Task #10115 (closed)
Opened 11 years ago
Closed 11 years ago
Bug: Cellr images very slow rendering
Reported by: | bpindelski | Owned by: | bpindelski |
---|---|---|---|
Priority: | major | Milestone: | OMERO-4.4.7 |
Component: | Insight | Version: | n.a. |
Keywords: | fs | Cc: | ux@…, fs@… |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description
Imported all images from the cellr/colin folder. Thumbnails generated ok, but browsing time points when there is more than 10 seems to be too much for gretzky. Clicking on the time point slider in the Image Viewer doesn't change the rendered image.
Image name: cellr/colin/07-06-21/07-06-21_d.mtb [FITC]
Server: gretzky
Build: OMERO.insight-4.4.4-766-7e18246-dirty-ice33-b111-mac
Change History (6)
comment:1 Changed 11 years ago by jburel
- Milestone changed from Unscheduled to OMERO-4.5
comment:2 Changed 11 years ago by jmoore
- Cc ux@… fs@… added
- Owner changed from jburel to bpindelski
comment:3 Changed 11 years ago by bpindelski
Josh, I seem to have found the culprit. Today it's still the same (i.e. I can't view any time point greater than 4), but managed to tail -f Blitz-0.log on gretzky. When browsing an image with T > 4, the following errors appear in the server log:
java.lang.RuntimeException: ome.io.nio.DimensionsOutOfBoundsException: T '4' greater than sizeT '4'. at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:248) at omeis.providers.re.GreyScaleStrategy.renderAsPackedInt(GreyScaleStrategy.java:153) at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:511) at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:478) at sun.reflect.GeneratedMethodAccessor1439.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:592) 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:116) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) at $Proxy108.renderAsPackedInt(Unknown Source) at sun.reflect.GeneratedMethodAccessor1439.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:592) 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 $Proxy108.renderAsPackedInt(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:592) 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:150) at ome.services.blitz.impl.RenderingEngineI.renderAsPackedInt_async(RenderingEngineI.java:332) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:592) 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:59) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) at $Proxy110.renderAsPackedInt_async(Unknown Source) at omero.api._RenderingEngineTie.renderAsPackedInt_async(_RenderingEngineTie.java:288) at omero.api._RenderingEngineDisp.___renderAsPackedInt(_RenderingEngineDisp.java:502) at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1680) at IceInternal.Incoming.invoke(Incoming.java:159) at Ice.ConnectionI.invokeAll(ConnectionI.java:2037) at Ice.ConnectionI.message(ConnectionI.java:972) at IceInternal.ThreadPool.run(ThreadPool.java:577) at IceInternal.ThreadPool.access$100(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) Caused by: ome.io.nio.DimensionsOutOfBoundsException: T '4' greater than sizeT '4'. at ome.io.bioformats.BfPixelsWrapper.checkBounds(BfPixelsWrapper.java:111) at ome.io.bioformats.BfPixelsWrapper.getPlane(BfPixelsWrapper.java:265) at ome.io.bioformats.BfPixelBuffer.getPlane(BfPixelBuffer.java:179) at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:230)
comment:4 Changed 11 years ago by jburel
it looks like an index problem during the import. Then it is impossible to generate the image.
comment:5 Changed 11 years ago by bpindelski
Closing. This has been an issue pointed out by Melissa and has now been fixed.
comment:6 Changed 11 years ago by bpindelski
- Resolution set to fixed
- Status changed from new to closed
Blazej, could you re-try today and see if it's equally slow. My thinking is that there are fewer people working today. If it still is slow, perhaps check the server log for OOMs. Thanks.
Note: please CC minimally fs@.. for any fs-related tickets.