Re: Re past 2.0 with terracotta?

Altaweel, Mark R. wrote:

It's not very clear exactly what is going on from the stack trace. Have you manipulated the tc-config.xml file in any way to change the topology. It seems like it is not finding this topologyObservers field.

Mark
On Jan 20, 2011, at 7:00 PM, charlie1kimo wrote:

>
> Hi all,
> sorry for kind of spamming the forum, but I really want to get terracotta
> feature to work and I think I am almost there.
>
> For clustering purpose, I've created a StartRWorker with main method to
> start the worker JVM instances, along with routingIDs = localhost1, 2, 3, 4.
> (I started 4 instances of JVMs).
> Then now I want to start master and dataGridManager to feed those 4 JVMs
> into the simulation. So I've put those 4 routerIDs in, and start the master
> and workers (because dataGridManager needs to have a List of workers) in the
> GUI simulation. Now I got two errors:
>
> While starting master, the error is:
> Starting...:
>  list with routing IDs         = [ localhost1 localhost2 localhost3 localhost4 ]
>  routing ID for fail-over node = localhost4
> 2011-01-20 16:47:50,533 ERROR - OnLoad execute script failed for: class
> org.terracotta.message.topology.DefaultTopology error: self
> .topologyObservers  line: 3; Sourced file: inline evaluation of: ``
> self.topologyObservers = n . . . '' : Field access: bsh.ReflectError: No
> such field: topologyObservers
> ERROR [AWT-EventQueue-0] 2011-01-20 16:47:50,571
> repast.simphony.demo.terracotta.TerracottaContextBuilder - Problems reading
> in router in master
> java.lang.NullPointerException
>        at
> org.terracotta.message.topology.DefaultTopology.getOrCreatePipeFor(DefaultTopology.java:65)
>        at
> org.terracotta.masterworker.AbstractMaster.doRegister(AbstractMaster.java:134)
>        at
> org.terracotta.masterworker.AbstractMaster.<init>(AbstractMaster.java:58)
>        at
> org.terracotta.workmanager.AbstractWorkManager.<init>(AbstractWorkManager.java:50)
>        at
> org.terracotta.workmanager.statik.StaticWorkManager.<init>(StaticWorkManager.java:40)
>        at
> repast.simphony.terracotta.datagrid.DataGridMaster.<init>(DataGridMaster.java:88)
>        at
> repast.simphony.terracotta.datagrid.StartMaster.startExample(StartMaster.java:52)
>        at biomod.fcc.ISCM.ISCMBuilder.build(ISCMBuilder.java:59)
>        at
> repast.simphony.dataLoader.engine.ClassNameContextBuilder.build(ClassNameContextBuilder.java:41)
>        ...
>        (below are the stack trace to some GUI codes)
>
> While starting workers, the error is:
> -- starting workers...
> 2011-01-20 16:47:50,598 ERROR - OnLoad execute script failed for: class
> org.terracotta.message.topology.DefaultTopology error: self
> .topologyObservers  line: 3; Sourced file: inline evaluation of: ``
> self.topologyObservers = n . . . '' : Field access: bsh.ReflectError: No
> such field: topologyObservers
> Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException:
> Width (-1) and height (-1) cannot be <= 0
>        at
> java.awt.image.DirectColorModel.createCompatibleWritableRaster(DirectColorModel.java:999)
>        at java.awt.image.BufferedImage.<init>(BufferedImage.java:312)
>        at repast.simphony.ui.widget.IconRotator.rotate(IconRotator.java:51)
>        at repast.simphony.ui.widget.IconRotator.access$0(IconRotator.java:47)
>        at
> repast.simphony.ui.widget.IconRotator$1.actionPerformed(IconRotator.java:32)
>        at javax.swing.Timer.fireActionPerformed(Timer.java:271)
>        at javax.swing.Timer$DoPostEvent.run(Timer.java:201)
>        at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
>        at java.awt.EventQueue.dispatchEvent(EventQueue.java:597)
>        at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
>        at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
>        at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
>        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
>        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
>        at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
>
>
> It seems like starting master is having a BIGGER issue with topology
> settings, and starting workers might just have something wrong with the
> simulation initialization...but I am not sure.
