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August 23, 2019

Java problems under Linux Log Out | Topics | Search
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Vidar R. Jensen
Unregistered guest
Posted on Friday, November 07, 2014 - 3:53 am:   

Observation: Most of the time it is not possible to view the geometry of previous jobs selected from the Job Manager. It is possible to create new jobs and build molecules, but it is not possible to choose engine or to export the geometry subsequent to building a structure.
Platform: Ubuntu 12.04 LTS, running Mozilla Firefox 33.0, with Oracle Java (TM) Plugin 10.72.2.
WebMO: 14.0.007e.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 426
Registered: 11-2006
Posted on Friday, November 07, 2014 - 11:03 am:   

Do you receive any error messages / popups, etc.? Please check with the Javascript and Java error consoles.
Vidar R. Jensen
Unregistered guest
Posted on Friday, November 07, 2014 - 3:48 pm:   

No error messages or popups; nothing happens. Where do I find the Javascript and Java error consoles?
JR Schmidt
Moderator
Username: Schmidt

Post Number: 427
Registered: 11-2006
Posted on Friday, November 07, 2014 - 9:03 pm:   

Javascript errors can be found in the console. Go to the firefox "menu" (upper right), click developer, then console.

The Java console can be enabled as follows:
https://www.java.com/en/download/help/enable_console_linux.xml
Vidar R. Jensen
Unregistered guest
Posted on Monday, November 10, 2014 - 4:56 am:   

I built, symmetrized, and cleaned up the geometry of a water molecule. Then I chose "Choose engine".
The content of the Java Console at that point was:
Java Plug-in 10.72.2.14
Using JRE version 1.7.0_72-b14 Java HotSpot(TM) 64-Bit Server VM
User home directory = /Home/siv2/nkjvj
----------------------------------------------------
c: clear console window
f: finalize objects on finalization queue
g: garbage collect
h: display this help message
l: dump classloader list
m: print memory usage
o: trigger logging
q: hide console
r: reload policy configuration
s: dump system and deployment properties
t: dump thread list
v: dump thread stack
x: clear classloader cache
0-5: set trace level to <n>
----------------------------------------------------
Principal Axes are non-degenerate


+ ELEMENTS FOUND:

C2 with a rating of 0.000000
sigma with a rating of 0.000000
sigma with a rating of 0.000000

+ POINT GROUP FOUND:

{ E, 2sigma, C2 }

***************************
1. C2v: 2.6493494208177222E-15
***************************
2. Cs: 0.0
3. C2: 3.636721891222372E-15
4. C1: 0.0

The JavaScript errors are:
uncaught exception: Liveconnect call for Applet ID 2 is not allowed in this JVM instance

Choosing Export Molecule generates exactly the same error message.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 428
Registered: 11-2006
Posted on Monday, November 10, 2014 - 10:58 am:   

Please try our demo server at https://www.webmo.net/demoserver/cgi-bin/webmo/login.cgi

to see if you experience the same issues.

I find no problem with the most recent Java on either the WebMO 15 or 14.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 429
Registered: 11-2006
Posted on Monday, November 10, 2014 - 5:21 pm:   

To follow up:

I fired up a virtual machine and can replicate the problem. Unfortunately it appears to be an ORACLE / JAVA bug. The appear to have broken security changes they made in the past. Oddly, this ONLY effects Linux, not Windows or Mac.

I don't have a perfect workaround, other than to install Java 7u67 (the previous Java version prior to 7u71), which is unaffected. Note that I found it necessary to physically delete Java 7u71 to prevent that version from being used.

