Server won't start - Ubuntu 10.04 OMERO 4.4.3 Ice 3.4

[fuho]

I followed this one viewtopic.php?f=5&t=665

With the exception of installing Ice3.4 and latest OMERO with Ice 3.4.

Java I installed this way:

add-apt-repository ppa:ferramroberto/java
apt-get update
apt-get install sun-java6-jdk

https://www.openmicroscopy.org/site/sup ... linux.html I have read, or maybe just one of it's other versions. But to install OMERO I used information from sticky in this forum, thinking that would be the most upd to date version.

Do you see what exactly is the problem? I could reinstall the server with a differrent distro, but I am somehow confortamble with Ubuntu and using Fedora 4 for example would force me to use use system I don't know/am not comfortable with.

Thanks for your time, I really appreciate your help. I am sure you know what it feels when you are stuck with no-one to talk to without any help

[fuho]

So I have been trying to figure out what is going on the whole day. I reinstalled the server to Ubuntu 12.04 LTS and installed Java manually from Oracle web which didn't help. So I reinstalled again and am trying to stick to official repositories as much as possible. This time I have ZeroC-ice34, OpenJDK-6-jdk and jre and installed OMERO 4.4.3.b5 and still have the same problem.

When I try and start it with "omero admin startasync" and immediately start checking what is going on with "omero admin dianostics" I can see that Blitz-0, DropBox, Indexer-0, PixelData-0, Processor-0 and Tables-0 are "activating" (most are probably waiting for just one of them to start)

Then PixelData or Indexer-0 times out first. And after these two the rest times out too and I have icegrindnode running but no Blitz-0.

The log's don't make me smarter at all, can I switch on some extra verbosity? Where?

What is the best way to bring the whole setup to near new state? Delete logs and var/master/?

How can I run components one by one to see which is is the troublemaker and what seems to be the problem?

[rleigh]

jUsing OpenJDK6 and Ice 3.4 on Ubuntu is just fine for running the server (so long as you downloaded the "ice34" variant of the server, and not "ice33").

In case it's a fault with the JVM, it might be worth testing a few small java programs by hand to see of you can run anything at all, even just a basic "hello world" type program. Also, make sure to run "sudo update-alternatives --config java" and if openjdk6 is not already the default, then choose it.

It might be worth looking at other factors which might prevent startup, including:

process limits (data, nofile, nproc, rss, stack) (are any being exceeded?)
memory usage (are they being killed due to being out of memory?)
security (selinux/apparmor)

If bad things are happening, check the logs in /var/log (kern.log, messages, syslog) to see if anything is being reported.

To check the limits, run "ulimit -a".
To check memory usage, run e.g. "free" or "top" as you start up omero.
For security stuff, if it's being logged as a problem, you can try disabling it as a temporary workaround.

It may be the case that none of the above are at fault; these are just suggestions.


Regards,
Roger

[cxallan]

If you've installed numerous JVMs and used numerous distributions on your system and you still have a crashing JVM I'd really suspect hardware issues. Have you run a memory test?

[fuho]

I have since reinstalled the server again (not sure if I mentioned it's a VPS -OpenVZ).
While reading the system logs in /var/log there were no errors at all. I will check I installed all the dependencies, will try to follow http://www.openmicroscopy.org/site/supp ... alkthrough as close as possible and then will report back.

I also tried the portable appliance and it worked, even if very slow (import of 7MB 4D tiff took about an hour) and I had to go in and start omero web myself.
Then I installed Ubuntu 12.04 desktop at home and got OMERO somewhat (web still doesn't work) working there, there I used Postgresql 9.1.

[cxallan]

A quick Google of segfaults in combination with OpenVZ unfortunately yields a lot of results. I'd expect everything you did was correct but your visualization infrastructure was tripping you up.

[fuho]

Well, anyways thanks for help guys/girls, I will have to give up at least for a while.

Last thing I did was double check I had all the environment variables set corectly, unistalled postgresql 8.4 and installed 9.1, set that up, double checked that I am using working sun java 6, checked the directories, deleted and unzipped the OMERO server again, set the config according to instructions, and ran it. After a while it timed out again, no interesting errors in logs, nothing at all in system logs.

