I thought java 1.7 is the recommended version.
On Sep 5, 2013, at 10:45 AM, Sho Uemura wrote:
> You should be able to use Java 1.6 now. (In theory you always could, but
> there was one stale package that was screwing that up.)
>
> Pushing this thread back to the list so it goes in the archives.
>
>
> On Thu, 5 Sep 2013, Kyle McCarty wrote:
>
>> This seems to work (at least until I get another version error, but I'll
>> have to get the server admin to fix that one). Thanks for your help! Once I
>> get an up-to-date Java version, I will attempt my analysis again and see if
>> I can get it going now.
>>
>>
>> On Thu, Sep 5, 2013 at 12:47 PM, Sho Uemura <[log in to unmask]> wrote:
>>
>>> Note: If you're running on background HPSTrackingDefaults.lcsim may not
>>> really do what you want; there's no trigger so many of your events won't
>>> have tracks. You really want to do readout and reconstruction separately if
>>> you're doing any sort of actual analysis. But it should run, which I think
>>> is all you care about at the moment.
>>>
>>>
>>> On Thu, 5 Sep 2013, Sho Uemura wrote:
>>>
>>> The process is simulation -> readout -> reconstruction -> analysis. SLIC
>>>> does the simulation, so you need to do readout and reconstruction.
>>>> HPSTrackingDefaults.lcsim (see bottom of the linked page) should do both.
>>>>
>>>> https://confluence.slac.**stanford.edu/display/hpsg/**
>>>> Running+Reconstruction<https://confluence.slac.stanford.edu/display/hpsg/Running+Reconstruction>
>>>>
>>>> On Thu, 5 Sep 2013, Kyle McCarty wrote:
>>>>
>>>> The input LCIO file is a file I generated from the data file
>>>>> "egs_0.0025x0_450na_100kb_1.**stdhep" which I believe is background
>>>>> data. I
>>>>> created it using
>>>>>
>>>>> ./slic -g
>>>>> /net/home/mccaky/hps/hps-**detectors/detectors/HPS-**
>>>>> Proposal2014-v4-6pt6/HPS-**Proposal2014-v4-6pt6.lcdd
>>>>> -i /net/taro/data/HPS/StdHep/6.**6GeV/beam/egs_0.0025x0_450na_**
>>>>> 100kb_1.stdhep
>>>>> -x -o hpsTest -r 10000
>>>>>
>>>>> Of course, this is just simulating the data, I suppose, and not
>>>>> reconstructing it, hence the error. What should I use to reconstruct the
>>>>> data for further analysis?
>>>>>
>>>>>
>>>>> On Thu, Sep 5, 2013 at 12:08 PM, Sho Uemura <[log in to unmask]>
>>>>> wrote:
>>>>>
>>>>> The third error - what's the input LCIO file? That steering file will
>>>>>> only
>>>>>> work with reconstruction output. The error is complaining that the
>>>>>> MatchedTracks (reconstructed tracks) collection doesn't exist.
>>>>>>
>>>>>>
>>>>>> On Thu, 5 Sep 2013, Sho Uemura wrote:
>>>>>>
>>>>>> The first error is my fault - the Confluence page example was missing
>>>>>> the
>>>>>>
>>>>>>> runNumber variable. Fixed.
>>>>>>>
>>>>>>> The second error refers to your Java version. If you get Java 1.7 you
>>>>>>> should be fine. In theory 1.6 is supposed to work but there are some
>>>>>>> packages that are stuck at the wrong version.
