calling external executor

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RITE Zhang

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Sep 2, 2020, 4:49:34 AM9/2/20
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Hi

I have encountered a problem for a long time.
In my python program using mpi4py, I need to spawn processes that call an external executor ('solver') as follows.

with open('log', 'wb') as outfile:
                p = subprocess.run(['./solver'], stdout=outfile, check=True) 


The problem is the code always going through the code, without really running the external executor. It gives the following error message.

subprocess.CalledProcessError: Command '['./solver']' returned non-zero exit status 15.

Rr if I use os.system('./solver'), it gets stuck


If not using mpi4py, for example, using multiprocessing, there is no problem. The solver itself does not use mpi.

I work under Linux.

Could anyone give a solution? Thank you.

Lisandro Dalcin

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Sep 2, 2020, 6:50:58 AM9/2/20
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What backend MPI implementation are you using?
Some MPI implementations have problems with the fork() system call, and that my be used by Python's subprocess module to implement its functionalities.

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Lisandro Dalcin
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Extreme Computing Research Center (ECRC)
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Yi Zhang

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Sep 2, 2020, 11:36:17 AM9/2/20
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Thank you. It seems mpich of conda.
It is a cluster with impi as default. I have tried to install mpi4py
with impi, however, always get failed, though I point mpicc to the
mpiicc of impi/bin.
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Lisandro Dalcin

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Sep 2, 2020, 12:01:57 PM9/2/20
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On Wed, 2 Sep 2020 at 18:36, Yi Zhang <zhang...@gmail.com> wrote:
Thank you. It seems mpich of conda.

I'm not sure what's going on. Could you send a minimal self-contained example reproducing the problem?
 
It is a cluster with impi as default. I have tried to install mpi4py
with impi, however, always get failed, though I point mpicc to the
mpiicc of impi/bin.

Oh, do not use mpiicc, just use plan "mpicc" (which in turn uses GCC). You probably need this because your Python was built with GCC, and the Intel compiler cannot understand some of the flags Python's distutils set. In short, there is absolutely no need to use the Intel compiler to build mpi4py. Using GCC is just fine, and it will save you some trouble.

Yi Zhang

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Sep 2, 2020, 9:43:24 PM9/2/20
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The problem is solved with your remind. Thank you.
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