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jmol stuck at "Initializing 3D display"

asked 2019-09-12 10:49:13 +0200

jipilab gravatar image

I have a freshly compiled version of sage 8.9.rc0. jmol used to work fine until I got it stuck at "Initializing 3D display"

sage: h = polytopes.regular_polygon(6)
sage: w = h.wedge(h.facets()[0])
sage: w.plot()
Launched jmol viewer for Graphics3d Object

The pop out window opens and then is stuck for eternity. This is annoying. I know that I could use a different viewer like threejs but it does not open a window in my browser (which is another unrelated issue). So I would really like jmol to just work as I expect it to...

(I also upgraded my debian from stretch to buster, but I do not think it is the problem since jmol starts fine outside of sage)

How to fix this?

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Same issue with Ubuntu 18.04 (OpenJDK 11.0.4).

eric_g gravatar imageeric_g ( 2019-09-12 23:22:46 +0200 )edit

For the record, the issue is fixed in SageMath 8.9, thanks to the update of Jmol performed in #25026.

eric_g gravatar imageeric_g ( 2019-10-12 15:35:52 +0200 )edit

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answered 2019-09-12 14:45:05 +0200

Emmanuel Charpentier gravatar image

updated 2019-09-13 21:01:24 +0200

I have the same problem anytime my Java engine is newer than Java 8 : our version of the jmol viewer works only with Java <= 8, whereas most current distros use Java >= 11. ISTR that a ticket is open about this (but I don't have the time to check it now...). EDIT : That's Trac#25026.

Workaround: use threejs (which has its own share of problems, BTW...).

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Another workaround is to run the code in a Jupyter notebook. There it is the JavaScript version of Jmol that is invoked, note the Java one, and it works (tested with Ubuntu 18.04).

eric_g gravatar imageeric_g ( 2019-09-12 23:25:28 +0200 )edit

This bug is another motivation for #22408. @Emmanuel_Charpentier: which "own share of problems" has threejs, given the recent improvements?

eric_g gravatar imageeric_g ( 2019-09-12 23:28:08 +0200 )edit

I'd also like to know what outstanding major problems there are with the Three.js viewer. Please add them to #22408 at your convenience.

paulmasson gravatar imagepaulmasson ( 2019-09-13 00:17:44 +0200 )edit

@ericg, @paulmasson: see my comment in the ticket.

Emmanuel Charpentier gravatar imageEmmanuel Charpentier ( 2019-09-13 21:25:41 +0200 )edit

Thanks! That explains why it was stuck indeed. I did create a dummy worksheet to execute my snippet of code and jsmol does work inside jupyter notebooks.

jipilab gravatar imagejipilab ( 2019-09-14 07:56:10 +0200 )edit

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Asked: 2019-09-12 10:49:13 +0200

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Last updated: Sep 13 '19