Re: [ice-dev] HDF5 Build Issue

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Re: [ice-dev] HDF5 Build Issue

From: Jay Jay Billings <jayjaybillings@xxxxxxxxx>
Date: Tue, 3 Feb 2015 11:25:50 -0500
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You can also put those flags in the run configuration of your pom file. Right click the pom, go to Run As->Run Configurations and then modify the environment in the "Environment" tab.

That being said, I'd follow Alex's instructions.

Thank you for disabling the wiki page Jordan. We will revert it as soon as they are approved. For the record, let me state one more time unequivocally:

Do NOT post "bulk" information about our dependencies, third party libraries or test files to the list, wiki, forums, website or any additional outlets until the CQs have been approved. In the case of a legitimate, single-scoped technical question, like Claire's, I will forward it to the list and it is OK to discuss it.

Jay

On Tue, Feb 3, 2015 at 11:16 AM, McCaskey, Alex <mccaskeyaj@xxxxxxxx> wrote:

Claire,

The Mac is funny when it comes to environment variables. If you’ve installed HDF Java correctly and exported the DYLD_LIBRARY_PATH correctly to point to where those jars are located, then you’re on the right track. Now to get it to play nicely with your Eclipse Application you can do one of two things:

1. In your .bash_profile in your home directory, add the following:
launchtcl setenv DYLD_LIBRARY_PATH $DYLD_LIBRARY_PATH

Then just run the command: source ~/.bash_profile.

This should tell the Mac application launch system about the environment variable, and Eclipse will have it when you go to build ICE.

2. Alternatively, you could alter the way your Eclipse Mac Application is launched in the following way:

Go to your Eclipse app directory, for me its

cd /Users/name/eclipse/Eclipse.app/Contents/MacOS

touch eclipse.sh

put these lines the new eclipse.sh shell script

#!/bin/sh

. ~/.bash_profile

logger "`dirname \"$0\"`/eclipse"

exec "`dirname \"$0\"`/eclipse" $@

And make sure you’ve exported your DYLD_LIBRARY_PATH to the correct paths. Then make it executable:

chmod +x eclipse.sh

Then cd .. to Contents, and edit the Info.plist file to say

<key>CFBundleExecutable</key>
<string>eclipse.sh</string>

instead of just eclipse. Then you have to re-register that Info.plist like this

/System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -v -f /Users/aqw/eclipse/Eclipse.app

Then every time you launch Eclipse, it will be launched with that script and you’re environment variables will be set.

I’ll be putting these instructions up on the wiki soon. Hope that helps and let me know if you have any further trouble.

Best,

Alex

On Feb 3, 2015, at 10:58 AM, Claire Saunders <clairesaunders1123@xxxxxxxxx<mailto:clairesaunders1123@xxxxxxxxx>> wrote:

Hi everyone,

I am building on my Mac. Here is the error message I am getting:
Thanks!

