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Unidata / thredds

THREDDS Data Server v4.6
https://www.unidata.ucar.edu/software/tds/v4.6/index.html
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dap4 test failing on travis #895

Open lesserwhirls opened 7 years ago

lesserwhirls commented 7 years ago

See http://unidata-tds.s3.amazonaws.com/Travis/5.0.0-4483/4483.1/classes/dap4.test.TestServlet.html

dap4.core.util.DapException: CDMDSP: cannot process: /home/travis/build/Unidata/thredds/dap4/d4tests/src/test/data/resources/testfiles/test_atomic_array.nc
    at dap4.cdm.dsp.CDMDSP.open(CDMDSP.java:142)
    at dap4.cdm.dsp.CDMDSP.open(CDMDSP.java:35)
    at dap4.servlet.DapCache.open(DapCache.java:94)
    at dap4.servlet.DapController.doDMR(DapController.java:307)
    at dap4.servlet.DapController.handleRequest(DapController.java:230)
    at thredds.server.dap4.Dap4Controller.handleRequest(Dap4Controller.java:73)
    at sun.reflect.GeneratedMethodAccessor23.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205)
    at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:133)
    at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:97)
    at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:827)
    at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:738)
    at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85)
    at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:963)
    at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:897)
    at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970)
    at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:861)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:687)
    at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:846)
    at org.springframework.test.web.servlet.TestDispatcherServlet.service(TestDispatcherServlet.java:65)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
    at org.springframework.mock.web.MockFilterChain$ServletFilterProxy.doFilter(MockFilterChain.java:167)
    at org.springframework.mock.web.MockFilterChain.doFilter(MockFilterChain.java:134)
    at org.springframework.test.web.servlet.MockMvc.perform(MockMvc.java:155)
    at dap4.test.DapTestCommon.perform(DapTestCommon.java:529)
    at dap4.test.TestServlet.dodmr(TestServlet.java:225)
    at dap4.test.TestServlet.doOneTest(TestServlet.java:207)
    at dap4.test.TestServlet.testServlet(TestServlet.java:188)
    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.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
    at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
    at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
    at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
    at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
    at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
    at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
    at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
    at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
    at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
    at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
    at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
    at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecuter.runTestClass(JUnitTestClassExecuter.java:114)
    at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecuter.execute(JUnitTestClassExecuter.java:57)
    at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassProcessor.processTestClass(JUnitTestClassProcessor.java:66)
    at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.processTestClass(SuiteTestClassProcessor.java:51)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
    at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
    at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32)
    at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93)
    at com.sun.proxy.$Proxy3.processTestClass(Unknown Source)
    at org.gradle.api.internal.tasks.testing.worker.TestWorker.processTestClass(TestWorker.java:109)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
    at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
    at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:147)
    at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:129)
    at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404)
    at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
    at org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:46)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: dap4.core.util.DapException: java.io.IOException: java.io.IOException: -101: NetCDF: HDF error
    at dap4.cdm.dsp.CDMDSP.createNetcdfFile(CDMDSP.java:1109)
    at dap4.cdm.dsp.CDMDSP.open(CDMDSP.java:138)
    ... 75 more
Caused by: java.io.IOException: java.io.IOException: -101: NetCDF: HDF error
    at ucar.nc2.NetcdfFile.open(NetcdfFile.java:512)
    at dap4.cdm.dsp.CDMDSP.createNetcdfFile(CDMDSP.java:1100)
    ... 76 more
Caused by: java.io.IOException: -101: NetCDF: HDF error
    at ucar.nc2.jni.netcdf.Nc4Iosp._open(Nc4Iosp.java:315)
    at ucar.nc2.jni.netcdf.Nc4Iosp.open(Nc4Iosp.java:292)
    at ucar.nc2.NetcdfFile.<init>(NetcdfFile.java:1649)
    at ucar.nc2.NetcdfFile.open(NetcdfFile.java:919)
    at ucar.nc2.NetcdfFile.open(NetcdfFile.java:509)
    ... 77 more
Jul 19, 2017 4:47:16 PM ucar.unidata.util.test.UnitTestCommon$STDIO printf
INFO: DMR Comparison

>>>> EMPTY TEST RESULT
DennisHeimbigner commented 7 years ago

This test is also failing in the same way on Jenkins. It works on my machine under intellij, so my speculation is that we need to upgrade the netcdf-c jna installation on travis and jenkins. We probably need to enable logging support for netcdf-4 when it is installed.

lesserwhirls commented 7 years ago

We are using 4.1.1, but could probably bump to 4.1.1.1. Or, should we wait until the next release of netCDF-C?

lesserwhirls commented 7 years ago

...my PR just passed on travis without issue...

https://travis-ci.org/lesserwhirls/thredds/builds/255838524?utm_source=email&utm_medium=notification

lesserwhirls commented 7 years ago

wait...it failed on the Unidata travis run

https://travis-ci.org/Unidata/thredds/builds/255838712?utm_source=github_status&utm_medium=notification

lesserwhirls commented 7 years ago

Ok, one ran on Ubuntu precise (Passed), the other ran on Trusty (failed). See Unidata/thredds#898. I just made a PR to pin our travis version to precise to keep thing going for now.

DennisHeimbigner commented 7 years ago

This is not good when the underlying OS [version] is involved in the failure.

lesserwhirls commented 7 years ago

I think it's because some of the os libraries that netCDF-C is linked against changed with the OS bump.

cwardgar commented 7 years ago

I can spin up a Vagrant box and quickly generate the new binaries. But weren't we waiting on a new version of netcdf-c? And didn't we want to build with certain flags enabled? Can I get a summary of all that?

lesserwhirls commented 7 years ago

Yeah, I thought we were waiting for the next release, so let's hold off until that happens. Travis is working again now that the version of Ubuntu is pinned. @DennisHeimbigner mentioned building with logging enabled, which would be the --enable-logging flag. Except for the CPPFLAGS and LDFLAGS in-line env variables, I don't think we need to use any other special flags on our test machines (no more --enable-threadsafe on the HDF build). Although, on our production machines, I turn off dap simply because it's not needed, so that one would be --disable-dap.

So, I would say, for netCDF-C specifically:

Everything else should be ok with vanilla or whatever the OS provides.

@DennisHeimbigner - where do the netCDF-C generated logs get dumped? It would be good to include those in the S3 Store (with a link in the testing output) so we can examine them after the tests run, much like we do on travis currently for output from our test suite.

DennisHeimbigner commented 7 years ago

That set of flags looks good. By default, the log output gets sent to stdout (or maybe stderr). However nothing is generated unless logging is turned on. The reason I would like it enabled is so we can turn it on as needed to help debug problems like the one in this issue. If it turns out that, for some reason, that log output is causing problems, then we can disable it again.