[sage-support] Re: Jmol problem with Chrome on Mac

2011-02-26 Thread Benjamin Jones
If you update Chrome and the Jmol package in Sage it will work. See
this newer thread:

http://groups.google.com/group/sage-support/browse_thread/thread/47046e1c81d75d24

--
Benjamin Jones

On Jan 27, 2:29 am, pong wypon...@gmail.com wrote:
 I just wonder if any one has any success in getting Jmol to run 
 insideChromeon a Mac.
 If so, please share how :-)

 It's well known that Java is buggy withChrome(perhaps the new
 firefox 4 as well) on Mac. On sagenb.org, for example, when I invoke
 anything that calls Jmol, sage simply complains that Java applet is
 not enabled. Even though I have already allowed all sites to run
 Javascripts.

 I know two more things:

 1)Chrome(or Chromium rather) does not have this problem on Linux.
 2) It appears thatChrome(on Mac) can run Javascripts on some other
 sites, for example, I can play Java games with it.

 Any idea on how to fix this? Thanks in advance.

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[sage-support] Re: jmol problem

2009-04-04 Thread Brian

My jmol plot at sagenb.org is working for me now:
http://www.sagenb.org/home/pub/423/

On Apr 3, 11:14 pm, William Stein wst...@gmail.com wrote:
 2009/4/3 Timothy Clemans timothy.clem...@gmail.com:



  I get the same. This historically has been a problem with the public
  notebook(s).

 I 100% disagree.   This has *not* historically been a problem with the
 public notebooks. I have used them millions of times with numerous
 browsers from many places to draw 3d plots using jmol.

 I just did the same plot on another public notebook server (on the
 same machine) and it works fine:

    http://demo2.sagenb.org/home/pub/3/

 There is a serious problem with the Linux install (or vmware virtual
 machine) that currently hosts sagenb.org, which manifest itself about
 2 days ago -- for some reason the OS is randomly killing processes.
 This could be the result of some sort of attack, or just some other
 problem; I don't know.   That's probably what is responsible for your
 graph at sagenb.org to not work.  I'm actually very 
 surprisedhttp://sagenb.orgis working at all.

 William
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[sage-support] Re: jmol problem

2009-04-04 Thread Carl Witty

On Apr 3, 10:14 pm, William Stein wst...@gmail.com wrote:
 2009/4/3 Timothy Clemans timothy.clem...@gmail.com:



  I get the same. This historically has been a problem with the public
  notebook(s).

 I 100% disagree.   This has *not* historically been a problem with the
 public notebooks. I have used them millions of times with numerous
 browsers from many places to draw 3d plots using jmol.

 I just did the same plot on another public notebook server (on the
 same machine) and it works fine:

    http://demo2.sagenb.org/home/pub/3/

 There is a serious problem with the Linux install (or vmware virtual
 machine) that currently hosts sagenb.org, which manifest itself about
 2 days ago -- for some reason the OS is randomly killing processes.
 This could be the result of some sort of attack, or just some other
 problem; I don't know.   That's probably what is responsible for your
 graph at sagenb.org to not work.  I'm actually very 
 surprisedhttp://sagenb.orgis working at all.

One reason for the OS to randomly kill processes is the Linux out-of-
memory killer (OOM killer for short).  Is there any chance that
sagenb.org is running out of RAM?  Are there any interesting messages
if you log in and type dmesg?

Actually, I just realized I could check this for myself, so I did... I
don't see anything about the OOM killer, but there is a recurring,
strange error message about BUG: soft lockup - CPU#0 stuck for 11s!
[python:8525].  I don't know what this means, or if it has anything
to do with this problem.

Carl
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[sage-support] Re: jmol problem

2009-04-04 Thread mabshoff



On Apr 4, 3:12 pm, Carl Witty carl.wi...@gmail.com wrote:
 On Apr 3, 10:14 pm, William Stein wst...@gmail.com wrote:

SNIP

 Actually, I just realized I could check this for myself, so I did... I
 don't see anything about the OOM killer, but there is a recurring,
 strange error message about BUG: soft lockup - CPU#0 stuck for 11s!
 [python:8525].  I don't know what this means, or if it has anything
 to do with this problem.