-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.eclipse.ice.io.hdf.test.HdfFileFactoryTester
/Users/claire/ICETests/ioData/test1.h5
java.lang.UnsatisfiedLinkError: no jhdf5 in java.library.path
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1886)
at java.lang.Runtime.loadLibrary0(Runtime.java:849)
at java.lang.System.loadLibrary(System.java:1088)
at ncsa.hdf.hdf5lib.H5.loadH5Lib(H5.java:347)
at ncsa.hdf.hdf5lib.H5.<clinit>(H5.java:274)
at ncsa.hdf.hdf5lib.HDF5Constants.<clinit>(HDF5Constants.java:28)
at ncsa.hdf.object.h5.H5File.<init>(H5File.java:99)
at ncsa.hdf.object.h5.H5File.<init>(H5File.java:132)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at java.lang.Class.newInstance(Class.java:374)
at ncsa.hdf.object.FileFormat.<clinit>(FileFormat.java:229)
at org.eclipse.ice.io.hdf.HdfFileFactory.createH5File(HdfFileFactory.java:65)
at org.eclipse.ice.io.hdf.test.HdfFileFactoryTester.checkFileOperations(HdfFileFactoryTester.java:81)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:53)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:123)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:104)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:164)
at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:110)
at org.apache.maven.surefire.booter.SurefireStarter.invokeProvider(SurefireStarter.java:175)
at org.apache.maven.surefire.booter.SurefireStarter.runSuitesInProcess(SurefireStarter.java:123)
at org.eclipse.tycho.surefire.osgibooter.OsgiSurefireBooter.run(OsgiSurefireBooter.java:85)
at org.eclipse.tycho.surefire.osgibooter.HeadlessTestApplication.run(HeadlessTestApplication.java:21)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.equinox.internal.app.EclipseAppContainer.callMethodWithException(EclipseAppContainer.java:587)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:198)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:354)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:181)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:636)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:591)
at org.eclipse.equinox.launcher.Main.run(Main.java:1450)
at org.eclipse.equinox.launcher.Main.main(Main.java:1426)
java.lang.NullPointerException
at org.eclipse.ice.io.hdf.HdfFileFactory.createH5File(HdfFileFactory.java:73)
at org.eclipse.ice.io.hdf.test.HdfFileFactoryTester.checkFileOperations(HdfFileFactoryTester.java:81)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:53)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:123)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:104)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:164)
at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:110)
at org.apache.maven.surefire.booter.SurefireStarter.invokeProvider(SurefireStarter.java:175)
at org.apache.maven.surefire.booter.SurefireStarter.runSuitesInProcess(SurefireStarter.java:123)
at org.eclipse.tycho.surefire.osgibooter.OsgiSurefireBooter.run(OsgiSurefireBooter.java:85)
at org.eclipse.tycho.surefire.osgibooter.HeadlessTestApplication.run(HeadlessTestApplication.java:21)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.equinox.internal.app.EclipseAppContainer.callMethodWithException(EclipseAppContainer.java:587)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:198)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:354)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:181)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:636)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:591)
at org.eclipse.equinox.launcher.Main.run(Main.java:1450)
at org.eclipse.equinox.launcher.Main.main(Main.java:1426)
Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec <<< FAILURE!
Running org.eclipse.ice.io.hdf.test.HdfIOFactoryTester
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.001 sec
Running org.eclipse.ice.io.hdf.test.HdfIORegistryTester
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec
Running org.eclipse.ice.io.hdf.test.HdfReaderFactoryTester
java.lang.NullPointerException
at org.eclipse.ice.io.hdf.HdfFileFactory.createH5File(HdfFileFactory.java:73)
at org.eclipse.ice.io.hdf.test.HdfReaderFactoryTester.checkGetters(HdfReaderFactoryTester.java:119)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:53)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:123)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:104)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:164)
at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:110)
at org.apache.maven.surefire.booter.SurefireStarter.invokeProvider(SurefireStarter.java:175)
at org.apache.maven.surefire.booter.SurefireStarter.runSuitesInProcess(SurefireStarter.java:123)
at org.eclipse.tycho.surefire.osgibooter.OsgiSurefireBooter.run(OsgiSurefireBooter.java:85)
at org.eclipse.tycho.surefire.osgibooter.HeadlessTestApplication.run(HeadlessTestApplication.java:21)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.equinox.internal.app.EclipseAppContainer.callMethodWithException(EclipseAppContainer.java:587)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:198)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:354)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:181)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:636)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:591)
at org.eclipse.equinox.launcher.Main.run(Main.java:1450)
at org.eclipse.equinox.launcher.Main.main(Main.java:1426)
java.lang.NullPointerException
at org.eclipse.ice.io.hdf.HdfFileFactory.createH5File(HdfFileFactory.java:73)
at org.eclipse.ice.io.hdf.test.HdfReaderFactoryTester.checkReaders(HdfReaderFactoryTester.java:292)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:53)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:123)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:104)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:164)
at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:110)
at org.apache.maven.surefire.booter.SurefireStarter.invokeProvider(SurefireStarter.java:175)
at org.apache.maven.surefire.booter.SurefireStarter.runSuitesInProcess(SurefireStarter.java:123)
at org.eclipse.tycho.surefire.osgibooter.OsgiSurefireBooter.run(OsgiSurefireBooter.java:85)
at org.eclipse.tycho.surefire.osgibooter.HeadlessTestApplication.run(HeadlessTestApplication.java:21)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.equinox.internal.app.EclipseAppContainer.callMethodWithException(EclipseAppContainer.java:587)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:198)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:354)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:181)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:636)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:591)
at org.eclipse.equinox.launcher.Main.run(Main.java:1450)
at org.eclipse.equinox.launcher.Main.main(Main.java:1426)
Tests run: 2, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec <<< FAILURE!
Running org.eclipse.ice.io.hdf.test.HdfWriterFactoryTester
java.lang.NullPointerException
at org.eclipse.ice.io.hdf.HdfFileFactory.createH5File(HdfFileFactory.java:73)
at org.eclipse.ice.io.hdf.test.HdfWriterFactoryTester.checkCreators(HdfWriterFactoryTester.java:98)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:53)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:123)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:104)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:164)
at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:110)
at org.apache.maven.surefire.booter.SurefireStarter.invokeProvider(SurefireStarter.java:175)
at org.apache.maven.surefire.booter.SurefireStarter.runSuitesInProcess(SurefireStarter.java:123)
at org.eclipse.tycho.surefire.osgibooter.OsgiSurefireBooter.run(OsgiSurefireBooter.java:85)
at org.eclipse.tycho.surefire.osgibooter.HeadlessTestApplication.run(HeadlessTestApplication.java:21)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.equinox.internal.app.EclipseAppContainer.callMethodWithException(EclipseAppContainer.java:587)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:198)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:354)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:181)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:636)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:591)
at org.eclipse.equinox.launcher.Main.run(Main.java:1450)
at org.eclipse.equinox.launcher.Main.main(Main.java:1426)
java.lang.NullPointerException
at org.eclipse.ice.io.hdf.HdfFileFactory.createH5File(HdfFileFactory.java:73)
at org.eclipse.ice.io.hdf.test.HdfWriterFactoryTester.checkWriters(HdfWriterFactoryTester.java:239)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:53)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:123)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:104)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:164)
at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:110)
at org.apache.maven.surefire.booter.SurefireStarter.invokeProvider(SurefireStarter.java:175)
at org.apache.maven.surefire.booter.SurefireStarter.runSuitesInProcess(SurefireStarter.java:123)
at org.eclipse.tycho.surefire.osgibooter.OsgiSurefireBooter.run(OsgiSurefireBooter.java:85)
at org.eclipse.tycho.surefire.osgibooter.HeadlessTestApplication.run(HeadlessTestApplication.java:21)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.equinox.internal.app.EclipseAppContainer.callMethodWithException(EclipseAppContainer.java:587)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:198)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:354)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:181)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:636)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:591)
at org.eclipse.equinox.launcher.Main.run(Main.java:1450)
at org.eclipse.equinox.launcher.Main.main(Main.java:1426)
Tests run: 2, Failures: 1, Errors: 1, Skipped: 0, Time elapsed: 0.005 sec <<< FAILURE!
Running org.eclipse.ice.io.ips.test.IPSReaderTester
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 sec
Running org.eclipse.ice.io.ips.test.IPSWriterTester
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec
Running org.eclipse.ice.io.serializable.test.IOServiceTester
[IOService Message] Adding FakeReader reader to the IOService Mapping.
[IOService Message] Adding FakeWriter writer to the IOService Mapping.
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec

Results :

Failed tests: checkFileOperations(org.eclipse.ice.io.hdf.test.HdfFileFactoryTester)
checkGetters(org.eclipse.ice.io.hdf.test.HdfReaderFactoryTester)
checkReaders(org.eclipse.ice.io.hdf.test.HdfReaderFactoryTester)
checkCreators(org.eclipse.ice.io.hdf.test.HdfWriterFactoryTester)

Tests in error:
checkWriters(org.eclipse.ice.io.hdf.test.HdfWriterFactoryTester)

Tests run: 10, Failures: 4, Errors: 1, Skipped: 1

[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] org.eclipse.ice.build ............................. SUCCESS [ 0.196 s]
[INFO] org.eclipse.ice.target.kepler ..................... SUCCESS [ 0.077 s]
[INFO] org.eclipse.ice.dependencies ...................... SUCCESS [ 0.684 s]
[INFO] org.eclipse.ice.datastructures .................... SUCCESS [ 0.104 s]
[INFO] org.eclipse.ice.io ................................ SUCCESS [ 0.058 s]
[INFO] org.eclipse.ice.materials ......................... SUCCESS [ 0.044 s]
[INFO] org.eclipse.ice.item .............................. SUCCESS [ 0.103 s]
[INFO] org.eclipse.ice.core .............................. SUCCESS [ 0.054 s]
[INFO] org.eclipse.ice.client ............................ SUCCESS [ 0.055 s]
[INFO] org.eclipse.ice.analysistool ...................... SUCCESS [ 0.039 s]
[INFO] org.eclipse.ice.client.compatibility .............. SUCCESS [ 0.046 s]
[INFO] org.eclipse.ice.reactor.plant ..................... SUCCESS [ 0.072 s]
[INFO] org.eclipse.ice.client.widgets.rcp ................ SUCCESS [ 0.163 s]

