Standard error
java.lang.UnsatisfiedLinkError: /tmp/libjhdf5.2.11.018431675893636658877.so: /tmp/libjhdf5.2.11.018431675893636658877.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform)
at java.base/jdk.internal.loader.NativeLibraries.load(Native Method)
at java.base/jdk.internal.loader.NativeLibraries$NativeLibraryImpl.open(NativeLibraries.java:388)
at java.base/jdk.internal.loader.NativeLibraries.loadLibrary(NativeLibraries.java:232)
at java.base/jdk.internal.loader.NativeLibraries.loadLibrary(NativeLibraries.java:174)
at java.base/java.lang.ClassLoader.loadLibrary(ClassLoader.java:2389)
at java.base/java.lang.Runtime.load0(Runtime.java:755)
at java.base/java.lang.System.load(System.java:1953)
at ncsa.hdf.hdf5lib.H5.loadH5Lib(H5.java:290)
at ncsa.hdf.hdf5lib.H5.<clinit>(H5.java:254)
at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87)
at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43)
at org.broadinstitute.hellbender.utils.hdf5.HDF5LibraryUnitTest.testIsSupported(HDF5LibraryUnitTest.java:34)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethodConsideringTimeout(MethodInvocationHelper.java:69)
at org.testng.internal.invokers.ConfigInvoker.invokeConfigurationMethod(ConfigInvoker.java:361)
at org.testng.internal.invokers.ConfigInvoker.invokeConfigurations(ConfigInvoker.java:296)
at org.testng.internal.invokers.TestMethodWorker.invokeBeforeClassMethods(TestMethodWorker.java:180)
at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:122)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
at org.testng.TestRunner.privateRun(TestRunner.java:829)
at org.testng.TestRunner.run(TestRunner.java:602)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
at org.testng.SuiteRunner.run(SuiteRunner.java:330)
at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
at org.testng.TestNG.runSuites(TestNG.java:1099)
at org.testng.TestNG.run(TestNG.java:1067)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
java.lang.UnsatisfiedLinkError: no jhdf5 in java.library.path: /usr/java/packages/lib:/usr/lib64:/lib64:/lib:/usr/lib
at java.base/java.lang.ClassLoader.loadLibrary(ClassLoader.java:2429)
at java.base/java.lang.Runtime.loadLibrary0(Runtime.java:818)
at java.base/java.lang.System.loadLibrary(System.java:1989)
at ncsa.hdf.hdf5lib.H5.loadH5Lib(H5.java:316)
at ncsa.hdf.hdf5lib.H5.<clinit>(H5.java:254)
at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87)
at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43)
at org.broadinstitute.hellbender.utils.hdf5.HDF5LibraryUnitTest.testIsSupported(HDF5LibraryUnitTest.java:34)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethodConsideringTimeout(MethodInvocationHelper.java:69)
at org.testng.internal.invokers.ConfigInvoker.invokeConfigurationMethod(ConfigInvoker.java:361)
at org.testng.internal.invokers.ConfigInvoker.invokeConfigurations(ConfigInvoker.java:296)
at org.testng.internal.invokers.TestMethodWorker.invokeBeforeClassMethods(TestMethodWorker.java:180)
at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:122)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
at org.testng.TestRunner.privateRun(TestRunner.java:829)
at org.testng.TestRunner.run(TestRunner.java:602)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
at org.testng.SuiteRunner.run(SuiteRunner.java:330)
at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
at org.testng.TestNG.runSuites(TestNG.java:1099)
at org.testng.TestNG.run(TestNG.java:1067)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
17:47:24.934 WARN HDF5Library - could not instantiate the HDF5 Library, due to an exception.