Looks like a bug in the Ubuntu kernel. According to

  
http://muffinresearch.co.uk/archives/2008/08/20/ubuntu-bug-soft-lockup-cpu0-stuck-for-11s/

updating to the latest kernel for 8.04LTS should make this go away.

 Carl

Cheers,

Michael
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[sage-support] Re: jmol problem

2009-04-03 Thread Timothy Clemans

I get the same. This historically has been a problem with the public
notebook(s).

On Sat, Apr 4, 2009 at 1:04 AM, Brian medo...@gmail.com wrote:

 When I go to this public worksheet, jmol renders as a black screen:
 http://sagenb.org/home/pub/422/

 Here is the output of the Java Console.

 Java Plug-in 1.6.0_12
 Using JRE version 1.6.0_12 Java HotSpot(TM) Client VM
 User home directory = E:\Documents and Settings\brian
 
 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
 
 Jmol applet jmolApplet0__1424380939856034__ destroyed
 Jmol applet jmolApplet0__1672076516679526__ initializing
 AppletRegistry.checkIn(jmolApplet0__1672076516679526__)
 applet context: -applet
 appletDocumentBase=http://sagenb.org/home/pub/422/
 appletCodeBase=http://sagenb.org/java/jmol/
 (C) 2008 Jmol Development
 Jmol Version 11.6.16  2008-11-24 13:39
 java.vendor:Sun Microsystems Inc.
 java.version:1.6.0_12
 os.name:Windows XP
 memory:6.6/7.9
 useCommandThread: false
 appletId:jmolApplet0__1672076516679526__
 urlImage=jar:http://sagenb.org/java/jmol/JmolApplet0.jar!/
 jmol75x29x8.gif
 FileManager opening http://sagenb.org/java/jmol/appletweb/SageMenu.mnu
 defaults = Jmol
 backgroundColor = black
 language=en_US
 FileManager opening 
 http://sagenb.org/home/pub/422/cells/13/sage0-size500.jmol?1238821371
 FileManager opening 
 http://sagenb.org/home/pub/422/sage0-size500-117612907.jmol.zip
 script compiler ERROR: command expected
 line 1 command 1 of SCRIPT:
           !DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.01//EN 
 script ERROR: script compiler ERROR: command expected
 line 1 command 1 of SCRIPT:
           !DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.01//EN 
 eval ERROR:
 line 2 command 2 of file /home/pub/422/cells/13/sage0-size500.jmol?
 1238821371:
         script  SCRIPT 
 line 1 command 1:
         script  /home/pub/422/cells/13/sage0-size500.jmol?
 1238821371 

 


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[sage-support] Re: jmol problem

2009-04-03 Thread William Stein

2009/4/3 Timothy Clemans timothy.clem...@gmail.com:

 I get the same. This historically has been a problem with the public
 notebook(s).

I 100% disagree.   This has *not* historically been a problem with the
public notebooks. I have used them millions of times with numerous
browsers from many places to draw 3d plots using jmol.

I just did the same plot on another public notebook server (on the
same machine) and it works fine:

http://demo2.sagenb.org/home/pub/3/

There is a serious problem with the Linux install (or vmware virtual
machine) that currently hosts sagenb.org, which manifest itself about
2 days ago -- for some reason the OS is randomly killing processes.
This could be the result of some sort of attack, or just some other
problem; I don't know.   That's probably what is responsible for your
graph at sagenb.org to not work.  I'm actually very surprised
http://sagenb.org is working at all.

William

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[sage-support] Re: Jmol problem

2009-03-08 Thread Kwankyu

I solved my problem just by reinstalling Firefox. ^^ Thank you anyway!