>>>>>>>
>>>>>>> On Thu, 5 Sep 2013, Kyle McCarty wrote:
>>>>>>>
>>>>>>> Thanks for the quick reply. The "-r" was indeed the reason for the
>>>>>>> error
>>>>>>>
>>>>>>>> I
>>>>>>>> was getting. I was trying to link to external files. I have attempted
>>>>>>>> to
>>>>>>>> run the commands now without the "-r" and no longer get the
>>>>>>>> MalformedURLException, but I now get different errors. Using the
>>>>>>>> sample
>>>>>>>> commands page (
>>>>>>>> https://confluence.slac.**stan**ford.edu/display/hpsg/**<http://stanford.edu/display/hpsg/**>
>>>>>>>> Running+Readout+Simulation<htt**ps://confluence.slac.stanford.**
>>>>>>>> edu/display/hpsg/Running+**Readout+Simulation<https://confluence.slac.stanford.edu/display/hpsg/Running+Readout+Simulation>
>>>>>>>>>
>>>>>>>> )
>>>>>>>> again to avoid any mistakes in my steering files, I ran:
>>>>>>>>
>>>>>>>> java -jar
>>>>>>>> /net/home/mccaky/hps/hps-java/****target/hps-java-1.7-**
>>>>>>>> SNAPSHOT-**bin.jar
>>>>>>>> /net/home/mccaky/hps/hps-java/****target/classes/org/lcsim/**hps/**
>>>>>>>> steering/readout/****TestRunReadoutToLcio.lcsim
>>>>>>>> -i filtered.slcio -DoutputFile=readout
>>>>>>>>
>>>>>>>> which gave the error
>>>>>>>>
>>>>>>>> Exception in thread "main" java.lang.RuntimeException: Variable not
>>>>>>>> defined: runNumber
>>>>>>>> at
>>>>>>>> org.lcsim.job.****JobControlManager.****substituteVariables(**
>>>>>>>> JobControlManager.java:609)
>>>>>>>> at
>>>>>>>> org.lcsim.job.****JobControlManager.****substituteVariables(**
>>>>>>>> JobControlManager.java:622)
>>>>>>>> at
>>>>>>>> org.lcsim.job.****JobControlManager.****substituteVariables(**
>>>>>>>> JobControlManager.java:622)
>>>>>>>> at
>>>>>>>> org.lcsim.job.****JobControlManager.****substituteVariables(**
>>>>>>>> JobControlManager.java:622)
>>>>>>>> at
>>>>>>>> org.lcsim.job.****JobControlManager.****substituteVariables(**
>>>>>>>> JobControlManager.java:568)
>>>>>>>> at org.lcsim.job.****JobControlManager.setup(**
>>>>>>>> JobControlManager.java:514)
>>>>>>>> at org.lcsim.job.****JobControlManager.setup(**
>>>>>>>> JobControlManager.java:492)
>>>>>>>> at org.lcsim.job.****JobControlManager.setup(**
>>>>>>>> JobControlManager.java:450)
>>>>>>>> at
>>>>>>>> org.lcsim.job.****JobControlManager.****parseCommandLineOptions(**
>>>>>>>> JobControlManager.java:322)
>>>>>>>> at org.lcsim.job.****JobControlManager.main(**
>>>>>>>> JobControlManager.java:168)
>>>>>>>>
>>>>>>>> and
>>>>>>>>
>>>>>>>> java -jar
>>>>>>>> /net/home/mccaky/hps/hps-java/****target/hps-java-1.7-**
>>>>>>>> SNAPSHOT-**bin.jar
>>>>>>>> /net/home/mccaky/hps/hps-java/****target/classes/org/lcsim/**hps/**
>>>>>>>> steering/readout/****HPS2014ReadoutToLcio.lcsim
>>>>>>>> -i hpsTest.slcio -DoutputFile=readout
>>>>>>>>
>>>>>>>> which gives the error
>>>>>>>>
>>>>>>>> java.lang.****UnsupportedClassVersionError: org/jlab/coda/jevio/****
>>>>>>>> EvioException
>>>>>>>> :
>>>>>>>> Unsupported major.minor version 51.0