One error log generated in OMERO.server [hs_err_pid21373.log]:

Code: Select all

root@dallas:/home/omero/OMERO.server# cat hs_err_pid21373.log
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  Internal Error (relocInfo_x86.cpp:77), pid=21373, tid=140438060611328
#  Error: ShouldNotReachHere()
#
# JRE version: 6.0_35-b10
# Java VM: Java HotSpot(TM) 64-Bit Server VM (20.10-b01 mixed mode linux-amd64 compressed oops)
# If you would like to submit a bug report, please visit:
#   http://java.sun.com/webapps/bugreport/crash.jsp
#

---------------  T H R E A D  ---------------

Current thread (0x00007fba4c0e0800):  JavaThread "C2 CompilerThread1" daemon [_thread_in_vm, id=21445, stack(0x00007fba48a73000,0x00007fba48b74000)]

Stack: [0x00007fba48a73000,0x00007fba48b74000],  sp=0x00007fba48b70ec0,  free space=1015k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
V  [libjvm.so+0x860395]  VMError::report_and_die()+0x265
V  [libjvm.so+0x3e5346]  report_should_not_reach_here(char const*, int)+0x46
V  [libjvm.so+0x77b079]  Relocation::pd_call_destination(unsigned char*)+0xb9
V  [libjvm.so+0x779630]  CallRelocation::fix_relocation_after_move(CodeBuffer const*, CodeBuffer*)+0x30
V  [libjvm.so+0x386b3c]  CodeBuffer::relocate_code_to(CodeBuffer*) const+0xec
V  [libjvm.so+0x386a22]  CodeBuffer::copy_code_to(CodeBlob*)+0x42
V  [libjvm.so+0x383448]  CodeBlob::CodeBlob(char const*, CodeBuffer*, int, int, int, int, OopMapSet*)+0xb8
V  [libjvm.so+0x6e86ab]  nmethod::nmethod(methodOopDesc*, int, int, int, CodeOffsets*, int, DebugInformationRecorder*, Dependencies*, CodeBuffer*, int, OopMapSet*, ExceptionHandlerTable*, ImplicitExceptionTable*, AbstractCompiler*, int)+0x4b
V  [libjvm.so+0x6e7932]  nmethod::new_nmethod(methodHandle, int, int, CodeOffsets*, int, DebugInformationRecorder*, Dependencies*, CodeBuffer*, int, OopMapSet*, ExceptionHandlerTable*, ImplicitExceptionTable*, AbstractCompiler*, int)+0x1b2
V  [libjvm.so+0x33dcef]  ciEnv::register_method(ciMethod*, int, CodeOffsets*, int, CodeBuffer*, int, OopMapSet*, ExceptionHandlerTable*, ImplicitExceptionTable*, AbstractCompiler*, int, bool, bool)+0x41f
V  [libjvm.so+0x39ef99]  Compile::Compile(ciEnv*, C2Compiler*, ciMethod*, int, bool, bool)+0x9b9
V  [libjvm.so+0x321d3e]  C2Compiler::compile_method(ciEnv*, ciMethod*, int)+0x9e
V  [libjvm.so+0x3a96aa]  CompileBroker::invoke_compiler_on_method(CompileTask*)+0x2ca
V  [libjvm.so+0x3a8f95]  CompileBroker::compiler_thread_loop()+0x355
V  [libjvm.so+0x821539]  compiler_thread_entry(JavaThread*, Thread*)+0x9
V  [libjvm.so+0x81aa41]  JavaThread::run()+0x121
V  [libjvm.so+0x711d1f]  java_start(Thread*)+0x13f


Current CompileTask:
C2:  42502 397      java.lang.AbstractStringBuilder.append(Ljava/lang/String;)Ljava/lang/AbstractStringBuilder; (60 bytes)