> I've search around and apparently the terracotta support in Repast is the
> old version of terracotta TIM modules, so it was really hard to find the
> documentations and support as well...
>
> It's really frustrated...
> so if anyone could provide some sort of directions or opinions that would be
> extremely helpful...
>
> Thank you.
>
> -Charlie-
>
>
> charlie1kimo wrote:
>>
>> Hi All,
>> so I've decided to try to implement terracotta feature on my own project.
>> That's why it took a while...
>> I am able to get the terracotta settings to run with my Repast project.
>> However, I believed the master and worker I setup did not start. I
>> couldn't see the connection on terracotta console.
>>
>> I basically implement the terracotta demo's codes into my project, and I
>> tried to go through the code and I couldn't find the source code of
>> org.terracotta.workmanager.DefaultWorker
>> I think there is something wrong in starting the master and workers...
>> Does anyone have some idea about this issues?
>>
>> Thanks a lot...
>>
>> -Charlie-
>>
>>
>> charlie1kimo wrote:
>>>
>>>
>>> Hi Mark,
>>> You actually pointed out some interesting thing...
>>> I converted this terracotta demo from Repast 1.2.0 to 2.0 beta, so I
>>> guess
>>> some of the package structure has been changed? This could be a problem.
>>>
>>> I spotted that in my repast.simphony.action.display_1.xml:
>>> ...
>>> <projectionDescriptors>
>>>  <entry>
>>>    <string>Terracotta Grid</string>
>>>    <repast.simphony.visualization.grid.GridProjectionDescriptor>
>>>      <proj class="repast.score.impl.SGridImpl"
>>> reference="../../../../projections/repast.score.impl.SGridImpl" />
>>>      <entry>
>>> ...
>>>
>>> I did a search on that class and its src, and I didn't find it in Repast
>>> 2.0
>>> beta. I believed that's the problem. Can anyone tell me where to find
>>> this
>>> grid implementation class in Repast 2.0? I'll report if this really IS
>>> the
>>> problem.
>>>
>>> Thank you guys very much
>>>
>>> -Charlie-
>>>
>>>
>>>
>>> Altaweel, Mark R. wrote:
>>>>
>>>> Seems like it can't find something called: terracottaGrid, but I believe
>>>> the name should be: "Terracotta Grid"
>>>>
>>>> Have you tried making that adjustment?
>>>>
>>>> Mark
>>>> On Jan 11, 2011, at 5:15 PM, charlie1kimo wrote:
>>>>
>>>>
>>>> Thank you for your reply, but I couldn't get repast with terracotta to
>>>> work
>>>> in eclipse, as I stated in my previous posts. The problem was the log4j
>>>> path
>>>> issue. When I used eclipse to run terracotta demo, repast runtime
>>>> library
>>>> is
>>>> using "repast.simphony.bin_and_src," which had log4j error. However,
>>>> when
>>>> I
>>>> modified the runtime library path using "repast.simphony.runtime" and
>>>> run
>>>> it
>>>> in the terminal. It can launch repast window just fine. Therefore the
>>>> debugging tools in eclipse is NOT useful to me... ...
>>>>
>>>> So I turned to command line tool -- jdb.
>>>> I was able to set the break points based on what I read in the source
>>>> codes
>>>> (which are from repast.simphony.bin_and_src"). Since the console output
>>>> stopped at "starting workers...," I was curious if some communication
>>>> process in terracotta got hung. Thus, I set the break point in all the
>>>> StartWorker method. However when I stepped through them, they seemed to
>>>> pass
>>>> just fine without any repetitive commands. (I checked the classes and
>>>> lines
>>>> each time when I stepped, so if there is a infinite loop I'll see...)
