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HPS-SOFTWARE  November 2012

HPS-SOFTWARE November 2012

Subject:

Re: OutOfMemory error in jevio?

From:

Sho Uemura <[log in to unmask]>

Reply-To:

Software for the Heavy Photon Search Experiment <[log in to unmask]>

Date:

Fri, 9 Nov 2012 18:59:45 -0800

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (167 lines)

No. That command line is correct (-jar if running the usual lcsim main(),
-cp if you're running a different class, e.g. TestRunEvioToLcio).

I haven't been able to reproduce this error. I'd try a different machine?

The error seems to be coming up when the EVIO file is loaded. Does the
same error show up if you try to run on a smaller EVIO file?


Possibly relevant:

https://issues.apache.org/bugzilla/show_bug.cgi?id=49326

But if this is actually the problem and it can't be resolved by blowing up
-Xmx, I think the fix needs to be in JEVIO. The above link mentions some
workarounds which I can try on Monday, assuming I'm able to reproduce this
bug.

What version of the JVM are you running? (java -version)

On Fri, 9 Nov 2012, Homer wrote:

> Hi Matt,
>
> Your message shows that your command was:
>> java -Xmx2048m -cp hps-java/target/hps-java-1.2-SNAPSHOT-bin.jar
> org.lcsim.hps.evio.TestRunEvioToLcio -x steering/TestRunOfflineRecon.lcsim
> /nfs/slac/g/hps/mgraham/DarkPhoton/testrun_data/hps_001349.evio.0
> -DoutputFile=recon.slcio -d HPS-TestRun-v3
>
> Shouldn't "-cp" be "-jar"?
>
> Cheers,
> Homer
>
>
>
> On Fri, 9 Nov 2012, Graham, Mathew Thomas wrote:
>
>>
>> This actually happens right away?I tried upping Xmx to no avail.
>>
>> On Nov 9, 2012, at 5:11 PM, Homer <[log in to unmask]> wrote:
>>
>>> Hi Matt,
>>>
>>> Is this reproducible on different machines?
>>> Have you tried -Xmx3192m? I'm having to push
>>> it this far for some JAS3 SiD work. When I was
>>> running the conversion at JLAB, the jobs would
>>> run for several 10 of thousands of events before
>>> dying on the mentioned error. Using -Xmx2048
>>> resolved that problem but there is clearly something
>>> that slowly consumes memory. This is somewhat normal
>>> and it may not be a leak. Recent code changes may
>>> have slightly increased the memory consumption rate.
>>> How many events do you succeed in processing before
>>> the crash?
>>>
>>> Cheers,
>>> Homer
>>>
>>>
>>> On Fri, 9 Nov 2012, McCormick, Jeremy I. wrote:
>>>
>>>> Hi, Matt.
>>>>
>>>> Do you know how to look at memory usage in Java?
>>>>
>>>> You'll might want to debug with something like this:
>>>>
>>>> ----
>>>>
>>>> Runtime runtime = Runtime.getRuntime();
>>>>
>>>> NumberFormat format = NumberFormat.getInstance();
>>>>
>>>> StringBuilder sb = new StringBuilder();
>>>> long maxMemory = runtime.maxMemory();
>>>> long allocatedMemory = runtime.totalMemory();
>>>> long freeMemory = runtime.freeMemory();
>>>>
>>>> sb.append("free memory: " + format.format(freeMemory / 1024) + "<br/>");
>>>> sb.append("allocated memory: " + format.format(allocatedMemory / 1024) +
>>>> "<br/>");
>>>> sb.append("max memory: " + format.format(maxMemory / 1024) + "<br/>");
>>>> sb.append("total free memory: " + format.format((freeMemory + (maxMemory
>>>> - allocatedMemory)) / 1024) + "<br/>");
>>>>
>>>> ----
>>>>
>>>> I took the above idea from here.
>>>>
>>>> http://stackoverflow.com/questions/74674/how-to-do-i-check-cpu-and-memory-usage-in-java
>>>>
>>>> You could make that a static method and call it at various points in
>>>> TestRunEvioToLcio or within one of your drivers in the .lcsim file you're
>>>> using.
>>>>
>>>> If memory is steadily increasing every event then this indicates some
>>>> systematic memory leak. If it looks fine and then explodes on one event,
>>>> that indicates some problem with the data of that event. For instance,
>>>> there could be a bogus (very large) value that gets into an array size
>>>> setting
>>>> due to corrupted data (e.g. when size of something is read from a data
>>>> block), which is often what happens to cause these kinds of problems.
>>>>
>>>> --Jeremy
>>>>
>>>> -----Original Message-----
>>>> From: Graham, Mathew Thomas
>>>> Sent: Friday, November 09, 2012 12:38 PM
>>>> To: Uemura, Sho; Omar Moreno; Per Hansson
>>>> Cc: McCormick, Jeremy I.
>>>> Subject: OutOfMemory error in jevio?
>>>>
>>>> I'm trying to run over data (from a pretty pristine hps-java build) like
>>>> this:
>>>> java -Xmx2048m -cp hps-java/target/hps-java-1.2-SNAPSHOT-bin.jar
>>>> org.lcsim.hps.evio.TestRunEvioToLcio -x
>>>> steering/TestRunOfflineRecon.lcsim
>>>> /nfs/slac/g/hps/mgraham/DarkPhoton/testrun_data/hps_001349.evio.0
>>>> -DoutputFile=recon.slcio -d HPS-TestRun-v3
>>>>
>>>>
>>>> and I get this...
>>>>
>>>> Exception in thread "main" java.lang.RuntimeException:
>>>> java.io.IOException: Map failed
>>>> at
>>>> org.lcsim.hps.evio.TestRunEvioToLcio.main(TestRunEvioToLcio.java:188)
>>>> Caused by: java.io.IOException: Map failed
>>>> at sun.nio.ch.FileChannelImpl.map(FileChannelImpl.java:748)
>>>> at org.jlab.coda.jevio.EvioReader.mapFile(EvioReader.java:323)
>>>> at org.jlab.coda.jevio.EvioReader.<init>(EvioReader.java:178)
>>>> at
>>>> org.lcsim.hps.evio.TestRunEvioToLcio.main(TestRunEvioToLcio.java:186)
>>>> Caused by: java.lang.OutOfMemoryError: Map failed
>>>> at sun.nio.ch.FileChannelImpl.map0(Native Method)
>>>> at sun.nio.ch.FileChannelImpl.map(FileChannelImpl.java:745)
>>>> ... 3 more
>>>>
>>>>
>>>> ...
>>>>
>>>> ########################################################################
>>>> Use REPLY-ALL to reply to list
>>>>
>>>> To unsubscribe from the HPS-SOFTWARE list, click the following link:
>>>> https://listserv.slac.stanford.edu/cgi-bin/wa?SUBED1=HPS-SOFTWARE&A=1
>>>>
>>
>>
>
> ########################################################################
> Use REPLY-ALL to reply to list
>
> To unsubscribe from the HPS-SOFTWARE list, click the following link:
> https://listserv.slac.stanford.edu/cgi-bin/wa?SUBED1=HPS-SOFTWARE&A=1
>

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