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.Mon, 07 Sep 2020 12:31:31 -0500jmol cannot run while plot3dhttps://ask.sagemath.org/question/31048/jmol-cannot-run-while-plot3d/ Well,the internet connection is terrible which makes me a mess...
I downloaded the source(version 6.9 in Ubuntu 12.04).When I typed these following in sage command line,I got a problem...
g(x,y)=x^2+y
plot3d(g(x,y),(x,1,3),(y,1,10))
It said something about jmol,so I went to get jmol,then invoked it again,however didn't work.IT SAYS:
**RuntimeError: jmol cannot run, no suitable java version found**
And I tried to call **jmol** in Terminal,it seemed to work well.
Does sage cann't find the right path?What should I do?
Wed, 25 Nov 2015 08:46:27 -0600https://ask.sagemath.org/question/31048/jmol-cannot-run-while-plot3d/Comment by A.P. for <p>Well,the internet connection is terrible which makes me a mess...
I downloaded the source(version 6.9 in Ubuntu 12.04).When I typed these following in sage command line,I got a problem...</p>
<pre><code>g(x,y)=x^2+y
plot3d(g(x,y),(x,1,3),(y,1,10))
</code></pre>
<p>It said something about jmol,so I went to get jmol,then invoked it again,however didn't work.IT SAYS:
<strong>RuntimeError: jmol cannot run, no suitable java version found</strong> <br/>
And I tried to call <strong>jmol</strong> in Terminal,it seemed to work well. <br/>
Does sage cann't find the right path?What should I do?</p>
https://ask.sagemath.org/question/31048/jmol-cannot-run-while-plot3d/?comment=31205#post-id-31205Did you restart Sage after installing `jmol`?Mon, 30 Nov 2015 10:07:22 -0600https://ask.sagemath.org/question/31048/jmol-cannot-run-while-plot3d/?comment=31205#post-id-31205Answer by toricweb for <p>Well,the internet connection is terrible which makes me a mess...
I downloaded the source(version 6.9 in Ubuntu 12.04).When I typed these following in sage command line,I got a problem...</p>
<pre><code>g(x,y)=x^2+y
plot3d(g(x,y),(x,1,3),(y,1,10))
</code></pre>
<p>It said something about jmol,so I went to get jmol,then invoked it again,however didn't work.IT SAYS:
<strong>RuntimeError: jmol cannot run, no suitable java version found</strong> <br/>
And I tried to call <strong>jmol</strong> in Terminal,it seemed to work well. <br/>
Does sage cann't find the right path?What should I do?</p>
https://ask.sagemath.org/question/31048/jmol-cannot-run-while-plot3d/?answer=41317#post-id-41317This is what I get it to work.
1. Run
> /usr/libexec/java_home -V
2. Identify version 8 of Java, and remove the others using a command like
> rm -rf /Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/
(with the version suitably changed; also you'll probably have to run this as sudo)
It turns out that JMol is incompatible with version 9, which I originally had. After getting rid of version 9, closing the shell session and restarting it, I am now able to plot 3d objects in Sagemath through JMol.Wed, 28 Feb 2018 14:39:40 -0600https://ask.sagemath.org/question/31048/jmol-cannot-run-while-plot3d/?answer=41317#post-id-41317Answer by slelievre for <p>Well,the internet connection is terrible which makes me a mess...
I downloaded the source(version 6.9 in Ubuntu 12.04).When I typed these following in sage command line,I got a problem...</p>
<pre><code>g(x,y)=x^2+y
plot3d(g(x,y),(x,1,3),(y,1,10))
</code></pre>
<p>It said something about jmol,so I went to get jmol,then invoked it again,however didn't work.IT SAYS:
<strong>RuntimeError: jmol cannot run, no suitable java version found</strong> <br/>
And I tried to call <strong>jmol</strong> in Terminal,it seemed to work well. <br/>
Does sage cann't find the right path?What should I do?</p>
https://ask.sagemath.org/question/31048/jmol-cannot-run-while-plot3d/?answer=31062#post-id-31062I suggest visiting http://java.com/en/download/installed8.jsp to check if your Java is up-to-date.
Another useful trick is to plot using threejs instead of the default Jmol.