[INFO] org.eclipse.ice.reactor ........................... SUCCESS [ 0.061 s]
[INFO] org.eclipse.ice.client.widgets .................... SUCCESS [ 0.186 s]
[INFO] org.eclipse.ice.client.test ....................... SUCCESS [ 6.673 s]
[INFO] org.eclipse.ice.client.widgets.moose .............. SUCCESS [ 0.126 s]
[INFO] org.eclipse.ice.reactor.sfr ....................... SUCCESS [ 0.054 s]
[INFO] org.eclipse.ice.reactorAnalyzer ................... SUCCESS [ 0.057 s]
[INFO] org.eclipse.ice.client.widgets.reactoreditor ...... SUCCESS [ 0.091 s]
[INFO] org.eclipse.ice.client.widgets.reactoreditor.test . SUCCESS [ 9.861 s]
[INFO] org.eclipse.ice.client.widgets.reactoreditor.grid . SUCCESS [ 0.054 s]
[INFO] org.eclipse.ice.client.widgets.reactoreditor.grid.test SUCCESS [ 0.044 s]
[INFO] org.eclipse.ice.client.widgets.reactoreditor.lwr .. SUCCESS [ 0.085 s]
[INFO] org.eclipse.ice.client.widgets.reactoreditor.lwr.test SUCCESS [ 3.890 s]
[INFO] org.eclipse.ice.client.widgets.reactoreditor.sfr .. SUCCESS [ 0.070 s]
[INFO] org.eclipse.ice.client.widgets.reactoreditor.sfr.test SUCCESS [ 3.762 s]
[INFO] org.eclipse.ice.client.widgets.test ............... SUCCESS [ 0.057 s]
[INFO] org.eclipse.ice.client.widgets.rcp.test ........... SUCCESS [ 0.048 s]
[INFO] org.eclipse.ice.client.rcp ........................ SUCCESS [ 0.055 s]
[INFO] org.eclipse.ice.datastructures.test ............... SUCCESS [ 27.947 s]
[INFO] org.eclipse.ice.core.test ......................... SUCCESS [ 2.652 s]
[INFO] org.eclipse.ice.persistence.xml ................... SUCCESS [ 0.034 s]
[INFO] org.eclipse.ice.item.test ......................... SUCCESS [ 9.458 s]
[INFO] org.eclipse.ice.caebat ............................ SUCCESS [ 0.040 s]
[INFO] org.eclipse.ice.persistence.xml.test .............. SUCCESS [ 20.052 s]
[INFO] org.eclipse.ice.io.test ........................... FAILURE [ 1.786 s]
[INFO] org.eclipse.ice.reactor.test ...................... SKIPPED
[INFO] org.eclipse.ice.reactor.sfr.test .................. SKIPPED
[INFO] org.eclipse.ice.reactor.plant.test ................ SKIPPED
[INFO] org.eclipse.ice.reactor.perspective ............... SKIPPED
[INFO] org.eclipse.ice.reactorAnalyzer.test .............. SKIPPED
[INFO] org.eclipse.ice.caebat.test ....................... SKIPPED
[INFO] org.eclipse.ice.kdd ............................... SKIPPED
[INFO] org.eclipse.ice.kdd.test .......................... SKIPPED
[INFO] org.eclipse.ice.proteus ........................... SKIPPED
[INFO] org.eclipse.ice.proteus.test ...................... SKIPPED
[INFO] org.eclipse.ice.mesh .............................. SKIPPED
[INFO] org.eclipse.ice.mesh.test ......................... SKIPPED
[INFO] org.eclipse.ice.nek5000 ........................... SKIPPED
[INFO] org.eclipse.ice.nek5000.test ...................... SKIPPED
[INFO] gov.lbnl.visit.swt ................................ SKIPPED
[INFO] org.eclipse.ice.viz ............................... SKIPPED
[INFO] org.eclipse.ice.viz.test .......................... SKIPPED
[INFO] org.eclipse.ice.viz.service ....................... SKIPPED
[INFO] org.eclipse.ice.viz.service.test .................. SKIPPED
[INFO] org.eclipse.ice.viz.service.visit ................. SKIPPED
[INFO] org.eclipse.ice.viz.service.visit.test ............ SKIPPED
[INFO] org.eclipse.ice.xolotl ............................ SKIPPED
[INFO] org.eclipse.ice.materials.test .................... SKIPPED
[INFO] org.eclipse.ice.materials.ui ...................... SKIPPED
[INFO] org.eclipse.ice.caebat.batml ...................... SKIPPED
[INFO] org.eclipse.ice.caebat.batml.test ................. SKIPPED
[INFO] org.eclipse.ice.sassena ........................... SKIPPED
[INFO] org.eclipse.ice.sassena.test ...................... SKIPPED
[INFO] org.eclipse.ice.reflectivity ...................... SKIPPED
[INFO] org.eclipse.ice.reflectivity.test ................. SKIPPED
[INFO] ICE Feature ....................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 05:23 min
[INFO] Finished at: 2015-02-03T10:56:58-05:00
[INFO] Final Memory: 174M/1632M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.eclipse.tycho:tycho-surefire-plugin:0.18.1:test (default-test) on project org.eclipse.ice.io.test: There are test failures.
[ERROR]

