cache coordinates about nglview HOT 17 CLOSED

Question: Why do we really need to sync coordinates originally?

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a proposed PR here: https://github.com/arose/nglview/pull/59/files

normal implementation by syncing coordinates

view = nv.show_pytraj()
view

turn cache on

view.caching()

--> fast

want to sync coordinate again?

view.uncaching()

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potential: let user to choose specific frames to cache. This is good for pytraj and MDAnalysis out-of-core trajectory/universe. User only need to load coordinates from disk to JavaScript once when caching is called.

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tried with 13008 atoms (DNA + waters). caching is dramatically faster.

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New issue: sending 30 MB data from Python to JS via Widget.send is really slow, costs me 16 s. ack.

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so two seperate issue:

• how to send a GB of data from Python to JS within seconds?
• how to use binary data?

for trajectory viewer, non-lagging viewing is important (at least for me).

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timing: sending list and bytes via Widget.send method

print(traj.xyz.shape, traj.xyz.dtype)

xyz = traj.xyz.flatten()

xyz_list = xyz.tolist()

xyz_bytes = xyz.tobytes()

(100, 5293, 3) float64

%%time
view.send(xyz_list)

CPU times: user 10.2 s, sys: 77 ms, total: 10.3 s
Wall time: 10.3 s

%%time
view.send(xyz_bytes)

CPU times: user 1.73 s, sys: 247 ms, total: 1.98 s
Wall time: 1.95 s

sending bytes is 5 times faster than sending list but still slow (1.95 s for 100 frames, 5293 atoms).

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from my benchmark, sending a dict of base64 data is 100 times faster than sending a Python list.

I am going this way.

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Out of curiosity when you send GB of data from python to js is that data copied?

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Out of curiosity when you send GB of data from python to js is that data copied?

Yes. But this should not be a problem for out-of-core back-end like MDAnalysis. Coordinates are only copied once when 'caching' is called and those are kept in memory (JS) for fast iteration.

But ideally, I just want Python and Javascript can share memory view, just like Python and C/C++.

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You could ask on the jupyter mailing list if they know a method to do that.

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• bokeh still have an open issue about DataView ans Python/JS stuff. :D
  bokeh/bokeh#2204

So I guess there is not.

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But ideally, I just want Python and Javascript can share memory view, just like Python and C/C++.

That is not going to happen, ever! At least not between a browser and Python. The browser is a sandbox for security reasons, so there will be no memory sharing.

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That is not going to happen, ever! At least not between a browser and Python. The browser is a sandbox for security reasons, so there will be no memory sharing.

yeah, right. So my work here is still useful. =)) #67

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@kain88-de @dotsdl I just update MDA support for new data transfer protocol in my new PR.

Let me know if the view play is reasonably fast or not.

PR: #67

should check branch: https://github.com/hainm/nglview/tree/on_msg_f32

That branch includes notebook test for MDA too, just run it.

The speed can be still improved (see @arose comment in that PR).

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note: if using view.caching() the viewer play is much smoother.

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done. Problem left is sending binary data.

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