Newbie: jmol black screen

[gary]

I've installed sage 2.11 on Kubuntu 7.10, and I'm poking around.

In the tutorial, sec 2.9.2 (?) there are 3D graphics examples using
jmol. When I run these (adding show(P) to the scripts) jmol reports
that it is starting, but all I get is a black rectangle with the
letters "jmol" in the lower right corner. I've got a newly installed
java: 1.6.0_05, I think.

I *can* see the demos on the jmol website. Also, I've installed the
vmware version on the same machine (dual boot) and everything there
seems to work ok.

any ideas ??
-gary

[mabshoff]

On Apr 21, 1:59 am, gary <gary.pa...@gmail.com> wrote:

Hi Gary,

This usually indicates that somewhere you end up using the GNU java
toolchain and that works less than stellar. Re VMWare: Is that VMWare
on Linux or Windows?

> any ideas ??

Not really, but IIRC there is some mechanism in Ubuntu land in general
to select the default java. I just don't know what it is :( and I will
be sure that somebody else knows ;)

> -gary

Cheers,

Michael

[gary]

Forgot to mention: executing the 3D script on the sagenb server with
the same browser works fine, also.

>
> any ideas ??
> -gary

[William Stein]

Which web browser are you using?

What exact command are you using to start the notebook?

If notebook(), try using inotebook() instead.

William

[Dan Drake]

On Sun, 20 Apr 2008 at 05:10PM -0700, mabshoff wrote:
> Not really, but IIRC there is some mechanism in Ubuntu land in general
> to select the default java. I just don't know what it is :( and I will
> be sure that somebody else knows ;)

In Debian-based systems, it's the "alternatives" system. See `man
update-alternatives`; you'll want to change the java alternative, I
think.

Dan

--
--- Dan Drake <dr...@mathsci.kaist.ac.kr>
----- KAIST Department of Mathematical Sciences
------- http://math.kaist.ac.kr/~drake

[gary]

On Apr 20, 8:20 pm, "William Stein" <wst...@gmail.com> wrote:

> On Sun, Apr 20, 2008 at 4:59 PM, gary <gary.pa...@gmail.com> wrote:
>
> > I've installed sage 2.11 on Kubuntu 7.10, and I'm poking around.
>
> > In the tutorial, sec 2.9.2 (?) there are 3D graphics examples using
> > jmol. When I run these (adding show(P) to the scripts) jmol reports
> > that it is starting, but all I get is a black rectangle with the
> > letters "jmol" in the lower right corner. I've got a newly installed
> > java: 1.6.0_05, I think.
>
> > I *can* see the demos on the jmol website. Also, I've installed the
> > vmware version on the same machine (dual boot) and everything there
> > seems to work ok.
>
> > any ideas ??
>
> Which web browser are you using?

Thanks for responding ...

firefox 2.0.0.13

> What exact command are you using to start the notebook?

./sage at bash, then notebook()

>
> If notebook(), try using inotebook() instead.

sage starts, inotebook() seems to start, but
The browser spins and spins, but a page is never loaded.

However, I do now notice something that may or may not be an error
when notebook() is executed.
Here's what I see: (below this is the output from inotebook() )
-----------------------------------------------------------


gap@gap-laptop:~/bin/sage$ ./sage
----------------------------------------------------------------------
| SAGE Version 2.11, Release Date: 2008-03-30 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------

sage: notebook()
The notebook files are stored in: /home/gap/.sage//sage_notebook
****************************************************
* *
* Open your web browser to https://localhost:8000 *
* *
****************************************************
There is an admin account. If you do not remember the password,
quit the notebook and type notebook(reset=True).
Removing stale pidfile /home/gap/.sage/sage_notebook/twistd.pd
2008/04/20 20:45 -0400 [-] Log opened.
2008/04/20 20:45 -0400 [-] twistd 2.5.0 (/home/gap/bin/sage/local/bin/
python 2.5.1) starting up
2008/04/20 20:45 -0400 [-] reactor class: <class
'twisted.internet.selectreactor.SelectReactor'>
2008/04/20 20:45 -0400 [-] Loading sage_notebook/twistedconf.tac...
2008/04/20 20:45 -0400 [-] Loaded.
2008/04/20 20:45 -0400 [-] twisted.web2.channel.http.HTTPFactory
starting on 8000
2008/04/20 20:45 -0400 [-] Starting factory
<twisted.web2.channel.http.HTTPFactory instance at 0x8a54ecc>
2008/04/20 20:45 -0400 [HTTPChannel,1,127.0.0.1] /home/gap/bin/sage/
local/lib/python2.5/site-packages/twisted/internet/defer.py:259:
exceptions.DeprecationWarning: Don't pass strings (like 'Bad token')
to failure.Failure (replacing with a DefaultException).
2008/04/20 20:45 -0400 [HTTPChannel,1,127.0.0.1] Exception rendering:
2008/04/20 20:45 -0400 [HTTPChannel,1,127.0.0.1] Unhandled Error
Traceback (most recent call last):
Failure: twisted.python.failure.DefaultException: Bad token

