Testing memory consumption of the MDAnalysis XTCReader vs MemoryReader. See https://github.com/MDAnalysis/mdanalysis/wiki/memory-profiling

xtc_vs_memreader.py

# -*- coding: utf-8 -*-
# load trajectory and iterate

import numpy as np
import tqdm
import MDAnalysis as mda

import gc


@profile
def analyze(u, start=None, stop=None, step=None):
    protein = u.select_atoms("protein")

    traj = u.trajectory[start:stop:step]
    results = np.empty((len(traj), 3))
    for i, ts in tqdm.tqdm(enumerate(traj)):
        results[i, :] = (ts.frame, ts.time, protein.radius_of_gyration())

    return results


@profile
def run(*args, **kwargs):
    start = kwargs.pop('start', None)
    stop =  kwargs.pop('stop', None)
    step = kwargs.pop('step', None)
    u = mda.Universe(*args, **kwargs)
    results = analyze(u, start=start, stop=stop, step=step)

    rgyr = results[:, 2]

    del u
    gc.collect()

    return rgyr.mean(), rgyr.std()


if __name__ == "__main__":
    import MDAnalysisData.datasets as data

    sim = data.fetch_nhaa_equilibrium()

    for repeat in range(3):
        results = run(sim.topology, sim.trajectory, step=10)
        print("file reader: repeat {0} (results = {1[0]} ± {1[1]} Å)".format(repeat, results))

    for repeat in range(3):
        results = run(sim.topology, sim.trajectory, in_memory=True, step=10)
        print("memory reader: repeat {0} (results = {1[0]} ± {1[1]} Å)".format(repeat, results))