{"action":"created","issue":{"url":"https://api.github.com/repos/Unidata/thredds/issues/518","repository_url":"https://api.github.com/repos/Unidata/thredds","labels_url":"https://api.github.com/repos/Unidata/thredds/issues/518/labels{/name}","comments_url":"https://api.github.com/repos/Unidata/thredds/issues/518/comments","events_url":"https://api.github.com/repos/Unidata/thredds/issues/518/events","html_url":"https://github.com/Unidata/thredds/issues/518","id":146413927,"number":518,"title":"HDF5 DataBTree Issue","user":{"login":"dblodgett-usgs","id":1492803,"avatar_url":"https://avatars.githubusercontent.com/u/1492803?v=3","gravatar_id":"","url":"https://api.github.com/users/dblodgett-usgs","html_url":"https://github.com/dblodgett-usgs","followers_url":"https://api.github.com/users/dblodgett-usgs/followers","following_url":"https://api.github.com/users/dblodgett-usgs/following{/other_user}","gists_url":"https://api.github.com/users/dblodgett-usgs/gists{/gist_id}","starred_url":"https://api.github.com/users/dblodgett-usgs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dblodgett-usgs/subscriptions","organizations_url":"https://api.github.com/users/dblodgett-usgs/orgs","repos_url":"https://api.github.com/users/dblodgett-usgs/repos","events_url":"https://api.github.com/users/dblodgett-usgs/events{/privacy}","received_events_url":"https://api.github.com/users/dblodgett-usgs/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/Unidata/thredds/labels/Area:%20HDF","name":"Area: HDF","color":"c5def5"},{"url":"https://api.github.com/repos/Unidata/thredds/labels/Note:%20User%20Visible%20Change","name":"Note: User Visible Change","color":"d4c5f9"},{"url":"https://api.github.com/repos/Unidata/thredds/labels/Type:%20Bug","name":"Type: Bug","color":"e99695"}],"state":"closed","locked":false,"assignee":{"login":"JohnLCaron","id":613568,"avatar_url":"https://avatars.githubusercontent.com/u/613568?v=3","gravatar_id":"","url":"https://api.github.com/users/JohnLCaron","html_url":"https://github.com/JohnLCaron","followers_url":"https://api.github.com/users/JohnLCaron/followers","following_url":"https://api.github.com/users/JohnLCaron/following{/other_user}","gists_url":"https://api.github.com/users/JohnLCaron/gists{/gist_id}","starred_url":"https://api.github.com/users/JohnLCaron/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JohnLCaron/subscriptions","organizations_url":"https://api.github.com/users/JohnLCaron/orgs","repos_url":"https://api.github.com/users/JohnLCaron/repos","events_url":"https://api.github.com/users/JohnLCaron/events{/privacy}","received_events_url":"https://api.github.com/users/JohnLCaron/received_events","type":"User","site_admin":false},"assignees":[{"login":"JohnLCaron","id":613568,"avatar_url":"https://avatars.githubusercontent.com/u/613568?v=3","gravatar_id":"","url":"https://api.github.com/users/JohnLCaron","html_url":"https://github.com/JohnLCaron","followers_url":"https://api.github.com/users/JohnLCaron/followers","following_url":"https://api.github.com/users/JohnLCaron/following{/other_user}","gists_url":"https://api.github.com/users/JohnLCaron/gists{/gist_id}","starred_url":"https://api.github.com/users/JohnLCaron/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JohnLCaron/subscriptions","organizations_url":"https://api.github.com/users/JohnLCaron/orgs","repos_url":"https://api.github.com/users/JohnLCaron/repos","events_url":"https://api.github.com/users/JohnLCaron/events{/privacy}","received_events_url":"https://api.github.com/users/JohnLCaron/received_events","type":"User","site_admin":false}],"milestone":null,"comments":43,"created_at":"2016-04-06T19:46:32Z","updated_at":"2016-08-05T01:17:12Z","closed_at":"2016-08-04T23:30:54Z","body":"This issue supercedes #501. \r\n\r\nI have found that I can reproduce the stack trace below with a reproducible workflow.\r\n\r\n1. Request data from an ncml union aggregation [1] of OPeNDAP source data and a local netcdf file.\r\n2. Request data from a data source that has 2-D coordinate axes. [2], [3].