ASKSAGE: Sage Q&A Forum - Individual question feedhttps://ask.sagemath.org/questions/Q&A Forum for SageenCopyright Sage, 2010. Some rights reserved under creative commons license.Sat, 12 Oct 2019 08:35:52 -0500jmol stuck at "Initializing 3D display"https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/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?Thu, 12 Sep 2019 03:49:13 -0500https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/Comment by eric_g for <p>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"</p>
<pre><code>sage: h = polytopes.regular_polygon(6)
sage: w = h.wedge(h.facets()[0])
sage: w.plot()
Launched jmol viewer for Graphics3d Object
</code></pre>
<p>The pop out window opens and then is stuck for eternity. This is annoying. I know that I could use a different viewer like <code>threejs</code> 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...</p>
<p>(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)</p>
<p>How to fix this?</p>
https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/?comment=48300#post-id-48300For the record, the issue is fixed in SageMath 8.9, thanks to the update of Jmol performed in [#25026](https://trac.sagemath.org/ticket/25026).Sat, 12 Oct 2019 08:35:52 -0500https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/?comment=48300#post-id-48300Comment by eric_g for <p>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"</p>
<pre><code>sage: h = polytopes.regular_polygon(6)
sage: w = h.wedge(h.facets()[0])
sage: w.plot()
Launched jmol viewer for Graphics3d Object
</code></pre>
<p>The pop out window opens and then is stuck for eternity. This is annoying. I know that I could use a different viewer like <code>threejs</code> 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...</p>
<p>(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)</p>
<p>How to fix this?</p>
https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/?comment=47864#post-id-47864Same issue with Ubuntu 18.04 (OpenJDK 11.0.4).Thu, 12 Sep 2019 16:22:46 -0500https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/?comment=47864#post-id-47864Answer by Emmanuel Charpentier for <p>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"</p>
<pre><code>sage: h = polytopes.regular_polygon(6)
sage: w = h.wedge(h.facets()[0])
sage: w.plot()
Launched jmol viewer for Graphics3d Object
</code></pre>
<p>The pop out window opens and then is stuck for eternity. This is annoying. I know that I could use a different viewer like <code>threejs</code> 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...</p>
<p>(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)</p>
<p>How to fix this?</p>
https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/?answer=47844#post-id-47844I 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](https://trac.sagemath.org/ticket/25026).
Workaround: use `threejs` (which has its own share of problems, BTW...).Thu, 12 Sep 2019 07:45:05 -0500https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/?answer=47844#post-id-47844Comment by jipilab for <p>I have the same problem anytime my Java engine is newer than Java 8 : our version of the <code>jmol</code> 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...). <strong>EDIT :</strong> That's <a href="https://trac.sagemath.org/ticket/25026">Trac#25026</a>.</p>
<p>Workaround: use <code>threejs</code> (which has its own share of problems, BTW...).</p>
https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/?comment=47912#post-id-47912Thanks! 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.Sat, 14 Sep 2019 00:56:10 -0500https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/?comment=47912#post-id-47912Comment by Emmanuel Charpentier for <p>I have the same problem anytime my Java engine is newer than Java 8 : our version of the <code>jmol</code> 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...). <strong>EDIT :</strong> That's <a href="https://trac.sagemath.org/ticket/25026">Trac#25026</a>.</p>
<p>Workaround: use <code>threejs</code> (which has its own share of problems, BTW...).</p>
https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/?comment=47906#post-id-47906@ericg, @paulmasson: see my [comment](https://trac.sagemath.org/ticket/22408#comment:69) in the ticket.Fri, 13 Sep 2019 14:25:41 -0500https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/?comment=47906#post-id-47906Comment by paulmasson for <p>I have the same problem anytime my Java engine is newer than Java 8 : our version of the <code>jmol</code> 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...). <strong>EDIT :</strong> That's <a href="https://trac.sagemath.org/ticket/25026">Trac#25026</a>.</p>
<p>Workaround: use <code>threejs</code> (which has its own share of problems, BTW...).</p>
https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/?comment=47868#post-id-47868I'd also like to know what outstanding major problems there are with the Three.js viewer. Please add them to [#22408](https://trac.sagemath.org/ticket/22408) at your convenience.Thu, 12 Sep 2019 17:17:44 -0500https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/?comment=47868#post-id-47868Comment by eric_g for <p>I have the same problem anytime my Java engine is newer than Java 8 : our version of the <code>jmol</code> 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...). <strong>EDIT :</strong> That's <a href="https://trac.sagemath.org/ticket/25026">Trac#25026</a>.</p>
<p>Workaround: use <code>threejs</code> (which has its own share of problems, BTW...).</p>
https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/?comment=47867#post-id-47867This bug is another motivation for [#22408](https://trac.sagemath.org/ticket/22408). @Emmanuel_Charpentier: which "own share of problems" has `threejs`, given the recent improvements?Thu, 12 Sep 2019 16:28:08 -0500https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/?comment=47867#post-id-47867Comment by eric_g for <p>I have the same problem anytime my Java engine is newer than Java 8 : our version of the <code>jmol</code> 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...). <strong>EDIT :</strong> That's <a href="https://trac.sagemath.org/ticket/25026">Trac#25026</a>.</p>
<p>Workaround: use <code>threejs</code> (which has its own share of problems, BTW...).</p>
https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/?comment=47865#post-id-47865Another 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).Thu, 12 Sep 2019 16:25:28 -0500https://ask.sagemath.org/question/47837/jmol-stuck-at-initializing-3d-display/?comment=47865#post-id-47865