Kwankyu
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[sage-support] Re: Jmol problem

2009-03-07 Thread Jason Grout

Kwankyu wrote:
 Hi,
 
 In my Sage 3.3 notebook on Mac OS 10.5/Firefox 3.07, Jmol 3d graphics
 are shown as just black rectangles. I know this was a problem that
 other people experienced. But is it now fixed? If this occurs only to
 me, how can I fix it?
 


Can you view some demos on the jmol website?

http://jmol.sourceforge.net/demo/atoms/

http://jmol.sourceforge.net/demo/animation/



Jason


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[sage-support] Re: Jmol problem

2009-03-07 Thread John Cremona

When I try to view the frst demo I get this (and similarly from within
Sage) in a yellow fram in the window.

You do not have Java applets enabled in your web browser, or your
browser is blocking this applet.
Check the warning message from your browser and/or enable Java applets in
your web browser preferences, or install the Java Runtime Environment
from www.java.com

In the past I tried several ways to solve this but to no avail: I *do*
have Java applets enabled in Firefox, there is no warning message from
Firefox, and I have all sorts of version of JRE installed (this is in
ubuntu).  I just gave up, since I can do without graphics, but it
would be nice to know what the problem is.

John Cremona

2009/3/7 Jason Grout jason-s...@creativetrax.com:

 Kwankyu wrote:
 Hi,

 In my Sage 3.3 notebook on Mac OS 10.5/Firefox 3.07, Jmol 3d graphics
 are shown as just black rectangles. I know this was a problem that
 other people experienced. But is it now fixed? If this occurs only to
 me, how can I fix it?



 Can you view some demos on the jmol website?

 http://jmol.sourceforge.net/demo/atoms/

 http://jmol.sourceforge.net/demo/animation/



 Jason


 


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[sage-support] Re: Jmol problem

2009-03-07 Thread Rob Beezer

John et al,

I've been doing without JMOL on 64-bit Ubuntu, since Sun had not made
a 64-bit plugin until just recently.  VERY inconvenient.  ;-)  I've
had similar frustrations as John with all sorts of JRE's around/
installed.

However, I got this new plugin installed last night in about 5
minutes.  The instructions might help others on different platforms -
the Sun download area has RPM's, etc.

Here is the Ubuntu thread, just follow the first poster's instructions
modified/adjusted to fit your situation.

http://ubuntuforums.org/showthread.php?t=1011899

Rob


On Mar 7, 6:57 am, John Cremona john.crem...@gmail.com wrote:
 When I try to view the frst demo I get this (and similarly from within
 Sage) in a yellow fram in the window.

 You do not have Java applets enabled in your web browser, or your
 browser is blocking this applet.
 Check the warning message from your browser and/or enable Java applets in
 your web browser preferences, or install the Java Runtime Environment
 fromwww.java.com

 In the past I tried several ways to solve this but to no avail: I *do*
 have Java applets enabled in Firefox, there is no warning message from
 Firefox, and I have all sorts of version of JRE installed (this is in
 ubuntu).  I just gave up, since I can do without graphics, but it
 would be nice to know what the problem is.

 John Cremona

 2009/3/7 Jason Grout jason-s...@creativetrax.com:



  Kwankyu wrote:
  Hi,

  In my Sage 3.3 notebook on Mac OS 10.5/Firefox 3.07, Jmol 3d graphics
  are shown as just black rectangles. I know this was a problem that
  other people experienced. But is it now fixed? If this occurs only to
  me, how can I fix it?

  Can you view some demos on the jmol website?

 http://jmol.sourceforge.net/demo/atoms/

 http://jmol.sourceforge.net/demo/animation/

  Jason
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[sage-support] Re: Jmol problem

2009-03-07 Thread gerhard

 with all sorts of JRE's
one possible reason for this problem is
the plugin firefox may be using.

check by typing
  about:plugins
in the title bar,
and make sure it is the plugin you expect
(sun's jre)
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[sage-support] Re: Jmol problem

2009-03-07 Thread John Cremona

That's interesting -- there is no java at all listed in the list of
plugins.  This is with 32-bit ubuntu.

