"embarrassingly parallel" programming using python and PBS on a cluster

Question

I have a function (neural network model) which produces figures. I wish to test several parameters, methods and different inputs (meaning hundreds of runs of the function) from python using PBS on a standard cluster with Torque.

Note: I tried parallelpython, ipython and such and was never completely satisfied, since I want something simpler. The cluster is in a given configuration that I cannot change and such a solution integrating python + qsub will certainly benefit to the community.

To simplify things, I have a simple function such as:

import myModule
def model(input, a= 1., N=100):
    do_lots_number_crunching(input, a,N)
    pylab.savefig('figure_' + input.name + '_' + str(a) + '_' + str(N) + '.png')

where input is an object representing the input, input.name is a string, anddo_lots_number_crunching may last hours.

My question is: is there a correct way to transform something like a scan of parameters such as

for a in pylab.linspace(0., 1., 100):
    model(input, a)

into "something" that would launch a PBS script for every call to the model function?

#PBS -l ncpus=1
#PBS -l mem=i1000mb
#PBS -l cput=24:00:00
#PBS -V
cd /data/work/
python experiment_model.py

I was thinking of a function that would include the PBS template and call it from the python script, but could not yet figure it out (decorator?).

Answer 1

pbs_python[1] could work for this. If experiment_model.py 'a' as an argument you could do

import pbs, os

server_name = pbs.pbs_default()
c = pbs.pbs_connect(server_name)

attopl = pbs.new_attropl(4)
attropl[0].name  = pbs.ATTR_l
attropl[0].resource = 'ncpus'
attropl[0].value = '1'

attropl[1].name  = pbs.ATTR_l
attropl[1].resource = 'mem'
attropl[1].value = 'i1000mb'

attropl[2].name  = pbs.ATTR_l
attropl[2].resource = 'cput'
attropl[2].value = '24:00:00'

attrop1[3].name = pbs.ATTR_V

script='''
cd /data/work/
python experiment_model.py %f
'''

jobs = []

for a in pylab.linspace(0.,1.,100):
    script_name = 'experiment_model.job' + str(a)
    with open(script_name,'w') as scriptf:
        scriptf.write(script % a)
    job_id = pbs.pbs_submit(c, attropl, script_name, 'NULL', 'NULL')
    jobs.append(job_id)
    os.remove(script_name)

 print jobs

[1]: https://subtrac.sara.nl/oss/pbs_python/wiki/TorqueUsage pbs_python

Answer 2

You can do this easily using jug (which I developed for a similar setup).

You'd write in file (e.g., model.py):

@TaskGenerator
def model(param1, param2):
     res = complex_computation(param1, param2)
     pyplot.coolgraph(res)


for param1 in np.linspace(0, 1.,100):
    for param2 in xrange(2000):
        model(param1, param2)

And that's it!

Now you can launch "jug jobs" on your queue: jug execute model.py and this will parallelise automatically. What happens is that each job will in, a loop, do something like:

while not all_done():
    for t in tasks in tasks_that_i_can_run():
        if t.lock_for_me(): t.run()

(It's actually more complicated than that, but you get the point).

It uses the filesystem for locking (if you're on an NFS system) or a redis server if you prefer. It can also handle dependencies between tasks.

This is not exactly what you asked for, but I believe it's a cleaner architechture to separate this from the job queueing system.