Can't start fresh WSO2-IS install, permission errors

Question

I'm having difficulty simply starting WSO2-IS 5.3.0.

Environment : Ubuntu 16.04 VM(Virtualbox) on Ubuntu 16.04 host.

I don't have much additional information, this is a fresh install on a fresh VM. I haven't changed any settings except for what's described in https://docs.wso2.com/display/IS530/Installing+on+Linux+or+OS+X

JAVA_HOME environment variable is set to /usr/java/jdk1.8.0_151
CARBON_HOME environment variable is set to /usr/local/bin/wso2is-5.3.0
rm: cannot remove '/usr/local/bin/wso2is-5.3.0/tmp/work': Permission denied
Using Java memory options: -Xms256m -Xmx1024m
log4j:ERROR setFile(null,true) call failed.
java.io.FileNotFoundException: /usr/local/bin/wso2is-5.3.0/repository/logs/wso2carbon.log (Permission denied)
    at java.io.FileOutputStream.open0(Native Method)
    at java.io.FileOutputStream.open(FileOutputStream.java:270)
    at java.io.FileOutputStream.(FileOutputStream.java:213)
    at java.io.FileOutputStream.(FileOutputStream.java:133)
    at org.apache.log4j.FileAppender.setFile(FileAppender.java:294)
    at org.apache.log4j.FileAppender.activateOptions(FileAppender.java:165)
    at org.apache.log4j.DailyRollingFileAppender.activateOptions(DailyRollingFileAppender.java:223)
    at org.apache.log4j.config.PropertySetter.activate(PropertySetter.java:307)
    at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:172)
    at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:104)
    at org.apache.log4j.PropertyConfigurator.parseAppender(PropertyConfigurator.java:842)
    at org.apache.log4j.PropertyConfigurator.parseCategory(PropertyConfigurator.java:768)
    at org.apache.log4j.PropertyConfigurator.configureRootCategory(PropertyConfigurator.java:648)
    at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:514)
    at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:580)
    at org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:526)
    at org.apache.log4j.LogManager.(LogManager.java:127)
    at org.apache.log4j.Logger.getLogger(Logger.java:104)
    at org.apache.commons.logging.impl.Log4JLogger.getLogger(Log4JLogger.java:262)
    at org.apache.commons.logging.impl.Log4JLogger.(Log4JLogger.java:108)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
    at org.apache.commons.logging.impl.LogFactoryImpl.createLogFromClass(LogFactoryImpl.java:1025)
    at org.apache.commons.logging.impl.LogFactoryImpl.discoverLogImplementation(LogFactoryImpl.java:844)
    at org.apache.commons.logging.impl.LogFactoryImpl.newInstance(LogFactoryImpl.java:541)
    at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactoryImpl.java:292)
    at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactoryImpl.java:269)
    at org.apache.commons.logging.LogFactory.getLog(LogFactory.java:655)
    at org.wso2.carbon.server.Main.(Main.java:34)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
    at java.lang.Class.newInstance(Class.java:442)
    at org.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:60)
    at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
log4j:ERROR Either File or DatePattern options are not set for appender [CARBON_LOGFILE].
log4j:ERROR setFile(null,true) call failed.
java.io.FileNotFoundException: /usr/local/bin/wso2is-5.3.0/repository/logs/patches.log (Permission denied)
    at java.io.FileOutputStream.open0(Native Method)
    at java.io.FileOutputStream.open(FileOutputStream.java:270)
    at java.io.FileOutputStream.(FileOutputStream.java:213)
    at java.io.FileOutputStream.(FileOutputStream.java:133)
    at org.apache.log4j.FileAppender.setFile(FileAppender.java:294)
    at org.apache.log4j.FileAppender.activateOptions(FileAppender.java:165)
    at org.apache.log4j.config.PropertySetter.activate(PropertySetter.java:307)
    at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:172)
    at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:104)
    at org.apache.log4j.PropertyConfigurator.parseAppender(PropertyConfigurator.java:842)
    at org.apache.log4j.PropertyConfigurator.parseCategory(PropertyConfigurator.java:768)
    at org.apache.log4j.PropertyConfigurator.parseCatsAndRenderers(PropertyConfigurator.java:672)
    at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:516)
    at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:580)
    at org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:526)
    at org.apache.log4j.LogManager.(LogManager.java:127)
    at org.apache.log4j.Logger.getLogger(Logger.java:104)
    at org.apache.commons.logging.impl.Log4JLogger.getLogger(Log4JLogger.java:262)
    at org.apache.commons.logging.impl.Log4JLogger.(Log4JLogger.java:108)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
    at org.apache.commons.logging.impl.LogFactoryImpl.createLogFromClass(LogFactoryImpl.java:1025)
    at org.apache.commons.logging.impl.LogFactoryImpl.discoverLogImplementation(LogFactoryImpl.java:844)
    at org.apache.commons.logging.impl.LogFactoryImpl.newInstance(LogFactoryImpl.java:541)
    at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactoryImpl.java:292)
    at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactoryImpl.java:269)
    at org.apache.commons.logging.LogFactory.getLog(LogFactory.java:655)
    at org.wso2.carbon.server.Main.(Main.java:34)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
    at java.lang.Class.newInstance(Class.java:442)
    at org.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:60)
    at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
log4j:ERROR setFile(null,true) call failed.
java.io.FileNotFoundException: /usr/local/bin/wso2is-5.3.0/repository/logs/wso2carbon-trace-messages.log (Permission denied)
    at java.io.FileOutputStream.open0(Native Method)
    at java.io.FileOutputStream.open(FileOutputStream.java:270)
    at java.io.FileOutputStream.(FileOutputStream.java:213)
    at java.io.FileOutputStream.(FileOutputStream.java:133)
    at org.apache.log4j.FileAppender.setFile(FileAppender.java:294)
    at org.apache.log4j.FileAppender.activateOptions(FileAppender.java:165)
    at org.apache.log4j.DailyRollingFileAppender.activateOptions(DailyRollingFileAppender.java:223)
    at org.apache.log4j.config.PropertySetter.activate(PropertySetter.java:307)
    at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:172)
    at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:104)
