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Task #2763 (closed)

Opened 9 years ago

Closed 9 years ago

BUG: Cannot retrieve the free space Feedback 2678

Reported by: omero-qa Owned by: cxallan
Priority: minor Milestone: OMERO-Beta4.2.1
Component: from QA Version: 4.1
Keywords: n.a. Cc: p.schregle@…, jburel
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by atarkowska)

​http://qa.openmicroscopy.org.uk/qa/feedback/2678/

Comment: Opening Disk Space when no data was there

This problem is related to ​http://loci.wisc.edu/trac/java/ticket/543

Change History (6)

comment:1 Changed 9 years ago by atarkowska

  • Cc jburel added
  • Description modified (diff)
  • Milestone changed from Unscheduled to OMERO-Beta4.2.1 
java.lang.Exception: org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data.
Cannot retrieve the free space


at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:729)


at org.openmicroscopy.shoola.env.data.OMEROGateway.getFreeSpace(OMEROGateway.java:3837)


at org.openmicroscopy.shoola.env.data.AdminServiceImpl.getSpace(AdminServiceImpl.java:141)


at org.openmicroscopy.shoola.env.data.views.calls.AdminLoader$1.doCall(AdminLoader.java:98)


at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:145)


at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)


at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)


at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)


at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)


at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)


at java.lang.Thread.run(Unknown Source)


Caused by: omero.ResourceError


serverStackTrace = "ome.conditions.ResourceError: Cannot run program "df": java.io.IOException: error=24, Too many open files


at ome.logic.RepositoryInfoImpl.getFreeSpaceInKilobytes(RepositoryInfoImpl.java:164)


at sun.reflect.GeneratedMethodAccessor374.invoke(Unknown Source)


at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)


at java.lang.reflect.Method.invoke(Method.java:616)


at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)


at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)


at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)


at ome.security.basic.EventHandler.invoke(EventHandler.java:144)


at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)


at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)


at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)


at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)


at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)


at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:222)


at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)


at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:111)


at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)


at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)


at $Proxy66.getFreeSpaceInKilobytes(Unknown Source)


at sun.reflect.GeneratedMethodAccessor374.invoke(Unknown Source)


at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)


at java.lang.reflect.Method.invoke(Method.java:616)


at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)


at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)


at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)


at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:83)


at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)


at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:40)


at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)


at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)


at $Proxy66.getFreeSpaceInKilobytes(Unknown Source)


at sun.reflect.GeneratedMethodAccessor385.invoke(Unknown Source)


at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)


at java.lang.reflect.Method.invoke(Method.java:616)


at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)


at ome.services.throttling.Callback.run(Callback.java:56)


at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)


at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:132)


at ome.services.blitz.impl.RepositoryInfoI.getFreeSpaceInKilobytes_async(RepositoryInfoI.java:42)


at omero.api._IRepositoryInfoTie.getFreeSpaceInKilobytes_async(_IRepositoryInfoTie.java:64)


at omero.api._IRepositoryInfoDisp.___getFreeSpaceInKilobytes(_IRepositoryInfoDisp.java:132)


at omero.api._IRepositoryInfoDisp.__dispatch(_IRepositoryInfoDisp.java:218)


at IceInternal.Incoming.invoke(Incoming.java:159)


at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)


at Ice.ConnectionI.message(ConnectionI.java:972)


at IceInternal.ThreadPool.run(ThreadPool.java:577)


at IceInternal.ThreadPool.access$100(ThreadPool.java:12)


at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)


"


serverExceptionClass = "ome.conditions.ResourceError"


message = "Cannot run program "df": java.io.IOException: error=24, Too many open files"


at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)


at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)


at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)


at java.lang.reflect.Constructor.newInstance(Unknown Source)


at java.lang.Class.newInstance0(Unknown Source)


at java.lang.Class.newInstance(Unknown Source)


at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)


at IceInternal.BasicStream.throwException(BasicStream.java:1632)


at IceInternal.Outgoing.throwUserException(Outgoing.java:442)


at omero.api._IRepositoryInfoDelM.getFreeSpaceInKilobytes(_IRepositoryInfoDelM.java:31)


at omero.api.IRepositoryInfoPrxHelper.getFreeSpaceInKilobytes(IRepositoryInfoPrxHelper.java:48)


at omero.api.IRepositoryInfoPrxHelper.getFreeSpaceInKilobytes(IRepositoryInfoPrxHelper.java:20)


at org.openmicroscopy.shoola.env.data.OMEROGateway.getFreeSpace(OMEROGateway.java:3835)


... 9 more


at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:158)


at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:245)


at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:217)


at org.openmicroscopy.shoola.agents.metadata.EditorLoader.handleException(EditorLoader.java:161)


at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:84)


at org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)


at java.awt.event.InvocationEvent.dispatch(Unknown Source)


at java.awt.EventQueue.dispatchEvent(Unknown Source)


at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)


at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)


at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)


at java.awt.EventDispatchThread.pumpEvents(Unknown Source)


at java.awt.EventDispatchThread.pumpEvents(Unknown Source)


at java.awt.EventDispatchThread.run(Unknown Source)

comment:2 Changed 9 years ago by atarkowska 

Traceback (most recent call last):

File "/home/omero/omero_dist/lib/python/django/core/handlers/base.py", line 92, in get_response
response = callback(request, *callback_args, **callback_kwargs)

