Hi all, I want to divide ENZO simulation into certain regions, do some operation and save some files in parallel. I used parallel_objects for this. If I use openMPI and do $mpirun -np 6 python script.py --parallel it works fine. But if I use MPT(a variety of MPICH, I think) and run the exact same command, it ignores --parallel and just does things in serial. Is this expected? I'm new to parallel computation, and kind of stuck here. Thanks for your help. Best regards, Semyeong
Hi Semyeong,
With the MPT module loaded, can you successfully import mpi4py? yt uses
mpi4py in the background to handle MPI communication. If you have openmpi
and MPT on the same system, it may be that you installed mpi4py using
openmpi rather than MPT. When yt tries to import mpi4py, that fails since
openmpi is not available.
Of course if there is only MPT available on your system, my guess is
probably incorrect.
Running the script I've pasted below should expose any issues with mpi4py:
from mpi4py import MPI
import sys
size = MPI.COMM_WORLD.Get_size()
rank = MPI.COMM_WORLD.Get_rank()
name = MPI.Get_processor_name()
sys.stdout.write(“Helloworld! I am process %d of %d on %s.\n” % (rank,
size, name))
Cheers,
Nathan
On Thu, Sep 26, 2013 at 4:32 PM, Semyeong Oh
Hi all,
I want to divide ENZO simulation into certain regions, do some operation and save some files in parallel. I used parallel_objects for this.
If I use openMPI and do $mpirun -np 6 python script.py --parallel it works fine.
But if I use MPT(a variety of MPICH, I think) and run the exact same command, it ignores --parallel and just does things in serial.
Is this expected? I'm new to parallel computation, and kind of stuck here. Thanks for your help.
Best regards, Semyeong
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Hi Nathan,
You were exactly right. It was which mpicc mpi4py was built with.
Thanks very much for the prompt response!
Best,
Semyeong
On Thu, Sep 26, 2013 at 7:38 PM, Nathan Goldbaum
Hi Semyeong,
With the MPT module loaded, can you successfully import mpi4py? yt uses mpi4py in the background to handle MPI communication. If you have openmpi and MPT on the same system, it may be that you installed mpi4py using openmpi rather than MPT. When yt tries to import mpi4py, that fails since openmpi is not available.
Of course if there is only MPT available on your system, my guess is probably incorrect.
Running the script I've pasted below should expose any issues with mpi4py:
from mpi4py import MPI import sys
size = MPI.COMM_WORLD.Get_size() rank = MPI.COMM_WORLD.Get_rank() name = MPI.Get_processor_name()
sys.stdout.write(“Helloworld! I am process %d of %d on %s.\n” % (rank, size, name))
Cheers,
Nathan
On Thu, Sep 26, 2013 at 4:32 PM, Semyeong Oh
wrote: Hi all,
I want to divide ENZO simulation into certain regions, do some operation and save some files in parallel. I used parallel_objects for this.
If I use openMPI and do $mpirun -np 6 python script.py --parallel it works fine.
But if I use MPT(a variety of MPICH, I think) and run the exact same command, it ignores --parallel and just does things in serial.
Is this expected? I'm new to parallel computation, and kind of stuck here. Thanks for your help.
Best regards, Semyeong
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_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
participants (2)
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Nathan Goldbaum
-
Semyeong Oh