    at org.apache.log4j.PropertyConfigurator.parseAppender(PropertyConfigurator.java:842)
    at org.apache.log4j.PropertyConfigurator.parseCategory(PropertyConfigurator.java:768)
    at org.apache.log4j.PropertyConfigurator.parseCatsAndRenderers(PropertyConfigurator.java:672)
    at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:516)
    at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:580)
    at org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:526)
    at org.apache.log4j.LogManager.(LogManager.java:127)
    at org.apache.log4j.Logger.getLogger(Logger.java:104)
    at org.apache.commons.logging.impl.Log4JLogger.getLogger(Log4JLogger.java:262)
    at org.apache.commons.logging.impl.Log4JLogger.(Log4JLogger.java:108)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
    at org.apache.commons.logging.impl.LogFactoryImpl.createLogFromClass(LogFactoryImpl.java:1025)
    at org.apache.commons.logging.impl.LogFactoryImpl.discoverLogImplementation(LogFactoryImpl.java:844)
    at org.apache.commons.logging.impl.LogFactoryImpl.newInstance(LogFactoryImpl.java:541)
    at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactoryImpl.java:292)
    at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactoryImpl.java:269)
    at org.apache.commons.logging.LogFactory.getLog(LogFactory.java:655)
    at org.wso2.carbon.server.Main.(Main.java:34)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
    at java.lang.Class.newInstance(Class.java:442)
    at org.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:60)
    at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
log4j:ERROR Either File or DatePattern options are not set for appender [CARBON_TRACE_LOGFILE].
[2017-11-22 17:16:33,708]  WARN {org.wso2.carbon.server.Main} -  Cannot write wso2carbon.pid file
[2017-11-22 17:16:33,713] ERROR {org.wso2.carbon.server.extensions.FragmentBundleCreator} -  Error occured while creating the log4j prop fragment bundle.
java.io.IOException: Fail to create the directory: /usr/local/bin/wso2is-5.3.0/tmp/jarsToBundles
    at org.wso2.carbon.server.util.Utils.copyFileToDir(Utils.java:494)
    at org.wso2.carbon.server.extensions.FragmentBundleCreator.perform(FragmentBundleCreator.java:70)
    at org.wso2.carbon.server.Main.invokeExtensions(Main.java:142)
    at org.wso2.carbon.server.Main.main(Main.java:92)
    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.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:63)
    at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
[2017-11-22 17:16:33,732] ERROR {org.wso2.carbon.server.extensions.DropinsBundleDeployer} -  Failed to create the directory: /usr/local/bin/wso2is-5.3.0/tmp/bundles_info_bcd7eb77-3295-4fac-8942-a5cde9d32434/bundles.info
java.io.IOException: Failed to create the directory: /usr/local/bin/wso2is-5.3.0/tmp/bundles_info_bcd7eb77-3295-4fac-8942-a5cde9d32434/bundles.info
    at org.wso2.carbon.server.extensions.DropinsBundleDeployer.updateBundlesInfoFile(DropinsBundleDeployer.java:323)
    at org.wso2.carbon.server.extensions.DropinsBundleDeployer.perform(DropinsBundleDeployer.java:87)
    at org.wso2.carbon.server.Main.invokeExtensions(Main.java:146)
    at org.wso2.carbon.server.Main.main(Main.java:92)
    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.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:63)
    at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
[2017-11-22 17:16:33,732] ERROR {org.wso2.carbon.server.extensions.DropinsBundleDeployer} -  Error occured while deploying bundles in the dropins directory
java.lang.Exception: Error occurred while updating the bundles.info file.
    at org.wso2.carbon.server.extensions.DropinsBundleDeployer.updateBundlesInfoFile(DropinsBundleDeployer.java:345)
    at org.wso2.carbon.server.extensions.DropinsBundleDeployer.perform(DropinsBundleDeployer.java:87)
    at org.wso2.carbon.server.Main.invokeExtensions(Main.java:146)
    at org.wso2.carbon.server.Main.main(Main.java:92)
    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.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:63)
    at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
Caused by: java.io.IOException: Failed to create the directory: /usr/local/bin/wso2is-5.3.0/tmp/bundles_info_bcd7eb77-3295-4fac-8942-a5cde9d32434/bundles.info
    at org.wso2.carbon.server.extensions.DropinsBundleDeployer.updateBundlesInfoFile(DropinsBundleDeployer.java:323)
    ... 9 more
[2017-11-22 17:16:33,735] ERROR {org.wso2.carbon.server.extensions.PatchInstaller} -  Error occurred while applying patches
java.io.IOException: No such file or directory
    at java.io.UnixFileSystem.createFileExclusively(Native Method)
    at java.io.File.createNewFile(File.java:1012)
    at org.wso2.carbon.server.util.PatchUtils.processPatches(PatchUtils.java:218)
    at org.wso2.carbon.server.extensions.PatchInstaller.perform(PatchInstaller.java:49)
    at org.wso2.carbon.server.Main.invokeExtensions(Main.java:149)
    at org.wso2.carbon.server.Main.main(Main.java:92)
    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.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:63)
    at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
[2017-11-22 17:16:33,736] ERROR {org.wso2.carbon.server.extensions.EclipseIniRewriter} -  Error while writing to file null.ini
java.io.FileNotFoundException: /usr/local/bin/wso2is-5.3.0/repository/components/default/null.ini (Permission denied)
    at java.io.FileOutputStream.open0(Native Method)
    at java.io.FileOutputStream.open(FileOutputStream.java:270)
    at java.io.FileOutputStream.(FileOutputStream.java:213)
    at java.io.FileOutputStream.(FileOutputStream.java:162)
    at java.io.FileWriter.(FileWriter.java:90)
    at org.wso2.carbon.server.extensions.EclipseIniRewriter.rewriteFile(EclipseIniRewriter.java:73)
    at org.wso2.carbon.server.extensions.EclipseIniRewriter.perform(EclipseIniRewriter.java:55)
    at org.wso2.carbon.server.Main.invokeExtensions(Main.java:152)
    at org.wso2.carbon.server.Main.main(Main.java:92)
    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.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:63)
    at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
!SESSION 2017-11-22 17:16:33.950 -----------------------------------------------
eclipse.buildId=unknown
java.version=1.8.0_151
java.vendor=Oracle Corporation
BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_US