File "/home/omero/omero_dist/lib/python/omeroweb/webadmin/views.py", line 204, in wrapped
return f(request, *args, **kwargs)

File "/home/omero/omero_dist/lib/python/omeroweb/webadmin/views.py", line 990, in drivespace
controller = BaseDriveSpace(conn)

File "/home/omero/omero_dist/lib/python/omeroweb/webadmin/controller/drivespace.py", line 35, in __init__
self.freeSpace = self.conn.getFreeSpace()

File "/home/omero/omero_dist/lib/python/omeroweb/extlib/gateway.py", line 262, in getFreeSpace
return rep_serv.getFreeSpaceInKilobytes() * 1024

File "/home/omero/omero_dist/lib/python/omero/gateway/__init__.py", line 1841, in wrapped
return inner(*args, **kwargs)

File "/home/omero/omero_dist/lib/python/omero/gateway/__init__.py", line 1774, in inner
return f(*args, **kwargs)

File "/home/omero/omero_dist/lib/python/omero_api_IRepositoryInfo_ice.py", line 89, in getFreeSpaceInKilobytes
return _M_omero.api.IRepositoryInfo._op_getFreeSpaceInKilobytes.invoke(self, ((), _ctx))

ResourceError: exception ::omero::ResourceError
{
serverStackTrace = ome.conditions.ResourceError: Cannot run program "df": java.io.IOException: error=24, Too many open files
at ome.logic.RepositoryInfoImpl.getFreeSpaceInKilobytes(RepositoryInfoImpl.java:164)
at sun.reflect.GeneratedMethodAccessor374.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.security.basic.EventHandler.invoke(EventHandler.java:144)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:222)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:111)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy66.getFreeSpaceInKilobytes(Unknown Source)
at sun.reflect.GeneratedMethodAccessor374.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:83)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:40)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy66.getFreeSpaceInKilobytes(Unknown Source)
at sun.reflect.GeneratedMethodAccessor385.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
at ome.services.throttling.Callback.run(Callback.java:56)
at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:132)
at ome.services.blitz.impl.RepositoryInfoI.getFreeSpaceInKilobytes_async(RepositoryInfoI.java:42)
at omero.api._IRepositoryInfoTie.getFreeSpaceInKilobytes_async(_IRepositoryInfoTie.java:64)
at omero.api._IRepositoryInfoDisp.___getFreeSpaceInKilobytes(_IRepositoryInfoDisp.java:132)
at omero.api._IRepositoryInfoDisp.__dispatch(_IRepositoryInfoDisp.java:218)
at IceInternal.Incoming.invoke(Incoming.java:159)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
at Ice.ConnectionI.message(ConnectionI.java:972)
at IceInternal.ThreadPool.run(ThreadPool.java:577)
at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)

serverExceptionClass = ome.conditions.ResourceError
message = Cannot run program "df": java.io.IOException: error=24, Too many open files
}


path:/webadmin/drivespace/,
GET:,
POST:,
COOKIES:{'sessionid': '464ceee26b1d31fe5d0b4a78baee48b7'},
META:{'AUTH_TYPE': None,
'CONTENT_LENGTH': 0,
'CONTENT_TYPE': None,
'GATEWAY_INTERFACE': 'CGI/1.1',
'HTTP_ACCEPT': 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8',
'HTTP_ACCEPT_CHARSET': 'ISO-8859-1,utf-8;q=0.7,*;q=0.7',
'HTTP_ACCEPT_ENCODING': 'gzip,deflate',
'HTTP_ACCEPT_LANGUAGE': 'en-us,en;q=0.5',
'HTTP_CONNECTION': 'keep-alive',
'HTTP_COOKIE': 'sessionid=464ceee26b1d31fe5d0b4a78baee48b7',
'HTTP_HOST': '141.52.175.71',
'HTTP_KEEP_ALIVE': '115',
'HTTP_REFERER': 'http://141.52.175.71/webadmin/experimenters/',
'HTTP_USER_AGENT': 'Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.2.8) Gecko/20100722 Firefox/3.6.8',
'PATH_INFO': u'/webadmin/drivespace/',
'PATH_TRANSLATED': None,
'QUERY_STRING': None,
'REMOTE_ADDR': '134.36.64.132',
'REMOTE_HOST': None,
'REMOTE_IDENT': None,
'REMOTE_USER': None,
'REQUEST_METHOD': 'GET',
'SCRIPT_NAME': '',
'SERVER_NAME': '127.0.0.1',
'SERVER_PORT': 80,
'SERVER_PROTOCOL': 'HTTP/1.1',
'SERVER_SOFTWARE': 'mod_python'}>

comment:3 Changed 9 years ago by atarkowska

  • Description modified (diff)

comment:4 Changed 9 years ago by atarkowska

  • Description modified (diff)
  • Owner changed from atarkowska to mlinkert-x

comment:5 Changed 9 years ago by jmoore

  • Owner changed from mlinkert-x to cxallan

This is not a bioformats issue, per-se, but rather an instance of the server running out of file handles. Chris recently responded to an email from Peter (​http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2010-September/001702.html), so giving this to him. If all the odds and ends are taken care of, this ticket can be closed.

comment:6 Changed 9 years ago by cxallan

  • Resolution set to fixed
  • Status changed from new to closed

Has been solved by addressing the issues with file handle leakage in #2764.

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