-----------------------------------------------------------------------------------------------------


sage: inotebook()
The notebook files are stored in: /home/gap/.sage//sage_notebook
WARNING: Running the notebook insecurely may be dangerous.
Make sure you know what you are doing.
**************************************************
* *
* Open your web browser to http://localhost:8000 *
* *
**************************************************
Removing stale pidfile /home/gap/.sage/sage_notebook/twistd.pd
2008/04/20 20:42 -0400 [-] Log opened.
2008/04/20 20:42 -0400 [-] twistd 2.5.0 (/home/gap/bin/sage/local/bin/
python 2.5.1) starting up
2008/04/20 20:42 -0400 [-] reactor class: <class
'twisted.internet.selectreactor.SelectReactor'>
2008/04/20 20:42 -0400 [-] Loading sage_notebook/twistedconf.tac...
2008/04/20 20:42 -0400 [-] Loaded.
2008/04/20 20:42 -0400 [-] twisted.web2.channel.http.HTTPFactory
starting on 8000
2008/04/20 20:42 -0400 [-] Starting factory
<twisted.web2.channel.http.HTTPFactory instance at 0x8a53ecc>
2008/04/20 20:45 -0400 [-] (Notebook cleanly saved. Press control-C
again to exit.)

>
> William

-gary

[gary]

On Apr 20, 8:52 pm, gary <gary.pa...@gmail.com> wrote:
> On Apr 20, 8:20 pm, "William Stein" <wst...@gmail.com> wrote:
>
>
>
> > On Sun, Apr 20, 2008 at 4:59 PM, gary <gary.pa...@gmail.com> wrote:
>
> > > I've installed sage 2.11 on Kubuntu 7.10, and I'm poking around

[...]

> > If notebook(), try using inotebook() instead.
>
> sage starts, inotebook() seems to start, but
> The browser spins and spins, but a page is never loaded.

Whoops, I just noticed the different URL, without the "s"
With that, the page loads, and behaves exactly like notebook()

Thanks again,
gary

[William Stein]

This means that with http://localhost:8000 it still does *not* work at all?

William

[gary]

On Apr 20, 9:02 pm, "William Stein" <wst...@gmail.com> wrote:

> On Sun, Apr 20, 2008 at 5:58 PM, gary <gary.pa...@gmail.com> wrote:
>
> > On Apr 20, 8:52 pm, gary <gary.pa...@gmail.com> wrote:
> > > On Apr 20, 8:20 pm, "William Stein" <wst...@gmail.com> wrote:
>
> > > > On Sun, Apr 20, 2008 at 4:59 PM, gary <gary.pa...@gmail.com> wrote:
>
> > > > > I've installed sage 2.11 on Kubuntu 7.10, and I'm poking around
>
> > [...]
>
> > > > If notebook(), try using inotebook() instead.
>
> > > sage starts, inotebook() seems to start, but
> > > The browser spins and spins, but a page is never loaded.
>
> > Whoops, I just noticed the different URL, without the "s"
> > With that, the page loads, and behaves exactly like notebook()
>
> > Thanks again,
>

> This means that withhttp://localhost:8000it still does *not* work at all?

No, sorry about the ambiguity.

http://localhost:8000 with inotebook() works fine *except* that the
jmol screens are black with the letters "jmol" in the lower right.