On Feb 3, 2015, at 10:51 AM, Wojtowicz, Anna <wojtowicza@xxxxxxxx<mailto:wojtowicza@xxxxxxxx>> wrote:

Yeah, once the CQs are approved, we will require the user to install HDF5 on their own accord, but the Java wrappers will be distributed as part of ICE.

Claire, for now, you also need to install HDF-Java/HDF-View: http://www.hdfgroup.org/products/java/release/download.html

I don’t know anything about Macs, but I know on Windows, the binary installation does not add the correct paths to the PATH variable. I manually need to add the /{HDF5 install}/lib and /{HDFJava install}/lib directories to my PATH.

Anna

From: ice-dev-bounces@xxxxxxxxxxx<mailto:ice-dev-bounces@xxxxxxxxxxx> [mailto:ice-dev-bounces@xxxxxxxxxxx] On Behalf Of Jay Jay Billings
Sent: Tuesday, February 03, 2015 10:41 AM
To: ice developer discussions
Subject: Re: [ice-dev] Fwd: HDF5 Build Issue

Our current build instructions do not discuss the third party libraries because they ate not approved yet. If that is the problem here, other than a simple setting or something, we need to take it off the list.

Jay

On Feb 3, 2015 10:35 AM, "Jordan Deyton" <deytonjh@xxxxxxxx<mailto:deytonjh@xxxxxxxx>> wrote:
Claire,

To re-iterate Jay's question... Windows, Mac, or Linux?

As a side note, I think the build instructions need to be updated to include HDF Java, not HDF5. HDF5 should only be required if you are building ICE IO. (HDF Java includes pre-compiled versions of HDF5 for its own use, but I'm not sure if they are statically linked.)

Jordan

Jordan Deyton

Oak Ridge National Laboratory

Telephone: (865) 574-1091<tel:%28865%29%20574-1091>

Email: deytonjh@xxxxxxxx<mailto:deytonjh@xxxxxxxx>

On 2/3/2015 5:32 AM, Jay Jay Billings wrote:

Claire,

Can you send the text error to the dev list please? Ate you building on your Mac?

Jay

---------- Forwarded message ----------
From: "Claire Saunders" <clairenicolesaunders@xxxxxxxxx<mailto:clairenicolesaunders@xxxxxxxxx>>
Date: Feb 3, 2015 12:09 AM
Subject: HDF5 Build Issue
To: "Jay Jay Billings" <jayjaybillings@xxxxxxxxx<mailto:jayjaybillings@xxxxxxxxx>>
Cc:

Hi Jay,

I am having issues with the build and the HDF5 libraries. I followed the script on http://wiki.eclipse.org/Getting_ICE#Prerequisites but I still can’t get it working. Is there anything else I am missing?

Thanks,
Claire

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Alex McCaskey
ORNL Computer Science Research
mccaskeyaj@xxxxxxxx<mailto:mccaskeyaj@xxxxxxxx>
(865) 574-8715

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Jay Jay Billings

Oak Ridge National Laboratory

Twitter Handle: @jayjaybillings

References:
- [ice-dev] Fwd: HDF5 Build Issue
  - From: Jay Jay Billings
- Re: [ice-dev] Fwd: HDF5 Build Issue
  - From: Jordan Deyton
- Re: [ice-dev] Fwd: HDF5 Build Issue
  - From: Jay Jay Billings
- Re: [ice-dev] Fwd: HDF5 Build Issue
  - From: Wojtowicz, Anna
- Re: [ice-dev] Fwd: HDF5 Build Issue
  - From: Claire Saunders
- Re: [ice-dev] HDF5 Build Issue
  - From: McCaskey, Alex

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