[petsc-users] petsc4py help with parallel execution

Thu Nov 15 11:07:49 CST 2018

On Thu, Nov 15, 2018 at 11:59 AM Ivan Voznyuk <ivan.voznyuk.work at gmail.com>
wrote:

> Hi Matthew,
>
> Does it mean that by using just command python3 simple_code.py (without
> mpiexec) you *cannot* obtain a parallel execution?
>

As I wrote before, its not impossible. You could be directly calling PMI,
but I do not think you are doing that.

> It s been 5 days we are trying to understand with my colleague how he
> managed to do so.
> It means that by using simply python3 simple_code.py he gets 8 processors
> workiing.
> By the way, we wrote in his code few lines:
> rank = PETSc.COMM_WORLD.Get_rank()
> size = PETSc.COMM_WORLD.Get_size()
> and we got rank = 0, size = 1
>

This is MPI telling you that you are only running on 1 processes.

> However, we compilator arrives to KSP.solve(), somehow it turns on 8
> processors.
>

Why do you think its running on 8 processes?

> This problem is solved on his PC in 5-8 sec (in parallel, using *python3
> simple_code.py*), on mine it takes 70-90 secs (in sequantial, but with
> the same command *python3 simple_code.py*)
>

I think its much more likely that there are differences in the solver (use
-ksp_view to see exactly what solver was used), then
to think it is parallelism. Moreover, you would never ever ever see that
much speedup on a laptop since all these computations
are bandwidth limited.

  Thanks,

     Matt

> So, conclusion is that on his computer this code works in the same way as
> scipy: all the code is executed in sequantial mode, but when it comes to
> solution of system of linear equations, it runs on all available
> processors. All this with just running python3 my_code.py (without any
> mpi-smth)
>
> Is it an exception / abnormal behavior? I mean, is it something irregular
> that you, developers, have never seen?
>
> Thanks and have a good evening!
> Ivan
>
> P.S. I don't think I know the answer regarding Scipy...
>
>
> On Thu, Nov 15, 2018 at 2:39 PM Matthew Knepley <knepley at gmail.com> wrote:
>
>> On Thu, Nov 15, 2018 at 8:07 AM Ivan Voznyuk <ivan.voznyuk.work at gmail.com>
>> wrote:
>>
>>> Hi Matthew,
>>> Thanks for your reply!
>>>
>>> Let me precise what I mean by defining few questions:
>>>
>>> 1. In order to obtain a parallel execution of simple_code.py, do I need
>>> to go with mpiexec python3 simple_code.py, or I can just launch python3
>>> simple_code.py?
>>>
>>
>> mpiexec -n 2 python3 simple_code.py
>>
>>
>>> 2. This simple_code.py consists of 2 parts: a) preparation of matrix b)
>>> solving the system of linear equations with PETSc. If I launch mpirun (or
>>> mpiexec) -np 8 python3 simple_code.py, I suppose that I will basically
>>> obtain 8 matrices and 8 systems to solve. However, I need to prepare only
>>> one matrix, but launch this code in parallel on 8 processors.
>>>
>>
>> When you create the Mat object, you give it a communicator (here
>> PETSC_COMM_WORLD). That allows us to distribute the data. This is all
>> covered extensively in the manual and the online tutorials, as well as the
>> example code.
>>
>>
>>> In fact, here attached you will find a similar code (scipy_code.py) with
>>> only one difference: the system of linear equations is solved with scipy.
>>> So when I solve it, I can clearly see that the solution is obtained in a
>>> parallel way. However, I do not use the command mpirun (or mpiexec). I just
>>> go with python3 scipy_code.py.
>>>
>>
>> Why do you think its running in parallel?
>>
>>   Thanks,
>>
>>      Matt
>>
>>
>>> In this case, the first part (creation of the sparse matrix) is not
>>> parallel, whereas the solution of system is found in a parallel way.
>>> So my question is, Do you think that it s possible to have the same
>>> behavior with PETSC? And what do I need for this?
>>>
>>> I am asking this because for my colleague it worked! It means that he
>>> launches the simple_code.py on his computer using the command python3
>>> simple_code.py (and not mpi-smth python3 simple_code.py) and he obtains a
>>> parallel execution of the same code.
>>>
>>> Thanks for your help!
>>> Ivan
>>>
>>>
>>> On Thu, Nov 15, 2018 at 11:54 AM Matthew Knepley <knepley at gmail.com>
>>> wrote:
>>>
>>>> On Thu, Nov 15, 2018 at 4:53 AM Ivan Voznyuk via petsc-users <
>>>> petsc-users at mcs.anl.gov> wrote:
>>>>
>>>>> Dear PETSC community,
>>>>>
>>>>> I have a question regarding the parallel execution of petsc4py.
>>>>>
>>>>> I have a simple code (here attached simple_code.py) which solves a
>>>>> system of linear equations Ax=b using petsc4py. To execute it, I use the
>>>>> command python3 simple_code.py which yields a sequential performance. With
>>>>> a colleague of my, we launched this code on his computer, and this time the
>>>>> execution was in parallel. Although, he used the same command python3
>>>>> simple_code.py (without mpirun, neither mpiexec).
>>>>>
>>>>> I am not sure what you mean. To run MPI programs in parallel, you need
>>>> a launcher like mpiexec or mpirun. There are Python programs (like nemesis)
>>>> that use the launcher API directly (called PMI), but that is not part of
>>>> petsc4py.
>>>>
>>>>   Thanks,
>>>>
>>>>      Matt
>>>>
>>>>> My configuration: Ubuntu x86_64 Ubuntu 16.04, Intel Core i7, PETSc
>>>>> 3.10.2, PETSC_ARCH=arch-linux2-c-debug, petsc4py 3.10.0 in virtualenv
>>>>>
>>>>> In order to parallelize it, I have already tried:
>>>>> - use 2 different PCs
>>>>> - use Ubuntu 16.04, 18.04
>>>>> - use different architectures (arch-linux2-c-debug, linux-gnu-c-debug,
>>>>> etc)
>>>>> - ofc use different configurations (my present config can be found in
>>>>> make.log that I attached here)
>>>>> - mpi from mpich, openmpi
>>>>>
>>>>> Nothing worked.
>>>>>
>>>>> Do you have any ideas?
>>>>>
>>>>> Thanks and have a good day,
>>>>> Ivan
>>>>>
>>>>> --
>>>>> Ivan VOZNYUK
>>>>> PhD in Computational Electromagnetics
>>>>>
>>>>
>>>>
>>>> --
>>>> What most experimenters take for granted before they begin their
>>>> experiments is infinitely more interesting than any results to which their
>>>> experiments lead.
>>>> -- Norbert Wiener
>>>>
>>>> https://www.cse.buffalo.edu/~knepley/
>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>
>>>
>>>
>>> --
>>> Ivan VOZNYUK
>>> PhD in Computational Electromagnetics
>>> +33 (0)6.95.87.04.55
>>> My webpage <https://ivanvoznyukwork.wixsite.com/webpage>
>>> My LinkedIn <http://linkedin.com/in/ivan-voznyuk-b869b8106>
>>>
>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>>
>> https://www.cse.buffalo.edu/~knepley/
>> <http://www.cse.buffalo.edu/~knepley/>
>>
>
>
> --
> Ivan VOZNYUK
> PhD in Computational Electromagnetics
> +33 (0)6.95.87.04.55
> My webpage <https://ivanvoznyukwork.wixsite.com/webpage>
> My LinkedIn <http://linkedin.com/in/ivan-voznyuk-b869b8106>
>

-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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