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!")