!ENTRY org.eclipse.osgi 4 0 2017-11-22 17:16:33.950
!MESSAGE Error reading configuration: Unable to create lock manager.
!STACK 0
java.io.IOException: Unable to create lock manager.
    at org.eclipse.osgi.storagemanager.StorageManager.open(StorageManager.java:699)
    at org.eclipse.osgi.internal.baseadaptor.BaseStorage.initFileManager(BaseStorage.java:226)
    at org.eclipse.osgi.internal.baseadaptor.BaseStorage.initialize(BaseStorage.java:160)
    at org.eclipse.osgi.baseadaptor.BaseAdaptor.initializeStorage(BaseAdaptor.java:123)
    at org.eclipse.osgi.framework.internal.core.Framework.(Framework.java:192)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.startup(EclipseStarter.java:263)
    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.wso2.carbon.server.CarbonLauncher.launch(CarbonLauncher.java:108)
    at org.wso2.carbon.server.Main.launchCarbon(Main.java:160)
    at org.wso2.carbon.server.Main.main(Main.java:94)
    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.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:63)
    at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)

user_515034 · Answer

The user who tries to start the Identity Server doesn't have write permission on /usr/local/bin/wso2is-5.3.0 path.

Grant write permission and start the pack. It's better if you choose some other location like /opt/wso2is-5.3.0

user_1645712 · Answer

The previous answer (from Abimaran) is basically right. The process needs rights to write into its own filesystem /usr/local/bin/wso2is-5.3.0 based on the user under which is the process running. The log claims the applicarion is unable to create multiple files.

I am little bit concerned about the location you've chosen for your product installation. /usr/local/bin/ is usually devoted to binaries and user with non-root privileges should have no write access to that location. Mainly if you have SELinux enabled, you may get restricted write acces from common processes despite the process owner is root.

And I strongly urge you don't run any application as root if it's really not necessary.

I usually choose locations like /opt or /srv for 3rd part products ( so you will have /opt/wso2is-5.3.0). You can create a dedicated user (or any non-root user will do), give ownership of the installation directory to the user and you are good to go (much better than from /usr/local/bin and running as root)

user_9002571 · Answer

BTW, you use a wrong version of JDK (jdk1.8.0_151) this one got several compatibility problems with wso2iot (go for the _144).

Do not use JDK1.8.0_151 due to a known issue. This issue is fixed in JDK 1.8.0_162-ea. However, use JDK 1.8.0_144 until the latter mentioned version is released

Can't start fresh WSO2-IS install, permission errors

3 Answers