---------------  P R O C E S S  ---------------

Java Threads: ( => current thread )
  0x00007fba4c5fe800 JavaThread "Ice.ThreadPool.Client-0" [_thread_in_native, id=21856, stack(0x00007fba2bade000,0x00007fba2bbdf000)]
  0x00007fba4c518000 JavaThread "Ice.EndpointHostResolverThread" [_thread_blocked, id=21855, stack(0x00007fba2bce7000,0x00007fba2bde8000)]
  0x00007fba4c7b8800 JavaThread "Ice.Timer" [_thread_blocked, id=21854, stack(0x00007fba2bde8000,0x00007fba2bee9000)]
  0x00007fba4c629000 JavaThread "Thread-1" daemon [_thread_blocked, id=21650, stack(0x00007fba48092000,0x00007fba48193000)]
  0x00007fba4c635000 JavaThread "perf4j-async-stats-appender-sink-CoalescingStatistics" daemon [_thread_blocked, id=21644, stack(0x00007fba48193000,0x00007fba48294000)]
  0x00007fba4c0e3000 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=21446, stack(0x00007fba48972000,0x00007fba48a73000)]
=>0x00007fba4c0e0800 JavaThread "C2 CompilerThread1" daemon [_thread_in_vm, id=21445, stack(0x00007fba48a73000,0x00007fba48b74000)]
  0x00007fba4c0de000 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=21443, stack(0x00007fba48b74000,0x00007fba48c75000)]
  0x00007fba4c0dc000 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=21441, stack(0x00007fba48c75000,0x00007fba48d76000)]
  0x00007fba4c0c0000 JavaThread "Finalizer" daemon [_thread_blocked, id=21429, stack(0x00007fba48eff000,0x00007fba49000000)]
  0x00007fba4c0be000 JavaThread "Reference Handler" daemon [_thread_blocked, id=21428, stack(0x00007fba50027000,0x00007fba50128000)]
  0x00007fba4c007800 JavaThread "main" [_thread_in_Java, id=21415, stack(0x00007fba51383000,0x00007fba51484000)]

Other Threads:
  0x00007fba4c0b7000 VMThread [stack: 0x00007fba50128000,0x00007fba50229000] [id=21419]
  0x00007fba4c0ee000 WatcherThread [stack: 0x00007fba48871000,0x00007fba48972000] [id=21447]

VM state:not at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread:  ([mutex/lock_event])
[0x00007fba4c003cb0] CodeCache_lock - owner thread: 0x00007fba4c0e0800
[0x00007fba4c005330] Compile_lock - owner thread: 0x00007fba4c0e0800
[0x00007fba4c005430] MethodCompileQueue_lock - owner thread: 0x00007fba4c0e0800

Heap
def new generation   total 36928K, used 29725K [0x00000000d8000000, 0x00000000da810000, 0x00000000e2aa0000)
  eden space 32832K,  78% used [0x00000000d8000000, 0x00000000d99075e8, 0x00000000da010000)
  from space 4096K,  99% used [0x00000000da410000, 0x00000000da80fff8, 0x00000000da810000)
  to   space 4096K,   0% used [0x00000000da010000, 0x00000000da010000, 0x00000000da410000)
tenured generation   total 81936K, used 49309K [0x00000000e2aa0000, 0x00000000e7aa4000, 0x00000000f8000000)
   the space 81936K,  60% used [0x00000000e2aa0000, 0x00000000e5ac7430, 0x00000000e5ac7600, 0x00000000e7aa4000)
compacting perm gen  total 25728K, used 25487K [0x00000000f8000000, 0x00000000f9920000, 0x0000000100000000)
   the space 25728K,  99% used [0x00000000f8000000, 0x00000000f98e3c40, 0x00000000f98e3e00, 0x00000000f9920000)
No shared spaces configured.

Code Cache  [0x00007fba49000000, 0x00007fba49270000, 0x00007fba4c000000)
total_blobs=652 nmethods=358 adapters=246 free_code_cache=48902016 largest_free_block=38336