John

2009/3/7 gerhard ge01...@yahoo.de:

 with all sorts of JRE's
 one possible reason for this problem is
 the plugin firefox may be using.

 check by typing
      about:plugins
 in the title bar,
 and make sure it is the plugin you expect
 (sun's jre)
 


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[sage-support] Re: Jmol problem

2009-03-07 Thread Rob Beezer

I'd forgotten that about:plugins is so useful.

Do you know the Debian/Ubuntu alternatives scheme?  Its a way to
specify a system-wide default editor, etc.  See  man update-
alternatives

On Ubuntu Hardy 8.04 I had to use (as root)

update-alternatives  --config   xulrunner-1.9-javaplugin.so

You can see the possible alternatives via
ls -al /etc/alternatives.   The update-alternatives command manages
asll these symbolic links.

You want to have the xul-runner thing point to a Sun plug in, not an
Open JDK or IcedTea or some such thing. You'll probably get some
choices.  (Presuming you have the right packages installed.)

THEN check about:plugins after a restart of Firefox.  Good luck.  ;-)





On Mar 7, 12:43 pm, John Cremona john.crem...@gmail.com wrote:
 That's interesting -- there is no java at all listed in the list of
 plugins.  This is with 32-bit ubuntu.

 John

 2009/3/7 gerhard ge01...@yahoo.de:



  with all sorts of JRE's
  one possible reason for this problem is
  the plugin firefox may be using.

  check by typing
       about:plugins
  in the title bar,
  and make sure it is the plugin you expect
  (sun's jre)
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[sage-support] Re: Jmol problem

2009-03-07 Thread Jason Grout

John Cremona wrote:
 Thanks for the detailed instructions.  I have never heard of
 xulrunner.  Something of that name was installed but I installed a
 newer (?) version using synaptic.  I also used update-alternatives to
 get java to point to the sun version.  Now I have this:
 
 j...@ubuntu%sudo update-alternatives  --display  java
 java - status is manual.
  link currently points to /usr/lib/jvm/java-6-sun/jre/bin/java
 /usr/lib/jvm/java-6-openjdk/jre/bin/java - priority 1061
  slave java.1.gz: /usr/lib/jvm/java-6-openjdk/jre/man/man1/java.1.gz
 /usr/bin/gij-4.2 - priority 42
  slave java.1.gz: /usr/share/man/man1/gij-4.2.1.gz
 /usr/lib/jvm/java-6-sun/jre/bin/java - priority 63
  slave java.1.gz: /usr/lib/jvm/java-6-sun/jre/man/man1/java.1.gz
 Current `best' version is /usr/lib/jvm/java-6-openjdk/jre/bin/java.
 
 j...@ubuntu%sudo update-alternatives  --display  xulrunner
 xulrunner - status is auto.
  link currently points to /usr/bin/xulrunner-1.9
 /usr/bin/xulrunner-1.9 - priority 50
 /usr/lib/xulrunner/xulrunner - priority 50
 Current `best' version is /usr/bin/xulrunner-1.9.
 
 I don't know what 'best' means, it still seems to like the look of the
 open jdk for java.
 
 After all this and restarting firefox there is still no mention of
 java in about:plugins.  I find it hard to believe that it is not there
 since the Preferences setting for jave is enabled and surely there
 are many other web things which would not work without java (gmail for
 a start).

Gmail almost surely uses javascript, not java, which is different.

Jason


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[sage-support] Re: Jmol problem

2009-03-07 Thread Rob Beezer

John,

java will point to something to run java programs locally on your
machine.

I think xulrunner is some Firefox/Mozilla thing.

You want a java *plugin* for Firefox.

Try the combo deal:

update-alternatives  --config   xulrunner-1.9-javaplugin.so

and pick the one that looks like it comes from Sun.

