[ome-users] Omero Blitz error
josh.moore at gmx.de
josh.moore at gmx.de
Tue Feb 17 22:16:42 GMT 2009
Paulo Almeida writes:
> Hi Josh,
Hi Paulo
> That seems to be the problem indeed. I installed the 3.3 version of
> Ice and I think it compiled just fine. I say 'think' because the
> test fails, due to a missing test/integration.exe file, but the
> rest seems successful. I am pasting the final output lines for you
> to see:
>
> dist:
> Copying 2153 files to /home/cgl/OMERO_test/OMERO/dist
> Copied 333 empty directories to 4 empty directories
> under /home/cgl/OMERO_test/OMERO/dist
> Updating jar: /home/cgl/OMERO_test/OMERO/dist/blitz/services.jar
> Building jar: /home/cgl/OMERO_test/OMERO/dist/omero.ear
>
> BUILD SUCCESSFUL
> Total time: 40 minutes 12 seconds
Congratulations! :)
> + java_omero integration
...
> test-compile:
> scons: Reading SConscript files ...
> Checking for C++ header file Ice/Ice.h... (cached) yes
> Checking for boost_unit_test...(cached) no
> scons: done reading SConscript files.
> scons: Building targets ...
> scons: `test' is up to date.
> scons: done building targets.
>
> BUILD FAILED
> /home/cgl/OMERO_test/OMERO/build.xml:197: The following error occurred while
> executing this line:
> /home/cgl/OMERO_test/OMERO/build.xml:184: The following error occurred while
> executing this line:
> /home/cgl/OMERO_test/OMERO/components/antlib/resources/global.xml:74: The
> following error occurred while executing this line:
> /home/cgl/OMERO_test/OMERO/components/tools/OmeroCpp/build.xml:46: Execute
> failed: java.io.IOException: Cannot run program "test/integration.exe" (in
> directory "/home/cgl/OMERO_test/OMERO/components/tools/OmeroCpp"):
> java.io.IOException: error=2, No such file or directory
Right. These are the integration tests which you definitely don't
need. Copying hudson.sh and removing the later build steps
(integration, findbugs, javadoc) would probably be the easiest path
for you. If we cannot find another workaround for what looks to be a
64bit build issue, we'll be providing a similar bash script ourselves.
> Thank you,
> Paulo
You're more than welcome.
~J.
> On Tuesday 17 February 2009 15:50:49 you wrote:
> > Paulo Almeida writes:
> > > Hi Josh,
> >
> > Paulo,
> >
> > that was helpful, thanks. The error you are getting with hudson.sh is
> > a different one:
> >
> > public static IceInternal.DispatchStatus
> > ^
> > /home/cgl/OMERO_test/OMERO/components/blitz/generated/omero/model/Job.java:
> >559: cannot find symbol symbol : class DispatchStatus
> > location: package IceInternal
> > public static IceInternal.DispatchStatus
> > ^
> >
> > This points to mismatched Ice versions. Can you verify:
> >
> > $ slice2java --version
> > 3.3.0
> >
> > I added a ticket:
> >
> > https://trac.openmicroscopy.org.uk/omero/ticket/1185
> >
> > for adding a check to the build. Thanks again.
> >
> > Best wishes,
> > ~Josh.
> >
> > > I'm sending the output of hudson.sh. I just replaced the BUILD_NUMBER
> > > variable with '1' and ran the script. It suggested using
> > > -Xlint:unchecked for details; should I do that, or is this output
> > > enough?
> > >
> > > Also, I ran:
> > >
> > > sh hudson.sh 2>&1 > hudson.txt
> > >
> > > hudson.txt is the result of that and console.txt is what was written to
> > > the console as the script ran.
> > >
> > > I'm sending this offlist as you suggested, but feel free to reply on the
> > > list if it may help others.
> > >
> > > Thanks,
> > > Paulo
> > >
> > > > Paulo Almeida writes:
> > > > > Hi Josh,
> > > >
> > > > Hi Paulo,
> > > >
> > > > > I tried that export in hudson.sh and it still fails with the same
> > > >
> > > > error. I
> > > >
> > > > > also tried to run hudson.sh itself, just to see what happened and
> > > > > it
> > > >
> > > > also
> > > >
> > > > > failed (although from what I read of the script I don't know if I
> > > > > was supposed to run it).
> > > > >
> > > > > We are building on 64-bit Linux (kernel is 2.6.26 amd64), with java
> > > > > version giving me this:
> > > > >
> > > > > java version "1.6.0_12"
> > > > > Java(TM) SE Runtime Environment (build 1.6.0_12-b04)
> > > > > Java HotSpot(TM) 64-Bit Server VM (build 11.2-b01, mixed mode)
> > > >
> > > > Thanks for the info. Could you possibly run hudson.sh and send me the
> > > > output, offlist if you'd prefer?
> > > >
> > > > > Thank you,
> > > > > Paulo
> > > >
> > > > Cheers,
> > > > ~j.
> > > >
> > > > > > Paulo Almeida writes:
> > > > > > > Hi,
> > > > > >
> > > > > > Hi Paulo,
> > > > > >
> > > > > > > We are trying to install Omero/Omero Blitz and we get a java
> > > > > > > error
> > > >
> > > > when
> > > >
> > > > > > > running:
> > > > > > >
> > > > > > > java -Xms512m -Xmx1512m -XX:+UseConcMarkSweepGC
> > > >
> > > > -XX:+CMSIncrementalMode
> > > >
> > > > > > > -XX:+PrintGCDetails -XX:+PrintGCTimeStamps omero
> > > > > > >
> > > > > > > We tried just "java omero" first, the switches were for
> > > > > > > debugging.
> > > >
> > > > We
> > > >
> > > > > > also
> > > > > >
> > > > > > > used -XX:-UseGCOverheadLimit , but it gave the same error. The
> > > >
> > > > computer
> > > >
> > > > > > > still had a lot of memory available.
> > > > > >
> > > > > > This is a problem we've also run into on certain platforms. What
> > > > > > are you building on? To workaround, take a look at
> > > > > > OMERO_HOME/hudson.sh which performs the continuous builds.
> > > > > > Specifically:
> > > > > >
> > > > > > export JAVA_OPTS=${JAVA_OPTS:-"-Xmx600M -Djavac.maxmem=600M
> > > > > > -Djavadoc.maxmem=600M -XX:MaxPermSize=256m"}
> > > > > >
> > > > > > are the settings we use.
> > > > > >
> > > > > > Best wishes,
> > > > > > ~Josh.
> > > > > >
> > > > > > > The stack trace follows:
> > > > > > >
> > > > > > > -----------
> > > > > > > The system is out of resources.
> > > > > > > Consult the following stack trace for details.
> > > > > > > java.lang.OutOfMemoryError: GC overhead limit exceeded
> > > > > > > at
> > > > > > > com.sun.tools.javac.code.Scope$ImportScope.makeEntry(Scope.jav
> > > > > > >a:385) at com.sun.tools.javac.code.Scope.enter(Scope.java:196)
> > > > > > > at
> > > > > > > com.sun.tools.javac.comp.MemberEnter$2.importFrom(MemberEnter.
> > > > > > >java:198) at
> > > > > > > com.sun.tools.javac.comp.MemberEnter$2.enterAnnotation(MemberE
> > > > > > >nter.java:203) at
> > > >
> > > > com.sun.tools.javac.comp.Annotate.flush(Annotate.java:95)
> > > >
> > > > > > > at
> > > > > >
> > > > > > com.sun.tools.javac.comp.Annotate.enterDone(Annotate.java:87)
> > > > > >
> > > > > > > at
> > > > > > > com.sun.tools.javac.comp.Enter.complete(Enter.java:472) at
> > > > > > > com.sun.tools.javac.comp.Enter.main(Enter.java:429) at
> > > > > > > com.sun.tools.javac.main.JavaCompiler.enterTrees(JavaCompiler.
> > > > > > >java:819) at
> > > > > > > com.sun.tools.javac.main.JavaCompiler.compile(JavaCompiler.jav
> > > > > > >a:727) at com.sun.tools.javac.main.Main.compile(Main.java:353)
> > > > > > > at com.sun.tools.javac.main.Main.compile(Main.java:279) at
> > > > > > > com.sun.tools.javac.main.Main.compile(Main.java:270) at
> > > > > > > com.sun.tools.javac.Main.compile(Main.java:69) at
> > > > > > > com.sun.tools.javac.Main.main(Main.java:54)
> > > > > > >
> > > > > > > BUILD FAILED
> > > > > > > /home/cgl/OMERO_test/OMERO_blitz/build.xml:108: The following
> > > >
> > > > error
> > > >
> > > > > > > occurred while executing this line:
> > > > > > > /home/cgl/OMERO_test/OMERO_blitz/components/antlib/resources/g
> > > > > > >lobal.xml:74: The following error occurred while executing this
> > > > > > > line:
> > > > > > > /home/cgl/OMERO_test/OMERO_blitz/components/blitz/build.xml:25
> > > > > > >:
> > > >
> > > > The
> > > >
> > > > > > > following error occurred while executing this line:
> > > > > > > /home/cgl/OMERO_test/OMERO_blitz/components/antlib/resources/l
> > > > > > >ifecycle.xml:122: Compile failed; see the compiler error output
> > > > > > > for details.
> > > > > > >
> > > > > > > Total time: 2 minutes 48 seconds
> > > > > > > Heap
> > > > > > > par new generation total 38336K, used 13664K
> > > >
> > > > [0x00007f5c5b4f0000,
> > > >
> > > > > > > 0x00007f5c5de80000, 0x00007f5c5de80000)
> > > > > > > eden space 34112K, 34% used [0x00007f5c5b4f0000,
> > > >
> > > > 0x00007f5c5c080cc0,
> > > >
> > > > > > > 0x00007f5c5d640000)
> > > > > > > from space 4224K, 43% used [0x00007f5c5da60000,
> > > >
> > > > 0x00007f5c5dc27638,
> > > >
> > > > > > > 0x00007f5c5de80000)
> > > > > > > to space 4224K, 0% used [0x00007f5c5d640000,
> > > >
> > > > 0x00007f5c5d640000,
> > > >
> > > > > > > 0x00007f5c5da60000)
> > > > > > > concurrent mark-sweep generation total 481728K, used 12149K
> > > > > > > [0x00007f5c5de80000, 0x00007f5c7b4f0000, 0x00007f5cb9cf0000)
> > > > > > > concurrent-mark-sweep perm gen total 63544K, used 38348K
> > > > > > > [0x00007f5cb9cf0000, 0x00007f5cbdafe000, 0x00007f5cbf0f0000)
> > > > > > >
> > > > > > > Thanks,
> > > > > > > Paulo
>
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