Switching from .dat file writing to pickling

[ricalessandri]

Writing the results in a .dat file is one way of doing this.
I think the more python way of doing it, would be to pickle the results.
But either is fine.

Originally posted by @InnocentBug in #171 (comment)

e.g.

PySAGES/examples/hoomd-blue/ann/butane_ann.py

Lines 301 to 303 in f5bffa5

	# write free energy to file
	dih_vs_A = np.stack([mesh[:, 0], A[:, 0]], axis=1)
	np.savetxt("butane-fe.dat", dih_vs_A, header='"dih" "Free energy"')

[ricalessandri]

May be a basic question but ... shouldn't this just be:

    import pickle

    ...
    # Analysis: Calculate free energy
    result = pysages.analyze(run_result)
    fes_fn = result["fes_fn"]

    # Pickle
    pickle.dump( result, open("result.pickle", "wb") )
    ...

?

I'm getting:

  File "adp_SpectralABF.py", line 133, in main
    pickle.dump( result, open("result.pickle", "wb") )
AttributeError: Can't pickle local object 'analyze.<locals>.build_fes_fn.<locals>.<lambda>'

[InnocentBug]

Hmm, too bad.
that is a function it can’t pickle.
we probably have to rework this a bit.
Wither return data instead of a function.
or make it a pickable functor

[pabloferz]

I believe that what we have guaranteed so far to be pickeable are the raw Results and not the analysis results. This might not be ideal, but performing analysis is generally cheap compared to running whole biased simulations, Of course, we might want to improve upon that in the future, but so far it should give us something reasonable to work with.

[ricalessandri]

🤔 also raw_results seems to not work. The following:

import pickle
...
raw_result = pysages.run(method, generate_simulation, args.time_steps)
...
pickle.dump( raw_result, open("raw_result.pickle", "wb") )

Gives:

Traceback (most recent call last):
  File "adp_SpectralABF.py", line 137, in <module>
    main(sys.argv[1:])
  File "adp_SpectralABF.py", line 104, in main
    pickle.dump( raw_result, open("raw_result.pickle", "wb") )
_pickle.PicklingError: Can't pickle <class 'pysages.methods.core.Result[<class 'pysages.methods.spectral_abf.SpectralABF'>]'>: attribute lookup Result[<class 'pysages.methods.spectral_abf.SpectralABF'>] on pysages.methods.core failed

[ricalessandri]

With #235 merged, I should now do this.

[InnocentBug]

Is this is active?

[ricalessandri]

I think this is only partially complete (i.e., only part of the examples have been converted). I should get back to this. Not sure whether we want to move this "issue" to the PySAGES-examples repo, though?

[pabloferz]

Yeah. It does make sense to have one issue within PySAGES-examples, but I would like us to use the serialization support we have now here as well, just in case someone stumbles upon these examples right now.