For this, you could do:
sage: g = lambda x, y: x^2 + y
sage: plot3d(g, (1, 3), (1, 10), viewer='threejs')Wed, 25 Nov 2015 10:59:11 -0600https://ask.sagemath.org/question/31048/jmol-cannot-run-while-plot3d/?answer=31062#post-id-31062Comment by PHPirates for <p>I suggest visiting <a href="http://java.com/en/download/installed8.jsp">http://java.com/en/download/installed...</a> to check if your Java is up-to-date.</p>
<p>Another useful trick is to plot using threejs instead of the default Jmol.</p>
<p>For this, you could do:</p>
<pre><code>sage: g = lambda x, y: x^2 + y
sage: plot3d(g, (1, 3), (1, 10), viewer='threejs')
</code></pre>
https://ask.sagemath.org/question/31048/jmol-cannot-run-while-plot3d/?comment=53361#post-id-53361@slelievre I don't remember, and I don't have that Windows system anymore. However, I can say it works fine in Firefox under Linux, Sage 9.1.Mon, 07 Sep 2020 12:31:31 -0500https://ask.sagemath.org/question/31048/jmol-cannot-run-while-plot3d/?comment=53361#post-id-53361Comment by slelievre for <p>I suggest visiting <a href="http://java.com/en/download/installed8.jsp">http://java.com/en/download/installed...</a> to check if your Java is up-to-date.</p>
<p>Another useful trick is to plot using threejs instead of the default Jmol.</p>
<p>For this, you could do:</p>
<pre><code>sage: g = lambda x, y: x^2 + y
sage: plot3d(g, (1, 3), (1, 10), viewer='threejs')
</code></pre>
https://ask.sagemath.org/question/31048/jmol-cannot-run-while-plot3d/?comment=49166#post-id-49166@PHPirates -- was that with Firefox?
Viewing SageMath Three.js 3d plots in Firefox on Windows
did not work in SageMath <= 8.9. But it worked in other browsers.
This problem was reported as
- [Sage-Windows issue 38: viewer='threejs' does not work in Firefox](https://github.com/sagemath/sage-windows/issues/38)
and fixed in
- [Sage Trac ticket 28801: Fix ThreeJS script paths for Firefox on Windows](https://trac.sagemath.org/ticket/28801)
which was [merged in Sage 9.0.beta9](https://groups.google.com/d/topic/sage-release/p3mnazZ58HQ).
So, when Sage 9.0 comes out, viewing Three.js 3d plots in Firefox on Windows will work.Tue, 24 Dec 2019 08:35:35 -0600https://ask.sagemath.org/question/31048/jmol-cannot-run-while-plot3d/?comment=49166#post-id-49166Comment by PHPirates for <p>I suggest visiting <a href="http://java.com/en/download/installed8.jsp">http://java.com/en/download/installed...</a> to check if your Java is up-to-date.</p>
<p>Another useful trick is to plot using threejs instead of the default Jmol.</p>
<p>For this, you could do:</p>
<pre><code>sage: g = lambda x, y: x^2 + y
sage: plot3d(g, (1, 3), (1, 10), viewer='threejs')
</code></pre>
https://ask.sagemath.org/question/31048/jmol-cannot-run-while-plot3d/?comment=42480#post-id-42480... or use `viewer='tachyon'` when threejs also doesn't work (Windows 8, Sage 8.1).Sat, 02 Jun 2018 06:52:46 -0500https://ask.sagemath.org/question/31048/jmol-cannot-run-while-plot3d/?comment=42480#post-id-42480Answer by Anik Samiur Rahman for <p>Well,the internet connection is terrible which makes me a mess...
I downloaded the source(version 6.9 in Ubuntu 12.04).When I typed these following in sage command line,I got a problem...</p>
<pre><code>g(x,y)=x^2+y
plot3d(g(x,y),(x,1,3),(y,1,10))
</code></pre>
<p>It said something about jmol,so I went to get jmol,then invoked it again,however didn't work.IT SAYS:
<strong>RuntimeError: jmol cannot run, no suitable java version found</strong> <br/>
And I tried to call <strong>jmol</strong> in Terminal,it seemed to work well. <br/>
Does sage cann't find the right path?What should I do?</p>
https://ask.sagemath.org/question/31048/jmol-cannot-run-while-plot3d/?answer=49968#post-id-49968This can also happen due to mismatched java version number. The java version expected by sage is declared in "~/.local/lib/python2.7/site-packages/sage/interfaces/jmoldata.py" There, in the "JmolData" class at "is_jvm_available" function you'll find the code responsible for java version check.
<p>java_version = re.search("version.*[11][.][06]", version)</p>
See, I've changed the version number to 11.06, it previously was 1.78(=[1][.][78]). Then voila, JMol started working normally.Tue, 18 Feb 2020 13:26:47 -0600https://ask.sagemath.org/question/31048/jmol-cannot-run-while-plot3d/?answer=49968#post-id-49968