Hi Adam,
can you provide us additional logging? (looking for something which cancel
the directory walking if available).
In general, when dealing with similar big datasets, configuring stores via
REST would be better.
You can take a look on these page to get some information on that topic:
http://docs.geoserver.org/stable/en/user/rest/examples/curl.html#uploading-and-modifying-a-image-mosaic
http://geoserver.geo-solutions.it/edu/en/multidim/rest/index.html
As an instance, you could start configuring a store on top of a set of
sample granules and then harvest additional ones.
Please, let us know.
Cheers,
Daniele
On Sun, Mar 19, 2017 at 11:26 PM, Adam Steer <adam.st...@anu.edu.au> wrote:
> Hi all
>
> I’m attempting to create a very large imagemosaic in Geoserver 2.10.2.
>
> The process goes like:
>
> 1. add the MODIS sinusoidal projection (http://spatialreference.org/
> ref/sr-org/6974/geoserver/) to user_projections and netcdf_projections
> 2. use CreateIndexer.jar (http://geoserver.geo-solutions.it/downloads/
> releases/2.8.x-netcdf/CreateIndexer.jar) to generate an indexer.xml and
> _auxiliary.xml for the underlying files
> 3. check that permissions are all correct on the data store (a directory
> of many netCDF files)
> 4. check that my datastore.propoerties file is all correct
> 5. use the imagemosaic web UI create a store
>
> What happens? Geoserver dutifully trundles off, tells me it’s busy and
> starts writing to the relevant database tables.
>
> The tables have data, including geometries:
>
> --
> select * from bare_soil limit 10;
> fid |
> the_geom
> | imageindex |
> location |
> time
> -----+------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> --------------+------------+--------------------------------
> ----------------------------------------------------+---------------------
> 1 | 01030000000100000005000000D2F3B5D18E1673C100E0D6EF17F86CC0D2
> F3B5D18E1673C13964C84576F83041A3754DF1F80672C13964C84576F830
> 41A3754DF1F80672C100E0D6EF17F86CC0D2F3B5D18E1673C100E0D6EF17F86CC0 |
> 80 | /local/geoserver_data/gdata/fr5/FC.v302.MCD43A4/FC.v302.
> MCD43A4.h00v08.2000.005.nc | 2000-02-18 11:00:00
> 2 | 01030000000100000005000000D2F3B5D18E1673C100E0D6EF17F86CC0D2
> F3B5D18E1673C13964C84576F83041A3754DF1F80672C13964C84576F830
> 41A3754DF1F80672C100E0D6EF17F86CC0D2F3B5D18E1673C100E0D6EF17F86CC0 |
> 81 | /local/geoserver_data/gdata/fr5/FC.v302.MCD43A4/FC.v302.
> MCD43A4.h00v08.2000.005.nc | 2000-02-26 11:00:00
>
>
> …and the geometries actually hold data (whether they are correct I have to
> check - but for the moment I dangerously assume that they are):
>
> select st_astext(the_geom) from bare_soil limit 10;
>
> st_astext
> ------------------------------------------------------------
> ------------------------------------------------------------
> -----------------------------------------------------------------
> POLYGON((-20015341.106922 -231.752921981504,-20015341.106922
> 1112182.27258898,-18902927.081411 1112182.27258898,-18902927.081411
> -231.752921981504,-20015341.106922 -231.752921981504))
> POLYGON((-20015341.106922 -231.752921981504,-20015341.106922
> 1112182.27258898,-18902927.081411 1112182.27258898,-18902927.081411
> -231.752921981504,-20015341.106922 -231.752921981504))
>
> ….but no store is ever created.
>
> There are just over 9k tiles, in 4D (ie each tile has X, Y, and time
> axes). The DB tables get to about 51mb for each ‘layer’ publishable from
> the tiles.
>
> The only clue I have found in catalina.out is this:
>
> [gce.imagemosaic] - Unable to close indexingnull
>
> …which leads to a post about geoserver needing an EPSG: code:
> https://osgeo-org.atlassian.net/browse/GEOS-7201 - but this is apparently
> resolved.
>
> Geoserver’s own log (geoserver-home/logs/geoserver.log) shows me that the
> mosaic construction is cancelled (see below).
>
> Do I need to:
>
> a. give geoserver more resources?
> b. somehow give tomcat more time before it kills processes (no idea if
> this is a setting I can change or if it’s even relevant)
> c. provide more detail?