Dynamic libraries:
40000000-40009000 r-xp 00000000 09:7f 50210447                           /usr/lib/jvm/java-6-sun-1.6.0.35/jre/bin/java
40108000-4010a000 rwxp 00008000 09:7f 50210447                           /usr/lib/jvm/java-6-sun-1.6.0.35/jre/bin/java
41c67000-41c88000 rwxp 00000000 00:00 0                                  [heap]
d8000000-da810000 rwxp 00000000 00:00 0
da810000-e2aa0000 rwxp 00000000 00:00 0
e2aa0000-e7aa4000 rwxp 00000000 00:00 0
e7aa4000-f8000000 rwxp 00000000 00:00 0
f8000000-f9920000 rwxp 00000000 00:00 0
f9920000-100000000 rwxp 00000000 00:00 0
7fba2bade000-7fba2bae1000 ---p 00000000 00:00 0
7fba2bae1000-7fba2bbdf000 rwxp 00000000 00:00 0
7fba2bbdf000-7fba2bbe6000 r-xp 00000000 09:7f 50210260                   /usr/lib/jvm/java-6-sun-1.6.0.35/jre/lib/amd64/libnio.so
7fba2bbe6000-7fba2bce5000 ---p 00007000 09:7f 50210260                   /usr/lib/jvm/java-6-sun-1.6.0.35/jre/lib/amd64/libnio.so
7fba2bce5000-7fba2bce7000 rwxp 00006000 09:7f 50210260                   /usr/lib/jvm/java-6-sun-1.6.0.35/jre/lib/amd64/libnio.so
7fba2bce7000-7fba2bcea000 ---p 00000000 00:00 0
7fba2bcea000-7fba2bde8000 rwxp 00000000 00:00 0
7fba2bde8000-7fba2bdeb000 ---p 00000000 00:00 0
7fba2bdeb000-7fba2bee9000 rwxp 00000000 00:00 0
7fba2bee9000-7fba2befc000 r-xp 00000000 09:7f 50210304                   /usr/lib/jvm/java-6-sun-1.6.0.35/jre/lib/amd64/libnet.so
7fba2befc000-7fba2bffd000 ---p 00013000 09:7f 50210304                   /usr/lib/jvm/java-6-sun-1.6.0.35/jre/lib/amd64/libnet.so
7fba2bffd000-7fba2c000000 rwxp 00014000 09:7f 50210304                   /usr/lib/jvm/java-6-sun-1.6.0.35/jre/lib/amd64/libnet.so
7fba2c000000-7fba2cdad000 rwxp 00000000 00:00 0
7fba2cdad000-7fba30000000 ---p 00000000 00:00 0
7fba30000000-7fba30021000 rwxp 00000000 00:00 0
7fba30021000-7fba34000000 ---p 00000000 00:00 0
7fba34000000-7fba34021000 rwxp 00000000 00:00 0
7fba34021000-7fba38000000 ---p 00000000 00:00 0
7fba38000000-7fba3985d000 rwxp 00000000 00:00 0
7fba3985d000-7fba3c000000 ---p 00000000 00:00 0
7fba3c000000-7fba3c021000 rwxp 00000000 00:00 0
7fba3c021000-7fba40000000 ---p 00000000 00:00 0
7fba40000000-7fba40021000 rwxp 00000000 00:00 0
7fba40021000-7fba44000000 ---p 00000000 00:00 0
7fba44000000-7fba44196000 rwxp 00000000 00:00 0
7fba44196000-7fba48000000 ---p 00000000 00:00 0
7fba48092000-7fba48095000 ---p 00000000 00:00 0
7fba48095000-7fba48193000 rwxp 00000000 00:00 0
7fba48193000-7fba48196000 ---p 00000000 00:00 0
7fba48196000-7fba48294000 rwxp 00000000 00:00 0
7fba48294000-7fba4829a000 r-xp 00000000 09:7f 50210229                   /usr/lib/jvm/java-6-sun-1.6.0.35/jre/lib/amd64/libmanagement.so
7fba4829a000-7fba48399000 ---p 00006000 09:7f 50210229                   /usr/lib/jvm/java-6-sun-1.6.0.35/jre/lib/amd64/libmanagement.so
7fba48399000-7fba4839b000 rwxp 00005000 09:7f 50210229                   /usr/lib/jvm/java-6-sun-1.6.0.35/jre/lib/amd64/libmanagement.so
7fba4839b000-7fba483a0000 r-xs 00010000 09:7f 49947577                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/xml-apis-ext.jar
7fba483a0000-7fba483a3000 r-xs 00012000 09:7f 49947574                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/spring-security-ldap.jar
7fba483a3000-7fba483ad000 r-xs 00041000 09:7f 49947573                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/spring-security-core.jar
7fba483ad000-7fba483b0000 r-xs 00025000 09:7f 49947572                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/spring-security-config.jar
7fba483b0000-7fba483b8000 r-xs 00034000 09:7f 49947571                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/spring-ldap.jar
7fba483b8000-7fba483c5000 r-xs 000d0000 09:7f 49947566                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/server.jar
7fba483c5000-7fba483d9000 r-xs 000e3000 09:7f 49947576                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/xercesImpl.jar
7fba483d9000-7fba483eb000 r-xs 0019c000 09:7f 49947575                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/xalan.jar
7fba483eb000-7fba483ef000 r-xs 0006c000 09:7f 49947570                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/specification.jar
7fba483ef000-7fba483f7000 r-xs 00028000 09:7f 49947578                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/xml-apis.jar
7fba483f7000-7fba483fa000 r-xs 00041000 09:7f 49947565                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/serializer.jar
7fba483fa000-7fba483fc000 r-xs 00011000 09:7f 49947563                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/romio.jar
7fba483fc000-7fba483fe000 r-xs 00012000 09:7f 49947562                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/rendering.jar
