    0.000    0.125    0.000 {len}
        3    0.040    0.013    2.079    0.693 xmlrpclib.py:1041(dumps)
        1    0.029    0.029    0.029    0.029 {method 'fill' of '
numpy.ndarray' objects}
        3    0.002    0.001    9.642    3.214 xmlrpclib.py:1427(__request)
        3    0.002    0.001    9.644    3.215 xmlrpclib.py:1146(__call__)
        1    0.001    0.001    9.815    9.815 multienginexmlrpc.py
:946(scatterAll)
       21    0.000    0.000    6.076    0.289 socket.py:321(readline)
        1    0.000    0.000    9.891    9.891 test.py:2(<module>)

Looks like it's pickling the array and sending it as a string. I think
mpi4py can send numerical arrays without pickling, so perhaps I don't have
it installed properly?

Thanks,
Anand
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