All fixed. Ready for release.
On Tue, Sep 7, 2010 at 5:19 PM, Nicolas Vervelle <nverve...@gmail.com>wrote:
> Yes, I was wondering if there was a purpose on removing/adding elements one
> at a time.
> Collections have built-in methods to add all the elements (or some
> elements) of an other collection.
>
> Nico
>
> On Tue, Sep 7, 2010 at 11:54 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> It's easier just to not use an iterator -- get the keys as an array and
>> run through them. I'll work on it tonight.
>>
>> On Tue, Sep 7, 2010 at 12:58 PM, Nicolas Vervelle <nverve...@gmail.com>wrote:
>>
>>> Hi Bob,
>>>
>>> I have just looked into the code involved, and I believe it's not a
>>> multithread problem.
>>> It's simply that we're iterating over a Map and incorrectly removing
>>> elements from it.
>>>
>>> The Map.remove() shouldn't be called when iterating over the keySet.
>>> The javadoc for keySet() says the results are undefined.
>>>
>>> Maybe replacing (twice) :
>>>
>>> Iterator<String> e = messageQueue.keySet().iterator();
>>> while (e.hasNext()) {
>>> String statusName = e.next();
>>> List<List<Object>> record = messageQueue.remove(statusName);
>>> msgList.add(record);
>>> }
>>>
>>> by something like (not tested) :
>>>
>>> Iterator<Entry<String, List<List<Object>>>> e =
>>> messageQueue.entrySet().iterator();
>>> while (e.hasNext()) {
>>> Entry<String, List<List<Object>>> record = e.next();
>>> e.remove();
>>> msgList.add(record.getValue());
>>> }
>>>
>>> I don't know how to test the modification, so I haven't done it.
>>>
>>> Nico
>>>
>>>
>>> On Tue, Sep 7, 2010 at 6:26 PM, Robert Hanson <hans...@stolaf.edu>wrote:
>>>
>>>> Oh, interesting! ConcurrentModificationException. Yes, (Nico) we might
>>>> need to look into that. That means that two independent threads are trying
>>>> to update the same Java object and have collided. It would indeed be unique
>>>> to Jmol 12.1, I think.
>>>>
>>>> I'll look into it this evening if Nico hasn't tracked it down by then.
>>>> Nico, do we need to synchronize that?
>>>>
>>>> Bob
>>>>
>>>> On Tue, Sep 7, 2010 at 9:52 AM, Alexander Rose <
>>>> alexander.r...@weirdbyte.de> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>>
>>>>> In the 12.1 development branch (starting with 12.1.2), the applet
>>>>> throws an exception upon calling jmolScriptWait( ... ).
>>>>>
>>>>> http://weirdbyte.de/jmol-test/html/security.html
>>>>>
>>>>> The exception occurs on both, the signed and the unsigned applet.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Firefox on Ubuntu 10.04, Java 1.6.0_18
>>>>>
>>>>> java.lang.reflect.InvocationTargetException
>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>>> at
>>>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>>>>> at
>>>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>>>> at java.lang.reflect.Method.invoke(Method.java:616)
>>>>> at
>>>>> sun.applet.PluginAppletSecurityContext$4.run(PluginAppletSecurityContext.java:699)
>>>>> at java.security.AccessController.doPrivileged(Native Method)
>>>>> at
>>>>> sun.applet.PluginAppletSecurityContext.handleMessage(PluginAppletSecurityContext.java:696)
>>>>> at
>>>>> sun.applet.AppletSecurityContextManager.handleMessage(AppletSecurityContextManager.java:69)
>>>>> at
>>>>> sun.applet.PluginStreamHandler.handleMessage(PluginStreamHandler.java:273)
>>>>> at
>>>>> sun.applet.PluginMessageHandlerWorker.run(PluginMessageHandlerWorker.java:82)
>>>>> Caused by: java.util.ConcurrentModificationException
>>>>> at java.util.Hashtable$Enumerator.next(Hashtable.java:1048)
>>>>> at org.jmol.viewer.StatusManager.getStatusChanged(Unknown
>>>>> Source)
>>>>> at org.jmol.viewer.Viewer.getStatusChanged(Unknown Source)
>>>>> at org.jmol.viewer.PropertyManager.getPropertyAsObject(Unknown
>>>>> Source)
>>>>> at org.jmol.viewer.PropertyManager.getProperty(Unknown Source)
>>>>> at org.jmol.viewer.Viewer.getProperty(Unknown Source)
>>>>> at org.jmol.viewer.Viewer.getProperty(Unknown Source)
>>>>> at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
>>>>> at org.jmol.viewer.Viewer.scriptWait(Unknown Source)
>>>>> at org.jmol.applet.Jmol.scriptProcessor(Unknown Source)
>>>>> at org.jmol.applet.Jmol.scriptWait(Unknown Source)
>>>>> at JmolApplet.scriptWait(Unknown Source)
>>>>> ... 10 more
>>>>> Error on Java side: null
>>>>>
>>>>>
>>>>>
>>>>> Firefox 3.6 on Mac OSX 10.6, Java 1.6.0_20
>>>>>
