Using Multiple processors to speed up simulation

[codepujan]

Is there any way I can speed up the diffusion simulation leveraging the multiple cores I have in my machine. I want to speed up a single experiment, for a relatively larger net. Is there any way for optimization already existing. Regards,

[GiulioRossetti]

Unfortunately, for the moment it is not possible to parallelize a single experiment, only pools. However, we will consider this request for a future release!

[codepujan]

Thank you Sir, It would be a very powerful tool of utility. Till then, what do you suggest for working with relatively larger networks? I am working with a network that has 3862396 nodes and 4953798 edges. Models like SIR, SIS are relatively on waitable time, but SEIR, SWIR take a lot of time. Any tips on them large networks.

[GiulioRossetti]

One thing that might help, if you are storing your graph in a networkx object, is switching to igraph. Since the latest release ndlib natively supports both graph libraries.

[codepujan]

Would working on the same network with igraph give me speedup over Networkx?

[GiulioRossetti]

For sure igraph handles better graphs of that size than networkx (especially regarding memory consumption). Networkx implementation is pure python while igraph is c-based: maybe this will help a little bit.

[codepujan]

Thank you. Are there any updated docs on how to run the model on IGraph ?

[GiulioRossetti]

Actually, no docs for the moment (we're working on it). However, you have only to load the graph in igraph instead of in networkx: ndlib (since v5.0) will work as usual without requiring any adjustment to your code.

[codepujan]

@GiulioRossetti Sir , I tried doing it the most simple way , as :

from igraph import * g=Graph.Erdos_Renyi(1000,0.1) import ndlib.models.epidemics.SIRModel as sir model = sir.SIRModel(g)

But I'm having the error as :

[GiulioRossetti]

Sorry, the examples in the docs are a little our of synch w.r.t. the latest version. Change your code in

import ndlib.models.epidemics as ep

then use instantiate the model on the graph using

model = ep.SIRModel(g)

[codepujan]

I tried doing the exact same thing , but I am getting the error as :

My NDLIB version is : 5.0.0 My Python-Igraph version is : 0.7.1.post6

[GiulioRossetti]

I'll try to replicate your issue as asap.

However, there's something strange in your screen: it seems you are running everything under python 2.7 while the ndlib package has only been released for python 3. Can you change your evironment?

[codepujan]

I tried doing it using python3 environment as well, facing the same issue !!

[GiulioRossetti]

Ok, I think I figured it out. When reading networks from file igraph saves node ids into a 'name' attribute so as to be able to remap node ids while compacting the adjacency matrix. Conversely, when generating synthetic graphs (as ER) it doesn't store such information.

To address your issue on the ER graph just do the following:

g = Graph.Erdos_Renyi(1000, 0.1)
g.vs["name"] = list(range(g.vcount()))

Then, everything will work fine.

[codepujan]

I'll try to replicate your issue as asap.

However, there's something strange in your screen: it seems you are running everything under python 2.7 while the ndlib package has only been released for python 3. Can you change your evironment?

I had been previously making use of the library using Python2 (using NetworkX ).

[koujiangheng]

def all_nodes_influence_sim(g, p, sim_time=50):
    result_list = []
    process_list = []
    with futures.ProcessPoolExecutor(max_workers=10) as executor:
        for node in g.nodes:
            process_list.append(executor.submit(
                __mean_single_node_infection, g, node, p, sim_time))
        for process in tqdm(process_list, desc="compute single node ic value"):
            result_list.append(process.result())
    return result_list

def __mean_single_node_infection(g, node, p, sim_time):
    result_list = []
    process_list = []
    with futures.ProcessPoolExecutor(max_workers=10) as executor:
        for i in range(sim_time):
            # process_list.append(executor.submit(
            #     __single_node_ic_sim, g, node, p))
            process_list.append(executor.submit(
                __single_node_lt_sim, g, node, p))
        for process in process_list:
            result_list.append(process.result())
    return np.mean(result_list)

def __single_node_lt_sim(g: nx.Graph, node: int, p: float):
    model = ep.ThresholdModel(g)
    if(node not in g.nodes):
        raise Exception("node are not in this graph")
    config = mc.Configuration()
    nodes = []
    nodes.append(node)
    config.add_model_initial_configuration('Infected', nodes)
    for e in g.edges():
        config.add_edge_configuration("threshold", e, p)

    model.set_initial_status(config)
    iterations = model.iteration_bunch(100)
    infected = iterations[-1]["node_count"][1]
    return infected

This is how I writing into multiprocess, the experiment I did is that I need a influence value on all nodes