Hi folks,
I’ve just done a fresh install of spark-2.0.2 and hail from today’s git. On executing the Hail tests, all but two passed: LinearMixedRegressionSuite.lmmLargeExampleTest and eigSymDSuite.eigSymTest. On review of both, /hail/build/reports/tests/classes/is.hail.methods.LinearMixedRegressionSuite.html
and /hail/build/reports/tests/classes/is.hail.stats.eigSymDSuite.html
show the same (verbatim):
breeze.linalg.MatrixNotSymmetricException: Matrix is not symmetric
at breeze.linalg.package$$anonfun$requireSymmetricMatrix$1$$anonfun$apply$mcVI$sp$1.apply$mcVI$sp(package.scala:122)
at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:160)
at breeze.linalg.package$$anonfun$requireSymmetricMatrix$1.apply$mcVI$sp(package.scala:120)
at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:160)
at breeze.linalg.package$.requireSymmetricMatrix(package.scala:120)
at breeze.linalg.cholesky$ImplCholesky_DM$.apply(cholesky.scala:25)
at breeze.linalg.cholesky$ImplCholesky_DM$.apply(cholesky.scala:16)
at breeze.generic.UFunc$class.apply(UFunc.scala:48)
at breeze.linalg.cholesky$.apply(cholesky.scala:15)
at is.hail.methods.LinearMixedRegressionSuite.lmmLargeExampleTest(LinearMixedRegressionSuite.scala:200)
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:497)
at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
at org.testng.internal.Invoker.invokeMethod(Invoker.java:696)
at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:882)
at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1189)
at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
at org.testng.TestRunner.privateRun(TestRunner.java:767)
at org.testng.TestRunner.run(TestRunner.java:617)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:348)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:343)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:305)
at org.testng.SuiteRunner.run(SuiteRunner.java:254)
at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
at org.testng.TestNG.runSuitesSequentially(TestNG.java:1224)
at org.testng.TestNG.runSuitesLocally(TestNG.java:1149)
at org.testng.TestNG.run(TestNG.java:1057)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:133)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:83)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61)
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:497)
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$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93)
at com.sun.proxy.$Proxy2.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:120)
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:497)
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.MessageHub$Handler.run(MessageHub.java:377)
at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:54)
at org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:40)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)```
Any troubleshooting tips?
Cheers!
CanWood