3d plotting using Jmol: black screen of death

[Benjamin Jones]

3d plotting using Jmol: black screen of death

I've read through all the Jmol problem threads here that I could find,
back to    2008, and I can't find an answer to the "Jmol produces a blank,               
black display" problem I'm about to describe. So here is a new thread.
...

I've been having a frustrating time making 3d plots using Jmol for a while now. I have
a server setup running Debian and various versions of the Sage notebook on
different ports. I'm connecting to the server mainly with a newish
MacBook Pro (OS X 10.6.8) using Firefox 11 or Chrome
18.0.1025.151.

I experience the following thing, over and over again.
1. I connect to the notebook
2. I start a new worksheet
3. I type cube() into the first cell and evaluate
4. Jmol loads, I see a cube. Great!
5. I Save and Quit, go do something else, maybe shut the lid on my
laptop, etc.
6. I load the worksheet just made. Where the Jmol applet displays
there is only a black screen.
7. Re-evaluating the cell returns the same black display.
8. Quitting browser, clearing cache, cookies, rebooting computer, has
no effect.
9. I notice that one I get the "black screen of death" once, I get it
in every other old worksheet containing a Jmol applet and in every new
worksheet I produce until some later indeterminate time when it starts
working again.

In trying to isolate the problem, or just to find a Sage / Sagenb
version where 3d plotting with Jmol works consistently, I collected
some data which I post below. I haven't come to any conclusion yet,
but I'd really like to track this problem down. I find that using sageng.org
basically always works (all platforms / browser combos below work there)
so I guess one question is what magic is going on there with regards to
Jmol and the notebook that I can't get using sage-4.8 + instructions at
trac #11080?

   - Note: Mac = Mac OS X 10.6.8, Linux = Fedora 16 VM
   - Note: on Mac and Linux, all examples at
     http://jmol.sourceforge.net/demo/ WORK fine.
   - Note: When I say WORK, I means the plots load always, can be
     reloaded, at will, anytime. When I say FAILS, I mean that it
     might work the first time the plot is made, but I get black
     screen of death or some other bad behavior thereafter.

= Data =

== MY SERVER ==

   - Sage 4.7.1
     - Mac
       - FAILS in FF 11 (black screen, menus work but no data)
       - FAILS in Chrome 18.0.1025.151 (black screen, menus work but no data)
     - Linux
       - FAILS in FF 11 (black screen, red error "No atoms found for file string type 
         Xyz")
     - Windows 7
       - WORKS on one machine, FAILS on another  in FF 11
       - WORKS in IE (both machines!?!?)

   - Sage 4.8 + new notebook at #11080 (applied months ago)
     - Mac
       - FAILS in FF 11 (black screen, menus work but no data)
       - FAILS in Chrome 18.0.1025.151 (black screen, menus work but no data)
     - Linux
       - FAILS in FF 11

   - Sage 4.8 (stock)
     - Mac
       - WORKS in FF 11
       - WORKS in Crome 18.0.1025.151
     - Linux
       - FAILS in FF 11 (black screen, red error "No atoms found for file string type")
   - Sage 5.0.beta13 + new notebook at #11080 (applied 2012-04-09)
     - Mac
       - FAILS in FF 11 (black screen, menus work but no data)
       - FAILS in Chrome 18.0.1025.151 (black screen, menus work but no data)
     - Linux
       - WORKS in FF 11
     - Windows 7
       - WORKS in FF 11
       - WORKS in IE (!?!?)

== REMOTE SERVERS ==

   - sagenb.org (sage-4.8 + ???)
     - Mac
       - WORKS in Chrome 18.0.1025.151
     - Linux (Fed 16 VM)
       - WORKS in FF 11

   - test.sagenb.org (sage-5.0.beta11 + ???)
     - Mac
       - WORKS in FF 11
       - WORKS in Chrome 18
     - Linux
       - FAILS in FF 11 (Loading Jmol applet counts up forever..)
       - FAILS in Chrome 18 (tab crashes "he's dead, Jim!")

[P Purkayastha]

You have given a lot of information except for one important thing: what is the java you have installed? The jmol applet is most reliable and tested only on Sun/Oracle java.

[Benjamin Jones]

Yes, good point. I meant to include that:

Mac runs the java that Apple ships with 10.6.8:

java version "1.6.0_31"
Java(TM) SE Runtime Environment (build 1.6.0_31-b04-413-10M3623)
Java HotSpot(TM) 64-Bit Server VM (build 20.6-b01-413, mixed mode)

Fedora Linux VM runs the java that Fedora 16 ships with:

java version "1.6.0_24"
OpenJDK Runtime Environment (IcedTea 1.11.1)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

I don't have access to the Windows machine right now, but I'm 99%
positive it has a recent Sun/Oracle java 1.6.0 release.

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

... so the Java isntallation on the Linux machine might be the cause
of the problems there (the red error messages in the table below).
But, it still leaves the problem I have on Mac OS X in Firefox and
that my colleagues have on Windows 7 in Firefox.

--
Benjamin Jones

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[P Purkayastha]

FYI, I have not had a failing jmol for well over a year on Linux - Gentoo Linux x64 and Ubuntu minimal 11.10 (which was earlier 11.04). In both machines I run sun java. Currently on the Gentoo machine the java is sun-jdk-1.6.0.31.

[Benjamin Jones]

 
I believe I've solved my problem so I thought I'd post here in case other people run into it.

Problem: I connect via https to local Sage notebook server. The local server has a self-signed SSL certificate. Some Java installations (in particular the default Java installed on my Mac OS X 10.6.8 MacBookPro) has a problem re-verifying the self-signed certificate when a worksheet with a Jmol applet is reloaded or refreshed.

Solution: Install the self-signed certificate for the local Sage notebook server into the list of Java's trusted certificates on the client machine (do this for each client machine and each self-signed cert needed). For example, on my MacBook I did:

mac> export JAVA_HOME=/Library/Java/Home
mac> cd $JAVA_HOME
mac> sudo bin/keytool -import -trustcacerts -alias <CERT_NAME> -file <CERT_FILE> -keystore lib/security/cacerts

where I had previously exported my Sage server's self-signed certificate to the file <CERT_FILE> on my mac and <CERT_NAME> is a name for the certificate in the keystore (I used "SageCA")

After doing this, I have no Jmol problems in Mac OS X on the given Sage notebook server.

--
Benjamin Jones