>>>> The
>>>> step result terminated at some gui method call and it seemed to
>>>> initialize
>>>> just fine, except missing a display for this terracotta demo.
>>>>
>>>> Now I started to suspect this problem is the DISPLAY issue, since I can
>>>> press "step" and "run" in the repast window after initialized. Are you
>>>> guys
>>>> sure the display will be automatically initialized by this demo??? I was
>>>> curious because I didn't see any Displays in "scenario tree" even after
>>>> initialized. I remembered in some demo I tried I had to manually create
>>>> display...
>>>>
>>>> So I tried to create one through Repast window, and it failed to create
>>>> the
>>>> display due to:
>>>> ...
>>>> Caused by: java.lang.RuntimeException: Projection 'terracottaGrid' not
>>>> found.
>>>>   at
>>>> repast.simphony.visualization.engine.AbstractDisplayCreator.createLayout(AbstractDisplayCreator.java:51)
>>>>   at
>>>> repast.simphony.visualization.engine.DisplayCreatorOGL2D.createDisplay(DisplayCreatorOGL2D.java:62)
>>>> ...38 more
>>>> ...
>>>>
>>>> I'll attach the full error log of creating display here:
>>>> http://old.nabble.com/file/p30648864/errorDisplay.log errorDisplay.log
>>>>
>>>> Any helps on this? I really REALLY would like to get this feature to
>>>> work,
>>>> and I think I am almost there.
>>>> Thanks for all your helps so far!!!
>>>>
>>>> -Charlie-
>>>>
>>>>
>>>> North, Michael wrote:
>>>>
>>>> Thank you for using Repast! All of the Repast source code is accessible
>>>> through the repast.simphony.bin_and_src.jar in the
>>>> plugins/repast.simphony.bin_and_src_2.0.0 directory. By default the
>>>> source
>>>> code in the JAR file is linked in so the Eclipse debugger can trace
>>>> through it.
>>>>
>>>> Repast does quite a bit of work for you on startup. As such, I would
>>>> start
>>>> to debug your model by putting a breakpoint in your own code near the
>>>> area
>>>> of interest rather than in the Repast code itself. A short guide on
>>>> using
>>>> the Eclipse debugger can be found here:
>>>>
>>>>   http://www.ibm.com/developerworks/library/os-ecbug/
>>>>
>>>> Mike
>>>>
>>>> On 1/7/11 5:44 PM, "charlie1kimo"
>>>> <ChenYiChen@lbl.gov<mailto:ChenYiChen@lbl.gov>> wrote:
>>>>
>>>>
>>>> Unfortunately, I can't find a way to let the code goes steps by steps in
>>>> eclipse debugger, since I think the debugger required the source codes,
>>>> and
>>>> I think repast.runtime.Main only has "class."...
>>>> or it could also be I am not familiar with eclipse debugger, any
>>>> solutions
>>>> of how to debug this are welcome.
>>>>
>>>> However, I did a java stack trace using jstack tool. Here are the
>>>> threads
>>>> dumped before Repast simulation initialization (which is just openning
>>>> repast windows and waiting user to do things), and after I initialized
>>>> the
>>>> Repast simulation.
>>>> I called the logs before and after in the file name, and I'll attached
>>>> it
>>>> here.
>>>> I figured 4 threads were generated after I pressed the "initialize"
>>>> button,
>>>> by simply doing a diff on the thread dumps. They are threads 16 ~ 19.
>>>> I don't quite understand what those packages ( such as
>>>> bytecode.ManageImpl,
>>>> concurrent.LinkedBlockingQueue ) for in the process of parallelization.
>>>> But
>>>> it seems like I have a possible deadlock in creating sharing objects???
>>>> The weird thing is when I used jconsole to debug these threads, it
>>>> didn't
>>>> think there are deadlock anywhere...so I really don't know what's going
>>>> on
>>>> here...
