Re: [Yade-users] [Question #647852]: Using openmp in a python script.

[Bruno Chareyre]

Question #647852 on Yade changed:
https://answers.launchpad.net/yade/+question/647852

Bruno Chareyre proposed the following answer:
>so I re-phrase my question: Is there a possible way on how I could loop
through the objects and addforces every timestep without compromising on
the performance?

Does it mean that the question is unrelated to OpenMP, and that the real 
problem is the inefficiency of python loops (not a surprise)?
A cure could be to implement the loops in c++, i.e. give a python array to a 
yade module and let it loop (in c++) through the data and set values.

Bruno

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Re: [Yade-users] [Question #647852]: Using openmp in a python script.

[Gary Pekmezi]

Question #647852 on Yade changed:
https://answers.launchpad.net/yade/+question/647852

Status: Open => Answered

Gary Pekmezi proposed the following answer:
Deepak,

I think you will need to load a multiprocessing library first, then you
can loop through Yade objects using a multiprocessing pool [1] instead
of the single-threaded sequential for loop you are currently using.

For example, instead of:

for b in O.bodies:
  pvel.append(b.state.vel); prot.append(b.state.angVel)

you would do something like (please note it's just a sample, I haven't
tested it):

import multiprocessing as mp
def appVel(i):
pvel[i] = (O.bodies)[i].state.vel
prot[i] = (O.bodies)[i].state.angVel
if __name__=="__main__":
numBods = len(O.bodies)
pvel = mp.Array('d',range(numBods))
prot = mp.Array('d',range(numBods))
p=mp.Pool(numThreads)
p.map(appVel,range(0,numBods))


[1] https://docs.python.org/2/library/multiprocessing.html

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Re: [Yade-users] [Question #647852]: Using openmp in a python script.

[Chareyre]

Question #647852 on Yade changed:
https://answers.launchpad.net/yade/+question/647852

Chareyre proposed the following answer:
Hello Deepak, did you try a parallel 'hello world' with mpi nesting openmp
on the same system? Maybe even without python. I would make sure this one
is as expected before diving into more complex situations.
B

Le 13 juil. 2017 5:18 PM, "Deepak"  a
écrit :

> New question #647852 on Yade:
> https://answers.launchpad.net/yade/+question/647852
>
> Hello,
>
> I currently run Yade by importing it in a python script as explained in
> [1].
> However I am unable to utilize more than 1 core(for yade) in my
> simulations, I've tried the method described in [2], and I don't see any
> difference and I've also tried setting 'ompThreads=(N)' in the engines and
> I see no effect. (There are around 50k particles in the simulation)
>
> I run yade in parallel with another application under MPI as follows  :
> mpiexec -n 1 python yade : - n 12 app2
>
> Is there a way I could get openmp working in such a situation?
>
> (I had disabled LINSOLV, LBMFLOW,BLAS during compilation as suggested in
> here [3])
>
> [1] https://yade-dem.org/doc/user.html#importing-yade-in-other-
> python-applications
> [2]https://answers.launchpad.net/yade/+question/271679
> [3]https://answers.launchpad.net/yade/+question/247865
>
> Thanks,
> deepak
>
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Re: [Yade-users] [Question #647852]: Using openmp in a python script.

[Gary Pekmezi]

Question #647852 on Yade changed:
https://answers.launchpad.net/yade/+question/647852

Status: Open => Answered

Gary Pekmezi proposed the following answer:
The first thing I notice, is that there is only 1 mpi process for
python, so only 1 core. I don't believe there will be any speedup with
only one core beyond maybe 2-3 simultaneous processes.

One other thing to consider, is setting the environment variable
OMP_NUM_THREADS before running the mpiexec command.

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[Yade-users] [Question #647852]: Using openmp in a python script.

[Deepak]

New question #647852 on Yade:
https://answers.launchpad.net/yade/+question/647852

Hello, 

I currently run Yade by importing it in a python script as explained in [1]. 
However I am unable to utilize more than 1 core(for yade) in my simulations, 
I've tried the method described in [2], and I don't see any difference and I've 
also tried setting 'ompThreads=(N)' in the engines and I see no effect. (There 
are around 50k particles in the simulation)

I run yade in parallel with another application under MPI as follows  : 
mpiexec -n 1 python yade : - n 12 app2 

Is there a way I could get openmp working in such a situation?

(I had disabled LINSOLV, LBMFLOW,BLAS during compilation as suggested in here 
[3])

[1] 
https://yade-dem.org/doc/user.html#importing-yade-in-other-python-applications 
[2]https://answers.launchpad.net/yade/+question/271679
[3]https://answers.launchpad.net/yade/+question/247865

Thanks, 
deepak

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