On Tuesday, April 10, 2012 7:40:51 PM UTC-5, Benjamin Jones wrote: > > 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 = > > > 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 -- To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to sage-support+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-support URL: http://www.sagemath.org