Rob

On Mar 7, 2:22 pm, John Cremona john.crem...@gmail.com wrote:
 Thanks for the detailed instructions.  I have never heard of
 xulrunner.  Something of that name was installed but I installed a
 newer (?) version using synaptic.  I also used update-alternatives to
 get java to point to the sun version.  Now I have this:

 j...@ubuntu%sudo update-alternatives  --display  java
 java - status is manual.
  link currently points to /usr/lib/jvm/java-6-sun/jre/bin/java
 /usr/lib/jvm/java-6-openjdk/jre/bin/java - priority 1061
  slave java.1.gz: /usr/lib/jvm/java-6-openjdk/jre/man/man1/java.1.gz
 /usr/bin/gij-4.2 - priority 42
  slave java.1.gz: /usr/share/man/man1/gij-4.2.1.gz
 /usr/lib/jvm/java-6-sun/jre/bin/java - priority 63
  slave java.1.gz: /usr/lib/jvm/java-6-sun/jre/man/man1/java.1.gz
 Current `best' version is /usr/lib/jvm/java-6-openjdk/jre/bin/java.

 j...@ubuntu%sudo update-alternatives  --display  xulrunner
 xulrunner - status is auto.
  link currently points to /usr/bin/xulrunner-1.9
 /usr/bin/xulrunner-1.9 - priority 50
 /usr/lib/xulrunner/xulrunner - priority 50
 Current `best' version is /usr/bin/xulrunner-1.9.

 I don't know what 'best' means, it still seems to like the look of the
 open jdk for java.

 After all this and restarting firefox there is still no mention of
 java in about:plugins.  I find it hard to believe that it is not there
 since the Preferences setting for jave is enabled and surely there
 are many other web things which would not work without java (gmail for
 a start).

 The jmol demo page shows exactly the same message as before.

 Never mind,

 John

 2009/3/7 Rob Beezer goo...@beezer.cotse.net:



  I'd forgotten that about:plugins is so useful.

  Do you know the Debian/Ubuntu alternatives scheme?  Its a way to
  specify a system-wide default editor, etc.  See  man update-
  alternatives

  On Ubuntu Hardy 8.04 I had to use (as root)

  update-alternatives  --config   xulrunner-1.9-javaplugin.so

  You can see the possible alternatives via
  ls -al /etc/alternatives.   The update-alternatives command manages
  asll these symbolic links.

  You want to have the xul-runner thing point to a Sun plug in, not an
  Open JDK or IcedTea or some such thing. You'll probably get some
  choices.  (Presuming you have the right packages installed.)

  THEN check about:plugins after a restart of Firefox.  Good luck.  ;-)

  On Mar 7, 12:43 pm, John Cremona john.crem...@gmail.com wrote:
  That's interesting -- there is no java at all listed in the list of
  plugins.  This is with 32-bit ubuntu.

  John

  2009/3/7 gerhard ge01...@yahoo.de:

   with all sorts of JRE's
   one possible reason for this problem is
   the plugin firefox may be using.

   check by typing
        about:plugins
   in the title bar,
   and make sure it is the plugin you expect
   (sun's jre)
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[sage-support] Re: Jmol problem

2009-03-07 Thread John Cremona

Problem solved.  When I did

update-alternatives  --config   xulrunner-1.9-javaplugin.so

it complained that there was no such alternative.  Googling that file
name led me to ubuntu forums and hence to the package name
sun-java6-plugin, which I did not have installed.  So I installed it,
restarted firefox, and now it works!

I'm sure it is worth putting this information into the FAQ list, even
if it only applies to ubuntu machines:  for jmol to work you need to
have the package sun-java6-plugin installed.

thanks for your help, now I can demo Sage's animated 3D graphics to people!

John

2009/3/7 Rob Beezer goo...@beezer.cotse.net:

 John,

 java will point to something to run java programs locally on your
 machine.

 I think xulrunner is some Firefox/Mozilla thing.