I will explore other workarounds, but it may be a waiting game until Oracle fixes the problem.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 430
Registered: 11-2006
Posted on Monday, November 10, 2014 - 9:01 pm:   

Another alternative:

OpenJDK (on which Oracle's Java is based) appears to work without any issuses. This should by installable via apt-get or yum.
Vidar R. Jensen
Unregistered guest
Posted on Tuesday, November 11, 2014 - 3:06 am:   

Yes, I get the same kind of error message "uncaught exception: Liveconnect call for Applet ID 1 is not allowed in this JVM instance" when using your demo server. Unfortunately, it is not very likely that I can persuade our system administration to downgrade the Oracle Java, or to install OpenJDK: I have already pushed considerable to have them install the latest Oracle Java and to get rid of OpenJDK - since this is the "mantra" in many of your replies to those who report issues with WebMO on this forum. The question now is whether you have reported this bug to Oracle already?
JR Schmidt
Moderator
Username: Schmidt

Post Number: 433
Registered: 11-2006
Posted on Saturday, November 15, 2014 - 1:48 pm:   

It appears the above referenced Java bug was already reported to OpenJDK, which develops the code on which both OpenJDK an Oracle's Java are based:

https://bugs.openjdk.java.net/browse/JDK-8064677?page=com.atlassian.streams.streams-jira-plugin:activity-stream-issue-tab
Kevin Range
Unregistered guest
Posted on Friday, February 06, 2015 - 3:47 pm:   

This is not fixed in 7u76. The OpenJDK bug you referenced above was closed as a dupe of a bug I can't seem to find on their bug tracking system.
Kevin Range
Unregistered guest
Posted on Friday, February 06, 2015 - 4:02 pm:   

8u31 doesn't work either.
Kevin Range
Unregistered guest
Posted on Friday, February 06, 2015 - 4:53 pm:   

Openjdk works:

java version "1.7.0_75"
OpenJDK Runtime Environment (IcedTea 2.5.4) (7u75-2.5.4-1~trusty1)
OpenJDK 64-Bit Server VM (build 24.75-b04, mixed mode)

with icedtea version 1.5-1ubuntu1
John Keller
Unregistered guest
Posted on Wednesday, February 25, 2015 - 6:06 pm:   

A few more details...
Neither java-8u31 and java-7u75 from the Oracle website (that is, jdk-7u75-linux-x64.tar.gz or jre-8u31-x64.tar.gz) allow me to visualize a molecule on recent WebMO webservers using a Linux CentOS client. However, they *do* allow one to see Jmol webpages and molecules. Anyway, the Oracle java can removed by simply (as su) deleting the /usr/java folder and removing the link to libnpjp2.so from the /usr/lib64/mozilla/plugins folder.

Kevin Range's post indicated that the openjdk-java and icedtea web plugin do allow one to visualize WebMO molecules, although one still must still click through various security warnings. So as su, do

# yum list iced*
# yum list java*

This will show you what is installed, as well as what is available for download.
Actually, icedtea requires java-1.7.0-openjdk as a dependency, so you will get both by doing:

#yum install icedtea-web.x86_64

After installing you will notice that the libjavaplugin.so file is automatically installed in the /usr/lib64/mozilla/plugins folder. Therefore it is not necessary to insert the link as discussed on the WebMO browser support webpage.

Client OS: CentOS 6.5
Browser: Mozilla Firefox 31.4.0
Server WebMO: 15.0.003p
John Keller
Unregistered guest
Posted on Wednesday, February 25, 2015 - 6:20 pm:   

Correction: what is installed is a link to another link /etc/alternatives/libjavaplugin.so, which is itself a link to /usr/lib64/IcedTeaPlugin.so
John Keller
Unregistered guest
Posted on Wednesday, February 25, 2015 - 6:25 pm:   

Kevin Range's detailed procedure, which he indicated could be copied into this forum for Ubuntu users, is as follows:

# sudo apt-get install openjdk-7-jre
# sudo apt-get install icedtea-7-plugin

then perhaps you should do:

# sudo update-alternatives --config java

and select /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java as your java

and

# sudo update-alternatives --config mozilla-javaplugin.so

and select /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/IcedTeaPlugin.so as your java-plugin for firefox

restart firefox and test it out.

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