-g

>
> William

[gary]

On Apr 20, 9:20 pm, gary <gary.pa...@gmail.com> wrote:
> On Apr 20, 9:02 pm, "William Stein" <wst...@gmail.com> wrote:
>
>
>
> > On Sun, Apr 20, 2008 at 5:58 PM, gary <gary.pa...@gmail.com> wrote:
>
> > > On Apr 20, 8:52 pm, gary <gary.pa...@gmail.com> wrote:
> > > > On Apr 20, 8:20 pm, "William Stein" <wst...@gmail.com> wrote:
>
> > > > > On Sun, Apr 20, 2008 at 4:59 PM, gary <gary.pa...@gmail.com> wrote:
>
> > > > > > I've installed sage 2.11 on Kubuntu 7.10, and I'm poking around
>
> > > [...]
>
> > > > > If notebook(), try using inotebook() instead.
>
> > > > sage starts, inotebook() seems to start, but
> > > > The browser spins and spins, but a page is never loaded.
>
> > > Whoops, I just noticed the different URL, without the "s"
> > > With that, the page loads, and behaves exactly like notebook()
>
> > > Thanks again,
>

> > This means that withhttp://localhost:8000itstill does *not* work at all?

>
> No, sorry about the ambiguity.
>

> http://localhost:8000with inotebook() works fine *except* that the

> jmol screens are black with the letters "jmol" in the lower right.
>
> -g

Here's something:
the Java console reports an error:
------------------------------------------------------------------------------------------------------
Init Jmol
language=en_US
Jmol applet jmolApplet0[533848364848684]
AppletRegistry.checkIn(jmolApplet0[533848364848684])
urlImage=jar:https://localhost:8000/java/jmol/JmolApplet0.jar!/
jmol75x29x8.gif
(C) 2007 Jmol Development
Jmol Version 11.5.2 2007-12-20 06:37
java.vendor:Sun Microsystems Inc.
java.version:1.6.0_05
os.name:Linux
memory:3.6/5.2
appletId:jmolApplet0
appletDocumentBase=https://localhost:8000/doc/live/tut/node22.html
appletCodeBase=https://localhost:8000/java/jmol/
FileManager opening https://localhost:8000/home/_sage_/18/cells/1/sage0-size500.jmol?3
FileManager opening https://localhost:8000/doc/live/tut/sage0-size500-22631843.jmol.zip
script ERROR: java.io.FileNotFoundException:
https://localhost:8000/doc/live/tut/sage0-size500-22631843.jmol.zip
eval ERROR:
----line 2 command 2 of file /home/_sage_/18/cells/1/sage0-
size500.jmol?3:
script "SCRIPT" <<
----line 1 command 1 of file null:
script "/home/_sage_/18/cells/1/sage0-size500.jmol?3" <<

---------------------------------------------------------------------------------------------------------------------
I checked permissions in case a temporary file can't be written ...
it looks like they are correct.
I'll check that again more closely tomorrow when I'm more alert.

-g




>
>
>
> > William

[gary]

On Apr 20, 10:15 pm, gary <gary.pa...@gmail.com> wrote:
>
> Here's something:
> the Java console reports an error:
> ------------------------------------------------------------------------------------------------------
> Init Jmol
> language=en_US
> Jmol applet jmolApplet0[533848364848684]
> AppletRegistry.checkIn(jmolApplet0[533848364848684])
> urlImage=jar:https://localhost:8000/java/jmol/JmolApplet0.jar!/
> jmol75x29x8.gif
> (C) 2007 Jmol Development
> Jmol Version 11.5.2 2007-12-20 06:37
> java.vendor:Sun Microsystems Inc.
> java.version:1.6.0_05
> os.name:Linux
> memory:3.6/5.2
> appletId:jmolApplet0
> appletDocumentBase=https://localhost:8000/doc/live/tut/node22.html
> appletCodeBase=https://localhost:8000/java/jmol/
> FileManager openinghttps://localhost:8000/home/_sage_/18/cells/1/sage0-size500.jmol?3
> FileManager openinghttps://localhost:8000/doc/live/tut/sage0-size500-22631843.jmol.zip

Are the above three lines fishy?

I downloaded the binary sage 2.11
I put my sage directory in /home/gap/bin I call it sage, so I have
everything in /home/gap/bin/sage
But what exactly does https://localhost:8000 point to?

I have no /home/gap/bin/sage/doc/live/tut
But I do have a /home/gap/bin/sage/doc/tut
Yet the browser finds a file at https://localhost:8000/doc/live/tut/node22.html

There is *no* /home/gap/bin/sage/java/jmol
There *is* a /home/gap/bin/sage/local/java/jmol

I can't find a home directory anywhere, execpt /home, and that has no
_sage_

Are these issues problems?

Perhaps I should install from source? or set some environment
variables?

??,
-gary

[William Stein]

A dynamic web server. There is no a priori mapping from what that
web server serves to your filesystem. Not all webserver just
serve up static pages mapped by a filesystem.

-- william

--
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org