>>>>>>>> at java.lang.ClassLoader.****defineClass1(Native Method)
>>>>>>>> at java.lang.ClassLoader.****defineClass(ClassLoader.java:***
>>>>>>>> *634)
>>>>>>>> at
>>>>>>>> java.security.****SecureClassLoader.defineClass(****
>>>>>>>> SecureClassLoader.java:142)
>>>>>>>> at java.net.URLClassLoader.****defineClass(URLClassLoader.**
>>>>>>>> java:277)
>>>>>>>> at java.net.URLClassLoader.****access$000(URLClassLoader.****
>>>>>>>> java:73)
>>>>>>>> at java.net.URLClassLoader$1.run(****URLClassLoader.java:212)
>>>>>>>> at java.security.****AccessController.doPrivileged(****Native
>>>>>>>> Method)
>>>>>>>> at java.net.URLClassLoader.****findClass(URLClassLoader.java:*
>>>>>>>> ***205)
>>>>>>>> at java.lang.ClassLoader.****loadClass(ClassLoader.java:****
>>>>>>>> 321)
>>>>>>>> at sun.misc.Launcher$****AppClassLoader.loadClass(**
>>>>>>>> Launcher.java:294)
>>>>>>>> at java.lang.ClassLoader.****loadClass(ClassLoader.java:****
>>>>>>>> 266)
>>>>>>>> at
>>>>>>>> org.lcsim.hps.evio.****TestRunTriggeredReconToLcio.****startOfData(**
>>>>>>>> TestRunTriggeredReconToLcio.****java:82)
>>>>>>>> at org.lcsim.util.Driver.****startOfData(Driver.java:172)
>>>>>>>> at org.lcsim.util.DriverAdapter.***
>>>>>>>> *start(DriverAdapter.java:92)
>>>>>>>> at
>>>>>>>> org.freehep.record.loop.****AbstractLoopListener.process(****
>>>>>>>> AbstractLoopListener.java:22)
>>>>>>>> at
>>>>>>>> org.freehep.record.loop.****DefaultRecordLoop.****fireLoopEvents(**
>>>>>>>> DefaultRecordLoop.java:125)
>>>>>>>> at
>>>>>>>> org.freehep.record.loop.****DefaultRecordLoop.execute(**
>>>>>>>> DefaultRecordLoop.java:561)
>>>>>>>> at org.lcsim.util.loop.LCSimLoop.****loop(LCSimLoop.java:153)
>>>>>>>> at org.lcsim.job.****JobControlManager.run(**
>>>>>>>> JobControlManager.java:393)
>>>>>>>> at org.lcsim.job.****JobControlManager.main(**
>>>>>>>> JobControlManager.java:169)
>>>>>>>>
>>>>>>>> Finally, I also tried the command
>>>>>>>>
>>>>>>>> java -jar
>>>>>>>> /net/home/mccaky/hps/hps-java/****target/hps-java-1.7-**
>>>>>>>> SNAPSHOT-**bin.jar
>>>>>>>> /net/home/mccaky/hps/hps-java/****target/classes/org/lcsim/**hps/**
>>>>>>>> steering/analysis/****StarterAnalysis.lcsim
>>>>>>>> -i hpsTest.slcio -DoutputFile=readout
>>>>>>>>
>>>>>>>> which starts to run, unlike the others which crash immediately, but it
>>>>>>>> crashes as soon as Event 0 is printed with the error
>>>>>>>>
>>>>>>>> java.lang.****IllegalArgumentException: Unknown event component
>>>>>>>> MatchedTracks
>>>>>>>> at hep.physics.event.BaseEvent.****get(BaseEvent.java:48)
>>>>>>>> at org.lcsim.event.base.****BaseLCSimEvent.get(**
>>>>>>>> BaseLCSimEvent.java:105)
>>>>>>>> at
>>>>>>>> org.lcsim.hps.examples.****StarterAnalysisDriver.****processTracks(**
>>>>>>>> StarterAnalysisDriver.java:87)
>>>>>>>> at
>>>>>>>> org.lcsim.hps.examples.****StarterAnalysisDriver.process(****
>>>>>>>> StarterAnalysisDriver.java:45)
>>>>>>>> at org.lcsim.util.Driver.****doProcess(Driver.java:273)
