repsimtools 0.0.1

Tools for parallel simulation with git source control.

Reproducible Simulation Tools

This is a helper tool to quickly build large dumb parallel simulation or processing in a reproducible way.

• Parallelization is done using ipyparallel
• Results are saved in human friendly JSON format, as soon as collected
• Provided the main project is versioned with git, the state of the repo is checked prior to simulation. If the repo is dirty, simulation is aborted
• The results are tagged with the commit number
• A basic interface displays how many loops have been done, how much time has ellapsed, approximately how long is left
• Options allow to run a single loop or in serial mode (without using ipyparallel) for debugging
• All the arguments and parameters for the simulation are saved along the results

Basics

The code to repeat is isolated in a function taking as single argument a list args . This list args contains all the parameters that vary from loop to loop. The global parameters, that are always the same during all loops of the simulation are stored in a Python dictionary called parameters.

Every script created with rrtools comes with a list of options that can be accessed through the help command

$ python examples/test_simulation.py --help

usage: test_simulation.py [-h] [-d DIR] [-p PROFILE] [-t] [-s] [--dummy]
                          parameters

Dummy test simulation

positional arguments:
  parameters            JSON file containing simulation parameters

optional arguments:
  -h, --help            show this help message and exit
  -d DIR, --dir DIR     directory to store sim results
  -p PROFILE, --profile PROFILE
                        ipython profile of cluster
  -t, --test            test mode, runs a single loop of the simulation
  -s, --serial          run in a serial loop, ipyparallel not called
  --dummy               tags the directory as dummy, can be used for running
                        small batches

If using a cluster of ipyparallel engines is not available, it is possible to run everything in a simple loop using the -s of --serial option.

For debugging, the -t or --test option runs only 2 loops of all.

Using the --dummy option will tag the results with dummy tag, which is useful to make sure we distinguish test runs from the real simulation results.

Example

A simple example is availble in examples folder. It can be run like this

python examles/test_simulation.py examples/test_simulation.json

The python file contains the function definitions for the different parts

import os
import itertools

import rrtools

# find the absolute path to this file
base_dir = os.path.abspath(os.path.split(__file__)[0])

def init(parameters):
    '''
    This function takes as unique positional argument a Python
    dictionary of global parameters for the simulation.
    This lets the user add some parameters computed in software
    to the dictionary. The update dictionary will be saved
    along the simulation output.

    This updated dictionary is later availbable in the global namespace of
    parallel_loop and gen_args functions.

    Parameters
    ----------
    parameters: dict
      The global simulation parameters
    '''
    parameters['lower_bound'] = 0


def parallel_loop(args):
    '''
    This is the heart of the parallel simulation. This function is what is repeated
    a large number of time.

    Parameters
    ----------
    args: list
        A list of arguments whose combination is unique to one loop of the simulation.
    '''
    global parameters
    import time

    # split arguments
    timeout = args[0]
    key = args[1]

    time.sleep(timeout)
    
    return dict(key=key, timeout=timeout, secret=parameters['secret'])

def gen_args(parameters):
    '''
    This function is called once before the simulation to generate
    the list of arguments combinations to try.

    For example say that you have arguments x=1,2,3 and y=2,3 for your parallel
    loop and you want to try all combinations. Then this function
    can generate the list
    args = [[1,2], [1,3], [2,2], [2,3], [3,2], [3,3]]

    Paramters
    ---------
    parameters: dict
        The Python dictionary of globaly simulation parameters. This can
        typically contain the range of values for the arguments to sweep.
    '''

    timeouts = range(parameters['max_timeout'])
    keys = range(parameters['max_int'])

    return list(itertools.product(timeouts, keys))


if __name__ == '__main__':

    rrtools.run(parallel_loop, gen_args, func_init=init,
        base_dir=base_dir, results_dir='data/',
        description='Dummy test simulation')

The JSON file contains global simulation parameters.

{
  "max_timeout": 10,
  "max_int": 2,
  "secret": "helloworld"
}

Control the Number of Threads

When using outer loop level parallelism, it is important that the inner loop does not use parallel processing. When using numpy for the processing, it is thus important to disable multi-threading in the BLAS library used. This can be achieved by setting the number of threads to one using environment variables.

• Openblas OPENBLAS_NUM_THREADS=1
• MKL MKL_NUM_THREADS=1 or directly in the code using the mkl.set_num_threads(1) function.

If not, the outer threads might compete with the inner threads for resources, and the overall simulation becomes very slow. Resource usage is most efficient when sufficiently many outer loops can run in parallel.

Author

Robin Scheibler contact

License

Copyright (c) 2018 Robin Scheibler

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.