[petsc-users] petsc4py help with parallel execution

Thu Nov 15 10:59:29 CST 2018

Hi Matthew,

Does it mean that by using just command python3 simple_code.py (without
mpiexec) you *cannot* obtain a parallel execution?
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
However, we compilator arrives to KSP.solve(), somehow it turns on 8
processors.
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*)

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>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20181115/b07d2a38/attachment.html>