>
> It’s a single geoserver instance, with Xms 8g, Xmx 8g, G1Gc garbage
> collection, on a 16GB/8CPU VM. I can make some swap space (it’s on SSD),
> and expand the heap size if needed - but that might be silly Java
> management.
>
> Thoughts/suggestions welcome!
>
> Thanks
>
> Adam
>
>
> —
> (geoserver.log output)
> 2017-03-18 20:52:36,788 WARN [gce.imagemosaic] - Failure occurred while
> collecting the granules
> org.apache.commons.io.DirectoryWalker$CancelException: Operation Cancelled
> at org.apache.commons.io.DirectoryWalker.checkIfCancelled(
> DirectoryWalker.java:395)
> at org.apache.commons.io.DirectoryWalker.walk(
> DirectoryWalker.java:368)
> at org.apache.commons.io.DirectoryWalker.walk(
> DirectoryWalker.java:335)
> at org.geotools.gce.imagemosaic.ImageMosaicDirectoryWalker$
> MosaicDirectoryWalker.<init>(ImageMosaicDirectoryWalker.java:114)
> at org.geotools.gce.imagemosaic.ImageMosaicDirectoryWalker.run(
> ImageMosaicDirectoryWalker.java:197)
> at org.geotools.gce.imagemosaic.Utils.createMosaic(Utils.java:450)
> at org.geotools.gce.imagemosaic.Utils.checkSource(Utils.java:1310)
> at org.geotools.gce.imagemosaic.ImageMosaicReader.
> initReaderFromURL(ImageMosaicReader.java:532)
> at org.geotools.gce.imagemosaic.ImageMosaicReader.<init>(
> ImageMosaicReader.java:479)
> at org.geotools.gce.imagemosaic.ImageMosaicFormat.getReader(
> ImageMosaicFormat.java:502)
> at org.geotools.gce.imagemosaic.ImageMosaicFormat.getReader(
> ImageMosaicFormat.java:97)
> at org.geoserver.catalog.ResourcePool.getGridCoverageReader(
> ResourcePool.java:1493)
> at org.geoserver.catalog.ResourcePool.getGridCoverageReader(
> ResourcePool.java:1423)
> at org.geoserver.catalog.impl.CoverageStoreInfoImpl.
> getGridCoverageReader(CoverageStoreInfoImpl.java:59)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke(
> NativeMethodAccessorImpl.java:62)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(
> DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:498)
> at org.geoserver.catalog.impl.ModificationProxy.invoke(
> ModificationProxy.java:147)
> at com.sun.proxy.$Proxy13.getGridCoverageReader(Unknown Source)
> at org.geoserver.web.data.layer.NewLayerPageProvider.
> getItemsInternal(NewLayerPageProvider.java:95)
> at org.geoserver.web.data.layer.NewLayerPageProvider.getItems(
> NewLayerPageProvider.java:61)
> at org.geoserver.web.wicket.GeoServerDataProvider.fullSize(
> GeoServerDataProvider.java:243)
> at org.geoserver.web.wicket.GeoServerTablePanel$
> PagerDelegate.updateMatched(GeoServerTablePanel.java:583)
> at org.geoserver.web.wicket.GeoServerTablePanel$
> PagerDelegate.<init>(GeoServerTablePanel.java:576)
> at org.geoserver.web.wicket.GeoServerTablePanel.<init>(
> GeoServerTablePanel.java:176)
> at org.geoserver.web.wicket.GeoServerTablePanel.<init>(
> GeoServerTablePanel.java:97)
> at org.geoserver.web.data.layer.NewLayerPage$1.<init>(
> NewLayerPage.java:105)
> at org.geoserver.web.data.layer.NewLayerPage.<init>(
> NewLayerPage.java:105)
> at org.geoserver.web.data.store.CoverageStoreNewPage.
> onSuccessfulSave(CoverageStoreNewPage.java:86)
> at org.geoserver.web.data.store.CoverageStoreNewPage.onSave(
> CoverageStoreNewPage.java:74)
> at org.geoserver.web.data.store.AbstractCoverageStorePage$1.
> onSubmit(AbstractCoverageStorePage.java:122)
> at org.apache.wicket.ajax.markup.html.form.AjaxSubmitLink$1.