7fba483fe000-7fba48402000 r-xs 0005b000 09:7f 49947561                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/quartz.jar
7fba48402000-7fba48405000 r-xs 00016000 09:7f 49947552                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/org.springframework.context.support.jar
7fba48405000-7fba48408000 r-xs 0000e000 09:7f 49947547                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/omero-shares.jar
7fba48408000-7fba48411000 r-xs 0005f000 09:7f 49947545                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ome-java.jar
7fba48411000-7fba48412000 r-xs 00016000 09:7f 49947544                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ome-io.jar
7fba48412000-7fba4842d000 r-xs 00255000 09:7f 49947543                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/netcdf.jar
7fba4842d000-7fba48433000 r-xs 00055000 09:7f 49947539                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/mail.jar
7fba48433000-7fba48440000 r-xs 00086000 09:7f 49947531                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/jts.jar
7fba48440000-7fba48442000 r-xs 00001000 09:7f 49947530                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/jsr107cache.jar
7fba48442000-7fba48444000 r-xs 00009000 09:7f 49947528                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/java-image-scaling.jar
7fba48444000-7fba48445000 r-xs 0000d000 09:7f 49947527                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/java-getopt.jar
7fba48445000-7fba48447000 r-xs 00007000 09:7f 49947524                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ini4j.jar
7fba48447000-7fba4847e000 r-xs 0029c000 09:7f 49947523                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ice.jar
7fba4847e000-7fba48483000 r-xs 0003f000 09:7f 49947522                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ice-freeze.jar
7fba48483000-7fba4848d000 r-xs 0007e000 09:7f 49947521                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ice-db.jar
7fba4848d000-7fba48491000 r-xs 00049000 09:7f 49947516                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/grib.jar
7fba48491000-7fba48493000 r-xs 00002000 09:7f 49947515                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/geronimo-spec-jta.jar
7fba48493000-7fba48498000 r-xs 0003c000 09:7f 49947514                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ehcache.jar
7fba48498000-7fba4849a000 r-xs 00009000 09:7f 49947511                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-pool.jar
7fba4849a000-7fba4849f000 r-xs 00040000 09:7f 49947509                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-lang.jar
7fba4849f000-7fba484a2000 r-xs 00018000 09:7f 49947508                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-io.jar
7fba484a2000-7fba484a8000 r-xs 00045000 09:7f 49947507                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-httpclient.jar
7fba484a8000-7fba484aa000 r-xs 0000a000 09:7f 49947505                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-codec.jar
7fba484aa000-7fba484b0000 r-xs 00077000 09:7f 49947560                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/postgresql.jar
7fba484b0000-7fba484b7000 r-xs 00031000 09:7f 49947557                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/org.springframework.transaction.jar
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7fba52d77000-7fba52d78000 r-xs 00006000 09:7f 49947494                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/asm.jar
7fba52d78000-7fba52d7a000 r-xs 00003000 09:7f 49947493                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/asm-attrs.jar
7fba52d7a000-7fba52d7c000 r-xs 0000c000 09:7f 49947491                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/activation.jar
7fba52d7c000-7fba52d7e000 r-xs 0000e000 09:7f 49947489                   /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/FontBox.jar
7fba52d7e000-7fba52d86000 rwxs 00000000 09:7f 48498665                   /tmp/hsperfdata_omero/21373
7fba52d86000-7fba52d87000 rwxp 00000000 00:00 0
7fba52d87000-7fba52d88000 r-xp 00000000 00:00 0
7fba52d88000-7fba52d8a000 rwxp 00000000 00:00 0
7fba52d8a000-7fba52d8b000 r-xp 00022000 09:7f 48499236                   /lib/x86_64-linux-gnu/ld-2.15.so
7fba52d8b000-7fba52d8d000 rwxp 00023000 09:7f 48499236                   /lib/x86_64-linux-gnu/ld-2.15.so
7ffff5a78000-7ffff5a8d000 rwxp 00000000 00:00 0                          [stack]
7ffff5bfe000-7ffff5c00000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