>>>>>>>> at org.lcsim.util.Driver.****processChildren(Driver.java:****
>>>>>>>> 284)
>>>>>>>> at org.lcsim.util.Driver.process(****Driver.java:198)
>>>>>>>> at
>>>>>>>> org.lcsim.util.DriverAdapter.****recordSupplied(DriverAdapter.**
>>>>>>>> **java:74)
>>>>>>>> at
>>>>>>>> org.freehep.record.loop.****DefaultRecordLoop.****consumeRecord(**
>>>>>>>> DefaultRecordLoop.java:832)
>>>>>>>> at
>>>>>>>> org.freehep.record.loop.****DefaultRecordLoop.loop(**
>>>>>>>> DefaultRecordLoop.java:668)
>>>>>>>> at
>>>>>>>> org.freehep.record.loop.****DefaultRecordLoop.execute(**
>>>>>>>> DefaultRecordLoop.java:566)
>>>>>>>> at org.lcsim.util.loop.LCSimLoop.****loop(LCSimLoop.java:153)
>>>>>>>> at org.lcsim.job.****JobControlManager.run(**
>>>>>>>> JobControlManager.java:393)
>>>>>>>> at org.lcsim.job.****JobControlManager.main(**
>>>>>>>> JobControlManager.java:169)
>>>>>>>>
>>>>>>>> I assume that I am still doing something incorrectly, but now the
>>>>>>>> errors
>>>>>>>> seem to be all different. Any ideas?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Kyle
>>>>>>>>
>>>>>>>>
>>>>>>>> On Thu, Sep 5, 2013 at 11:47 AM, Sho Uemura <[log in to unmask]>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>> This error means hps-java can't find your steering file.
>>>>>>>>
>>>>>>>>>
>>>>>>>>> If you use the -r option, the steering file path is a Java resource
>>>>>>>>> path -
>>>>>>>>> it refers to a file you compiled into the jar. But if you're
>>>>>>>>> modifying
>>>>>>>>> steering files, it's better to not use "-r" so you don't have to
>>>>>>>>> rebuild
>>>>>>>>> every time you change your steering file - I think that's what you
>>>>>>>>> wanted
>>>>>>>>> here.
>>>>>>>>>
>>>>>>>>> So use the same command, but drop the "-r".
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Thu, 5 Sep 2013, Kyle McCarty wrote:
>>>>>>>>>
>>>>>>>>> Hello,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> I am trying to run hps-java and am getting some errors.
>>>>>>>>>> Specifically,
>>>>>>>>>> I am
>>>>>>>>>> receiving a "java.net.******MalformedURLException" error when I
>>>>>>>>>> try to
>>>>>>>>>> run a
>>>>>>>>>> steering file through the software. As an example, I tried running
>>>>>>>>>> the
>>>>>>>>>> sample commands on the website to make sure that it wasn't something
>>>>>>>>>> weird
>>>>>>>>>> in my steering file. I ran the command
>>>>>>>>>>
>>>>>>>>>> java -jar
>>>>>>>>>> /net/home/mccaky/hps/hps-java/******target/hps-java-1.7-****
>>>>>>>>>> SNAPSHOT-**bin.jar
>>>>>>>>>> -r
>>>>>>>>>> /net/home/mccaky/hps/hps-java/******target/classes/org/lcsim/***
>>>>>>>>>> *hps/**
>>>>>>>>>> steering/readout/******TestRunReadoutToLcio.lcsim
>>>>>>>>>> -i filtered.slcio -DoutputFile=readout
>>>>>>>>>>
>>>>>>>>>> This crashed giving the error message
>>>>>>>>>>
>>>>>>>>>> Exception in thread "main" java.lang.RuntimeException:
>>>>>>>>>> java.net.MalformedURLException
