Current Implementation of Universe Pickling

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Photo by Billy Huyn.

To achieve a flawless implementation of parallelism, in the first stage of GSoC project, we aimed at Universe serialization.

Universe is serialized by serializing each necessary compartment— _topology, _trajectory, anchor_name; a new Universe is reconstructed with these elements.

Here is how a Universe can be (un)pickled with its current state saved:

    u = MDAnalysis.Universe(topology, trajectory)
    u_pickled = pickle.loads(pickle.dumps(u))
    u_pickled.ts.frame == u.trajectory.ts.frame == 5

With a picklable Universe at hand, we can delve into parallel analysis. This is a very simple example:

    def cog(u, ag, frame_id):
        return ag.center_of_geometry()

    u = MDAnalysis.Universe(GRO, XTC)
    ag = u.atoms[2:5]

    p = multiprocessing.Pool(2)
    result = np.array([p.apply(cog, args=(u, ag, i))
                       for i in range(u.n_frames)])

Note to make sure Atomgroup finds its anchored Universe after pickling, the Universe has to be pickled first.

Below is some notes for the developers to implement serialization to the new readers in the future.

To make sure every Trajectory reader can be successfully serialized, we implement picklable I/O classes (see :ref:implemented-fileio). When the file is pickled, filename and other necessary attributes of the open file handle are saved. On unpickling, the file is opened by filename. This means that for a successful unpickle, the original file still has to be accessible with its filename. To retain the current frame of the trajectory, _read_frame(previous frame) will be called during unpickling.

  • File Access

If the new reader uses util.anyopen() (e.g. PDB), the reading handler can be pickled without modification. If the new reader uses I/O classes from other package (e.g. GSD), and cannot be pickled natively, create a new picklable class inherited from the file class in that package (e.g. GSDPicklable), adding __getstate__, __setstate__ functions to allow file handler serialization.

  • To seek or not to seek

Some I/O class supports seek and tell functions to allow the file to be pickled with an offset. It is normally not needed for MDAnalysis with random access. But if error occurs, find a way to make the offset work.

  • Miscellaneous

If pickle still fails due to some unpicklable attributes, try to find a way to pickle those, or write custom __getstate__ and __setstate__ methods for the reader.

If the new reader is written in Cython, read lib.formats.libmdaxdr and lib.formats.libdcd files as references.

  • Tests

If the test for the new reader uses BaseReaderTest, whether the current timestep information is saved, and whether its relative position is maintained, i.e. next() read the right next timestep, are already tested.

If the new reader accesses the file with util.anyopen, add necessary testes inside parallelism/ for the reader.

If the new reader accessed the file with new picklable I/O class, add necessary tests inside utils/ for I/O class, parallelism/ for the reader.