> onSubmit(AjaxSubmitLink.java:110)
> at org.apache.wicket.ajax.form.AjaxFormSubmitBehavior$
> AjaxFormSubmitter.onSubmit(AjaxFormSubmitBehavior.java:215)
> at org.apache.wicket.markup.html.form.Form.delegateSubmit(Form.
> java:1307)
> at org.apache.wicket.markup.html.form.Form.process(Form.java:974)
> at org.apache.wicket.markup.html.form.Form.onFormSubmitted(
> Form.java:795)
> at org.apache.wicket.ajax.form.AjaxFormSubmitBehavior.onEvent(
> AjaxFormSubmitBehavior.java:171)
> at org.apache.wicket.ajax.AjaxEventBehavior.respond(
> AjaxEventBehavior.java:155)
> at org.apache.wicket.ajax.AbstractDefaultAjaxBehavior.onRequest(
> AbstractDefaultAjaxBehavior.java:588)
> at sun.reflect.GeneratedMethodAccessor210.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(
> DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:498)
> at org.apache.wicket.RequestListenerInterface.internalInvoke(
> RequestListenerInterface.java:258)
> at org.apache.wicket.RequestListenerInterface.invoke(
> RequestListenerInterface.java:241)
> at org.apache.wicket.core.request.handler.
> ListenerInterfaceRequestHandler.invokeListener(
> ListenerInterfaceRequestHandler.java:248)
> at org.apache.wicket.core.request.handler.
> ListenerInterfaceRequestHandler.respond(ListenerInterfaceRequestHandle
> r.java:234)
> at org.apache.wicket.request.cycle.RequestCycle$
> HandlerExecutor.respond(RequestCycle.java:865)
> at org.apache.wicket.request.RequestHandlerStack.execute(
> RequestHandlerStack.java:64)
> at org.apache.wicket.request.cycle.RequestCycle.execute(
> RequestCycle.java:265)
> at org.apache.wicket.request.cycle.RequestCycle.
> processRequest(RequestCycle.java:222)
> at org.apache.wicket.request.cycle.RequestCycle.
> processRequestAndDetach(RequestCycle.java:293)
> at org.apache.wicket.protocol.http.WicketFilter.
> processRequestCycle(WicketFilter.java:261)
> at org.apache.wicket.protocol.http.WicketFilter.
> processRequest(WicketFilter.java:203)
> at org.apache.wicket.protocol.http.WicketServlet.doPost(
> WicketServlet.java:159)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
> at org.springframework.web.servlet.mvc.ServletWrappingController.
> handleRequestInternal(ServletWrappingController.java:158)
> at org.springframework.web.servlet.mvc.AbstractController.
> handleRequest(AbstractController.java:147)
> at org.springframework.web.servlet.mvc.
> SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter
> .java:50)
> at org.springframework.web.servlet.DispatcherServlet.
> doDispatch(DispatcherServlet.java:959)
> at org.springframework.web.servlet.DispatcherServlet.
> doService(DispatcherServlet.java:893)
> at org.springframework.web.servlet.FrameworkServlet.
> processRequest(FrameworkServlet.java:968)
> at org.springframework.web.servlet.FrameworkServlet.
> doPost(FrameworkServlet.java:870)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
> at org.springframework.web.servlet.FrameworkServlet.
> service(FrameworkServlet.java:844)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
> at org.apache.catalina.core.ApplicationFilterChain.
> internalDoFilter(ApplicationFilterChain.java:303)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(
> ApplicationFilterChain.java:208)
> at org.apache.tomcat.websocket.server.WsFilter.doFilter(
> WsFilter.java:52)
> at org.apache.catalina.core.ApplicationFilterChain.
> internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(
> ApplicationFilterChain.java:208)
> at org.geoserver.filters.ThreadLocalsCleanupFilter.doFilter(
> ThreadLocalsCleanupFilter.java:28)
> at org.apache.catalina.core.ApplicationFilterChain.
> internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(
> ApplicationFilterChain.java:208)
> at org.geoserver.filters.SpringDelegatingFilter$Chain.doFilter(
> SpringDelegatingFilter.java:75)
> at org.geoserver.wms.animate.AnimatorFilter.doFilter(
> AnimatorFilter.java:71)
> at org.geoserver.filters.SpringDelegatingFilter$Chain.doFilter(
> SpringDelegatingFilter.java:71)
> at org.geoserver.flow.controller.IpBlacklistFilter.doFilter(
> IpBlacklistFilter.java:94)
> at org.geoserver.filters.SpringDelegatingFilter$Chain.doFilter(
> SpringDelegatingFilter.java:71)
> at org.geoserver.flow.ControlFlowCallback.doFilter(
> ControlFlowCallback.java:252)
> at org.geoserver.filters.SpringDelegatingFilter$Chain.doFilter(
> SpringDelegatingFilter.java:71)
> at org.geoserver.filters.SpringDelegatingFilter.doFilter(
> SpringDelegatingFilter.java:46)
> at org.apache.catalina.core.ApplicationFilterChain.
> internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(
> ApplicationFilterChain.java:208)
> at org.geoserver.platform.AdvancedDispatchFilter.doFilter(
> AdvancedDispatchFilter.java:50)
> at org.apache.catalina.core.ApplicationFilterChain.
> internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(
> ApplicationFilterChain.java:208)
> at org.springframework.security.web.FilterChainProxy$
> VirtualFilterChain.doFilter(FilterChainProxy.java:316)
> at org.geoserver.security.filter.GeoServerCompositeFilter$
> NestedFilterChain.doFilter(GeoServerCompositeFilter.java:69)
> at org.springframework.security.web.access.intercept.
> FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:126)
> at org.springframework.security.web.access.intercept.
> FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:90)
> at org.geoserver.security.filter.GeoServerCompositeFilter$
> NestedFilterChain.doFilter(GeoServerCompositeFilter.java:73)
> at org.geoserver.security.filter.GeoServerCompositeFilter.
> doFilter(GeoServerCompositeFilter.java:92)
> at org.springframework.security.web.FilterChainProxy$
> VirtualFilterChain.doFilter(FilterChainProxy.java:330)
> at org.geoserver.security.filter.GeoServerCompositeFilter$
> NestedFilterChain.doFilter(GeoServerCompositeFilter.java:69)
> at org.springframework.security.web.access.
> ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:114)
> at org.geoserver.security.filter.GeoServerCompositeFilter$
> NestedFilterChain.doFilter(GeoServerCompositeFilter.java:73)
> at org.geoserver.security.filter.GeoServerCompositeFilter.
> doFilter(GeoServerCompositeFilter.java:92)
> at org.springframework.security.web.FilterChainProxy$
> VirtualFilterChain.doFilter(FilterChainProxy.java:330)
> at org.geoserver.security.filter.GeoServerAnonymousAuthenticati
> onFilter.doFilter(GeoServerAnonymousAuthenticationFilter.java:54)
> at org.springframework.security.web.FilterChainProxy$
> VirtualFilterChain.doFilter(FilterChainProxy.java:330)
> at org.geoserver.security.filter.GeoServerCompositeFilter$
> NestedFilterChain.doFilter(GeoServerCompositeFilter.java:69)
> at org.springframework.security.web.authentication.
> AbstractAuthenticationProcessingFilter.doFilter(
> AbstractAuthenticationProcessingFilter.java:205)
> at org.geoserver.security.filter.GeoServerCompositeFilter$
> NestedFilterChain.doFilter(GeoServerCompositeFilter.java:73)
> at org.geoserver.security.filter.GeoServerCompositeFilter.
> doFilter(GeoServerCompositeFilter.java:92)
> at org.geoserver.security.filter.GeoServerUserNamePasswordAuthe
> nticationFilter.doFilter(GeoServerUserNamePasswordAuthe
> nticationFilter.java:116)
> at org.springframework.security.web.FilterChainProxy$
> VirtualFilterChain.doFilter(FilterChainProxy.java:330)
> at org.geoserver.security.filter.GeoServerCompositeFilter$
> NestedFilterChain.doFilter(GeoServerCompositeFilter.java:69)
> at org.springframework.security.web.authentication.rememberme.
> RememberMeAuthenticationFilter.doFilter(RememberMeAuthenticationFilter
> .java:157)
> at org.geoserver.security.filter.GeoServerCompositeFilter$
> NestedFilterChain.doFilter(GeoServerCompositeFilter.java:73)
> at org.geoserver.security.filter.GeoServerCompositeFilter.
> doFilter(GeoServerCompositeFilter.java:92)
> at org.springframework.security.web.FilterChainProxy$
> VirtualFilterChain.doFilter(FilterChainProxy.java:330)
> at org.geoserver.security.filter.GeoServerCompositeFilter$
> NestedFilterChain.doFilter(GeoServerCompositeFilter.java:69)
> at org.springframework.security.web.context.
> SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilt
> er.java:91)
> at org.geoserver.security.filter.GeoServerSecurityContextPersis
> tenceFilter$1.doFilter(GeoServerSecurityContextPersistenceFilter.java:53)
> at org.geoserver.security.filter.GeoServerCompositeFilter$
> NestedFilterChain.doFilter(GeoServerCompositeFilter.java:73)
> at org.geoserver.security.filter.GeoServerCompositeFilter.
> doFilter(GeoServerCompositeFilter.java:92)
> at org.springframework.security.web.FilterChainProxy$
> VirtualFilterChain.doFilter(FilterChainProxy.java:330)
> at org.springframework.security.web.FilterChainProxy.
> doFilterInternal(FilterChainProxy.java:213)
> at org.springframework.security.web.FilterChainProxy.doFilter(
> FilterChainProxy.java:176)
> at org.geoserver.security.GeoServerSecurityFilterChainPr
> oxy.doFilter(GeoServerSecurityFilterChainProxy.java:152)
> at org.springframework.web.filter.DelegatingFilterProxy.
> invokeDelegate(DelegatingFilterProxy.java:346)
> at org.springframework.web.filter.DelegatingFilterProxy.doFilter(
> DelegatingFilterProxy.java:262)
> at org.apache.catalina.core.ApplicationFilterChain.
> internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(
> ApplicationFilterChain.java:208)
> at org.geoserver.filters.LoggingFilter.doFilter(
> LoggingFilter.java:87)
> at org.apache.catalina.core.ApplicationFilterChain.
> internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(
> ApplicationFilterChain.java:208)
> at org.geoserver.filters.GZIPFilter.doFilter(GZIPFilter.java:42)
> at org.apache.catalina.core.ApplicationFilterChain.
> internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(
> ApplicationFilterChain.java:208)
> at org.geoserver.filters.SessionDebugFilter.doFilter(
> SessionDebugFilter.java:48)
> at org.apache.catalina.core.ApplicationFilterChain.
> internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(
> ApplicationFilterChain.java:208)
> at org.geoserver.filters.FlushSafeFilter.doFilter(
> FlushSafeFilter.java:44)
> at org.apache.catalina.core.ApplicationFilterChain.
> internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(
> ApplicationFilterChain.java:208)
> at org.springframework.web.filter.CharacterEncodingFilter.
> doFilterInternal(CharacterEncodingFilter.java:121)
> at org.springframework.web.filter.OncePerRequestFilter.
> doFilter(OncePerRequestFilter.java:107)
> at org.apache.catalina.core.ApplicationFilterChain.
> internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(
> ApplicationFilterChain.java:208)
> at org.apache.catalina.core.StandardWrapperValve.invoke(
> StandardWrapperValve.java:220)
> at org.apache.catalina.core.StandardContextValve.invoke(
> StandardContextValve.java:122)
> at org.apache.catalina.authenticator.AuthenticatorBase.invoke(
> AuthenticatorBase.java:505)
> at org.apache.catalina.core.StandardHostValve.invoke(
> StandardHostValve.java:169)
> at org.apache.catalina.valves.ErrorReportValve.invoke(
> ErrorReportValve.java:103)
> at org.apache.catalina.valves.AccessLogValve.invoke(
> AccessLogValve.java:956)
> at org.apache.catalina.core.StandardEngineValve.invoke(
> StandardEngineValve.java:116)
> at org.apache.catalina.connector.CoyoteAdapter.service(
> CoyoteAdapter.java:436)
> at org.apache.coyote.ajp.AjpAprProcessor.process(
> AjpAprProcessor.java:188)
> at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.
> process(AbstractProtocol.java:625)
> at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.
> doRun(AprEndpoint.java:2517)
> at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.
> run(AprEndpoint.java:2506)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
> at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(
> TaskThread.java:61)
> at java.lang.Thread.run(Thread.java:745)
>
> ------------------------------------------------------------
> ------------------
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--
==
GeoServer Professional Services from the experts! Visit
http://goo.gl/it488V for more information.
==
Ing. Daniele Romagnoli
Senior Software Engineer
GeoSolutions S.A.S.
Via di Montramito 3/A
55054 Massarosa (LU)
Italy
phone: +39 0584 962313
fax: +39 0584 1660272
http://www.geo-solutions.it
http://twitter.com/geosolutions_it
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