Found the 64-bit executable:
[yakut01] ~/myhps/release $ file
/afs/slac/package/java/amd64_linux/jdk1.6/bin/java
/afs/slac/package/java/amd64_linux/jdk1.6/bin/java: ELF 64-bit LSB executable,
AMD x86-64, version 1 (SYSV), for GNU/Linux 2.4.0, dynamically linked (uses
shared libs), not stripped
[yakut01] ~/myhps/release $ /afs/slac/package/java/amd64_linux/jdk1.6/bin/java
-Xmx2048m -cp hps-java/target/hps-java-1.2-SNAPSHOT-bin.jar
org.lcsim.hps.evio.TestRunEvioToLcio -x
hps-java/src/main/resources/org/lcsim/hps/steering/TestRunOfflineRecon-o1.lcsim
~/hps3/data/testrun/runs/evio/hps_001349.evio.0 -DoutputFile=recon.slcio -d
HPS-TestRun-v3 | more
No input files in XML file.
No input files provided by XML or command line. Dry run will be enabled.
Loading the SVT bad channels for run -1
Opening file /u/ey/homer/hps3/data/testrun/runs/evio/hps_001349.evio.0
block number out of sequence, got 1 expecting 2
Prestart event: time 1337323692 - Thu May 17 23:48:12 PDT 2012, run 1349, run
type 31
Reading calibrations for date: Thu May 17 23:48:12 PDT 2012
Use this calibration from Fri May 11 14:30:14 PDT 2012:
calibSVT/20120511_1.dat.base
Reading calibrations for date: Thu May 17 23:48:12 PDT 2012
Use this calibration from Fri Dec 31 21:43:14 PST 1999: calibSVT/default.tp
Loading the SVT bad channels for run 1349
File daqmap/svt1349.badchannels was not found! Continuing with only QA bad
channels
Loading SVT gains ...
Go event: time 1337323714 - Thu May 17 23:48:34 PDT 2012, event count so far 0
reading ECal DAQ map
reading ECal bad channels
Crate 2, slot 19, channel 13 not found in map
Crate 2, slot 19, channel 14 not found in map
Crate 2, slot 19, channel 15 not found in map
Layer: 9 FPGA: 2 Hybrid: 2
Layer: 8 FPGA: 2 Hybrid: 0
Layer: 7 FPGA: 2 Hybrid: 1
Layer: 6 FPGA: 1 Hybrid: 1
Layer: 5 FPGA: 1 Hybrid: 2
Layer: 4 FPGA: 0 Hybrid: 2
Layer: 3 FPGA: 1 Hybrid: 0
Layer: 2 FPGA: 0 Hybrid: 0
Layer: 10 FPGA: 5 Hybrid: 0
Layer: 1 FPGA: 0 Hybrid: 1
Layer: 9 FPGA: 6 Hybrid: 2
Layer: 8 FPGA: 6 Hybrid: 0
Layer: 7 FPGA: 6 Hybrid: 1
Layer: 6 FPGA: 3 Hybrid: 1
Layer: 5 FPGA: 3 Hybrid: 2
Layer: 4 FPGA: 4 Hybrid: 2
Layer: 3 FPGA: 3 Hybrid: 0
Layer: 2 FPGA: 4 Hybrid: 0
Layer: 10 FPGA: 5 Hybrid: 2
Layer: 1 FPGA: 4 Hybrid: 1
SVTEvioReader_RTH: The data size is 8
Data 0: 1
Data 1: 146475195
Data 2: 268374015
Data 3: 146081978
Data 4: 268374014
Data 5: 145557681
...
Data 6: 268374015
Data 7: 0
SVTEvioReader_RTH: The temperatures are:
Temp 0: 2235.0
Temp 1: 2235.0
Temp 2: 4095.0
Temp 3: 4095.0
Temp 4: 2234.0
Temp 5: 2229.0
Temp 6: 4094.0
Temp 7: 4095.0
Temp 8: 2225.0
Temp 9: 2221.0
Temp 10: 4095.0
Temp 11: 4095.0
SVTEvioReader_RTH: The data size is 228
Data 0: 1
Data 1: 145492142
Data 2: 268374014
Data 3: 148179138
Data 4: 268374015
Data 5: 146409673
Data 6: 268374015
go Matt go
On Fri, 9 Nov 2012, Homer wrote:
> [yakut01] ~/myhps/release $
> /afs/slac/package/java/amd64_linux26/jdk1.6/bin/java -Xmx2048m -cp
> hps-java/target/hps-java-1.2-SNAPSHOT-bin.jar
> org.lcsim.hps.evio.TestRunEvioToLcio -x
> hps-java/src/main/resources/org/lcsim/hps/steering/TestRunOfflineRecon-o1.lcsim
> ~/hps3/data/testrun/runs/evio/hps_001349.evio.0 -DoutputFile=recon.slcio -d
> HPS-TestRun-v3
> No input files in XML file.
> No input files provided by XML or command line. Dry run will be enabled.
> Loading the SVT bad channels for run -1
> Opening file /u/ey/homer/hps3/data/testrun/runs/evio/hps_001349.evio.0
> Exception in thread "main" java.lang.RuntimeException: java.io.IOException:
> Map failed
> at
> org.lcsim.hps.evio.TestRunEvioToLcio.main(TestRunEvioToLcio.java:185)
> 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:183)
> 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
>
> Note!:
> [yakut01] ~/myhps/release $ file
> /afs/slac/package/java/amd64_linux26/jdk1.6/bin/java
> /afs/slac/package/java/amd64_linux26/jdk1.6/bin/java: ELF 32-bit LSB
> executable, Intel 80386, version 1 (SYSV), for GNU/Linux 2.2.5, dynamically
> linked (uses shared libs), not stripped
>
>
> On Fri, 9 Nov 2012, Sho Uemura wrote:
>
>> 'kay, the problem is that EvioReader (a JEVIO class) reads EVIO files by
>> mapping the entire file into a single byte buffer.
>>
>> If you're running a 32-bit JVM ("java -version" will tell you) you
>> apparently can't memory-map more than 1.3 GB or so at a time. Run 1351 is
>> barely under the line; the files that are failing are 2 GB.
>>
>> Heap size is (mostly) unrelated to this problem. Allocating more heap will
>> not solve it.
>>
>> I couldn't reproduce because I'm running 64-bit. If the two of you can
>> confirm what JVM version you're running?
>>
>>
>> Fixes:
>>
>> For now, run a 64-bit JVM. All the SLAC public machines are 64-bit at this
>> point.
>>
>> If you're on 32-bit, don't run on really big EVIO files. If many people are
>> running into this issue, we could break up the EVIO files, or translate to
>> LCIO - the original EVIO files would of course be kept.
>>
>> Long-term, EvioReader needs to be rewritten so it does the right thing and
>> either reads sequentially or maps only chunks of the file at a time. We can
>> get the CODA people to do this, since it is legitimately a JEVIO bug and
>> not ours.
>>
>> On Fri, 9 Nov 2012, Graham, Mathew Thomas wrote:
>>
>>>>
>>>> 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?
>>>
>>> Ah?when I run on a smaller file it does work.
>>>
>>>
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>>>
>>
>
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