\r\n\r\nAfter some period of time (tens of minutes), this issue goes away for 2-d coordinate axis datasets that _have not_ been accessed producing the error. If the offending aggregation is accessed then the working dataset is accessed, it brakes like the others. That is, the databtree error is being cached in some way.\r\n\r\n[1] http://cida-test.er.usgs.gov/thredds/dodsC/stageiv/ncml/stageivRT.ncml.html\r\n    Grib collection: http://cida-test.er.usgs.gov/thredds/catalog/stageiv/01hRT/catalog.html\r\n    .ncml union can be downloaded here: http://cida-test.er.usgs.gov/thredds/catalog/stageiv/ncml/catalog.html\r\n[2] http://cida-test.er.usgs.gov/thredds/dodsC/UpperDeschutes.html\r\n    If the data behind this is needed, it is visible here: http://cida-test.er.usgs.gov/thredds/catalog/stageiv/symlinked_files/deschutes/catalog.html\r\n[3] http://cida-test.er.usgs.gov/thredds/dodsC/stageiv/symlinked_files/stageiv_archive.nc.html\r\n    This is a single NetCDF4 File here: http://cida-test.er.usgs.gov/thredds/catalog/stageiv/symlinked_files/catalog.html?dataset=examples/symlinked_files/stageiv_archive.nc\r\n\r\n```\r\n2016-04-06T13:35:44.315 -0500 [    408330][      44] ERROR - thredds.server.opendap.OpendapServlet - path2= /ncep_stageiv.ascii\r\njava.lang.NullPointerException\r\n    at ucar.unidata.io.RandomAccessFile.read_(RandomAccessFile.java:760) ~[cdm-4.6.5.jar:4.6.5]\r\n    at ucar.unidata.io.RandomAccessFile.readBuffer(RandomAccessFile.java:520) ~[cdm-4.6.5.jar:4.6.5]\r\n    at ucar.unidata.io.RandomAccessFile.seek(RandomAccessFile.java:508) ~[cdm-4.6.5.jar:4.6.5]\r\n    at ucar.nc2.iosp.hdf5.DataBTree$Node.<init>(DataBTree.java:170) ~[cdm-4.6.5.jar:4.6.5]\r\n    at ucar.nc2.iosp.hdf5.DataBTree$DataChunkIterator.<init>(DataBTree.java:135) ~[cdm-4.6.5.jar:4.6.5]\r\n    at ucar.nc2.iosp.hdf5.DataBTree.getDataChunkIteratorFilter(DataBTree.java:61) ~[cdm-4.6.5.jar:4.6.5]\r\n    at ucar.nc2.iosp.hdf5.H5tiledLayoutBB.<init>(H5tiledLayoutBB.java:110) ~[cdm-4.6.5.jar:4.6.5]\r\n    at ucar.nc2.iosp.hdf5.H5iosp.readData(H5iosp.java:162) ~[cdm-4.6.5.jar:4.6.5]\r\n    at ucar.nc2.iosp.hdf5.H5iosp.readData(H5iosp.java:141) ~[cdm-4.6.5.jar:4.6.5]\r\n    at ucar.nc2.NetcdfFile.readData(NetcdfFile.java:2009) ~[cdm-4.6.5.jar:4.6.5]\r\n    at ucar.nc2.Variable.reallyRead(Variable.java:913) ~[cdm-4.6.5.jar:4.6.5]\r\n    at ucar.nc2.Variable._read(Variable.java:898) ~[cdm-4.6.5.jar:4.6.5]\r\n    at ucar.nc2.Variable.read(Variable.java:709) ~[cdm-4.6.5.jar:4.6.5]\r\n    at ucar.nc2.dataset.VariableDS.reallyRead(VariableDS.java:557) ~[cdm-4.6.5.jar:4.6.5]\r\n    at ucar.nc2.dataset.VariableDS._read(VariableDS.java:537) ~[cdm-4.6.5.jar:4.6.5]\r\n    at ucar.nc2.Variable.read(Variable.java:709) ~[cdm-4.6.5.jar:4.6.5]\r\n    at ucar.nc2.Variable.read(Variable.java:683) ~[cdm-4.6.5.jar:4.6.5]\r\n    at thredds.server.opendap.NcSDArray.read(NcSDArray.java:115) ~[NcSDArray.class:?]\r\n    at opendap.servlet.AsciiWriter.writeAsc(AsciiWriter.java:107) ~[opendap-4.6.5.jar:4.6.5]\r\n    at opendap.servlet.AsciiWriter.toASCII(AsciiWriter.java:68) ~[opendap-4.6.5.jar:4.6.5]\r\n    at thredds.server.opendap.OpendapServlet.doGetASC(OpendapServlet.java:315) ~[OpendapServlet.class:?]\r\n    at thredds.server.opendap.OpendapServlet.doGet(OpendapServlet.java:220) [OpendapServlet.class:?]\r\n    at javax.servlet.http.HttpServlet.service(HttpServlet.java:621) [servlet-api.jar:?]\r\n    at javax.servlet.http.HttpServlet.service(HttpServlet.java:728) [servlet-api.jar:?]\r\n    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305) [catalina.jar:7.0.39]\r\n    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) [catalina.jar:7.0.39]\r\n    at thredds.servlet.filter.CookieFilter.doFilter(CookieFilter.java:55) [CookieFilter.class:?]\r\n    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) [catalina.jar:7.0.39]\r\n    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) [catalina.jar:7.0.39]\r\n    at thredds.servlet.filter.RequestQueryFilter.doFilter(RequestQueryFilter.java:118) [RequestQueryFilter.class:?]