pythonsupercomputersmpiexec

Supercomputer: Dead simple example of a program to run in supercomputer


I am learning how to use supercomputers to make the good use of resources. Let's say I have a python script, that will create a text file with given random number.

myfile.py

# Imports
import random,os

outdir = 'outputs'
if not os.path.exists(outdir):
    os.makedirs(outdir)

with open (outdir+'/temp.txt','w') as f :
    a = random.randint(0,9)
    f.write(str(a))

This will create only one text file in the local machine.
Is there any way I can use the multiple instances of this program, use multiple nodes and get multiple outputs?

I got a template for mpiexec in C program which looks like this, but I could not find any template for python program.

#PBS -N my_job
#PBS -l walltime=0:10:00
#PBS -l nodes=4:ppn=12
#PBS -j oe

cd $PBS_O_WORKDIR

mpicc -O2 mpi-hello.c -o mpi-hello

cp $PBS_O_WORKDIR/* $PFSDIR
cd $PFSDIR

mpiexec ./mpi-hello

cp $PFSDIR/* $PBS_O_WORKDIR

Note: On a single node using multiple cores I can write a bash script like this:

for i in `seq 1 10`;
    do
        python myfile.py && cp temp.txt outputs/out$i.txt &
    done

But I want to utilize different nodes.
Required output: outputs/out1.txt,out2.txt,out3.txt etc

Some related links are following:
https://www.osc.edu/sites/osc.edu/files/documentation/Batch%20Training%20-%2020150312%20-%20OSC.pdf
https://www.osc.edu/~kmanalo/multithreadedsubmission


Solution

  • Take a look to this link it may solve your problem

    http://materials.jeremybejarano.com/MPIwithPython/introMPI.html

    so your code may be something like:

    from mpi4py import MPI
    import random,os
    
    outdir = 'outputs'
    comm = MPI.COMM_WORLD
    rank = comm.Get_rank()
    
    if not os.path.exists(outdir):
        os.makedirs(outdir)
    
    with open (outdir+'/temp%s.txt' % rank,'w') as f :
        a = random.randint(0,9)
        f.write(str(a))
    

    and the pbs file:

    #!/bin/bash
    ################################################################################
    #PBS -N myfile.py
    #PBS -l nodes=7:ppn=4
    #PBS -l walltime=30:30:00:00
    #PBS -m bea
    ##PBS -M mail@mail.mail
    ###############################################################################
    
    cores=$(awk 'END {print NR}' $PBS_NODEFILE)
    mpirun -np $cores python myfile.py