>>>>> java.util.ConcurrentModificationException
>>>>> at java.util.Hashtable$Enumerator.next(Hashtable.java:1031)
>>>>> at org.jmol.viewer.StatusManager.getStatusChanged(Unknown
>>>>> Source)
>>>>> at org.jmol.viewer.Viewer.getStatusChanged(Unknown Source)
>>>>> at org.jmol.viewer.PropertyManager.getPropertyAsObject(Unknown
>>>>> Source)
>>>>> at org.jmol.viewer.PropertyManager.getProperty(Unknown Source)
>>>>> at org.jmol.viewer.Viewer.getProperty(Unknown Source)
>>>>> at org.jmol.viewer.Viewer.getProperty(Unknown Source)
>>>>> at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
>>>>> at org.jmol.viewer.Viewer.scriptWait(Unknown Source)
>>>>> at org.jmol.applet.Jmol.scriptProcessor(Unknown Source)
>>>>> at org.jmol.applet.Jmol.scriptWait(Unknown Source)
>>>>> at JmolApplet.scriptWait(Unknown Source)
>>>>> at netscape.oji.JNIRunnable.run(Native Method)
>>>>> at netscape.oji.LiveConnectProxy.run(LiveConnectProxy.java:48)
>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>>> at
>>>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>>>> at
>>>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>>>> at java.lang.reflect.Method.invoke(Method.java:597)
>>>>> at jep.LiveConnect$DoProxy.run(Unknown Source)
>>>>> at
>>>>> java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
>>>>> at java.awt.EventQueue.dispatchEvent(EventQueue.java:633)
>>>>> at
>>>>> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
>>>>> at
>>>>> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
>>>>> at
>>>>> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
>>>>> at
>>>>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
>>>>> at
>>>>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
>>>>> at
>>>>> java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
>>>>>
>>>>>
>>>>>
>>>>> Safari 5 on Mac OSX 10.6, Java 1.6.0_20
>>>>>
>>>>> Ignored exception: java.security.PrivilegedActionException:
>>>>> java.lang.reflect.InvocationTargetException
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Best
>>>>> Alex
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> This SF.net Dev2Dev email is sponsored by:
>>>>>
>>>>> Show off your parallel programming skills.
>>>>> Enter the Intel(R) Threading Challenge 2010.
>>>>> http://p.sf.net/sfu/intel-thread-sfd
>>>>> _______________________________________________
>>>>> Jmol-users mailing list
>>>>> jmol-us...@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Robert M. Hanson
>>>> Professor of Chemistry
>>>> St. Olaf College
>>>> 1520 St. Olaf Ave.
>>>> Northfield, MN 55057
>>>> http://www.stolaf.edu/people/hansonr
>>>> phone: 507-786-3107
>>>>
>>>>
>>>> If nature does not answer first what we want,
>>>> it is better to take what answer we get.
>>>>
>>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> This SF.net Dev2Dev email is sponsored by:
>>>>
>>>> Show off your parallel programming skills.
>>>> Enter the Intel(R) Threading Challenge 2010.
>>>> http://p.sf.net/sfu/intel-thread-sfd
>>>> _______________________________________________
>>>> Jmol-users mailing list
>>>> jmol-us...@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> This SF.net Dev2Dev email is sponsored by:
>>>
>>> Show off your parallel programming skills.
>>> Enter the Intel(R) Threading Challenge 2010.
>>> http://p.sf.net/sfu/intel-thread-sfd
>>> _______________________________________________
>>> Jmol-users mailing list
>>> jmol-us...@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net Dev2Dev email is sponsored by:
>>
>> Show off your parallel programming skills.
>> Enter the Intel(R) Threading Challenge 2010.
>> http://p.sf.net/sfu/intel-thread-sfd
>> _______________________________________________
>> Jmol-developers mailing list
>> Jmol-developers@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>
>
> ------------------------------------------------------------------------------
> This SF.net Dev2Dev email is sponsored by:
>
> Show off your parallel programming skills.
> Enter the Intel(R) Threading Challenge 2010.
> http://p.sf.net/sfu/intel-thread-sfd
> _______________________________________________
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
This SF.net Dev2Dev email is sponsored by:
Show off your parallel programming skills.
Enter the Intel(R) Threading Challenge 2010.
http://p.sf.net/sfu/intel-thread-sfd
_______________________________________________
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers
