[ome-users] trouble with thumbnails in omero web
Tjelvar Olsson (JIC)
Tjelvar.Olsson at jic.ac.uk
Thu Nov 12 15:19:43 GMT 2015
Hi Simon,
Thanks for the quick reply.
Running:
# yum install java-1.8.0-openjdk
# yum remove java-1.7.0
# yum remove java-1.7.0-openjdk-headless.x86_64
Followed by restarting omero and omero web solved the problem.
Below are the details of the server, prior to me applying the fix.
Thanks for your help,
Tjelvar
$ java -version
java version "1.7.0_91"
OpenJDK Runtime Environment (rhel-2.6.2.1.el7_1-x86_64 u91-b00)
OpenJDK 64-Bit Server VM (build 24.91-b01, mixed mode)
$ ./bin/omero admin diagnostics
================================================================================
OMERO Diagnostics 5.1.2-ice35-b45
================================================================================
WARNING:omero.util.UpgradeCheck:UPGRADE AVAILABLE:Please upgrade to 5.1.4 See http://trac.openmicroscopy.org.uk/omero for the latest version
Commands: java -version 1.7.0 (/usr/bin/java)
Commands: python -V 2.7.5 (/usr/bin/python)
Commands: icegridnode --version 3.5.1 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.5.1 (/usr/bin/icegridadmin)
Commands: psql --version 9.4.5 (/usr/bin/psql)
Server: icegridnode running
Server: Blitz-0 active (pid = 716, enabled)
Server: DropBox active (pid = 728, enabled)
Server: FileServer active (pid = 729, enabled)
Server: Indexer-0 active (pid = 764, enabled)
Server: MonitorServer active (pid = 737, enabled)
Server: OMERO.Glacier2 active (pid = 740, enabled)
Server: OMERO.IceStorm active (pid = 743, enabled)
Server: PixelData-0 active (pid = 749, enabled)
Server: Processor-0 active (pid = 734, enabled)
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)
Log dir: /home/omero/OMERO.server-5.1.2-ice35-b45/var/log exists
Log files: Blitz-0.log 366.0 MB errors=597 warnings=1661
Log files: DropBox.log 1.0 KB
Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log 3.0 MB errors=0 warnings=7
Log files: MonitorServer.log 1.0 KB
Log files: OMEROweb.log 3.0 MB errors=239 warnings=849
Log files: OMEROweb_request.log 107.0 KB errors=2 warnings=790
Log files: PixelData-0.log 1.0 MB errors=18 warnings=2
Log files: Processor-0.log 132.0 KB errors=7 warnings=0
Log files: Tables-0.log 2.0 KB errors=3 warnings=0
Log files: TestDropBox.log n/a
Log files: master.err 0.0 KB
Log files: master.out 0.0 KB
Log files: Total size 375.68 MB
Log files: Total size 375.68 MB
Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/root/bin:/usr/lib/jvm/jre/bin:/usr/share/Ice-3.5.1:/usr/bin:/home/omero/OMERO.server/bin
Environment:PYTHONPATH=(unset)
Environment:ICE_HOME=/usr/share/Ice-3.5.1
Environment:LD_LIBRARY_PATH=/usr/share/java:/usr/lib:/usr/local/lib
Environment:DYLD_LIBRARY_PATH=(unset)
OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir:'/OMERO' Exists? True Is writable? True
OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
JVM settings: Blitz -Xmx596m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer -Xmx397m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Pixeldata -Xmx596m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository -Xmx397m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions
OMERO.web status... [RUNNING] (PID 1006)
$ ./bin/omero config get --hide-password
omero.db.name=omero
omero.db.pass=********
omero.db.user=omero_db_user
omero.ldap.base=****
omero.ldap.config=true
omero.ldap.new_user_group=public
omero.ldap.urls=***
omero.ldap.user_filter=(objectClass=inetOrgPerson)
omero.ldap.user_mapping=omeName=uid,firstName=givenName,lastName=sn,email=mail
________________________________
From: ome-users [ome-users-bounces at lists.openmicroscopy.org.uk] on behalf of Simon Li [spli at dundee.ac.uk]
Sent: 12 November 2015 14:06
To: OME User Support List
Subject: Re: [ome-users] trouble with thumbnails in omero web
Hi Tjelvare
What version of Java are you using? We've come across a similar problem before:
https://trac.openmicroscopy.org/ome/ticket/12612
But it's reported as being fixed in the latest Java 8:
https://bugs.launchpad.net/ubuntu/+source/openjdk-8/+bug/1421501
(that bug report is for Ubuntu, but RHEL/CentOS should also have the updated Java)
Could you provide us with the output of:
- omero admin diagnostics
- omero config get --hide-password (just in case it's different from your ansible config)
Simon
On 12 November 2015 at 13:28, Tjelvar Olsson (JIC) <Tjelvar.Olsson at jic.ac.uk<mailto:Tjelvar.Olsson at jic.ac.uk>> wrote:
Hi,
I cannot currently view thumbnails in: OMERO.web 5.1.2-ice35-b45 running on a CentOS 7 VM, installed using an Ansible playbook developed earlier in the year:
https://github.com/JIC-CSB/omero-ansible
I've just realised that I cannot view thumbnails in the web interface. Looking at the OMERO.
I have appended some output from the OMEROweb.log that seemed relevant.
Any idea what is wrong with my installation?
Regards,
Tjelvare
2015-11-12 13:13:00,143 WARNI [ omero.gateway] (proc.24856) debug:4105 InternalException on <class 'omeroweb.webclient.webclient_gateway.OmeroWebSafeCallWrapper'> to <b1d90d71-3f90-4b72
-b3f8-858d3b3ef964omero.api.RenderingEngine> renderCompressed((object #0 (::omero::romio::PlaneDef)
{
slice = 0
x = 0
y = 0
z = 0
t = 0
region = <nil>
stride = 0
}, <ServiceOptsDict: {'omero.session.uuid': 'abe5fa60-6b2b-4ae6-b7b5-da97732ee258', 'omero.group': '-1', 'omero.client.uuid': '9984e28e-6cfd-4929-90ab-7815ff95c82f'}>), {})
Traceback (most recent call last):
File "/home/omero/OMERO.server/lib/python/omero/gateway/__init__.py", line 4123, in __call__
return self.f(*args, **kwargs)
File "/home/omero/OMERO.server/lib/python/omero_api_RenderingEngine_ice.py", line 307, in renderCompressed
return _M_omero.api.RenderingEngine._op_renderCompressed.invoke(self, ((_def, ), _ctx))
InternalException: exception ::omero::InternalException
{
serverStackTrace = ome.conditions.InternalException: Wrapped Exception: (java.lang.NoClassDefFoundError):
Could not initialize class com.sun.imageio.plugins.jpeg.JPEGImageWriter
at com.sun.imageio.plugins.jpeg.JPEGImageWriterSpi.createWriterInstance(JPEGImageWriterSpi.java:96)
at javax.imageio.spi.ImageWriterSpi.createWriterInstance(ImageWriterSpi.java:351)
at javax.imageio.ImageIO$ImageWriterIterator.next(ImageIO.java:843)
at javax.imageio.ImageIO$ImageWriterIterator.next(ImageIO.java:827)
at ome.logic.CompressImpl.compressToStream(CompressImpl.java:34)
at ome.services.RenderingBean.renderCompressed(RenderingBean.java:545)
at sun.reflect.GeneratedMethodAccessor1781.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy107.renderCompressed(Unknown Source)
at sun.reflect.GeneratedMethodAccessor1781.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy107.renderCompressed(Unknown Source)
at sun.reflect.GeneratedMethodAccessor2657.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
at ome.services.throttling.Callback.run(Callback.java:56)
at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:149)
at ome.services.blitz.impl.RenderingEngineI.renderCompressed_async(RenderingEngineI.java:339)
at sun.reflect.GeneratedMethodAccessor2656.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at omero.cmd.CallContext.invoke(CallContext.java:78)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy109.renderCompressed_async(Unknown Source)
at omero.api._RenderingEngineTie.renderCompressed_async(_RenderingEngineTie.java:276)
at omero.api._RenderingEngineDisp.___renderCompressed(_RenderingEngineDisp.java:575)
at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1667)
at IceInternal.Incoming.invoke(Incoming.java:222)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)
at Ice.ConnectionI.dispatch(ConnectionI.java:1258)
at Ice.ConnectionI.message(ConnectionI.java:1213)
at IceInternal.ThreadPool.run(ThreadPool.java:321)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
at java.lang.Thread.run(Thread.java:745)
serverExceptionClass = ome.conditions.InternalException
message = Wrapped Exception: (java.lang.NoClassDefFoundError):
Could not initialize class com.sun.imageio.plugins.jpeg.JPEGImageWriter
}
The University of Dundee is a registered Scottish Charity, No: SC015096
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