java.lang.UnsatisfiedLinkError: 'int ncsa.hdf.hdf5lib.H5.H5dont_atexit()'
at ncsa.hdf.hdf5lib.H5.H5dont_atexit(Native Method) ~[hdf5-java-bindings-1.2.0-hdf5_2.11.0.jar:1.2.0-hdf5_2.11.0]
at ncsa.hdf.hdf5lib.H5.loadH5Lib(H5.java:333) ~[hdf5-java-bindings-1.2.0-hdf5_2.11.0.jar:1.2.0-hdf5_2.11.0]
at ncsa.hdf.hdf5lib.H5.<clinit>(H5.java:254) ~[hdf5-java-bindings-1.2.0-hdf5_2.11.0.jar:1.2.0-hdf5_2.11.0]
at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) ~[hdf5-java-bindings-1.2.0-hdf5_2.11.0.jar:1.2.0-hdf5_2.11.0]
at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) ~[hdf5-java-bindings-1.2.0-hdf5_2.11.0.jar:1.2.0-hdf5_2.11.0]
at org.broadinstitute.hellbender.utils.hdf5.HDF5LibraryUnitTest.testIsSupported(HDF5LibraryUnitTest.java:34) ~[test/:?]
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) ~[?:?]
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.base/java.lang.reflect.Method.invoke(Method.java:568) ~[?:?]
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) ~[testng-7.7.0.jar:7.7.0]
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethodConsideringTimeout(MethodInvocationHelper.java:69) ~[testng-7.7.0.jar:7.7.0]
at org.testng.internal.invokers.ConfigInvoker.invokeConfigurationMethod(ConfigInvoker.java:361) ~[testng-7.7.0.jar:7.7.0]
at org.testng.internal.invokers.ConfigInvoker.invokeConfigurations(ConfigInvoker.java:296) ~[testng-7.7.0.jar:7.7.0]
at org.testng.internal.invokers.TestMethodWorker.invokeBeforeClassMethods(TestMethodWorker.java:180) ~[testng-7.7.0.jar:7.7.0]
at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:122) ~[testng-7.7.0.jar:7.7.0]
at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) [?:?]
at org.testng.TestRunner.privateRun(TestRunner.java:829) [testng-7.7.0.jar:7.7.0]
at org.testng.TestRunner.run(TestRunner.java:602) [testng-7.7.0.jar:7.7.0]
at org.testng.SuiteRunner.runTest(SuiteRunner.java:437) [testng-7.7.0.jar:7.7.0]
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) [testng-7.7.0.jar:7.7.0]
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) [testng-7.7.0.jar:7.7.0]
at org.testng.SuiteRunner.run(SuiteRunner.java:330) [testng-7.7.0.jar:7.7.0]
at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) [testng-7.7.0.jar:7.7.0]
at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) [testng-7.7.0.jar:7.7.0]
at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) [testng-7.7.0.jar:7.7.0]
at org.testng.TestNG.runSuitesLocally(TestNG.java:1176) [testng-7.7.0.jar:7.7.0]
at org.testng.TestNG.runSuites(TestNG.java:1099) [testng-7.7.0.jar:7.7.0]
at org.testng.TestNG.run(TestNG.java:1067) [testng-7.7.0.jar:7.7.0]
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) [gradle-testing-jvm-infrastructure-8.10.2.jar:8.10.2]
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) [gradle-testing-jvm-infrastructure-8.10.2.jar:8.10.2]
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) [gradle-testing-base-infrastructure-8.10.2.jar:8.10.2]
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) ~[?:?]
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.base/java.lang.reflect.Method.invoke(Method.java:568) ~[?:?]
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) [gradle-messaging-8.10.2.jar:8.10.2]
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) [gradle-messaging-8.10.2.jar:8.10.2]
at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) [gradle-messaging-8.10.2.jar:8.10.2]
at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) [gradle-messaging-8.10.2.jar:8.10.2]
at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) [?:?]
at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) [gradle-testing-base-infrastructure-8.10.2.jar:8.10.2]
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) [gradle-testing-base-infrastructure-8.10.2.jar:8.10.2]
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) [gradle-testing-base-infrastructure-8.10.2.jar:8.10.2]
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) [gradle-testing-base-infrastructure-8.10.2.jar:8.10.2]
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) [gradle-worker-main-8.10.2.jar:8.10.2]
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) [gradle-worker-main-8.10.2.jar:8.10.2]
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) [gradle-worker-main-8.10.2.jar:8.10.2]
at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) [gradle-worker.jar:?]
at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74) [gradle-worker.jar:?]