>>>>>>>>>> at org.lcsim.job.******JobControlManager.setup(**
>>>>>>>>>> JobControlManager.java:488)
>>>>>>>>>> at org.lcsim.job.******JobControlManager.setup(**
>>>>>>>>>> JobControlManager.java:461)
>>>>>>>>>> at
>>>>>>>>>> org.lcsim.job.******JobControlManager.******
>>>>>>>>>> parseCommandLineOptions(**
>>>>>>>>>> JobControlManager.java:315)
>>>>>>>>>> at org.lcsim.job.******JobControlManager.main(**
>>>>>>>>>> JobControlManager.java:168)
>>>>>>>>>> Caused by: java.net.MalformedURLException
>>>>>>>>>> at java.net.URL.<init>(URL.java:******617)
>>>>>>>>>> at java.net.URL.<init>(URL.java:******480)
>>>>>>>>>> at java.net.URL.<init>(URL.java:******429)
>>>>>>>>>> at
>>>>>>>>>> org.apache.xerces.impl.******XMLEntityManager.****
>>>>>>>>>> setupCurrentEntity(Unknown
>>>>>>>>>> Source)
>>>>>>>>>> at
>>>>>>>>>> org.apache.xerces.impl.******XMLVersionDetector.****
>>>>>>>>>> determineDocVersion(Unknown
>>>>>>>>>> Source)
>>>>>>>>>> at org.apache.xerces.parsers.******
>>>>>>>>>> XML11Configuration.parse(****
>>>>>>>>>> Unknown
>>>>>>>>>> Source)
>>>>>>>>>> at org.apache.xerces.parsers.******
>>>>>>>>>> XML11Configuration.parse(****
>>>>>>>>>> Unknown
>>>>>>>>>> Source)
>>>>>>>>>> at org.apache.xerces.parsers.******XMLParser.parse(Unknown
>>>>>>>>>> Source)
>>>>>>>>>> at org.apache.xerces.parsers.******
>>>>>>>>>> AbstractSAXParser.parse(****
>>>>>>>>>> Unknown
>>>>>>>>>> Source)
>>>>>>>>>> at org.apache.xerces.jaxp.******
>>>>>>>>>> SAXParserImpl$JAXPSAXParser.**
>>>>>>>>>> parse(Unknown
>>>>>>>>>> Source)
>>>>>>>>>> at org.jdom.input.SAXBuilder.******
>>>>>>>>>> build(SAXBuilder.java:453)
>>>>>>>>>> at org.jdom.input.SAXBuilder.******
>>>>>>>>>> build(SAXBuilder.java:770)
>>>>>>>>>> at org.lcsim.job.******JobControlManager.setup(**
>>>>>>>>>> JobControlManager.java:486)
>>>>>>>>>> ... 3 more
>>>>>>>>>> Caused by: java.lang.NullPointerException
>>>>>>>>>> at java.net.URL.<init>(URL.java:******522)
>>>>>>>>>> ... 15 more
>>>>>>>>>>
>>>>>>>>>> Note that "filtered.slcio" is in the directory which I ran the
>>>>>>>>>> command
>>>>>>>>>> from, and the preceding command
>>>>>>>>>>
>>>>>>>>>> java -cp /net/home/mccaky/hps/hps-java/******target/hps-java-1.7-**
>>>>>>>>>> SNAPSHOT-**
>>>>>>>>>> bin.jar
>>>>>>>>>> org.lcsim.hps.users.meeg.******FilterMCBunches hpsTest.slcio
>>>>>>>>>> filtered.slcio
>>>>>>>>>> -e250
>>>>>>>>>>
>>>>>>>>>> works perfectly. My version of the software was compiled last week,
>>>>>>>>>> so
>>>>>>>>>> it
>>>>>>>>>> should be very up-to-date.
>>>>>>>>>>
>>>>>>>>>> Since I got this same message any time I tried to put a steering
>>>>>>>>>> file
>>>>>>>>>> in,
>>>>>>>>>> I
>>>>>>>>>> assume that I am just doing something dumb and giving hps-java bad
>>>>>>>>>> information. Can you point me to where my mistake is?
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> Kyle McCarty
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>
>>>>
>>
>
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