>>>>
>>>> Here are the full thread dump logs:
>>>> http://old.nabble.com/file/p30619197/jstack_before.log jstack_before.log
>>>> http://old.nabble.com/file/p30619197/jstack_after.log jstack_after.log
>>>>
>>>> Does anyone has any ideas of what's going on? Any help would be highly
>>>> appreciated. Thanks!!!
>>>>
>>>> -Charlie-
>>>>
>>>>
>>>>
>>>>
>>>> Altaweel, Mark R. wrote:
>>>>
>>>> Do you know at what point the run gets hung? Is there a way to debug and
>>>> see where the code hangs?
>>>>
>>>> There should be a 2D display that comes up in the demo. It should show
>>>> agents moving around randomly more or less.
>>>>
>>>> Mark
>>>> On Jan 5, 2011, at 7:05 PM, charlie1kimo wrote:
>>>>
>>>>
>>>> Hi Mark,
>>>> First thanks for the quick reply.
>>>> I went through the stream of message in Feb 2009, and apparently the
>>>> problem
>>>> was not solved...
>>>> I still have trouble running repast with terracotta in eclipse because
>>>> of
>>>> the strange path look up issues (like repast was run in
>>>> repast.simphony.bin_and_src.jar when run with terracotta DSO, and was
>>>> run
>>>> in
>>>> repast.simphony.runtime.bin when run without terracotta), but at least
>>>> gave
>>>> me some ideas and directions to try for.
>>>>
>>>> So I actually combine my run parameters from with and without
>>>> terracotta,
>>>> and run it from the command line. Now terracotta client starts okay, it
>>>> connected to the sever, I can see the connection through terracotta
>>>> develop
>>>> console...etc. But when I make both master and worker to be localhost,
>>>> and
>>>> initialize the model, it's having the same problem as running without
>>>> terracotta. It's the problem with stuck at the "starting workers" step.
>>>> Here is the console output:
>>>>
>>>> 2011-01-05 16:58:29,409 INFO - Terracotta 3.4.0, as of 20101104-141154
>>>> (Revision 16614 by cruise@su10mo4 from 3.4)
>>>> 2011-01-05 16:58:29,804 INFO - Successfully loaded base configuration
>>>> from
>>>> file at
>>>>
>>>> '/data2/home/charlie/workspace/test_repast_terracotta_demo/testrepastter
>>>> racottademo.rs/tc-config.xml'.
>>>> 2011-01-05 16:58:29,995 INFO - Log file:
>>>> '/data2/home/charlie/terracotta/client-logs/terracotta-client.log'.
>>>> 2011-01-05 16:58:31,322 INFO - Connection successfully established to
>>>> server
>>>> at 127.0.0.1:9510
>>>> Starting...:
>>>> list with routing IDs         = [ localhost ]
>>>> routing ID for fail-over node = localhost
>>>> -- starting workers...
>>>>
>>>> There's something happened in client-log that lead to a
>>>> CommonShutDownHook,
>>>> which closed the local worker node I believed, but I am not sure what's
>>>> the
>>>> reason.
>>>>
>>>> I attached the server log and client log here for the reference
>>>> http://old.nabble.com/file/p30601758/terracotta-client.log
>>>> terracotta-client.log
>>>> http://old.nabble.com/file/p30601758/terracotta-server.log
>>>> terracotta-server.log
>>>>
>>>> Lastly, is this demo suppose to create display on its own? I tried to
>>>> create
>>>> a 2D display myself but it would crash the repast window...
>>>>
>>>> Thanks for the help!
>>>>
>>>> -Charlie-
>>>>
>>>>
>>>> Altaweel, Mark R. wrote:
>>>>
>>>> There is a similar problem by another user back from February 2009.
>>>>
>>>> I listed the link to the stream of messages below:
>>>>
>>>>
>>>> http://sourceforge.net/mailarchive/forum.php?thread_name=5FDF261785B44C
>>>> 4DB302979A658D006102AE3BA8%40spike.dis.anl.gov&forum_name=repast-intere
>>>> st
>>>>
>>>>
>>>> On Jan 4, 2011, at 8:40 PM, charlie1kimo wrote:
>>>>
>>>>
>>>> hmm...