 You want a java *plugin* for Firefox.

 Try the combo deal:

 update-alternatives  --config   xulrunner-1.9-javaplugin.so

 and pick the one that looks like it comes from Sun.

 Rob

 On Mar 7, 2:22 pm, John Cremona john.crem...@gmail.com wrote:
 Thanks for the detailed instructions.  I have never heard of
 xulrunner.  Something of that name was installed but I installed a
 newer (?) version using synaptic.  I also used update-alternatives to
 get java to point to the sun version.  Now I have this:

 j...@ubuntu%sudo update-alternatives  --display  java
 java - status is manual.
  link currently points to /usr/lib/jvm/java-6-sun/jre/bin/java
 /usr/lib/jvm/java-6-openjdk/jre/bin/java - priority 1061
  slave java.1.gz: /usr/lib/jvm/java-6-openjdk/jre/man/man1/java.1.gz
 /usr/bin/gij-4.2 - priority 42
  slave java.1.gz: /usr/share/man/man1/gij-4.2.1.gz
 /usr/lib/jvm/java-6-sun/jre/bin/java - priority 63
  slave java.1.gz: /usr/lib/jvm/java-6-sun/jre/man/man1/java.1.gz
 Current `best' version is /usr/lib/jvm/java-6-openjdk/jre/bin/java.

 j...@ubuntu%sudo update-alternatives  --display  xulrunner
 xulrunner - status is auto.
  link currently points to /usr/bin/xulrunner-1.9
 /usr/bin/xulrunner-1.9 - priority 50
 /usr/lib/xulrunner/xulrunner - priority 50
 Current `best' version is /usr/bin/xulrunner-1.9.

 I don't know what 'best' means, it still seems to like the look of the
 open jdk for java.

 After all this and restarting firefox there is still no mention of
 java in about:plugins.  I find it hard to believe that it is not there
 since the Preferences setting for jave is enabled and surely there
 are many other web things which would not work without java (gmail for
 a start).

 The jmol demo page shows exactly the same message as before.

 Never mind,

 John

 2009/3/7 Rob Beezer goo...@beezer.cotse.net:



  I'd forgotten that about:plugins is so useful.

  Do you know the Debian/Ubuntu alternatives scheme?  Its a way to
  specify a system-wide default editor, etc.  See  man update-
  alternatives

  On Ubuntu Hardy 8.04 I had to use (as root)

  update-alternatives  --config   xulrunner-1.9-javaplugin.so

  You can see the possible alternatives via
  ls -al /etc/alternatives.   The update-alternatives command manages
  asll these symbolic links.

  You want to have the xul-runner thing point to a Sun plug in, not an
  Open JDK or IcedTea or some such thing. You'll probably get some
  choices.  (Presuming you have the right packages installed.)

  THEN check about:plugins after a restart of Firefox.  Good luck.  ;-)

  On Mar 7, 12:43 pm, John Cremona john.crem...@gmail.com wrote:
  That's interesting -- there is no java at all listed in the list of
  plugins.  This is with 32-bit ubuntu.

  John

  2009/3/7 gerhard ge01...@yahoo.de:

   with all sorts of JRE's
   one possible reason for this problem is
   the plugin firefox may be using.

   check by typing
        about:plugins
   in the title bar,
   and make sure it is the plugin you expect
   (sun's jre)
 


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[sage-support] Re: Jmol problem

2009-03-07 Thread Rob Beezer

John,

Super!  Thanks for the information.  Yes, maybe I should add something
to the FAQ.  Spring break is in a week.  ;-)

The JMOL applet for the 3D plots is really powerful.  Jason Grout and
I have been passing worksheets back and forth for the multivariate
calculus courses we are teaching and they are *really* enhancing my
course.  They should all migrate to the Interact/Calculus section of
the wiki when we get a chance.

But Java is a pain to get working.  Right up there with the Flash
plugin.  Its always the proprietary bits. ;-)

Rob

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