VM Arguments:
jvm_args: -Xmx512M -XX:MaxPermSize=128m -Djava.awt.headless=true -Dlog4j.configuration=etc/log4j.xml -Domero.logfile=var/log/${omero.name}.log -Domero.name=Blitz-0
java_command: lib/server/blitz.jar --Ice.Config=/home/omero/OMERO.server-4.4.3-ice34-b5/var/master/servers/Blitz-0/config/config
Launcher Type: SUN_STANDARD

Environment Variables:
JAVA_HOME=/usr/lib/jvm/java-6-sun
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/lib/jvm/java-6-sun/bin:/usr/share/Ice-3.4.2:/usr/lib/postgresql/9.1/bin:/home/omero/OMERO.server/bin
LD_LIBRARY_PATH=/usr/lib/jvm/java-6-sun-1.6.0.35/jre/lib/amd64/server:/usr/lib/jvm/java-6-sun-1.6.0.35/jre/lib/amd64:/usr/lib/jvm/java-6-sun-1.6.0.35/jre/../lib/amd64:/usr/share/java:/usr/lib:
SHELL=/bin/bash

Signal Handlers:
SIGSEGV: [libjvm.so+0x860fc0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGBUS: [libjvm.so+0x860fc0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGFPE: [libjvm.so+0x70f520], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGPIPE: [libjvm.so+0x70f520], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGXFSZ: [libjvm.so+0x70f520], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGILL: [libjvm.so+0x70f520], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGUSR1: SIG_DFL, sa_mask[0]=0x00000000, sa_flags=0x00000000
SIGUSR2: [libjvm.so+0x711f50], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGHUP: SIG_IGN, sa_mask[0]=0x00000000, sa_flags=0x00000000
SIGINT: [libjvm.so+0x711f50], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGTERM: [libjvm.so+0x711f50], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGQUIT: [libjvm.so+0x711f50], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004


---------------  S Y S T E M  ---------------

OS:wheezy/sid

uname:Linux 2.6.32-042stab059.7 #1 SMP Tue Jul 24 19:12:01 MSK 2012 x86_64
libc:glibc 2.15 NPTL 2.15
rlimit: STACK 10240k, CORE 0k, NPROC 126889, NOFILE 4096, AS infinity
load average:15.17 13.88 14.35

/proc/meminfo:
MemTotal:        1048576 kB
MemFree:          127952 kB
Cached:           187672 kB
Active:           810220 kB
Inactive:          77448 kB
Active(anon):     689064 kB
Inactive(anon):    10932 kB
Active(file):     121156 kB
Inactive(file):    66516 kB
Unevictable:           0 kB
Mlocked:               0 kB
SwapTotal:             0 kB
SwapFree:              0 kB
Dirty:              1272 kB
Writeback:             0 kB
AnonPages:        699996 kB
Shmem:             36832 kB
Slab:              32848 kB
SReclaimable:      17648 kB
SUnreclaim:        15200 kB


CPU:total 1 (4 cores per cpu, 2 threads per core) family 6 model 58 stepping 9, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, ht

/proc/cpuinfo:
processor   : 0
vendor_id   : GenuineIntel
cpu family   : 6
model      : 58
model name   : Intel(R) Xeon(R) CPU E3-1230 V2 @ 3.30GHz
stepping   : 9
cpu MHz      : 3292.547
cache size   : 8192 KB
physical id   : 0
siblings   : 8
core id      : 0
cpu cores   : 4
apicid      : 0
initial apicid   : 0
fpu      : yes
fpu_exception   : yes
cpuid level   : 13
wp      : yes
flags      : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm sse4_1 sse4_2 x2apic popcnt aes xsave avx f16c rdrand lahf_lm ida arat epb xsaveopt pln pts dts tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms
bogomips   : 6585.09
clflush size   : 64
cache_alignment   : 64
address sizes   : 36 bits physical, 48 bits virtual
power management:



Memory: 4k page, physical 1048576k(127956k free), swap 0k(0k free)

vm_info: Java HotSpot(TM) 64-Bit Server VM (20.10-b01) for linux-amd64 JRE (1.6.0_35-b10), built on Aug 28 2012 16:21:56 by "java_re" with gcc 3.2.2 (SuSE Linux)

time: Mon Sep 17 20:01:53 2012
elapsed time: 42 seconds


If anyone sees something I should look into please let me know.

[cxallan]

As I mentioned above OpenVZ is known to have issues with Java on certain kernels. A couple threads for reference:

http://forum.openvz.org/index.php?t=msg&goto=43571&
https://freevps.us/thread-6197.html

There are numerous other threads that are a Google search away with a wide variety of OpenVZ issues with Java. I'd suggest that if you want to have a pain free OMERO experience you try a different virtualization approach.