>>>> I believed it wouldn't be a firewall issue here.
>>>> I could NOT run the demo with terracotta DSO because it was giving me
>>>> the
>>>> log4j error.
>>>> The repast windows wouldn't start, and the console just showed log4j
>>>> was
>>>> not
>>>> found and needed to be initialized.
>>>>
>>>> So I tried running the demo LOCALLY, which is just run the demo as a
>>>> standard java/repast application.
>>>> I put both my master and worker as "localhost," so it wouldn't have
>>>> the
>>>> firewall problem.
>>>> Somehow, running locally on localhost made "starting workers" hang.
>>>>
>>>> I've also tried the terracotta's HelloClusteredWorld sample on our
>>>> machine,
>>>> and I can start the clients within eclipse and connect to the
>>>> localhost
>>>> server, which means terracotta is working...
>>>>
>>>> I guess for some reasons when eclipse runs terracotta DSO project, it
>>>> missed
>>>> the path to find log4j?
>>>>
>>>> Any ideas about what happened would be highly appreciated
>>>>
>>>> Thanks
>>>>
>>>> -Charlie-
>>>>
>>>>
>>>> Altaweel, Mark R. wrote:
>>>>
>>>> One thing you might want to check is the firewall settings on your
>>>> remote
>>>> nodes. It sounds like some communication might be stalled some place
>>>> and
>>>> this might be preventing terracota from communicating between your
>>>> nodes.
>>>> The demo should have agents basically moving around the grid;
>>>> however,
>>>> outside of that there is not much behavior as this is just a demo of
>>>> using
>>>> terracotta.
>>>>
>>>> Also, if you might want to look at the repast.distributedBatch
>>>> plugin
>>>> (more info see:
>>>>
>>>> http://repast.sourceforge.net/docs/RepastParameterSweepsGettingStarte
>>>> d.pdf).
>>>> This enables distributed batch runs using multiple nodes, which
>>>> might
>>>> be
>>>> useful for the type of simulations you want to do.
>>>>
>>>> Mark
>>>> On Jan 4, 2011, at 6:50 PM, charlie1kimo wrote:
>>>>
>>>>
>>>> Hi all,
>>>> Recently I am trying to run repast with terracotta as well. I tried
>>>> to
>>>> get
>>>> the terracotta demo in repast package (the one with
>>>> AgentManager.java
>>>> and
>>>> DoSomeActionAgent.java) to work but to no avail.
>>>> Is this demo suppose to do something? or this demo is just a
>>>> template
>>>> for
>>>> putting terracotta in your project?
>>>>
>>>> Here's my test runs with terracott:
>>>> I've copied the terracotta demo into a separate project, and
>>>> started
>>>> from
>>>> there.
>>>> I configured the eclipse terracotta plugins and run configuration
>>>> to
>>>> read
>>>> the correct tc-config.xml as well.
>>>> Due to the bug in eclipse 64bit and terracotta plugin, I have to
>>>> start
>>>> the
>>>> terracotta server from command line, but that's ok because the
>>>> terracotta
>>>> server started fine; I can also connect to the terracotta managing
>>>> console.
>>>>
>>>> Then I ran this repast terracotta demo with DSO terracotta, and the
>>>> following is what I got:
>>>>
>>>> 2011-01-04 16:41:33,160 INFO - Terracotta 3.4.0, as of
>>>> 20101104-141154
>>>> (Revision 16614 by cruise@su10mo4 from 3.4)
>>>> 2011-01-04 16:41:33,566 INFO - Successfully loaded base
>>>> configuration
>>>> from
>>>> file at
>>>>
>>>> '/data2/home/charlie/workspace/test_repast_terracotta_demo/testrepas
>>>> tterracottademo.rs/tc-config.xml'.
>>>> 2011-01-04 16:41:33,753 INFO - Log file:
>>>>
>>>> '/data2/home/charlie/workspace/test_repast_terracotta_demo/terracott
>>>> a/client-logs/terracotta-client.log'.