\r\n    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) [catalina.jar:7.0.39]\r\n    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) [catalina.jar:7.0.39]\r\n    at thredds.servlet.filter.RequestCORSFilter.doFilterInternal(RequestCORSFilter.java:49) [RequestCORSFilter.class:?]\r\n    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]\r\n    at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344) [spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]\r\n    at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261) [spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]\r\n    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) [catalina.jar:7.0.39]\r\n    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) [catalina.jar:7.0.39]\r\n    at thredds.servlet.filter.RequestPathFilter.doFilter(RequestPathFilter.java:94) [RequestPathFilter.class:?]\r\n    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) [catalina.jar:7.0.39]\r\n    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) [catalina.jar:7.0.39]\r\n    at thredds.server.RequestBracketingLogMessageFilter.doFilter(RequestBracketingLogMessageFilter.java:81) [RequestBracketingLogMessageFilter.class:?]\r\n    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) [catalina.jar:7.0.39]\r\n    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) [catalina.jar:7.0.39]\r\n    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222) [catalina.jar:7.0.39]\r\n    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123) [catalina.jar:7.0.39]\r\n    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472) [catalina.jar:7.0.39]\r\n    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171) [catalina.jar:7.0.39]\r\n    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99) [catalina.jar:7.0.39]\r\n    at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:947) [catalina.jar:7.0.39]\r\n    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118) [catalina.jar:7.0.39]\r\n    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408) [catalina.jar:7.0.39]\r\n    at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1009) [tomcat-coyote.jar:7.0.39]\r\n    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:589) [tomcat-coyote.jar:7.0.39]\r\n    at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310) [tomcat-coyote.jar:7.0.39]\r\n    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_45]\r\n    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_45]\r\n    at java.lang.Thread.run(Thread.java:745) [?:1.8.0_45]\r\n```"},"comment":{"url":"https://api.github.com/repos/Unidata/thredds/issues/comments/237731278","html_url":"https://github.com/Unidata/thredds/issues/518#issuecomment-237731278","issue_url":"https://api.github.com/repos/Unidata/thredds/issues/518","id":237731278,"user":{"login":"dblodgett-usgs","id":1492803,"avatar_url":"https://avatars.githubusercontent.com/u/1492803?v=3","gravatar_id":"","url":"https://api.github.com/users/dblodgett-usgs","html_url":"https://github.com/dblodgett-usgs","followers_url":"https://api.github.com/users/dblodgett-usgs/followers","following_url":"https://api.github.com/users/dblodgett-usgs/following{/other_user}","gists_url":"https://api.github.com/users/dblodgett-usgs/gists{/gist_id}","starred_url":"https://api.github.com/users/dblodgett-usgs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dblodgett-usgs/subscriptions","organizations_url":"https://api.github.com/users/dblodgett-usgs/orgs","repos_url":"https://api.github.com/users/dblodgett-usgs/repos","events_url":"https://api.github.com/users/dblodgett-usgs/events{/privacy}","received_events_url":"https://api.github.com/users/dblodgett-usgs/received_events","type":"User","site_admin":false},"created_at":"2016-08-05T01:17:12Z","updated_at":"2016-08-05T01:17:12Z","body":"Will give it a whirl. Thanks for digging into this @cwardgar and @JohnLCaron !!!"}}
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