[ome-users] excessive time to upgrade database / cleanse
Olivier Miquel
olivier.miquel at mri.cnrs.fr
Fri Apr 29 14:30:01 BST 2016
Dear Mark,
I had tried to cleanse the binary repository, with no success. The
script died after several minutes of silence.
Is there an alternate way to achieve that?
Log :
omero at kansas:~$ /home/omero/apps/OMERO/OMERO.server/bin/omero admin
cleanse /home/omero/apps/OMERO/OMERO.data
Previous session expired for root on localhost:4064
Server: [localhost:4064]
Username: [root]
Password:
Created session 50852b9f-4f40-4dc2-ad14-b900a8527386
(root at localhost:4064). Idle timeout: 10 min. Current group: system
Traceback (most recent call last):
File "/home/omero/apps/OMERO/OMERO.server/bin/omero", line 125, in
<module>
rv = omero.cli.argv()
File "/home/omero/apps/OMERO/OMERO.server/lib/python/omero/cli.py",
line 1438, in argv
cli.invoke(args[1:])
File "/home/omero/apps/OMERO/OMERO.server/lib/python/omero/cli.py",
line 952, in invoke
stop = self.onecmd(line, previous_args)
File "/home/omero/apps/OMERO/OMERO.server/lib/python/omero/cli.py",
line 1029, in onecmd
self.execute(line, previous_args)
File "/home/omero/apps/OMERO/OMERO.server/lib/python/omero/cli.py",
line 1111, in execute
args.func(args)
File
"/home/omero/apps/OMERO/OMERO.server/lib/python/omero/plugins/admin.py",
line 1776, in cleanse
dry_run=args.dry_run)
File
"/home/omero/apps/OMERO/OMERO.server/lib/python/omero/util/cleanse.py",
line 242, in cleanse
delete_empty_dirs(proxy, root, client, dry_run)
File
"/home/omero/apps/OMERO/OMERO.server/lib/python/omero/util/cleanse.py",
line 250, in delete_empty_dirs
is_empty_dir(repo, '/', False, to_delete)
File
"/home/omero/apps/OMERO/OMERO.server/lib/python/omero/util/cleanse.py",
line 282, in is_empty_dir
is_empty_dir(repo, subdirectory, may_delete_subdir, empty_subdirs):
File
"/home/omero/apps/OMERO/OMERO.server/lib/python/omero/util/cleanse.py",
line 282, in is_empty_dir
is_empty_dir(repo, subdirectory, may_delete_subdir, empty_subdirs):
File
"/home/omero/apps/OMERO/OMERO.server/lib/python/omero/util/cleanse.py",
line 282, in is_empty_dir
is_empty_dir(repo, subdirectory, may_delete_subdir, empty_subdirs):
File
"/home/omero/apps/OMERO/OMERO.server/lib/python/omero/util/cleanse.py",
line 277, in is_empty_dir
for entry in repo.listFiles(directory):
File
"/home/omero/apps/OMERO/OMERO.server/lib/python/omero_Repositories_ice.py",
line 329, in listFiles
return _M_omero.grid.Repository._op_listFiles.invoke(self, ((path,
), _ctx))
Ice.UnknownException: exception ::Ice::UnknownException
{
unknown = ome.conditions.InternalException: Wrapped Exception:
(org.springframework.transaction.TransactionSystemException):
Could not roll back JDBC transaction; nested exception is
org.postgresql.util.PSQLException: This connection has been closed.
at
org.springframework.jdbc.datasource.DataSourceTransactionManager.doRollback(DataSourceTransactionManager.java:286)
at
org.springframework.transaction.support.AbstractPlatformTransactionManager.processRollback(AbstractPlatformTransactionManager.java:845)
at
org.springframework.transaction.support.AbstractPlatformTransactionManager.rollback(AbstractPlatformTransactionManager.java:822)
at
org.springframework.transaction.interceptor.TransactionAspectSupport.completeTransactionAfterThrowing(TransactionAspectSupport.java:430)
at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:112)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at
ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy70.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:443)
at
ome.services.blitz.repo.RepositoryDaoImpl.getOriginalFiles(RepositoryDaoImpl.java:439)
at
ome.services.blitz.repo.PublicRepositoryI.listFiles(PublicRepositoryI.java:263)
at
omero.grid._ManagedRepositoryTie.listFiles(_ManagedRepositoryTie.java:136)
at
omero.grid._RepositoryDisp.___listFiles(_RepositoryDisp.java:324)
at
omero.grid._ManagedRepositoryDisp.__dispatch(_ManagedRepositoryDisp.java:585)
at IceInternal.Incoming.invoke(Incoming.java:222)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)
at Ice.ConnectionI.dispatch(ConnectionI.java:1258)
at Ice.ConnectionI.message(ConnectionI.java:1213)
at IceInternal.ThreadPool.run(ThreadPool.java:321)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at
IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
at java.lang.Thread.run(Thread.java:745)
}
On 08/03/2016 10:19, Mark Carroll wrote:
> Dear Olivier,
>
>> Is there somewhere a script to check and clean the database?
>> Our omero.server is in production for about five years now and perhaps
>> we now need to clean some unused stuff in the database?
>
> What I'd been mentioning to Carnë in this thread about periodic VACUUMs
> and suchlike probably suffices for PostgreSQL; their documentation is
> good on this point. If we notice that our server has wrongly been
> leaving some kind of debris in the database then we usually include
> cleanup in upgrade scripts so it gets done for our users anyway in time;
> for instance, the upgrade that we've been discussing included some
> removal of uselessly duplicate rows from a large table.
>
> However, separately from the database, there is also the binary
> repository: it is probably worth glancing at the first part of
> https://www.openmicroscopy.org/site/support/omero/sysadmins/server-backup-and-restore.html
>
> which talks about cleaning files up before doing a backup. If you
> haven't run a "bin/omero admin cleanse" for a while then that might be
> something that's worth adding to your infrequent maintenance checklist.
>
> -- Mark
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
--
Olivier Miquel
Administrateur Système et Réseau
Plate-forme technologique MRI
Tel : 06.50.19.27.43
Mail:olivier.miquel at mri.cnrs.fr
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