>>>> 2011-01-04 16:41:35,126 INFO - Connection successfully established
>>>> to
>>>> server
>>>> at 127.0.0.1:9510
>>>> log4j:WARN No appenders could be found for logger
>>>> (MessageCenter.INTERNAL.saf.core.runtime.Boot).
>>>> log4j:WARN Please initialize the log4j system properly.
>>>>
>>>> Apparently it can connect to my server, but it died immediately
>>>> after
>>>> the
>>>> connection due to the famous log4j error. (seems lots of people
>>>> have
>>>> this
>>>> error)
>>>>
>>>> So I tried to run this demo without terracotta, and it seemed to
>>>> work,
>>>> except it hanged at "starting workers" when I initialized it:
>>>>
>>>> Starting...:
>>>> list with routing IDs      = [ localhost ]
>>>> routing ID for fail-over node = localhost
>>>> -- starting workers...
>>>>
>>>> Is this the right behavior for this demo? I have a feeling that
>>>> this
>>>> demo
>>>> is
>>>> actually doing NOTHING.
>>>> anyone has any ideas? In addition, I believed my log4j can be found
>>>> in
>>>> the
>>>> build path, since it ran without terracotta successfully, it just
>>>> hanged
>>>> at
>>>> the "starting workers."
>>>>
>>>> Lastly, some side notes for people who also testing this, when I
>>>> ran
>>>> this
>>>> demo without terracotta DSO, I have to input parameter for
>>>> "routerIDs."
>>>> "routerIDs" has to have at least 2 hosts, separated by comma.
>>>>
>>>> Thanks in advance for any suggestions
>>>>
>>>> -Charlie-
>>>>
>>>> --
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>>>> http://old.nabble.com/Repast-2.0-with-terracotta--tp30592413p30648864.html
>>>> Sent from the repast-interest mailing list archive at
>>>> Nabble.com<http://Nabble.com>.
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Protect Your Site and Customers from Malware Attacks
>>>> Learn about various malware tactics and how to avoid them. Understand
>>>> malware threats, the impact they can have on your business, and how you
>>>> can protect your company and customers by using code signing.
>>>> http://p.sf.net/sfu/oracle-sfdevnl
>>>> _______________________________________________
>>>> Repast-interest mailing list
>>>> Repast-interest@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/repast-interest
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Protect Your Site and Customers from Malware Attacks
>>>> Learn about various malware tactics and how to avoid them. Understand
>>>> malware threats, the impact they can have on your business, and how you
>>>> can protect your company and customers by using code signing.
>>>> http://p.sf.net/sfu/oracle-sfdevnl
>>>> _______________________________________________
>>>> Repast-interest mailing list
>>>> Repast-interest@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/repast-interest
>>>>
>>>>
>>>
>>> --
>>> View this message in context:
>>> http://old.nabble.com/Repast-2.0-with-terracotta--tp30592413p30654357.html
>>> Sent from the repast-interest mailing list archive at Nabble.com.
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Protect Your Site and Customers from Malware Attacks
>>> Learn about various malware tactics and how to avoid them. Understand
>>> malware threats, the impact they can have on your business, and how you
>>> can protect your company and customers by using code signing.
>>> http://p.sf.net/sfu/oracle-sfdevnl
>>> _______________________________________________
>>> Repast-interest mailing list
>>> Repast-interest@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/repast-interest
>>>
>>>
>>
>>
>
> --
> View this message in context: http://old.nabble.com/Repast-2.0-with-terracotta--tp30592413p30724916.html
> Sent from the repast-interest mailing list archive at Nabble.com.
>
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
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> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> Repast-interest mailing list
> Repast-interest@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/repast-interest


------------------------------------------------------------------------------
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires
February 28th, so secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsight-sfd2d
_______________________________________________
Repast-interest mailing list
Repast-interest@lists.sourceforge.net
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